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/Akhet-2.0.tar.gz/Akhet-2.0/docs/demo/details.rst
Details %%%%%%% development.ini =============== The config file contains the following settings which aren't in Pyramid's built-in scaffolds: * mako.directories: necessary when using Mako, to set the template search path. (Theoretically you don't need this if you specify renderers by asset spec rather than by relative path, but I couldn't get that to work.) * cache.\*: Beaker cache settings. These are not actually necessary because the demo never uses a cache, but they're here for demonstration. * session.\*: Beaker session settings. These are necessary if you use sessions or flash messages. Beaker supports several kinds of session persistence: in-memory, files, memcached, database, etc. The demo's configuration uses memory mode, which holds the sessions in memory until the application quits. It contains commented settings for file-based sessions, which is Pylons' default. Experienced developers seem to be choosing memcached mode nowadays. Memory sessions disappear when the server is restarted, and work only with multithreaded servers, not multiprocess servers. File-based sessions are persistent, but add the complications of a directory and permissions and maintenance. Memcached avoids all these problems, and it also scales to multiple parallel servers, which can all share a memcached session. If you copy the session configuration to your application, do change "session.secret" to a random string. This is used to help ensure the integrity of the session, to prevent people from hijacking it. Init module and main function ============================= The main function, in addition to the minimal Pyramid configuration, activates Beaker sessions and caching, and sets up templates, subscribers, routes, and a static route. The Beaker setup passes the ``settings`` dict to Beaker; that's how your settings are read. Pyramid cofigures Mako the same way behind the scenes, passing the settings to it. The "add_renderer" line tells Pyramid to recognize filenames ending in ".html" as Mako templates. The subscribers include we'll see in a minute. Activating static routes involves an include line and a "config.add_static_route" call. Helpers ======= The demo provides a Pylons-like helpers module, *akhet_demo/lib/helpers.py*. You can put utility functions here for use in your templates. The helper contains imports for WebHelper's HTML tag helpers, but they're commented out. (WebHelpers is a Python package containing generic functions for use in web applications and other applications.) I'm tempted to actually use the tag helpers in the site template but haven't done so yet. Most of WebHelpers works with Pyramid, including the popular ``webhelpers.html`` subpackage, ``webhelpers.text``, and ``webhelpers.number``. You'll have to add a WebHelpers dependency to your application if you want to use it. The only part of WebHelpers that doesn't work with Pyramid is the ``webhelpers.pylonslib`` subpackage, which depends on Pylons' special globals. Note that ``webhelpers.paginate`` requires a slightly different configuration with Pyramid than with Pylons, because ``pylons.url`` is not available. You'll have to supply a URL generator, perhaps using one of the convenience classes included in WebHelpers 1.3. Paginate's URL generator is *not* Akhet's URL generator: it's a different kind of class specific to the paginator's needs. Subscribers =========== *akhet_demo/subscribers.py* is unique to the demo. It sets up a URL generator and configures several Pylons-like globals for the template namespace. The only thing you need in here is the includeme function, which the application's main function invokes via the ``config.include(".subscribers")`` line. The ``add_renderer_globals`` subscriber configures the following variables for the template namespace: * ``h``: the helpers module. * ``r``: an alias for ``request``. * ``url``: the URL generator. It has commented code to configure "settings", "session", and "c" variables if you want those. For completeness, here are the system variables Pyramid 1.3 adds to the template namespace: * ``context``: the context. * ``renderer_name``: the name of the renderer. * ``renderer_info``: a ``RendererHelper`` object (defined in ``pyramid.renderers``). * ``request``: the request. * ``view``: the view. (A function or instance.) As a reminder, everything here is local to the current request. The URL generator is attached to the request object, and the renderer globals are set just before the renderer is invoked. These variables are all discarded at the end of the request. Views ===== The views module has a base class called ``Handler`` (but it's not related to "pyramid_handlers"). The index view demonstrates logging, optionally sets a flash message, and invokes a Mako template renderer. The demo pushes a flash message by calling ``self.request.session.flash()`` with the message text. By default this puts the message on the "info" queue, and it's displayed using an "info" CSS class. You can push the message onto a different queue by specifying the queue name as a second argument. But that's only useful if the template pops the messages from the other queue by name, otherwise they'll never be displayed. It's customary to name the queues according to the Python logging hierarchy: debug, info (notice), warn(ing), error, critical. The default stylesheet defines CSS classes with distinct styling for several of these levels. .. include:: ../links.rst
PypiClean
/LiliDB-1.0.3.tar.gz/LiliDB-1.0.3/README.md
# LiliDB *Lili* ("Small" in Toki Pona) it's a small Key-Value database library.<br> No third-party dependencies, pure Python and safe to use!<br> # Install ```sh # GIT+PIP pip install git+https://github.com/ZSendokame/LiliDB.git # PIP pip install LiliDB ``` # How to use ```py import lilidb db = lilidb.Database('database.json') db.set('key', 'value') db.dump() with db as db: db.set('with': 'Open, save and close file.') # You can use Threads! # and make errors... If an exception ocurrs, it automatically saves. ```
PypiClean
/Chives-0.0.1-py3-none-any.whl/chives/info.py
# import logging # logging.basicConfig(filename='logging.log', # format='%(asctime)s %(message)s', # filemode="w", level=logging.DEBUG) # 更新: # 1、可配置抓取的字段:f1.f2..fxxx # 2、可配置一次抓取的数量:'pz': 2000, # 3、可导出到Excel:spider.py # 4、剩余页码可配置是否开启 break # 5、可以设置分时数据是否开启,以及过滤条件 'ft': 1(全部,大于100手等), # 6、除中国股市外,其他地区无法获取分时数据 # 7、无法解析详情的包括:首页、自选股、特色行情、英股市场、期货市场 # 8、正常解析的包括:科创板、沪深个股、沪深板块、沪深指数、新三板、沪深港通、港股市场、 # 美股市场、全球指数、基金市场、债券市场、外汇市场、期权市场、黄金市场 # 9、大部分逻辑集中在crawList(self, tList)函数中,后面考虑拆分出来。 # 10、基本信息一栏加入了股吧的资讯和评论 # 11、只抓取分时数据的话约1.5个小时,但是record报错:pymongo.errors.DocumentTooLarge: 'update' command document too large # 12、requests_get()函数加入了缓存池的设计 #20200222: #AB股比价,AH股比价字段解析错误,期权字段解析错误; #全球指数有一个最新行情时间的字段没有解析,(所有行情公用一种表结构) # # loginParam={ 'com': { 'pn': 1, 'pz': 5000, 'po': 1, 'np': 1, 'fltt': 2, 'invt': 2, 'fid': 'f3', 'fs' :'m:1+t:23', 'fields' :'f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16,f17,f18,f19,f20,f21,f22,f23,f24,f25,f26,f27,f28,f29,f30,f31,f32,f33,f34,f35,f36,f37,f38,f39,f40,f41,f42,f43,f44,f45,f46,f47,f48,f49,f50,f62,f128,f136,f115,f152', #无限延伸? }, 'fs': { 'pageindex': 1, 'pagesize': 5000, #最大300 'sort': 1, 'ft': 1, #过滤条件>=?手 'code': 688159, 'market': 1, 'dpt': 'wzfscj', 'ut': '7eea3edcaed734bea9cbfc24409ed989', }, 'trends2': { 'iscr': 0, 'ndays': 1, 'fields1': 'f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13', 'fields2': 'f51,f52,f53,f54,f55,f56,f57,f58', 'secid': '1.600789', }, 'kline': { 'fqt': 0, 'end': '20500101', 'klt': 0, 'lmt': 120, 'fields1': 'f1,f2,f3,f4,f5', 'fields2': 'f51,f52,f53,f54,f55,f56,f57,f58', 'secid': '1.600789', }, 'fflow': { 'lmt': 100, 'klt': 101, 'fields1': 'f1,f2,f3,f7', 'fields2': 'f51,f52,f53,f54,f55,f56,f57,f58,f59,f60,f61,f62,f63,f64,f65', 'secid': '1.600789', }, 'info': { 'fltt': 2, 'invt': 2, 'volt': 2, 'fields': 'f43,f57,f58,f169,f170,f46,f44,f51,f168,f47,f164,f163,f116,f60,f45,f52,f50,f48,f167,f117,f71,f161,f49,f530,f135,f136,f137,f138,f139,f141,f142,f144,f145,f147,f148,f140,f143,f146,f149,f55,f62,f162,f92,f173,f104,f105,f84,f85,f183,f184,f185,f186,f187,f188,f189,f190,f191,f192,f107,f111,f86,f177,f78,f110,f262,f263,f264,f267,f268,f250,f251,f252,f253,f254,f255,f256,f257,f258,f266,f269,f270,f271,f273,f274,f275,f127,f199,f128,f198,f259,f260,f261,f171,f277,f278,f279,f288', 'secid': '1.600789', }, 'guba': { 'ps': 36, 'sorttype': 1, 'version': 200, 'code': 688159, 'product': 'Guba', 'plat': 'Web', }, } loginUrls = { 'proxyWeb': 'https://www.xicidaili.com/nn/', 'proxies': { 'http': 'http://104.224.154.185:8118', 'https': 'https://104.224.154.185:8118', }, 'url':'http://17.push2.eastmoney.com/api/qt/clist/get?', 'base':'http://quote.eastmoney.com', 'fs':'http://push2ex.eastmoney.com/getStockFenShi?', 'trends2':'http://push2his.eastmoney.com/api/qt/stock/trends2/get?', 'kline':'http://74.push2his.eastmoney.com/api/qt/stock/kline/get?', 'fflow':'http://push2.eastmoney.com/api/qt/stock/fflow/kline/get?', 'daykline':'http://push2his.eastmoney.com/api/qt/stock/fflow/daykline/get?', 'info':'http://push2.eastmoney.com/api/qt/stock/get?', 'guba':'http://gbapi.eastmoney.com/webarticlelist/api/Article/Articlelist?', } loginHeaders = { 'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/59.0.3071.86 Safari/537.36', 'Host': '17.push2.eastmoney.com', 'Accept-Encoding': 'gzip, deflate', 'Accept-Language': 'zh-CN,zh;q=0.8', 'Connection':'keep-alive' } loginCookie='' mainjs='''/*! 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f=window.location.href.split("#")[1];if("region_board"==f||"concept_board"==f||"industry_board"==f)0==this.ops.orderDur&&(this.tableHead[10].title="领涨股票",this.tableHead[10].key="f128",this.tableHead[11].key="f136",this.tableHead[11].color="f136",this.createHead(e,t),this.getDataBank(e,t,r)),1==this.ops.orderDur&&(this.tableHead[10].title="领跌股票",this.tableHead[10].key="f128",this.tableHead[11].key="f136",this.tableHead[11].color="f222",this.createHead(e,t),this.getDataBank(e,t,r));else{var o={PB:"市净率",MarketValue:"总市值",FlowCapitalValue:"流通市值",FlowCapitalValue:"流通市值",ChangePercent60Day:"60日涨跌幅",ChangePercent360Day:"年初至今涨跌幅",Speed:"涨速",FiveMinuteChangePercent:"5分钟涨跌",VolumeRate:"量比"};if(this.getParam("st")){for(var n=0;n<this.tableHead.length;n++){var i=this.tableHead[n].title;"总市值"!=i&&"流通市值"!=i&&"60日涨跌幅"!=i&&"年初至今涨跌幅"!=i&&"涨速"!=i&&"5分钟涨跌"!=i&&"量比"!=i||(this.tableHead[n].show=!1),i==o[this.getParam("st")]&&(this.tableHead[n].show=!0)}this.createHead(e,t),this.getDataBank(e,t,r)}else 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class="icon"></b></th>');else if("czYjl"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="纯债溢价率 = (转债最新价 – 纯债价值)/ 纯债价值" class="tooltip-f">纯债溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("hsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足回售触发条件时,可转债持有人有权将其持有的可转债全部或部分按债券面值加上当期应计利息的价格回售给公司" class="tooltip-f">回售触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("qsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足赎回触发条件时,公司有权按照债券面值加当期应计利息的价格赎回全部或部分未转股的可转债" class="tooltip-f">强赎触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("dqShj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="公司有权以债券发行说明书中规定的到期赎回价买回其发行在外债券" class="tooltip-f">到期赎回价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span>'+a.title+'</span><b class="icon"></b></th>');else if("zgValue"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股价值=正股价/转股价*100" class="tooltip-f">转股价值<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("zgYjb"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股溢价率 = (转债最新价 – 转股价值)/ 转股价值" class="tooltip-f">转股溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("czYjl"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" 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class="help-icon"></em></span></span><b class="icon"></b></th>');else i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span>'+a.title+'</span><b class="icon"></b></th>');else if("zgValue"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股价值=正股价/转股价*100" class="tooltip-f">转股价值<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("zgYjb"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股溢价率 = (转债最新价 – 转股价值)/ 转股价值" class="tooltip-f">转股溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("czYjl"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="纯债溢价率 = (转债最新价 – 纯债价值)/ 纯债价值" class="tooltip-f">纯债溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("hsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足回售触发条件时,可转债持有人有权将其持有的可转债全部或部分按债券面值加上当期应计利息的价格回售给公司" class="tooltip-f">回售触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("qsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足赎回触发条件时,公司有权按照债券面值加当期应计利息的价格赎回全部或部分未转股的可转债" class="tooltip-f">强赎触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("dqShj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="公司有权以债券发行说明书中规定的到期赎回价买回其发行在外债券" class="tooltip-f">到期赎回价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" 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a=window.location.href.split("#")[1];"region_board"==a||"concept_board"==a||"industry_board"==a?(0==o.ops.orderDur&&(o.tableHead[10].title="领涨股票",o.tableHead[10].key="f128",o.tableHead[11].key="f136",o.tableHead[11].color="f136",o.createHead(e,r),o.getDataBank(e,r,f)),1==o.ops.orderDur&&(o.tableHead[10].title="领跌股票",o.tableHead[10].key="f207",o.tableHead[11].key="f222",o.tableHead[11].color="f222",o.createHead(e,r),o.getDataBank(e,r,f))):(o.createHead(e,r),o.getDataBank(e,r,f))}})},l.prototype.addEventSelect=function(e,r){var f=this;t("#custom-fields").change(function(){for(var o=t(this).val(),n={PB:"市净率",MarketValue:"总市值",FlowCapitalValue:"流通市值",ChangePercent60Day:"60日涨跌幅",ChangePercent360Day:"年初至今涨跌幅",Speed:"涨速",FiveMinuteChangePercent:"5分钟涨跌",VolumeRate:"量比"},a=0;a<f.tableHead.length;a++){var i=f.tableHead[a].title;"市净率"!=i&&"总市值"!=i&&"流通市值"!=i&&"60日涨跌幅"!=i&&"年初至今涨跌幅"!=i&&"涨速"!=i&&"5分钟涨跌"!=i&&"量比"!=i||(f.tableHead[a].show=!1),i==n[o]&&(f.tableHead[a].show=!0)}f.createHead(e,r),f.createBody(e,r)})},l.prototype.setBody=function(e,t,r){var f=this;if(f.body=t,1==f.ops.zixuan){if(r)o(r);else i.getDefaultStocks().then(function(e){o(e)});function o(t){if(t){f.zixuanList=t.split(",");for(var r=0;r<f.body.length;r++){var o=f.body[r],n=o.f13+"."+o.f12,a=!1;a=!!f.in_array(n,f.zixuanList),o.isZisuan=a}f.createBody(e)}}}f.createBody(e)},l.prototype.add=function(e){t(e+"-table").on("click",".addzx",function(){var e=t(this),r=t(this).attr("data-myscode");i.add(r).then(function(t){1==t&&(e.addClass("hide"),e.removeClass("show"),e.siblings(".delzx").addClass("show"),e.siblings(".delzx").removeClass("hide"))})}),t("#optional-blocks-wrapper").off(),t("#optional-blocks-wrapper").on("click",".addzx",function(e){var r=t(this),f=t(this).attr("data-myscode");i.add(f).then(function(e){1==e&&(r.addClass("hide"),r.removeClass("show"),r.siblings(".delzx").addClass("show"),r.siblings(".delzx").removeClass("hide"))}),e.stopPropagation()})},l.prototype.del=function(e){t(e+"-table").on("click",".delzx",function(){var e=t(this),r=t(this).attr("data-myscode");i.del(r).then(function(t){e.addClass("hide"),e.removeClass("show"),e.siblings(".addzx").addClass("show"),e.siblings(".addzx").removeClass("hide")})}),t("#optional-blocks-wrapper").on("click",".delzx",function(){var e=t(this),r=t(this).attr("data-myscode");i.del(r).then(function(t){e.addClass("hide"),e.removeClass("show"),e.siblings(".addzx").addClass("show"),e.siblings(".addzx").removeClass("hide")})})},l.prototype.getKcbHQData=function(e){var r={secids:e,pz:20,pi:0,ut:"bd1d9ddb04089700cf9c27f6f7426281",po:1,fields:"f2,f3,f4,f5,f6,f12",fltt:2,invt:2,np:1};return 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f=t(r);f.html("");for(var o=this.body,n=this.tableHead,a=0;a<o.length;a++){var i=o[a],s=t("<tr></tr>");a%2==0?s.addClass("odd"):s.addClass("even");for(var l=0;l<n.length;l++){var u=n[l];if(u&&1==u.show){var c="",d=t("<td></td>");if("名称"==u.title||"领涨股"==u.title||"领跌股"==u.title||"主力流入最大股"==u.title)d=t("<td class='mywidth'></td>");if("板块名称"==u.title||"领涨股票"==u.title||"领跌股票"==u.title)d=t("<td class='mywidth3'></td>");if("名称"==u.title&&"usindex_name"==u.name)if(5==i.f107)d=t("<td class='mywidth' style='text-align:left;padding-left:5px;'><em class='circle' title='已收盘'>●</em></td>");else if(3==i.f107)d=t("<td class='mywidth' style='text-align:left;padding-left:5px;'><em class='circle' title='盘中休息'>●</em></td>");else d=t("<td class='mywidth' style='text-align:left;padding-left:5px;'><em class='trading' title='交易中'>●</em></td>");if("最新价"==u.title||"涨跌幅"==u.title)d=t("<td class='mywidth2'></td>");if("相关链接"==u.title&&"Links"==u.name)d=t('<td class=" listview-col-Links"><a 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f=r(79);e.exports={futures:f.futures,stocks:f.stocks,bankuai:f.bankuai,zijinliu:f.zijinliu,zijinliuGegu:f.zijinliuGegu,hushenAStock:f.hushenAStock,hushenStockKcb:f.hushenStockKcb,shhkBoard:f.shhkBoard,staqnetBoard:f.staqnetBoard,indexsh:f.indexsh,neeqstocks:f.neeqstocks,hkstocks:f.hkstocks,hkshstocks:f.hkshstocks,abgu:f.abgu,ahgu:f.ahgu,ahgu2:f.ahgu2,ahgu3:f.ahgu3,hkindex:f.hkindex,usstocks:f.usstocks,usindex:f.usindex,globalamerica:f.globalamerica,globalamerica2:f.globalamerica2,globalamericaOz:f.globalamericaOz,globalamerica3:f.globalamerica3,globalamerica4:f.globalamerica4,conceptboard:f.conceptboard,conceptboardDatil:f.conceptboardDatil,hsgt:f.hsgt,qhsc_jq:f.qhsc_jq,fundcloseend:f.fundcloseend,fundcloseend2:f.fundcloseend2,bond:f.bond,bondnew:f.bondnew,forex:f.forex,forex2:f.forex2,qqsc:f.qqsc,gold:f.gold,gold2:f.gold2,hsbk:f.hsbk,hsbkd:f.hsbkd,hsbklz:f.hsbklz,hszs:f.hszs,hszs2:f.hszs2,mgsc:f.mgsc,mgsc3:f.mgsc3,bondmine:f.bondmine,indexqh:f.indexqh,indexqhNew:f.indexqhNew,zjs:f.zjs,gjqh:f.gjqh,hjqh:f.hjqh,whpj:f.whpj,ggsc:f.ggsc,Zqzqzs:f.Zqzqzs,opsnewgu:f.opsnewgu,hkadr:f.hkadr,hkstocks_cp_asc:f.hkstocks_cp_asc,sh_a_cp_desc:f.sh_a_cp_desc,AB5MinChangePercent:f.AB5MinChangePercent,ABTurnoverRate:f.ABTurnoverRate,ABVolumeRate:f.ABVolumeRate,ABAmplitude:f.ABAmplitude,ABAmount:f.ABAmount,ABPE:f.ABPE,ABPB:f.ABPB,ABFlowCapitalValue:f.ABFlowCapitalValue,ABMarketValue:f.ABMarketValue,AB60DayChangePercent:f.AB60DayChangePercent,AB360DayChangePercent:f.AB360DayChangePercent,ABSpeed:f.ABSpeed,BoardsCPAsc:f.BoardsCPAsc,BoardsCPAscd:f.BoardsCPAscd,BoardsTurnoverRate:f.BoardsTurnoverRate,BoardsSpeed:f.BoardsSpeed,BoardsAmount:f.BoardsAmount,CommonVolume:f.CommonVolume,CommonAmount:f.CommonAmount,BoardsPosition:f.BoardsPosition,MainCaptialFlow:f.MainCaptialFlow,FFRanking:f.FFRanking,BoardsCaptialFlow:f.BoardsCaptialFlow,fullscreenlist:f.fullscreenlist}},function(e,t,r){var f=r(80);e.exports={bankuai:{fields:"f1,f2,f3,f14,f12,f13,f62,f128,f136,f152",head:[{title:"名称",key:"f14",order:!1,href:"<a href='//quote.eastmoney.com/center/boardlist.html#boards-{{0}}1' title='{{1}}'></a>",data:["f12","f14"],show:!0,newcb:function(e){return f.txtPoint(e)}},{title:"涨跌幅",key:"f3",color:"f3",order:!1,fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},show:!0},{title:"主力净流入",key:"f62",color:"f62",order:!1,cb:function(e,t){return f.formatNumberIndex(e)},show:!0},{title:"领涨股",key:"f128",order:!1,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}' title='{{2}}'></a>",data:["f141","f140","f128"],show:!0,newcb:function(e){return f.txtPoint(e)}},{title:"涨跌幅",key:"f136",color:"f136",order:!1,fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},show:!0}],sumcount:5},zijinliu:{fields:"f1,f2,f3,f14,f12,f13,f62,f128,f136,f152,f184",head:[{title:"名称",key:"f14",order:!1,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}' 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href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Name"},{title:"相关链接",key:"",order:!1,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Links"},{title:"最新价",key:"f2",fixedkey:"f1",newcb:function(e,t){return f.formatNumberFlag(e,t)},color:"_f18",order:!0,show:!0,name:"Close"},{title:"涨跌幅",key:"f3",fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f3",order:!0,show:!0,name:"ChangePercent"},{title:"涨跌额",key:"f4",fixedkey:"f1",color:"f4",order:!0,show:!0,name:"Change",newcb:function(e,t){return f.formatNumberFlag(e,t)}},{title:"成交量(手)",key:"f5",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!0,name:"Volume"},{title:"成交额",key:"f6",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!0,name:"Amount"},{title:"振幅",key:"f7",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!0,name:"Amplitude"},{title:"最高",key:"f15",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Hign"},{title:"最低",key:"f16",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Low"},{title:"今开",key:"f17",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Open"},{title:"昨收",key:"f18",fixedkey:"f1",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"PreviousClose"},{title:"量比",key:"f10",order:!0,cb:function(e,t){return f.formatNumberHSGGLB(e)},show:!0,name:"VolumeRate"},{title:"换手率",key:"f8",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!0,name:"TurnoverRate"},{title:"市盈率(动态)",key:"f9",order:!0,show:!0,cb:function(e,t){return f.formatNumberSyl(e)},name:"PERation"},{title:"市净率",key:"f23",order:!0,show:!0,cb:function(e,t){return f.formatNumberSyl(e)},name:"PB"},{title:"总市值",key:"f20",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!1},{title:"流通市值",key:"f21",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!1},{title:"60日涨跌幅",key:"f24",order:!0,fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f24",show:!1},{title:"年初至今涨跌幅",key:"f25",fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f25",order:!0,show:!1},{title:"涨速",key:"f22",color:"f22",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!1},{title:"5分钟涨跌",key:"f11",color:"f11",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!1},{title:"加自选",key:"addzixuan",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Links"}],sumcount:20},hushenStockKcb:{fields:"f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f12,f13,f14,f15,f16,f17,f18,f20,f21,f23,f24,f25,f22,f11,f62,f128,f136,f115,f152",head:[{title:"序号",type:"seq",show:!0,name:"number"},{title:"代码",key:"f12",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Code"},{title:"名称",key:"f14",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Name"},{title:"相关链接",key:"",order:!1,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Links"},{title:"最新价",key:"f2",fixedkey:"f1",newcb:function(e,t){return f.formatNumberFlag(e,t)},color:"_f18",order:!0,show:!0,name:"Close"},{title:"涨跌幅",key:"f3",fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f3",order:!0,show:!0,name:"ChangePercent"},{title:"涨跌额",key:"f4",fixedkey:"f1",color:"f4",order:!0,show:!0,name:"Change",newcb:function(e,t){return f.formatNumberFlag(e,t)}},{title:"成交量(手)",key:"f5",order:!0,cb:function(e,t){return f.kcbMyformatNum(e)},show:!0,name:"Volume"},{title:"成交额",key:"f6",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!0,name:"Amount"},{title:"振幅",key:"f7",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!0,name:"Amplitude"},{title:"最高",key:"f15",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Hign"},{title:"最低",key:"f16",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Low"},{title:"今开",key:"f17",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Open"},{title:"昨收",key:"f18",fixedkey:"f1",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"PreviousClose"},{title:"量比",key:"f10",order:!0,cb:function(e,t){return f.formatNumberHSGGLB(e)},show:!0,name:"VolumeRate"},{title:"换手率",key:"f8",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!0,name:"TurnoverRate"},{title:"市盈率(动态)",key:"f9",order:!0,show:!0,cb:function(e,t){return f.formatNumberSyl(e)},name:"PERation"},{title:"市净率",key:"f23",order:!0,show:!0,cb:function(e,t){return f.formatNumberSyl(e)},name:"PB"},{title:"总市值",key:"f20",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!1},{title:"流通市值",key:"f21",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!1},{title:"60日涨跌幅",key:"f24",order:!0,fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f24",show:!1},{title:"年初至今涨跌幅",key:"f25",fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f25",order:!0,show:!1},{title:"涨速",key:"f22",color:"f22",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!1},{title:"5分钟涨跌",key:"f11",color:"f11",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!1},{title:"加自选",key:"addzixuan",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Links"}],sumcount:20},opsnewgu:{fields:"f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f12,f13,f14,f15,f16,f17,f18,f20,f21,f23,f24,f25,f26,f22,f11,f62,f128,f136,f115,f152",head:[{title:"序号",type:"seq",show:!0,name:"number"},{title:"代码",key:"f12",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Code"},{title:"名称",key:"f14",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Name"},{title:"相关链接",key:"",order:!1,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Links"},{title:"最新价",key:"f2",fixedkey:"f1",newcb:function(e,t){return f.formatNumberFlag(e,t)},color:"_f18",order:!0,show:!0,name:"Close"},{title:"涨跌幅",key:"f3",fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f3",order:!0,show:!0,name:"ChangePercent"},{title:"涨跌额",key:"f4",fixedkey:"f1",color:"f4",order:!0,show:!0,name:"Change",newcb:function(e,t){return f.formatNumberFlag(e,t)}},{title:"成交量(手)",key:"f5",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!0,name:"Volume"},{title:"成交额",key:"f6",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!0,name:"Amount"},{title:"振幅",key:"f7",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!0,name:"Amplitude"},{title:"最高",key:"f15",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Hign"},{title:"最低",key:"f16",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Low"},{title:"今开",key:"f17",fixedkey:"f1",color:"_f18",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"Open"},{title:"昨收",key:"f18",fixedkey:"f1",order:!0,newcb:function(e,t){return f.formatNumberFlag(e,t)},show:!0,name:"PreviousClose"},{title:"换手率",key:"f8",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!0,name:"TurnoverRate"},{title:"市盈率(动态)",key:"f9",order:!0,show:!0,cb:function(e,t){return f.formatNumberSyl(e)},name:"PERation"},{title:"市净率",key:"f23",order:!0,show:!0,cb:function(e,t){return f.formatNumberSyl(e)},name:"PB"},{title:"上市时间",key:"f26",order:!0,show:!0,name:"shtime",cb:function(e,t){return f.formatNumber3(e)}},{title:"总市值",key:"f20",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!1},{title:"流通市值",key:"f21",order:!0,cb:function(e,t){return f.formatNumber(e)},show:!1},{title:"60日涨跌幅",key:"f24",order:!0,fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f24",show:!1},{title:"年初至今涨跌幅",key:"f25",fixedkey:"f152",newcb:function(e,t){return f.formatNumberIndexZdf(e,t)},color:"f25",order:!0,show:!1},{title:"涨速",key:"f22",color:"f22",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!1},{title:"5分钟涨跌",key:"f11",color:"f11",order:!0,cb:function(e,t){return f.formatNumber2(e)},show:!1},{title:"量比",key:"f10",order:!0,cb:function(e,t){return f.formatNumberHSGGLB(e)},show:!1,name:"VolumeRate"},{title:"加自选",key:"addzixuan",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f13","f12"],show:!0,name:"Links"}],sumcount:20},abgu:{fields:"f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f12,f13,f14,f15,f16,f17,f18,f20,f21,f23,f24,f25,f22,f11,f62,f128,f136,f115,f152,f201,f202,f203,f196,f197,f199,f195,f200",head:[{title:"序号",type:"seq",show:!0,name:"number"},{title:"B股代码",key:"f201",order:!0,href:"<a href='//quote.eastmoney.com/unify/r/{{0}}.{{1}}'></a>",data:["f202","f201"],show:!0,name:"Code"},{title:"名称",key:"f203",order:!0,href:"<a 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o=this;o.page.onPage=function(n){o.ops.index=n,n>r&&(o.ops.index=r),o.getDataBank(e,t,f)}},i.prototype.hoverFn=function(){t("#digest-industry").show(),t("#digest-concept").hide(),t("#digest-region").hide(),t("#digest-industry").hover(function(){t("#digest-industry").show(),t("#digest-concept").hide(),t("#digest-region").hide()}),t("#digest-concept").hover(function(){t("#digest-industry").hide(),t("#digest-concept").show(),t("#digest-region").hide()}),t("#digest-region").hover(function(){t("#digest-industry").hide(),t("#digest-concept").hide(),t("#digest-region").show()})},i.prototype.getQihuo=function(e,t,r){0!=this.getParam("sr")&&1!=this.getParam("sr")||(this.ops.orderDur=!0),-1==this.getParam("sr")&&(this.ops.orderDur=!1);var f=window.location.href.split("#")[1];if("region_board"==f||"concept_board"==f||"industry_board"==f)0==this.ops.orderDur&&(this.tableHead[10].title="领涨股票",this.tableHead[10].key="f128",this.tableHead[11].key="f136",this.tableHead[11].color="f136",this.createHead(e,t),this.getDataBank(e,t,r)),1==this.ops.orderDur&&(this.tableHead[10].title="领跌股票",this.tableHead[10].key="f128",this.tableHead[11].key="f136",this.tableHead[11].color="f222",this.createHead(e,t),this.getDataBank(e,t,r));else{var o={PB:"市净率",MarketValue:"总市值",FlowCapitalValue:"流通市值",FlowCapitalValue:"流通市值",ChangePercent60Day:"60日涨跌幅",ChangePercent360Day:"年初至今涨跌幅",Speed:"涨速",FiveMinuteChangePercent:"5分钟涨跌",VolumeRate:"量比"};if(this.getParam("st")){for(var n=0;n<this.tableHead.length;n++){var a=this.tableHead[n].title;"总市值"!=a&&"流通市值"!=a&&"60日涨跌幅"!=a&&"年初至今涨跌幅"!=a&&"涨速"!=a&&"5分钟涨跌"!=a&&"量比"!=a||(this.tableHead[n].show=!1),a==o[this.getParam("st")]&&(this.tableHead[n].show=!0)}this.createHead(e,t),this.getDataBank(e,t,r)}else this.createHead(e,t),this.getDataBank(e,t,r)}},i.prototype.createHead=function(e,r){for(var f=this.tableHead,o=t('<tr role="row"></tr>'),n=0;n<f.length;n++){var a=f[n];if(a&&1==a.show){if("序号"==a.title||"加自选"==a.title||0==a.order)var i=t('<th style="" class="listview-col-'+a.name+' sorting_disabled" rowspan="1" colspan="1" aria-label="'+a.title+'"><span style="color:#333">'+a.title+'</span><b class="icon"></b></th>');else if(a.key==this.ops.order)if(1==this.ops.orderDur)if("zgValue"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股价值=正股价/转股价*100" class="tooltip-f">转股价值<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("zgYjb"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股溢价率 = (转债最新价 – 转股价值)/ 转股价值" class="tooltip-f">转股溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("czYjl"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="纯债溢价率 = (转债最新价 – 纯债价值)/ 纯债价值" class="tooltip-f">纯债溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("hsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足回售触发条件时,可转债持有人有权将其持有的可转债全部或部分按债券面值加上当期应计利息的价格回售给公司" class="tooltip-f">回售触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("qsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足赎回触发条件时,公司有权按照债券面值加当期应计利息的价格赎回全部或部分未转股的可转债" class="tooltip-f">强赎触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("dqShj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="公司有权以债券发行说明书中规定的到期赎回价买回其发行在外债券" class="tooltip-f">到期赎回价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else i=t('<th style="" class="listview-col-'+a.name+' sorting_asc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span>'+a.title+'</span><b class="icon"></b></th>');else if("zgValue"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股价值=正股价/转股价*100" class="tooltip-f">转股价值<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("zgYjb"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股溢价率 = (转债最新价 – 转股价值)/ 转股价值" class="tooltip-f">转股溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("czYjl"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="纯债溢价率 = (转债最新价 – 纯债价值)/ 纯债价值" class="tooltip-f">纯债溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("hsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足回售触发条件时,可转债持有人有权将其持有的可转债全部或部分按债券面值加上当期应计利息的价格回售给公司" class="tooltip-f">回售触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("qsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足赎回触发条件时,公司有权按照债券面值加当期应计利息的价格赎回全部或部分未转股的可转债" class="tooltip-f">强赎触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("dqShj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="公司有权以债券发行说明书中规定的到期赎回价买回其发行在外债券" class="tooltip-f">到期赎回价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else i=t('<th style="" class="listview-col-'+a.name+' sorting_desc" rowspan="1" colspan="1" aria-label="'+a.title+'"><span>'+a.title+'</span><b class="icon"></b></th>');else if("zgValue"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股价值=正股价/转股价*100" class="tooltip-f">转股价值<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("zgYjb"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="转股溢价率 = (转债最新价 – 转股价值)/ 转股价值" class="tooltip-f">转股溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("czYjl"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="纯债溢价率 = (转债最新价 – 纯债价值)/ 纯债价值" class="tooltip-f">纯债溢价率<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("hsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足回售触发条件时,可转债持有人有权将其持有的可转债全部或部分按债券面值加上当期应计利息的价格回售给公司" class="tooltip-f">回售触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("qsCfj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="满足赎回触发条件时,公司有权按照债券面值加当期应计利息的价格赎回全部或部分未转股的可转债" class="tooltip-f">强赎触发价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else if("dqShj"==a.name)i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span><span title="公司有权以债券发行说明书中规定的到期赎回价买回其发行在外债券" class="tooltip-f">到期赎回价<em class="help-icon"></em></span></span><b class="icon"></b></th>');else i=t('<th style="" class="listview-col-'+a.name+' sorting" rowspan="1" colspan="1" aria-label="'+a.title+'"><span>'+a.title+'</span><b class="icon"></b></th>');i.attr("data-key",a.key),o.append(i)}}t(e).find("table thead").html(""),t(e).find("table thead").append(o)},i.prototype.getDataBank=function(e,r,o){var n=this,a=this.ops,i=(this.config,{orderBy:a.order,sort:a.orderDur?"asc":"desc",pageSize:a.pageSize,pageIndex:a.index-1,blockName:a.blockName});f(i,a.url,function(f){var i=f.list;if(i){var s=i;try{a.sc!=undefined&&(s=i.map(function(e){return e.sc=a.sc,e}))}catch(c){}var l=f.total,u=Math.ceil(l/a.pageSize);if(a.sumPage=u,u>1)n.page.setOps({index:a.index,sumPage:a.sumPage}),n.pageClick(e,r,u,o),t(".dataTables_paginate").show();else t(".dataTables_paginate").hide();n.setBody(e,s,o)}else s=[],t(".dataTables_paginate").hide(),n.setBody(e,s,o)})},i.prototype.addEvent=function(e,r,f){var o=this;t(e).find("thead").off(),t(e).find("thead").on("click","th",function(){var n=t(this).attr("data-key");n&&"addzixuan"!=n&&(n==o.ops.order?o.ops.orderDur=!o.ops.orderDur:(o.ops.order=n,o.ops.orderDur=!0),o.createHead(e,r),o.getDataBank(e,r,f))})},i.prototype.setBody=function(e,t,r){var f=this;if(f.body=t,1==f.ops.zixuan){if(r)o(r);else a.getDefaultStocks().then(function(e){o(e)});function o(t){if(t){f.zixuanList=t.split(",");for(var r=0;r<f.body.length;r++){var o=f.body[r],n=o.f13+"."+o.f12,a=!1;a=!!f.in_array(n,f.zixuanList),o.isZisuan=a}f.createBody(e)}}}f.createBody(e)},i.prototype.getParam=function(e){var t=location.search,r={};if(""!=t)for(var f,o,n=(t=t.substring(1,t.length)).split("&"),a=0;a<n.length;a++)f=n[a].substring(0,n[a].indexOf("=")),o=n[a].substring(n[a].indexOf("=")+1,n[a].length),r[f]=o;return"undefined"!=typeof r[e]?r[e]:null},i.prototype.formatData=function(){for(var e=this.body,t=["f2","f4","f15","f16","f17","f18","f28","f31","f32"].join(",")+",",r=["f3","f7","f8","f9","f10","f11","f22","f23","f24","f25","f33"].join(",")+",",f=["f115"].join(",")+",",o=0,n=e.length;o<n;o++){var a=e[o],i=Math.pow(10,a.f1);for(var s in a)if(t.indexOf(s+",")>-1&&(a[s]=(a[s]/i).toFixed(a.f1)),r.indexOf(s+",")>-1&&(a[s]=(a[s]/100).toFixed(2)),f.indexOf(s+",")>-1){var l=Math.pow(10,a.f152);a[s]=(a[s]/l).toFixed(a.f152)}}},i.prototype.createBody=function(e){var r=t(e+"-table").find("tbody");0==r.length&&(r=t(e).find("tbody"));var f=t(r);f.html("");for(var o=this.body,n=this.tableHead,a=0;a<o.length;a++){var i=o[a],s=t("<tr></tr>");a%2==0?s.addClass("odd"):s.addClass("even");for(var l=0;l<n.length;l++){var u=n[l];if(u&&1==u.show){var c="",d=t("<td></td>");if("名称"==u.title||"领涨股"==u.title||"领跌股"==u.title||"主力流入最大股"==u.title)d=t("<td class='mywidth'></td>");if("板块名称"==u.title||"领涨股票"==u.title||"领跌股票"==u.title)d=t("<td 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f(o.usstocks).Bankuai("#table_wrapper","b:MK0218");break;case"us_media":new f(o.usstocks).Bankuai("#table_wrapper","b:MK0220");break;case"us_automotive_energy":new f(o.usstocks).Bankuai("#table_wrapper","b:MK0219");break;case"us_manufacture_retail":new f(o.usstocks).Bankuai("#table_wrapper","b:MK0221");break;case"us_chinese_internet":new f(o.usstocks).Bankuai("#table_wrapper","b:MK0202");break;case"global_asia":new f(o.globalamerica).Bankuai("#table_wrapper","i:1.000001,i:0.399001,i:0.399005,i:0.399006,i:1.000300,i:100.HSI,i:100.HSCEI,i:124.HSCCI,i:100.TWII,i:100.N225,i:100.KOSPI200,i:100.KS11,i:100.STI,i:100.SENSEX,i:100.KLSE,i:100.SET,i:100.PSI,i:100.KSE100,i:100.VNINDEX,i:100.JKSE,i:100.CSEALL");break;case"global_america":new f(o.globalamerica).Bankuai("#table_wrapper","i:100.DJIA,i:100.SPX,i:100.NDX,i:100.TSX,i:100.BVSP,i:100.MXX");break;case"global_euro":new f(o.globalamerica).Bankuai("#table_wrapper","i:100.SX5E,i:100.FTSE,i:100.MCX,i:100.AXX,i:100.FCHI,i:100.GDAXI,i:100.RTS,i:100.IBEX,i:100.PSI20,i:100.OMXC20,i:100.BFX,i:100.AEX,i:100.WIG,i:100.OMXSPI,i:100.SSMI,i:100.HEX,i:100.OSEBX,i:100.ATX,i:100.MIB,i:100.ASE,i:100.ICEXI,i:100.PX,i:100.ISEQ");break;case"global_australia":new f(o.globalamerica).Bankuai("#table_wrapper","i:100.AS51,i:100.AORD,i:100.NZ50");break;case"global_qtzs":new f(o.globalamerica).Bankuai("#table_wrapper","i:100.UDI,i:100.BDI,i:100.CRB");break;case"futures_cffex":var r={type:"zjs",order:"zdf",url:a.qihuourl+"/list/8"};new n(r).Qihuo("#table_wrapper");break;case"futures_cffex-_TS":r={type:"zjs",order:"zdf",url:a.qihuourl+"/list/variety/8/6"};new n(r).Qihuo("#table_wrapper");break;case"futures_cffex-_T":r={type:"zjs",order:"zdf",url:a.qihuourl+"/list/variety/8/4"};new n(r).Qihuo("#table_wrapper");break;case"futures_cffex-_TF":r={type:"zjs",order:"zdf",url:a.qihuourl+"/list/variety/8/5"};new n(r).Qihuo("#table_wrapper");break;case"futures_cffex-_IF":r={type:"zjs",order:"zdf",url:a.qihuourl+"/list/variety/8/2"};new n(r).Qihuo("#table_wrapper");break;case"futures_cffex-_IH":r={type:"zjs",order:"zdf",url:a.qihuourl+"/list/variety/8/3"};new n(r).Qihuo("#table_wrapper");break;case"futures_cffex-_IC":r={type:"zjs",order:"zdf",url:a.qihuourl+"/list/variety/8/1"};new n(r).Qihuo("#table_wrapper");break;case"hk_index_futures":r={type:"gjs",order:"name",orderDur:"1",url:a.qihuourl+"/list/HKINDEXF"};new n(r).Qihuo("#table_wrapper");break;case"hk_stock_futures":r={type:"gjs_gpqh",order:"name",orderDur:"1",url:a.qihuourl+"/list/HKSTOCKF"};new n(r).Qihuo("#table_wrapper");break;case"HCF_CUS":r={type:"gjs",order:"name",orderDur:"1",url:a.qihuourl+"/list/HKCNYF"};new n(r).Qihuo("#table_wrapper");break;case"HMFS_LRP":r={type:"gjs",order:"name",orderDur:"1",url:a.qihuourl+"/list/HKMETALFS"};new n(r).Qihuo("#table_wrapper");break;case"futures_global":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/COMEX,NYMEX,COBOT,SGX,NYBOT,LME,MDEX,TOCOM,IPE"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-comex":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/COMEX"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-nymex":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/NYMEX"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-cobot":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/COBOT"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-sgx":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/SGX"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-nybot":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/NYBOT"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-lme":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/LME"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-mdex":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/MDEX"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-tocom":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/TOCOM"};new n(r).Qihuo("#table_wrapper");break;case"futures_global-ipe":r={type:"gjqh",order:"zdf",url:a.qihuourl+"/list/IPE"};new n(r).Qihuo("#table_wrapper");break;case"futures_finance":r={blockName:"financial",type:"gjqh",order:"zdf",url:a.qihuourl+"/list/block"};new n(r).Qihuo("#table_wrapper");break;case"futures_energy":r={blockName:"energy",type:"gjqh",order:"zdf",url:a.qihuourl+"/list/block"};new n(r).Qihuo("#table_wrapper");break;case"futures_metal":r={blockName:"metal",type:"gjqh",order:"zdf",url:a.qihuourl+"/list/block"};new n(r).Qihuo("#table_wrapper");break;case"futures_farmproduce":r={blockName:"agricultural",type:"gjqh",order:"zdf",url:a.qihuourl+"/list/block"};new n(r).Qihuo("#table_wrapper");break;case"fund_close_end":new f(o.fundcloseend).Bankuai("#table_wrapper","e:19");break;case"fund_etf":new f(o.fundcloseend).Bankuai("#table_wrapper","b:MK0021,b:MK0022,b:MK0023,b:MK0024");break;case"fund_lof":new f(o.fundcloseend).Bankuai("#table_wrapper","b:MK0404,b:MK0405,b:MK0406,b:MK0407");break;case"bond_index":new f(o.bond).Bankuai("#table_wrapper","i:1.000012,i:1.000013,i:1.000022,i:1.000061,i:0.395021,i:0.395022,i:0.395031,i:0.395032,i:0.399481");break;case"bond_sh":new f(o.bond).Bankuai("#table_wrapper","m:1+t:4");break;case"bond_national_sh":new f(o.bondnew).Bankuai("#table_wrapper","m:1+b:MK0351");break;case"bond_enterprise_sh":new f(o.bondnew).Bankuai("#table_wrapper","m:1+b:MK0353");break;case"bond_convertible_sh":new f(o.bond).Bankuai("#table_wrapper","m:1+b:MK0354");break;case"bond_sz":new f(o.bond).Bankuai("#table_wrapper","m:0+t:8");break;case"bond_national_sz":new f(o.bondnew).Bankuai("#table_wrapper","m:0+b:MK0351");break;case"bond_enterprise_sz":new f(o.bondnew).Bankuai("#table_wrapper","m:0+b:MK0353");break;case"bond_convertible_sz":new f(o.bond).Bankuai("#table_wrapper","m:0+b:MK0354");break;case"bond_sh_buyback":new f(o.bondnew).Bankuai("#table_wrapper","m:1+b:MK0356");break;case"bond_sz_buyback":new f(o.bondnew).Bankuai("#table_wrapper","m:0+b:MK0356");break;case"forex_all":new f(o.forex).Bankuai("#table_wrapper","m:119,m:120,m:121,m:133");break;case"forex_basic":new f(o.forex).Bankuai("#table_wrapper","b:MK0300");break;case"forex_cross":new f(o.forex).Bankuai("#table_wrapper","b:MK0301");break;case"forex_cny":new f(o.forex).Bankuai("#table_wrapper","m:120,m:121,m:133");break;case"forex_cnyc":new f(o.forex).Bankuai("#table_wrapper","m:120");break;case"forex_cnyi":new f(o.forex).Bankuai("#table_wrapper","m:121+t:1");break;case"forex_cnyb":new f(o.forex).Bankuai("#table_wrapper","m:121+t:2");break;case"forex_cnh":new f(o.forex).Bankuai("#table_wrapper","m:133");break;case"forex_exchange_icbc":new f(o.whpj).Bankuai("#table_wrapper","m:162+s:1");break;case"forex_exchange_abc":new f(o.whpj).Bankuai("#table_wrapper","m:162+s:2");break;case"forex_exchange_boc":new f(o.whpj).Bankuai("#table_wrapper","m:162+s:4");break;case"forex_exchange_ccb":new f(o.whpj).Bankuai("#table_wrapper","m:162+s:8");break;case"forex_exchange_bcm":new f(o.whpj).Bankuai("#table_wrapper","m:162+s:16");break;case"forex_exchange_cmb":new f(o.whpj).Bankuai("#table_wrapper","m:162+s:32");break;case"options_sh50etf_all":new f(o.qqsc).Bankuai("#table_wrapper","m:10");break;case"options_szetf_all":case"options_sz300etf_all":new f(o.qqsc).Bankuai("#table_wrapper","m:12");break;case"options_sh50etf_call":new f(o.qqsc).Bankuai("#table_wrapper","m:10+t:173");break;case"options_sh50etf_put":new f(o.qqsc).Bankuai("#table_wrapper","m:10+t:174");break;case"options_shfe_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/SHFEOPTION"};new n(r).Qihuo("#table_wrapper");break;case"options_cu_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/SHFEOPTION/1"};new n(r).Qihuo("#table_wrapper");break;case"options_ru_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/SHFEOPTION/2"};new n(r).Qihuo("#table_wrapper");break;case"options_au_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/151/3"};new n(r).Qihuo("#table_wrapper");break;case"options_dce_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/DCEOPTION"};new n(r).Qihuo("#table_wrapper");break;case"options_beanpulp_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/DCEOPTION/1"};new n(r).Qihuo("#table_wrapper");break;case"options_c_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/DCEOPTION/2"};new n(r).Qihuo("#table_wrapper");break;case"options_t_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/DCEOPTION/3"};new n(r).Qihuo("#table_wrapper");break;case"options_czce_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/CZCEOPTION"};new n(r).Qihuo("#table_wrapper");break;case"options_sugar_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/CZCEOPTION/1"};new n(r).Qihuo("#table_wrapper");break;case"options_cf_all":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/CZCEOPTION/2"};new n(r).Qihuo("#table_wrapper");break;case"options_cf_ta":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/CZCEOPTION/4"};new n(r).Qihuo("#table_wrapper");break;case"options_cf_ma":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/CZCEOPTION/3"};new n(r).Qihuo("#table_wrapper");break;case"options_cf_cp":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/variety/CZCEOPTION/5"};new n(r).Qihuo("#table_wrapper");break;case"options_cffex_all":case"options_cffex_io":r={type:"qqsc",order:"zdf",url:a.qihuourl+"/list/11",sc:11};new 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true if we are in IE8 or IE9 return (window.XDomainRequest && (window.XMLHttpRequest && new XMLHttpRequest().responseType === undefined)) ? true : false; } global[evsImportName] = EventSource; })(window); /***/ }), /***/ "./src/modules/old_f1/index.js": /*!*************************************!*\ !*** ./src/modules/old_f1/index.js ***! \*************************************/ /*! no static exports found */ /***/ (function(module, exports, __webpack_require__) { __webpack_require__(/*! ../ie_sse_polyfill */ "./src/modules/ie_sse_polyfill/index.js"); var template = __webpack_require__(/*! ../template */ "./src/modules/template/index.js") // var marge = require('lodash/merge'); var marge = _.merge; $(function () { drawTable(); setInterval(refresh, 30 * 1000); //setInterval(loadQuote, 10*1000); loadQuote(); JuadeIe7(); filterFun(); clickFun(); // isRong(); var suggest = new suggest2017({ inputid: "search_box", offset: { left: -91, top: 5 } }); }); function refresh() { var option = argFun(); drawTable(option); // loadQuote(); } //区分ie7 function JuadeIe7() { //增加判断浏览器是否为ie7及以下 if (document.all && !document.querySelector) { setInterval(loadQuote, 30 * 1000); } else { sseHeadData(); } } function argFun() { var option = {}; $(".bigOrder dd input[type=radio]").each(function () { if ($(this).prop("checked")) { // option.gtvolume = $(this).val(); var gtvolume = $(this).val(); if(gtvolume == '100') { option.ft = 2 } else if(gtvolume == '200') { option.ft = 3 } else if(gtvolume == '500') { option.ft = 4 } else if(gtvolume == '1000') { option.ft = 5 } else if(gtvolume == '2000') { option.ft = 6 } else if(gtvolume == '5000') { option.ft = 7 } else if(gtvolume == '10000') { option.ft = 8 } else { option.ft = 1 } } }); option.sort = $("#reverseInput").val(); option.pageindex = Number($(".curPage").html()) - 1; //console.log(option) return option; } //青色=绿色=1=#00ffff,紫色=红色=2=ff00ff 先判断方向再判断大于20万 1是涨 -1是跌 0是没跌没涨 //增加newflag 倒序无需执行分页 //分时成交 function drawTable(option, newflag) { var _default = { "pageindex": 0, "id": stockEnity.stockId, "sort": 1, "ft": 1 } var _option = $.extend(_default, option); _option.code = getCode(); _option.market = getMarket(); if (_option.pageindex == -1) { return; } // var url = "http://61.152.230.32:1981/getStockFenShi?pagesize=144&ut=7eea3edcaed734bea9cbfc24409ed989&dpt=wzfscj" var url = "http://push2ex.eastmoney.com/getStockFenShi?pagesize=144&ut=7eea3edcaed734bea9cbfc24409ed989&dpt=wzfscj" $.ajax({ url: url, dataType: "jsonp", jsonp: "cb", data: _option, success: function (json) { if (json.data) { // console.log('分时时间') // console.log(json) var count = Math.ceil(json.data.tc / 144); var kcbFlag = json.data.ct; if(count == 0) { count = 1; } // console.log(count) var data = json.data.data, pc = Dealprice(json.data.cp); var list1 = [], list2 = [], list3 = [], list4 = []; var html_1 = "", html_2 = "", html_3 = "", html_4 = ""; var dir = "", color = "", otherColor = "", chje = ""; if (!data && data.length == 0 && typeof data == "string") { return; } for (var i = 0; i < data.length; i++) { var preItems = data[i-1]; var items = data[i]; color = Dealprice(items.p) - pc == 0 ? "" : Dealprice(items.p) - pc > 0 ? "red" : Dealprice(items.p) - pc < 0 ? "green" : ""; chje = items.v * 100 * Dealprice(items.p); if (items.bs == "1") { otherColor = chje > 200000 ? "blue" : "green"; } else if (items.bs == "2") { otherColor = chje > 200000 ? "purple" : "red"; } else { otherColor = ""; } //箭头 if (items.bs != "4") { if(preItems) { if (items.p > preItems.p) { dir = "red"; } else if (items.p < preItems.p) { dir = "green"; } else { dir = ""; } }else { dir = ""; } } else { dir = ""; items.v = "-"; color = ""; } //判断是否是科创板 手数做不同处理 var new_cjs = items.v; if(kcbFlag == 1) { new_cjs = kcbMyformatNum(new_cjs); // console.log(new_cjs) }else { new_cjs = new_cjs; } if (i < 36) { list1.push({ "time": DealTime(items.t), "close": Dealprice(items.p), "coloseColor": color, "num": new_cjs, "fontColor": otherColor, "dir": dir }); } if (i > 35 && i < 72) { list2.push({ "time": DealTime(items.t), "close": Dealprice(items.p), "coloseColor": color, "num": new_cjs, "fontColor": otherColor, "dir": dir }); } if (i > 71 && i < 108) { list3.push({ "time": DealTime(items.t), "close": Dealprice(items.p), "coloseColor": color, "num": new_cjs, "fontColor": otherColor, "dir": dir }); } if (i > 107 && i < 144) { list4.push({ "time": DealTime(items.t), "close": Dealprice(items.p), "coloseColor": color, "num": new_cjs, "fontColor": otherColor, "dir": dir }); } } var html_1 = template("tmp", { list: list1 }); var html_2 = template("tmp", { list: list2 }); var html_3 = template("tmp", { list: list3 }); var html_4 = template("tmp", { list: list4 }); $("#listTable1 tbody").html(html_1); $("#listTable2 tbody").html(html_2); $("#listTable3 tbody").html(html_3); $("#listTable4 tbody").html(html_4); if(newflag !== false) { pageFun(count, _option.pageindex); } } } }) } //科创板成交量 function kcbMyformatNum(num) { if (num == '-') { return '-'; } if (num == undefined || isNaN(num)) { return ''; } var hz = ''; var num2 = ''; try { if (num >= 0 && num <= 99.999999999) { num2 = parseFloat(num).toFixed(2); } else if (num >= 100 && num <= 999) { num2 = parseFloat(num).toFixed(1); } else if (num >= 1000) { // num2 = parseFloat(num).toFixed(0); if (num > 10000 && num < 100000000) { num2 = (num / 10000).toFixed(2) + "万"; } else if (num > 100000000) { num2 = (num / 100000000).toFixed(2) + "亿"; } else if (num == 0) { num2 = '-'; } else { num2 = num.toFixed(0); } } return num2.toString() + hz; } catch (error) { return '-'; } } //处理价格 function Dealprice(val) { try { val = val/1000; return val.toFixed(2); } catch(e) { return '-' } } //处理时间 function DealTime(val) { try { val = '' + val; if(val.length == 5) { val = '0' + val; } return val.substr(0,2) + ':' + val.substr(2,2) + ':' + val.substr(4,2) } catch(e) { return '-' } } //翻页的html function pageFun(count, page) { var count = Number(count); var page = Number(page); if (count == 0) { page = 0; } var obj = { "curPage": page, "prev": page == 0 ? 0 : page - 1 , "next": page == count ? count : page + 1, "count": count }; var lstxt = obj.curPage + 1; //ie7 $(".prevPage").attr("mypage", obj.prev); // $(".prevPage").attr("value", obj.prev); $(".nextPage").attr("mypage", obj.next); $(".lastPage").attr("mypage", obj.count-1); $(".curPage").text(lstxt); $(".count").text(obj.count); if (count == page+1) { $(".lastPage").removeClass("canClick"); $(".arrowR").hide(); $(".nextPage").removeClass("canClick"); } else { $(".lastPage").addClass("canClick"); $(".nextPage").addClass("canClick"); $(".arrowR").show(); } if (page+1 == 1) { $(".fistPage").removeClass("canClick"); $(".prevPage").removeClass("canClick"); $(".arrowL").hide(); } else { $(".fistPage").addClass("canClick"); $(".prevPage").addClass("canClick"); $(".arrowL").show(); } if (count == 0) { $(".liPage").removeClass("canClick"); $(".arrowR").hide(); $(".arrowL").hide(); } } //筛选、倒序 function filterFun() { $(".bigOrder input[type=radio]").change(function () { var option = {}; // console.log('筛选大单:',$(this).val()) // option.gtvolume = $(this).val(); var gtvolume = $(this).val(); if(gtvolume == '100') { option.ft = 2 } else if(gtvolume == '200') { option.ft = 3 } else if(gtvolume == '500') { option.ft = 4 } else if(gtvolume == '1000') { option.ft = 5 } else if(gtvolume == '2000') { option.ft = 6 } else if(gtvolume == '5000') { option.ft = 7 } else if(gtvolume == '10000') { option.ft = 8 } else { option.ft = 1 } option.sort = $("#reverseInput").val(); drawTable(option); }); $(".reverseDiv input[type=checkbox]").change(function () { var option = {}; if ($(this).prop("checked")) { $(this).val("2"); } else { $(this).val("1"); } option.sort = $("#reverseInput").val(); //option.page = Number($(".curPage").html()); //argFun() var _option = $.extend(argFun(), option); drawTable(_option, false); }); } //点击事件 function clickFun() { $(".goBtn").click(function () { var val = Number($(".go").val()); var curPage = Number($(".PageNavBtm .curPage").text()); var lastPage = Number($(".PageNavBtm .lastPage").attr("mypage")); if (val == "" || val > lastPage+1 || val < 1 || isNaN(val) > 0 || val == curPage) { $(".go").val(""); return; } var option = {}; option.pageindex = val-1; var _option = $.extend(argFun(), option); drawTable(_option); $(".go").val(""); }); $(".liPage").click(function () { $(".go").val(""); if ($(this).hasClass("canClick")) { var val = $(this).attr("mypage"); var option = {}; option.pageindex = val; var _option = $.extend(argFun(), option); drawTable(_option); } }); $(".go").keydown(function (e) { var keyCode = e.keyCode ? e.keyCode : e.which ? e.which : e.charCode; //兼容IE 火狐 谷歌 if (keyCode == 13) { $(".goBtn").trigger("click"); return false; } }); $(".mobile-icon").mouseover(function () { $(".QRcode-div").show(); }); $(".mobile-icon").mouseout(function () { $(".QRcode-div").hide(); }); } //快速行情 function loadQuote() { var options = { "id": stockEnity.stockId } var secid = getMarket() + '.' + getCode(); // var _url = "//nuff.eastmoney.com/EM_Finance2015TradeInterface/JS.ashx?token=beb0a0047196124721f56b0f0ff5a27c"; var url = 'http://push2.eastmoney.com/api/qt/stock/get?ut=fa5fd1943c7b386f172d6893dbfba10b&invt=2&fltt=2&fields=f1,f43,f57,f58,f169,f170,f46,f44,f51,f168,f47,f116,f60,f45,f52,f50,f48,f167,f117,f71,f161,f49,f162,f107,f86,f177,f127,f199,f128,f80,f152,f110,f111,f107,f285,f286,f262,f263,f256,f257,f269,f270&secid=' + secid; $.ajax({ url: url, // data: options, dataType: "jsonp", jsonp: "cb", success: function (json) { // console.log(json) var items = json.data; if (!items || items.length == 0 || typeof items == "string") { return; } if(items) { formatHead(json); renderContent(items); renderRong(items); renderGenming(); } } }); } //sse function sseHeadData() { var secid = getMarket() + '.' + getCode(); //正式地址 var url = "http://" + (Math.floor(Math.random() * 99) + 1) +".push2.eastmoney.com/api/qt/stock/sse?ut=fa5fd1943c7b386f172d6893dbfba10b&invt=2&fltt=2&fields=f1,f43,f57,f58,f169,f170,f46,f44,f51,f168,f47,f116,f60,f45,f52,f50,f48,f167,f117,f71,f161,f49,f162,f107,f86,f177,f127,f199,f128,f80,f152,f110,f111,f107,f285,f286,f262,f263,f256,f257,f269,f270&secid=" + secid; var evtSource = new EventSource(url); evtSource.onmessage = function (msg) { var obj = JSON.parse(msg.data) var items = msg.data; if (obj.data) { formatHead(obj); } } } //head format var headSourceData; function formatHead(data) { // console.log(data); if(data.full == 1 && data.data){ headSourceData = data.data; } else if(data.full == 0 && data.data ){ if(headSourceData) { headSourceData = marge(headSourceData, data.data); } } renderHead(headSourceData); } function renderHead(items) { var list = [ { "name": "zxj", "item": items.f43 == "-" ? "-" : (items.f43).toFixed(items.f152), "color": getColor(items.f170) }, { "name": "zde", "item": items.f169 == "-" ? "-" : (items.f169).toFixed(items.f152), "color": getColor(items.f170) }, { "name": "zdf", "item": items.f170 == "-" ? "-" : (items.f170).toFixed(items.f152) + "%", "color": getColor(items.f170) }, { "name": "jk", "item": items.f46 == "-" ? "-" : (items.f46).toFixed(items.f152), "color": getColor(items.f46 - items.f60) }, { "name": "zs", "item": items.f60 == "-" ? "-" : (items.f60).toFixed(items.f152)}, { "name": "zg", "item": items.f44 == "-" ? "-" : (items.f44).toFixed(items.f152), "color": getColor(items.f44 - items.f60) }, { "name": "zd", "item": items.f45 == "-" ? "-" : (items.f45).toFixed(items.f152), "color": getColor(items.f45 - items.f60) }, { "name": "zt", "item": items.f51 == "-" ? "-" : (items.f51).toFixed(2), "color": getColor(items.f51 - items.f60) }, { "name": "dt", "item": items.f52 == "-" ? "-" : (items.f52).toFixed(2), "color": getColor(items.f52 - items.f60) }, { "name": "hs", "item": items.f168 == "-" ? "-" : items.f168 + "%" }, { "name": "lb", "item": items.f50 == "-" ? "-" : (items.f50).toFixed(2)}, { "name": "cjl", "item": items.f47 == "-" ? "-" : NumbericFormat(items.f47) }, { "name": "cje", "item": items.f48 == "-" ? "-" : NumbericFormat(items.f48) }, { "name": "sy", "item": items.f162 == "-" ? "-" : (items.f162).toFixed(2)}, { "name": "sj", "item": items.f167 == "-" ? "-" : (items.f167).toFixed(2)}, { "name": "zsz", "item": items.f116 == "-" ? "-" : NumbericFormat(items.f116) }, { "name": "ltsz", "item": items.f117 == "-" ? "-" : NumbericFormat(items.f117) } ]; for (var i = 0; i < list.length; i++) { var name = $("#" + list[i].name); name.text(list[i].item); name.removeClass("red").removeClass("green").addClass(list[i].color); } //箭头颜色 onChangeDataRender(items.f170); //时间 if(items.f86) { var d = new Date(items.f86 * 1000); //("0" + (d.getMonth() + 1)).slice(-2) d.getMinutes() d.getMinutes() d.getSeconds() var whichDay = ''; if(d.getDay() == 0) { whichDay = '星期天'; } else if(d.getDay() == 1) { whichDay = '星期一'; } else if(d.getDay() == 2) { whichDay = '星期二'; } else if(d.getDay() == 3) { whichDay = '星期三'; } else if(d.getDay() == 4) { whichDay = '星期四'; } else if(d.getDay() == 5) { whichDay = '星期五'; }else if(d.getDay() == 6) { whichDay = '星期六'; } youWant = d.getFullYear() + '-' + (("0" + (d.getMonth() + 1)).slice(-2)) + '-' + (("0" + (d.getDate())).slice(-2)) + ' ' + whichDay + ' ' + ("0" + (d.getHours())).slice(-2) + ':' + ("0" + (d.getMinutes())).slice(-2) + ':' + ("0" + (d.getSeconds())).slice(-2); $("#day").html('(' + youWant + ')'); } //判断若字数过长 字体变小 if(items.f43 >= 1000) { $("#zxj").css("font-size", "23px") } } function renderContent(items) { var obj = { "market": items.f107, "code": items.f57, "name": items.f58, "id": items.f107 + items.f57, "time": '111' } $(".n1").attr("href", "http://data.eastmoney.com/zlsj/detail/" + obj["code"] + "-1.html"); if(obj["name"]) { $(".n2").text("查看" + obj["name"] + "买卖点"); $(".n3").text(obj["name"] + "股价预警") $(".quote_title_0").text(obj["name"]); } $(".quote_title_1").text(obj["code"]); var src = "//pifm3.eastmoney.com/EM_Finance2014PictureInterface/RC.ashx?url=http://m.quote.eastmoney.com/stock," + obj["code"] + ".shtml"; $(".QRcode-div img").attr("src", src); //ie8 if(obj["code"] && obj["name"]) { // $("title").text(obj["name"] + obj["code"] + "股票价格_行情_走势图—东方财富网"); document.title = obj["name"] + obj["code"] + "股票价格_行情_走势图—东方财富网"; } } function renderRong(items) { //融 和港股通 // if(items.f177 & 64) { // $(".rongi").show(); // $(".rongi a").attr("href", "http://data.eastmoney.com/rzrq/detail/" + items.f57 + ".html"); // } else { // $(".rongi").hide(); // } // if (items.f177 & 1024) { // $("#sgt_icon").show(); // $("#hgt_icon").hide(); // } else if (items.f177 & 512){ // $("#sgt_icon").hide(); // $("#hgt_icon").show(); // } if (items.f110 == 1 && items.f111 == 2) { $("#jys-box").show().find("b ").text("沪主板"); $("#jys-box").attr("title", "该股票在沪主板上市"); $("#jys-box").find("a").attr("href", "//quote.eastmoney.com/center/gridlist.html#sh_a_board") } if (items.f110 == 0 && items.f111 == 6) { $("#jys-box").show().find("b ").text("深主板"); $("#jys-box").attr("title", "该股票在深主板上市"); $("#jys-box").find("a").attr("href", "//quote.eastmoney.com/center/gridlist.html#sz_a_board") } if (items.f107 == 0 && items.f111 == 13) { $("#jys-box").show().find("b ").text("中小板"); $("#jys-box").attr("title", "该股票在中小板上市"); $("#jys-box").find("a").attr("href", "//quote.eastmoney.com/center/gridlist.html#sme_board") } if (items.f107 == 0 && items.f111 == 80) { $("#jys-box").show().find("b ").text("创业板"); $("#jys-box").attr("title", "该股票在创业板上市"); $("#jys-box").find("a").attr("href", "//quote.eastmoney.com/center/gridlist.html#gem_board") } if ((items.f177) & 512) { $("#hgt_icon").show() } else { if ((items.f177) & 1024) { $("#sgt_icon").show() } } if(items.f107 == 1 && items.f111 == 23) { $("#kcb").show() }else { $("#kcb").hide() } if ((items.f177) & 64) { $("#rong").show(); $("#rong a").attr("href", "http://data.eastmoney.com/rzrq/detail/" + items.f57 + ".html"); } else { $("#rong").hide() } if (items.f177 & 32768) { $("#hlt").show().find("b ").text("沪伦通"); $("#hlt").attr("title", "该股票为沪伦通标的"); $("#hlt").find("a").attr("href", "http://quote.eastmoney.com/uk/" + items.f286 + "." + items.f285 + ".html"); $("#GDR").show().find("b ").text("GDR"); $("#GDR").attr("title", "该股票存在关联的GDR(全球存托凭证)"); $("#GDR").find("a").attr("href", "http://quote.eastmoney.com/uk/" + items.f286 + "." + items.f285 + ".html") } var marketzhai = items.f263 == "1" ? "sh" : "sz"; if (items.f262 && items.f262 != "-") { $("#Z-box").show().find("b").text("可转债"); $("#Z-box").attr("title", "点击查看关联可转债行情"); $("#Z-box").find("a").attr("href", "http://quote.eastmoney.com/bond/" + marketzhai + items.f262 + ".html") } else { $("#Z-box").hide() } var marketH = items.f257; if (items.f256 && items.f256 != "-") { $("#H-box").show().find("b").text("H股"); $("#H-box").attr("title", "点击查看关联H股行情"); $("#H-box").find("a").attr("href", "http://quote.eastmoney.com/unify/r/" + marketH + "." + items.f256) } else { $("#H-box").hide() } var marketB = items.f270 == "1" ? "sh" : "sz"; if (items.f269 && items.f269 != "-") { $("#B-box").show().find("b ").text("B股"); $("#B-box").attr("title", "点击查看关联B股行情"); $("#B-box").find("a").attr("href", "http://quote.eastmoney.com/" + marketB + items.f269 + ".html") } else { $("#B-box").hide() } // } //更名 function renderGenming() { var _this = this; var code = getCode(); $.ajax({ url: "http://dcfm.eastmoney.com/em_mutisvcexpandinterface/api/js/get?type=ABLS_MB&token=70f12f2f4f091e459a279469fe49eca5&filter=(scode=%27" + code + "%27)&st=changedate", dataType: "jsonp", scriptCharset: "utf-8", accept: "json", success: function(json) { if (json.length > 1) { $("#stock_change_name").show(); $("#stock_change_name .rongi").css("display", "block"); var html = "<span class=usedName>" + json[0].sname + "</span> <span class='usedName'>&gt;&gt;&gt;</span>"; for (var i = 1; i < json.length - 1; i++) { html += '<span class="usedName">' + json[i].sname + '<span class="hasDate">(' + json[i].changedate.substring(0, 9).replace(/\//g, "-") + ")</span></span><span class='usedName'>&gt;&gt;&gt;</span>" } html += '<span class="usedName">' + json[json.length - 1].sname + '<span class="hasDate">(' + json[json.length - 1].changedate.substring(0, 9).replace(/\//g, "-") + ")</span></span>"; $("#stock_change_name .shorthandInfo").html(html) $("#stock_change_name").hover(function() { // console.log('777'); $(".comNameExInfo").show(); $(".arrowUp").show(); }, function() { $(".comNameExInfo").hide(); }) $(".closeBtn").click(function() { $(".comNameExInfo").hide(); }) } } }) } function onChangeDataRender(item) { if (item != 0 && item != "-") { if (item > 0) { $("#arrow-find").removeClass("down-arrow").addClass("up-arrow"); } else { $("#arrow-find").removeClass("up-arrow").addClass("down-arrow"); } } if(item == 0){ $("#arrow-find").removeClass("up-arrow").removeClass("down-arrow"); } } function getParam(name) { var urlpara = location.search; var par = {}; if (urlpara != "") { urlpara = urlpara.substring(1, urlpara.length); var para = urlpara.split("&"); var parname; var parvalue; for (var i = 0; i < para.length; i++) { parname = para[i].substring(0, para[i].indexOf("=")); parvalue = para[i].substring(para[i].indexOf("=") + 1, para[i].length); par[parname] = parvalue; } } if (typeof (par[name]) != "undefined") { return par[name]; } else { return null; } } //获取code和market function getCode() { var code; if(getParam('code')) { code = getParam('code'); }else if(getParam('newcode')) { code = getParam('newcode').split('.')[1]; } else if(getParam('id')) { code = getParam('id').substr(0,6); } return code; } function getMarket() { var market; if(getParam('market')) { var newmarket = getParam('market') == 2 ? 0 : 1; market = newmarket; }else if(getParam('newcode')) { market = getParam('newcode').split('.')[0]; }else if(getParam('id')) { market = getParam('id').substr(6); var newmarket = market == 2 ? 0 : 1; market = newmarket; } return market } function gw_now(time, id) { var str = time.replace(/-/g, "/"); var _date = new Date(str); var year = _date.getFullYear(); var month = gw_now_addzero(_date.getMonth() + 1); var day = gw_now_addzero(_date.getDate()); var hour = gw_now_addzero(_date.getHours()); var minute = gw_now_addzero(_date.getMinutes()); var second = gw_now_addzero(_date.getSeconds()); var week = ""; switch (_date.getDay()) { case 0: week = "星期天"; break case 1: week = "星期一"; break case 2: week = "星期二"; break case 3: week = "星期三"; break case 4: week = "星期四"; break case 5: week = "星期五"; break case 6: week = "星期六"; break } var Time = year + "-" + month + "-" + day + " " + week + " " + hour + ":" + minute + ":" + second; $(id).html('(' + Time + ')') } function gw_now_addzero(temp) { if (temp < 10) return "0" + temp; else return temp; } function getColor(str) { var context = str.toString(); context = context.replace("%", ""); if (context == 0 || isNaN(context)) { return ""; } else if (context > 0) { return "red"; } else { return "green"; } } //融和沪深股通 function isRong() { var _url = "//nufm.dfcfw.com/EM_Finance2014NumericApplication/JS.aspx?type=CT&sty=MCSS&st=z&js=((x))&token=883df69e21fd8fe57ebf53dd71aae25f&cmd=" + stockEnity.stockId $.ajax({ url: _url, dataType: "jsonp", jsonp: "cb", success: function (json) { if (typeof json !== "string") return; var data = json.split(","); if (data[4] == "深股通") { $("#sgt_icon").show(); $("#hgt_icon").hide(); } else if (data[4] == "沪股通"){ $("#sgt_icon").hide(); $("#hgt_icon").show(); } if (data[5] == "True") { $(".rongi").show(); $(".rongi a").attr("href", "http://data.eastmoney.com/rzrq/detail/" + data[1] + ".html"); } else { $(".rongi").hide(); } } }) } function NumbericFormat(string) { var context = Number(string); //var fushu = false; if (!isNaN(context)) { var item = parseInt(string); if ((item > 0 && item < 1e4) || (item < 0 && item > -1e4)) { return item; } else if ((item > 0 && item < 1e6) || (item < 0 && item > -1e6)) { item = item / 10000; return item.toFixed(2) + "万"; } else if ((item > 0 && item < 1e7) || (item < 0 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/AMAS_sb-1.0.1-py3-none-any.whl/AMAS/recommender.py
# import collections import compress_pickle import copy import fnmatch import itertools import libsbml import numpy as np import os import pandas as pd import re from AMAS import annotation_maker as am from AMAS import constants as cn from AMAS import iterator as it from AMAS import tools from AMAS import species_annotation as sa from AMAS import reaction_annotation as ra ELEMENT_TYPES = ['species', 'reaction'] class Recommender(object): def __init__(self, libsbml_fpath=None, libsbml_cl=None, model_specs=None): """ Parameters ---------- libsbml_cl: libsbml.SBMLDocument A libsbml document class instance libsbml_fpath: str File path of an SBML model mdoel_specs: tuple/list Iterable object of two tuples including model specifications """ # Document will be updated and saved if chosen. self.sbml_document = None # First of all, collect model information from libsbml model # and send the informaton to create species/reaction annotations fname = None if libsbml_fpath: spec_tuple, reac_tuple = self._parseSBML(libsbml_fpath) # basically split fpath and use the last one fname = libsbml_fpath.split('/')[-1] elif libsbml_cl: spec_tuple, reac_tuple = self._parseSBML(libsbml_cl) elif model_specs: spec_tuple = model_specs[0] reac_tuple = model_specs[1] else: spec_tuple = None reac_tuple = None self.fname = fname self.species = sa.SpeciesAnnotation(inp_tuple=spec_tuple) self.reactions = ra.ReactionAnnotation(inp_tuple=reac_tuple) # Below are elements to interact with user self.current_type = None self.just_displayed = None self.selection = {val:dict() for val in ELEMENT_TYPES} def getDataFrameFromRecommendation(self, rec, show_url=False): """ Get a pandas dataframe from a single recommendation. Parameters ---------- rec: cn.Recommendation show_url: bool If False, omit this column Returns ------- :str """ cands = [val[0] for val in rec.candidates] match_scores = [val[1] for val in rec.candidates] labels = rec.labels # index starts from 1; df = pd.DataFrame({'annotation':cands, cn.DF_MATCH_SCORE_COL:match_scores, 'label':labels}) df.index.name = rec.id if show_url: urls = rec.urls df['url'] = urls return df def getRecommendationFromDataFrame(self, df): """ Convert dataframe back to namedtuple Recommendation. WARNING: it may not work with empty dataframe, so be careful. Parameters ---------- df: pandas.DataFrame element_type: str 'species' or 'reaction' Returns ------- Recommendation (namedtuple) """ cands_tups = list(zip(df['annotation'], df['match score'])) one_annotation = cands_tups[0][0] # indicating species if one_annotation[:4] == 'CHEB': default_url = cn.CHEBI_DEFAULT_URL url_digit = 6 # indicating reaction elif one_annotation[:4] == 'RHEA': default_url = cn.RHEA_DEFAULT_URL url_digit = 5 return cn.Recommendation(df.index.name, list(zip(df['annotation'], df['match score'])), [default_url + val[url_digit:] for val in df['annotation']], list(df['label'])) def getMarkdownFromRecommendation(self, rec, show_url=False): """ Get a markdown using a cn.Recommendation or pandas.DataFrame. Parameters ---------- rec: cn.Recommendation/pandas.DataFrame show_url: bool If False, omit this column Returns ------- :str """ if isinstance(rec, pd.DataFrame): # to deepcopy so original data doesn't get changed # in line 156. df = copy.deepcopy(rec) idx_name = df.index.name.split(' ') rec_id = idx_name[0] else: df = self.getDataFrameFromRecommendation(rec, show_url) rec_id = rec.id # In markdown, title is shown separately, # so index name with element ID is removed; df.index.name=None df_str = df.to_markdown(tablefmt="grid", floatfmt=".03f", index=True) # Centering and adding the title len_first_line = len(df_str.split('\n')[0]) title_line = rec_id title_line = title_line.center(len_first_line) df_str = title_line + '\n' + df_str return df_str def getSpeciesRecommendation(self, pred_str=None, pred_id=None, method='cdist', mssc='top', cutoff=0.0, update=True, get_df=False): """ Predict annotations of species using the provided string or ID. If pred_str is given, directly use the string; if pred_id is given, determine the appropriate name using the species ID. Algorithmically, it is a special case of self.getSpeciesListRecommendation. Parameters ---------- pred_str: str Species name to predict annotation with pred_id: str ID of species (search for name using it) method: str One of ['cdist', 'edist'] 'cdist' represents Cosine Similarity 'edist' represents Edit Distance. Default method id 'cdist' mssc: match score selection criteria 'top' will recommend candidates with the highest match score above cutoff 'above' will recommend all candidates with match scores above cutoff cutoff: float Cutoff value; only candidates with match score at or above the cutoff will be recommended. update: bool If true, update existing species annotations (i.e., replace or create new entries) in self.species.candidates and self.species.formula get_df: bool If true, return a pandas.DataFrame. If False, return a cn.Recommendation Returns ------- cn.Recommendation (namedtuple) / str """ if pred_str: result = self.getSpeciesListRecommendation(pred_strs=[pred_str], method=method, mssc=mssc, cutoff=cutoff, update=update, get_df=get_df) elif pred_id: result = self.getSpeciesListRecommendation(pred_ids=[pred_id], method=method, mssc=mssc, cutoff=cutoff, update=update, get_df=get_df) return result[0] def getSpeciesIDs(self, pattern=None, regex=False): """ Returns Species IDs that match the pattern. The pattern is given as glob If none is given, returns all available species that exist in the model. Parameters --------- pattern: str/None string pattern reges: bool if True, use regex if False, use glob Returns ------- list-str/None None returned if no match was found """ # list of species ids specs = list(self.species.names.keys()) # returns a list of ids thta match pattern, if None, return all if pattern is None: return specs else: if regex: re_pattern = pattern else: re_pattern = fnmatch.translate(pattern) matched = [re.match(re_pattern, val) for val in specs] filt_matched = [val.group(0) for val in matched if val] if len(filt_matched)>0: return filt_matched else: return None def getSpeciesListRecommendation(self, pred_strs=None, pred_ids=None, method='cdist', mssc='top', cutoff=0.0, update=True, get_df=False): """ Get annotation of multiple species, given as a list (or an iterable object). self.getSpeciesRecommendation is applied to each element. Parameters ---------- pred_strs: str-list :Species names to predict annotations with pred_ids: str-list :Species IDs to predict annotations with (model info should have been already loaded) method: str One of ['cdist', 'edist'] 'cdist' represents Cosine Similarity 'edist' represents Edit Distance. Default method id 'cdist' mssc: match score selection criteria 'top' will recommend candidates with the highest match score above cutoff 'above' will recommend all candidates with match scores above cutoff cutoff: float Cutoff value; only candidates with match score at or above the cutoff will be recommended. update: bool :If true, update the current annotations (i.e., replace or create new entries) in self.species.candidates and self.species.formula get_df: bool If True, return a list of pandas.DataFrame. If False, return a list of cn.Recommendation Returns ------- list-Recommendation (list-namedtuple) / list-str """ scoring_methods = {'edist': self.species.getEScores, 'cdist': self.species.getCScores} if pred_strs: ids_dict = {k:k for k in pred_strs} inp_strs = pred_strs elif pred_ids: ids_dict = {k:self.species.getNameToUse(inp_id=k) \ for k in pred_ids} inp_strs = [ids_dict[k] for k in ids_dict.keys()] pred_res = scoring_methods[method](inp_strs=inp_strs, mssc=mssc, cutoff=cutoff) result = [] for spec in ids_dict.keys(): urls = [cn.CHEBI_DEFAULT_URL + val[0][6:] for val in pred_res[ids_dict[spec]]] labels = [cn.REF_CHEBI2LABEL[val[0]] for val in pred_res[ids_dict[spec]]] one_recom = cn.Recommendation(spec, [(val[0], np.round(val[1], cn.ROUND_DIGITS)) \ for val in pred_res[ids_dict[spec]]], urls, labels) result.append(one_recom) if update: _ = self.species.updateSpeciesWithRecommendation(one_recom) if get_df: return [self.getDataFrameFromRecommendation(rec=val) \ for val in result] else: return result def getReactionRecommendation(self, pred_id, use_exist_species_annotation=False, spec_res=None, spec_method='cdist', mssc='top', cutoff=0.0, update=True, get_df=False): """ Predict annotations of reactions using the provided IDs (argument). Can be either singular (string) or plural Parameters ---------- pred_id: str A single ID of reaction to annotate use_exist_speices_annotation: bool If True, use existing species annotation spec_res: list-cn.Recommendation If provided, species will not be predicted for remaining species spec_method: str Method to use if to directly predict species annotation; if 'cdist' Cosine Similarity if 'edist' Edit distance mssc: match score selection criteria 'top' will recommend candidates with the highest match score above cutoff 'above' will recommend all candidates with match scores above cutoff cutoff: float Cutoff value; only candidates with match score at or above the cutoff will be recommended. update: bool If true, update existing species annotations (i.e., replace or create new entries) in self.reactions.candidates get_df: bool If True, return a pandas DataFrame. If False, return a cn.Recommendation Returns ------- Recommendation (namedtuple) / str """ result = self.getReactionListRecommendation(pred_ids=[pred_id], use_exist_species_annotation=use_exist_species_annotation, spec_res=spec_res, spec_method=spec_method, mssc=mssc, cutoff=cutoff, update=update, get_df=get_df) return result[0] def getReactionIDs(self, pattern=None, by_species=False, regex=False): """ Get IDs of reactions based on the pattern. If by_species is True, it retrieves all reaction with the species that match the pattern; if False, it searches based on the ID of reactions Parameters --------- pattern: str Pattern by_species: bool If True, find species with pattern If False, find reaction IDs regex: bool If True, use regex expression If False, convert it to regex. """ reacts = list(self.reactions.reaction_components.keys()) if pattern is None: return reacts # returns a list of ids thta match pattern, if None, return all if regex: re_pattern = pattern else: re_pattern = fnmatch.translate(pattern) if by_species: specs2use = self.getSpeciesIDs(pattern=re_pattern, regex=True) if any(specs2use): comp_items = list(self.reactions.reaction_components.items()) result = [val[0] for val in comp_items \ if any(set(val[1]).intersection(specs2use))] # if no species match was found else: return None else: matched = [re.match(re_pattern, val) for val in reacts] result = [val.group(0) for val in matched if val] return result def getReactionListRecommendation(self, pred_ids, use_exist_species_annotation=False, spec_res=None, spec_method='cdist', mssc='top', cutoff=0.0, update=True, get_df=False): """ Get annotation of multiple reactions. Instead of applying getReactionRecommendation for each reaction, it'll predict all component species first and proceed (this will reduce computational cost). Parameters ---------- pred_ids: str-list For now, it only accommodates calling by reaction IDs. use_exist_species_annotation: tool If True, search existing annotation for species and predict the remaining species spec_res: list-cn.Recommendation If provided, species will not be predicted for remaining species spec_method: str Method to use if to directly predict species annotation; if 'cdist' Cosine Similarity if 'edist' Edit distance mssc: match score selection criteria 'top' will recommend candidates with the highest match score above cutoff 'above' will recommend all candidates with match scores above cutoff cutoff: float Cutoff value; only candidates with match score at or above the cutoff will be recommended. update: bool If true, update existing species annotations (i.e., replace or create new entries) in self.reactions.candidates get_df: bool If True, return a list of pandas DataFrames. If False, return a list of cn.Recommendation Returns ------- list-Reccommendation (list-namedtuple) / list-str """ # First, collect all species IDs to annotate specs_to_annotate = list(set(itertools.chain(*[self.reactions.reaction_components[val] \ for val in pred_ids]))) if use_exist_species_annotation: pred_formulas = {val:self.species.exist_annotation_formula[val] \ for val in specs_to_annotate \ if val in self.species.exist_annotation_formula.keys()} else: pred_formulas = {} remaining_species = [val for val in specs_to_annotate if val not in pred_formulas.keys()] # Get annotation of collected species if len(remaining_species) > 0: if spec_res: spec_results = [val for val in spec_res if val.id in remaining_species] else: # No updates; use MSSC Top, cutoff 0.0. spec_results = self.getSpeciesListRecommendation(pred_ids=remaining_species, update=False, method=spec_method) for one_recom in spec_results: chebis = [val[0] for val in one_recom.candidates] forms = list(set([cn.REF_CHEBI2FORMULA[k] \ for k in chebis if k in cn.REF_CHEBI2FORMULA.keys()])) pred_formulas[one_recom.id] = forms # Predict reaction annotations. pred_res = self.reactions.getRScores(spec_dict=pred_formulas, reacs=pred_ids, mssc=mssc, cutoff=cutoff) result = [] for reac in pred_res.keys(): urls = [cn.RHEA_DEFAULT_URL + val[0][5:] for val in pred_res[reac]] labels = [cn.REF_RHEA2LABEL[val[0]] for val in pred_res[reac]] one_recom = cn.Recommendation(reac, [(val[0], np.round(val[1], cn.ROUND_DIGITS)) \ for val in pred_res[reac]], urls, labels) result.append(one_recom) if update: self.reactions.candidates = pred_res if get_df: return [self.getDataFrameFromRecommendation(rec=val) \ for val in result] else: return result def _parseSBML(self, sbml): """ Parse SBML file and return two tuples, for species and reactions respecitvely, equivalent to model_specs. Can use either libsbml.Document class or a file path. Parameters ---------- sbml: str(filepath)/libsbml.Document Returns ------- (tuple, tuple): Two tuples to create species/reaction annotation classes (species_tuple, reaction_tuple) """ if isinstance(sbml, str): reader = libsbml.SBMLReader() # Reading the model string file with open(sbml, 'r') as f: model_str = f.read() self.sbml_document = reader.readSBMLFromString(model_str) elif isinstance(sbml, libsbml.SBMLDocument): self.sbml_document = sbml model = self.sbml_document.getModel() exist_spec_annotation = tools.extractExistingSpeciesAnnotation(model) species_names = {val.getId():val.name for val in model.getListOfSpecies()} species_tuple = (species_names, exist_spec_annotation) # reac_exist_annotation = tools.extractExistingReactionAnnotation(inp_model=model) # Next, reaction components for each reaction reac_components = {val.getId():list(set([k.species for k in val.getListOfReactants()]+\ [k.species for k in val.getListOfProducts()])) \ for val in model.getListOfReactions()} reaction_tuple = (reac_components, reac_exist_annotation) return species_tuple, reaction_tuple def getSpeciesStatistics(self, mssc='top', cutoff=0.0, model_mean=True): """ Get recall and precision of species in a model, for both species and reactions. This method works only if there exists annotation in model; otherwise None will be returned. In the result, values will be returned after rounding to the two decimal places. Parameters ---------- mssc: str match score selection criteria 'top' will recommend candidates with the highest match score above cutoff 'above' will recommend all candidates with match scores above cutoff cutoff: float Cutoff value; only candidates with match score at or above the cutoff will be recommended. model_mean: bool If True, get single float values for recall/precision. If False, get a dictionary for recall/precision. Returns ------- None/dict Return None if there is nothing to evaluate (i.e., if there is no existing model annotation) """ # get dictionary of formulas if they exist refs = {val:self.species.exist_annotation_formula[val] \ for val in self.species.exist_annotation_formula.keys() \ if self.species.exist_annotation_formula[val]} specs2eval = list(refs.keys()) if len(specs2eval) == 0: return None preds_comb = self.getSpeciesListRecommendation(pred_ids=specs2eval, mssc=mssc, cutoff=cutoff) chebi_preds = {val.id:[k[0] for k in val.candidates] \ for val in preds_comb} preds = {k:[cn.REF_CHEBI2FORMULA[val] for val in chebi_preds[k] \ if val in cn.REF_CHEBI2FORMULA.keys()] \ for k in chebi_preds.keys()} recall = tools.getRecall(ref=refs, pred=preds, mean=model_mean) precision = tools.getPrecision(ref=refs, pred=preds, mean=model_mean) return {cn.RECALL: recall, cn.PRECISION: precision} def getReactionStatistics(self, model_mean=True, mssc='top', cutoff=0.0): """ Get recall and precision of reactions in a model, for both species and reactions. This method works only if there exists annotation in model; otherwise None will be returned. In the result, values will be returned after rounding to the two decimal places. Parameters ---------- mssc: str match score selection criteria 'top' will recommend candidates with the highest match score above cutoff 'above' will recommend all candidates with match scores above cutoff cutoff: float Cutoff value; only candidates with match score at or above the cutoff will be recommended. model_mean: bool If True, get single float values for recall/precision. If False, get a dictionary for recall/precision. Returns ------- None/dict Return None if there is nothing to evaluate (i.e., if there is no existing model annotation) """ # For reactions, component species should be # predicted first. refs = self.reactions.exist_annotation if len(refs) == 0: return None specs2pred = list(set(itertools.chain(*([self.reactions.reaction_components[val] for val in refs.keys()])))) ## Use mssc top, cutoff 0.0. preds_comb = self.getSpeciesListRecommendation(pred_ids=specs2pred, mssc='top', cutoff=0.0) chebi_preds = {val.id:[k[0] for k in val.candidates] \ for val in preds_comb} specs_predicted = {k:[cn.REF_CHEBI2FORMULA[val] for val in chebi_preds[k] \ if val in cn.REF_CHEBI2FORMULA.keys()] \ for k in chebi_preds.keys()} reac_preds = self.reactions.getRScores(spec_dict=specs_predicted, reacs=refs.keys(), mssc='top', cutoff=0.0) preds = {k:[val[0] for val in reac_preds[k]] for k in reac_preds.keys()} recall = tools.getRecall(ref=refs, pred=preds, mean=model_mean) precision = tools.getPrecision(ref=refs, pred=preds, mean=model_mean) return {cn.RECALL: recall, cn.PRECISION: precision} def filterDataFrameByThreshold(self, df, min_score): """ Filter dataframe by min_score (threshold), and returns the result; Note that if no item meets the threshold, it'll still return an empty dataframe. Paramters --------- df: pd.DataFrame min_score: float (0.0-1.0) Returns ------- pd.DataFrame """ scores = df[cn.DF_MATCH_SCORE_COL] filt_idx = scores[scores>=min_score].index filt_df = df.loc[filt_idx, :] return filt_df def autoSelectAnnotation(self, df, cutoff=0.0, mssc='top'): """ Choose annotations based on the set threshold; (1) if None meets the threshold, return an empty frame (2) if multiple meet the threshold, (a) if method is 'best': (i) find the highest match score among them (ii) return all above match score == highest_match_score (b) if method is 'all': (i) return all that is at or above min_score Parameters ---------- df: pandas.DataFrame cutoff: float (0.0-1.0) Match score cutoff mssc: str Match score selection criteria; either 'top' or 'above'. Returns ------- pandas.DataFrame if nothing matched, an empty dataframe is returned """ scores = df[cn.DF_MATCH_SCORE_COL] # max_score: highest match score that exists # min_score: cutoff max_score = np.max(scores) if max_score < cutoff: # this will create an empty dataframe filt_idx = scores[scores>=cutoff].index elif mssc=='top': filt_idx = scores[scores==max_score].index else: filt_idx = scores[scores>=cutoff].index filt_df = df.loc[filt_idx, :] return filt_df def recommendAnnotation(self, mssc='top', cutoff=0.0, optimize=False, outtype='table'): """ Combine recommendSpecies and recommendReactions methods; can optimize. Parameters ---------- mssc: str cutoff: float optiimize: bool outtype: str If 'table', returns recommendation table if 'sbml', returns an updated SBML model. Returns ------- pandas.DataFrame / str """ pred_spec = self.getSpeciesListRecommendation(pred_ids=self.getSpeciesIDs(), mssc=mssc, cutoff=cutoff, get_df=True) pred_reac = self.getReactionListRecommendation(pred_ids=self.getReactionIDs(), mssc=mssc, cutoff=cutoff, get_df=True) if optimize: res_tab = self.optimizePrediction(pred_spec=pred_spec, pred_reac=pred_reac) else: s_df = self.getRecomTable(element_type='species', recommended=pred_spec) r_df = self.getRecomTable(element_type='reaction', recommended=pred_reac) res_tab = pd.concat([s_df, r_df], ignore_index=True) if outtype == 'table': return res_tab elif outtype == 'sbml': res_sbml = self.getSBMLDocument(sbml_document=self.sbml_document, chosen=res_tab, auto_feedback=True) return libsbml.writeSBMLToString(res_sbml) def recommendReactions(self, ids=None, min_len=0, mssc='top', cutoff=0.0, outtype='table'): """ Recommend one or more ids of reactions and returns a single dataframe or a list of dataframes. Parameters ---------- ids: str/list-str If None, recommend all reactionos. min_len: int Minimum number of reaction components to be returned for results mssc: str match score selection criteria. 'top' or 'above' cutoff: float MSSC cutoff outtype: str Either 'table' or 'sbml'. 'table' will return a pandas.DataFrame 'sbml' will return an sbml string Returns ------- None """ self.updateCurrentElementType('reaction') if isinstance(ids, str): reacs = [ids] elif ids is None: reacs = self.getReactionIDs() else: reacs = ids filt_reacs = [val for val in reacs \ if len(self.reactions.reaction_components[val])>=min_len] if len(filt_reacs) == 0: print("No reaction after the element filter.\n") return None pred = self.getReactionListRecommendation(pred_ids=filt_reacs, mssc=mssc, cutoff=cutoff, get_df=True) res_table = self.getRecomTable(element_type='reaction', recommended=pred) if outtype == 'table': return res_table elif outtype == 'sbml': res_sbml = self.getSBMLDocument(sbml_document=self.sbml_document, chosen=res_table, auto_feedback=True) return libsbml.writeSBMLToString(res_sbml) return None def recommendSpecies(self, ids=None, min_len=0, mssc='top', cutoff=0.0, outtype='table'): """ Recommend one or more ids of species and returns a single dataframe or a list of dataframes. Parameters ---------- ids: str/list-str If None, will predict all min_len: int Minimum length of species name to be returned for results mssc: str Match score selection criteria. cutoff: match score cutoff If None given, returns all values. outtype: str Either 'table' or 'sbml'. 'table' will return a pandas.DataFrame 'sbml' will return an sbml string Returns ------- : pd.DataFrame/str/None Either """ self.updateCurrentElementType('species') if isinstance(ids, str): specs = [ids] elif ids is None: specs = self.getSpeciesIDs() else: specs = ids filt_specs = [val for val in specs \ if len(self.species.getNameToUse(val))>=min_len] if len(filt_specs) == 0: print("No species after the element filter.\n") return None pred = self.getSpeciesListRecommendation(pred_ids=filt_specs, mssc=mssc, cutoff=cutoff, get_df=True) res_table = self.getRecomTable(element_type='species', recommended=pred) if outtype == 'table': return res_table elif outtype == 'sbml': res_sbml = self.getSBMLDocument(sbml_document=self.sbml_document, chosen=res_table, auto_feedback=True) return libsbml.writeSBMLToString(res_sbml) return None def updateCurrentElementType(self, element_type): """ Updating self.current_type indicator; updated when recommendSpecies or recommendReactions is called; Parameters ---------- element_type: str Either 'species' or 'reaction' """ self.current_type = element_type def updateJustDisplayed(self, df_dict): """ Used it every time result is shown to user. called by /recommendSpecies/recommendReactions/ /selectAnnotation/ For now, always in the format as pandas.DataFrame. Parameters ---------- df_dict: dict() Dictionary of pandas.DataFrame Returns ------- None """ self.just_displayed = df_dict def selectAnnotation(self, choice=None): """ Based on the previous recommendation, determine the annotations to store. If 'all' given in choice[1], select all. Parameters ---------- choice: tuple/list-tuple (str, int) [(element ID, choice number)] """ # assumes self.just_displayced is {id: pd.dataframe} sel_id = choice[0] sel_idx = choice[1] df = self.just_displayed[choice[0]] if sel_idx == 'all': result = df else: if isinstance(sel_idx, int): chosen = [sel_idx] else: chosen = sel_idx result = df.loc[chosen, :] # Now, update the selected annotation self.updateSelection(sel_id, result) print("Selection updated.") return None def updateSelection(self, sel_id, sel_df): """ Direct result of selectAnnotation; filtered or non-filtered dictionary of dataframes. By calling SaveFile, All selected annotations will be saved as an .xml file. Parameters ---------- sel_id: str sel_df: pandas.DataFrame """ self.selection[self.current_type].update({sel_id: sel_df}) def displaySelection(self): """ To assist user, display all selected annotations from self.selection. """ for one_type in ELEMENT_TYPES: type_selection = self.selection[one_type] for k in type_selection.keys(): print(self.getMarkdownFromRecommendation(type_selection[k])+"\n") def getRecomTable(self, element_type, recommended): """ Extend the dataframe using results obtained by self.get....ListRecommendation. A new, extended dataframe will be returned; to be either saved as CSV or shown to the user. Parameters ---------- element_type: str either 'species' or 'reaction' recommended: list-pandas.DataFrame result of get....ListRecommendation method Returns ------- :pandas.DataFrame a single dataframe (not a list of dataframes) """ etype = element_type model = self.sbml_document.getModel() TYPE_EXISTING_ATTR = {'species': self.species.exist_annotation, 'reaction': self.reactions.exist_annotation} ELEMENT_FUNC = {'species': model.getSpecies, 'reaction': model.getReaction} TYPE_LABEL = {'species': cn.REF_CHEBI2LABEL, 'reaction': cn.REF_RHEA2LABEL} pd.set_option('display.max_colwidth', 255) edfs = [] for one_edf in recommended: element_id = one_edf.index.name if one_edf.shape[0] == 0: continue annotations = list(one_edf['annotation']) match_scores = list(one_edf[cn.DF_MATCH_SCORE_COL]) labels = list(one_edf['label']) # if there is existing annotation among predicted candidates; if element_id in TYPE_EXISTING_ATTR[etype].keys(): existings = [1 if val in TYPE_EXISTING_ATTR[etype][element_id] else 0 \ for idx, val in enumerate(one_edf['annotation'])] upd_annotation = ['keep' if val in TYPE_EXISTING_ATTR[etype][element_id] else 'ignore' \ for idx, val in enumerate(one_edf['annotation'])] annotation2add_raw = [val for val in TYPE_EXISTING_ATTR[etype][element_id] \ if val not in list(one_edf['annotation'])] # only use existing annotation that exists in the label dictionaries annotation2add = [val for val in annotation2add_raw \ if val in TYPE_LABEL[etype].keys()] # if there doesn't exist existing annotation among predicted candidates; else: existings = [0] * len(annotations) upd_annotation = ['ignore'] * len(annotations) annotation2add = [] # handling existing annotations that were not predicted for new_anot in annotation2add: annotations.append(new_anot) if etype=='reaction': match_scores.append(self.getMatchScoreOfRHEA(element_id, new_anot)) labels.append(cn.REF_RHEA2LABEL[new_anot]) elif etype=='species': match_scores.append(self.getMatchScoreOfCHEBI(element_id, new_anot)) labels.append(cn.REF_CHEBI2LABEL[new_anot]) existings.append(1) upd_annotation.append('keep') new_edf = pd.DataFrame({'type': [etype]*len(annotations), 'id': [element_id]*len(annotations), 'display name': [ELEMENT_FUNC[etype](element_id).name]*len(annotations), 'meta id': [ELEMENT_FUNC[etype](element_id).meta_id]*len(annotations), 'annotation': annotations, 'annotation label': labels, cn.DF_MATCH_SCORE_COL: match_scores, 'existing': existings, cn.DF_UPDATE_ANNOTATION_COL: upd_annotation}) edfs.append(new_edf) res = pd.concat(edfs, ignore_index=True) res.insert(0, 'file', self.fname) return res def getSBMLDocument(self, sbml_document, chosen, auto_feedback=False): """ Create an updated SBML document based on the feedback. If auto_feedback is True, replace 'ignore' with 'add' and subsequently update the file. Parameters ---------- sbml_document: libsbml.SBMLDocument chosen: pandas.DataFrame Returns ------- str SBML document """ model = sbml_document.getModel() if auto_feedback: chosen.replace('ignore', 'add', inplace=True) ELEMENT_FUNC = {'species': model.getSpecies, 'reaction': model.getReaction} element_types = list(np.unique(chosen['type'])) for one_type in element_types: maker = am.AnnotationMaker(one_type) ACTION_FUNC = {'delete': maker.deleteAnnotation, 'add': maker.addAnnotation} df_type = chosen[chosen['type']==one_type] uids = list(np.unique(df_type['id'])) meta_ids = {val:list(df_type[df_type['id']==val]['meta id'])[0] for val in uids} # going through one id at a time for one_id in uids: orig_str = ELEMENT_FUNC[one_type](one_id).getAnnotationString() df_id = df_type[df_type['id']==one_id] dels = list(df_id[df_id[cn.DF_UPDATE_ANNOTATION_COL]=='delete'].loc[:, 'annotation']) adds_raw = list(df_id[df_id[cn.DF_UPDATE_ANNOTATION_COL]=='add'].loc[:, 'annotation']) # existing annotations to be kept keeps = list(df_id[df_id[cn.DF_UPDATE_ANNOTATION_COL]=='keep'].loc[:, 'annotation']) # TODO: remove RHEA adds_raw = list(set(adds_raw + keeps)) adds = [] for one_add in adds_raw: # if it is rhea, only store number if one_add[:4].lower()=='rhea': adds.append(one_add[5:]) # if it is else, store as it is else: adds.append(one_add) # if type is 'reaction', need to map rhea terms back to ec/kegg terms to delete them. if one_type == 'reaction': rhea_del_terms = list(set(itertools.chain(*[tools.getAssociatedTermsToRhea(val) for val in dels]))) deled = maker.deleteAnnotation(rhea_del_terms, orig_str) elif one_type == 'species': deled = maker.deleteAnnotation(dels, orig_str) added = maker.addAnnotation(adds, deled, meta_ids[one_id]) ELEMENT_FUNC[one_type](one_id).setAnnotation(added) return sbml_document def optimizePrediction(self, pred_spec, pred_reac): """ Optimize prediction using iteration. Parameters ---------- pred_spec: list-DataFrame Result of getSpeciesListRecommendation with get_df=True pred_reac: list-DataFrame Result of getReactionListRecommendation with get_df=True reactions_to_update: list IDs of reactions Returns ------- fin_spec_recom: Recommendation (namedtuple) fin_reac_recom: Recommendation (namedtuple) """ # filtering out reactions that can be updated filt_reac = [val for val in pred_reac if val.shape[0]>0] filt_reac_ids = [val.index.name for val in filt_reac] spec_formulas = dict() for one_rec in pred_spec: formulas = list(set([cn.REF_CHEBI2FORMULA[k] \ for k in one_rec['annotation'] \ if k in cn.REF_CHEBI2FORMULA.keys()])) spec_formulas[one_rec.index.name] = formulas anot_iter = it.Iterator(cur_spec_formula=spec_formulas, reaction_cl=self.reactions, reactions_to_update=filt_reac_ids) res_iter = anot_iter.match() recoms_tobe_added = [] for one_spec in res_iter.keys(): pred_reac_ids = [val.index.name for val in pred_reac] reacs_using_one_spec = [val for val in pred_reac_ids \ if one_spec in self.reactions.reaction_components[val]] filt_pred_reac = [val for val in pred_reac if val.index.name in reacs_using_one_spec] # match score of reactions using that species # average of the [very first match score from each candidaets set] adj_match_score = np.mean([val['match score'].iloc[0] for val in filt_pred_reac]) cands = res_iter[one_spec] scores = [adj_match_score for val in cands] labels = [cn.REF_CHEBI2LABEL[val] for val in cands] adj_recom = pd.DataFrame({'annotation': cands, 'match score': scores, 'label': labels}) adj_recom.index.name = one_spec recoms_tobe_added.append(adj_recom) upd_spec_dfs = recoms_tobe_added + \ [val for val in pred_spec if val.index.name not in res_iter.keys()] # need to be converted back to namedtuple DataFrame upd_spec_recom = [self.getRecommendationFromDataFrame(val) for val in upd_spec_dfs] upd_reac_dfs = self.getReactionListRecommendation(pred_ids=filt_reac_ids, spec_res=upd_spec_recom, get_df=True) s_df = self.getRecomTable(element_type='species', recommended=upd_spec_dfs) r_df = self.getRecomTable(element_type='reaction', recommended=upd_reac_dfs) return pd.concat([s_df, r_df], ignore_index=True) def saveToCSV(self, obj, fpath="recommendation.csv"): """ Save a completed dataframe to csv. Doesn't proceed if obj is None, which indicates it didn't pass the element filter. Parameters ---------- obj: pandas.DataFrame Object that can be saved to csv. fpath: str Path of the csv file to be saved. """ if isinstance(obj, pd.DataFrame): obj.to_csv(fpath, index=False) # print a summary message for one_type in ELEMENT_TYPES: saved_elements = list(np.unique(obj[obj['type']==one_type]['id'])) self.printSummary(saved_elements, one_type) # def saveToSBML(self, # fpath='model_amas_annotations.xml', # option='augment'): # """ # Update and save model; # How to distinguish species vs. reactions? # by using self.current_element_type. # If option is 'augment', # it'll add candidate annotations to # existing annotation string. # If option is 'replace', # create a new annotation string and # replace whatevers exists. # Default to 'augment'. # Call annotation maker; # Parameters # ---------- # fpath: str # Path to save file # option: str # Either 'augment' or 'replace' # """ # model = self.sbml_document.getModel() # ELEMENT_FUNC = {'species': model.getSpecies, # 'reaction': model.getReaction} # # dictionary with empty lists; # saved_elements = {k:[] for k in ELEMENT_TYPES} # for one_type in ELEMENT_TYPES: # type_selection = self.selection[one_type] # maker = am.AnnotationMaker(one_type) # sel2save = type_selection # for one_k in sel2save.keys(): # one_element = ELEMENT_FUNC[one_type](one_k) # meta_id = one_element.meta_id # df = sel2save[one_k] # # cands2save = list(df['annotation']) # cands2save = [] # for val2save in list(df['annotation']): # if val2save[:4].lower() == 'rhea': # cands2save.append(val2save[5:]) # else: # cands2save.append(val2save) # if cands2save: # if option == 'augment': # orig_annotation = one_element.getAnnotationString() # annotation_str = maker.addAnnotation(cands2save, # orig_annotation, # meta_id) # elif option == 'replace': # annotation_str = maker.getAnnotationString(cands2save, meta_id) # one_element.setAnnotation(annotation_str) # saved_elements[one_type].append(one_k) # else: # continue # # finally, write the sbml document # libsbml.writeSBMLToFile(self.sbml_document, fpath) # # Summary message # for one_type in ELEMENT_TYPES: # self.printSummary(saved_elements[one_type], one_type) def printSummary(self, saved, element_type): """ Print out a summary of saved element IDs and numbers. Parameters ---------- saved: list-str List of elements saved. element_type: str 'species' or 'reaction' """ plural_str = {'species': '', 'reaction': '(s)'} num_saved = len(saved) if num_saved == 0: return None print("Annotation recommended for %d %s%s:\n[%s]\n" %\ (num_saved, element_type, plural_str[element_type], ', '.join(saved))) def getMatchScoreOfCHEBI(self, inp_id, inp_chebi): """ Calculate match score of a species (by ID) with a ChEBI term. This is to inform user of how well it matches with a specific ChEBI term. If the ChEBI term somehow doesn't exist in the dictionary, 0.0 will be returned. Parameters ---------- inp_id: str ID of a species inp_chebi: str A ChEBI term. Returns ------- res: float """ inp_str = self.species.getNameToUse(inp_id) scores = self.species.getCScores(inp_strs=[inp_str], mssc='above', cutoff=0.0)[inp_str] # searching for the match score res = next((np.round(v[1], cn.ROUND_DIGITS) \ for v in scores if v[0] == inp_chebi), 0.0) return res def getMatchScoreOfRHEA(self, inp_id, inp_rhea): """ Calculate match score of a reaction (by ID) with a Rhea term. This is to inform user of how well it matches with a specific Rhea term. Parameters ---------- inp_id: str ID of a species inp_rhea: str A Rhea term. Returns ------- res_match_score: float """ specs2predict = self.reactions.reaction_components[inp_id] spec_results = self.getSpeciesListRecommendation(pred_ids=specs2predict, update=False, method='cdist', mssc='top', cutoff=0.0) pred_formulas = dict() for one_spec_res in spec_results: chebis = [val[0] for val in one_spec_res.candidates] forms = list(set([cn.REF_CHEBI2FORMULA[k] \ for k in chebis if k in cn.REF_CHEBI2FORMULA.keys()])) pred_formulas[one_spec_res.id] = forms scores = self.reactions.getRScores(spec_dict=pred_formulas, reacs=[inp_id], mssc='above', cutoff=0.0)[inp_id] # searching for the match score res = next((np.round(v[1], cn.ROUND_DIGITS) \ for v in scores if v[0] == inp_rhea), 0.0) return res
PypiClean
/FastNLP-1.0.1.tar.gz/FastNLP-1.0.1/fastNLP/modules/torch/decoder/crf.py
__all__ = [ "ConditionalRandomField", "allowed_transitions" ] from typing import Union, List, Tuple import torch from torch import nn from ....core.metrics.span_f1_pre_rec_metric import _get_encoding_type_from_tag_vocab, _check_tag_vocab_and_encoding_type from ....core.vocabulary import Vocabulary def allowed_transitions(tag_vocab:Union[Vocabulary, dict], encoding_type:str=None, include_start_end:bool=False) -> List[Tuple[int, int]]: r""" 给定一个 ``id`` 到 ``label`` 的映射表,返回所有可以跳转的 ``(from_tag_id, to_tag_id)`` 列表。 :param tag_vocab: 支持类型为 tag 或 tag-label 。只有 tag 的,比如 ``"B"`` 、 ``"M"``,也可以是 ``"B-NN"`` 、 ``"M-NN"``, tag 和 label之间一定要用 ``"-"`` 隔开。如果传入 :class:`dict` ,格式需要形如 ``{0:"O", 1:"B-tag1"}`` ,即 **index 在前,tag 在后** 。 :param encoding_type: 支持 ``["bio", "bmes", "bmeso", "bioes", None]``。默认为 ``None``,通过 ``tag_vocab`` 自动推断 :param include_start_end: 是否包含开始与结尾的转换。比如在 ``bio`` 中, ``b/o`` 可以在开头,但是 ``i`` 不能在开头; - 为 ``True`` -- 返回的结果中会包含 ``(start_idx, b_idx), (start_idx, o_idx)`` ,但是不包含 ``(start_idx, i_idx)`` ; 其中 ``start_idx=len(id2label)``,``end_idx=len(id2label)+1`` ; - 为 ``False`` , 返回的结果中不含与开始结尾相关的内容; :return: 一系列元组构成的列表,内部的 :class:`Tuple` 是可以进行跳转的 ``(from_tag_id, to_tag_id)``。 """ if encoding_type is None: encoding_type = _get_encoding_type_from_tag_vocab(tag_vocab) else: encoding_type = encoding_type.lower() _check_tag_vocab_and_encoding_type(tag_vocab, encoding_type) pad_token = '<pad>' unk_token = '<unk>' if isinstance(tag_vocab, Vocabulary): id_label_lst = list(tag_vocab.idx2word.items()) pad_token = tag_vocab.padding unk_token = tag_vocab.unknown else: id_label_lst = list(tag_vocab.items()) num_tags = len(tag_vocab) start_idx = num_tags end_idx = num_tags + 1 allowed_trans = [] if include_start_end: id_label_lst += [(start_idx, 'start'), (end_idx, 'end')] def split_tag_label(from_label): from_label = from_label.lower() if from_label in ['start', 'end']: from_tag = from_label from_label = '' else: from_tag = from_label[:1] from_label = from_label[2:] return from_tag, from_label for from_id, from_label in id_label_lst: if from_label in [pad_token, unk_token]: continue from_tag, from_label = split_tag_label(from_label) for to_id, to_label in id_label_lst: if to_label in [pad_token, unk_token]: continue to_tag, to_label = split_tag_label(to_label) if _is_transition_allowed(encoding_type, from_tag, from_label, to_tag, to_label): allowed_trans.append((from_id, to_id)) return allowed_trans def _is_transition_allowed(encoding_type, from_tag, from_label, to_tag, to_label): r""" :param str encoding_type: 支持"BIO", "BMES", "BEMSO", 'bioes'。 :param str from_tag: 比如"B", "M"之类的标注tag. 还包括start, end等两种特殊tag :param str from_label: 比如"PER", "LOC"等label :param str to_tag: 比如"B", "M"之类的标注tag. 还包括start, end等两种特殊tag :param str to_label: 比如"PER", "LOC"等label :return: bool,能否跃迁 """ if to_tag == 'start' or from_tag == 'end': return False encoding_type = encoding_type.lower() if encoding_type == 'bio': r""" 第一行是to_tag, 第一列是from_tag. y任意条件下可转,-只有在label相同时可转,n不可转 +-------+---+---+---+-------+-----+ | | B | I | O | start | end | +-------+---+---+---+-------+-----+ | B | y | - | y | n | y | +-------+---+---+---+-------+-----+ | I | y | - | y | n | y | +-------+---+---+---+-------+-----+ | O | y | n | y | n | y | +-------+---+---+---+-------+-----+ | start | y | n | y | n | n | +-------+---+---+---+-------+-----+ | end | n | n | n | n | n | +-------+---+---+---+-------+-----+ """ if from_tag == 'start': return to_tag in ('b', 'o') elif from_tag in ['b', 'i']: return any([to_tag in ['end', 'b', 'o'], to_tag == 'i' and from_label == to_label]) elif from_tag == 'o': return to_tag in ['end', 'b', 'o'] else: raise ValueError("Unexpect tag {}. Expect only 'B', 'I', 'O'.".format(from_tag)) elif encoding_type == 'bmes': r""" 第一行是to_tag, 第一列是from_tag,y任意条件下可转,-只有在label相同时可转,n不可转 +-------+---+---+---+---+-------+-----+ | | B | M | E | S | start | end | +-------+---+---+---+---+-------+-----+ | B | n | - | - | n | n | n | +-------+---+---+---+---+-------+-----+ | M | n | - | - | n | n | n | +-------+---+---+---+---+-------+-----+ | E | y | n | n | y | n | y | +-------+---+---+---+---+-------+-----+ | S | y | n | n | y | n | y | +-------+---+---+---+---+-------+-----+ | start | y | n | n | y | n | n | +-------+---+---+---+---+-------+-----+ | end | n | n | n | n | n | n | +-------+---+---+---+---+-------+-----+ """ if from_tag == 'start': return to_tag in ['b', 's'] elif from_tag == 'b': return to_tag in ['m', 'e'] and from_label == to_label elif from_tag == 'm': return to_tag in ['m', 'e'] and from_label == to_label elif from_tag in ['e', 's']: return to_tag in ['b', 's', 'end'] else: raise ValueError("Unexpect tag type {}. Expect only 'B', 'M', 'E', 'S'.".format(from_tag)) elif encoding_type == 'bmeso': if from_tag == 'start': return to_tag in ['b', 's', 'o'] elif from_tag == 'b': return to_tag in ['m', 'e'] and from_label == to_label elif from_tag == 'm': return to_tag in ['m', 'e'] and from_label == to_label elif from_tag in ['e', 's', 'o']: return to_tag in ['b', 's', 'end', 'o'] else: raise ValueError("Unexpect tag type {}. Expect only 'B', 'M', 'E', 'S', 'O'.".format(from_tag)) elif encoding_type == 'bioes': if from_tag == 'start': return to_tag in ['b', 's', 'o'] elif from_tag == 'b': return to_tag in ['i', 'e'] and from_label == to_label elif from_tag == 'i': return to_tag in ['i', 'e'] and from_label == to_label elif from_tag in ['e', 's', 'o']: return to_tag in ['b', 's', 'end', 'o'] else: raise ValueError("Unexpect tag type {}. Expect only 'B', 'I', 'E', 'S', 'O'.".format(from_tag)) else: raise ValueError("Only support BIO, BMES, BMESO, BIOES encoding type, got {}.".format(encoding_type)) class ConditionalRandomField(nn.Module): r""" 条件随机场。提供 :meth:`forward` 以及 :meth:`viterbi_decode` 两个方法,分别用于 **训练** 与 **inference** 。 :param num_tags: 标签的数量 :param include_start_end_trans: 是否考虑各个 tag 作为开始以及结尾的分数。 :param allowed_transitions: 内部的 ``Tuple[from_tag_id(int), to_tag_id(int)]`` 视为允许发生的跃迁,其他没 有包含的跃迁认为是禁止跃迁,可以通过 :func:`allowed_transitions` 函数得到;如果为 ``None`` ,则所有跃迁均为合法。 """ def __init__(self, num_tags:int, include_start_end_trans:bool=False, allowed_transitions:List=None): super(ConditionalRandomField, self).__init__() self.include_start_end_trans = include_start_end_trans self.num_tags = num_tags # the meaning of entry in this matrix is (from_tag_id, to_tag_id) score self.trans_m = nn.Parameter(torch.randn(num_tags, num_tags)) if self.include_start_end_trans: self.start_scores = nn.Parameter(torch.randn(num_tags)) self.end_scores = nn.Parameter(torch.randn(num_tags)) if allowed_transitions is None: constrain = torch.zeros(num_tags + 2, num_tags + 2) else: constrain = torch.full((num_tags + 2, num_tags + 2), fill_value=-10000.0, dtype=torch.float) has_start = False has_end = False for from_tag_id, to_tag_id in allowed_transitions: constrain[from_tag_id, to_tag_id] = 0 if from_tag_id==num_tags: has_start = True if to_tag_id==num_tags+1: has_end = True if not has_start: constrain[num_tags, :].fill_(0) if not has_end: constrain[:, num_tags+1].fill_(0) self._constrain = nn.Parameter(constrain, requires_grad=False) def _normalizer_likelihood(self, logits, mask): r"""Computes the (batch_size,) denominator term for the log-likelihood, which is the sum of the likelihoods across all possible state sequences. :param logits:FloatTensor, ``[max_len, batch_size, num_tags]`` :param mask:ByteTensor, ``[max_len, batch_size]`` :return:FloatTensor, ``[batch_size,]`` """ seq_len, batch_size, n_tags = logits.size() alpha = logits[0] if self.include_start_end_trans: alpha = alpha + self.start_scores.view(1, -1) flip_mask = mask.eq(False) for i in range(1, seq_len): emit_score = logits[i].view(batch_size, 1, n_tags) trans_score = self.trans_m.view(1, n_tags, n_tags) tmp = alpha.view(batch_size, n_tags, 1) + emit_score + trans_score alpha = torch.logsumexp(tmp, 1).masked_fill(flip_mask[i].view(batch_size, 1), 0) + \ alpha.masked_fill(mask[i].eq(True).view(batch_size, 1), 0) if self.include_start_end_trans: alpha = alpha + self.end_scores.view(1, -1) return torch.logsumexp(alpha, 1) def _gold_score(self, logits, tags, mask): r""" Compute the score for the gold path. :param logits: FloatTensor, ``[max_len, batch_size, num_tags]`` :param tags: LongTensor, ``[max_len, batch_size]`` :param mask: ByteTensor, ``[max_len, batch_size]`` :return:FloatTensor, ``[batch_size.]`` """ seq_len, batch_size, _ = logits.size() batch_idx = torch.arange(batch_size, dtype=torch.long, device=logits.device) seq_idx = torch.arange(seq_len, dtype=torch.long, device=logits.device) # trans_socre [L-1, B] mask = mask.eq(True) flip_mask = mask.eq(False) trans_score = self.trans_m[tags[:seq_len - 1], tags[1:]].masked_fill(flip_mask[1:, :], 0) # emit_score [L, B] emit_score = logits[seq_idx.view(-1, 1), batch_idx.view(1, -1), tags].masked_fill(flip_mask, 0) # score [L-1, B] score = trans_score + emit_score[:seq_len - 1, :] score = score.sum(0) + emit_score[-1].masked_fill(flip_mask[-1], 0) if self.include_start_end_trans: st_scores = self.start_scores.view(1, -1).repeat(batch_size, 1)[batch_idx, tags[0]] last_idx = mask.long().sum(0) - 1 ed_scores = self.end_scores.view(1, -1).repeat(batch_size, 1)[batch_idx, tags[last_idx, batch_idx]] score = score + st_scores + ed_scores # return [B,] return score def forward(self, feats: "torch.FloatTensor", tags: "torch.LongTensor", mask: "torch.ByteTensor") -> "torch.FloatTensor": r""" 用于计算 ``CRF`` 的前向 loss,返回值为一个形状为 ``[batch_size,]`` 的 :class:`torch.FloatTensor` ,可能需要 :func:`mean` 求得 loss 。 :param feats: 特征矩阵,形状为 ``[batch_size, max_len, num_tags]`` :param tags: 标签矩阵,形状为 ``[batch_size, max_len]`` :param mask: 形状为 ``[batch_size, max_len]`` ,为 **0** 的位置认为是 padding。 :return: ``[batch_size,]`` """ feats = feats.transpose(0, 1) tags = tags.transpose(0, 1).long() mask = mask.transpose(0, 1).float() all_path_score = self._normalizer_likelihood(feats, mask) gold_path_score = self._gold_score(feats, tags, mask) return all_path_score - gold_path_score def viterbi_decode(self, logits: "torch.FloatTensor", mask: "torch.ByteTensor", unpad=False): r"""给定一个 **特征矩阵** 以及 **转移分数矩阵** ,计算出最佳的路径以及对应的分数 :param logits: 特征矩阵,形状为 ``[batch_size, max_len, num_tags]`` :param mask: 标签矩阵,形状为 ``[batch_size, max_len]`` ,为 **0** 的位置认为是 padding。如果为 ``None`` ,则认为没有 padding。 :param unpad: 是否将结果删去 padding: - 为 ``False`` 时,返回的是 ``[batch_size, max_len]`` 的张量 - 为 ``True`` 时,返回的是 :class:`List` [:class:`List` [ :class:`int` ]], 内部的 :class:`List` [:class:`int` ] 为每个 sequence 的 label ,已经除去 pad 部分,即每个 :class:`List` [ :class:`int` ] 的长度是这个 sample 的有效长度。 :return: (paths, scores)。 - ``paths`` -- 解码后的路径, 其值参照 ``unpad`` 参数. - ``scores`` -- :class:`torch.FloatTensor` ,形状为 ``[batch_size,]`` ,对应每个最优路径的分数。 """ batch_size, max_len, n_tags = logits.size() seq_len = mask.long().sum(1) logits = logits.transpose(0, 1).data # L, B, H mask = mask.transpose(0, 1).data.eq(True) # L, B flip_mask = mask.eq(False) # dp vpath = logits.new_zeros((max_len, batch_size, n_tags), dtype=torch.long) vscore = logits[0] # bsz x n_tags transitions = self._constrain.data.clone() transitions[:n_tags, :n_tags] += self.trans_m.data if self.include_start_end_trans: transitions[n_tags, :n_tags] += self.start_scores.data transitions[:n_tags, n_tags + 1] += self.end_scores.data vscore += transitions[n_tags, :n_tags] trans_score = transitions[:n_tags, :n_tags].view(1, n_tags, n_tags).data end_trans_score = transitions[:n_tags, n_tags+1].view(1, 1, n_tags).repeat(batch_size, 1, 1) # bsz, 1, n_tags # 针对长度为1的句子 vscore += transitions[:n_tags, n_tags+1].view(1, n_tags).repeat(batch_size, 1) \ .masked_fill(seq_len.ne(1).view(-1, 1), 0) for i in range(1, max_len): prev_score = vscore.view(batch_size, n_tags, 1) cur_score = logits[i].view(batch_size, 1, n_tags) + trans_score score = prev_score + cur_score.masked_fill(flip_mask[i].view(batch_size, 1, 1), 0) # bsz x n_tag x n_tag # 需要考虑当前位置是该序列的最后一个 score += end_trans_score.masked_fill(seq_len.ne(i+1).view(-1, 1, 1), 0) best_score, best_dst = score.max(1) vpath[i] = best_dst # 由于最终是通过last_tags回溯,需要保持每个位置的vscore情况 vscore = best_score.masked_fill(flip_mask[i].view(batch_size, 1), 0) + \ vscore.masked_fill(mask[i].view(batch_size, 1), 0) # backtrace batch_idx = torch.arange(batch_size, dtype=torch.long, device=logits.device) seq_idx = torch.arange(max_len, dtype=torch.long, device=logits.device) lens = (seq_len - 1) # idxes [L, B], batched idx from seq_len-1 to 0 idxes = (lens.view(1, -1) - seq_idx.view(-1, 1)) % max_len ans = logits.new_empty((max_len, batch_size), dtype=torch.long) ans_score, last_tags = vscore.max(1) ans[idxes[0], batch_idx] = last_tags for i in range(max_len - 1): last_tags = vpath[idxes[i], batch_idx, last_tags] ans[idxes[i + 1], batch_idx] = last_tags ans = ans.transpose(0, 1) if unpad: paths = [] for idx, max_len in enumerate(lens): paths.append(ans[idx, :max_len + 1].tolist()) else: paths = ans return paths, ans_score
PypiClean
/Hikka_Pyro-2.0.66-py3-none-any.whl/pyrogram/methods/advanced/save_file.py
import asyncio import functools import inspect import io import logging import math import os from hashlib import md5 from pathlib import PurePath from typing import Union, BinaryIO, Callable import pyrogram from pyrogram import StopTransmission from pyrogram import raw from pyrogram.session import Session log = logging.getLogger(__name__) class SaveFile: async def save_file( self: "pyrogram.Client", path: Union[str, BinaryIO], file_id: int = None, file_part: int = 0, progress: Callable = None, progress_args: tuple = () ): """Upload a file onto Telegram servers, without actually sending the message to anyone. Useful whenever an InputFile type is required. .. note:: This is a utility method intended to be used **only** when working with raw :obj:`functions <pyrogram.api.functions>` (i.e: a Telegram API method you wish to use which is not available yet in the Client class as an easy-to-use method). .. include:: /_includes/usable-by/users-bots.rst Parameters: path (``str`` | ``BinaryIO``): The path of the file you want to upload that exists on your local machine or a binary file-like object with its attribute ".name" set for in-memory uploads. file_id (``int``, *optional*): In case a file part expired, pass the file_id and the file_part to retry uploading that specific chunk. file_part (``int``, *optional*): In case a file part expired, pass the file_id and the file_part to retry uploading that specific chunk. progress (``Callable``, *optional*): Pass a callback function to view the file transmission progress. The function must take *(current, total)* as positional arguments (look at Other Parameters below for a detailed description) and will be called back each time a new file chunk has been successfully transmitted. progress_args (``tuple``, *optional*): Extra custom arguments for the progress callback function. You can pass anything you need to be available in the progress callback scope; for example, a Message object or a Client instance in order to edit the message with the updated progress status. Other Parameters: current (``int``): The amount of bytes transmitted so far. total (``int``): The total size of the file. *args (``tuple``, *optional*): Extra custom arguments as defined in the ``progress_args`` parameter. You can either keep ``*args`` or add every single extra argument in your function signature. Returns: ``InputFile``: On success, the uploaded file is returned in form of an InputFile object. Raises: RPCError: In case of a Telegram RPC error. """ if path is None: return None async def worker(session): while True: data = await queue.get() if data is None: return try: await session.invoke(data) except Exception as e: log.error(e) part_size = 512 * 1024 if isinstance(path, (str, PurePath)): fp = open(path, "rb") elif isinstance(path, io.IOBase): fp = path else: raise ValueError("Invalid file. Expected a file path as string or a binary (not text) file pointer") file_name = getattr(fp, "name", "file.jpg") fp.seek(0, os.SEEK_END) file_size = fp.tell() fp.seek(0) if file_size == 0: raise ValueError("File size equals to 0 B") file_size_limit_mib = 4000 if self.me.is_premium else 2000 if file_size > file_size_limit_mib * 1024 * 1024: raise ValueError(f"Can't upload files bigger than {file_size_limit_mib} MiB") file_total_parts = int(math.ceil(file_size / part_size)) is_big = file_size > 10 * 1024 * 1024 pool_size = 3 if is_big else 1 workers_count = 4 if is_big else 1 is_missing_part = file_id is not None file_id = file_id or self.rnd_id() md5_sum = md5() if not is_big and not is_missing_part else None pool = [ Session( self, await self.storage.dc_id(), await self.storage.auth_key(), await self.storage.test_mode(), is_media=True ) for _ in range(pool_size) ] workers = [self.loop.create_task(worker(session)) for session in pool for _ in range(workers_count)] queue = asyncio.Queue(16) try: for session in pool: await session.start() fp.seek(part_size * file_part) while True: chunk = fp.read(part_size) if not chunk: if not is_big and not is_missing_part: md5_sum = "".join([hex(i)[2:].zfill(2) for i in md5_sum.digest()]) break if is_big: rpc = raw.functions.upload.SaveBigFilePart( file_id=file_id, file_part=file_part, file_total_parts=file_total_parts, bytes=chunk ) else: rpc = raw.functions.upload.SaveFilePart( file_id=file_id, file_part=file_part, bytes=chunk ) await queue.put(rpc) if is_missing_part: return if not is_big and not is_missing_part: md5_sum.update(chunk) file_part += 1 if progress: func = functools.partial( progress, min(file_part * part_size, file_size), file_size, *progress_args ) if inspect.iscoroutinefunction(progress): await func() else: await self.loop.run_in_executor(self.executor, func) except StopTransmission: raise except Exception as e: log.error(e, exc_info=True) else: if is_big: return raw.types.InputFileBig( id=file_id, parts=file_total_parts, name=file_name, ) else: return raw.types.InputFile( id=file_id, parts=file_total_parts, name=file_name, md5_checksum=md5_sum ) finally: for _ in workers: await queue.put(None) await asyncio.gather(*workers) for session in pool: await session.stop() if isinstance(path, (str, PurePath)): fp.close()
PypiClean
/FreePyBX-1.0-RC1.tar.gz/FreePyBX-1.0-RC1/freepybx/public/js/dojox/grid/enhanced/plugins/NestedSorting.js
define("dojox/grid/enhanced/plugins/NestedSorting",["dojo/_base/declare","dojo/_base/array","dojo/_base/connect","dojo/_base/lang","dojo/_base/html","dojo/_base/event","dojo/_base/window","dojo/keys","dojo/query","dojo/string","../_Plugin","../../EnhancedGrid"],function(_1,_2,_3,_4,_5,_6,_7,_8,_9,_a,_b,_c){ var _d=_1("dojox.grid.enhanced.plugins.NestedSorting",_b,{name:"nestedSorting",_currMainSort:"none",_currRegionIdx:-1,_a11yText:{"dojoxGridDescending":"&#9662;","dojoxGridAscending":"&#9652;","dojoxGridAscendingTip":"&#1784;","dojoxGridDescendingTip":"&#1783;","dojoxGridUnsortedTip":"x"},constructor:function(){ this._sortDef=[]; this._sortData={}; this._headerNodes={}; this._excludedColIdx=[]; this.nls=this.grid._nls; this.grid.setSortInfo=function(){ }; this.grid.setSortIndex=_4.hitch(this,"_setGridSortIndex"); this.grid.getSortIndex=function(){ }; this.grid.getSortProps=_4.hitch(this,"getSortProps"); if(this.grid.sortFields){ this._setGridSortIndex(this.grid.sortFields,null,true); } this.connect(this.grid.views,"render","_initSort"); this.initCookieHandler(); this.subscribe("dojox/grid/rearrange/move/"+this.grid.id,_4.hitch(this,"_onColumnDnD")); },onStartUp:function(){ this.inherited(arguments); this.connect(this.grid,"onHeaderCellClick","_onHeaderCellClick"); this.connect(this.grid,"onHeaderCellMouseOver","_onHeaderCellMouseOver"); this.connect(this.grid,"onHeaderCellMouseOut","_onHeaderCellMouseOut"); },_onColumnDnD:function(_e,_f){ if(_e!=="col"){ return; } var m=_f,obj={},d=this._sortData,p; var cr=this._getCurrentRegion(); this._blurRegion(cr); var idx=this._getRegionHeader(cr).getAttribute("idx"); for(p in m){ if(d[p]){ obj[m[p]]=d[p]; delete d[p]; } if(p===idx){ idx=m[p]; } } for(p in obj){ d[p]=obj[p]; } var c=this._headerNodes[idx]; this._currRegionIdx=_2.indexOf(this._getRegions(),c.firstChild); this._initSort(false); },_setGridSortIndex:function(_10,_11,_12){ if(_4.isArray(_10)){ var i,d,_13; for(i=0;i<_10.length;i++){ d=_10[i]; _13=this.grid.getCellByField(d.attribute); if(!_13){ console.warn("Invalid sorting option, column ",d.attribute," not found."); return; } if(_13["nosort"]||!this.grid.canSort(_13.index,_13.field)){ console.warn("Invalid sorting option, column ",d.attribute," is unsortable."); return; } } this.clearSort(); _2.forEach(_10,function(d,i){ _13=this.grid.getCellByField(d.attribute); this.setSortData(_13.index,"index",i); this.setSortData(_13.index,"order",d.descending?"desc":"asc"); },this); }else{ if(!isNaN(_10)){ if(_11===undefined){ return; } this.setSortData(_10,"order",_11?"asc":"desc"); }else{ return; } } this._updateSortDef(); if(!_12){ this.grid.sort(); } },getSortProps:function(){ return this._sortDef.length?this._sortDef:null; },_initSort:function(_14){ var g=this.grid,n=g.domNode,len=this._sortDef.length; _5.toggleClass(n,"dojoxGridSorted",!!len); _5.toggleClass(n,"dojoxGridSingleSorted",len===1); _5.toggleClass(n,"dojoxGridNestSorted",len>1); if(len>0){ this._currMainSort=this._sortDef[0].descending?"desc":"asc"; } var idx,_15=this._excludedCoIdx=[]; this._headerNodes=_9("th",g.viewsHeaderNode).forEach(function(n){ idx=parseInt(n.getAttribute("idx"),10); if(_5.style(n,"display")==="none"||g.layout.cells[idx]["nosort"]||(g.canSort&&!g.canSort(idx,g.layout.cells[idx]["field"]))){ _15.push(idx); } }); this._headerNodes.forEach(this._initHeaderNode,this); this._initFocus(); if(_14){ this._focusHeader(); } },_initHeaderNode:function(_16){ _5.toggleClass(_16,"dojoxGridSortNoWrap",true); var _17=_9(".dojoxGridSortNode",_16)[0]; if(_17){ _5.toggleClass(_17,"dojoxGridSortNoWrap",true); } if(_2.indexOf(this._excludedCoIdx,_16.getAttribute("idx"))>=0){ _5.addClass(_16,"dojoxGridNoSort"); return; } if(!_9(".dojoxGridSortBtn",_16).length){ this._connects=_2.filter(this._connects,function(_18){ if(_18._sort){ _3.disconnect(_18); return false; } return true; }); var n=_5.create("a",{className:"dojoxGridSortBtn dojoxGridSortBtnNested",title:_a.substitute(this.nls.sortingState,[this.nls.nestedSort,this.nls.ascending]),innerHTML:"1"},_16.firstChild,"last"); n.onmousedown=_6.stop; n=_5.create("a",{className:"dojoxGridSortBtn dojoxGridSortBtnSingle",title:_a.substitute(this.nls.sortingState,[this.nls.singleSort,this.nls.ascending])},_16.firstChild,"last"); n.onmousedown=_6.stop; }else{ var a1=_9(".dojoxGridSortBtnSingle",_16)[0]; var a2=_9(".dojoxGridSortBtnNested",_16)[0]; a1.className="dojoxGridSortBtn dojoxGridSortBtnSingle"; a2.className="dojoxGridSortBtn dojoxGridSortBtnNested"; a2.innerHTML="1"; _5.removeClass(_16,"dojoxGridCellShowIndex"); _5.removeClass(_16.firstChild,"dojoxGridSortNodeSorted"); _5.removeClass(_16.firstChild,"dojoxGridSortNodeAsc"); _5.removeClass(_16.firstChild,"dojoxGridSortNodeDesc"); _5.removeClass(_16.firstChild,"dojoxGridSortNodeMain"); _5.removeClass(_16.firstChild,"dojoxGridSortNodeSub"); } this._updateHeaderNodeUI(_16); },_onHeaderCellClick:function(e){ this._focusRegion(e.target); if(_5.hasClass(e.target,"dojoxGridSortBtn")){ this._onSortBtnClick(e); _6.stop(e); this._focusRegion(this._getCurrentRegion()); } },_onHeaderCellMouseOver:function(e){ if(!e.cell){ return; } if(this._sortDef.length>1){ return; } if(this._sortData[e.cellIndex]&&this._sortData[e.cellIndex].index===0){ return; } var p; for(p in this._sortData){ if(this._sortData[p]&&this._sortData[p].index===0){ _5.addClass(this._headerNodes[p],"dojoxGridCellShowIndex"); break; } } if(!_5.hasClass(_7.body(),"dijit_a11y")){ return; } var i=e.cell.index,_19=e.cellNode; var _1a=_9(".dojoxGridSortBtnSingle",_19)[0]; var _1b=_9(".dojoxGridSortBtnNested",_19)[0]; var _1c="none"; if(_5.hasClass(this.grid.domNode,"dojoxGridSingleSorted")){ _1c="single"; }else{ if(_5.hasClass(this.grid.domNode,"dojoxGridNestSorted")){ _1c="nested"; } } var _1d=_1b.getAttribute("orderIndex"); if(_1d===null||_1d===undefined){ _1b.setAttribute("orderIndex",_1b.innerHTML); _1d=_1b.innerHTML; } if(this.isAsc(i)){ _1b.innerHTML=_1d+this._a11yText.dojoxGridDescending; }else{ if(this.isDesc(i)){ _1b.innerHTML=_1d+this._a11yText.dojoxGridUnsortedTip; }else{ _1b.innerHTML=_1d+this._a11yText.dojoxGridAscending; } } if(this._currMainSort==="none"){ _1a.innerHTML=this._a11yText.dojoxGridAscending; }else{ if(this._currMainSort==="asc"){ _1a.innerHTML=this._a11yText.dojoxGridDescending; }else{ if(this._currMainSort==="desc"){ _1a.innerHTML=this._a11yText.dojoxGridUnsortedTip; } } } },_onHeaderCellMouseOut:function(e){ var p; for(p in this._sortData){ if(this._sortData[p]&&this._sortData[p].index===0){ _5.removeClass(this._headerNodes[p],"dojoxGridCellShowIndex"); break; } } },_onSortBtnClick:function(e){ var _1e=e.cell.index; if(_5.hasClass(e.target,"dojoxGridSortBtnSingle")){ this._prepareSingleSort(_1e); }else{ if(_5.hasClass(e.target,"dojoxGridSortBtnNested")){ this._prepareNestedSort(_1e); }else{ return; } } _6.stop(e); this._doSort(_1e); },_doSort:function(_1f){ if(!this._sortData[_1f]||!this._sortData[_1f].order){ this.setSortData(_1f,"order","asc"); }else{ if(this.isAsc(_1f)){ this.setSortData(_1f,"order","desc"); }else{ if(this.isDesc(_1f)){ this.removeSortData(_1f); } } } this._updateSortDef(); this.grid.sort(); this._initSort(true); },setSortData:function(_20,_21,_22){ var sd=this._sortData[_20]; if(!sd){ sd=this._sortData[_20]={}; } sd[_21]=_22; },removeSortData:function(_23){ var d=this._sortData,i=d[_23].index,p; delete d[_23]; for(p in d){ if(d[p].index>i){ d[p].index--; } } },_prepareSingleSort:function(_24){ var d=this._sortData,p; for(p in d){ delete d[p]; } this.setSortData(_24,"index",0); this.setSortData(_24,"order",this._currMainSort==="none"?null:this._currMainSort); if(!this._sortData[_24]||!this._sortData[_24].order){ this._currMainSort="asc"; }else{ if(this.isAsc(_24)){ this._currMainSort="desc"; }else{ if(this.isDesc(_24)){ this._currMainSort="none"; } } } },_prepareNestedSort:function(_25){ var i=this._sortData[_25]?this._sortData[_25].index:null; if(i===0||!!i){ return; } this.setSortData(_25,"index",this._sortDef.length); },_updateSortDef:function(){ this._sortDef.length=0; var d=this._sortData,p; for(p in d){ this._sortDef[d[p].index]={attribute:this.grid.layout.cells[p].field,descending:d[p].order==="desc"}; } },_updateHeaderNodeUI:function(_26){ var _27=this._getCellByNode(_26); var _28=_27.index; var _29=this._sortData[_28]; var _2a=_9(".dojoxGridSortNode",_26)[0]; var _2b=_9(".dojoxGridSortBtnSingle",_26)[0]; var _2c=_9(".dojoxGridSortBtnNested",_26)[0]; _5.toggleClass(_2b,"dojoxGridSortBtnAsc",this._currMainSort==="asc"); _5.toggleClass(_2b,"dojoxGridSortBtnDesc",this._currMainSort==="desc"); if(this._currMainSort==="asc"){ _2b.title=_a.substitute(this.nls.sortingState,[this.nls.singleSort,this.nls.descending]); }else{ if(this._currMainSort==="desc"){ _2b.title=_a.substitute(this.nls.sortingState,[this.nls.singleSort,this.nls.unsorted]); }else{ _2b.title=_a.substitute(this.nls.sortingState,[this.nls.singleSort,this.nls.ascending]); } } var _2d=this; function _2e(){ var _2f="Column "+(_27.index+1)+" "+_27.field; var _30="none"; var _31="ascending"; if(_29){ _30=_29.order==="asc"?"ascending":"descending"; _31=_29.order==="asc"?"descending":"none"; } var _32=_2f+" - is sorted by "+_30; var _33=_2f+" - is nested sorted by "+_30; var _34=_2f+" - choose to sort by "+_31; var _35=_2f+" - choose to nested sort by "+_31; _2b.setAttribute("aria-label",_32); _2c.setAttribute("aria-label",_33); var _36=[_2d.connect(_2b,"onmouseover",function(){ _2b.setAttribute("aria-label",_34); }),_2d.connect(_2b,"onmouseout",function(){ _2b.setAttribute("aria-label",_32); }),_2d.connect(_2c,"onmouseover",function(){ _2c.setAttribute("aria-label",_35); }),_2d.connect(_2c,"onmouseout",function(){ _2c.setAttribute("aria-label",_33); })]; _2.forEach(_36,function(_37){ _37._sort=true; }); }; _2e(); var _38=_5.hasClass(_7.body(),"dijit_a11y"); if(!_29){ _2c.innerHTML=this._sortDef.length+1; _2c.title=_a.substitute(this.nls.sortingState,[this.nls.nestedSort,this.nls.ascending]); if(_38){ _2a.innerHTML=this._a11yText.dojoxGridUnsortedTip; } return; } if(_29.index||(_29.index===0&&this._sortDef.length>1)){ _2c.innerHTML=_29.index+1; } _5.addClass(_2a,"dojoxGridSortNodeSorted"); if(this.isAsc(_28)){ _5.addClass(_2a,"dojoxGridSortNodeAsc"); _2c.title=_a.substitute(this.nls.sortingState,[this.nls.nestedSort,this.nls.descending]); if(_38){ _2a.innerHTML=this._a11yText.dojoxGridAscendingTip; } }else{ if(this.isDesc(_28)){ _5.addClass(_2a,"dojoxGridSortNodeDesc"); _2c.title=_a.substitute(this.nls.sortingState,[this.nls.nestedSort,this.nls.unsorted]); if(_38){ _2a.innerHTML=this._a11yText.dojoxGridDescendingTip; } } } _5.addClass(_2a,(_29.index===0?"dojoxGridSortNodeMain":"dojoxGridSortNodeSub")); },isAsc:function(_39){ return this._sortData[_39].order==="asc"; },isDesc:function(_3a){ return this._sortData[_3a].order==="desc"; },_getCellByNode:function(_3b){ var i; for(i=0;i<this._headerNodes.length;i++){ if(this._headerNodes[i]===_3b){ return this.grid.layout.cells[i]; } } return null; },clearSort:function(){ this._sortData={}; this._sortDef.length=0; },initCookieHandler:function(){ if(this.grid.addCookieHandler){ this.grid.addCookieHandler({name:"sortOrder",onLoad:_4.hitch(this,"_loadNestedSortingProps"),onSave:_4.hitch(this,"_saveNestedSortingProps")}); } },_loadNestedSortingProps:function(_3c,_3d){ this._setGridSortIndex(_3c); },_saveNestedSortingProps:function(_3e){ return this.getSortProps(); },_initFocus:function(){ var f=this.focus=this.grid.focus; this._focusRegions=this._getRegions(); if(!this._headerArea){ var _3f=this._headerArea=f.getArea("header"); _3f.onFocus=f.focusHeader=_4.hitch(this,"_focusHeader"); _3f.onBlur=f.blurHeader=f._blurHeader=_4.hitch(this,"_blurHeader"); _3f.onMove=_4.hitch(this,"_onMove"); _3f.onKeyDown=_4.hitch(this,"_onKeyDown"); _3f._regions=[]; _3f.getRegions=null; this.connect(this.grid,"onBlur","_blurHeader"); } },_focusHeader:function(e){ if(this._currRegionIdx===-1){ this._onMove(0,1,null); }else{ this._focusRegion(this._getCurrentRegion()); } try{ _6.stop(e); } catch(e){ } return true; },_blurHeader:function(e){ this._blurRegion(this._getCurrentRegion()); return true; },_onMove:function(_40,_41,e){ var _42=this._currRegionIdx||0,_43=this._focusRegions; var _44=_43[_42+_41]; if(!_44){ return; }else{ if(_5.style(_44,"display")==="none"||_5.style(_44,"visibility")==="hidden"){ this._onMove(_40,_41+(_41>0?1:-1),e); return; } } this._focusRegion(_44); var _45=this._getRegionView(_44); _45.scrollboxNode.scrollLeft=_45.headerNode.scrollLeft; },_onKeyDown:function(e,_46){ if(_46){ switch(e.keyCode){ case _8.ENTER: case _8.SPACE: if(_5.hasClass(e.target,"dojoxGridSortBtnSingle")||_5.hasClass(e.target,"dojoxGridSortBtnNested")){ this._onSortBtnClick(e); } } } },_getRegionView:function(_47){ var _48=_47; while(_48&&!_5.hasClass(_48,"dojoxGridHeader")){ _48=_48.parentNode; } if(_48){ return _2.filter(this.grid.views.views,function(_49){ return _49.headerNode===_48; })[0]||null; } return null; },_getRegions:function(){ var _4a=[],_4b=this.grid.layout.cells; this._headerNodes.forEach(function(n,i){ if(_5.style(n,"display")==="none"){ return; } if(_4b[i]["isRowSelector"]){ _4a.push(n); return; } _9(".dojoxGridSortNode,.dojoxGridSortBtnNested,.dojoxGridSortBtnSingle",n).forEach(function(_4c){ _4c.setAttribute("tabindex",0); _4a.push(_4c); }); },this); return _4a; },_focusRegion:function(_4d){ if(!_4d){ return; } var _4e=this._getCurrentRegion(); if(_4e&&_4d!==_4e){ this._blurRegion(_4e); } var _4f=this._getRegionHeader(_4d); _5.addClass(_4f,"dojoxGridCellSortFocus"); if(_5.hasClass(_4d,"dojoxGridSortNode")){ _5.addClass(_4d,"dojoxGridSortNodeFocus"); }else{ if(_5.hasClass(_4d,"dojoxGridSortBtn")){ _5.addClass(_4d,"dojoxGridSortBtnFocus"); } } _4d.focus(); this.focus.currentArea("header"); this._currRegionIdx=_2.indexOf(this._focusRegions,_4d); },_blurRegion:function(_50){ if(!_50){ return; } var _51=this._getRegionHeader(_50); _5.removeClass(_51,"dojoxGridCellSortFocus"); if(_5.hasClass(_50,"dojoxGridSortNode")){ _5.removeClass(_50,"dojoxGridSortNodeFocus"); }else{ if(_5.hasClass(_50,"dojoxGridSortBtn")){ _5.removeClass(_50,"dojoxGridSortBtnFocus"); } } _50.blur(); },_getCurrentRegion:function(){ return this._focusRegions?this._focusRegions[this._currRegionIdx]:null; },_getRegionHeader:function(_52){ while(_52&&!_5.hasClass(_52,"dojoxGridCell")){ _52=_52.parentNode; } return _52; },destroy:function(){ this._sortDef=this._sortData=null; this._headerNodes=this._focusRegions=null; this.inherited(arguments); }}); _c.registerPlugin(_d); return _d; });
PypiClean
/Chameleon-4.1.0.tar.gz/Chameleon-4.1.0/src/chameleon/zpt/template.py
from functools import partial from hashlib import sha256 from os.path import dirname from ..astutil import Symbol from ..compiler import ExpressionEngine from ..i18n import simple_translate from ..loader import TemplateLoader from ..tal import RepeatDict from ..tales import DEFAULT_MARKER from ..tales import ExistsExpr from ..tales import ExpressionParser from ..tales import ImportExpr from ..tales import NotExpr from ..tales import ProxyExpr from ..tales import PythonExpr from ..tales import StringExpr from ..tales import StructureExpr from ..template import BaseTemplate from ..template import BaseTemplateFile from .program import MacroProgram try: bytes except NameError: bytes = str class PageTemplate(BaseTemplate): """Constructor for the page template language. Takes a string input as the only positional argument:: template = PageTemplate("<div>Hello, ${name}.</div>") Configuration (keyword arguments): ``auto_reload`` Enables automatic reload of templates. This is mostly useful in a development mode since it takes a significant performance hit. ``default_expression`` Set the default expression type. The default setting is ``python``. ``encoding`` The default text substitution value is a string. Pass an encoding to allow encoded byte string input (e.g. UTF-8). ``boolean_attributes`` Attributes included in this set are treated as booleans: if a true value is provided, the attribute value is the attribute name, e.g.:: boolean_attributes = {"selected"} If we insert an attribute with the name "selected" and provide a true value, the attribute will be rendered:: selected="selected" If a false attribute is provided (including the empty string), the attribute is dropped. The special return value ``default`` drops or inserts the attribute based on the value element attribute value. ``translate`` Use this option to set a translation function. Example:: def translate(msgid, domain=None, mapping=None, default=None, context=None): ... return translation Note that if ``target_language`` is provided at render time, the translation function must support this argument. ``implicit_i18n_translate`` Enables implicit translation for text appearing inside elements. Default setting is ``False``. While implicit translation does work for text that includes expression interpolation, each expression must be simply a variable name (e.g. ``${foo}``); otherwise, the text will not be marked for translation. ``implicit_i18n_attributes`` Any attribute contained in this set will be marked for implicit translation. Each entry must be a lowercase string. Example:: implicit_i18n_attributes = set(['alt', 'title']) ``on_error_handler`` This is an optional exception handler that is invoked during the "on-error" fallback block. ``strict`` Enabled by default. If disabled, expressions are only required to be valid at evaluation time. This setting exists to provide compatibility with the reference implementation which compiles expressions at evaluation time. ``trim_attribute_space`` If set, additional attribute whitespace will be stripped. ``restricted_namespace`` True by default. If set False, ignored all namespace except chameleon default namespaces. It will be useful working with attributes based javascript template renderer like VueJS. Example: <div v-bind:id="dynamicId"></div> <button v-on:click="greet">Greet</button> <button @click="greet">Greet</button> ``tokenizer`` None by default. If provided, this tokenizer is used instead of the default (which is selected based on the template mode parameter.) ``value_repr`` This can be used to override the default value representation function which is used to format values when formatting an exception output. The function must not raise an exception (it should be safe to call with any value). ``default_marker`` This default marker is used as the marker object bound to the `default` name available to any expression. The semantics is such that if an expression evaluates to the marker object, the default action is used; for an attribute expression, this is the static attribute text; for an element this is the static element text. If there is no static text then the default action is similar to an expression result of `None`. Output is of type ``str``. """ expression_types = { 'python': PythonExpr, 'string': StringExpr, 'not': NotExpr, 'exists': ExistsExpr, 'import': ImportExpr, 'structure': StructureExpr, } default_expression = 'python' translate = staticmethod(simple_translate) encoding = None boolean_attributes = set() mode = "xml" implicit_i18n_translate = False implicit_i18n_attributes = set() trim_attribute_space = False enable_data_attributes = False enable_comment_interpolation = True on_error_handler = None restricted_namespace = True tokenizer = None default_marker = Symbol(DEFAULT_MARKER) def __init__(self, body, **config): self.macros = Macros(self) super().__init__(body, **config) def __getitem__(self, name): return self.macros[name] @property def builtins(self): return self._builtins() @property def engine(self): return partial( ExpressionEngine, self.expression_parser, default_marker=self.default_marker, ) @property def expression_parser(self): return ExpressionParser(self.expression_types, self.default_expression) def parse(self, body): return MacroProgram( body, self.mode, self.filename, escape=True if self.mode == "xml" else False, default_marker=self.default_marker, boolean_attributes=self.boolean_attributes, implicit_i18n_translate=self.implicit_i18n_translate, implicit_i18n_attributes=self.implicit_i18n_attributes, trim_attribute_space=self.trim_attribute_space, enable_data_attributes=self.enable_data_attributes, enable_comment_interpolation=self.enable_comment_interpolation, restricted_namespace=self.restricted_namespace, tokenizer=self.tokenizer ) def render(self, encoding=None, **_kw): """Render template to string. If providd, the ``encoding`` argument overrides the template default value. Additional keyword arguments are passed as template variables. In addition, some also have a special meaning: ``translate`` This keyword argument will override the default template translate function. ``target_language`` This will be used as the default argument to the translate function if no `i18n:target` value is provided. If not provided, the `translate` function will need to negotiate a language based on the provided context. """ translate = _kw.get('translate') if translate is None: translate = self.translate # This should not be necessary, but we include it for # backward compatibility. if translate is None: translate = type(self).translate encoding = encoding if encoding is not None else self.encoding if encoding is not None: def translate(msgid, txl=translate, encoding=encoding, **kwargs): if isinstance(msgid, bytes): msgid = bytes.decode(msgid, encoding) return txl(msgid, **kwargs) def decode(inst, encoding=encoding): return bytes.decode(inst, encoding, 'ignore') else: decode = bytes.decode target_language = _kw.get('target_language') setdefault = _kw.setdefault setdefault("__translate", translate) setdefault("__convert", partial(translate, target_language=target_language)) setdefault("__decode", decode) setdefault("target_language", None) setdefault("__on_error_handler", self.on_error_handler) # Make sure we have a repeat dictionary if 'repeat' not in _kw: _kw['repeat'] = RepeatDict({}) return super().render(**_kw) def include(self, *args, **kwargs): self.cook_check() self._render(*args, **kwargs) def digest(self, body, names): hex = super().digest(body, names) if isinstance(hex, str): hex = hex.encode('utf-8') digest = sha256(hex) digest.update(';'.join(names).encode('utf-8')) for attr in ( 'trim_attribute_space', 'implicit_i18n_translate', 'strict' ): v = getattr(self, attr) digest.update( (";{}={}".format(attr, str(v))).encode('ascii') ) return digest.hexdigest()[:32] def _builtins(self): return { 'template': self, 'macros': self.macros, 'nothing': None, } class PageTemplateFile(PageTemplate, BaseTemplateFile): """File-based constructor. Takes a string input as the only positional argument:: template = PageTemplateFile(absolute_path) Note that the file-based template class comes with the expression type ``load`` which loads templates relative to the provided filename. Below are listed the configuration arguments specific to file-based templates; see the string-based template class for general options and documentation: Configuration (keyword arguments): ``loader_class`` The provided class will be used to create the template loader object. The default implementation supports relative and absolute path specs. The class must accept keyword arguments ``search_path`` (sequence of paths to search for relative a path spec) and ``default_extension`` (if provided, this should be added to any path spec). ``prepend_relative_search_path`` Inserts the path relative to the provided template file path into the template search path. The default setting is ``True``. ``search_path`` If provided, this is used as the search path for the ``load:`` expression. It must be a string or an iterable yielding a sequence of strings. """ expression_types = PageTemplate.expression_types.copy() expression_types['load'] = partial( ProxyExpr, '__loader', ignore_prefix=False ) prepend_relative_search_path = True def __init__(self, filename, search_path=None, loader_class=TemplateLoader, **config): if search_path is None: search_path = [] else: if isinstance(search_path, str): search_path = [search_path] else: search_path = list(search_path) def post_init(): # If the flag is set (this is the default), prepend the path # relative to the template file to the search path if self.prepend_relative_search_path: path = dirname(self.filename) search_path.insert(0, path) loader = loader_class(search_path=search_path, **config) template_class = type(self) # Bind relative template loader instance to the same template # class, providing the same keyword arguments. self._loader = loader.bind(template_class) super().__init__( filename, post_init_hook=post_init, **config ) def _builtins(self): d = super()._builtins() d['__loader'] = self._loader return d class PageTextTemplate(PageTemplate): """Text-based template class. Takes a non-XML input:: template = PageTextTemplate("Hello, ${name}.") This is similar to the standard library class ``string.Template``, but uses the expression engine to substitute variables. """ mode = "text" class PageTextTemplateFile(PageTemplateFile): """File-based constructor.""" mode = "text" def render(self, **vars): result = super().render(**vars) return result.encode(self.encoding or 'utf-8') class Macro: __slots__ = "include", def __init__(self, render): self.include = render class Macros: __slots__ = "template", def __init__(self, template): self.template = template def __getitem__(self, name): name = name.replace('-', '_') self.template.cook_check() try: function = getattr(self.template, "_render_%s" % name) except AttributeError: raise KeyError( "Macro does not exist: '%s'." % name) return Macro(function) @property def names(self): self.template.cook_check() result = [] for name in self.template.__dict__: if name.startswith('_render_'): result.append(name[8:]) return result
PypiClean
/Nuitka_fixed-1.1.2-cp310-cp310-win_amd64.whl/nuitka/plugins/standard/AntiBloatPlugin.py
import ast import re from nuitka.containers.OrderedDicts import OrderedDict from nuitka.Errors import NuitkaForbiddenImportEncounter from nuitka.plugins.PluginBase import NuitkaPluginBase from nuitka.utils.ModuleNames import ModuleName from nuitka.utils.Yaml import getYamlPackageConfiguration class NuitkaPluginAntiBloat(NuitkaPluginBase): plugin_name = "anti-bloat" plugin_desc = ( "Patch stupid imports out of widely used library modules source codes." ) @staticmethod def isAlwaysEnabled(): return True def __init__( self, noinclude_setuptools_mode, noinclude_pytest_mode, noinclude_unittest_mode, noinclude_ipython_mode, noinclude_default_mode, custom_choices, show_changes, ): # Many details, due to many repetitive arguments, pylint: disable=too-many-branches self.show_changes = show_changes # Default manually to default argument value: if noinclude_setuptools_mode is None: noinclude_setuptools_mode = noinclude_default_mode if noinclude_pytest_mode is None: noinclude_pytest_mode = noinclude_default_mode if noinclude_unittest_mode is None: noinclude_unittest_mode = noinclude_default_mode if noinclude_ipython_mode is None: noinclude_ipython_mode = noinclude_default_mode self.config = getYamlPackageConfiguration() self.handled_modules = OrderedDict() # These should be checked, to allow disabling anti-bloat contents. self.control_tags = OrderedDict() if noinclude_setuptools_mode != "allow": self.handled_modules["setuptools"] = noinclude_setuptools_mode self.handled_modules["setuptools_scm"] = noinclude_setuptools_mode else: self.control_tags["use_setuptools"] = True if noinclude_pytest_mode != "allow": self.handled_modules["pytest"] = noinclude_pytest_mode self.handled_modules["nose2"] = noinclude_pytest_mode self.handled_modules["nose"] = noinclude_pytest_mode else: self.control_tags["use_pytest"] = True if noinclude_unittest_mode != "allow": self.handled_modules["unittest"] = noinclude_unittest_mode else: self.control_tags["use_unittest"] = True if noinclude_ipython_mode != "allow": self.handled_modules["IPython"] = noinclude_ipython_mode else: self.control_tags["use_ipython"] = True for custom_choice in custom_choices: if ":" not in custom_choice: self.sysexit( "Error, malformed value '%s' for '--noinclude-custom-mode' used." % custom_choice ) module_name, mode = custom_choice.rsplit(":", 1) if mode not in ("error", "warning", "nofollow", "allow", "bytecode"): self.sysexit( "Error, illegal mode given '%s' in '--noinclude-custom-mode=%s'" % (mode, custom_choice) ) self.handled_modules[ModuleName(module_name)] = mode def getCacheContributionValues(self, module_name): config = self.config.get(module_name, section="anti-bloat") if config: yield str(config) @classmethod def addPluginCommandLineOptions(cls, group): group.add_option( "--show-anti-bloat-changes", action="store_true", dest="show_changes", default=False, help="""\ Annotate what changes are by the plugin done.""", ) group.add_option( "--noinclude-setuptools-mode", action="store", dest="noinclude_setuptools_mode", choices=("error", "warning", "nofollow", "allow"), default=None, help="""\ What to do if a 'setuptools' or import is encountered. This package can be big with dependencies, and should definitely be avoided. Also handles 'setuptools_scm'.""", ) group.add_option( "--noinclude-pytest-mode", action="store", dest="noinclude_pytest_mode", choices=("error", "warning", "nofollow", "allow"), default=None, help="""\ What to do if a 'pytest' import is encountered. This package can be big with dependencies, and should definitely be avoided. Also handles 'nose' imports.""", ) group.add_option( "--noinclude-unittest-mode", action="store", dest="noinclude_unittest_mode", choices=("error", "warning", "nofollow", "allow"), default=None, help="""\ What to do if a unittest import is encountered. This package can be big with dependencies, and should definitely be avoided.""", ) group.add_option( "--noinclude-IPython-mode", action="store", dest="noinclude_ipython_mode", choices=("error", "warning", "nofollow", "allow"), default=None, help="""\ What to do if a IPython import is encountered. This package can be big with dependencies, and should definitely be avoided.""", ) group.add_option( "--noinclude-default-mode", action="store", dest="noinclude_default_mode", choices=("error", "warning", "nofollow", "allow"), default="warning", help="""\ This actually provides the default "warning" value for above options, and can be used to turn all of these on.""", ) group.add_option( "--noinclude-custom-mode", action="append", dest="custom_choices", default=[], help="""\ What to do if a specific import is encountered. Format is module name, which can and should be a top level package and then one choice, "error", "warning", "nofollow", e.g. PyQt5:error.""", ) def _onModuleSourceCode(self, module_name, anti_bloat_config, source_code): # Complex dealing with many cases, pylint: disable=too-many-branches,too-many-locals,too-many-statements description = anti_bloat_config.get("description", "description not given") # To allow detection if it did anything. change_count = 0 context = {} context_code = anti_bloat_config.get("context", "") if type(context_code) in (tuple, list): context_code = "\n".join(context_code) # We trust the yaml files, pylint: disable=eval-used,exec-used context_ready = not bool(context_code) for replace_src, replace_code in anti_bloat_config.get( "replacements", {} ).items(): # Avoid the eval, if the replace doesn't hit. if replace_src not in source_code: continue if replace_code: if not context_ready: try: exec(context_code, context) except Exception as e: # pylint: disable=broad-except self.sysexit( "Error, cannot execute context code '%s' due to: %s" % (context_code, e) ) context_ready = True try: replace_dst = eval(replace_code, context) except Exception as e: # pylint: disable=broad-except self.sysexit( "Error, cannot evaluate code '%s' in '%s' due to: %s" % (replace_code, context_code, e) ) else: replace_dst = "" if type(replace_dst) is not str: self.sysexit( "Error, expression needs to generate string, not %s" % type(replace_dst) ) old = source_code source_code = source_code.replace(replace_src, replace_dst) if old != source_code: change_count += 1 for replace_src, replace_dst in anti_bloat_config.get( "replacements_plain", {} ).items(): old = source_code source_code = source_code.replace(replace_src, replace_dst) if old != source_code: change_count += 1 for replace_src, replace_dst in anti_bloat_config.get( "replacements_re", {} ).items(): old = source_code source_code = re.sub(replace_src, replace_dst, source_code) if old != source_code: change_count += 1 append_code = anti_bloat_config.get("append_result", "") if type(append_code) in (tuple, list): append_code = "\n".join(append_code) if append_code: if not context_ready: exec(context_code, context) context_ready = True try: append_result = eval(append_code, context) except Exception as e: # pylint: disable=broad-except self.sysexit( "Error, cannot evaluate code '%s' in '%s' due to: %s" % (append_code, context_code, e) ) source_code += "\n" + append_result change_count += 1 append_plain = anti_bloat_config.get("append_plain", "") if type(append_plain) in (tuple, list): append_plain = "\n".join(append_plain) if append_plain: source_code += "\n" + append_plain change_count += 1 if change_count > 0 and self.show_changes: self.info( "Handling module '%s' with %d change(s) for: %s." % (module_name.asString(), change_count, description) ) module_code = anti_bloat_config.get("module_code", None) if module_code is not None: assert not change_count if self.show_changes: self.info( "Handling module '%s' with full replacement : %s." % (module_name.asString(), description) ) source_code = module_code return source_code def onModuleSourceCode(self, module_name, source_code): for anti_bloat_config in self.config.get(module_name, section="anti-bloat"): if self.evaluateCondition( full_name=module_name, condition=anti_bloat_config.get("when", "True"), # Allow disabling config for a module with matching control tags. control_tags=self.control_tags, ): source_code = self._onModuleSourceCode( module_name=module_name, anti_bloat_config=anti_bloat_config, source_code=source_code, ) return source_code def _onFunctionBodyParsing( self, module_name, anti_bloat_config, function_name, body ): context = {} context_code = anti_bloat_config.get("context", "") if type(context_code) in (tuple, list): context_code = "\n".join(context_code) # We trust the yaml files, pylint: disable=eval-used,exec-used context_ready = not bool(context_code) replace_code = anti_bloat_config.get("change_function", {}).get(function_name) if replace_code == "un-callable": replace_code = """'raise RuntimeError("Must not call %s.%s")'""" % ( module_name, function_name, ) if replace_code is not None: if not context_ready: exec(context_code, context) context_ready = True try: replacement = eval(replace_code, context) except Exception as e: # pylint: disable=broad-except self.sysexit( "Error, cannot evaluate code '%s' in '%s' due to: %s" % (replace_code, context_code, e) ) # Single node is required, extract the generated module body with # single expression only statement value or a function body. replacement = ast.parse(replacement).body[0] if type(replacement) is ast.Expr: if type(replacement.value) is ast.Lambda: body[:] = [ast.Return(replacement.value.body)] else: body[:] = [ast.Return(replacement.value)] elif type(replacement) is ast.Raise: body[:] = [replacement] else: body[:] = replacement.body if self.show_changes: self.info( "Updated module '%s' function '%s'." % (module_name.asString(), function_name) ) def onFunctionBodyParsing(self, module_name, function_name, body): config = self.config.get(module_name, section="anti-bloat") if config: for anti_bloat_config in config: self._onFunctionBodyParsing( module_name=module_name, anti_bloat_config=anti_bloat_config, function_name=function_name, body=body, ) def onModuleRecursion(self, module_name, module_filename, module_kind): for handled_module_name, mode in self.handled_modules.items(): if module_name.hasNamespace(handled_module_name): # Make sure the compilation aborts. if mode == "error": raise NuitkaForbiddenImportEncounter(module_name) if mode == "warning": self.warning("Unwanted import of '%s' encountered." % module_name) def onModuleEncounter(self, module_name, module_filename, module_kind): for handled_module_name, mode in self.handled_modules.items(): if module_name.hasNamespace(handled_module_name): # Either issue a warning, or pretend the module doesn't exist for standalone or # at least will not be included. if mode == "nofollow": if self.show_changes: self.info( "Forcing import of '%s' to not be followed." % module_name ) return ( False, "user requested to not follow '%s' import" % module_name, ) # Do not provide an opinion about it. return None def decideCompilation(self, module_name): for handled_module_name, mode in self.handled_modules.items(): if mode != "bytecode": continue if module_name.hasNamespace(handled_module_name): return "bytecode"
PypiClean
/NREL_reVX-0.3.53-py3-none-any.whl/reVX/config/turbine_flicker.py
from reV.config.base_analysis_config import AnalysisConfig class TurbineFlickerConfig(AnalysisConfig): """Config framework for turbine flicker calculation""" NAME = 'TurbineFlicker' REQUIREMENTS = ('excl_fpath', 'res_fpath', 'hub_height', 'rotor_diameter') def __init__(self, config): """ Parameters ---------- config : str | dict Path to config .json or pre-extracted config input dictionary. """ super().__init__(config) self._default_tm_dset = 'techmap_wtk' self._default_resolution = 128 self._default_grid_cell_size = 90 self._default_max_flicker_exclusion_range = "10x" self._default_building_threshold = 0 self._default_flicker_threshold = 30 self._default_hsds_flag = False @property def excl_fpath(self): """Get the exclusions .h5 file path (required).""" return self['excl_fpath'] @property def res_fpath(self): """Get the resource .h5 file path (required).""" return self['res_fpath'] @property def regulations_fpath(self): """Get regulations .csv path""" return self.get('regulations_fpath', None) @property def building_layer(self): """Get the building layer name.""" return self.get('building_layer', None) @property def hub_height(self): """ Get the turbine hub-height for which shadow flicker will be computed. """ return self['hub_height'] @property def rotor_diameter(self): """ Get turbine rotor diameter for which shadow flicker will be computed. """ return self['rotor_diameter'] @property def tm_dset(self): """Get the techmap dataset name.""" return self.get('tm_dset', self._default_tm_dset) @property def resolution(self): """Get the supply curve resolution.""" return self.get('resolution', self._default_resolution) @property def grid_cell_size(self): """Get the length (m) of a side of each grid cell in `excl_fpath`.""" return self.get('grid_cell_size', self._default_grid_cell_size) @property def max_flicker_exclusion_range(self): """ Get the max distance (m) that flicker exclusions will extend in any of the cardinal directions. """ return self.get('max_flicker_exclusion_range', self._default_max_flicker_exclusion_range) @property def building_threshold(self): """ Get the threshold for which buildings are identified in the building_layer. """ return self.get('building_threshold', self._default_building_threshold) @property def flicker_threshold(self): """ Get the threshold at which shadow flicker will lead to an exclusions, values are in hours """ return self.get('flicker_threshold', self._default_flicker_threshold) @property def out_layer(self): """ Get the output layer name under which turbine flicker exclusions will be saved """ return self.get('out_layer', None) @property def replace(self): """Get replace flag""" return self.get('replace', False) @property def hsds(self): """Get hsds flag""" return self.get('hsds', self._default_hsds_flag)
PypiClean
/ALP4lib-1.0.1.tar.gz/ALP4lib-1.0.1/README.md
# ALP4lib ALP4lib is a Python module to control Vialux DMDs based on ALP4.X API. This is not an independant open source module, it uses the .ddl files provided by [Vialux](http://www.vialux.de/en/). This software is experimental, use it at your own risk. ## What is it? This module wraps the basic function of the Vialux dlls to control a digitial micro-mirror device with a Vialux board. Vialux provides dlls and also modules for Matlab and Labview but not for Python. This code is tested with a device using the 4.3 version of the ALP API, other versions may have issues. LED control related functions are not implemented. Please read the ALP API description provided with the [Vialux](http://www.vialux.de/en/) ALP installation. ## Requirements * Windows 32 or 64, * Vialux drivers and the ALP4.X dll files available for download on [Vialux website](http://www.vialux.de/en/), * Compatible Python 2.7 and 3.X. ## Citing the code If the code was helpful to your work, please consider citing it: [![DOI](https://zenodo.org/badge/70229567.svg)](https://zenodo.org/badge/latestdoi/70229567) ## Installation ### Manual installation Just copy the ALP4.py file in the working directory. ### Automatic installation To automatically download and copy the module in the python directory (so it can be available from anywhere), run the command: ```shell pip install ALP4lib ``` or ```shell easy_install ALP4lib ``` ### Installation from source (Github) To install the latest version from Github, clone the repository, and install the package with the the following command. ```shell script python setup.py install ``` Instead of the normal installation, if you want to install ALP4lib in [development mode](https://setuptools.readthedocs.io/en/latest/userguide/development_mode.html), use: ```shell script python setup.py develop ``` ## Copy the .dll The win32 ALPX.dll files should be directly in the working directory and the win64 dll with the same name in a /x64 subfolder. Alternatively, a different dll directory can be set at the initialization of the DMD handler object. The dlls have the following names respectively for the 4.1, 4.2 and 4.3 versions of the ALP API: 'alp41.dll', 'alp42.dll' and 'alp4395.dll'. ## A simple example ```python import numpy as np from ALP4 import * import time # Load the Vialux .dll DMD = ALP4(version = '4.3') # Initialize the device DMD.Initialize() # Binary amplitude image (0 or 1) bitDepth = 1 imgBlack = np.zeros([DMD.nSizeY,DMD.nSizeX]) imgWhite = np.ones([DMD.nSizeY,DMD.nSizeX])*(2**8-1) imgSeq = np.concatenate([imgBlack.ravel(),imgWhite.ravel()]) # Allocate the onboard memory for the image sequence DMD.SeqAlloc(nbImg = 2, bitDepth = bitDepth) # Send the image sequence as a 1D list/array/numpy array DMD.SeqPut(imgData = imgSeq) # Set image rate to 50 Hz DMD.SetTiming(pictureTime = 20000) # Run the sequence in an infinite loop DMD.Run() time.sleep(10) # Stop the sequence display DMD.Halt() # Free the sequence from the onboard memory DMD.FreeSeq() # De-allocate the device DMD.Free() ```
PypiClean
/OctoBot-Services-1.6.2.tar.gz/OctoBot-Services-1.6.2/octobot_services/interfaces/util/util.py
import threading import octobot_commons.logging as logging import octobot_commons.constants as commons_constants import octobot_trading.api as trading_api import octobot_services.interfaces as interfaces def get_exchange_managers(bot_api=None, independent_backtesting=None, trading_exchanges_only=True): if bot_api is not None: return _filter_exchange_manager(trading_api.get_exchange_managers_from_exchange_ids( bot_api.get_exchange_manager_ids()), trading_exchanges_only) elif independent_backtesting is not None: try: import octobot.api as api return _filter_exchange_manager( trading_api.get_exchange_managers_from_exchange_ids( api.get_independent_backtesting_exchange_manager_ids(independent_backtesting)), trading_exchanges_only) except ImportError: logging.get_logger("octobot_services/interfaces/util/util.py").error( "get_exchange_managers requires OctoBot package installed") else: return _filter_exchange_manager(interfaces.AbstractInterface.get_exchange_managers(), trading_exchanges_only) def _filter_exchange_manager(exchange_managers, trading_exchanges_only): if trading_exchanges_only: return trading_api.get_trading_exchanges(exchange_managers) return exchange_managers def run_in_bot_main_loop(coroutine, blocking=True, log_exceptions=True, timeout=commons_constants.DEFAULT_FUTURE_TIMEOUT): if blocking: return interfaces.get_bot_api().run_in_main_asyncio_loop(coroutine, log_exceptions=log_exceptions, timeout=timeout) else: threading.Thread( target=interfaces.get_bot_api().run_in_main_asyncio_loop, name=f"run_in_bot_main_loop {coroutine.__name__}", args=(coroutine,), kwargs={"timeout": timeout} ).start() def run_in_bot_async_executor(coroutine): return interfaces.get_bot_api().run_in_async_executor(coroutine)
PypiClean
/Newcalls-0.0.1-cp37-cp37m-win_amd64.whl/newcalls/node_modules/util-deprecate/README.md
util-deprecate ============== ### The Node.js `util.deprecate()` function with browser support In Node.js, this module simply re-exports the `util.deprecate()` function. In the web browser (i.e. via browserify), a browser-specific implementation of the `util.deprecate()` function is used. ## API A `deprecate()` function is the only thing exposed by this module. ``` javascript // setup: exports.foo = deprecate(foo, 'foo() is deprecated, use bar() instead'); // users see: foo(); // foo() is deprecated, use bar() instead foo(); foo(); ``` ## License (The MIT License) Copyright (c) 2014 Nathan Rajlich <[email protected]> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
PypiClean
/Bluebook-0.0.1.tar.gz/Bluebook-0.0.1/pylot/component/views/contact_page.py
from pylot import (Pylot, utils, route, abort, redirect, request, url_for) from pylot.component import (mailer, recaptcha) def contact_page(**kwargs): template_dir = kwargs["template_dir"] if "template_dir" \ in kwargs else "Pylot/ContactPage" template_page = template_dir + "/%s.html" def wrapper(view): @view.extends__ @route("contact", methods=["GET", "POST"], endpoint="ContactPage") def contact(self): if request.method == "POST": error_message = None email = request.form.get("email") subject = request.form.get("subject") message = request.form.get("message") name = request.form.get("name") contact_email = self.get_config__("CONTACT_PAGE_EMAIL_RECIPIENT") if recaptcha.verify(): if not email or not subject or not message: error_message = "All fields are required" elif not utils.is_valid_email(email): error_message = "Invalid email address" if error_message: self.flash_error__(error_message) else: mailer.send_template("contact-us.txt", to=contact_email, reply_to=email, mail_from=email, mail_subject=subject, mail_message=message, mail_name=name ) self.flash_success__("Message sent successfully! We'll get in touch with you soon.") else: self.flash_error__("Invalid security code") return redirect(url_for("ContactPage")) else: self.set_meta__(title="Contact Us") return self.render(view_template=template_page % "contact") return view return wrapper
PypiClean
/ARGs_OAP-2.3.2.tar.gz/ARGs_OAP-2.3.2/ARGs_OAP/bin/bbmap/muxbyname.sh
usage(){ echo " Written by Brian Bushnell Last modified June 22, 2016 Description: Multiplexes reads from multiple files after renaming them based on their initial file. Opposite of demuxbyname. Usage: muxbyname.sh in=<file,file,file...> out=<output file> Input files may also be given without an in= prefix, so that you can use wildcards: muxbyname.sh *.fastq out=muxed.fastq Standard parameters: in=<file,file> A list of input files. in2=<file,file> Read 2 input if reads are in paired files. out=<file> Primary output, or read 1 output. out2=<file> Read 2 output if reads are in paired files. overwrite=f (ow) Set to false to force the program to abort rather than overwrite an existing file. showspeed=t (ss) Set to 'f' to suppress display of processing speed. ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster. Processing parameters: None yet! Java Parameters: -Xmx This will set Java's memory usage, overriding autodetection. -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. The max is typically 85% of physical memory. -eoom This flag will cause the process to exit if an out-of-memory exception occurs. Requires Java 8u92+. -da Disable assertions. Please contact Brian Bushnell at [email protected] if you encounter any problems. " } #This block allows symlinked shellscripts to correctly set classpath. pushd . > /dev/null DIR="${BASH_SOURCE[0]}" while [ -h "$DIR" ]; do cd "$(dirname "$DIR")" DIR="$(readlink "$(basename "$DIR")")" done cd "$(dirname "$DIR")" DIR="$(pwd)/" popd > /dev/null #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" CP="$DIR""current/" z="-Xmx400m" z2="-Xms400m" set=0 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then usage exit fi calcXmx () { source "$DIR""/calcmem.sh" setEnvironment parseXmx "$@" } calcXmx "$@" muxbyname() { local CMD="java $EA $EOOM $z -cp $CP driver.RenameAndMux $@" echo $CMD >&2 eval $CMD } muxbyname "$@"
PypiClean
/BigJob-0.64.5.tar.gz/BigJob-0.64.5/docs/source/tutorial/index.rst
######## Tutorial ######## This tutorial will walk you through the installation as well as the most important features of BigJob. Many of these examples illustrate common workflow usages as well as distributed data movement. **Prerequisites:** * You are familiar with Linux or UNIX * You can read and write Python code * You can use SSH and understand how public and private keys work * You understand the basic concepts of distributed computing **You will learn how to:** * Install BigJob into user space on your own machine or XSEDE resource * Learn to submit multiple jobs through a 'container job' to either your local machine or a remote resource * Write a program that runs multiple jobs to form a simple ensemble workflow * Write programs that demonstrate more complex, frequently used workflows * Use file transfer capabilities to transfer input files to the location of an executable **Contents:** .. toctree:: :numbered: :maxdepth: 1 part1 part2 part3 part4 table
PypiClean
/AmFast-0.5.3-r541.tar.gz/AmFast-0.5.3-r541/amfast/remoting/gae_subscription_manager.py
import pickle from google.appengine.ext import db import amfast from subscription_manager import Subscription, SubscriptionManager class GaeSubscription(db.Model, Subscription): """A client's subscription to a topic, persisted in a Google Datastore.""" @classmethod def getKeyName(cls, connection_id, client_id, topic): return ':'.join((connection_id, client_id, topic)) connection_id = db.StringProperty(required=True) client_id = db.StringProperty(required=True) topic = db.StringProperty(required=True) class GaeMessageBody(db.Model): """Flex message body persisted in a Google Datastore.""" p_message = db.BlobProperty(required=True) class GaeMessageMetadata(db.Model): """Flex message metadata persisted in a Google Datastore.""" time_to_live = db.FloatProperty(required=True) timestamp = db.FloatProperty(required=True) topic = db.StringProperty(required=True) message_body = db.ReferenceProperty(reference_class=GaeMessageBody, required=True) class GaeSubscriptionManager(SubscriptionManager): """Stores subscriptions in Google DataStore.""" def reset(self): query = GaeSubscription.all(keys_only=True) for result in query: db.delete(result) query = GaeMessageMetadata.all(keys_only=True) for result in query: db.delete(result) query = GaeMessageBody.all(keys_only=True) for result in query: db.delete(result) def subscribe(self, connection_id, client_id, topic, sub_topic=None, selector=None): """Add a subscription to a topic.""" topic = SubscriptionManager.getTopicKey(topic, sub_topic) key_name = GaeSubscription.getKeyName(connection_id, client_id, topic) subscription = GaeSubscription(key_name=key_name, connection_id=connection_id, client_id=client_id, topic=topic) subscription.put() def unSubscribe(self, connection_id, client_id, topic, sub_topic=None): """Remove a subscription from a topic.""" topic = SubscriptionManager.getTopicKey(topic, sub_topic) key_name = GaeSubscription.getKeyName(connection_id, client_id, topic) subscription = GaeSubscription.get_by_key_name(key_name) db.delete(subscription) def deleteConnection(self, connection): """Delete connection-subscription information.""" query = GaeSubscription.all(keys_only=True) query.filter('connection_id = ', connection.id) db.delete(query) def persistMessage(self, msg): """Save message object.""" # Remove connection data, # so that it is not pickled tmp_connection = getattr(msg, 'connection', None) if tmp_connection is not None: msg.connection = None message_body = GaeMessageBody(p_message=pickle.dumps(msg)) message_body.put() message_data = GaeMessageMetadata(timestamp=msg.timestamp, time_to_live=float(msg.timeToLive), topic=self.getMessageTopicKey(msg), message_body=message_body) message_data.put() # Restore connection attr. if tmp_connection is not None: msg.connection = tmp_connection def iterConnectionSubscriptions(self, connection): """Iterate through all Subscriptions that belong to a specific connection.""" query = GaeSubscription.all() query.filter('connection_id = ', connection.id) return query def iterSubscribers(self, topic, sub_topic=None): """Iterate through all connection ids subscribed to a topic.""" topic = SubscriptionManager.getTopicKey(topic, sub_topic) connection_ids = {} # Keep track of unique IDs. query = GaeSubscription.all() query.filter('topic = ', topic) for subscription in query: if subscription.connection_id in connection_ids: continue connection_ids[subscription.connection_id] = True yield subscription.connection_id def pollMessages(self, topic, cutoff_time, current_time): """Retrieves all qeued messages, and discards expired messages. arguments: =========== * topic - string, Topic to find messages for. * cutoff_time - float, epoch time, only messages published after this time will be returned. * current_time - float, epoch time, used to determine if a message is expired. """ query = GaeMessageMetadata.all() query.filter('topic = ', topic) query.filter('timestamp > ', cutoff_time) query.order('timestamp') for message_data in query: yield pickle.loads(message_data.message_body.p_message) def deleteExpiredMessages(self, cutoff_time): query = GaeMessageMetadata.all(keys_only=True) query.filter('timestamp < ', cutoff_time) for result in query: db.delete(result)
PypiClean
/CsuPTMD-1.0.12.tar.gz/CsuPTMD-1.0.12/PTMD/maskrcnn_benchmark/engine/trainer.py
import datetime import logging import time import torch import torch.distributed as dist from PTMD.maskrcnn_benchmark.utils.comm import get_world_size from PTMD.maskrcnn_benchmark.utils.metric_logger import MetricLogger from apex import amp def reduce_loss_dict(loss_dict): """ Reduce the loss dictionary from all processes so that process with rank 0 has the averaged results. Returns a dict with the same fields as loss_dict, after reduction. """ world_size = get_world_size() if world_size < 2: return loss_dict with torch.no_grad(): loss_names = [] all_losses = [] for k in sorted(loss_dict.keys()): loss_names.append(k) all_losses.append(loss_dict[k]) all_losses = torch.stack(all_losses, dim=0) dist.reduce(all_losses, dst=0) if dist.get_rank() == 0: # only main process gets accumulated, so only divide by # world_size in this case all_losses /= world_size reduced_losses = {k: v for k, v in zip(loss_names, all_losses)} return reduced_losses def do_train( model, data_loader, optimizer, scheduler, checkpointer, device, checkpoint_period, arguments, ): logger = logging.getLogger("maskrcnn_benchmark.trainer") logger.info("Start training") meters = MetricLogger(delimiter=" ") max_iter = len(data_loader) start_iter = arguments["iteration"] model.train() start_training_time = time.time() end = time.time() for iteration, (images, targets, _) in enumerate(data_loader, start_iter): data_time = time.time() - end iteration = iteration + 1 arguments["iteration"] = iteration scheduler.step() images = images.to(device) targets = [target.to(device) for target in targets] loss_dict = model(images, targets) losses = sum(loss for loss in loss_dict.values()) # reduce losses over all GPUs for logging purposes loss_dict_reduced = reduce_loss_dict(loss_dict) losses_reduced = sum(loss for loss in loss_dict_reduced.values()) meters.update(loss=losses_reduced, **loss_dict_reduced) optimizer.zero_grad() # Note: If mixed precision is not used, this ends up doing nothing # Otherwise apply loss scaling for mixed-precision recipe with amp.scale_loss(losses, optimizer) as scaled_losses: scaled_losses.backward() optimizer.step() batch_time = time.time() - end end = time.time() meters.update(time=batch_time, data=data_time) eta_seconds = meters.time.global_avg * (max_iter - iteration) eta_string = str(datetime.timedelta(seconds=int(eta_seconds))) if iteration % 20 == 0 or iteration == max_iter: logger.info( meters.delimiter.join( [ "eta: {eta}", "iter: {iter}", "{meters}", "lr: {lr:.6f}", "max mem: {memory:.0f}", ] ).format( eta=eta_string, iter=iteration, meters=str(meters), lr=optimizer.param_groups[0]["lr"], memory=torch.cuda.max_memory_allocated() / 1024.0 / 1024.0, ) ) if iteration % checkpoint_period == 0: checkpointer.save("model_{:07d}".format(iteration), **arguments) if iteration == max_iter: checkpointer.save("model_final", **arguments) total_training_time = time.time() - start_training_time total_time_str = str(datetime.timedelta(seconds=total_training_time)) logger.info( "Total training time: {} ({:.4f} s / it)".format( total_time_str, total_training_time / (max_iter) ) )
PypiClean
/crosscat-0.1.55-cp27-none-macosx_10_6_intel.whl/crosscat/IPClusterEngine.py
import functools # from IPython.parallel import Client # import crosscat import crosscat.LocalEngine as LE def partialize(func, args_dict, dview): # why is this push necessary? dview.push(args_dict, block=True) helper = functools.partial(func, **args_dict) return helper class IPClusterEngine(LE.LocalEngine): """A simple interface to the Cython-wrapped C++ engine IPClusterEngine """ def __init__(self, config_filename=None, profile=None, seed=None, sshkey=None, packer='json'): """Initialize a IPClusterEngine Do IPython.parallel operations to set up cluster and generate mapper. """ super(IPClusterEngine, self).__init__(seed=seed) rc = Client(config_filename, profile=profile, sshkey=sshkey, packer=packer) # FIXME: add a warning if environment in direct view is not 'empty'? # else, might become dependent on an object created in # environemnt in a prior run dview = rc.direct_view() lview = rc.load_balanced_view() with dview.sync_imports(local=True): import crosscat mapper = lambda f, tuples: self.lview.map(f, *tuples) # if you're trying to debug issues, consider clearning to start fresh # rc.clear(block=True) # self.rc = rc self.dview = dview self.lview = lview self.mapper = mapper self.do_initialize = None self.do_analyze = None return def get_initialize_arg_tuples(self, M_c, M_r, T, initialization, row_initialization, n_chains): args_dict = dict(M_c=M_c, M_r=M_r, T=T, initialization=initialization, row_initialization=row_initialization) do_initialize = partialize(crosscat.LocalEngine._do_initialize, args_dict, self.dview) seeds = [self.get_next_seed() for seed_idx in range(n_chains)] arg_tuples = [seeds] # self.do_initialize = do_initialize return arg_tuples def get_analyze_arg_tuples(self, M_c, T, X_L, X_D, kernel_list=(), n_steps=1, c=(), r=(), max_iterations=-1, max_time=-1, diagnostic_func_dict=None, every_N=1): n_chains = len(X_L) args_dict = dict(M_c=M_c, T=T, kernel_list=kernel_list, n_steps=n_steps, c=c, r=r, max_iterations=max_iterations, max_time=max_time, diagnostic_func_dict=diagnostic_func_dict, every_N=every_N) do_analyze = partialize(crosscat.LocalEngine._do_analyze_with_diagnostic, args_dict, self.dview) seeds = [self.get_next_seed() for seed_idx in range(n_chains)] arg_tuples = [seeds, X_L, X_D] # self.do_analyze = do_analyze return arg_tuples
PypiClean
/FaceRecogAI-0.1.tar.gz/FaceRecogAI-0.1/README.rst
A brief into to this package. This was made to practice CV2 image processing, as well as simplify the process of including facial recognition and blurring in my further projects which will feature them commonly. There are 3 functions in the package right now, with more to be added, with different principles, including deep learning and others, such as video camera systems as well. 1. detect_face(img_file): It contains a simple Haar cascade recognition system utilized by OpenCV. Creates a rectangle around the face 2. block_face(img_file): It contains a simple Haar cascade recognition system utilized by OpenCV. Creates a rectangle around the face filled in, as to block the face with a white screen. 3. blur_face(img_file): It contains a simple Haar cascade recognition system utilized by OpenCV. Creates a rectangle-shaped blur around the face using Gaussian blur.
PypiClean
/FlaskCms-0.0.4.tar.gz/FlaskCms-0.0.4/flask_cms/static/js/ace/theme-vibrant_ink.js
ace.define("ace/theme/vibrant_ink",["require","exports","module","ace/lib/dom"], function(require, exports, module) { exports.isDark = true; exports.cssClass = "ace-vibrant-ink"; exports.cssText = ".ace-vibrant-ink .ace_gutter {\ background: #1a1a1a;\ color: #BEBEBE\ }\ .ace-vibrant-ink .ace_print-margin {\ width: 1px;\ background: #1a1a1a\ }\ .ace-vibrant-ink {\ background-color: #0F0F0F;\ color: #FFFFFF\ }\ .ace-vibrant-ink .ace_cursor {\ color: #FFFFFF\ }\ .ace-vibrant-ink .ace_marker-layer .ace_selection {\ background: #6699CC\ }\ .ace-vibrant-ink.ace_multiselect .ace_selection.ace_start {\ box-shadow: 0 0 3px 0px #0F0F0F;\ border-radius: 2px\ }\ .ace-vibrant-ink .ace_marker-layer .ace_step {\ background: rgb(102, 82, 0)\ }\ .ace-vibrant-ink .ace_marker-layer .ace_bracket {\ margin: -1px 0 0 -1px;\ border: 1px solid #404040\ }\ .ace-vibrant-ink .ace_marker-layer .ace_active-line {\ background: #333333\ }\ .ace-vibrant-ink .ace_gutter-active-line {\ background-color: #333333\ }\ .ace-vibrant-ink .ace_marker-layer .ace_selected-word {\ border: 1px solid #6699CC\ }\ .ace-vibrant-ink .ace_invisible {\ color: #404040\ }\ .ace-vibrant-ink .ace_keyword,\ .ace-vibrant-ink .ace_meta {\ color: #FF6600\ }\ .ace-vibrant-ink .ace_constant,\ .ace-vibrant-ink .ace_constant.ace_character,\ .ace-vibrant-ink .ace_constant.ace_character.ace_escape,\ .ace-vibrant-ink .ace_constant.ace_other {\ color: #339999\ }\ .ace-vibrant-ink .ace_constant.ace_numeric {\ color: #99CC99\ }\ .ace-vibrant-ink .ace_invalid,\ .ace-vibrant-ink .ace_invalid.ace_deprecated {\ color: #CCFF33;\ background-color: #000000\ }\ .ace-vibrant-ink .ace_fold {\ background-color: #FFCC00;\ border-color: #FFFFFF\ }\ .ace-vibrant-ink .ace_entity.ace_name.ace_function,\ .ace-vibrant-ink .ace_support.ace_function,\ .ace-vibrant-ink .ace_variable {\ color: #FFCC00\ }\ .ace-vibrant-ink .ace_variable.ace_parameter {\ font-style: italic\ }\ .ace-vibrant-ink .ace_string {\ color: #66FF00\ }\ .ace-vibrant-ink .ace_string.ace_regexp {\ color: #44B4CC\ }\ .ace-vibrant-ink .ace_comment {\ color: #9933CC\ }\ .ace-vibrant-ink .ace_entity.ace_other.ace_attribute-name {\ font-style: italic;\ color: #99CC99\ }\ .ace-vibrant-ink .ace_indent-guide {\ background: url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAACCAYAAACZgbYnAAAAEklEQVQImWNgYGBgYNDTc/oPAALPAZ7hxlbYAAAAAElFTkSuQmCC) right repeat-y\ }"; var dom = require("../lib/dom"); dom.importCssString(exports.cssText, exports.cssClass); });
PypiClean
/DLTA-AI-1.1.tar.gz/DLTA-AI-1.1/DLTA_AI_app/mmdetection/configs/common/mstrain_3x_coco.py
_base_ = '../_base_/default_runtime.py' # dataset settings dataset_type = 'CocoDataset' data_root = 'data/coco/' img_norm_cfg = dict( mean=[123.675, 116.28, 103.53], std=[58.395, 57.12, 57.375], to_rgb=True) # In mstrain 3x config, img_scale=[(1333, 640), (1333, 800)], # multiscale_mode='range' train_pipeline = [ dict(type='LoadImageFromFile'), dict(type='LoadAnnotations', with_bbox=True), dict( type='Resize', img_scale=[(1333, 640), (1333, 800)], multiscale_mode='range', keep_ratio=True), dict(type='RandomFlip', flip_ratio=0.5), dict(type='Normalize', **img_norm_cfg), dict(type='Pad', size_divisor=32), dict(type='DefaultFormatBundle'), dict(type='Collect', keys=['img', 'gt_bboxes', 'gt_labels']), ] test_pipeline = [ dict(type='LoadImageFromFile'), dict( type='MultiScaleFlipAug', img_scale=(1333, 800), flip=False, transforms=[ dict(type='Resize', keep_ratio=True), dict(type='RandomFlip'), dict(type='Normalize', **img_norm_cfg), dict(type='Pad', size_divisor=32), dict(type='ImageToTensor', keys=['img']), dict(type='Collect', keys=['img']), ]) ] # Use RepeatDataset to speed up training data = dict( samples_per_gpu=2, workers_per_gpu=2, train=dict( type='RepeatDataset', times=3, dataset=dict( type=dataset_type, ann_file=data_root + 'annotations/instances_train2017.json', img_prefix=data_root + 'train2017/', pipeline=train_pipeline)), val=dict( type=dataset_type, ann_file=data_root + 'annotations/instances_val2017.json', img_prefix=data_root + 'val2017/', pipeline=test_pipeline), test=dict( type=dataset_type, ann_file=data_root + 'annotations/instances_val2017.json', img_prefix=data_root + 'val2017/', pipeline=test_pipeline)) evaluation = dict(interval=1, metric='bbox') # optimizer optimizer = dict(type='SGD', lr=0.02, momentum=0.9, weight_decay=0.0001) optimizer_config = dict(grad_clip=None) # learning policy # Experiments show that using step=[9, 11] has higher performance lr_config = dict( policy='step', warmup='linear', warmup_iters=500, warmup_ratio=0.001, step=[9, 11]) runner = dict(type='EpochBasedRunner', max_epochs=12)
PypiClean
/LibRecommender-limited-0.6.6.6.tar.gz/LibRecommender-limited-0.6.6.6/libreco/algorithms/fm.py
from itertools import islice import os import numpy as np import pandas as pd import tensorflow.compat.v1 as tf from tensorflow.keras.initializers import ( truncated_normal as tf_truncated_normal ) from .base import Base, TfMixin from ..data.data_generator import DataGenFeat from ..evaluation.evaluate import EvalMixin from ..utils.tf_ops import ( reg_config, dropout_config, lr_decay_config, multi_sparse_combine_embedding ) from ..utils.sampling import NegativeSampling from ..utils.misc import count_params from ..feature import ( get_predict_indices_and_values, get_recommend_indices_and_values, features_from_dict, add_item_features ) tf.disable_v2_behavior() class FM(Base, TfMixin, EvalMixin): """ Note this implementation is actually a mixture of FM and NFM, since it uses one dense layer in the final output """ user_variables = ["linear_user_feat", "pairwise_user_feat"] item_variables = ["linear_item_feat", "pairwise_item_feat"] sparse_variables = ["linear_sparse_feat", "pairwise_sparse_feat"] dense_variables = ["linear_dense_feat", "pairwise_dense_feat"] def __init__( self, task, data_info=None, embed_size=16, n_epochs=20, lr=0.01, lr_decay=False, reg=None, batch_size=256, num_neg=1, use_bn=True, dropout_rate=None, batch_sampling=False, multi_sparse_combiner="sqrtn", seed=42, lower_upper_bound=None, tf_sess_config=None ): Base.__init__(self, task, data_info, lower_upper_bound) TfMixin.__init__(self, tf_sess_config) EvalMixin.__init__(self, task, data_info) self.task = task self.data_info = data_info self.embed_size = embed_size self.n_epochs = n_epochs self.lr = lr self.lr_decay = lr_decay self.reg = reg_config(reg) self.batch_size = batch_size self.num_neg = num_neg self.use_bn = use_bn self.dropout_rate = dropout_config(dropout_rate) self.batch_sampling = batch_sampling self.n_users = data_info.n_users self.n_items = data_info.n_items self.seed = seed self.user_consumed = data_info.user_consumed self.sparse = self._decide_sparse_indices(data_info) self.dense = self._decide_dense_values(data_info) if self.sparse: self.sparse_feature_size = self._sparse_feat_size(data_info) self.sparse_field_size = self._sparse_field_size(data_info) self.multi_sparse_combiner = self._check_multi_sparse( data_info, multi_sparse_combiner) self.true_sparse_field_size = self._true_sparse_field_size( data_info, self.sparse_field_size, self.multi_sparse_combiner) if self.dense: self.dense_field_size = self._dense_field_size(data_info) self.all_args = locals() def _build_model(self): self.graph_built = True tf.set_random_seed(self.seed) self.labels = tf.placeholder(tf.float32, shape=[None]) self.is_training = tf.placeholder_with_default(False, shape=[]) self.linear_embed, self.pairwise_embed = [], [] self._build_user_item() if self.sparse: self._build_sparse() if self.dense: self._build_dense() linear_embed = tf.concat(self.linear_embed, axis=1) pairwise_embed = tf.concat(self.pairwise_embed, axis=1) # linear_term = tf.reduce_sum(linear_embed, axis=1, # keepdims=True) # B * 1 linear_term = tf.layers.dense(linear_embed, units=1, activation=None) # B * K pairwise_term = 0.5 * tf.subtract( tf.square(tf.reduce_sum(pairwise_embed, axis=1)), tf.reduce_sum(tf.square(pairwise_embed), axis=1) ) # For original FM, just add K dim together: # pairwise_term = 0.5 * tf.reduce_sum(pairwise_term, axis=1) if self.use_bn: pairwise_term = tf.layers.batch_normalization( pairwise_term, training=self.is_training) pairwise_term = tf.layers.dense(inputs=pairwise_term, units=1, activation=tf.nn.elu) self.output = tf.squeeze(tf.add(linear_term, pairwise_term)) count_params() def _build_user_item(self): self.user_indices = tf.placeholder(tf.int32, shape=[None]) self.item_indices = tf.placeholder(tf.int32, shape=[None]) linear_user_feat = tf.get_variable( name="linear_user_feat", shape=[self.n_users + 1, 1], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) linear_item_feat = tf.get_variable( name="linear_item_feat", shape=[self.n_items + 1, 1], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) pairwise_user_feat = tf.get_variable( name="pairwise_user_feat", shape=[self.n_users + 1, self.embed_size], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) pairwise_item_feat = tf.get_variable( name="pairwise_item_feat", shape=[self.n_items + 1, self.embed_size], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) # print(linear_embed.get_shape().as_list()) linear_user_embed = tf.nn.embedding_lookup(linear_user_feat, self.user_indices) linear_item_embed = tf.nn.embedding_lookup(linear_item_feat, self.item_indices) self.linear_embed.extend([linear_user_embed, linear_item_embed]) pairwise_user_embed = tf.expand_dims( tf.nn.embedding_lookup(pairwise_user_feat, self.user_indices), axis=1) pairwise_item_embed = tf.expand_dims( tf.nn.embedding_lookup(pairwise_item_feat, self.item_indices), axis=1 ) self.pairwise_embed.extend([pairwise_user_embed, pairwise_item_embed]) def _build_sparse(self): self.sparse_indices = tf.placeholder( tf.int32, shape=[None, self.sparse_field_size]) linear_sparse_feat = tf.get_variable( name="linear_sparse_feat", shape=[self.sparse_feature_size], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) pairwise_sparse_feat = tf.get_variable( name="pairwise_sparse_feat", shape=[self.sparse_feature_size, self.embed_size], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) if (self.data_info.multi_sparse_combine_info and self.multi_sparse_combiner in ("sum", "mean", "sqrtn")): linear_sparse_embed = multi_sparse_combine_embedding( self.data_info, linear_sparse_feat, self.sparse_indices, self.multi_sparse_combiner, 1) pairwise_sparse_embed = multi_sparse_combine_embedding( self.data_info, pairwise_sparse_feat, self.sparse_indices, self.multi_sparse_combiner, self.embed_size) else: linear_sparse_embed = tf.nn.embedding_lookup( # B * F1 linear_sparse_feat, self.sparse_indices) pairwise_sparse_embed = tf.nn.embedding_lookup( # B * F1 * K pairwise_sparse_feat, self.sparse_indices) self.linear_embed.append(linear_sparse_embed) self.pairwise_embed.append(pairwise_sparse_embed) def _build_dense(self): self.dense_values = tf.placeholder( tf.float32, shape=[None, self.dense_field_size]) dense_values_reshape = tf.reshape( self.dense_values, [-1, self.dense_field_size, 1]) batch_size = tf.shape(self.dense_values)[0] linear_dense_feat = tf.get_variable( name="linear_dense_feat", shape=[self.dense_field_size], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) pairwise_dense_feat = tf.get_variable( name="pairwise_dense_feat", shape=[self.dense_field_size, self.embed_size], initializer=tf_truncated_normal(0.0, 0.03), regularizer=self.reg) # B * F2 linear_dense_embed = tf.tile(linear_dense_feat, [batch_size]) linear_dense_embed = tf.reshape( linear_dense_embed, [-1, self.dense_field_size]) linear_dense_embed = tf.multiply( linear_dense_embed, self.dense_values) pairwise_dense_embed = tf.expand_dims(pairwise_dense_feat, axis=0) # B * F2 * K pairwise_dense_embed = tf.tile( pairwise_dense_embed, [batch_size, 1, 1]) pairwise_dense_embed = tf.multiply( pairwise_dense_embed, dense_values_reshape) self.linear_embed.append(linear_dense_embed) self.pairwise_embed.append(pairwise_dense_embed) def _build_train_ops(self, **kwargs): if self.task == "rating": self.loss = tf.losses.mean_squared_error(labels=self.labels, predictions=self.output) elif self.task == "ranking": self.loss = tf.reduce_mean( tf.nn.sigmoid_cross_entropy_with_logits(labels=self.labels, logits=self.output) ) if self.reg is not None: reg_keys = tf.get_collection(tf.GraphKeys.REGULARIZATION_LOSSES) total_loss = self.loss + tf.add_n(reg_keys) else: total_loss = self.loss if self.lr_decay: n_batches = int(self.data_info.data_size / self.batch_size) self.lr, global_steps = lr_decay_config(self.lr, n_batches, **kwargs) else: global_steps = None optimizer = tf.train.AdamOptimizer(self.lr) optimizer_op = optimizer.minimize(total_loss, global_step=global_steps) update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS) self.training_op = tf.group([optimizer_op, update_ops]) self.sess.run(tf.global_variables_initializer()) def fit(self, train_data, verbose=1, shuffle=True, eval_data=None, metrics=None, **kwargs): self.show_start_time() if not self.graph_built: self._build_model() self._build_train_ops(**kwargs) if self.task == "ranking" and self.batch_sampling: self._check_has_sampled(train_data, verbose) data_generator = NegativeSampling(train_data, self.data_info, self.num_neg, self.sparse, self.dense, batch_sampling=True) else: data_generator = DataGenFeat(train_data, self.sparse, self.dense) self.train_feat(data_generator, verbose, shuffle, eval_data, metrics, **kwargs) self.assign_oov() def predict(self, user, item, feats=None, cold_start="average", inner_id=False): user, item = self.convert_id(user, item, inner_id) unknown_num, unknown_index, user, item = self._check_unknown(user, item) ( user_indices, item_indices, sparse_indices, dense_values ) = get_predict_indices_and_values( self.data_info, user, item, self.n_items, self.sparse, self.dense) if feats is not None: assert isinstance(feats, (dict, pd.Series)), ( "feats must be dict or pandas.Series.") assert len(user_indices) == 1, "only support single user for feats" sparse_indices, dense_values = features_from_dict( self.data_info, sparse_indices, dense_values, feats, "predict") feed_dict = self._get_feed_dict(user_indices, item_indices, sparse_indices, dense_values, None, False) preds = self.sess.run(self.output, feed_dict) if self.task == "rating": preds = np.clip(preds, self.lower_bound, self.upper_bound) elif self.task == "ranking": preds = 1 / (1 + np.exp(-preds)) if unknown_num > 0 and cold_start == "popular": preds[unknown_index] = self.default_prediction return preds def recommend_user(self, user, n_rec, user_feats=None, item_data=None, cold_start="average", inner_id=False): user_id = self._check_unknown_user(user, inner_id) if user_id is None: if cold_start == "average": user_id = self.n_users elif cold_start == "popular": return self.data_info.popular_items[:n_rec] else: raise ValueError(user) ( user_indices, item_indices, sparse_indices, dense_values ) = get_recommend_indices_and_values( self.data_info, user_id, self.n_items, self.sparse, self.dense) if user_feats is not None: assert isinstance(user_feats, (dict, pd.Series)), ( "feats must be dict or pandas.Series.") sparse_indices, dense_values = features_from_dict( self.data_info, sparse_indices, dense_values, user_feats, "recommend") if item_data is not None: assert isinstance(item_data, pd.DataFrame), ( "item_data must be pandas DataFrame") assert "item" in item_data.columns, ( "item_data must contain 'item' column") sparse_indices, dense_values = add_item_features( self.data_info, sparse_indices, dense_values, item_data) feed_dict = self._get_feed_dict(user_indices, item_indices, sparse_indices, dense_values, None, False) recos = self.sess.run(self.output, feed_dict) if self.task == "ranking": recos = 1 / (1 + np.exp(-recos)) consumed = set(self.user_consumed[user_id]) count = n_rec + len(consumed) ids = np.argpartition(recos, -count)[-count:] rank = sorted(zip(ids, recos[ids]), key=lambda x: -x[1]) recs_and_scores = islice( (rec if inner_id else (self.data_info.id2item[rec[0]], rec[1]) for rec in rank if rec[0] not in consumed), n_rec ) return list(recs_and_scores) def save(self, path, model_name, manual=True, inference_only=False): if not os.path.isdir(path): print(f"file folder {path} doesn't exists, creating a new one...") os.makedirs(path) self.save_params(path) if manual: self.save_variables(path, model_name, inference_only) else: self.save_tf_model(path, model_name) @classmethod def load(cls, path, model_name, data_info, manual=True): if manual: return cls.load_variables(path, model_name, data_info) else: return cls.load_tf_model(path, model_name, data_info)
PypiClean
/Nuitka_fixed-1.1.2-cp310-cp310-win_amd64.whl/nuitka/build/inline_copy/lib/scons-4.4.0/SCons/Node/Alias.py
import collections import SCons.Errors import SCons.Node import SCons.Util from SCons.Util import hash_signature class AliasNameSpace(collections.UserDict): def Alias(self, name, **kw): if isinstance(name, SCons.Node.Alias.Alias): return name try: a = self[name] except KeyError: a = SCons.Node.Alias.Alias(name, **kw) self[name] = a return a def lookup(self, name, **kw): try: return self[name] except KeyError: return None class AliasNodeInfo(SCons.Node.NodeInfoBase): __slots__ = ('csig',) current_version_id = 2 field_list = ['csig'] def str_to_node(self, s): return default_ans.Alias(s) def __getstate__(self): """ Return all fields that shall be pickled. Walk the slots in the class hierarchy and add those to the state dictionary. If a '__dict__' slot is available, copy all entries to the dictionary. Also include the version id, which is fixed for all instances of a class. """ state = getattr(self, '__dict__', {}).copy() for obj in type(self).mro(): for name in getattr(obj,'__slots__',()): if hasattr(self, name): state[name] = getattr(self, name) state['_version_id'] = self.current_version_id try: del state['__weakref__'] except KeyError: pass return state def __setstate__(self, state): """ Restore the attributes from a pickled state. """ # TODO check or discard version del state['_version_id'] for key, value in state.items(): if key not in ('__weakref__',): setattr(self, key, value) class AliasBuildInfo(SCons.Node.BuildInfoBase): __slots__ = () current_version_id = 2 class Alias(SCons.Node.Node): NodeInfo = AliasNodeInfo BuildInfo = AliasBuildInfo def __init__(self, name): super().__init__() self.name = name self.changed_since_last_build = 1 self.store_info = 0 def str_for_display(self): return '"' + self.__str__() + '"' def __str__(self): return self.name def make_ready(self): self.get_csig() really_build = SCons.Node.Node.build is_up_to_date = SCons.Node.Node.children_are_up_to_date def is_under(self, dir): # Make Alias nodes get built regardless of # what directory scons was run from. Alias nodes # are outside the filesystem: return 1 def get_contents(self): """The contents of an alias is the concatenation of the content signatures of all its sources.""" childsigs = [n.get_csig() for n in self.children()] return ''.join(childsigs) def sconsign(self): """An Alias is not recorded in .sconsign files""" pass # # # def build(self): """A "builder" for aliases.""" pass def convert(self): try: del self.builder except AttributeError: pass self.reset_executor() self.build = self.really_build def get_csig(self): """ Generate a node's content signature, the digested signature of its content. node - the node cache - alternate node to use for the signature cache returns - the content signature """ try: return self.ninfo.csig except AttributeError: pass contents = self.get_contents() csig = hash_signature(contents) self.get_ninfo().csig = csig return csig default_ans = AliasNameSpace() SCons.Node.arg2nodes_lookups.append(default_ans.lookup) # Local Variables: # tab-width:4 # indent-tabs-mode:nil # End: # vim: set expandtab tabstop=4 shiftwidth=4:
PypiClean
/IsaBelaMora-0.0.0.tar.gz/IsaBelaMora-0.0.0/README.txt
ScriptSupreme is a cutting-edge software designed to revolutionize the way screenwriters, playwrights, and novelists bring their stories to life. With its powerful suite of features, ScriptSupreme offers a seamless and intuitive writing experience, allowing you to focus on your creativity and storytelling. The software includes a robust set of tools for organizing your ideas, structuring your plot, and developing your characters. With its user-friendly interface, you can easily navigate through your work, create outlines, and visualize your story arc. ScriptSupreme also features an advanced AI-powered tool that can suggest improvements to your writing based on style, tone, and grammar. With this feature, you can quickly identify areas where your writing can be improved and refine your prose to perfection. Whether you're a seasoned professional or just starting out, ScriptSupreme is the perfect tool to take your writing to the next level. So why wait? Download ScriptSupreme today and start creating the stories you've always dreamed of.
PypiClean
/CADET-Process-0.7.3.tar.gz/CADET-Process-0.7.3/CADETProcess/optimization/individual.py
import hashlib from addict import Dict import numpy as np from CADETProcess import CADETProcessError from CADETProcess.dataStructure import StructMeta from CADETProcess.dataStructure import Float, Vector def hash_array(array): """Compute a hash value for an array of floats using the sha256 hash function. Parameters ---------- array : numpy.ndarray An array of floats. Returns ------- str A hash value as a string of hexadecimal characters. Examples -------- >>> import numpy as np >>> hash_array(np.array([1, 2.0])) '3dfc9d56e04dcd01590f48b1b57c9ed9fecb1e94e11d3c3f13cf0fd97b7a9f0f' """ array = np.asarray(array) return hashlib.sha256(array.tobytes()).hexdigest() class Individual(metaclass=StructMeta): """Set of variables evaluated during Optimization. Attributes ---------- x : list Variable values. f : list Objective values. g : list Nonlinear constraint values. m : list Meta score values. cv : list Nonlinear constraints violation. cv_tol : float Tolerance for constraints violation. See Also -------- CADETProcess.optimization.Population """ x = Vector() x_untransformed = Vector() f = Vector() g = Vector() m = Vector() cv = Vector() cv_tol = Float() def __init__( self, x, f=None, g=None, m=None, cv=None, cv_tol=0, x_untransformed=None, independent_variable_names=None, objective_labels=None, contraint_labels=None, meta_score_labels=None, variable_names=None): self.x = x self.f = f self.g = g self.m = m if cv is None: cv = g self.cv = cv if cv_tol is None: cv_tol = self.n_g*[0] self.cv_tol = cv_tol if x_untransformed is None: x_untransformed = x variable_names = independent_variable_names self.x_untransformed = x_untransformed if isinstance(variable_names, np.ndarray): variable_names = [s.decode() for s in variable_names] self.variable_names = variable_names if isinstance(independent_variable_names, np.ndarray): independent_variable_names = [s.decode() for s in independent_variable_names] self.independent_variable_names = independent_variable_names if isinstance(objective_labels, np.ndarray): objective_labels = [s.decode() for s in objective_labels] self.objective_labels = objective_labels if isinstance(contraint_labels, np.ndarray): contraint_labels = [s.decode() for s in contraint_labels] self.contraint_labels = contraint_labels if isinstance(meta_score_labels, np.ndarray): meta_score_labels = [s.decode() for s in meta_score_labels] self.meta_score_labels = meta_score_labels self.id = hash_array(self.x) @property def is_evaluated(self): """bool: Return True if individual has been evaluated. False otherwise.""" if self.f is None: return False else: return True @property def is_feasible(self): """bool: Return False if any constraint is not met. True otherwise.""" if self.cv is not None and np.any(np.array(self.cv) > self.cv_tol): return False else: return True @property def n_x(self): return len(self.x) @property def n_f(self): if self.f is None: return 0 return len(self.f) @property def n_g(self): if self.g is None: return 0 else: return len(self.g) @property def n_m(self): if self.m is None: return 0 else: return len(self.m) @property def dimensions(self): """tuple: Individual dimensions (n_x, n_f, n_g)""" return (self.n_x, self.n_f, self.n_g, self.n_m) def dominates(self, other): """Determine if individual dominates other. Parameters ---------- other : Individual Other individual Returns ------- dominates : bool True if objectives of "self" are not strictly worse than the corresponding objectives of "other" and at least one objective is strictly better. False otherwise """ if not self.is_evaluated: raise CADETProcessError("Individual needs to be evaluated first.") if not other.is_evaluated: raise CADETProcessError("Other individual needs to be evaluated first.") if self.is_feasible and not other.is_feasible: return True if not self.is_feasible and not other.is_feasible: if np.any(self.cv < other.cv): return True if self.m is not None: self_values = self.m other_values = other.m else: self_values = self.f other_values = other.f if np.any(self_values > other_values): return False if np.any(self_values < other_values): return True return False def is_similar(self, other, tol=1e-1): """Determine if individual is similar to other. Parameters ---------- other : Individual Other individual tol : float, optional Relative tolerance parameter. To reduce number of entries, a rather high rtol is chosen. Returns ------- is_similar : bool True if individuals are close to each other. False otherwise """ if tol is None: return False similar_x = self.is_similar_x(other, tol) similar_f = self.is_similar_f(other, tol) if self.g is not None: similar_g = self.is_similar_g(other, tol) else: similar_g = True if self.m is not None: similar_m = self.is_similar_m(other, tol) else: similar_m = True return similar_x and similar_f and similar_g and similar_m def is_similar_x(self, other, tol=1e-1): """Determine if individual is similar to other based on parameter values. Parameters ---------- other : Individual Other individual tol : float Relative tolerance parameter. To reduce number of entries, a rather high rtol is chosen. Returns ------- is_similar : bool True if parameters are close to each other. False otherwise """ similar_x = np.allclose(self.x, other.x, rtol=tol) return similar_x def is_similar_f(self, other, tol=1e-1): """Determine if individual is similar to other based on objective values. Parameters ---------- other : Individual Other individual tol : float Relative tolerance parameter. To reduce number of entries, a rather high rtol is chosen. Returns ------- is_similar : bool True if parameters are close to each other. False otherwise """ similar_f = np.allclose(self.f, other.f, rtol=tol) return similar_f def is_similar_g(self, other, tol=1e-1): """Determine if individual is similar to other based on constraint values. Parameters ---------- other : Individual Other individual tol : float Relative tolerance parameter. To reduce number of entries, a rather high rtol is chosen. Returns ------- is_similar : bool True if parameters are close to each other. False otherwise """ similar_g = np.allclose(self.g, other.g, rtol=tol) return similar_g def is_similar_m(self, other, tol=1e-1): """Determine if individual is similar to other based on meta score values. Parameters ---------- other : Individual Other individual tol : float Relative tolerance parameter. To reduce number of entries, a rather high rtol is chosen. Returns ------- is_similar : bool True if parameters are close to each other. False otherwise """ similar_m = np.allclose(self.m, other.m, rtol=tol) return similar_m def __str__(self): return str(list(self.x)) def __repr__(self): if self.g is None: return f'{self.__class__.__name__}({self.x}, {self.f})' else: return f'{self.__class__.__name__}({self.x}, {self.f}, {self.g})' def to_dict(self): """Convert individual to a dictionary. Returns ------- dict: A dictionary representation of the individual's attributes. """ data = Dict() data.x = self.x data.f = self.f if self.g is not None: data.g = self.g if self.cv is not None: data.cv = self.cv if self.m is not None: data.m = self.m data.x_untransformed = self.x_untransformed data.variable_names = self.variable_names data.independent_variable_names = self.independent_variable_names if self.objective_labels is not None: data.objective_labels = self.objective_labels if self.contraint_labels is not None: data.contraint_labels = self.contraint_labels if self.meta_score_labels is not None: data.meta_score_labels = self.meta_score_labels return data @classmethod def from_dict(cls, data): """Create Individual from dictionary representation of its attributes. Parameters ---------- data : dict A dictionary representation of the individual's attributes. Returns ------- individual Individual idual created from the dictionary. """ return cls(**data)
PypiClean
/CleverSheep-0.7.6.tar.gz/CleverSheep-0.7.6/README.txt
=================================== A collection of re-usable packages. =================================== Introduction ============ This is the top-level package for various other general purpose packages. It exists in order keep the other packages tidily hidden within a single name space. It is not recommended CleverSheep be used for new projects. For more details see https://gitlab.com/LCaraccio/clever-sheep Installation ============ Run './setup.py build' and './setup.py install' Dependencies ============ Mostly you only need Python, but... 1. The curses library is used and on some Linux distributions 'pycurses' is not installed by default. 2. If you are using tornado or twisted as your event loop manager they will need to be installed 3. six.
PypiClean
/BigJob2-0.54.post73.tar.gz/BigJob2-0.54.post73/pilot/filemanagement/irods_adaptor.py
import urlparse import datetime import errno import sys import os import stat import logging import traceback import time import re import shutil import pdb import glob import pexpect # This is for local debugging! sys.path.insert(0, os.path.join(os.path.dirname(__file__), "../..")) import saga from pilot.api import State from bigjob import logger class iRodsFileAdaptor(object): """ BigData File Management for Pilot Data Supports pilot data on top of iRods. Assumption: working iRods installation irods://localhost/${OSG_DATA}/?vo=<vo>&resource-group=<resource-group> """ def __init__(self, resource_url, security_context=None, pilot_data_description=None): self.resource_url = saga.Url(resource_url) query_string = self.resource_url.query self.localpath = self.resource_url.path self.vo = re.search("(?<=vo=)(.*)([&\b]{1})", query_string).group(1) self.resource_group = re.search("(?<=resource-group=)(.*)[&\b$]?", query_string).group(1) logger.debug("VO: %s, Resource Group: %s"%(self.vo, self.resource_group)) self.is_local = self.__is_local() def __is_local(self): # test whether path contains environment variable match = re.search("\$\{(.*)\}", self.localpath) if match: env_var = match.group(1) logger.debug("Found: " + env_var + " in URL.") logger.debug("Env list: " + str(os.environ)) if os.environ.has_key(env_var): self.localpath = re.sub(r'\$\{.*\}', os.environ[env_var], self.localpath) #self.localpath = os.environ[env_var] logger.debug("Expanding URL Path to: " + self.localpath) return True logger.debug("No expansion in: " + self.localpath) return False def get_security_context(self): """ Returns security context that needs to be available on the distributed node in order to access this Pilot Data """ return None def initialize_pilotdata(self): pass def get_pilotdata_size(self): # unlimited size return None def delete_pilotdata(self): self.__state=State.Done def get_state(self): return self.__state def create_du(self, du_id): logger.debug("create iRods collection: " + du_id) if self.is_local: command = "mkdir %s"%(os.path.join(self.localpath, du_id)) else: command = "imkdir %s"%(du_id) self.__run_command(command) def put_du(self, du): start = time.time() logger.debug("Copy DU to iRod") du_items = du.list() for i in du_items.keys(): try: local_filename=du_items[i]["local"] remote_path = os.path.join(str(du.id), os.path.basename(local_filename)) logger.debug("copy %s to %s"%(local_filename, remote_path)) self._put_file(local_filename, remote_path) except: logger.debug("Could not copy: " + str(i)) logger.debug("Finished Put DU in: " + str(time.time()-start) + " sec.") def get_du(self, du, target_url): #du_id = "du-7370d7b5-ed0b-11e1-95df-705681b3df0f" start = time.time() du_id = du.id logger.debug("Get DU: " + str(du_id)) if self.is_local: command = "cp -r %s %s"%(os.path.join(self.localpath, du_id), target_url) source_path = os.path.join(self.localpath, du_id, "*") target_path = target_url logger.debug("Target and source host are localhost. Processing: %s" %(source_path)) expanded_path = glob.glob(source_path) logger.debug("Expanded path: " + str(expanded_path)) for path in expanded_path: if os.path.isdir(path): logger.debug("Source path %s is directory"%path) files = os.listdir(path) for i in files: try: os.symlink(os.path.join(files, i), target_path) os.chmod(os.path.join(target_path, os.path.basename(path)), 0777) except: self.__print_traceback() else: try: os.symlink(path, os.path.join(target_path, os.path.basename(path))) os.chmod(os.path.join(target_path, os.path.basename(path)), 0777) except: self.__print_traceback() else: command = "iget -f -r %s %s"%(du_id, target_url) logger.debug(command) self.__run_command(command) full_path = os.path.join(target_url, du_id) #logger.debug("Path: " + str(full_path) + " Exists: " + str(os.path.exists(full_path))) #while os.path.exists(full_path)==False: # time.sleep(1) for i in os.listdir(full_path): try: logger.debug("chmod " + str(i)) os.chmod(os.path.join(full_path, i), 0777) logger.debug("move " + str(i)) shutil.move(os.path.join(full_path, i), target_url) except: self.__print_traceback() shutil.rmtree(full_path, ignore_errors=True) #time.sleep(2) #if target_url==".": # target_url = os.getcwd() #command = "mv %s/* %s"%(os.path.join(target_url, du_id), target_url) #self.__run_command(command) logger.debug("Finished Get DU " + du.id + " in: " + str(time.time()-start) + " sec.") def copy_du(self, du, pd_new): remote_url = pd_new.resource_url + "/" + str(du.id) local_url = self.resource_url + "/" + str(du.id) self.copy_du_to_url(du, local_url, remote_url) def remove_du(self, du): if self.is_local: command = "rm -rf %s"%(os.path.join(self.localpath, du.id)) else: command = "irm %s"%du.id self.__run_command(command) ########################################################################### # Pure File Management APIs def _put_file(self, source, target): logger.debug("Put file: %s to %s"%(source, target)) start = time.time() if self.is_local: command = "cp -r %s %s"%(source, target) else: command = "iput -f -R %s %s %s"%(self.resource_group, source, target) self.__run_command(command) put_time = time.time() - start number_replica = 0 if self.is_local==False: #pdb.set_trace() home_directory= self.__run_command("ipwd")[0].strip() full_filename = os.path.join(home_directory, target) command = "irepl-osg -f %s -G %s"%(full_filename, self.resource_group) output = self.__run_command(command) for i in output: if i.find("copied") > 0 or i.find("replica")>0: number_replica = number_replica + 1 rep_time = time.time() - start - put_time logger.info("Upload;Replication;Total;File Size;Backend;Number Replica;Timestamp: %f;%f;%f;%d;%s;%d;%s"%(put_time, rep_time, time.time()-start, os.path.getsize(source), self.resource_group, number_replica, datetime.datetime.today().isoformat())) def transfer(self, source_url, target_url): pass def create_remote_directory(self, target_url): return True ########################################################################### def __run_command(self, command): logger.debug(command) child = pexpect.spawn(command, timeout=None) output = child.readlines() logger.debug("Run %s Output: %s"%(command, str(output))) child.close() return output def __print_traceback(self): exc_type, exc_value, exc_traceback = sys.exc_info() print "*** print_tb:" traceback.print_tb(exc_traceback, limit=1, file=sys.stderr) print "*** print_exception:" traceback.print_exception(exc_type, exc_value, exc_traceback, limit=2, file=sys.stderr) def test_irods(): irods = iRodsFileAdaptor("irods://gw68/${OSG_DATA}/osg/home/luckow/?vo=osg&resource-group=osgGridFtpGroup") irods.initialize_pilotdata() irods.create_du("du-7370d7b5-ed0b-11e1-95df-705681b3df0f") irods._put_file("test.txt", "du-7370d7b5-ed0b-11e1-95df-705681b3df0f/test.txt") irods.get_du("du-7370d7b5-ed0b-11e1-95df-705681b3df0f", "export") if __name__ == "__main__": test_irods()
PypiClean
/CoreTracker-1.5.3.tar.gz/CoreTracker-1.5.3/coretracker/settings/settings.py
import parameters import Bio.SubsMat.MatrixInfo as MatrixInfo AVAILABLE_MAT = MatrixInfo.available_matrices + ['identity'] class Settings(): """Contains global settings for the current run of CoReTracker""" def __init__(self): pass def set(self, **kwargs): """Set settings values from a dict""" EXCLUDE_AA = kwargs.get('EXCLUDE_AA', parameters.EXCLUDE_AA) # list of aa to exclude self.EXCLUDE_AA_FROM = kwargs.get( 'EXCLUDE_AA_FROM', parameters.EXCLUDE_AA_FROM) # list of accepted aa self.AA_LETTERS = "".join( [aa for aa in "ACDEFGHIKLMNPQRSTVWY" if aa not in EXCLUDE_AA]) self.AA_MAJORITY_THRESH = kwargs.get( # Set min frequency per column to use an aa as the most predominant 'AA_MAJORITY_THRESH', parameters.AA_MAJORITY_THRESH) # whether or not analysis should be restricted to suspected species self.LIMIT_TO_SUSPECTED_SPECIES = False try: self.LIMIT_TO_SUSPECTED_SPECIES = kwargs.get( 'LIMIT_TO_SUSPECTED_SPECIES', parameters.LIMIT_TO_SUSPECTED_SPECIES) except: pass # old method of finding suspected species by count self.FREQUENCY_THRESHOLD = kwargs.get( 'FREQUENCY_THRESHOLD', parameters.FREQUENCY_THRESHOLD) # minimum aa substitution to consider reassignment as validation # this is use to filter out false positive self.COUNT_THRESHOLD = kwargs.get( 'COUNT_THRESHOLD', parameters.COUNT_THRESHOLD) # minimum codon presence in reassigned position to make prediction self.CODON_COUNT_THRESHOLD = kwargs.get( 'CODON_COUNT_THRESHOLD', parameters.CODON_COUNT_THRESHOLD) # default genetic code to use self.GENETIC_CODE = kwargs.get( 'GENETIC_CODE', parameters.GENETIC_CODE) # whether or not codon in mixte position should be shown in the report self.SHOW_MIXTE_CODONS = kwargs.get( 'SHOW_MIXTE_CODONS', parameters.SHOW_MIXTE_CODONS) # whether or not filtered position should be shown self.SHOW_GLOBAL_CODON_DATA = kwargs.get( 'SHOW_GLOBAL_CODON_DATA', parameters.SHOW_GLOBAL_CODON_DATA) # Add a suffix to each leaf if colors is not available self.ADD_LABEL_TO_LEAF = kwargs.get( 'ADD_LABEL_TO_LEAF', parameters.ADD_LABEL_TO_LEAF) # Add number inside the piechart self.ADD_NUMBER_PIE = kwargs.get( 'ADD_NUMBER_PIE', parameters.ADD_NUMBER_PIE) # whether or not consensus should be used for the likelihood self.USE_CONSENSUS_FOR_LIKELIHOOD = kwargs.get( 'USE_CONSENSUS_FOR_LIKELIHOOD', parameters.USE_CONSENSUS_FOR_LIKELIHOOD) # save filtered alignment self.SAVE_ALIGN = kwargs.get('SAVE_ALIGN', parameters.SAVE_ALIGN) # do not output results for no predicted reassignment self.SKIP_EMPTY = kwargs.get('SKIP_EMPTY', parameters.SKIP_EMPTY) # if global alignment should be used to find the suspected list self.USE_GLOBAL = kwargs.get( 'USE_GLOBAL', parameters.USE_GLOBAL) # hidden parameter for debug purpose self.MODEL_TYPE = kwargs.get( 'MODEL_TYPE', parameters.MODEL_TYPE) # hmm loop self.HMMLOOP = kwargs.get( 'HMMLOOP', parameters.HMMLOOP) # choose algorithm for computing the suspected species self.MODE = kwargs.get('MODE', parameters.MODE) # choose matrix to compute substitution, default is blosum62 self.MATRIX = kwargs.get('MATRIX', parameters.MATRIX) if self.MATRIX not in AVAILABLE_MAT: self.MATRIX = "blosum62" try: self.SUBMAT = getattr(MatrixInfo, self.MATRIX) except: self.SUBMAT = getattr(MatrixInfo, "blosum62") # alpha to use , default is 0.05 self.CONF = kwargs.get('CONF', parameters.CONF) or 0.05 self.STARTDIST = kwargs.get('STARTDIST', parameters.STARTDIST) self.SHOW_ALL = kwargs.get('SHOW_ALL', parameters.SHOW_ALL) self.FORCED_CHI2 = kwargs.get('FORCED_CHI2', parameters.FORCED_CHI2) # output format. Should be pdf for the moment self.IMAGE_FORMAT = "pdf" # The following are the binaries setting for HMMER package self.hmmbuild = kwargs.get('HMMBUILD', 'hmmbuild') # self.eslalimask = kwargs.get('eslalimask', 'esl-alimask') # self.eslalimanip = kwargs.get('eslalimanip', 'esl-alimanip') # this can be used next version for a better filtering # not need right now self.hmmalign = kwargs.get('HMMALIGN', 'hmmalign') # default values for supplemental data self.VALIDATION = True self.COMPUTE_POS = False self.SCALE = 1.0 self.PROTFORMAT = kwargs.get('PROTFORMAT', parameters.PROTFORMAT) self.DNAFORMAT = kwargs.get('DNAFORMAT', parameters.DNAFORMAT) self.OUTDIR = "" def get_external_binaries(self): ext = [self.hmmbuild, self.hmmalign] return ext def fill(self, params): if isinstance(params, dict): self.set(**params) else: self.__dict__.update(params.__dict__) def update_params(self, **kwargs): for k, v in kwargs.items(): if k == 'MATRIX' and v in AVAILABLE_MAT: self.__dict__[k] = v if v != "identity": self.__dict__['MATRIX'] = getattr(MatrixInfo, v) else: self.__dict__[k] = v
PypiClean
/AsyncDex-1.1.tar.gz/AsyncDex-1.1/asyncdex/models/chapter_list.py
import asyncio from collections import defaultdict from datetime import datetime from functools import partial from typing import Any, Callable, Dict, Iterable, List, Optional, TYPE_CHECKING, Tuple, Union from natsort import natsort_keygen from .abc import ModelList from .aggregate import MangaAggregate, VolumeAggregate from .chapter import Chapter from .group import Group from .pager import Pager from .user import User from ..constants import routes from ..enum import DuplicateResolutionAlgorithm from ..list_orders import MangaFeedListOrder from ..utils import InclusionExclusionPair, Interval, return_date_string if TYPE_CHECKING: from .manga import Manga def _chapter_attr_map(items: List[Chapter], attr: str): return {getattr(item, attr): item for item in items} def _get_smallest_creation_time(items: List[Chapter]): return sorted(((item.created_at, item) for item in items), key=lambda i: i[0])[0] def _check_values(set1: set, set2: set) -> int: """This checks how many of the values present inside of the first set are in the second set.""" match = 0 if set1.issuperset(set2): match += 1 for item in set2: if set1.issuperset({item}): match += 1 return match def _resolve_duplicates( chapter_list: List[Chapter], algo: List[DuplicateResolutionAlgorithm], specific_groups: Optional[Iterable[Group]], specific_users: Optional[Iterable[User]], ): """Actually does the duplicate resolving.""" last_chapter: Optional[set] = None specific_groups = specific_groups or [] specific_users = specific_users or [] chapter_dict: Dict[Optional[str], List[Chapter]] = defaultdict(list) final = ChapterList(chapter_list[0].manga) for item in chapter_list: chapter_dict[item.number].append(item) final.extend(chapter_dict.pop(None, [])) # We grouped up the chapters by number for logical sorting. if DuplicateResolutionAlgorithm.VIEWS_ASC in algo or DuplicateResolutionAlgorithm.VIEWS_DESC in algo: raise NotImplementedError("MangaDex API does not return views yet, sorry!") duplicate_last_prios = _check_values( { DuplicateResolutionAlgorithm.VIEWS_ASC, DuplicateResolutionAlgorithm.VIEWS_DESC, DuplicateResolutionAlgorithm.CREATION_DATE_ASC, DuplicateResolutionAlgorithm.CREATION_DATE_DESC, }, set(algo), ) if duplicate_last_prios > 1: raise ValueError("The lowest-priority operations cannot be combined.") elif not duplicate_last_prios: algo.append(DuplicateResolutionAlgorithm.CREATION_DATE_ASC) for chapter_num, items in chapter_dict.items(): # Now the sorting begins. matches_found = items if last_chapter is not None and DuplicateResolutionAlgorithm.PREVIOUS_GROUP in algo: # Determine the priority. Obviously, if the last chapter was made by one group, that's easy. But if # multiple groups contributed towards a chapter, we would want to match chapters made by only one of the # multiple groups. Use a priority system to determine who gets to move on set_group = defaultdict(list) for item in matches_found: set_match_prio = _check_values(set(item.groups), last_chapter) if set_match_prio: set_group[set_match_prio].append(item) if set_group: matches_found = sorted(set_group.items(), key=lambda i: i[0])[0][1] if len(matches_found) > 1 and DuplicateResolutionAlgorithm.SPECIFIC_GROUP in algo: # Either we did not go the last time or there were more than one chapter with the same group priority. # Now we try if the "Specific Group" strategy was chosen. matches = list(filter(lambda chapter: _check_values(set(item.groups), set(specific_groups)), matches_found)) if len(matches) > 0: matches_found = matches else: final.append(matches_found[0]) continue if len(matches_found) > 1 and DuplicateResolutionAlgorithm.SPECIFIC_USER in algo: matches = list(filter(lambda chapter: item.user in specific_users, matches_found)) if len(matches) > 0: matches_found = matches else: final.append(matches_found[0]) continue if len(matches_found) > 1: if DuplicateResolutionAlgorithm.CREATION_DATE_ASC in algo: final.append(sorted(matches_found, key=lambda chapter: chapter.created_at)[0]) elif DuplicateResolutionAlgorithm.CREATION_DATE_DESC in algo: final.append(sorted(matches_found, key=lambda chapter: chapter.created_at, reverse=True)[0]) elif DuplicateResolutionAlgorithm.VIEWS_ASC in algo: # final.append(sorted(matches_found, key=lambda chapter: chapter.created_at)[0]) raise NotImplementedError("DuplicateResolutionAlgorithm.VIEWS_ASC not implemented.") elif DuplicateResolutionAlgorithm.VIEWS_DESC in algo: # final.append(sorted(matches_found, key=lambda chapter: chapter.created_at)[0]) raise NotImplementedError("DuplicateResolutionAlgorithm.VIEWS_DESC not implemented.") else: final.append(matches_found[0]) return final class ChapterList(ModelList[Chapter]): """An object representing a list of chapters from a manga. .. versionadded:: 0.3 :param entries: Pre-fill the ChapterList with the given entries. :type entries: Iterable[Chapter] """ manga: "Manga" """The :class:`.Manga` that this chapter list belongs to.""" def __init__(self, manga: "Manga", *, entries: Optional[Iterable[Chapter]] = None): super().__init__(entries or []) self.manga = manga async def get( self, *, languages: Optional[List[str]] = None, created_after: Optional[datetime] = None, updated_after: Optional[datetime] = None, published_after: Optional[datetime] = None, order: Optional[MangaFeedListOrder] = None, limit: Optional[int] = None, ): """Gets the list of chapters. .. versionchanged:: 0.5 * Parameter ``locales`` was renamed to ``languages`` .. deprecated:: 0.5 Parameter ``locales`` .. versionchanged:: 1.0 Parameter ``locales`` was removed. :param languages: The languages to filter by. :type languages: List[str] :param created_after: Get chapters created after this date. .. note:: The datetime object needs to be in UTC time. It does not matter if the datetime if naive or timezone aware. :type created_after: datetime :param updated_after: Get chapters updated after this date. .. note:: The datetime object needs to be in UTC time. It does not matter if the datetime if naive or timezone aware. :type updated_after: datetime :param published_after: Get chapters published after this date. .. note:: The datetime object needs to be in UTC time. It does not matter if the datetime if naive or timezone aware. :type published_after: datetime :param order: The order to sort the chapters. .. versionadded:: 0.5 :type order: MangaFeedListOrder .. versionadded:: 0.5 :param limit: Only return up to this many chapters. :type limit: int """ params = {} if languages: params["translatedLanguage"] = languages if created_after: params["createdAtSince"] = return_date_string(created_after) if updated_after: params["updatedAtSince"] = return_date_string(updated_after) if published_after: params["publishAtSince"] = return_date_string(published_after) self.manga.client._add_order(params, order) async for item in Pager( routes["manga_chapters"].format(id=self.manga.id), Chapter, self.manga.client, params=params, limit_size=500, limit=limit, ): item.manga = self.manga if item in self: self[self.index(item)] = item else: self.append(item) async def get_new( self, *, languages: Optional[List[str]] = None, created_after: Optional[datetime] = None, updated_after: Optional[datetime] = None, published_after: Optional[datetime] = None, order: Optional[MangaFeedListOrder] = None, limit: Optional[int] = None, ) -> "ChapterList": """A method that gets chapters but returns a new ChapterList. .. versionadded:: 0.5 :param languages: The languages to filter by. :type languages: List[str] :param created_after: Get chapters created after this date. .. note:: The datetime object needs to be in UTC time. It does not matter if the datetime if naive or timezone aware. :type created_after: datetime :param updated_after: Get chapters updated after this date. .. note:: The datetime object needs to be in UTC time. It does not matter if the datetime if naive or timezone aware. :type updated_after: datetime :param published_after: Get chapters published after this date. .. note:: The datetime object needs to be in UTC time. It does not matter if the datetime if naive or timezone aware. :type published_after: datetime :param order: The order to sort the chapters. :type order: MangaFeedListOrder :param limit: Only return up to this many chapters. :type limit: int :return: A new chapter list. :rtype: ChapterList """ cl = type(self)(self.manga) await cl.get( languages=languages, created_after=created_after, updated_after=updated_after, published_after=published_after, order=order, limit=limit, ) return cl def filter( self, *, languages: Optional[List[str]] = None, creation_time: Optional[Interval[datetime]] = None, update_time: Optional[Interval[datetime]] = None, publish_time: Optional[Interval[datetime]] = None, views: Optional[Interval[int]] = None, has_number: Optional[bool] = None, chapter_number_range: Optional[Interval[float]] = None, chapter_numbers: Optional[InclusionExclusionPair[Optional[float]]] = None, remove_duplicates: bool = False, duplicate_strategy: Optional[List[DuplicateResolutionAlgorithm]] = None, duplicate_strategy_groups: Optional[List[Group]] = None, duplicate_strategy_users: Optional[List[User]] = None, groups: Optional[InclusionExclusionPair[Group]] = None, users: Optional[InclusionExclusionPair[User]] = None, read: Optional[bool] = None, volumes: Optional[InclusionExclusionPair[int]] = None, ) -> "ChapterList": """Filter the chapter list and return a new :class:`.ChapterList`. Calling this method without specifying any additional filtering mechanisms will return a shallow copy of the list. The order of the filter will be as follows: #. Filter the datetimes first #. Filter by the intervals #. Filter by the inclusion and exclusion pairs #. Filter duplicates .. versionchanged:: 0.5 Parameter ``locales`` was renamed to ``languages`` .. deprecated:: 0.5 Parameter ``locales`` .. versionchanged:: 1.0 Parameter ``locales`` was removed. :param languages: The languages that should be present in the chapters. :type languages: List[str] :param creation_time: An :class:`.Interval` representing the bounds of the chapter's creation time. :attr:`.Interval.min` will select all chapters created **after** the given time, and :attr:`.Interval.max` will select all chapters created **before** the given time. .. note:: The datetime objects needs to be a non-timezone aware datetime in UTC time. A datetime in any timezone can be converted to a naive UTC timezone by: .. code-block:: python from datetime import timezone # dt is the datetime object. utc_naive = dt.astimezone(timezone.utc).replace(tzinfo=None) Example intervals: .. code-block:: python from asyncdex import Interval min_interval = Interval(min=datetime.datetime(2021, 1, 1)) max_interval = Interval(max=datetime.datetime(2021, 1, 1)) both = Interval(datetime.datetime(2021, 1, 1), datetime.datetime(2021, 5, 1)) :type creation_time: Interval[datetime] :param update_time: An :class:`.Interval` representing the bounds of the chapter's update time. :attr:`.Interval.min` will select all chapters updated **after** the given time, and :attr:`.Interval.max` will select all chapters updated **before** the given time. .. note:: The datetime objects needs to be a non-timezone aware datetime in UTC time. A datetime in any timezone can be converted to a naive UTC timezone by: .. code-block:: python from datetime import timezone # dt is the datetime object. utc_naive = dt.astimezone(timezone.utc).replace(tzinfo=None) Example intervals: .. code-block:: python from asyncdex import Interval min_interval = Interval(min=datetime.datetime(2021, 1, 1)) max_interval = Interval(max=datetime.datetime(2021, 1, 1)) both = Interval(datetime.datetime(2021, 1, 1), datetime.datetime(2021, 5, 1)) :type update_time: Interval[datetime] :param publish_time: An :class:`.Interval` representing the bounds of the chapter's publish time. :attr:`.Interval.min` will select all chapters published **after** the given time, and :attr:`.Interval.max` will select all chapters published **before** the given time. .. note:: The datetime objects needs to be a non-timezone aware datetime in UTC time. A datetime in any timezone can be converted to a naive UTC timezone by: .. code-block:: python from datetime import timezone # dt is the datetime object. utc_naive = dt.astimezone(timezone.utc).replace(tzinfo=None) Example intervals: .. code-block:: python min_interval = Interval(min=datetime.datetime(2021, 1, 1)) max_interval = Interval(max=datetime.datetime(2021, 1, 1)) both = Interval(datetime.datetime(2021, 1, 1), datetime.datetime(2021, 5, 1)) :type publish_time: Interval[datetime] :param views: An :class:`.Interval` of the views that a manga can have. .. warning:: The MangaDex API does not return views yet, so specifying something for this parameter will result in :class:`.NotImplementedError` being raised. Example intervals: .. code-block:: python from asyncdex import Interval min_interval = Interval(min=100) max_interval = Interval(max=25000) both = Interval(100, 25000) :type views: Interval[int] :param has_number: Only select chapters with valid numbers. :type has_number: bool :param chapter_number_range: An :class:`.Interval` of the number of the chapter. .. note:: Chapters without a number will be given a provisional number of 0 when sorted. Example intervals: .. code-block:: python from asyncdex import Interval min_interval = Interval(min=2) max_interval = Interval(max=20.5) both = Interval(2, 20.5) :type chapter_number_range: Interval[float] :param chapter_numbers: An :class:`.InclusionExclusionPair` denoting the chapter numbers that are either included or excluded. .. note:: Chapters without a number will be given a provisional number of 0 when sorted. Example inclusion/exclusion pairs: .. code-block:: python from asyncdex import InclusionExclusionPair include = InclusionExclusionPair(include=[5, 6]) exclude = InclusionExclusionPair(exclude=[7, 8, 9.5]) :type chapter_numbers: InclusionExclusionPair[float] :param remove_duplicates: Whether or not to remove duplicate chapters, ie chapters with the same chapter number. .. note:: This will not take languages into consideration. Make sure to specify a locale in the ``languages`` parameter if you want duplicates filtered for a specific locale. :type remove_duplicates: bool :param duplicate_strategy: The list of strategies used to resolve duplicates. See the values in :class:`.DuplicateResolutionAlgorithm` to find the possible algorithms. By default, the strategy of choosing the previous group and the strategy of choosing the first chapter chronologically when there is no previous group will be used. .. note:: If an adequate strategy is not found for dealing with certain chapters, the fallback mechanism of selecting the chapter that was created first will be used. :type duplicate_strategy: List[DuplicateResolutionAlgorithm] :param duplicate_strategy_groups: The groups to use for :attr:`.DuplicateResolutionAlgorithm.SPECIFIC_GROUP`. .. note:: If the group is not present in all the chapters for a specific number, an alternate resolution algorithm will be used. Use the ``include_groups`` param if you only want chapters from that group. :type duplicate_strategy_groups: List[Group] :param duplicate_strategy_users: The users to use for :attr:`.DuplicateResolutionAlgorithm.SPECIFIC_USER`. .. note:: If the user is not present in all the chapters for a specific number, an alternate resolution algorithm will be used. Use the ``include_users`` param if you only want chapters from that user. :type duplicate_strategy_users: List[User] :param users: An :class:`.InclusionExclusionPair` denoting the users to include/exclude from the listing. :type users: InclusionExclusionPair[User] :param groups: An :class:`.InclusionExclusionPair` denoting the groups to include/exclude from the listing. :type groups: InclusionExclusionPair[Group] :param read: Whether or not the manga is read. .. versionadded:: 0.5 :type read: bool :param volumes: An :class:`.InclusionExclusionPair` denoting the volumes to include/exclude from the listing. .. versionadded:: 0.5 :type volumes: InclusionExclusionPair[int] :return: A filtered :class:`.ChapterList`. .. note:: The filtered list is not cached in :attr:`.Manga.chapters`. :rtype: ChapterList """ base: Iterable[Chapter] = self.copy() options = ( languages, creation_time, update_time, publish_time, views, has_number, chapter_number_range, chapter_numbers, duplicate_strategy, duplicate_strategy_groups, duplicate_strategy_users, groups, users, read, volumes, ) if options.count(None) == len(options) and not remove_duplicates: return ChapterList(self.manga, entries=self.copy()) duplicate_strategy = duplicate_strategy or [ DuplicateResolutionAlgorithm.PREVIOUS_GROUP, DuplicateResolutionAlgorithm.CREATION_DATE_ASC, ] if languages: base = filter(lambda chapter: chapter.language in languages, base) if has_number: base = filter(lambda chapter: chapter.number is not None, base) if creation_time: base = filter(lambda chapter: chapter.created_at in creation_time, base) if update_time: base = filter(lambda chapter: chapter.created_at in update_time, base) if publish_time: base = filter(lambda chapter: chapter.created_at in publish_time, base) if views: raise NotImplementedError("Views not implemented in the MangaDex API.") # base = filter(lambda chapter: chapter.views in views, base) if chapter_number_range: base = filter(lambda chapter: chapter.number in chapter_number_range, base) if chapter_numbers: base = filter(lambda chapter: chapter_numbers.matches_include_exclude_pair(chapter.number), base) if groups: base = filter( lambda chapter: _check_values(set(chapter.groups), set(groups.include)) and not _check_values(set(chapter.groups), set(groups.exclude)), base, ) if users: base = filter(lambda chapter: users.matches_include_exclude_pair(chapter.user), base) if read is not None: base = filter(lambda chapter: chapter.read == read, base) if volumes: base = filter(lambda chapter: volumes.matches_include_exclude_pair(chapter.volume), base) final = list(base) if remove_duplicates: final = _resolve_duplicates(final, duplicate_strategy, duplicate_strategy_groups, duplicate_strategy_users) return type(self)(self.manga, entries=final) def __repr__(self) -> str: """Provide a string representation of the object. :return: The string representation :rtype: str """ return f"{type(self).__name__}{super().__repr__()}" def sort(self, *, key: Optional[Callable[[Chapter], Any]] = None, reverse: bool = False): """Sort the ChapterList. This uses a natural sorting algorithm to sort the chapters. :param key: An optional key if you want to override the sorting key used by the class. :type key: Callable[[Chapter], Any] :param reverse: Whether or not to reverse the list. :type reverse: bool """ super().sort(key=key or natsort_keygen(key=lambda chapter: chapter.name), reverse=reverse) async def download_all( self, *, skip_bad: bool = True, folder_format: str = "{manga}/{chapter_num}{separator}{title}", file_format: str = "{num}", as_bytes_list: bool = False, overwrite: bool = True, retries: int = 3, use_data_saver: bool = False, ssl_only: bool = False, ) -> Dict[Chapter, Optional[List[str]]]: """Download all chapters in the list. .. versionadded:: 0.4 :param skip_bad: Whether or not to skip bad chapters. Defaults to True. :type skip_bad: bool :param folder_format: The format of the folder to create for the chapter. The folder can already be existing. The default format is ``{manga}/{chapter_num}{separator}{chapter_title}``. .. note:: Specify ``.`` if you want to save the pages in the current folder. Available variables: * ``{manga}``: The name of the manga. If the chapter's manga object does not contain a title object, it will be fetched. * ``{chapter_num}``: The number of the chapter, if it exists. * ``{separator}``: A separator if both the chapter's number and title exists. * ``{title}``: The title of the chapter, if it exists. :type folder_format: str :param file_format: The format of the individual image file names. The default format is ``{num}``. .. note:: The file extension is applied automatically from the real file name. There is no need to include it. Available variables: * ``{num}``: The numbering of the image files starting from 1. This respects the order the images are in inside of :attr:`.page_names`. * ``{num0}``: The same as ``{num}`` but starting from 0. * ``{name}``: The actual filename of the image from :attr:`.page_names`, without the file extension. :type file_format: str :param as_bytes_list: Whether or not to return the pages as a list of raw bytes. Setting this parameter to ``True`` will ignore the value of the ``folder_format`` parameter. :type as_bytes_list: bool :param overwrite: Whether or not to override existing files with the same name as the page. Defaults to ``True``. :type overwrite: bool :param retries: How many times to retry a chapter if a MD@H node does not let us download the pages. Defaults to ``3``. :type retries: int :param use_data_saver: Whether or not to use the data saver pages or the normal pages. Defaults to ``False``. :type use_data_saver: bool :param ssl_only: Whether or not the given URL has port ``443``. Useful if your firewall blocks outbound connections to ports that are not port ``443``. Defaults to ``False``. .. note:: This will lower the pool of available clients and can cause higher download times. :type ssl_only: bool :raises: :class:`aiohttp.ClientResponseError` if there is an error after all retries are exhausted. :return: A dictionary mapping consisting of :class:`.Chapter` objects as keys and the data from that chapter's :meth:`.download_chapter` method. If ``skip_bad`` is True, chapters with exceptions will have ``None`` instead of a list of bytes. :rtype: List[Optional[List[bytes]]] """ tasks = [ asyncio.create_task( item.download_chapter( folder_format=folder_format, file_format=file_format, as_bytes_list=as_bytes_list, overwrite=overwrite, retries=retries, use_data_saver=use_data_saver, ssl_only=ssl_only, ) ) for item in self ] data = await asyncio.gather(*tasks, return_exceptions=skip_bad) return_mapping = {} for num, item in enumerate(data): if isinstance(item, BaseException): item = None return_mapping[self[num]] = item return return_mapping def group_by_volumes(self) -> Dict[Optional[str], "ChapterList"]: """Creates a dictionary mapping volume numbers to chapters. .. versionadded:: 0.5 :return: A dictionary where the keys are volume numbers and the values are a list of :class:`.Chapter` objects. :rtype: Dict[Optional[str], ChapterList] """ dd = defaultdict(partial(ChapterList, self.manga)) for item in self: dd[item.volume].append(item) return dict(dd) def group_by_numbers(self) -> Dict[Optional[str], "ChapterList"]: """Creates a dictionary mapping chapter numbers to chapters. .. versionadded:: 0.5 :return: A dictionary where the keys are chapter numbers and the values are a list of :class:`.Chapter` objects. :rtype: Dict[Optional[str], ChapterList] """ dd = defaultdict(partial(ChapterList, self.manga)) for item in self: dd[item.number].append(item) return dict(dd) def group_by_volume_and_chapters(self) -> Dict[Tuple[Optional[str], Optional[str]], "ChapterList"]: """Creates a dictionary mapping volume numbers and chapter numbers to chapters. .. versionadded:: 0.5 :return: A dictionary where the keys are a tuple of volume and chapter numbers and the values are a list of :class:`.Chapter` objects. :rtype: Dict[Tuple[Optional[str], Optional[str]], ChapterList] """ dd = defaultdict(partial(ChapterList, self.manga)) for item in self: dd[(item.volume, item.number)].append(item) return dict(dd) def calculate_aggregate(self) -> MangaAggregate: """Calculates an aggregate of the chapters contained. .. versionadded:: 0.5 :return: The aggregate of the chapters. :rtype: MangaAggregate """ ma = MangaAggregate() for (volume_number, chapter_number), chapter in self.group_by_volume_and_chapters().items(): ma.setdefault(volume_number, VolumeAggregate()).setdefault(chapter_number, 0) ma[volume_number][chapter_number] += 1 return ma def languages(self) -> List[str]: """Get the list of languages that exist in the chapter list. .. versionadded:: 0.5 :return: A list of languages. :rtype: List[str] """ return list({item.language for item in self}) def _update_read_data(self, data: Dict[str, Union[str, List[str]]]): id_mapping = self.id_map() for id in data["data"]: if id in id_mapping: id_mapping[id].read = True async def get_read(self): """Gets the list of chapters which are read. Chapters whose IDs are found in this list will be set as read. |auth| .. versionadded:: 0.5 """ self.manga.client.raise_exception_if_not_authenticated("GET", routes["manga_read"]) r = await self.manga.client.request("GET", routes["manga_read"].format(id=self.manga.id)) self.manga._check_404(r) json = await r.json() r.close() self._update_read_data(json) async def fetch_all(self): await self.manga.client.batch_chapters(*self)
PypiClean
/DLTA-AI-1.1.tar.gz/DLTA-AI-1.1/DLTA_AI_app/mmdetection/mmdet/models/plugins/pixel_decoder.py
import torch import torch.nn as nn import torch.nn.functional as F from mmcv.cnn import PLUGIN_LAYERS, Conv2d, ConvModule, caffe2_xavier_init from mmcv.cnn.bricks.transformer import (build_positional_encoding, build_transformer_layer_sequence) from mmcv.runner import BaseModule, ModuleList @PLUGIN_LAYERS.register_module() class PixelDecoder(BaseModule): """Pixel decoder with a structure like fpn. Args: in_channels (list[int] | tuple[int]): Number of channels in the input feature maps. feat_channels (int): Number channels for feature. out_channels (int): Number channels for output. norm_cfg (:obj:`mmcv.ConfigDict` | dict): Config for normalization. Defaults to dict(type='GN', num_groups=32). act_cfg (:obj:`mmcv.ConfigDict` | dict): Config for activation. Defaults to dict(type='ReLU'). encoder (:obj:`mmcv.ConfigDict` | dict): Config for transorformer encoder.Defaults to None. positional_encoding (:obj:`mmcv.ConfigDict` | dict): Config for transformer encoder position encoding. Defaults to dict(type='SinePositionalEncoding', num_feats=128, normalize=True). init_cfg (:obj:`mmcv.ConfigDict` | dict): Initialization config dict. Default: None """ def __init__(self, in_channels, feat_channels, out_channels, norm_cfg=dict(type='GN', num_groups=32), act_cfg=dict(type='ReLU'), init_cfg=None): super().__init__(init_cfg=init_cfg) self.in_channels = in_channels self.num_inputs = len(in_channels) self.lateral_convs = ModuleList() self.output_convs = ModuleList() self.use_bias = norm_cfg is None for i in range(0, self.num_inputs - 1): lateral_conv = ConvModule( in_channels[i], feat_channels, kernel_size=1, bias=self.use_bias, norm_cfg=norm_cfg, act_cfg=None) output_conv = ConvModule( feat_channels, feat_channels, kernel_size=3, stride=1, padding=1, bias=self.use_bias, norm_cfg=norm_cfg, act_cfg=act_cfg) self.lateral_convs.append(lateral_conv) self.output_convs.append(output_conv) self.last_feat_conv = ConvModule( in_channels[-1], feat_channels, kernel_size=3, padding=1, stride=1, bias=self.use_bias, norm_cfg=norm_cfg, act_cfg=act_cfg) self.mask_feature = Conv2d( feat_channels, out_channels, kernel_size=3, stride=1, padding=1) def init_weights(self): """Initialize weights.""" for i in range(0, self.num_inputs - 2): caffe2_xavier_init(self.lateral_convs[i].conv, bias=0) caffe2_xavier_init(self.output_convs[i].conv, bias=0) caffe2_xavier_init(self.mask_feature, bias=0) caffe2_xavier_init(self.last_feat_conv, bias=0) def forward(self, feats, img_metas): """ Args: feats (list[Tensor]): Feature maps of each level. Each has shape of (batch_size, c, h, w). img_metas (list[dict]): List of image information. Pass in for creating more accurate padding mask. Not used here. Returns: tuple: a tuple containing the following: - mask_feature (Tensor): Shape (batch_size, c, h, w). - memory (Tensor): Output of last stage of backbone.\ Shape (batch_size, c, h, w). """ y = self.last_feat_conv(feats[-1]) for i in range(self.num_inputs - 2, -1, -1): x = feats[i] cur_feat = self.lateral_convs[i](x) y = cur_feat + \ F.interpolate(y, size=cur_feat.shape[-2:], mode='nearest') y = self.output_convs[i](y) mask_feature = self.mask_feature(y) memory = feats[-1] return mask_feature, memory @PLUGIN_LAYERS.register_module() class TransformerEncoderPixelDecoder(PixelDecoder): """Pixel decoder with transormer encoder inside. Args: in_channels (list[int] | tuple[int]): Number of channels in the input feature maps. feat_channels (int): Number channels for feature. out_channels (int): Number channels for output. norm_cfg (:obj:`mmcv.ConfigDict` | dict): Config for normalization. Defaults to dict(type='GN', num_groups=32). act_cfg (:obj:`mmcv.ConfigDict` | dict): Config for activation. Defaults to dict(type='ReLU'). encoder (:obj:`mmcv.ConfigDict` | dict): Config for transorformer encoder.Defaults to None. positional_encoding (:obj:`mmcv.ConfigDict` | dict): Config for transformer encoder position encoding. Defaults to dict(type='SinePositionalEncoding', num_feats=128, normalize=True). init_cfg (:obj:`mmcv.ConfigDict` | dict): Initialization config dict. Default: None """ def __init__(self, in_channels, feat_channels, out_channels, norm_cfg=dict(type='GN', num_groups=32), act_cfg=dict(type='ReLU'), encoder=None, positional_encoding=dict( type='SinePositionalEncoding', num_feats=128, normalize=True), init_cfg=None): super(TransformerEncoderPixelDecoder, self).__init__( in_channels, feat_channels, out_channels, norm_cfg, act_cfg, init_cfg=init_cfg) self.last_feat_conv = None self.encoder = build_transformer_layer_sequence(encoder) self.encoder_embed_dims = self.encoder.embed_dims assert self.encoder_embed_dims == feat_channels, 'embed_dims({}) of ' \ 'tranformer encoder must equal to feat_channels({})'.format( feat_channels, self.encoder_embed_dims) self.positional_encoding = build_positional_encoding( positional_encoding) self.encoder_in_proj = Conv2d( in_channels[-1], feat_channels, kernel_size=1) self.encoder_out_proj = ConvModule( feat_channels, feat_channels, kernel_size=3, stride=1, padding=1, bias=self.use_bias, norm_cfg=norm_cfg, act_cfg=act_cfg) def init_weights(self): """Initialize weights.""" for i in range(0, self.num_inputs - 2): caffe2_xavier_init(self.lateral_convs[i].conv, bias=0) caffe2_xavier_init(self.output_convs[i].conv, bias=0) caffe2_xavier_init(self.mask_feature, bias=0) caffe2_xavier_init(self.encoder_in_proj, bias=0) caffe2_xavier_init(self.encoder_out_proj.conv, bias=0) for p in self.encoder.parameters(): if p.dim() > 1: nn.init.xavier_uniform_(p) def forward(self, feats, img_metas): """ Args: feats (list[Tensor]): Feature maps of each level. Each has shape of (batch_size, c, h, w). img_metas (list[dict]): List of image information. Pass in for creating more accurate padding mask. Returns: tuple: a tuple containing the following: - mask_feature (Tensor): shape (batch_size, c, h, w). - memory (Tensor): shape (batch_size, c, h, w). """ feat_last = feats[-1] bs, c, h, w = feat_last.shape input_img_h, input_img_w = img_metas[0]['batch_input_shape'] padding_mask = feat_last.new_ones((bs, input_img_h, input_img_w), dtype=torch.float32) for i in range(bs): img_h, img_w, _ = img_metas[i]['img_shape'] padding_mask[i, :img_h, :img_w] = 0 padding_mask = F.interpolate( padding_mask.unsqueeze(1), size=feat_last.shape[-2:], mode='nearest').to(torch.bool).squeeze(1) pos_embed = self.positional_encoding(padding_mask) feat_last = self.encoder_in_proj(feat_last) # (batch_size, c, h, w) -> (num_queries, batch_size, c) feat_last = feat_last.flatten(2).permute(2, 0, 1) pos_embed = pos_embed.flatten(2).permute(2, 0, 1) # (batch_size, h, w) -> (batch_size, h*w) padding_mask = padding_mask.flatten(1) memory = self.encoder( query=feat_last, key=None, value=None, query_pos=pos_embed, query_key_padding_mask=padding_mask) # (num_queries, batch_size, c) -> (batch_size, c, h, w) memory = memory.permute(1, 2, 0).view(bs, self.encoder_embed_dims, h, w) y = self.encoder_out_proj(memory) for i in range(self.num_inputs - 2, -1, -1): x = feats[i] cur_feat = self.lateral_convs[i](x) y = cur_feat + \ F.interpolate(y, size=cur_feat.shape[-2:], mode='nearest') y = self.output_convs[i](y) mask_feature = self.mask_feature(y) return mask_feature, memory
PypiClean
/BPMN_RPA-7.1.2.tar.gz/BPMN_RPA-7.1.2/BPMN_RPA/Scripts/FTP.py
import ftplib import pickle # The BPMN-RPA FTP module is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # The BPMN-RPA FTP module is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <https://www.gnu.org/licenses/>. # # The BPMN-RPA FTP module is based on the Python ftplib module, which is licensed under the MIT license: # Copyright (c) 2007 Giampaolo Rodola class FTP: def __init__(self, host, user, password): """ Create a new FTP connection. :param host: The host name or IP address of the FTP server. :param user: The user name to connect with. :param password: The password to connect with. """ self.user = user self.password = password self.ftp = None self.host = host self.__connect__() def __connect__(self): """ Internal function to connect to the FTP server. """ self.ftp = ftplib.FTP() # open FTP connection self.ftp.connect(self.host, 21) # login self.ftp.login(self.user, self.password) def __is_picklable__(self, obj: any) -> bool: """ Internal function to determine if the object is pickable. :param obj: The object to check. :return: True or False """ try: pickle.dumps(obj) return True except Exception as e: return False def __getstate__(self): """ Internal function for serialization """ state = self.__dict__.copy() for key, val in state.items(): if not self.__is_picklable__(val): state[key] = str(val) return state def __setstate__(self, state): """ Internal function for deserialization :param state: The state to set to the 'self' object of the class """ self.__dict__.update(state) self.__connect__() def close_ftp(self): """ Close FTP connection. """ self.ftp.close() def download_ftp_file(self, remote_file, local_file): """ Download a file from the FTP server. :param remote_file: The full path to the file to download. :param local_file: The full path to the file to create. """ # download file with open(local_file, 'wb') as f: self.ftp.retrbinary('RETR ' + remote_file, f.write) def upload_ftp_file(self, local_file, remote_file): """ Upload a file to the FTP server. :param local_file: The full path to the file to upload. :param remote_file: The full path to the file to create. """ # upload file self.ftp.storbinary("STOR " + remote_file, open(local_file, 'rb')) def list_ftp_files(self, path): """ List the files in a folder on the FTP server. :param path: The full path to the folder to list. :return: A list of files in the folder. """ # list files in directory self.ftp.cwd(path) return self.ftp.nlst() def list_ftp_files_with_wildcard(self, path, wildcard): """ List the files in a folder with a specific wildcard on the FTP server. :param path: The full path to the folder to list. :param wildcard: The wildcard of the files to return. :return: A list of files in the folder. """ files = [] self.ftp.cwd(path) for file in self.ftp.nlst(): if file.startswith(wildcard): files.append(file) return files def copy_ftp_file(self, source, destination): """ Copy a file on the FTP server. :param source: The full path to the file to copy. :param destination: The full path to the destination. """ # download file with open(destination, 'wb') as f: self.ftp.retrbinary('RETR ' + source, f.write) def move_ftp_file(self, source, destination): """ Move a file on the FTP server. :param source: The full path to the file to move. :param destination: The full path to the destination. """ # download file with open(destination, 'wb') as f: self.ftp.retrbinary('RETR ' + source, f.write) # delete file self.ftp.delete(source) def delete_ftp_file(self, path): """ Delete a file from the FTP server. :param path: The full path to the file to delete. """ # delete file self.ftp.delete(path) def delete_ftp_folder(self, path): """ Delete a folder on the FTP server. :param path: The full path to the folder to delete. """ # delete folder and its contents self.ftp.rmd(path) def create_ftp_folder(self, path): """ Create a folder on the FTP server. :param path: The full path to the folder to create. """ # create folder self.ftp.mkd(path) def rename_ftp_file(self, source, destination): """ Rename a file on the FTP server. :param source: The full path to the file to rename. :param destination: The full path to the destination. """ # rename file self.ftp.rename(source, destination) def rename_ftp_folder(self, source, destination): """ Rename a folder on the FTP server. :param source: The full path to the folder to rename. :param destination: The full path to the destination. """ # rename folder self.ftp.rename(source, destination) def get_ftp_file_size(self, path): """ Get the size of a file on the FTP server. :param path: The full path to the file. :return: The size of the file. """ # get file size return self.ftp.size(path) def get_ftp_folder_size(self, path): """ Get the size of a folder on the FTP server. :param path: The full path to the folder. :return: The size of the folder. """ # get folder size size = 0 self.ftp.cwd(path) for file in self.ftp.nlst(): size += self.ftp.size(file) return size def get_ftp_file_timestamp(self, path): """ Get the timestamp of a file on the FTP server. :param path: The full path to the file. :return: The timestamp of the file. """ # get file timestamp return self.ftp.sendcmd("MDTM " + path) def get_ftp_folder_timestamp(self, path): """ Get the timestamp of a folder on the FTP server. :param path: The full path to the folder. :return: The timestamp of the folder. """ # get folder timestamp return self.ftp.sendcmd("MDTM " + path) def get_ftp_file_permissions(self, path): """ Get the permissions of a file on the FTP server. :param path: The full path to the file. :return: The permissions of the file. """ # get file permissions return self.ftp.sendcmd("SITE CHMOD " + path) def get_ftp_folder_permissions(self, path): """ Get the permissions of a folder on the FTP server. :param path: The full path to the folder. :return: The permissions of the folder. """ # get folder permissions return self.ftp.sendcmd("SITE CHMOD " + path) def set_ftp_file_permissions(self, path, permissions): """ Set the permissions of a file on the FTP server. :param path: The full path to the file. :param permissions: The permissions to set. """ # set file permissions self.ftp.sendcmd("SITE CHMOD " + permissions + " " + path) def set_ftp_folder_permissions(self, path, permissions): """ Set the permissions of a folder on the FTP server. :param path: The full path to the folder. :param permissions: The permissions to set. """ # set folder permissions self.ftp.sendcmd("SITE CHMOD " + permissions + " " + path) def get_ftp_file_owner(self, path): """ Get the owner of a file on the FTP server. :param path: The full path to the file. :return: The owner of the file. """ # get file owner return self.ftp.sendcmd("SITE CHOWN " + path) def get_ftp_folder_owner(self, path): """ Get the owner of a folder on the FTP server. :param path: The full path to the folder. :return: The owner of the folder. """ # get folder owner return self.ftp.sendcmd("SITE CHOWN " + path) def set_ftp_file_owner(self, path, owner): """ Set the owner of a file on the FTP server. :param path: The full path to the file. :param owner: The owner to set. """ # set file owner self.ftp.sendcmd("SITE CHOWN " + owner + " " + path) def set_ftp_folder_owner(self, path, owner): """ Set the owner of a folder on the FTP server. :param path: The full path to the folder. :param owner: The owner to set. """ # set folder owner self.ftp.sendcmd("SITE CHOWN " + owner + " " + path) def get_ftp_file_group(self, path): """ Get the group of a file on the FTP server. :param path: The full path to the file. :return: The group of the file. """ # get file group return self.ftp.sendcmd("SITE CHGRP " + path) def get_ftp_folder_group(self, path): """ Get the group of a folder on the FTP server. :param path: The full path to the folder. :return: The group of the folder. """ # get folder group return self.ftp.sendcmd("SITE CHGRP " + path) def set_ftp_file_group(self, path, group): """ Set the group of a file on the FTP server. :param path: The full path to the file. :param group: The group to set. """ # set file group self.ftp.sendcmd("SITE CHGRP " + group + " " + path) def set_ftp_folder_group(self, path, group): """ Set the group of a folder on the FTP server. :param path: The full path to the folder. :param group: The group to set. """ # set folder group self.ftp.sendcmd("SITE CHGRP " + group + " " + path) def get_ftp_file_md5(self, path): """ Get the MD5 hash of a file on the FTP server. :param path: The full path to the file. :return: The MD5 hash of the file. """ # get file md5 return self.ftp.sendcmd("SITE MD5 " + path) def get_ftp_folder_md5(self, path): """ Get the MD5 hash of a folder on the FTP server. :param path: The full path to the folder. :return: The MD5 hash of the folder. """ # get folder md5 return self.ftp.sendcmd("SITE MD5 " + path) def change_working_directory(self, path): """ Change the working directory on the FTP server. :param path: The full path to the folder. """ # change working directory self.ftp.cwd(path) def get_working_directory(self): """ Get the working directory on the FTP server. :return: The working directory. """ # get working directory return self.ftp.pwd()
PypiClean
/IsoCon-0.3.3.tar.gz/IsoCon-0.3.3/modules/correction_module.py
import signal from multiprocessing import Pool import multiprocessing as mp import sys import math import copy import random from collections import Counter from modules.functions import create_multialignment_matrix, create_position_frequency_matrix def correct_strings(partition_alignments, seq_to_acc, ccs_dict, step, nr_cores = 1, verbose = False): S_prime = {} S_prime_quality = {} partition_unique_seq_to_acc = {} for m, partition in partition_alignments.items(): partition_unique_seq_to_acc[m] = {} partition_unique_seq_to_acc[m][m] = seq_to_acc[m] for s in partition: if s in seq_to_acc: s_accessions = seq_to_acc[s] partition_unique_seq_to_acc[m][s] = s_accessions if ccs_dict: partitioned_ccs_dict = {} for m, partition in partition_alignments.items(): partitioned_ccs_dict[m] = {} for s in partition: if s in seq_to_acc: s_accessions = seq_to_acc[s] for s_acc in s_accessions: partitioned_ccs_dict[m][s_acc] = ccs_dict[s_acc] else: partitioned_ccs_dict = {} for m, partition in partition_alignments.items(): partitioned_ccs_dict[m] = {} if nr_cores == 1: for m, partition in sorted(partition_alignments.items()): S_prime_partition, S_prime_quality_vectors = correct_to_consensus_helper( ((m, partition, partition_unique_seq_to_acc[m], step, verbose, partitioned_ccs_dict[m]), {}) ) for acc, s in S_prime_partition.items(): assert acc not in S_prime S_prime[acc] = s for acc, qual_vector in S_prime_quality_vectors.items(): S_prime_quality[acc] = qual_vector else: ####### parallelize statistical tests ######### # pool = Pool(processes=mp.cpu_count()) original_sigint_handler = signal.signal(signal.SIGINT, signal.SIG_IGN) signal.signal(signal.SIGINT, original_sigint_handler) pool = Pool(processes=nr_cores) try: res = pool.map_async(correct_to_consensus_helper, [ ( (m, partition, partition_unique_seq_to_acc[m], step, verbose, partitioned_ccs_dict[m]), {}) for m, partition in partition_alignments.items() if len(partition) > 1 ] ) S_prime_partition_dicts =res.get(999999999) # Without the timeout this blocking call ignores all signals. except KeyboardInterrupt: print("Caught KeyboardInterrupt, terminating workers") pool.terminate() sys.exit() else: # print("Normal termination") pool.close() pool.join() for S_prime_partition, S_prime_quality_vectors in S_prime_partition_dicts: for acc, s in S_prime_partition.items(): assert acc not in S_prime S_prime[acc] = s for acc, qual_vector in S_prime_quality_vectors.items(): S_prime_quality[acc] = qual_vector return S_prime, S_prime_quality def correct_to_consensus_helper(arguments): args, kwargs = arguments if args[5]: print("Correction with ccs probabilities") return correct_to_consensus_ccs_qual(*args, **kwargs) else: return correct_to_consensus(*args[:-1], **kwargs), {} def annotate_with_quality_values(alignment_matrix, seq_to_acc, ccs_dict): alignment_matrix_of_qualities = {} alignment_matrix_of_max_qualities = {} for s in alignment_matrix: s_accessions = seq_to_acc[s] all_quals = [ ccs_dict[s_acc].qual for s_acc in s_accessions ] sum_quals_vector = [sum(t) for t in zip(*all_quals)] max_quals_vector = [max(t) for t in zip(*all_quals)] # sum all probabilities from all reads equal to s here using all accessions in s to acc s_to_acc list_sum_quals = [] list_max_quals = [] current_pos_in_s = 0 for j in range(len(alignment_matrix[s])): # print(current_pos_in_s, len(sum_quals_vector) ) current_quality = sum_quals_vector[current_pos_in_s] current_max_quality = max_quals_vector[current_pos_in_s] list_sum_quals.append(current_quality) list_max_quals.append(current_max_quality) char_at_pos = alignment_matrix[s][j] if char_at_pos != "-": if current_pos_in_s < len(sum_quals_vector) - 1: current_pos_in_s += 1 alignment_matrix_of_qualities[s] = list_sum_quals alignment_matrix_of_max_qualities[s] = list_max_quals PFM_qualities = [] PFM_max_qualities = [] for j in range(len(alignment_matrix[s])): # for each column PFM_qualities.append({"A": 0, "C": 0, "G": 0, "T": 0, "-": 0}) PFM_max_qualities.append({"A": 0, "C": 0, "G": 0, "T": 0, "-": 0}) for s in alignment_matrix_of_qualities: nucl = alignment_matrix[s][j] sum_quality_at_position = alignment_matrix_of_qualities[s][j] PFM_qualities[j][nucl] += sum_quality_at_position max_quality_at_position = alignment_matrix_of_max_qualities[s][j] PFM_max_qualities[j][nucl] += max_quality_at_position # get all the differences to majority here list_of_majority_nucleotides = [] for j in range(len(PFM_qualities)): max_v_j = max(PFM_qualities[j], key = lambda x: PFM_qualities[j][x] ) majority_count = PFM_qualities[j][max_v_j] max_v_j_set = set([v for v in PFM_qualities[j] if PFM_qualities[j][v] == majority_count ]) all_major = "".join(max_v_j_set) list_of_majority_nucleotides.append(all_major) assert len(list_of_majority_nucleotides) == len(PFM_qualities) global_all_difference_qualities = [] for s in alignment_matrix: s_aligned_vector = alignment_matrix[s] for j in range(len(s_aligned_vector)): if s_aligned_vector[j] not in list_of_majority_nucleotides[j] and len(list_of_majority_nucleotides[j]) == 1: global_all_difference_qualities.append(alignment_matrix_of_qualities[s][j]) global_all_difference_qualities.sort() if len(global_all_difference_qualities) > 0: global_correction_threshold = global_all_difference_qualities[ int( math.ceil( len(global_all_difference_qualities)/2.0) ) - 1 ] else: global_correction_threshold = -1 print("nothing to correct!") print("GLOBAL QUAL THRESH:", global_correction_threshold) return alignment_matrix_of_qualities, PFM_qualities, PFM_max_qualities, global_correction_threshold def correct_to_consensus_ccs_qual(m, partition, seq_to_acc, step, ccs_dict): S_prime_partition = {} S_prime_quality_vector = {} N_t = sum([container_tuple[3] for s, container_tuple in partition.items()]) # total number of sequences in partition if len(partition) > 1: # all strings has not converged alignment_matrix = create_multialignment_matrix(m, partition) PFM = create_position_frequency_matrix(alignment_matrix, partition) for s_before in partition: s_after = "".join([n for n in alignment_matrix[s_before] if n != "-"]) assert s_before == s_after # print(len(partition), N_t) alignment_matrix_of_qualities, PFM_qualities, PFM_max_qualities, global_correction_threshold = annotate_with_quality_values(alignment_matrix, seq_to_acc, ccs_dict) assert len(alignment_matrix_of_qualities) == len(alignment_matrix) if global_correction_threshold < 0: return S_prime_partition, S_prime_quality_vector majority_vector = [] for j in range(len(PFM_qualities)): max_v_j = max(PFM_qualities[j], key = lambda x: PFM_qualities[j][x] ) majority_count = PFM_qualities[j][max_v_j] max_v_j_set = set([v for v in PFM_qualities[j] if PFM_qualities[j][v] == majority_count ]) all_major = "".join(max_v_j_set) majority_vector.append( all_major ) assert len(majority_vector) == len(PFM_qualities) ############################ ############################ for s in sorted(partition): if partition[s][3] > 1: # at least 2 identical sequences --> its a nearest_neighbor of the partition, has converged, and should not be corrected print("not correcting converged sequence!") continue s_alignment_in_matrix = alignment_matrix[s] # s_min = 0 for i, p in enumerate(s_alignment_in_matrix): if p != "-": s_min = i break for i, p in enumerate(s_alignment_in_matrix[::-1]): if p != "-": s_max = len(s_alignment_in_matrix) - i break print("S", s_min, s_max) s_quals = alignment_matrix_of_qualities[s] # ALL POSITIONS with sum of probabilities lower than the largest probability minority_positions = [ (j,majority_vector[j], s_alignment_in_matrix[j]) for j in range(len(majority_vector)) if s_alignment_in_matrix[j] not in majority_vector[j] and s_min <= j <= s_max ] minority_positions_correctable = [ j for j in range(len(majority_vector)) if (len(majority_vector[j]) == 1 and majority_vector[j] != s_alignment_in_matrix[j] ) ] minority_positions_correctable = [ (j, PFM_qualities[j][ s_alignment_in_matrix[j] ]) for j in minority_positions_correctable ] nr_pos_to_correct = int(math.ceil( len(minority_positions_correctable) * 0.5)) # (step/ float(step +1)) )) # print("positions to correct:", nr_pos_to_correct) if nr_pos_to_correct == 0: print("Edit distance to nearest_neighbor:", partition[s][0], "is nearest_neighbor:", s ==m, "Minority positions:", minority_positions) continue if len(minority_positions_correctable) == 0: print("no unambiguous majority positions") continue minority_positions_correctable.sort(key=lambda x: x[1]) print(len(minority_positions_correctable) ,minority_positions_correctable) _, quality_threshold_to_correct = minority_positions_correctable[ nr_pos_to_correct - 1 ] minority_positions_to_correct = [ (j, qual_j) for j, qual_j in minority_positions_correctable if qual_j <= quality_threshold_to_correct ] print(quality_threshold_to_correct, len(minority_positions_to_correct)) # minority_positions_to_correct = [ (j, qual_j) for j, qual_j in minority_positions_correctable if qual_j <= global_correction_threshold ] # print("actual:", len(minority_positions_to_correct)) # minority_positions_to_correct = sorted(minority_positions_correctable, key=lambda x: x[1])[:nr_pos_to_correct] # sorted list with the smallest probabilities first # print(minority_positions_to_correct) s_new = alignment_matrix[s] s_qual_new = alignment_matrix_of_qualities[s] for j, qual_j in minority_positions_to_correct: highest_prob_character_at_j = majority_vector[j] assert len(majority_vector[j]) == 1 s_new[j] = highest_prob_character_at_j s_qual_new[j] = PFM_max_qualities[j][highest_prob_character_at_j] s_modified = "".join([nucl for nucl in s_new if nucl != "-" ]) s_qual_modified = [s_qual_new[j] for j in range(len(s_new)) if s_new[j] != "-" ] # only unique strings can change in this step accessions_of_s = seq_to_acc[s] for acc in accessions_of_s: S_prime_partition[acc] = s_modified S_prime_quality_vector[acc] = s_qual_modified else: print("Partition converged: Partition size(unique strings):{0}, partition support: {1}.".format(len(partition), N_t)) return S_prime_partition, S_prime_quality_vector def correct_to_consensus(m, partition, seq_to_acc, step, verbose): S_prime_partition = {} N_t = sum([container_tuple[3] for s, container_tuple in partition.items()]) # total number of sequences in partition # if N_t == 2: # print("Partition has size", N_t, "no meaningful correction can be done") # for s, container_tuple in partition.items(): # print(seq_to_acc[s]) if len(partition) > 1 and N_t > 2: # all strings has not converged alignment_matrix = create_multialignment_matrix(m, partition) PFM = create_position_frequency_matrix(alignment_matrix, partition) for s_before in partition: s_after = "".join([n for n in alignment_matrix[s_before] if n != "-"]) assert s_before == s_after # consensus_alignment = [ max(PFM[j], key=lambda k: PFM[j][k]) for j in range(len(PFM))] # print("nearest_neighbor errors:", math.ceil(min([ partition[s][0] for s in partition if partition[s][3] > 1 or s !=m ]) / 2.0) ) # frozen_positions = get_frozen_positions(alignment_matrix[m]) ## TEST LOG ERROR TYPES ####### c_del = 0 c_ins = 0 c_subs = 0 majority_vector = [] temp_majority_string = "" for j in range(len(PFM)): max_v_j = max(PFM[j], key = lambda x: PFM[j][x] ) if max_v_j != "-": temp_majority_string += max_v_j majority_count = PFM[j][max_v_j] max_v_j_set = set([v for v in PFM[j] if PFM[j][v] == majority_count ]) all_major = "".join(max_v_j_set) majority_vector.append( all_major ) if len(max_v_j_set) > 1: continue # DO not count errors where majority position is ambigous since we don't know the true majority here for v in PFM[j]: if max_v_j == "-": if v != max_v_j: c_ins += PFM[j][v] else: if v != max_v_j: if v == "-": c_del += PFM[j][v] else: c_subs += PFM[j][v] if verbose: print("Partition error types:", c_del, c_ins, c_subs, "depth:", N_t ) assert len(majority_vector) == len(PFM) ############################ for s in sorted(partition): if partition[s][3] > 1: # at least 2 identical sequences --> its a nearest_neighbor of the partition, has converged, and should not be corrected continue nr_pos_to_correct2 = int(math.ceil(partition[s][0] / 2.0)) #decide how many errors we should correct here s_alignment_in_matrix = alignment_matrix[s] minority_positions = [ (j,majority_vector[j], s_alignment_in_matrix[j]) for j in range(len(majority_vector)) if s_alignment_in_matrix[j] not in majority_vector[j] ] nr_pos_to_correct = int(math.ceil( len([ 1 for j in range(len(majority_vector)) if (len(majority_vector[j]) == 1 and majority_vector[j] != s_alignment_in_matrix[j] ) ]) * 0.5)) # (step/ float(step +1)) )) # print("positions to correct:", nr_pos_to_correct) if verbose: if nr_pos_to_correct == 0: print("Edit distance to nearest_neighbor:", partition[s][0], "is nearest_neighbor:", s ==m, "Minority positions:", minority_positions) if nr_pos_to_correct2 > 0 and nr_pos_to_correct == 0: print("Edit distance to nearest_neighbor: {0}, {1} minority positions, correcting no position. Length partition (unique): {2}, total seqs: {3}".format(partition[s][0], len(minority_positions), len(partition), N_t)) # for s in partition: # print(s) # print([ (j,majority_vector[j], s_alignment_in_matrix[j], PFM[j]) for j in range(len(majority_vector)) if majority_vector[j] != s_alignment_in_matrix[j] ]) if nr_pos_to_correct == 0: continue # find the position probabilities of the alignment of s in PFM ###################### ORIGINAL CORRECTION ###################################### # pos_freqs_for_s = [] # for j in range(len(PFM)): # pos_freqs_for_s.append( (j, PFM[j][s_alignment_in_matrix[j]]) ) # pos_freqs_for_s.sort(key=lambda x: x[1]) # sort with respect to smallest frequencies # pos, highest_freq_of_error_to_correct = pos_freqs_for_s[ nr_pos_to_correct - 1 ] # end_position_in_list = nr_pos_to_correct # pp = nr_pos_to_correct # while pos_freqs_for_s[pp][1] == highest_freq_of_error_to_correct: # end_position_in_list += 1 # pp += 1 # J = [j for j, freq in random.sample(pos_freqs_for_s[:end_position_in_list], nr_pos_to_correct)] ############################################################ ############################################################ ########### TEST WEIGHTING EACH MINORITY POSITION BY IT'S OBSERVED FREQUENCY THROUGHOUT THE ALIGNMENTS TO THE nearest_neighbor ################ pos_freqs_for_s_mod = [] for j in range(len(PFM)): majority_variant = majority_vector[j] v_j = s_alignment_in_matrix[j] if v_j == majority_variant or len(majority_variant) > 1: # no correction of majority position or ambigous majority! continue else: if majority_variant == "-": pos_freqs_for_s_mod.append( (j, PFM[j][v_j] / float(max(c_ins, 1) ) )) elif v_j == "-": pos_freqs_for_s_mod.append( (j, PFM[j][v_j] / float(max(c_del, 1) ) )) else: pos_freqs_for_s_mod.append( (j, PFM[j][v_j] / float(max(c_subs, 1) ) )) # max_v_j = max(PFM[j], key = lambda x: PFM[j][x] ) # if max_v_j == v_j: # pos_freqs_for_s_mod.append( (j, PFM[j][v_j] / float(1)) ) # elif max_v_j == "-": # pos_freqs_for_s_mod.append( (j, PFM[j][v_j] / float(max(c_ins, 1) ) )) # elif v_j == "-": # pos_freqs_for_s_mod.append( (j, PFM[j][v_j] / float(max(c_del, 1) ) )) # else: # pos_freqs_for_s_mod.append( (j, PFM[j][v_j] / float(max(c_subs, 1) ) )) if len(pos_freqs_for_s_mod) == 0: continue pos_freqs_for_s_mod.sort(key=lambda x: x[1]) # sort with respect to smallest frequencies if len(pos_freqs_for_s_mod) < nr_pos_to_correct: end_position_in_list = len(pos_freqs_for_s_mod) else: pos, highest_freq_of_error_to_correct = pos_freqs_for_s_mod[ nr_pos_to_correct - 1 ] end_position_in_list = nr_pos_to_correct for pp in range(nr_pos_to_correct, len(pos_freqs_for_s_mod)): # print(pos_freqs_for_s_mod[pp][1], highest_freq_of_error_to_correct) if pos_freqs_for_s_mod[pp][1] > highest_freq_of_error_to_correct: break else: end_position_in_list += 1 # J = [j for j, freq in random.sample(pos_freqs_for_s_mod[:end_position_in_list], nr_pos_to_correct)] J_temp = [j for j, freq in pos_freqs_for_s_mod[:end_position_in_list]] # print("end pos:", end_position_in_list) ############################################# s_new = alignment_matrix[s] for j in J_temp: # if j in frozen_positions: # # print("tried to correct in frozen positions") # continue old_nucl = s_new[j] highest_prob_character_at_j = majority_vector[j] assert len(majority_vector[j]) == 1 # highest_prob_character_at_j = max(PFM[j], key=lambda k: PFM[j][k]) if highest_prob_character_at_j == old_nucl: # choose the other highest on if tie (should happen only when partition consist of two sequences) print("Highest count nucl was about to be corrected.") # pmf_j_minus_variant = copy.deepcopy(PFM[j]) # del pmf_j_minus_variant[old_nucl] # highest_prob_character_at_j = max(pmf_j_minus_variant, key=lambda k: pmf_j_minus_variant[k]) # print("correcting", s_new[j], "to", highest_prob_character_at_j ) s_new[j] = highest_prob_character_at_j s_modified = "".join([nucl for nucl in s_new if nucl != "-" ]) # only unique strings can change in this step accessions_of_s = seq_to_acc[s] for acc in accessions_of_s: S_prime_partition[acc] = s_modified elif len(partition) > 1: ed = 0 for s in partition: if partition[s][0] > ed: ed = partition[s][0] if verbose: print("Partition could not be corrected: Partition size(unique strings):{0}, partition support: {1}, edit distance:{2}.".format(len(partition), N_t, ed)) else: if verbose: print("Partition converged: Partition size(unique strings):{0}, partition support: {1}.".format(len(partition), N_t)) return S_prime_partition # def get_frozen_positions(m_in_alignment_matrix): # """ # positions in Multialingment matrix where there are insels longer than 2 bp w.r.t. nearest_neighbor, these regions are prone to errors in alingments and # we wait to correct these in another partition where they are hopefully split into several true partitions. # """ # frozen_pos = set() # ins_count = 0 # ins_pos = set() # for j in range(len(m_in_alignment_matrix)): # if m_in_alignment_matrix[j] == "-": # ins_count += 1 # ins_pos.add(j) # else: # if ins_count > 4: # always padded, so indel of length 2 be will be of length 4 in alignment matrixx - # for k in ins_pos: # frozen_pos.add(k) # ins_count = 0 # ins_pos = set() # print("frozen:", len(frozen_pos), "tot:", len(m_in_alignment_matrix) ) # return frozen_pos
PypiClean
/MeleeUploader-1.22.2.tar.gz/MeleeUploader-1.22.2/README.md
# Melee-YouTube-Uploader A YouTube Uploader for my Melee recordings A modified version of FRC-YouTube-Uploader for Video Game Tournaments. **IMPORTANT NOTE** This application **DOES NOT/CANNOT** support enabling monetization due to YouTube's API restrictions. Thus by default videos are uploaded as unlisted so you can set monetization settings before making them public. Optionally you can update monetization settings as they are uploaded without breaking anything. ## To Do - Automate creation of thumbnails - Slippi Integration (plan is to allow pulling characters from the slippi stream, additional ideas are appreciated). - Maybe other stuff ## Contributing PRs are appreciated and will be reviewed quickly, the only code quality standard I have is to follow PEP8 standard except for the line length. If you have trouble understanding my code just ask me. ## Questions and Support I am always open to help setup the program or fix any techincal issues you may have. Please send me a DM on twitter with your issue and I'll get you sorted out. ## Current Feature Set: - Upload videos - Manual or automatic file selection - Queue and dequeue Videos to upload (Queue items can be modified) - Add relevant YouTube tags - Make and add to playlists - Load old uploads from history - Save a queue to be uploaded later - Melee, Ultimate, Smash 64, Rivals of Aether, Splatoon<sup>\*</sup> and Custom Character Lists - Hook into Scoreboard Assistant, Stream Control, Streameta, and OBS - Automatic Updates (sometimes) <sup>\*</sup>There are no characters in the list, but this does set splatoon specific tags which are useful ## How to Setup - Video Version: https://youtu.be/zrcf4t_qk5A 1. Install [Python 3.7+](https://www.python.org/downloads/) for your OS with the PATH added and make sure there are no other versions of Python 3. 2. Install the program by typing `pip3 install -I meleeuploader` into Command Prompt/Terminal. If you want untested features you can download the repo and install with `pip3 install -I /path/to/repo` 3. Start the program by running `meleeuploader` for the Melee character list or `smashuploader` for the Ultimate character list in Command Prompt/Terminal. 4. Select the YouTube profile you would like to use for the first authentication request and then any google account for the second authentication request. If the second one fails, close your web browser and then run the command to open the program again. 5. Add in the necessary info in the Event Values and Match Values tabs 6. Hit submit when the match finishes. 7. Update forms with the next match's info. 8. Repeat steps 5-7 and enjoy not having to deal with YouTube's front end 🎉. ### Create Your Own Credentials In the future I will not be including YouTube API credentials with this project. So here is a guide to create your own credentials. 1. Open the [Google Developer Console](https://console.developers.google.com/) 2. Hit the `Select Project` button near the top and create a new project. 3. Once the project is created, select the project. 4. Hit the `Enable APIs and Services` button and enable the YouTube Data API V3 and the Google Sheets API. 5. Once the APIs are enabled it will tell you to create credentials and there will be a button to press. 6. Google will ask you to setup an Oauth consent screen. Set the consent screen to internal and then only add an application name. Hit save to exit that page and then click `Credentials` on the left tab. 7. Hit `Create Credentials` -> `OAuth client ID`, select other from the options given, and then type any name you want. Hit save. 8. Select the name of your new credentials in the `OAuth 2.0 Client IDs` section. Then select `Download JSON` at the top. 9. Once you have downloaded your credentails remember to rename them `client_secrets.json` (if you don't see the `.json` when renaming the file just use `client_secrets`) and put the file in `C:\Users\[Your Username]\` or, if you are on macOS or Unix, whatever `echo ~` returns in terminal. macOS users can also just do `open ~` to open a Finder window at that directory. 10. If you already created YouTube Account credentials for the program, open the program and select `Settings -> Remove YouTube Credentials` ### Additional Setup Options #### Windows If you want to launch the application easily, you can find the exe by hitting the Windows key and typing `meleeuploader`, if that doesn't show the option to run the command then you can probably find the exe at `C:\Users\[Your Username]\AppData\Local\Programs\Python\Python37\Scripts\`. Pinning the exe to the taskbar allows quick access to the program. If you would like to have no console window on your screen, you will need to find out where your pythonw.exe file is (it should be in the same place your python.exe) and create a shortcut to it. Then open the shortcut properties window and edit the target to include `-m meleeuploader` for Melee, `-m meleeuploader ult` for Ultimate, `-m meleeuploader 64` for 64, `-m meleeuploader rivals` for Rivals, or `-m meleeuploader splatoon` for Splatoon at the end. This can then be pinned to your taskbar for easy access. This method does not allow authenticating yourself so you will have to fall back to CMD/Terminal for that part. #### Mac and Unix `meleeuploader &` if you want to hide the terminal window. There are probably ways to launch the program quicker, but I don't use macOS/Linux for uploading. ## How to use each field ### Required `Event Name`, `Title Format`, `Video Privacy`, `File`, `Match Type`, and `Player Tags` are the only required fields for uploading any file. #### File File is able to be used as either a file or directory input. Because of how the input selector is setup you will need to either type out the directory address or select a file within the directory you wish to use and then you can delete the filename from the field. If you select a directory the field will not be cleared after submission. When using the directory feature, it will find the newest file in the directory you give it, so make sure no other files are written to this folder other than the recordings. This is best used for uploading or queueing videos during an event. #### Title Format All the options support no characters and the available options can be expanded upon on request. ### Optional #### Match Type Prefix and Suffix These are fairly self explanatory, you can add a bit of text before and after the `Match Type`. When submitting the video the `Prefix` is kept while the `Suffix` is cleared. #### Sponsor Tag This field will be added to the player tag like so `{sponsor} | {player}` resulting in names like `TSM | Leffen`. #### Characters Melee characters are currently ordered by tier list placing, according to the 2021 PGStats tier list. Ultimate characters are currently ordered by the default character select screen without echo stacking. If you don't add any characters for either player, both players will not have characters in the title. Characters that are selected will be in the order they are shown in the list, not the selected order (unfortunate issue with the GUI framework). You can swap the character list using the menu bar or load the preferred character list by using `meleeuploader` for Melee, `smashuploader` for Ultimate, `s64uploader` for Smash 64, `rivalsuploader` for Rivals, and `splatoonuploader` for Splatoon. There is also the option to load your own character list, instructions can be found at the bottom. #### YouTube PlaylistID The URL of the playlist after creation can be put here, the program will trim it to just the part it needs. The URL should look like `https://www.youtube.com/playlist?list=PLSCJwgNAP2cXdlHlwbZr38JDHuuc8vx_s`, if the address has a string with `PL` at the start, it should work. If you want to generate a playlist you can also do that by typing in a playlist name. Make sure it doesn't contain "PL" anywhere in the name otherwise it will fail. #### Bracket Link Adds a direct link to the bracket at the top of the description. Any URL will work here, just make sure to include `https://` so YouTube users can click on the link in the description. #### Tags If you want to add additional tags, for a specific event or your channel, add them here. Separate the tags with commas and don't worry about leading or trailing spaces. Also multiple tags about the game selected and the players are added by the program so don't add any related to those in this field. #### Description Additional text can be added to the description here, it will go between the bracket link and the credit text. If you would like to put the bracket link in a different spot, don't input anything in `Bracket Link` and instead insert your format in `Description`. #### Submit The submit button does a lot, it adds submission to queue, clears fields in match values that aren't generally needed for consecutive matches, and prevents you from adding submissions that don't meet the minimum criteria. ## How to use advanced features - Video Version: https://youtu.be/mw0sP7YJVfE ### History - Fixing an upload that didn't work History was built so I could fix uploads that exceeded the title limit on YouTube (100 characters). This actually happens very rarely now because I've employed a number of tricks to minify the title as much as possible. By loading the history window from the menubar, you can double click any row in the list to reload the form with the values you inputted for that submission. Every submission will create a new entry, but the history window is only updated on load, you will need to close and reopen it to see new entries. ### Queue - Saving uploads for later Queue was built so I could upload VODs after an event because the venue didn't have the bandwidth to support streaming and uploading simultaneously. Queue refers to the list of upcoming uploads in the status tab. By selecting `Toggle Uploads` you can toggle the uploading function, but continue to add entries to the queue. Once you have finished adding all the VODs you want to upload, selecting `Save Queue` will write the entire queue to your disk to be loaded later on. Finally, using `Load Queue` will load the entire queue file and start uploading immediately. You can also load the queue on startup by running `<uploader command> -q`. This will instantly load whatever is in the queue and start uploading. If you don't want to start uploading then you should use the usual method. Items in the queue can also be modified by double clicking the queue item in the queue list and then changing one of the cells in the right column of the window that appears. ### Scoreboard Assistant Websocket - Never retype anything SA Websocket was built so I could avoid retyping information that I put into Scoreboard Assistant. To enable the websocket open the `Settings` menu tab and select the `Enable Websocket` option. Just make sure that SA is open before you start the websocket. The program will pull from the `Player 1`, `Player 2`, and `Match` fields. The `Match` field will be parsed to find which of the match types defined in the program are a substring, then it will split the input at the substring and update `Match Prefix` and `Match Suffix` with whatever is left over. For example, `Doubles - Winners R1` as the input would result in `Doubles -` and `R1` being the prefix and suffix respectively. There is also support for character selection if you use stock icons from this [link](https://drive.google.com/file/d/1L8M-4FUDcQo-2cuh1Ak_VabJSQlWz8B_/view?usp=sharing). ### StreamControl and Streameta Integration This integration is similar to the SA websocket but is done by polling a file or HTTP endpoint respectively. The SC integration is flexible, just map your `streamcontrol.json` to the fields in the uploader. ### OBS Websocket - Never submit manually I've set it up so once recording has been stopped, you can have the application either submit the information that is currently inputted or stop updating the form if you are using a SA/SC/Streameta hook. This combined with `SA Websocket` or `SC/Streameta Integration` makes it effortless to quickly queue sets without touching the program In addition to enabling the settings you will need to update OBS with the websocket plugin found here: https://github.com/obsproject/obs-websocket ### Custom Character List You can add your own custom character lists by putting comma separated names in a file called `.smash_custom_list.txt` in the smashuploader config folder which is in your root directory. If you don't know where your root directory is, open the program and select `Characters -> Custom` and the program will make a blank text file where it is supposed to be.
PypiClean
/Kiwiii-server-0.7.0.tar.gz/Kiwiii-server-0.7.0/kiwiii/worker.py
from concurrent import futures as cf import threading from tornado import gen, process from tornado.queues import Queue PROCESSES = process.cpu_count() class Worker(object): """General-purpose multiprocess worker Args: args: iterable task array func: task processor """ def __init__(self, args, func): self.args = args self.func = func self.interruption_requested = False self._queue = Queue(PROCESSES * 2) @gen.coroutine def run(self): self.on_start() with cf.ThreadPoolExecutor(PROCESSES) as tp: for p in range(PROCESSES): tp.submit(self._consumer()) with cf.ProcessPoolExecutor(PROCESSES) as pp: for i, a in enumerate(self.args): yield self._queue.put(pp.submit(self.func, a)) if self.interruption_requested: yield self._queue.join() self.on_interrupted() return yield self._queue.join() self.status = -1 self.on_finish() @gen.coroutine def _consumer(self): while True: f = yield self._queue.get() res = yield f with threading.Lock(): self.on_task_done(res) self._queue.task_done() def on_task_done(self, res): pass def on_interrupted(self): pass def on_finish(self): pass def interrupt(self): print("Interruption requested...") self.interruption_requested = True class WorkerQueue(object): def __init__(self): self.queue = Queue() self.current_worker_id = None self.current_worker = None self.queued_ids = [] self.aborted_ids = [] self._dispatcher() def put(self, id_, worker): """ Put a job to the queue """ self.queued_ids.append(id_) self.queue.put_nowait((id_, worker)) def abort(self, id_): if id_ in self.queued_ids: self.aborted_ids.append(id_) elif id_ == self.current_worker_id: self.current_worker.interrupt() def status(self, id_): if id_ in self.queued_ids: return "Queued" elif id_ == self.current_worker_id: return self.current_worker.status else: return "Completed" @gen.coroutine def _dispatcher(self): while 1: id_, worker = yield self.queue.get() self.queued_ids.remove(id_) if id_ in self.aborted_ids: self.aborted_ids.remove(id_) continue self.current_worker_id = id_ self.current_worker = worker yield self.current_worker.run() self.current_worker_id = None self.current_worker = None
PypiClean
/125softNLP-0.0.1-py3-none-any.whl/pysoftNLP/kashgari/processors/base_processor.py
# author: BrikerMan # contact: [email protected] # blog: https://eliyar.biz # file: base_processor.py # time: 2019-05-21 11:27 import collections import logging import operator from typing import List, Optional, Union, Dict, Any import numpy as np from tensorflow.python.keras.preprocessing.sequence import pad_sequences from pysoftNLP.kashgari import utils class BaseProcessor(object): """ Corpus Pre Processor class """ def __init__(self, **kwargs): self.token2idx: Dict[str, int] = kwargs.get('token2idx', {}) self.idx2token: Dict[int, str] = dict([(v, k) for (k, v) in self.token2idx.items()]) self.token2count: Dict = {} self.label2idx: Dict[str, int] = kwargs.get('label2idx', {}) self.idx2label: Dict[int, str] = dict([(v, k) for (k, v) in self.label2idx.items()]) self.token_pad: str = kwargs.get('token_pad', '<PAD>') self.token_unk: str = kwargs.get('token_unk', '<UNK>') self.token_bos: str = kwargs.get('token_bos', '<BOS>') self.token_eos: str = kwargs.get('token_eos', '<EOS>') self.dataset_info: Dict[str, Any] = kwargs.get('dataset_info', {}) self.add_bos_eos: bool = kwargs.get('add_bos_eos', False) self.sequence_length = kwargs.get('sequence_length', None) self.min_count = kwargs.get('min_count', 3) def info(self): return { 'class_name': self.__class__.__name__, 'config': { 'label2idx': self.label2idx, 'token2idx': self.token2idx, 'token_pad': self.token_pad, 'token_unk': self.token_unk, 'token_bos': self.token_bos, 'token_eos': self.token_eos, 'dataset_info': self.dataset_info, 'add_bos_eos': self.add_bos_eos, 'sequence_length': self.sequence_length }, 'module': self.__class__.__module__, } def analyze_corpus(self, corpus: Union[List[List[str]]], labels: Union[List[List[str]], List[str]], force: bool = False): rec_len = sorted([len(seq) for seq in corpus])[int(0.95 * len(corpus))] self.dataset_info['RECOMMEND_LEN'] = rec_len if len(self.token2idx) == 0 or force: self._build_token_dict(corpus, self.min_count) if len(self.label2idx) == 0 or force: self._build_label_dict(labels) def _build_token_dict(self, corpus: List[List[str]], min_count: int = 3): """ Build token index dictionary using corpus Args: corpus: List of tokenized sentences, like ``[['I', 'love', 'tf'], ...]`` min_count: """ token2idx = { self.token_pad: 0, self.token_unk: 1, self.token_bos: 2, self.token_eos: 3 } token2count = {} for sentence in corpus: for token in sentence: count = token2count.get(token, 0) token2count[token] = count + 1 self.token2count = token2count # 按照词频降序排序 sorted_token2count = sorted(token2count.items(), key=operator.itemgetter(1), reverse=True) token2count = collections.OrderedDict(sorted_token2count) for token, token_count in token2count.items(): if token not in token2idx and token_count >= min_count: token2idx[token] = len(token2idx) self.token2idx = token2idx self.idx2token = dict([(value, key) for key, value in self.token2idx.items()]) logging.debug(f"build token2idx dict finished, contains {len(self.token2idx)} tokens.") self.dataset_info['token_count'] = len(self.token2idx) def _build_label_dict(self, corpus: Union[List[List[str]], List[str]]): raise NotImplementedError def process_x_dataset(self, data: List[List[str]], max_len: Optional[int] = None, subset: Optional[List[int]] = None) -> np.ndarray: if max_len is None: max_len = self.sequence_length if subset is not None: target = utils.get_list_subset(data, subset) else: target = data numerized_samples = self.numerize_token_sequences(target) return pad_sequences(numerized_samples, max_len, padding='post', truncating='post') def process_y_dataset(self, data: Union[List[List[str]], List[str]], max_len: Optional[int], subset: Optional[List[int]] = None) -> np.ndarray: raise NotImplementedError def numerize_token_sequences(self, sequences: List[List[str]]): raise NotImplementedError def numerize_label_sequences(self, sequences: List[List[str]]) -> List[List[int]]: raise NotImplementedError def reverse_numerize_label_sequences(self, sequence, **kwargs): raise NotImplementedError def __repr__(self): return f"<{self.__class__}>" def __str__(self): return self.__repr__() if __name__ == "__main__": print("Hello world")
PypiClean
/DjangoDjangoAppCenter-0.0.11-py3-none-any.whl/AppCenter/simpleui/static/admin/simpleui-x/elementui/umd/locale/sk.js
(function (global, factory) { if (typeof define === "function" && define.amd) { define('element/locale/sk', ['module', 'exports'], factory); } else if (typeof exports !== "undefined") { factory(module, exports); } else { var mod = { exports: {} }; factory(mod, mod.exports); global.ELEMENT.lang = global.ELEMENT.lang || {}; global.ELEMENT.lang.sk = mod.exports; } })(this, function (module, exports) { 'use strict'; exports.__esModule = true; exports.default = { el: { colorpicker: { confirm: 'OK', clear: 'Zmazať' }, datepicker: { now: 'Teraz', today: 'Dnes', cancel: 'Zrušiť', clear: 'Zmazať', confirm: 'OK', selectDate: 'Vybrať dátum', selectTime: 'Vybrať čas', startDate: 'Dátum začiatku', startTime: 'Čas začiatku', endDate: 'Dátum konca', endTime: 'Čas konca', prevYear: 'Predošlý rok', nextYear: 'Ďalší rok', prevMonth: 'Predošlý mesiac', nextMonth: 'Ďalší mesiac', day: 'Deň', week: 'Týždeň', month: 'Mesiac', year: 'Rok', month1: 'Január', month2: 'Február', month3: 'Marec', month4: 'Apríl', month5: 'Máj', month6: 'Jún', month7: 'Júl', month8: 'August', month9: 'September', month10: 'Október', month11: 'November', month12: 'December', weeks: { sun: 'Ne', mon: 'Po', tue: 'Ut', wed: 'St', thu: 'Št', fri: 'Pi', sat: 'So' }, months: { jan: 'Jan', feb: 'Feb', mar: 'Mar', apr: 'Apr', may: 'Máj', jun: 'Jún', jul: 'Júl', aug: 'Aug', sep: 'Sep', oct: 'Okt', nov: 'Nov', dec: 'Dec' } }, select: { loading: 'Načítavanie', noMatch: 'Žiadna zhoda', noData: 'Žiadne dáta', placeholder: 'Vybrať' }, cascader: { noMatch: 'Žiadna zhoda', loading: 'Načítavanie', placeholder: 'Vybrať', noData: 'Žiadne dáta' }, pagination: { goto: 'Choď na', pagesize: 'na stranu', total: 'Všetko {total}', pageClassifier: '' }, messagebox: { title: 'Správa', confirm: 'OK', cancel: 'Zrušiť', error: 'Neplatný vstup' }, upload: { deleteTip: 'pre odstránenie stisni klávesu Delete', delete: 'Vymazať', preview: 'Prehliadať', continue: 'Pokračovať' }, table: { emptyText: 'Žiadne dáta', confirmFilter: 'Potvrdiť', resetFilter: 'Zresetovať', clearFilter: 'Všetko', sumText: 'Spolu' }, tree: { emptyText: 'Žiadne dáta' }, transfer: { noMatch: 'Žiadna zhoda', noData: 'Žiadne dáta', titles: ['Zoznam 1', 'Zoznam 2'], filterPlaceholder: 'Filtrovať podľa', noCheckedFormat: '{total} položiek', hasCheckedFormat: '{checked}/{total} označených' }, image: { error: 'FAILED' // to be translated }, pageHeader: { title: 'Back' // to be translated } } }; module.exports = exports['default']; });
PypiClean
/Lantz-0.3.zip/Lantz-0.3/lantz/drivers/andor/neo.py
import ctypes as ct import numpy as np from lantz import Feat, Action, Q_ from lantz.foreign import RetStr, RetTuple from .andor import Andor class Neo(Andor): """Neo Andor CMOS Camera """ def initialize(self): super().initialize() self.flush() self.fan_speed = 1 self.width ,self.height = self.sensor_size self.length = self.width * self.height self.clock_rate = 100 self.pixel_encoding = 32 self.imagesizebytes = self.getint("ImageSizeBytes") self.userbuffer = ct.create_string_buffer(' ' * self.imagesizebytes) @Feat(None, values={32: 'Mono32', 64: 'Mono64'}) def pixel_encoding(self, value): """Pixel encoding. """ self.setenumstring("PixelEncoding", value) @Feat() def sensor_size(self): width = self.getint("SensorWidth") height = self.getint("SensorHeight") return width, height @Feat(None, values={100: '100 MHz', 200: '200 MHz', 280: '280 MHz'}) def clock_rate(self, value): """Pixel clock rate """ self.setenumstring("PixelReadoutRate", value) @Feat(None) def fan_peed(self, value = 1): """Fan speed. """ self.setenumerated("FanSpeed", value) @Feat() def sensor_temp(self): """Sensor temperature. """ return self.getfloat("SensorTemperature") @Feat() def exposure_time(self): """Get exposure time. """ return self.getfloat("ExposureTime") @exposure_time.setter def exposure_time(self, exposure): self.setfloat("ExposureTime", exposure) @Feat(None) def roi(self, width_height_top_left): """Set region of interest """ width, height, top, left = width_height_top_left self.setint("AOIWidth", width) self.setint("AOILeft", left) self.setint("AOIHeight", height) self.setint("AOITop", top) @Action() def take_image(self): """Image acquisition. """ self.queuebuffer(self.userbuffer, self.imagesizebytes) self.command("AcquisitionStart") self.waitbuffer(*RetStr(1)) self.command("AcquisitionStop") self.flush() image = np.fromstring(self.userbuffer, dtype=np.uint32, count=self.length) image.shape = (self.height, self.width) return image @Action() def take_image(self, numbuff, numframes): """Image acquisition with circular buffer. """ imagesizebytes = self.getint("ImageSizeBytes") userbuffer = [] for i in range(numbuff): userbuffer.append(ct.create_string_buffer(' ' * imagesizebytes)) self.queuebuffer(userbuffer, imagesizebytes) self.command("AcquisitionStart") for i in range(numbuff): self.waitbuffer(*RetStr(1)) self.queuebuffer(userbuffer[i], imagesizebytes) self.command("AcquisitionStop") self.flush() image = np.fromstring(userbuffer[0], dtype=np.uint32, count=self.length) image.shape = (self.height, self.width) return image
PypiClean
/Diofant-0.14.0a2.tar.gz/Diofant-0.14.0a2/diofant/printing/str.py
from __future__ import annotations import typing import mpmath.libmp as mlib from mpmath.libmp import prec_to_dps from ..core import Integer, Mul, Pow, Rational, S, oo from ..core.mul import _keep_coeff from ..sets import Reals from ..utilities import default_sort_key from .defaults import DefaultPrinting from .precedence import PRECEDENCE, precedence from .printer import Printer class StrPrinter(Printer): """Str printer.""" printmethod = '_diofantstr' _default_settings: dict[str, typing.Any] = { 'order': None, 'full_prec': 'auto', } _relationals: dict[str, str] = {} def parenthesize(self, item, level): if precedence(item) <= level: return '(%s)' % self._print(item) else: return self._print(item) def stringify(self, args, sep, level=0): return sep.join([self.parenthesize(item, level) for item in args]) def emptyPrinter(self, expr): if isinstance(expr, str): return expr elif hasattr(expr, '__str__') and not issubclass(expr.__class__, DefaultPrinting): return str(expr) else: return repr(expr) def _print_Add(self, expr, order=None): if self.order == 'none': terms = list(expr.args) else: terms = expr.as_ordered_terms(order=order or self.order) PREC = precedence(expr) l = [] for term in terms: t = self._print(term) if t.startswith('-'): sign = '-' t = t[1:] else: sign = '+' if precedence(term) < PREC: l.extend([sign, f'({t})']) else: l.extend([sign, t]) sign = l.pop(0) if sign == '+': sign = '' return sign + ' '.join(l) def _print_BooleanTrue(self, expr): return 'true' def _print_BooleanFalse(self, expr): return 'false' def _print_Not(self, expr): return '~%s' % self.parenthesize(expr.args[0], PRECEDENCE['Not']) def _print_And(self, expr): return self.stringify(expr.args, ' & ', PRECEDENCE['BitwiseAnd']) def _print_Or(self, expr): return self.stringify(expr.args, ' | ', PRECEDENCE['BitwiseOr']) def _print_Basic(self, expr): l = [self._print(o) for o in expr.args] return expr.__class__.__name__ + '(%s)' % ', '.join(l) def _print_BlockMatrix(self, B): return self._print(B.blocks) def _print_Catalan(self, expr): return 'Catalan' def _print_ComplexInfinity(self, expr): return 'zoo' def _print_Derivative(self, expr): return 'Derivative(%s)' % ', '.join(map(self._print, expr.args)) def _print_dict(self, d): keys = sorted(d, key=default_sort_key) items = [] for key in keys: item = f'{self._print(key)}: {self._print(d[key])}' items.append(item) return '{%s}' % ', '.join(items) def _print_Dict(self, expr): return self._print_dict(expr) def _print_RandomDomain(self, d): return 'Domain: ' + self._print(d.as_boolean()) def _print_Dummy(self, expr): return '_' + expr.name def _print_EulerGamma(self, expr): return 'EulerGamma' def _print_Exp1(self, expr): return 'E' def _print_ExprCondPair(self, expr): return f'({expr.expr}, {expr.cond})' def _print_FiniteSet(self, s): s = sorted(s, key=default_sort_key) if len(s) > 10: printset = s[:3] + ['...'] + s[-3:] else: printset = s return '{' + ', '.join(self._print(el) for el in printset) + '}' def _print_Function(self, expr): return expr.func.__name__ + '(%s)' % self.stringify(expr.args, ', ') def _print_GeometryEntity(self, expr): # GeometryEntity is special -- it's base is tuple return str(expr) def _print_GoldenRatio(self, expr): return 'GoldenRatio' def _print_ImaginaryUnit(self, expr): return 'I' def _print_Infinity(self, expr): return 'oo' def _print_Integral(self, expr): def _xab_tostr(xab): if len(xab) == 1: return self._print(xab[0]) else: return self._print((xab[0],) + tuple(xab[1:])) L = ', '.join([_xab_tostr(l) for l in expr.limits]) return f'Integral({self._print(expr.function)}, {L})' def _print_Interval(self, i): if i.left_open: left = '(' else: left = '[' if i.right_open: right = ')' else: right = ']' return f'{left}{self._print(i.start)}, {self._print(i.end)}{right}' def _print_Inverse(self, I): return '%s^-1' % self.parenthesize(I.arg, PRECEDENCE['Pow']) def _print_Lambda(self, obj): args, expr = obj.args if len(args) == 1: return f'Lambda({args.args[0]}, {expr})' else: arg_string = ', '.join(self._print(arg) for arg in args) return f'Lambda(({arg_string}), {expr})' def _print_LatticeOp(self, expr): args = sorted(expr.args, key=default_sort_key) return expr.func.__name__ + '(%s)' % ', '.join(self._print(arg) for arg in args) def _print_Limit(self, expr): e, z, z0, dir = expr.args if dir == -1: return f'Limit({e}, {z}, {z0})' elif dir == Reals: return f'Limit({e}, {z}, {z0}, dir=Reals)' else: return f'Limit({e}, {z}, {z0}, dir={dir})' def _print_list(self, expr): return '[%s]' % self.stringify(expr, ', ') def _print_MatrixBase(self, expr): return expr._format_str(self) def _print_MatrixElement(self, expr): return self._print(expr.parent) + f'[{expr.i}, {expr.j}]' def _print_MatrixSlice(self, expr): def strslice(x): x = list(x) if x[2] == 1: del x[2] if x[1] == x[0] + 1: del x[1] if x[0] == 0: x[0] = '' return ':'.join(map(self._print, x)) return (self._print(expr.parent) + '[' + strslice(expr.rowslice) + ', ' + strslice(expr.colslice) + ']') def _print_Mul(self, expr): prec = precedence(expr) c, e = expr.as_coeff_Mul() if c < 0: expr = _keep_coeff(-c, e) sign = '-' else: sign = '' a = [] # items in the numerator b = [] # items that are in the denominator (if any) if self.order != 'none': args = expr.as_ordered_factors() else: # use make_args in case expr was something like -x -> x args = Mul.make_args(expr) multiple_ones = len([x for x in args if x == 1]) > 1 # Gather args for numerator/denominator for item in args: if item.is_commutative and item.is_Pow and item.exp.is_Rational and item.exp.is_negative: if item.exp != -1: b.append(Pow(item.base, -item.exp, evaluate=False)) else: b.append(Pow(item.base, -item.exp)) elif item.is_Rational and item is not oo: if item.numerator != 1 or multiple_ones: a.append(Rational(item.numerator)) if item.denominator != 1: b.append(Rational(item.denominator)) else: a.append(item) a = a or [Integer(1)] a_str = [self.parenthesize(x, prec) for x in a] b_str = [self.parenthesize(x, prec) for x in b] if len(b) == 0: return sign + '*'.join(a_str) elif len(b) == 1: return sign + '*'.join(a_str) + '/' + b_str[0] else: return sign + '*'.join(a_str) + '/(%s)' % '*'.join(b_str) def _print_MatMul(self, expr): return '*'.join([self.parenthesize(arg, precedence(expr)) for arg in expr.args]) def _print_HadamardProduct(self, expr): return '.*'.join([self.parenthesize(arg, precedence(expr)) for arg in expr.args]) def _print_MatAdd(self, expr): return ' + '.join([self.parenthesize(arg, precedence(expr)) for arg in expr.args]) def _print_NaN(self, expr): return 'nan' def _print_NegativeInfinity(self, expr): return '-oo' def _print_Order(self, expr): if all(p == 0 for p in expr.point) or not expr.variables: if len(expr.variables) <= 1: return 'O(%s)' % self._print(expr.expr) else: return 'O(%s)' % self.stringify((expr.expr,) + expr.variables, ', ', 0) else: return 'O(%s)' % self.stringify(expr.args, ', ', 0) def _print_Cycle(self, expr): """We want it to print as Cycle in doctests for which a repr is required. With __repr__ defined in Cycle, interactive output gives Cycle form but during doctests, the dict's __repr__ form is used. Defining this _print function solves that problem. >>> Cycle(1, 2) # will print as a dict without this method Cycle(1, 2) """ return expr.__repr__() def _print_Permutation(self, expr): from ..combinatorics import Cycle, Permutation if Permutation.print_cyclic: if not expr.size: return 'Permutation()' # before taking Cycle notation, see if the last element is # a singleton and move it to the head of the string s = Cycle(expr)(expr.size - 1).__repr__()[len('Cycle'):] last = s.rfind('(') if not last == 0 and ',' not in s[last:]: s = s[last:] + s[:last] return f'Permutation{s}' else: s = expr.support() if not s: if expr.size < 5: return 'Permutation(%s)' % str(expr.array_form) return f'Permutation([], size={expr.size})' trim = str(expr.array_form[:s[-1] + 1]) + f', size={expr.size}' use = full = str(expr.array_form) if len(trim) < len(full): use = trim return f'Permutation({use})' def _print_TensorIndex(self, expr): return expr._print() def _print_TensorHead(self, expr): return expr._print() def _print_Tensor(self, expr): return expr._print() def _print_TensMul(self, expr): return expr._print() def _print_TensAdd(self, expr): return expr._print() def _print_PermutationGroup(self, expr): p = [' %s' % str(a) for a in expr.args] return 'PermutationGroup([\n%s])' % ',\n'.join(p) def _print_Pi(self, expr): return 'pi' def _print_PolyElement(self, poly): return poly._str(self, PRECEDENCE, '%s**%d', '*') def _print_FracElement(self, frac): if frac.denominator == 1: return self._print(frac.numerator) else: numer = self.parenthesize(frac.numerator, PRECEDENCE['Add']) denom = self.parenthesize(frac.denominator, PRECEDENCE['Atom']-1) return numer + '/' + denom def _print_Poly(self, expr): terms, gens = [], expr.gens for monom, coeff in expr.terms(): s_monom = [] for i, exp in enumerate(monom): if exp > 0: if exp == 1: s_monom.append(self._print(gens[i])) else: s_monom.append(self.parenthesize(gens[i], PRECEDENCE['Atom'] - 1) + f'**{exp:d}') s_monom = '*'.join(s_monom) if coeff.is_Add: if s_monom: s_coeff = '(' + self._print(coeff) + ')' else: s_coeff = self._print(coeff) else: if s_monom: if coeff == 1: terms.extend(['+', s_monom]) continue if coeff == -1: terms.extend(['-', s_monom]) continue s_coeff = self._print(coeff) if not s_monom: s_term = s_coeff else: s_term = s_coeff + '*' + s_monom if s_term.startswith('-'): terms.extend(['-', s_term[1:]]) else: terms.extend(['+', s_term]) if not terms: terms.extend(['+', '0']) modifier = terms.pop(0) if modifier == '-': terms[0] = '-' + terms[0] format = expr.__class__.__name__ + '(%s, %s' from ..polys.polyerrors import PolynomialError try: format += ', modulus=%s' % expr.get_modulus() except PolynomialError: format += f", domain='{expr.domain}'" format += ')' return format % (' '.join(terms), ', '.join(self._print(s) for s in expr.gens)) def _print_ProductSet(self, p): return ' x '.join(self._print(set) for set in p.sets) def _print_AlgebraicElement(self, expr): return self._print(expr.parent.to_expr(expr)) def _print_ModularInteger(self, expr): return f'{expr.rep}' def _print_GaloisFieldElement(self, expr): from ..domains import ZZ_python return 'GF(%s, %s)(%s)' % (expr.parent.characteristic, expr.mod.set_domain(ZZ_python).all_coeffs(), int(expr)) def _print_Pow(self, expr, rational=False): PREC = precedence(expr) if not expr.exp.is_Float and expr.exp == Rational(1, 2) and not rational: return 'sqrt(%s)' % self._print(expr.base) if expr.is_commutative and not expr.exp.is_Float: if -expr.exp == Rational(1, 2) and not rational: return '1/sqrt(%s)' % self._print(expr.base) if expr.exp == -1: return '1/%s' % self.parenthesize(expr.base, PREC) e = self.parenthesize(expr.exp, PREC) if (self.printmethod == '_diofantrepr' and expr.exp.is_Rational and not expr.exp.is_Integer): # The parenthesized exp should be '(Rational(a, b))' so strip # parens, but just check to be sure. return f'{self.parenthesize(expr.base, PREC)}**{e[1:-1]}' return f'{self.parenthesize(expr.base, PREC)}**{e}' def _print_Mod(self, expr): PREC = precedence(expr) a, b = expr.args return f'{self.parenthesize(a, PREC)}%{self.parenthesize(b, PREC)}' def _print_MatPow(self, expr): PREC = precedence(expr) return '%s**%s' % (self.parenthesize(expr.base, PREC), self.parenthesize(expr.exp, PREC)) def _print_ImmutableDenseNDimArray(self, expr): return str(expr) _print_ImmutableSparseNDimArray = _print_ImmutableDenseNDimArray _print_MutableDenseNDimArray = _print_ImmutableDenseNDimArray _print_MutableSparseNDimArray = _print_ImmutableDenseNDimArray def _print_Integer(self, expr): return str(expr.numerator) def _print_Rational(self, expr): if expr.denominator == 1: return str(expr.numerator) else: return f'{expr.numerator}/{expr.denominator}' def _print_Float(self, expr): prec = expr._prec if prec < 5: dps = 0 else: dps = prec_to_dps(expr._prec) if self._settings['full_prec'] is True: strip = False elif self._settings['full_prec'] is False: strip = True elif self._settings['full_prec'] == 'auto': strip = self._print_level > 1 else: raise NotImplementedError rv = mlib.to_str(expr._mpf_, dps, strip_zeros=strip) if rv.startswith('-.0'): rv = '-0.' + rv[3:] elif rv.startswith('.0'): rv = '0.' + rv[2:] elif rv.startswith('+'): rv = rv[1:] return rv def _print_Relational(self, expr): charmap = { '==': 'Eq', '!=': 'Ne', } if expr.rel_op in charmap: return f'{charmap[expr.rel_op]}({expr.lhs}, {expr.rhs})' return '%s %s %s' % (self.parenthesize(expr.lhs, precedence(expr)), self._relationals.get(expr.rel_op) or expr.rel_op, self.parenthesize(expr.rhs, precedence(expr))) def _print_RootOf(self, expr): p = self._print_Add(expr.expr, order='lex') if expr.free_symbols: return f'RootOf({p}, {expr.poly.gen}, {expr.index:d})' else: return f'RootOf({p}, {expr.index:d})' def _print_RootSum(self, expr): args = [self._print_Add(expr.expr, order='lex')] if expr.fun is not S.IdentityFunction: args.append(self._print(expr.fun)) return 'RootSum(%s)' % ', '.join(args) def _print_GroebnerBasis(self, basis): cls = basis.__class__.__name__ exprs = [self._print_Add(arg, order=basis.order) for arg in basis.exprs] exprs = '[%s]' % ', '.join(exprs) gens = [self._print(gen) for gen in basis.gens] domain = "domain='%s'" % self._print(basis.domain) order = "order='%s'" % self._print(basis.order) args = [exprs] + gens + [domain, order] return '%s(%s)' % (cls, ', '.join(args)) def _print_frozenset(self, s): items = sorted(s, key=default_sort_key) args = ', '.join(self._print(item) for item in items) if args: args = '{%s}' % args return f'{type(s).__name__}({args})' def _print_set(self, expr): if expr == set(): return 'set()' return '{%s}' % self.stringify(sorted(expr, key=default_sort_key), ', ') def _print_Sum(self, expr): def _xab_tostr(xab): return self._print((xab[0],) + tuple(xab[1:])) L = ', '.join([_xab_tostr(l) for l in expr.limits]) return f'Sum({self._print(expr.function)}, {L})' def _print_Symbol(self, expr): return expr.name _print_BaseSymbol = _print_Symbol _print_MatrixSymbol = _print_Symbol _print_RandomSymbol = _print_Symbol def _print_Identity(self, expr): return 'I' def _print_ZeroMatrix(self, expr): return '0' def _print_str(self, expr): return expr def _print_tuple(self, expr): if len(expr) == 1: return '(%s,)' % self._print(expr[0]) else: return '(%s)' % self.stringify(expr, ', ') def _print_Tuple(self, expr): return self._print_tuple(expr) def _print_Monomial(self, expr): if expr.gens: return '*'.join(['%s**%s' % (gen, exp) for gen, exp in zip(expr.gens, expr)]) else: return self._print_tuple(expr) def _print_Transpose(self, T): return '%s.T' % self.parenthesize(T.arg, PRECEDENCE['Pow']) def _print_Union(self, expr): return ' U '.join(self._print(set) for set in expr.args) def _print_Complement(self, expr): return r' \ '.join(self._print(set) for set in expr.args) def _print_Wild(self, expr): return expr.name + '_' def _print_WildFunction(self, expr): return expr.name + '_' def _print_Zero(self, expr): return '0' def _print_BaseScalarField(self, field): return field._coord_sys._names[field._index] def _print_BaseVectorField(self, field): return f'e_{field._coord_sys._names[field._index]}' def _print_Differential(self, diff): field = diff._form_field if hasattr(field, '_coord_sys'): return f'd{field._coord_sys._names[field._index]}' else: return 'd(%s)' % self._print(field) def _print_Tr(self, expr): # TODO : Handle indices return '%s(%s)' % ('Tr', self._print(expr.args[0])) def _print_Domain(self, expr): return expr.rep def sstr(expr, **settings): """Returns the expression as a string. For large expressions where speed is a concern, use the setting order='none'. Examples ======== >>> sstr(Eq(a + b, 0)) 'Eq(a + b, 0)' """ p = StrPrinter(settings) s = p.doprint(expr) return s class StrReprPrinter(StrPrinter): """(internal) -- see sstrrepr""" def _print_str(self, expr): return repr(expr) def sstrrepr(expr, **settings): """Return expr in mixed str/repr form. i.e. strings are returned in repr form with quotes, and everything else is returned in str form. This function could be useful for hooking into sys.displayhook """ p = StrReprPrinter(settings) s = p.doprint(expr) return s
PypiClean
/DigitalRover-0.0.1.tar.gz/DigitalRover-0.0.1/src/experimental/wayback/wayback.py
# https://opensourceseo.org/find-list-old-urls-domain-using-wayback-cdx-api/ # https://web.archive.org/web/20090420095939/https://twitter.com/realDonaldTrump # https://web.archive.org/cdx/search/cdx?url=twitter.com/realDonaldTrump # https://archive.org/web/researcher/cdx_file_format.php # https://support.archive-it.org/hc/en-us/articles/115001790023-Access-Archive-It-s-Wayback-index-with-the-CDX-C-API # Format Of Files # --------------- # Canonized URL # Date # Original URL # Mime Type of Original Document # Response Code # Old Style Checksum # Length # Example Command # curl "https://web.archive.org/cdx/search/cdx?url=twitter.com/realDonaldTrump" > realDonaldTrump.url # Generate Commands # dolt sql -q "select concat('curl \"https://web.archive.org/cdx/search/cdx?url=twitter.com/', twitter_handle, '\" > ', twitter_handle, '.url') as commands from total_tweets;" -r csv > urls.csv # 20090420095939 # For Unmodified Pages - https://web.archive.org/web/20090420095939id_/http://twitter.com:80/realDonaldTrump # May Want Modified Pages For Media # For Tweet 1346928882595885058 # https://web.archive.org/web/20210106212653/https://video.twimg.com/ext_tw_video/1346928794456776705/pu/vid/1280x720/xJsJiUTRa-ggqL1D.mp4 import os from typing import Optional import pandas as pd import requests list_folder: str = "working/archive-me" temp_files: list = os.listdir(list_folder) files: list = [] # Remove Non-URL Files for file in temp_files: if ".url" in file: files.append(file) if not os.path.exists('working/wayback'): os.makedirs('working/wayback') for file in files: download_folder_stripped: str = str(file).rstrip(".url") download_folder: str = os.path.join('working/wayback', download_folder_stripped) if not os.path.exists(download_folder): print(f"Creating: {download_folder}") os.makedirs(download_folder) print(f"Downloading Archives For {download_folder_stripped}") contents: pd.DataFrame = pd.read_csv(filepath_or_buffer=os.path.join(list_folder, file), header=None, delimiter=" ", usecols=[0, 1, 2, 3, 4, 5, 6], names=["canonized_url", "date", "original_url", "mime_type", "response_code", "old_checksum", "length"]) # https://web.archive.org/web/20090420095939id_/http://twitter.com:80/realDonaldTrump contents["raw_url"] = "https://web.archive.org/web/" + contents["date"].astype(str) + "id_/" + contents["original_url"].astype(str) contents["archive_url"] = "https://web.archive.org/web/" + contents["date"].astype(str) + "/" + contents["original_url"].astype(str) print(contents) contents.to_csv(path_or_buf=os.path.join(list_folder, download_folder_stripped + ".csv")) contents.drop_duplicates(inplace=True, subset=["old_checksum"]) # Headers headers: dict = { 'User-Agent': 'Chrome/90', # python-requests/2.25.1 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive' } total: int = len(contents.index) count: int = 1 for row in contents.itertuples(): # TODO: Means To Skip Already Downloaded Files (Doesn't Handle Multiple Different Files On Same Date) # if os.path.exists(os.path.join(download_folder, str(row.date) + "-archive.html")): # print(f"Page {count}/{total} - Skipping {row.date} From {download_folder_stripped}") # count += 1 # continue try: if not os.path.exists(os.path.join(download_folder, str(row.date) + "-raw.html")): # https://twitter.com/AlexisEvelyn42/status/1350405163048169475 r = requests.get(row.raw_url, allow_redirects=True, headers=headers) r_page = open(mode="w", file=os.path.join(download_folder, str(row.date) + "-raw.html")) r_page.writelines(r.text) r_page.close() print(f"Raw Page {count}/{total} - Saved {row.date} From {download_folder_stripped}") else: print(f"Raw Page {count}/{total} - Skipping {row.date} From {download_folder_stripped}") except: print(f"Failed To Download Raw Page!!! Logging!!! Page: {download_folder_stripped}/{row.date}") failed_log = open(mode="a", file='working/wayback/failed-download.txt') failed_log.writelines(f"Raw - {download_folder_stripped}/{row.date}\n") failed_log.close() # exit(1) try: if not os.path.exists(os.path.join(download_folder, str(row.date) + "-archive.html")): a = requests.get(row.archive_url, allow_redirects=True, headers=headers) a_page = open(mode="w", file=os.path.join(download_folder, str(row.date) + "-archive.html")) a_page.writelines(a.text) a_page.close() print(f"Archive Page {count}/{total} - Saved {row.date} From {download_folder_stripped}") else: print(f"Archive Page {count}/{total} - Skipping {row.date} From {download_folder_stripped}") except: print(f"Failed Connection!!! Page: {download_folder_stripped}/{row.date}") failed_log = open(mode="a", file='working/wayback/failed-download.txt') failed_log.writelines(f"Archive - {download_folder_stripped}/{row.date}\n") failed_log.close() # exit(1) # print(f"Page {count}/{total} - Saved {row.date} From {download_folder_stripped}") count += 1
PypiClean
/observations-0.1.4.tar.gz/observations-0.1.4/observations/yelp17.py
from __future__ import absolute_import from __future__ import division from __future__ import print_function import json import numpy as np import os def yelp17(path, categories=None): """Load Yelp reviews from the Yelp Dataset Challenge in 2017. It contains ~4.1 million reviews, ~1 million users, and ~144,000 businesses from cities in the UK, Germany, Canada, and the US. We only load the review's text and its rating. Args: path: str. Path to directory which stores file. Filename is `yelp_dataset_challenge_round9/`. categories: str or list of str, optional. Business categories to include reviews from. It is case-sensitive, e.g., "Restaurants". Default is to include all categories. Returns: Tuple of list x_train and np.ndarray y_train. Each pair of elements corresponds to the review text and its rating. """ if isinstance(categories, str): categories = [categories] path = os.path.expanduser(path) path = os.path.join(path, 'yelp_dataset_challenge_round9') if not os.path.exists(path): url = 'https://www.yelp.com/dataset_challenge' raise IOError("Files not found. Downloading requires explicit permission. " "See {}".format(e, url)) if categories is not None: business = {} with open(os.path.join(path, 'yelp_academic_dataset_business.json')) as f: for line in f: data = json.loads(line) business[data['business_id']] = data['categories'] x_train = [] y_train = [] with open(os.path.join(path, 'yelp_academic_dataset_review.json')) as f: for line in f: data = json.loads(line) if categories is None: x_train.append(data['text']) y_train.append(data['stars']) else: business_categories = business.get(data['business_id']) if business_categories and \ any(cat in categories for cat in business_categories): x_train.append(data['text']) y_train.append(data['stars']) y_train = np.array(y_train, dtype=np.int) return x_train, y_train
PypiClean
/MagicBus-4.1.2.tar.gz/MagicBus-4.1.2/magicbus/plugins/signalhandler.py
import os import signal as _signal import sys from magicbus.compat import basestring class SignalHandler(object): """Register bus channels (and listeners) for system signals. You can modify what signals your application listens for, and what it does when it receives signals, by modifying :attr:`SignalHandler.handlers`, a dict of {signal name: callback} pairs. The default set is:: handlers = {'SIGTERM': self.bus.transition("EXITED"), 'SIGHUP': self.handle_SIGHUP, 'SIGUSR1': self.bus.transition("IDLE"); self.bus.transition("RUN"), } The :func:`SignalHandler.handle_SIGHUP`` method calls execv if the process is daemonized, but exits if the process is attached to a TTY. This is because Unix window managers tend to send SIGHUP to terminal windows when the user closes them. Feel free to add signals which are not available on every platform. The :class:`SignalHandler` will ignore errors raised from attempting to register handlers for unknown signals. """ handlers = {} """A map from signal names (e.g. 'SIGTERM') to handlers.""" signals = {} """A map from signal numbers to names.""" for k, v in vars(_signal).items(): if k.startswith('SIG') and not k.startswith('SIG_'): signals[v] = k del k, v def __init__(self, bus): self.bus = bus # Set default handlers self.handlers = {'SIGTERM': self.handle_SIGTERM, 'SIGHUP': self.handle_SIGHUP, 'SIGUSR1': self.bus.graceful, } if sys.platform[:4] == 'java': del self.handlers['SIGUSR1'] self.handlers['SIGUSR2'] = self.bus.graceful self.bus.log('SIGUSR1 cannot be set on the JVM platform. ' 'Using SIGUSR2 instead.') self.handlers['SIGINT'] = self._jython_SIGINT_handler self._previous_handlers = {} def _jython_SIGINT_handler(self, signum=None, frame=None): # See http://bugs.jython.org/issue1313 self.bus.log('Keyboard Interrupt: shutting down bus') self.bus.transition('EXITED') def subscribe(self): self.bus.subscribe('ENTER', self.subscribe_handlers) def subscribe_handlers(self): """Subscribe self.handlers to signals.""" for sig, func in self.handlers.items(): try: self.set_handler(sig, func) except ValueError: pass # Only run after Daemonizer.ENTER (65) subscribe_handlers.priority = 70 def unsubscribe(self): """Unsubscribe self.handlers from signals.""" for signum, handler in self._previous_handlers.items(): signame = self.signals[signum] if handler is None: self.bus.log('Restoring %s handler to SIG_DFL.' % signame) handler = _signal.SIG_DFL else: self.bus.log('Restoring %s handler %r.' % (signame, handler)) try: our_handler = _signal.signal(signum, handler) if our_handler is None: self.bus.log('Restored old %s handler %r, but our ' 'handler was not registered.' % (signame, handler), level=30) except ValueError: self.bus.log('Unable to restore %s handler %r.' % (signame, handler), level=40, traceback=True) def set_handler(self, signal, listener=None): """Subscribe a handler for the given signal (number or name). If the optional 'listener' argument is provided, it will be subscribed as a listener for the given signal's channel. If the given signal name or number is not available on the current platform, ValueError is raised. """ if isinstance(signal, basestring): signum = getattr(_signal, signal, None) if signum is None: raise ValueError('No such signal: %r' % signal) signame = signal else: try: signame = self.signals[signal] except KeyError: raise ValueError('No such signal: %r' % signal) signum = signal prev = _signal.signal(signum, self._handle_signal) self._previous_handlers[signum] = prev if listener is not None: self.bus.log('Listening for %s.' % signame) self.bus.subscribe(signame, listener) def _handle_signal(self, signum=None, frame=None): """Python signal handler (self.set_handler subscribes it for you).""" signame = self.signals[signum] self.bus.log('Caught signal %s.' % signame) self.bus.publish(signame) def handle_SIGTERM(self): """Transition to the EXITED state.""" self.bus.log('SIGTERM caught. Exiting.') self.bus.transition('EXITED') def handle_SIGHUP(self): """Restart if daemonized, else exit.""" if os.isatty(sys.stdin.fileno()): # not daemonized (may be foreground or background) self.bus.log('SIGHUP caught but not daemonized. Exiting.') self.bus.transition('EXITED') else: self.bus.log('SIGHUP caught while daemonized. Restarting.') self.bus.restart()
PypiClean
/Files.com-1.0.1051-py3-none-any.whl/files_sdk/models/api_key.py
import builtins import datetime from files_sdk.api import Api from files_sdk.list_obj import ListObj from files_sdk.exceptions import InvalidParameterError, MissingParameterError, NotImplementedError class ApiKey: default_attributes = { 'id': None, # int64 - API Key ID 'descriptive_label': None, # string - Unique label that describes this API key. Useful for external systems where you may have API keys from multiple accounts and want a human-readable label for each key. 'description': None, # string - User-supplied description of API key. 'created_at': None, # date-time - Time which API Key was created 'expires_at': None, # date-time - API Key expiration date 'key': None, # string - API Key actual key string 'last_use_at': None, # date-time - API Key last used - note this value is only updated once per 3 hour period, so the 'actual' time of last use may be up to 3 hours later than this timestamp. 'name': None, # string - Internal name for the API Key. For your use. 'path': None, # string - Folder path restriction for this api key. This must be slash-delimited, but it must neither start nor end with a slash. Maximum of 5000 characters. 'permission_set': None, # string - Permissions for this API Key. Keys with the `desktop_app` permission set only have the ability to do the functions provided in our Desktop App (File and Share Link operations). Additional permission sets may become available in the future, such as for a Site Admin to give a key with no administrator privileges. If you have ideas for permission sets, please let us know. 'platform': None, # string - If this API key represents a Desktop app, what platform was it created on? 'url': None, # string - URL for API host. 'user_id': None, # int64 - User ID for the owner of this API Key. May be blank for Site-wide API Keys. } def __init__(self, attributes=None, options=None): if not isinstance(attributes, dict): attributes = {} if not isinstance(options, dict): options = {} self.set_attributes(attributes) self.options = options def set_attributes(self, attributes): for (attribute, default_value) in ApiKey.default_attributes.items(): setattr(self, attribute, attributes.get(attribute, default_value)) def get_attributes(self): return {k: getattr(self, k, None) for k in ApiKey.default_attributes if getattr(self, k, None) is not None} # Parameters: # name - string - Internal name for the API Key. For your use. # description - string - User-supplied description of API key. # expires_at - string - API Key expiration date # permission_set - string - Permissions for this API Key. Keys with the `desktop_app` permission set only have the ability to do the functions provided in our Desktop App (File and Share Link operations). Additional permission sets may become available in the future, such as for a Site Admin to give a key with no administrator privileges. If you have ideas for permission sets, please let us know. def update(self, params = None): if not isinstance(params, dict): params = {} if hasattr(self, "id") and self.id: params['id'] = self.id else: raise MissingParameterError("Current object doesn't have a id") if "id" not in params: raise MissingParameterError("Parameter missing: id") if "id" in params and not isinstance(params["id"], int): raise InvalidParameterError("Bad parameter: id must be an int") if "name" in params and not isinstance(params["name"], str): raise InvalidParameterError("Bad parameter: name must be an str") if "description" in params and not isinstance(params["description"], str): raise InvalidParameterError("Bad parameter: description must be an str") if "expires_at" in params and not isinstance(params["expires_at"], str): raise InvalidParameterError("Bad parameter: expires_at must be an str") if "permission_set" in params and not isinstance(params["permission_set"], str): raise InvalidParameterError("Bad parameter: permission_set must be an str") response, _options = Api.send_request("PATCH", "/api_keys/{id}".format(id=params['id']), params, self.options) return response.data def delete(self, params = None): if not isinstance(params, dict): params = {} if hasattr(self, "id") and self.id: params['id'] = self.id else: raise MissingParameterError("Current object doesn't have a id") if "id" not in params: raise MissingParameterError("Parameter missing: id") if "id" in params and not isinstance(params["id"], int): raise InvalidParameterError("Bad parameter: id must be an int") response, _options = Api.send_request("DELETE", "/api_keys/{id}".format(id=params['id']), params, self.options) return response.data def destroy(self, params = None): self.delete(params) def save(self): if hasattr(self, "id") and self.id: self.update(self.get_attributes()) else: new_obj = create(self.get_attributes(), self.options) self.set_attributes(new_obj.get_attributes()) # Parameters: # user_id - int64 - User ID. Provide a value of `0` to operate the current session's user. # cursor - string - Used for pagination. When a list request has more records available, cursors are provided in the response headers `X-Files-Cursor-Next` and `X-Files-Cursor-Prev`. Send one of those cursor value here to resume an existing list from the next available record. Note: many of our SDKs have iterator methods that will automatically handle cursor-based pagination. # per_page - int64 - Number of records to show per page. (Max: 10,000, 1,000 or less is recommended). # sort_by - object - If set, sort records by the specified field in either `asc` or `desc` direction (e.g. `sort_by[expires_at]=desc`). Valid fields are `expires_at`. # filter - object - If set, return records where the specified field is equal to the supplied value. Valid fields are `expires_at`. # filter_gt - object - If set, return records where the specified field is greater than the supplied value. Valid fields are `expires_at`. # filter_gteq - object - If set, return records where the specified field is greater than or equal the supplied value. Valid fields are `expires_at`. # filter_lt - object - If set, return records where the specified field is less than the supplied value. Valid fields are `expires_at`. # filter_lteq - object - If set, return records where the specified field is less than or equal the supplied value. Valid fields are `expires_at`. def list(params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} if "user_id" in params and not isinstance(params["user_id"], int): raise InvalidParameterError("Bad parameter: user_id must be an int") if "cursor" in params and not isinstance(params["cursor"], str): raise InvalidParameterError("Bad parameter: cursor must be an str") if "per_page" in params and not isinstance(params["per_page"], int): raise InvalidParameterError("Bad parameter: per_page must be an int") if "sort_by" in params and not isinstance(params["sort_by"], dict): raise InvalidParameterError("Bad parameter: sort_by must be an dict") if "filter" in params and not isinstance(params["filter"], dict): raise InvalidParameterError("Bad parameter: filter must be an dict") if "filter_gt" in params and not isinstance(params["filter_gt"], dict): raise InvalidParameterError("Bad parameter: filter_gt must be an dict") if "filter_gteq" in params and not isinstance(params["filter_gteq"], dict): raise InvalidParameterError("Bad parameter: filter_gteq must be an dict") if "filter_lt" in params and not isinstance(params["filter_lt"], dict): raise InvalidParameterError("Bad parameter: filter_lt must be an dict") if "filter_lteq" in params and not isinstance(params["filter_lteq"], dict): raise InvalidParameterError("Bad parameter: filter_lteq must be an dict") return ListObj(ApiKey,"GET", "/api_keys", params, options) def all(params = None, options = None): list(params, options) def find_current(params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} response, options = Api.send_request("GET", "/api_key", params, options) return ApiKey(response.data, options) # Parameters: # id (required) - int64 - Api Key ID. def find(id, params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} params["id"] = id if "id" in params and not isinstance(params["id"], int): raise InvalidParameterError("Bad parameter: id must be an int") if "id" not in params: raise MissingParameterError("Parameter missing: id") response, options = Api.send_request("GET", "/api_keys/{id}".format(id=params['id']), params, options) return ApiKey(response.data, options) def get(id, params = None, options = None): find(id, params, options) # Parameters: # user_id - int64 - User ID. Provide a value of `0` to operate the current session's user. # name - string - Internal name for the API Key. For your use. # description - string - User-supplied description of API key. # expires_at - string - API Key expiration date # permission_set - string - Permissions for this API Key. Keys with the `desktop_app` permission set only have the ability to do the functions provided in our Desktop App (File and Share Link operations). Additional permission sets may become available in the future, such as for a Site Admin to give a key with no administrator privileges. If you have ideas for permission sets, please let us know. # path - string - Folder path restriction for this api key. def create(params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} if "user_id" in params and not isinstance(params["user_id"], int): raise InvalidParameterError("Bad parameter: user_id must be an int") if "name" in params and not isinstance(params["name"], str): raise InvalidParameterError("Bad parameter: name must be an str") if "description" in params and not isinstance(params["description"], str): raise InvalidParameterError("Bad parameter: description must be an str") if "expires_at" in params and not isinstance(params["expires_at"], str): raise InvalidParameterError("Bad parameter: expires_at must be an str") if "permission_set" in params and not isinstance(params["permission_set"], str): raise InvalidParameterError("Bad parameter: permission_set must be an str") if "path" in params and not isinstance(params["path"], str): raise InvalidParameterError("Bad parameter: path must be an str") response, options = Api.send_request("POST", "/api_keys", params, options) return ApiKey(response.data, options) # Parameters: # expires_at - string - API Key expiration date # name - string - Internal name for the API Key. For your use. # permission_set - string - Permissions for this API Key. Keys with the `desktop_app` permission set only have the ability to do the functions provided in our Desktop App (File and Share Link operations). Additional permission sets may become available in the future, such as for a Site Admin to give a key with no administrator privileges. If you have ideas for permission sets, please let us know. def update_current(params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} if "expires_at" in params and not isinstance(params["expires_at"], str): raise InvalidParameterError("Bad parameter: expires_at must be an str") if "name" in params and not isinstance(params["name"], str): raise InvalidParameterError("Bad parameter: name must be an str") if "permission_set" in params and not isinstance(params["permission_set"], str): raise InvalidParameterError("Bad parameter: permission_set must be an str") response, options = Api.send_request("PATCH", "/api_key", params, options) return ApiKey(response.data, options) # Parameters: # name - string - Internal name for the API Key. For your use. # description - string - User-supplied description of API key. # expires_at - string - API Key expiration date # permission_set - string - Permissions for this API Key. Keys with the `desktop_app` permission set only have the ability to do the functions provided in our Desktop App (File and Share Link operations). Additional permission sets may become available in the future, such as for a Site Admin to give a key with no administrator privileges. If you have ideas for permission sets, please let us know. def update(id, params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} params["id"] = id if "id" in params and not isinstance(params["id"], int): raise InvalidParameterError("Bad parameter: id must be an int") if "name" in params and not isinstance(params["name"], str): raise InvalidParameterError("Bad parameter: name must be an str") if "description" in params and not isinstance(params["description"], str): raise InvalidParameterError("Bad parameter: description must be an str") if "expires_at" in params and not isinstance(params["expires_at"], str): raise InvalidParameterError("Bad parameter: expires_at must be an str") if "permission_set" in params and not isinstance(params["permission_set"], str): raise InvalidParameterError("Bad parameter: permission_set must be an str") if "id" not in params: raise MissingParameterError("Parameter missing: id") response, options = Api.send_request("PATCH", "/api_keys/{id}".format(id=params['id']), params, options) return ApiKey(response.data, options) def delete_current(params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} response, _options = Api.send_request("DELETE", "/api_key", params, options) return response.data def delete(id, params = None, options = None): if not isinstance(params, dict): params = {} if not isinstance(options, dict): options = {} params["id"] = id if "id" in params and not isinstance(params["id"], int): raise InvalidParameterError("Bad parameter: id must be an int") if "id" not in params: raise MissingParameterError("Parameter missing: id") response, _options = Api.send_request("DELETE", "/api_keys/{id}".format(id=params['id']), params, options) return response.data def destroy(id, params = None, options = None): delete(id, params, options) def new(*args, **kwargs): return ApiKey(*args, **kwargs)
PypiClean
/Mopidy_Advanced_Scrobbler-2.1.0-py3-none-any.whl/mopidy_advanced_scrobbler/_commands/db/sync_corrections.py
from __future__ import annotations import enum from typing import TYPE_CHECKING, Tuple from urllib.parse import urlparse import questionary from prompt_toolkit.completion import FuzzyWordCompleter from rich.table import Table, box from mopidy_advanced_scrobbler._commands import AbortCommand, Counter from mopidy_advanced_scrobbler._commands.db import ( attach_external_db, connect_internal_db, verify_external_db, ) from mopidy_advanced_scrobbler._commands.output import stderr, stdout if TYPE_CHECKING: from argparse import Namespace from mopidy_advanced_scrobbler.db import Connection load_both_differ_query = """ SELECT main.corrections.track_uri, main.corrections.title as main_title, main.corrections.artist as main_artist, main.corrections.album as main_album, ext.corrections.title as ext_title, ext.corrections.artist as ext_artist, ext.corrections.album as ext_album FROM main.corrections INNER JOIN ext.corrections ON ext.corrections.track_uri = main.corrections.track_uri WHERE main_title != ext_title OR main_artist != ext_artist OR main_album != ext_album """ update_correction_query = """ UPDATE {0}.corrections SET title = ?, artist = ?, album = ? WHERE track_uri = ? """ load_only_in_main_query = """ SELECT main.corrections.track_uri, main.corrections.title, main.corrections.artist, main.corrections.album FROM main.corrections LEFT JOIN ext.corrections ON ext.corrections.track_uri = main.corrections.track_uri WHERE ext.corrections.track_uri IS NULL """ load_only_in_ext_query = """ SELECT ext.corrections.track_uri, ext.corrections.title, ext.corrections.artist, ext.corrections.album FROM ext.corrections LEFT JOIN main.corrections ON main.corrections.track_uri = ext.corrections.track_uri WHERE main.corrections.track_uri IS NULL """ class DataMismatchChoiceEnum(enum.Enum): CHOOSE_INTERNAL = enum.auto() CHOOSE_EXTERNAL = enum.auto() MANUAL_EDIT = enum.auto() SKIP_TRACK = enum.auto() class DataMismatchCounterEnum(enum.Enum): UPDATE = enum.auto() SKIP = enum.auto() choice_choose_internal = questionary.Choice( title="Use Internal Values", value=DataMismatchChoiceEnum.CHOOSE_INTERNAL, ) choice_choose_external = questionary.Choice( title="Use External Values", value=DataMismatchChoiceEnum.CHOOSE_EXTERNAL, ) choice_manual_edit = questionary.Choice( title="Manually Edit Values", value=DataMismatchChoiceEnum.MANUAL_EDIT, ) choice_skip = questionary.Choice( title="Skip Track", value=DataMismatchChoiceEnum.SKIP_TRACK, ) def make_differ_table(result) -> Table: table = Table(title=result["track_uri"], show_footer=False, box=box.HEAVY_HEAD, show_lines=True) table.add_column(header="", style="bold") table.add_column(header="Internal") table.add_column(header="External") table.add_row("Title", result["main_title"], result["ext_title"]) table.add_row("Artist", result["main_artist"], result["ext_artist"]) table.add_row("Album", result["main_album"], result["ext_album"]) return table def run(args: Namespace, config): verify_external_db(args.external_db, config) db = connect_internal_db(config) attach_external_db(db, args.external_db) differ_counter: Counter[DataMismatchCounterEnum] = Counter() try: sync_both_differ(db, differ_counter, include_filesystem_uris=args.include_filesystem_uris) finally: updated_count = differ_counter.get(DataMismatchCounterEnum.UPDATE) if updated_count > 0: stdout.print(f"Updated {updated_count} entries!", style="success") else: stdout.print("No entries were updated.", style="notice") skipped_count = differ_counter.get(DataMismatchCounterEnum.SKIP) if skipped_count > 0: stdout.print(f"Skipped {skipped_count} entries.", style="notice") sync_only_in_main(db, include_filesystem_uris=args.include_filesystem_uris) sync_only_in_ext(db, include_filesystem_uris=args.include_filesystem_uris) stdout.print("Success!", style="success") return 0 def sync_both_differ( db: Connection, counter: Counter[DataMismatchCounterEnum], *, include_filesystem_uris: bool = False, ): stdout.print( "Synchronising differences between existing entries in both databases.", style="notice" ) results = db.execute(load_both_differ_query) for result in results: track_uri = result["track_uri"] parsed_track_uri = urlparse(track_uri) if not parsed_track_uri.scheme: stderr.print( f"Invalid track URI found in internal corrections database: {track_uri}", style="warning", ) continue elif parsed_track_uri.scheme in ("file", "local"): if not include_filesystem_uris: continue table = make_differ_table(result) stdout.print(table) response = questionary.select( message="", choices=(choice_choose_internal, choice_choose_external, choice_manual_edit), ).ask() if response is None: raise AbortCommand if response == DataMismatchChoiceEnum.CHOOSE_INTERNAL: update_ext_from_main(db, result) elif response == DataMismatchChoiceEnum.CHOOSE_EXTERNAL: update_main_from_ext(db, result) elif response == DataMismatchChoiceEnum.MANUAL_EDIT: while True: title, artist, album = edit_values(result) if questionary.confirm("Empty album correct?", auto_enter=False).ask(): break update_both(db, track_uri, title, artist, album) elif response == DataMismatchChoiceEnum.SKIP_TRACK: counter.incr(DataMismatchCounterEnum.SKIP) continue else: stderr.print("Unrecognised option.", style="error") raise AbortCommand counter.incr(DataMismatchCounterEnum.UPDATE) def update_ext_from_main(db: Connection, result): db.execute( update_correction_query.format("ext"), (result["main_title"], result["main_artist"], result["main_album"], result["track_uri"]), ) def update_main_from_ext(db: Connection, result): db.execute( update_correction_query.format("main"), (result["ext_title"], result["ext_artist"], result["ext_album"], result["track_uri"]), ) def update_both(db: Connection, track_uri: str, title: str, artist: str, album: str): with db: db.execute("BEGIN") db.execute( update_correction_query.format("main"), (title, artist, album, track_uri), ) db.execute( update_correction_query.format("ext"), (title, artist, album, track_uri), ) def edit_values(result) -> Tuple[str, str, str]: title = "" while title == "": if result["main_title"] == result["ext_title"]: default = result["main_title"] else: default = "" title = questionary.text( "Title:", default=default, completer=FuzzyWordCompleter([result["main_title"], result["ext_title"]]), ).ask() if title is None: raise AbortCommand title = title.strip() artist = "" while artist == "": if result["main_artist"] == result["ext_artist"]: default = result["main_artist"] else: default = "" artist = questionary.text( "Artist:", default=default, completer=FuzzyWordCompleter([result["main_artist"], result["ext_artist"]]), ).ask() if artist is None: raise AbortCommand artist = artist.strip() while True: if result["main_album"] == result["ext_album"]: default = result["main_album"] else: default = "" album = questionary.text( "Album:", default=default, completer=FuzzyWordCompleter([result["main_album"], result["ext_album"]]), ).ask() if album is None: raise AbortCommand album = album.strip() if album != "": break if questionary.confirm("Are you sure?", auto_enter=False).ask(): break return title, artist, album def sync_only_in_main(db: Connection, *, include_filesystem_uris: bool = False) -> int: stdout.print("Copying entries only in internal database to external database.", style="notice") insert_query = "INSERT INTO ext.corrections (track_uri, title, artist, album)" query = f"{insert_query} {load_only_in_main_query}" if not include_filesystem_uris: query += ( " AND main.corrections.track_uri NOT LIKE 'file:%'" " AND main.corrections.track_uri NOT LIKE 'local:%'" ) cursor = db.execute(query) entry_count = cursor.rowcount if entry_count > 0: stdout.print(f"Copied {entry_count} entries!", style="success") else: stdout.print("No entries were copied.", style="notice") return entry_count def sync_only_in_ext(db: Connection, *, include_filesystem_uris: bool = False) -> int: stdout.print("Copying entries only in external database to internal database.", style="notice") insert_query = "INSERT INTO main.corrections (track_uri, title, artist, album)" query = f"{insert_query} {load_only_in_ext_query}" if not include_filesystem_uris: query += ( " AND ext.corrections.track_uri NOT LIKE 'file:%'" " AND ext.corrections.track_uri NOT LIKE 'local:%'" ) cursor = db.execute(query) entry_count = cursor.rowcount if entry_count > 0: stdout.print(f"Copied {entry_count} entries!", style="success") else: stdout.print("No entries were copied.", style="notice") return entry_count __all__ = ("run",)
PypiClean
/DynaMIT-1.1.5.tar.gz/DynaMIT-1.1.5/dynamit/rnaForesterSearcher.py
from __future__ import print_function from __future__ import division from builtins import str import os, math, re import subprocess from subprocess import CalledProcessError import dynamit.motifSearcher import dynamit.utils class RNAforesterSearcher(dynamit.motifSearcher.MotifSearcher): """Class implementing a RNAforester RNA secondary structure motif search component, running this tool on the provided input sequences and providing its processed motifs and instances as results. """ def __init__(self): """Initialize all class attributes with their default values. """ super(self.__class__, self).__init__() self.searcherName = "RNAforester" self.path = "" self.params = "" self.structureFilename = "" def setConfiguration(self, path, params): """Loads the searcher parameters specified in the configuration file. Args: path: path of the RNAforester executable file. params: parameters to be passed to RNAforester along with the sequences filename. Returns: Returns 0 if everything went fine, 1 and an error message otherwise. """ self.path = path self.params = params # if params contain a semi-colon, then the first part is the # actual parameters, the second one is a filename containing # secondary structure predictions (RNAfold format) to be used # instead of letting RNAforester predict them. if self.params.find(";") >= 0: inf = self.params.split(";") self.params = inf[0] self.structureFilename = inf[1] return 0 def runSearch(self, sequencesFilename): """Performs motif search by executing the RNAforester secondary structure motif search tool and processing its results to provide motifs and related instances. Args: sequencesFilename: input sequences filename for this run. Returns: Returns a list of strings representing identified motif matches if everything went fine (details on results filenames, etc., are printed to the console); returns 1 and an error message otherwise. """ # convert sequences file to single line sequences FASTA singleLineFilename = os.path.splitext(sequencesFilename)[0] + \ "_singleLine.fasta" if (dynamit.utils.makeSingleLineFASTA(sequencesFilename, singleLineFilename) != 0): print("[ERROR] Unable to create single line sequences file.") return 1 # compose the complete command-line for launching RNAforester. completePath = os.path.join(self.path, "RNAforester") + \ " -p -m " + self.params # if a filename containing secondary structure predictions # (RNAfold format) was specified in the parameters, then # use this file as input instead of letting RNAforester predict them. if self.structureFilename != "": completePath = os.path.join(self.path, "RNAforester") + \ " -m " + self.params + " " + self.structureFilename # prepare sequences dictionary to be later passed # to processRNAforesterResults sequences = dict([(seqRecord.description, str(seqRecord.seq)) \ for seqRecord in dynamit.utils.getSequencesRecords(singleLineFilename)]) try: # open input and output files for RNAforester. inSeqsHandle = open(singleLineFilename) # if a filename containing secondary structure predictions # (RNAfold format) was specified in the parameters, then # use this file as input instead of letting RNAforester predict them. if self.structureFilename != "": inSeqsHandle.close() inSeqsHandle = open(self.structureFilename) outResultsHandle = open(singleLineFilename + ".RNAforester", "wb") # launch RNAforester and wait for its execution to # complete (store its stderr for use if an error happens). callOutput = subprocess.check_output(completePath, shell=True, stderr=subprocess.STDOUT, stdin=inSeqsHandle) # write results to the output file and close it. outResultsHandle.write(callOutput) outResultsHandle.close() # check if RNAforester results exist if os.path.isfile(singleLineFilename + ".RNAforester"): # extract results print(" [RNAforesterSearcher] Search completed.") self.searchResults = self._processRNAforesterResults(sequences, singleLineFilename + ".RNAforester") else: print("[ERROR] Could not find RNAforester results file.") return 1 # remove cluster.dot and test.out files (generated by RNAforester) # but not needed in this context. if os.path.isfile("cluster.dot"): os.remove("cluster.dot") if os.path.isfile("test.out"): os.remove("test.out") print(" [RNAforesterSearcher] Execution completed.") return self.searchResults except CalledProcessError as e: # inform about the error that happened, and abort searcher execution. print("[ERROR] RNAforester execution terminated with an error:" + e.output) return 1 finally: # close input and output files. inSeqsHandle.close() if outResultsHandle: outResultsHandle.close() def _processRNAforesterResults(self, sequences, resultsFilename): """ Process results contained in RNAforester output files to produce a table for subsequent DynaMIT phases. Args: sequences: a dictionary of sequences (id is key, sequence is value). resultsFilename: the RNAforester results filename. Returns: Returns a list of strings, one per motif match, containing motif sequence, sequence id, match position, etc. """ print(" [RNAforesterSearcher] Processing results: <", \ os.path.basename(resultsFilename), ">") try: with open(resultsFilename) as f: lines = f.readlines() processedResults = [] isInResults = False isInCluster = False resultsStart = 0 motifConsensus = "" motifScore = 0 motifStructConsensus = "" i = 0 while i < len(lines): line = lines[i].rstrip('\n') if isInResults: # we have collected the motif consensus and are # now processing its instances if (line == '\n') or line.startswith(" "): # we are done mapping instances, so return the results isInResults = False isInCluster = False else: # maps current instance to its position on the sequence, # then add it to results info = re.split(r'\s+', line) # get the match full sequence ID. fullSeqID = dynamit.utils.getFullSequenceID(sequences, info[0], 0) fullSeqID = info[0] if fullSeqID == -1 else fullSeqID # remove gaps to find the motif instance position and, if # original sequences contained "T"s replace Us in RNAforester. noGapsSeq = info[1].replace("-", "").replace("U", "T") \ if sequences[fullSeqID].find("T") >= 0 \ else info[1].replace("-", "") motifStart = sequences[fullSeqID].find(noGapsSeq) + 1 # if the motif instance was not found on the sequence, we # likely selected the wrong full sequence ID, so try again # systematically on all sequence until found. if motifStart == 0: for seqId, seq in list(sequences.items()): if seqId.startswith(info[0]): motifStart = seq.find(noGapsSeq) + 1 if motifStart > 0: fullSeqID = seqId break # add the instance to the searcher results. processedResults.append(motifConsensus + \ "\tstructure\t" + self.searcherName + \ "\t" + fullSeqID + "\t" + str(motifStart) + \ "\t" + str(motifStart + len(info[1])) + \ "\t" + motifScore + "\t" + motifStructConsensus) if line.startswith("RNA Structure Cluster Nr"): # we have reached the portion of the file containing motifs instances, # so skip additional lines, store the motif score and the starting # lines of motifs instances and go on, we will go back to instances # after collecting the motif consensus motifScore = lines[i+1].rstrip('\n').split(':')[1].lstrip(' ') motifScore = str(math.log(float(motifScore), 2)) i += 4 resultsStart = i isInCluster = True continue if line.startswith("Consensus sequence/structure:") and isInCluster: # we have reached the portion of the file containing the # motif consensus, so get its stucture/sequence representation. i += 11 motifConsensus = lines[i].rstrip('\n').lstrip(' ').replace("U", "T") motifStructConsensus = lines[i+1].rstrip('\n').lstrip(' ') # now that we have the consensus, move back to motif # instances to record these i = resultsStart isInResults = True continue i += 1 return processedResults except (IOError, IndexError, KeyError, RuntimeError, ValueError) as e: print(" [RNAforesterSearcher] Unexpected error: %s" % str(e)) return 1
PypiClean
/EVE-SRP-0.12.11.tar.gz/EVE-SRP-0.12.11/src/evesrp/views/divisions.py
from __future__ import absolute_import from flask import url_for, render_template, redirect, abort, flash, request,\ Blueprint, current_app from flask_babel import gettext, lazy_gettext from flask_login import login_required, fresh_login_required, current_user from flask_wtf import Form import six from six.moves import map from sqlalchemy.orm.exc import NoResultFound, MultipleResultsFound from wtforms.fields import StringField, SubmitField, HiddenField, SelectField,\ Label from wtforms.validators import InputRequired, AnyOf, NumberRange from ..models import db from ..auth import PermissionType from ..auth.models import Division, Permission, Entity from ..util import jsonify, varies blueprint = Blueprint('divisions', __name__) @blueprint.route('/') @fresh_login_required def permissions(): """Show a page listing all divisions. """ if current_user.admin: return render_template('divisions.html', divisions=Division.query.all()) if current_user.has_permission(PermissionType.admin): admin_permissions = current_user.permissions.filter_by( permission=PermissionType.admin).values(Permission.division_id) admin_permissions = map(lambda x: x[0], admin_permissions) divisions = db.session.query(Division).\ filter(Division.id.in_(admin_permissions)) return render_template('divisions.html', divisions=divisions) return render_template('permissions.html') return abort(403) class AddDivisionForm(Form): # TRANS: On a form for creating a new division, this is a label for the # TRANS: name of the division. name = StringField(lazy_gettext(u'Division Name'), validators=[InputRequired()]) # TRANS: On a form for creating a new division, this is a button for # TRANS: creating a new division (by submitting the form). submit = SubmitField(lazy_gettext(u'Create Division')) @blueprint.route('/add/', methods=['GET', 'POST']) @fresh_login_required def add_division(): """Present a form for adding a division and also process that form. Only accesible to adminstrators. """ if not current_user.admin: return abort(403) form = AddDivisionForm() if form.validate_on_submit(): division = Division(form.name.data) db.session.add(division) db.session.commit() return redirect(url_for('.get_division_details', division_id=division.id)) return render_template('form.html', form=form, # TRANS: The title for a page for creating new divisions. title=gettext(u'Create Division')) class ChangeEntity(Form): form_id = HiddenField(default='entity') id_ = HiddenField() name = StringField() permission = HiddenField(validators=[AnyOf(list(PermissionType.values()))]) action = HiddenField(validators=[AnyOf(('add', 'delete'))]) #: List of tuples enumerating attributes that can be transformed/linked. #: Mainly used as the choices argument to :py:class:`~.SelectField` transformer_choices = [ ('', u''), # TRANS: Label for fields showing the name of a pilot. ('pilot', lazy_gettext(u'Pilot')), # TRANS: Label for the corporation a pilot is in. ('corporation', lazy_gettext(u'Corporation')), # TRANS: Label for the alliance a pilot is in. ('alliance', lazy_gettext(u'Alliance')), # TRANS: Label for the solar system a loss occured in. ('system', lazy_gettext(u'Solar System')), # TRANS: Label for the constellation a loss occured in. ('constellation', lazy_gettext(u'Constellation')), # TRANS: Label for the region a loss occured in. ('region', lazy_gettext(u'Region')), # TRANS: Label for the type of ship that was lost. ('ship_type', lazy_gettext(u'Ship')), # TRANS: Label for the status a request is in (ex: Unevaluated, Approved) ('status', lazy_gettext(u'Request Status')), ] class ChangeTransformer(Form): form_id = HiddenField(default='transformer') # TRANS: The a label for a selection field for selecting which attribute # TRANS: to transform. See the translation for 'Attribute Transformer'. attribute = SelectField(lazy_gettext(u'Attribute'), choices=transformer_choices) # TRANS: The label for a selection field for selecting the transformer for # TRANS: an attribute. See the translation for 'Attribute Transformer'. transformer = SelectField(lazy_gettext(u'Transformer'), choices=[]) def transformer_choices(attr): """Conveniece function for generating a list of transformer option tuples. :param attr str: the name of the attribute to make a list for. :return: A list of tuples suitable for the choices argument of\ :py:class:`StringField` :rtype: list """ default_transformers = [ ('none', 'None'), ] choices = default_transformers if attr in current_app.url_transformers: for transformer in current_app.url_transformers[attr]: choices.append((transformer, transformer)) return choices @blueprint.route('/<int:division_id>/', methods=['GET']) @fresh_login_required @varies('Accept', 'X-Requested-With') def get_division_details(division_id=None, division=None): """Generate a page showing the details of a division. Shows which groups and individuals have been granted permissions to each division. Only accesible to administrators. :param int division_id: The ID number of the division """ if division is None: division = Division.query.get_or_404(division_id) if not current_user.admin and not \ current_user.has_permission(PermissionType.admin, division): abort(403) if request.is_json or request.is_xhr: return jsonify(division._json(True)) return render_template( 'division_detail.html', division=division, entity_form=ChangeEntity(formdata=None), transformer_form=ChangeTransformer(formdata=None), ) def _modify_division_entity(division): """Handle POST requests for adding/removing entities form a Division.""" form = ChangeEntity() if form.validate(): entity = None if form.id_.data != '': current_app.logger.debug("Looking up entity by ID: {}".format( form.id_.data)) entity = Entity.query.get(form.id_.data) if entity is None: # TRANS: This is an error message when there's a problem # TRANS: granting a permission to a user or group # TRANS: (collectively called 'entities'). The '#' is not # TRANS: special, but the '%s(in_num)d' will be replaced with # TRANS: the ID number that was attempted to be added. flash(gettext(u"No entity with ID #%(id_num)d.", id_num=form.id_.data), category=u'error') else: current_app.logger.debug(u"Looking up entity by name: '{}'"\ .format(form.name.data)) try: entity = Entity.query.filter_by( name=form.name.data).one() except NoResultFound: # TRANS: Error message when a user or group with a given name # TRANS: cannot be found. flash(gettext(u"No entities with the name '%(name)s' found.", name=form.name.data), category=u'error') except MultipleResultsFound: # TRANS: Error message when multiple users and/or groups are # TRANS: found with a given name. flash(gettext( u"Multiple entities with the name '%(name)s' found.", name=form.name.data), category=u'error') else: current_app.logger.debug("entity lookup success") if entity is None: return get_division_details(division=division), 404, None # The entity has been found, create the query for the requested # Permission. permission_type = PermissionType.from_string( form.permission.data) permission_query = Permission.query.filter_by( division=division, entity=entity, permission=permission_type) # The response for both add and delete actions depends on whether the # Permission is found, so look it up first. try: permission = permission_query.one() except NoResultFound: if form.action.data == 'add': db.session.add( Permission(division, permission_type, entity)) # TRANS: Message show when granting a permission to a user or # TRANS: group. flash(gettext(u"%(name)s is now a %(role)s.", name=entity, role=permission_type.description.lower()), category=u"info") elif form.action.data == 'delete': # TRANS: Message shown when trying to remove a permission from # TRANS: a user, but that user didn't have that permission # TRANS: already. flash(gettext(u"%(name)s is not a %(role)s.", name=entity, role=permission_type.description.lower()), category=u"warning") else: if form.action.data == 'delete': permission_query.delete() # TRANS: Confirmation message shown when revoking a permission # TRANS: from a user or group. flash(gettext(u"%(name)s is no longer a %(role)s.", name=entity, role=permission_type.description.lower()), category=u"info") elif form.action.data == 'add': flash(gettext(u"%(name)s is now a %(role)s.", name=entity, role=permission_type.description.lower()), category=u"info") db.session.commit() else: for field_name, errors in six.iteritems(form.errors): errors = u", ".join(errors) # TRANS: Error message that is shown when one or more fields of a # TRANS: form are shown. flash(gettext(u"Errors for %(field_name)s: %(error)s.", field_name=field_name, error=errors), u'error') current_app.logger.info("Malformed entity permission POST: {}".format( form.errors)) return get_division_details(division=division) def _modify_division_transformer(division): """Handle POST requests for changing the Transformers for a Division.""" form = ChangeTransformer() # Set the form's choices attr = form.attribute.data form.transformer.choices = transformer_choices(attr) # Check form and go from there if form.validate(): name = form.transformer.data if name == 'none': division.transformers[attr] = None else: # Get the specific map of transformers for the attribute attr_transformers = current_app.url_transformers[attr] # Get the new transformer division.transformers[attr] = attr_transformers[name] # Explicitly add the TransformerRef to the session db.session.add(division.division_transformers[attr]) db.session.commit() # TRANS: Confirmation message shown when a transformer for an # TRANS: attribute has been set. flash(gettext(u"'%(attribute)s' set to '%(transformer)s'.", attribute=attr, transformer=name), u'message') else: for field_name, errors in six.iteritems(form.errors): errors = u", ".join(errors) # TRANS: Generic error message shown for the fields in a form. flash(gettext(u"Errors for %(field_name)s: %(error)s.", field_name=field_name, error=errors), u'error') current_app.logger.info("Malformed division transformer POST: {}". format(form.errors)) return get_division_details(division=division) @blueprint.route('/<int:division_id>/', methods=['POST']) @fresh_login_required def modify_division(division_id): """Dispatches modification requests to the specialized view function for that operation. """ division = Division.query.get_or_404(division_id) if not current_user.admin and not \ current_user.has_permission(PermissionType.admin, division): abort(403) form_id = request.form.get('form_id') if form_id == 'entity': return _modify_division_entity(division) elif form_id == 'transformer': return _modify_division_transformer(division) else: current_app.logger.warn("Invalid division modification POST: {}" .format(request.form)) abort(400) @blueprint.route('/<int:division_id>/transformers/') @blueprint.route('/<int:division_id>/transformers/<attribute>/') @login_required def list_transformers(division_id, attribute=None): """API method to get a list of transformers for a division. :param division_id int: the ID of the division to look up :param attribute str: a specific attribute to look up. Optional. :return: JSON """ division = Division.query.get_or_404(division_id) if not current_user.admin and not \ current_user.has_permission(PermissionType.admin, division): abort(403) if attribute is None: attrs = six.iterkeys(current_app.url_transformers) else: attrs = (attribute,) choices = {} for attr in attrs: raw_choices = transformer_choices(attr) current = division.transformers.get(attr, None) if current is not None: choices[attr] = \ [(c[0], c[1], c[1] == current.name) for c in raw_choices] else: choices[attr] = \ [(c[0], c[1], False) for c in raw_choices] return jsonify(choices)
PypiClean
/LDtoolsets-0.0.14.tar.gz/LDtoolsets-0.0.14/nbs/00_Genodata.ipynb
``` # default_exp genodata #hide %load_ext autoreload %autoreload 2 ``` # Genodata module > read and extract genodata ``` #export import numpy as np import pandas as pd import dask.array as da from bgen_reader import open_bgen from pandas_plink import read_plink from pandas_plink.bed_reader import lib, ffi try: from pybgen.parallel import ParallelPyBGEN as PyBGEN except: print('Can not import ParallelPyBGEN. import PyBGEN instead') from pybgen import PyBGEN #export from math import floor from pathlib import Path from typing import Optional, Union from tqdm import tqdm from numpy import ascontiguousarray, empty, float32, float64, nan_to_num, uint8, uint64, arange, full from xarray import DataArray from pandas import DataFrame, array # export def read_bgen(file, sample_file=None,pybgen=True): '''the function to read genotype data''' if pybgen: bg = PyBGEN(file,probs_only=True) bim = [] for i,t in enumerate(bg.iter_variant_info()): bim.append([int(t.chrom),t.name,0.0,t.pos,t.a1,t.a2,i]) bim = pd.DataFrame(bim,columns=['chrom','snp','cm','pos','a0','a1','i']) bim.snp = 'chr'+bim[['chrom','pos','a0','a1']].astype(str).agg(':'.join, axis=1) else: bg = open_bgen(file,verbose=False) snp,aa0,aa1 = [],[],[] for c,p,alleles in zip(bg.chromosomes,bg.positions,bg.allele_ids): a0,a1 = alleles.split(',') aa0.append(a0) aa1.append(a1) snp.append(':'.join(['chr'+str(int(c)),str(p),a0,a1])) # '05' first change to int, then change to str bim = pd.DataFrame({'chrom':bg.chromosomes.astype(int),'snp':snp,'pos':bg.positions,'a0':aa0,'a1':aa1}) if sample_file is None: fam = None else: fam = pd.read_csv(sample_file, header=0, delim_whitespace=True, quotechar='"',skiprows=1) fam.columns = ['fid','iid','missing','sex'] #Fix me fam = fam return bim,fam,bg #export def read_bim(fn): header = ["chrom", "snp", "cm","pos","a0", "a1"] df = pd.read_csv(fn,delim_whitespace=True,header=None,names=header,compression=None,engine="c",iterator=False) df["i"] = range(df.shape[0]) return df # export def bgen2dask(bgen,index,step=500): '''The function to covert bgen to dask array''' genos = [] n = len(index) for i in range(0,n,step): onecode_geno = bgen.read(index[i:min(n,i+step)]) #samples x variants geno = onecode_geno.argmax(axis=2).astype(np.int8) genos.append(da.from_array(geno)) return(da.concatenate(genos,axis=1).T) # export def pybgen_region(bgen,region,step=100): genos,geno=[],[] i = 1 for _,v in bgen.iter_variants_in_region('0'+str(region[0]) if region[0]<10 else str(region[0]),region[1],region[2]): if i % step == 0: genos.append(da.from_array(geno)) geno = [] geno.append(v.argmax(axis=1).astype(np.int8)) i += 1 genos.append(da.from_array(geno)) return(da.concatenate(genos,axis=0)) # export def extract_bed(geno,idx,row=True,step=500,region=None): #row = True by variants, row = False by samples if isinstance(geno,da.core.Array): if row: geno = geno[idx,:] else: geno = geno[:,idx] elif isinstance(geno,PyBGEN): geno = pybgen_region(geno,region,step) else: if row: #must be numric index if type(list(idx)[0]) is bool: pd_idx = pd.Series(idx) idx = list(pd_idx[pd_idx].index) geno = bgen2dask(geno,idx,step) else: geno = geno.read() # read all variants geno = geno[:,idx] return geno # export class Genodata: def __init__(self,geno_path,sample_path=None): self.bim,self.fam,self.bed = self.read_geno(geno_path,sample_path) def __repr__(self): return "bim:% s \n fam:% s \n bed:%s" % (self.bim, self.fam, self.bed) def read_geno(self,geno_file,sample_file): if geno_file.endswith('.bed'): bim,fam,bed = read_plink(geno_file[:-4], verbose=False) bim.snp = 'chr'+bim[['chrom','pos','a0','a1']].astype(str).agg(':'.join, axis=1) elif geno_file.endswith('.bgen'): if sample_file is None: sample_file = geno_file.replace('.bgen', '.sample') bim,fam,bed = read_bgen(geno_file,sample_file) else: raise ValueError('Plesae provide the genotype files with PLINK binary format or BGEN format') bim.chrom = bim.chrom.astype(int) bim.pos = bim.pos.astype(int) return bim,fam,bed def geno_in_stat(self,stat,notin=False): '''The function to find an overlap region between geno data with sumstat''' variants = stat.SNP self.extractbyvariants(variants,notin) def geno_in_unr(self,unr): '''The function to find an overlap samples between geno data with unr''' samples = unr.IID self.extractbysamples(samples) def extractbyregion(self,region): bim = self.bim idx = (bim.chrom == region[0]) & (bim.pos >= region[1]) & (bim.pos <= region[2]) print('this region',region,'has',sum(idx),'SNPs in Genodata') if sum(idx) == 0: raise ValueError('The extraction is empty') #update bim,bed self.extractbyidx(idx,row=True,region=region) def extractbyvariants(self,variants,notin=False): #variants is list or pd.Series idx = self.bim.snp.isin(variants) if notin: idx = idx == False if sum(idx) == 0: raise ValueError('The extraction is empty') #update bim,bed self.extractbyidx(idx,row=True) def extractbysamples(self,samples,notin=False): #samples is list or pd.Series samples = pd.Series(samples,dtype=str) idx = self.fam.iid.astype(str).isin(samples) if notin: idx = idx == False if sum(idx) == 0: raise ValueError('The extraction is empty') #update fam,bed self.extractbyidx(idx,row=False) def extractbyidx(self,idx,row=True,region=None): '''get subset of genodata by index if index is numbers, the order of genodata will be sorted by the order of index. if row = True, extract by variants. Otherwise, extract by samples.''' idx = list(idx) self.idx = idx if row: #update bim if type(idx[0]) is bool: self.bim = self.bim[idx] else: self.bim = self.bim.iloc[idx] else: #update fam if type(idx[0]) is bool: self.fam = self.fam[idx] else: self.fam = self.fam.iloc[idx] self.bed = extract_bed(self.bed,idx,row,region=region) def export_plink(self, bed: Union[str, Path], bim: Optional[Union[str, Path]] = None, fam: Optional[Union[str, Path]] = None,row: str = "variant",verbose: bool = True): bed = Path(bed) if bim is None: bim = bed.with_suffix(".bim") if fam is None: fam = bed.with_suffix(".fam") bim = Path(bim) fam = Path(fam) write_bed(bed, self.bed, row, verbose) _echo("Writing FAM... ", end="", disable=not verbose) write_fam(fam, self.fam) _echo("done.", disable=not verbose) _echo("Writing BIM... ", end="", disable=not verbose) write_bim(bim, self.bim) _echo("done.", disable=not verbose) #export def write_plink( G, bed: Union[str, Path], bim: Optional[Union[str, Path]] = None, fam: Optional[Union[str, Path]] = None, row: str = "variant", verbose: bool = True, ): """ Write PLINK 1 binary files into a data array. A PLINK 1 binary file set consists of three files: - BED: containing the genotype. - BIM: containing variant information. - FAM: containing sample information. The user must provide the genotype (dosage) via a :class:`xarray.DataArray` matrix with data type :const:`numpy.float32` or :const:`numpy.float64`. That matrix must have two named dimensions: **sample** and **variant**. The only allowed values for the genotype are: :const:`0`, :const:`1`, :const:`2`, and :data:`math.nan`. Parameters ---------- G Genotype with bim, bed, and fam. bed Path to a BED file. bim Path to a BIM file.It defaults to :const:`None`, in which case it will try to be inferred. fam Path to a FAM file. It defaults to :const:`None`, in which case it will try to be inferred. major It can be either :const:`"sample"` or :const:`"variant"` (recommended and default). Specify the matrix layout on the BED file. verbose :const:`True` for progress information; :const:`False` otherwise. """ if G.bed.ndim != 2: raise ValueError("G has to be bidimensional") bed = Path(bed) if bim is None: bim = bed.with_suffix(".bim") if fam is None: fam = bed.with_suffix(".fam") bim = Path(bim) fam = Path(fam) write_bed(bed, G.bed, row, verbose) _echo("Writing FAM... ", end="", disable=not verbose) write_fam(fam, G.fam) _echo("done.", disable=not verbose) _echo("Writing BIM... ", end="", disable=not verbose) write_bim(bim, G.bim) _echo("done.", disable=not verbose) def _echo(msg: str, end: str = "\n", disable: bool = False): if not disable: print(msg, end=end, flush=True) def write_fam(filepath: Path, df): cols = ["fid", "iid", "father","mother","gender","trait"] df = df[cols] df.to_csv( filepath, index=False, sep="\t", header=False, encoding="ascii", line_terminator="\n", ) def write_bim(filepath: Path, df): cols = ["chrom","snp","cm","pos","a0","a1"] df = df[cols] df.to_csv( filepath, index=False, sep="\t", header=False, encoding="ascii", line_terminator="\n", ) #export def write_bed(filepath: Path, G, row='variant', verbose=True): """ Write BED file. It assumes that ``X`` is a variant-by-sample matrix. """ if not isinstance(G,da.core.Array): G = da.asanyarray(G) if row != "variant": G = G.T row_code = 1 if row == "variant" else 0 e = lib.write_bed_header(str(filepath).encode(), row_code) if e != 0: raise RuntimeError(f"Failure while writing BED file {filepath}.") nrows = G.shape[0] ncols = G.shape[1] row_chunk = max(1, floor((1024 * 1024 * 256) / ncols)) row_chunk = min(row_chunk, nrows) G = G.rechunk((row_chunk, ncols)) row_start = 0 for chunk in tqdm(G.chunks[0], "Writing BED", disable=not verbose): data = G[row_start : row_start + chunk, :].compute() if data.dtype not in [float32, float64]: msg = "Unsupported data type. " msg += "Please, provide a dosage matrix in either " msg += "float32 or float64 format." raise ValueError(msg) _write_bed_chunk(filepath, data) row_start += chunk def _write_bed_chunk(filepath: Path, X): base_type = uint8 base_size = base_type().nbytes base_repr = "uint8_t" nan_to_num(X, False, 3.0) G = ascontiguousarray(X, base_type) assert G.flags.aligned strides = empty(2, uint64) strides[:] = G.strides strides //= base_size e = lib.write_bed_chunk( str(filepath).encode(), G.shape[1], G.shape[0], ffi.cast(f"{base_repr} *", G.ctypes.data), ffi.cast("uint64_t *", strides.ctypes.data), ) if e != 0: raise RuntimeError(f"Failure while writing BED file {filepath}.") write_plink(geno,'test.bed') from pandas_plink import read_plink1_bin geno1 = Genodata('test.bed') geno1 ``` # Test ``` geno_path ='/home/dmc2245/UKBiobank/data/exome_files/project_VCF/072721_run/plink/ukb23156_c1.merged.filtered.bed' region = [5,272741,1213528-900000] geno_path = 'MWE_region_extraction/ukb23156_c5.merged.filtered.5_272741_1213528.bed' sumstats_path = 'MWE_region_extraction/090321_UKBB_Hearing_aid_f3393_expandedwhite_6436cases_96601ctrl_PC1_2_f3393.regenie.snp_stats' pheno_path = None unr_path = 'MWE_region_extraction/UKB_genotypedatadownloaded083019.090221_sample_variant_qc_final_callrate90.filtered.extracted.white_europeans.filtered.092821_ldprun_unrelated.filtered.prune.txt' imp_geno_path = 'MWE_region_extraction/ukb_imp_chr5_v3_05_272856_1213643.bgen' imp_sumstats_path = 'MWE_region_extraction/100521_UKBB_Hearing_aid_f3393_expandedwhite_15601cases_237318ctrl_500k_PC1_PC2_f3393.regenie.snp_stats' imp_ref = 'hg19' output_sumstats = 'test.snp_stats' output_LD = 'test_corr.csv' #main(region,geno_path,sumstats_path,pheno_path,unr_path,imp_geno_path,imp_sumstats_path,imp_ref,output_sumstats,output_LD) from pandas_plink import Chunk Chunk(512,512) exome_geno.extractbyvariants(exome_geno.bim.snp[:50]) exome_geno.extractbysamples(exome_geno.fam.iid[:60]) from LDtools.sumstat import * region = [5, 272741, 1213528] imput_sumstats = Sumstat('/home/dmc2245/UKBiobank/results/REGENIE_results/results_imputed_data/2021_10_07_f3393_500K/100521_UKBB_Hearing_aid_f3393_expandedwhite_15601cases_237318ctrl_500k_PC1_PC2_f3393.regenie.snp_stats.gz') imput_sumstats.extractbyregion(region) imput_sumstats bgen = PyBGEN(geno_file) sample_file = geno_file.replace('.bgen', '.sample') if not os.path.isfile(sample_file): if not os.path.isfile(${bgen_sample_path:r}): raise ValueError(f"Cannot find the matching sample file ``{sample_file}`` for ``{geno_file}``.\nYou can specify path to sample file for all BGEN files using ``--bgen-sample-path``.") else: sample_file = ${bgen_sample_path:r} bgen_fam = pd.read_csv(sample_file, header=0, delim_whitespace=True, quotechar='"',skiprows=1) bgen_fam.columns = ['fid','iid','missing','sex'] geno = [bgen,bgen_fam] #imp_geno_path = '/mnt/mfs/statgen/archive/UKBiobank_Yale_transfer/ukb39554_imputeddataset/ukb_imp_chr5_v3.bgen' bgen_sample_path = '/home/dmc2245/UKBiobank_Yale_transfer/ukb39554_imputeddataset/ukb32285_imputedindiv.sample' imput_geno = Genodata(imp_geno_path,bgen_sample_path) imput_geno.extractbyregion(region) imput_geno.extractbyvariants(list(imput_geno.bim.snp[10:20])) imput_geno.extractbysamples(list(imput_geno.fam.iid[50:100])) imput_geno region from pybgen import PyBGEN bgen = PyBGEN(imp_geno_path,probs_only=True) pybgen_region(bgen,region) for t,g in bgen.iter_variants_in_region('0'+str(region[0]) if region[0]<10 else str(region[0]),region[1],region[2]): print(t) import pandas as pd tmp = bgen.iter_variants() genos = [] for i,v in zip(range(bgen.nb_variants),bgen): geno = [] if i % 100000 ==0: geno.append(v.argmax(axis=1).astype(np.int8)) print(i,j) genos = [] n = len(index) for i in range(0,n,step): onecode_geno = bgen.read(index[i:min(n,i+step)]) #samples x variants geno = onecode_geno.argmax(axis=2).astype(np.int8) genos.append(da.from_array(geno)) 1002 %10000 tmp a = tmp.next() import numpy as np a[1] aa = a[1].argmax(axis=1).astype(np.int8) pd.Series(aa).value_counts() tmp = [] for i,t in enumerate(bgen.iter_variant_info()): tmp.append([int(t.chrom),t.name,0.0,t.pos,t.a1,t.a2,i]) tmp = pd.DataFrame(tmp,columns=['chrom','snp','cm','pos','a0','a1','i']) tmp.snp = 'chr'+tmp[['chrom','pos','a0','a1']].astype(str).agg(':'.join, axis=1) tmp list(bgen.iter_variant_info())[0] idx = imput_geno.idx if type(list(idx)[0]) is bool: pd_idx = pd.Series(idx) idx = list(pd_idx[pd_idx].index) len(idx) idx[1:10] imp_geno_path = 'MWE_region_extraction/ukb_imp_chr5_v3_05_272856_1213643.bgen' bgen = open_bgen(imp_geno_path) bgen.read(1) imp_geno_path = '/mnt/mfs/statgen/archive/UKBiobank_Yale_transfer/ukb39554_imputeddataset/ukb_imp_chr5_v3.bgen' bgen = open_bgen(imp_geno_path) bgen.read(1) imput_geno.bed bgen imput_geno.geno_in_stat(imput_sumstats.ss) read_bgen('/mnt/mfs/statgen/archive/UKBiobank_Yale_transfer/ukb39554_imputeddataset/ukb_imp_chr5_v3.bgen') ```
PypiClean
/EZFF-1.0.0.tar.gz/EZFF-1.0.0/examples/lj-gulp-serial/run.py
import ezff from ezff.interfaces import gulp, vasp import numpy as np # DEFINE GROUND TRUTHS gt_bulk_modulus = 1.1236 #GPa gt_structure = vasp.read_atomic_structure('ground_truths/POSCAR') def my_error_function(variable_values, template): myrank = ezff.get_pool_rank() # Configure GULP job. path = str(myrank) md_job = gulp.job(path=path) md_job.structure = gt_structure md_job.forcefield = ezff.generate_forcefield(template, variable_values, FFtype='SW') md_job.options['pbc'] = True md_job.options['relax_atoms'] = True md_job.options['relax_cell'] = True # Submit job and read output md_job.run() # Calculate errors in lattice constant and elastic modulus moduli = md_job.read_elastic_moduli() # 6X6 elastic modulus tensor inside a list of length 1 (for a single input structure) md_bulk_modulus = np.mean([moduli[0][i,i] for i in range(3)]) # Bulk modulus is sum of diagonal elements in moduli[0] bulk_modulus_error = np.linalg.norm(md_bulk_modulus - gt_bulk_modulus) # Error is the L2 norm of deviation from the ground truth value md_structure = md_job.read_structure() # Read relaxed structure after optimization error_abc, error_ang = ezff.error_lattice_constant(MD=md_structure, GT=gt_structure) # error_abc = error in lattice constants, error_ang = error in lattice angles latt_error = np.linalg.norm(error_abc[0]) # error in 'a' lattice constant return [latt_error, bulk_modulus_error] if __name__ == '__main__': obj = ezff.FFParam(error_function = my_error_function, num_errors = 2) obj.read_variable_bounds('variable_bounds') obj.read_forcefield_template('template') obj.set_algorithm('randomsearch_so', population_size = 32) obj.parameterize(num_epochs = 5) obj.set_algorithm('nsga2_mo_platypus', population_size = 32) obj.parameterize(num_epochs = 15)
PypiClean
/Kallithea-0.7.0.tar.gz/Kallithea-0.7.0/kallithea/lib/vcs/ssh/base.py
import datetime import logging import sys from kallithea.lib.auth import AuthUser, HasPermissionAnyMiddleware from kallithea.lib.utils2 import set_hook_environment from kallithea.model import db, meta log = logging.getLogger(__name__) class BaseSshHandler(object): # Protocol for setting properties: # Set by sub class: # vcs_type: 'hg' or 'git' # Set by make() / __init__(): # repo_name: requested repo name - only validated by serve() # Set by serve() - must not be accessed before: # db_repo: repository db object # authuser: user that has been authenticated - like request.authuser ... which isn't used here # allow_push: false for read-only access to the repo # Set defaults, in case .exit should be called early vcs_type = None repo_name = None @staticmethod def make(ssh_command): """Factory function. Given a command as invoked over SSH (and preserved in SSH_ORIGINAL_COMMAND when run as authorized_keys command), return a handler if the command looks ok, else return None. """ raise NotImplementedError def __init__(self, repo_name): self.repo_name = repo_name.rstrip('/') def serve(self, user_id, key_id, client_ip): """Verify basic sanity of the repository, and that the user is valid and has access - then serve the native VCS protocol for repository access.""" dbuser = db.User.get(user_id) if dbuser is None: self.exit('User %r not found' % user_id) self.authuser = AuthUser.make(dbuser=dbuser, ip_addr=client_ip) log.info('Authorized user %s from SSH %s trusting user id %s and key id %s for %r', dbuser, client_ip, user_id, key_id, self.repo_name) if self.authuser is None: # not ok ... but already kind of authenticated by SSH ... but not really not authorized ... self.exit('User %s from %s cannot be authorized' % (dbuser.username, client_ip)) ssh_key = db.UserSshKeys.get(key_id) if ssh_key is None: self.exit('SSH key %r not found' % key_id) ssh_key.last_seen = datetime.datetime.now() meta.Session().commit() if HasPermissionAnyMiddleware('repository.write', 'repository.admin')(self.authuser, self.repo_name): self.allow_push = True elif HasPermissionAnyMiddleware('repository.read')(self.authuser, self.repo_name): self.allow_push = False else: self.exit('Access to %r denied' % self.repo_name) self.db_repo = db.Repository.get_by_repo_name(self.repo_name) if self.db_repo is None: self.exit("Repository '%s' not found" % self.repo_name) assert self.db_repo.repo_name == self.repo_name # Set global hook environment up for 'push' actions. # For push actions, the action in global hook environment is used in # process_pushed_raw_ids (which it is called as Git post-receive hook, # or Mercurial 'changegroup' hook). # For pull actions, the actual hook in log_pull_action (called directly # on Git, or through the 'outgoing' Mercurial hook) is hardcoded to # ignore the environment action and always use 'pull'. set_hook_environment(self.authuser.username, client_ip, self.repo_name, self.vcs_type, 'push') self._serve() def _serve(self): """Serve the native protocol for repository access.""" raise NotImplementedError def exit(self, error): log.info('abort serving %s %s: %s', self.vcs_type, self.repo_name, error) sys.stderr.write('abort: %s\n' % error) sys.exit(1)
PypiClean
/ANYstructure-4.10.tar.gz/ANYstructure-4.10/any_files/load_factor_window.py
import tkinter as tk import os from _tkinter import TclError class CreateLoadFactorWindow: ''' self._load_factors_dict = {'dnva':[1.3,1.2,0.7], 'dnvb':[1,1,1.3], 'tanktest':[1,1,0]} # DNV loads factors ''' def __init__(self,master, app=None): super(CreateLoadFactorWindow, self).__init__() self._frame = master self._frame.wm_title("Load factor modifications here.") self._frame.geometry('800x800') self._frame.grab_set() self._app = app if __name__ == '__main__': self._load_factors_dict = {'dnva': [1.3, 1.2, 0.7], 'dnvb': [1, 1, 1.3], 'tanktest': [1, 1, 0]} # DNV loads factors else: self._load_factors_dict = app._load_factors_dict self.new_conda_lff1 = tk.DoubleVar() self.new_conda_lff2 = tk.DoubleVar() self.new_conda_lff3 = tk.DoubleVar() self.new_condb_lff1 = tk.DoubleVar() self.new_condb_lff2 = tk.DoubleVar() self.new_condb_lff3 = tk.DoubleVar() self.new_condtt_lff1 = tk.DoubleVar() self.new_condtt_lff2 = tk.DoubleVar() self.new_condtt_lff3 = tk.DoubleVar() self.new_change_default = tk.BooleanVar() self.new_change_existing = tk.BooleanVar() self.new_conda_lff1.set(self._load_factors_dict['dnva'][0]) self.new_conda_lff2.set(self._load_factors_dict['dnva'][1]) self.new_conda_lff3.set(self._load_factors_dict['dnva'][2]) self.new_condb_lff1.set(self._load_factors_dict['dnvb'][0]) self.new_condb_lff2.set(self._load_factors_dict['dnvb'][1]) self.new_condb_lff3.set(self._load_factors_dict['dnvb'][2]) self.new_condtt_lff1.set(self._load_factors_dict['tanktest'][0]) self.new_condtt_lff2.set(self._load_factors_dict['tanktest'][1]) self.new_condtt_lff3.set(self._load_factors_dict['tanktest'][2]) ent_w = 20 tk.Label(self._frame, text='Static and dynamic load factors is specified here', font='Verdana 15 bold')\ .grid(row = 1, column = 1, sticky = tk.W) tk.Label(self._frame, text='Note that DNV is used as reference, ' 'but the load factors can be any other rule set such as ISO.', font='Verdana 8 bold')\ .grid(row = 2, column = 1, sticky = tk.W) tk.Label(self._frame, text=' ', font='Verdana 8 bold')\ .grid(row = 3, column = 1, sticky = tk.W) tk.Label(self._frame, text='Condition a) - Static load factor "unknown loads"', font='Verdana 8 bold')\ .grid(row = 4, column = 1, sticky = tk.W) tk.Label(self._frame, text='Condition a) - Static load factor well defined loads', font='Verdana 8 bold')\ .grid(row = 5, column = 1, sticky = tk.W) tk.Label(self._frame, text='Condition a) - Dynamic load factor', font='Verdana 8 bold')\ .grid(row = 6, column = 1, sticky = tk.W) self.ent_conda_lf1 = tk.Entry(self._frame, textvariable=self.new_conda_lff1, width=ent_w) self.ent_conda_lf2 = tk.Entry(self._frame, textvariable=self.new_conda_lff2, width=ent_w) self.ent_conda_lf3 = tk.Entry(self._frame, textvariable=self.new_conda_lff3, width=ent_w) self.ent_conda_lf1.grid(row=4, column=2) self.ent_conda_lf2.grid(row=5, column=2) self.ent_conda_lf3.grid(row=6, column=2) tk.Label(self._frame, text=' ', font='Verdana 8 bold')\ .grid(row = 7, column = 1, sticky = tk.W) tk.Label(self._frame, text='Condition b) - Static load factor "unknown loads"', font='Verdana 8 bold')\ .grid(row = 8, column = 1, sticky = tk.W) tk.Label(self._frame, text='Condition b) - Static load factor well defined loads', font='Verdana 8 bold')\ .grid(row = 9, column = 1, sticky = tk.W) tk.Label(self._frame, text='Condition b) - Dynamic load factor', font='Verdana 8 bold')\ .grid(row = 10, column = 1, sticky = tk.W) self.ent_condb_lf1 = tk.Entry(self._frame, textvariable=self.new_condb_lff1, width=ent_w) self.ent_condb_lf2 = tk.Entry(self._frame, textvariable=self.new_condb_lff2, width=ent_w) self.ent_condb_lf3 = tk.Entry(self._frame, textvariable=self.new_condb_lff3, width=ent_w) self.ent_condb_lf1.grid(row=8, column=2) self.ent_condb_lf2.grid(row=9, column=2) self.ent_condb_lf3.grid(row=10, column=2) tk.Label(self._frame, text=' ', font='Verdana 8 bold')\ .grid(row = 11, column = 1, sticky = tk.W) tk.Label(self._frame, text='Tank test) - Static load factor "unknown loads"', font='Verdana 8 bold')\ .grid(row = 12, column = 1, sticky = tk.W) tk.Label(self._frame, text='Tank test) - Static load factor well defined loads', font='Verdana 8 bold')\ .grid(row = 13, column = 1, sticky = tk.W) tk.Label(self._frame, text='Tank test) - Dynamic load factor', font='Verdana 8 bold')\ .grid(row = 14, column = 1, sticky = tk.W) self.ent_condtt_lf1 = tk.Entry(self._frame, textvariable=self.new_condtt_lff1, width=ent_w) self.ent_condtt_lf2 = tk.Entry(self._frame, textvariable=self.new_condtt_lff2, width=ent_w) self.ent_condtt_lf3 = tk.Entry(self._frame, textvariable=self.new_condtt_lff3, width=ent_w) self.ent_condtt_lf1.grid(row=12, column=2) self.ent_condtt_lf2.grid(row=13, column=2) self.ent_condtt_lf3.grid(row=14, column=2) tk.Label(self._frame, text=' ', font='Verdana 8 bold')\ .grid(row = 15, column = 1, sticky = tk.W) # tk.Label(self._frame, text='Change all current load factors', font='Verdana 8 bold')\ # .grid(row = 16, column = 1, sticky = tk.W) # tk.Checkbutton(self._frame, variable=self.new_change_existing)\ # .grid(row=17, column=1, sticky = tk.W) # tk.Label(self._frame, text='Change default load factors', font='Verdana 8 bold')\ # .grid(row = 18, column = 1, sticky = tk.W) # tk.Checkbutton(self._frame, variable=self.new_change_default)\ # .grid(row=19, column=1, sticky=tk.W) # tk.Label(self._frame, text=' ', font='Verdana 8 bold')\ .grid(row = 16, column = 1, sticky = tk.W) destroy_and_return = tk.Button(self._frame, text='Return specified load factors and change existing', command=self.return_load_factors, bg='green', font='Verdana 12', fg='yellow') destroy_and_return.grid(row = 17, column = 1) tk.Label(self._frame, text=' ', font='Verdana 8 bold')\ .grid(row = 18, column = 1) try: img_file_name = 'img_dnv_load_combinations.gif' if os.path.isfile('images/' + img_file_name): file_path ='images/' + img_file_name else: file_path = app._root_dir + '/images/' + img_file_name photo_transverse = tk.PhotoImage(file=file_path) label_trans = tk.Label(self._frame, image=photo_transverse) label_trans.image = photo_transverse # keep a reference! label_trans.grid(row = 19, column = 1, columnspan = 2) except TclError: pass def return_load_factors(self): ''' self._load_factors_dict = {'dnva':[1.3,1.2,0.7], 'dnvb':[1,1,1.3], 'tanktest':[1,1,0]} # DNV loads factors :return: ''' self._load_factors_dict['dnva'] = [self.new_conda_lff1.get(), self.new_conda_lff2.get(), self.new_conda_lff3.get()] self._load_factors_dict['dnvb'] = [self.new_condb_lff1.get(), self.new_condb_lff2.get(), self.new_condb_lff3.get()] self._load_factors_dict['tanktest'] = [self.new_condtt_lff1.get(), self.new_condtt_lff2.get(), self.new_condtt_lff3.get()] if __name__ == '__main__': self._frame.destroy() print({'returned lf dict': self._load_factors_dict, 'change exisiting': self.new_change_existing.get(), 'change default': self.new_change_default.get()}) return self._app.on_close_load_factor_window({'returned lf dict': self._load_factors_dict, 'change exisiting': self.new_change_existing.get(), 'change default': self.new_change_default.get()}) self._frame.destroy() if __name__ == '__main__': root = tk.Tk() my_app = CreateLoadFactorWindow(root,app=None) root.mainloop()
PypiClean
/Joule-0.9.41.tar.gz/Joule-0.9.41/joule/controllers/follower_controller.py
import aiodns import aiohttp from aiohttp import web from sqlalchemy.orm import Session from joule.models import Follower from joule.api import TcpNode async def index(request: web.Request): db: Session = request.app["db"] followers = db.query(Follower) return web.json_response([f.to_json() for f in followers]) # Note: this is covered with e2e tests async def add(request: web.Request): # pragma: no cover """ Called by a Joule node to allow *this* node to control it Parameters: key(str): the API key to use base_uri(str): (optional) specify the URL of the follower port(int): specify the port Joule is using on the follower """ db: Session = request.app["db"] cafile = request.app["cafile"] if request.content_type != 'application/json': return web.Response(text='content-type must be application/json', status=400) body = await request.json() try: key = body["key"] port = body["port"] scheme = body["scheme"] base_uri = body["base_uri"] if "name_is_host" in body: location = scheme+"://" + body["name"] + ":" + str(port) + base_uri else: location = scheme+"://" + request.remote + ":" + str(port) + base_uri try: node = TcpNode("new_follower", location, key, cafile) info = await node.info() await node.close() follower_name = info.name except aiohttp.ClientError: return web.Response(text="no route to node", status=400) except ValueError as e: return web.Response(text=str(e), status=400) follower = Follower(key=key, location=location, name=follower_name) # update the follower if this is a repeat db.query(Follower).filter(Follower.location == follower.location).delete() db.add(follower) db.commit() except KeyError as e: return web.Response(text="Invalid request, missing [%s]" % str(e), status=400) except ValueError as e: return web.Response(text="Invalid request, bad argument format", status=400) return web.json_response(data={'name': request.app["name"]}) async def delete(request: web.Request): """ Remove the specified node from the list of followers """ db: Session = request.app["db"] try: name = request.query["name"] db.query(Follower).filter(name == name).delete() db.commit() except KeyError: return web.Response(text="specify name to remove", status=400) return web.Response(text="OK")
PypiClean
/NovalIDE-1.1.8-py3-none-any.whl/noval/util/objutils.py
import logging import traceback import sys import os import types import noval.util.utillang as utillang import noval.util.datetimeparser as datetimeparser from types import * import noval.util.utils as utils FUNCTION_HAS_ATTR = '_hasAttr' FUNCTION_GET_ATTR = '_getAttr' FUNCTION_SET_ATTR = '_setAttr' FUNCTION_DEL_ATTR = '_delAttr' try: ClassType DictionaryType long unicode InstanceType SliceType TypeType XRangeType basestring except: class _C: def _m(self): pass ClassType = type(_C) DictionaryType = dict long = int unicode = str _x = _C() InstanceType = type(_x) SliceType = slice TypeType = type XRangeType = range basestring = str def hasRawAttr(obj, name): if obj == None: return False if name != FUNCTION_HAS_ATTR and hasattr(obj, FUNCTION_HAS_ATTR): return obj._hasAttr(name) return obj.__dict__.has_key(name) def getRawAttr(obj, name): if name != FUNCTION_GET_ATTR and hasattr(obj, FUNCTION_GET_ATTR): return obj._getAttr(name) return obj.__dict__.get(name) def setRawAttr(obj, name, value): if name != FUNCTION_SET_ATTR and hasattr(obj, FUNCTION_SET_ATTR): obj._setAttr(name, value) else: obj.__dict__[name] = value def delRawAttr(obj, name): if name != FUNCTION_DEL_ATTR and hasattr(obj, FUNCTION_DEL_ATTR): obj._delAttr(name) else: del obj.__dict__[name] def getStaticAttr(obj, attr): if (isinstance(obj, types.TypeType)): classDesc = obj else: classDesc = obj.__class__ if (hasattr(classDesc, attr)): return getattr(classDesc, attr) return None def setStaticAttr(obj, attr, value): if (isinstance(obj, types.TypeType)): classDesc = obj else: classDesc = obj.__class__ setattr(classDesc, attr, value) def hasAttrFast(obj, name): if hasRawAttr(obj, name): return True if hasattr(obj, '_complexType'): complexType=obj._complexType element=complexType.findElement(name) if element: return True if hasattr(obj, name): return True return False def moduleForName(moduleName): module = None pathList = moduleName.split('.') if (len(moduleName) > 0): module = __import__(moduleName) for name in pathList[1:]: if (name in module.__dict__): module = module.__dict__[name] else: module = None break return module def typeForName(typeName): i = typeName.rfind('.') if (i >= 0): module = moduleForName(typeName[:i]) if (module != None): name = typeName[i+1:] if (name in module.__dict__): return module.__dict__[name] elif __builtin__.__dict__.has_key(typeName): return __builtin__.__dict__[typeName] return None def functionForName(functionName): ftype = typeForName(functionName) if (isinstance(ftype, (types.FunctionType, types.MethodType, types.BuiltinFunctionType, types.BuiltinMethodType))): return ftype return None def classForName(className): ctype = typeForName(className) if (isinstance(ctype, (types.ClassType, types.TypeType))): return ctype return None def newInstance(className, objargs=None): "dynamically create an object based on the className and return it." if not isinstance(objargs, list): objargs = [objargs] if className == "None": return None elif className == "bool": if ((len(objargs) < 1) or (objargs[0].lower() == "false") or (not objargs[0])): return False return True if className == "str" or className == "unicode": # don't strip: blanks are significant if len(objargs) > 0: try: if utils.is_py2(): return utillang.unescape(objargs[0]).encode() else: return utillang.unescape(objargs[0]) except: return "?" else: return "" if className == "date": return datetimeparser.parse(objargs[0], asdate=True) if className == "datetime": return datetimeparser.parse(objargs[0]) if className == "time": return datetimeparser.parse(objargs[0], astime=True) classtype = classForName(className) if (classtype == None): raise Exception("Could not find class %s" % className) if (len(objargs) > 0): return classtype(*objargs) else: return classtype() def getClassProperty(classType, propertyName): return getattr(classType, propertyName) def toDiffableRepr(value, maxLevel=None): if (value == None): return "None" if (maxLevel == None): maxLevel = 8 maxLevel -= 1 if (maxLevel < 0): return typeToString(value, PRINT_OBJ_DIFFABLE) ## if ((exclude != None) and not isinstance(value, (basestring, int))): ## for v in exclude: ## if (v is value): ## return "<recursive reference>" ## exclude.append(value) ## elif (isinstance(value, ObjectType) and hasattr(value, "__dict__")): ## if (exclude == None): ## exclude = [] ## s = "%s(%s)" % (type(value), toDiffableString(value.__dict__, exclude)) if (not isinstance(value, (bool, ClassType, complex, dict, DictionaryType, float, int, list, long, str, tuple, unicode, BuiltinFunctionType, BuiltinMethodType, CodeType, FrameType, FunctionType, GeneratorType, InstanceType, LambdaType, MethodType, ModuleType, SliceType, TracebackType, TypeType, XRangeType))): if (hasattr(value, "_toDiffableString")): s = value._toDiffableString(maxLevel) elif (hasattr(value, "__str__")): s = str(value) elif (hasattr(value, "__dict__")): s = "%s(%s)" % (type(value), toDiffableString(value.__dict__, maxLevel)) else: s = str(type(value)) ix2 = s.find(" object at 0x") if (ix2 > 0): ix = s.rfind(".") if (ix > 0): s = "<class %s>" %s[ix+1:ix2] elif (isinstance(value, bool)): if (value): return "True" else: return "False" elif (isinstance(value, (tuple, list))): items = [] for v in value: if (isinstance(v, basestring)): if (v.find("'") >= 0): items.append('"%s"' % v) else: items.append("'%s'" % v) else: items.append(toDiffableString(v, maxLevel)) s = "[" + ", ".join(items) + "]" elif (isinstance(value, dict)): items = [] for key, val in value.iteritems(): if (isinstance(val, UnicodeType)): items.append("'%s': u'%s'" % (key, toDiffableString(val, maxLevel))) elif (isinstance(val, basestring)): items.append("'%s': '%s'" % (key, toDiffableString(val, maxLevel))) else: items.append("'%s': %s" % (key, toDiffableString(val, maxLevel))) s = "{" + ", ".join(items) + "}" else: s = str(value) return s def toDiffableString(value, maxLevel=None): ## if (value == None): ## return "None" ## if ((exclude != None) and not isinstance(value, (basestring, int))): ## for v in exclude: ## if (v is value): ## return "<recursive reference>" ## exclude.append(value) s = toDiffableRepr(value, maxLevel) ds = "" i = s.find(" at 0x") start = 0 while (i >= 0): j = s.find(">", i) if (j < i): break ds += s[start:i] start = j i = s.find(" at 0x", start) ds = ds + s[start:] i = ds.find("\\src\\") if (i < 0): i = ds.find("/src/") else: ds = ds.replace("\\", "/") if (i > 0): i += 4 if (ds[i:i+5] == "\\php\\"): i += 4 elif (ds[i:i+8] == "\\python\\"): i += 7 ds = "filepath: ..." + ds[i:] return ds def toString(value, options=0): if ((options & PRINT_OBJ_DIFFABLE) > 0): return toDiffableString(value) elif (not isinstance(value, basestring)): return str(value) return value def typeToString(obj, options=0): if (isinstance(obj, BooleanType)): return "bool" elif (isinstance(obj, UnicodeType)): if ((options & PRINT_OBJ_DIFFABLE) > 0): return "string" return "unicode" elif (isinstance(obj, basestring)): return "string" elif (isinstance(obj, IntType)): return "int" elif (isinstance(obj, LongType)): if ((options & PRINT_OBJ_DIFFABLE) > 0): return "int" return "long" elif (isinstance(obj, FloatType)): return "float" elif (type(obj) == ListType): return "list" elif (isinstance(obj, DictType)): return "dict" elif (isinstance(obj, TupleType)): return "tuple" elif (isinstance(obj, InstanceType)): ## ds = str(type(obj)) ds = "<class %s.%s> " % (obj.__module__, obj.__class__.__name__) else: ds = str(type(obj)) if (options == 0): import activegrid.util.logger options = activegrid.util.logger.testMode(0, PRINT_OBJ_DIFFABLE) if ((options & PRINT_OBJ_DIFFABLE) > 0): if (ds.startswith("<class ")): ix = ds.rfind(".") if (ix < 0): ix = 8 ds = "<class %s>" % ds[ix+1:-2] return ds def nameToString(name, options=0): if (name.startswith("_v_")): return name[3:] if ((options & PRINT_OBJ_DIFFABLE) > 0): ix = name.find("__") if ((ix > 1) and name.startswith("_")): name = name[ix:] return toDiffableString(name) return name PRINT_OBJ_GETATTR = 1 PRINT_OBJ_HIDE_INTERNAL = 2 PRINT_OBJ_COMPACT = 4 PRINT_OBJ_NONONE = 8 PRINT_OBJ_DIFFABLE = 16 PRINT_OBJ_HIDE_EXCLUDED = 32 PRINT_OBJ_INTERNAL = 512 def printObject(out, object, name=None, indent=0, flags=0, exclude=None, remove=None, maxIndent=30): if (name == None): name = "" ## elif (name.endswith("_") and not name.endswith("__")): ## name = name[:-1] if ((remove != None) and (name in asDict(remove))): return False if ((maxIndent != None) and (indent > maxIndent)): print >> out, " "*indent, "%s: %s" % (name, toString(str(object), flags)), if ((flags & PRINT_OBJ_INTERNAL) == 0): print >> out return True finalNewLine = False printed = True if ((flags & (PRINT_OBJ_COMPACT | PRINT_OBJ_HIDE_EXCLUDED)) > 0): if ((exclude != None) and ((object in exclude) or (name in exclude))): return if ((flags & PRINT_OBJ_COMPACT) > 0): indent = 0 if ((flags & PRINT_OBJ_INTERNAL) == 0): finalNewLine = True flags |= PRINT_OBJ_INTERNAL if (object is None): if (flags & PRINT_OBJ_NONONE) == 0: print >> out, " "*indent, name, " = None", else: finalNewLine = False printed = False elif (name.startswith("_") and ((flags & PRINT_OBJ_HIDE_INTERNAL) > 0) and not name.startswith("_v_")): finalNewLine = False printed = False elif (isinstance(object, (list, tuple))): if ((exclude != None) and object in exclude): print >> out, " "*indent, name, " : ", typeToString(object, flags), " of length = ", len(object), " (already printed)", elif ((exclude != None) and name in exclude): print >> out, " "*indent, name, " : ", typeToString(object, flags), " of length = ", len(object), " (excluded)", else: if ((exclude != None) and (len(object) > 0)): exclude.append(object) print >> out, " "*indent, name, " : ", typeToString(object, flags), " of length = %d" % len(object), for i, o in enumerate(object): print >> out printObject(out, o, name="[%d]" % i, indent=indent+2, flags=flags, exclude=exclude, remove=remove, maxIndent=maxIndent) elif (isinstance(object, dict)): if ((exclude != None) and object in exclude): print >> out, " "*indent, name, " : ", typeToString(object, flags), " (already printed)", else: if ((exclude != None) and (len(object) > 0)): exclude.append(object) if (len(name) > 0): print >> out, " "*indent, name, if ((flags & PRINT_OBJ_COMPACT) == 0): print >> out indent += 2 print >> out, " "*indent, "{", if ((flags & PRINT_OBJ_COMPACT) == 0): print >> out keys = object.keys() keys.sort() for key in keys: if (key != None): n = key if (not (isinstance(n, basestring))): n = str(n) else: n = nameToString(n, flags) if ((not n.startswith("_") or ((flags & PRINT_OBJ_HIDE_INTERNAL) == 0))): if printObject(out, object[key], name=n, indent=indent+2, flags=(flags | PRINT_OBJ_INTERNAL), exclude=exclude, remove=remove, maxIndent=maxIndent): if ((flags & PRINT_OBJ_COMPACT) == 0): print >> out else: print >> out, ",", print >> out, " "*indent, "}", elif (hasattr(object, "__dict__")): if (name.startswith("_")): ## and ((flags & PRINT_OBJ_HIDE_INTERNAL) > 0)): print >> out, " "*indent, name, " : ", typeToString(object, flags), elif ((exclude != None) and ((object in exclude) or (object.__dict__ in exclude))): print >> out, " "*indent, name, " : ", typeToString(object, flags), " (already printed)", else: if (exclude != None): exclude.append(object) print >> out, " "*indent, name, " : ", typeToString(object, flags), if ((flags & PRINT_OBJ_GETATTR) == 0): if ((flags & PRINT_OBJ_COMPACT) == 0): print >> out printObject(out, object.__dict__, indent=indent, flags=flags, exclude=exclude, remove=remove, maxIndent=maxIndent) else: if ((flags & PRINT_OBJ_COMPACT) == 0): print >> out ## indent += 2 print >> out, " "*indent, "{", keys = object.__dict__.keys() keys.sort() printed = True for key in keys: if ((exclude != None) and (key in exclude)): continue if (printed and ((flags & PRINT_OBJ_COMPACT) == 0)): print >> out n = nameToString(key, flags) printed = printObject(out, getattr(object, n), name=n, indent=indent+2, flags=flags, exclude=exclude, remove=remove, maxIndent=maxIndent) if ((flags & PRINT_OBJ_COMPACT) == 0): print >> out print >> out, " "*indent, "}", elif (indent < 0): print >> out, object, elif isinstance(object, basestring): if ((exclude != None) and name in exclude): print >> out, " "*indent, name, " : ", typeToString(object, flags), " of length = ", len(object), " (excluded)", elif (len(object) > 100): object = toString(object, flags) print >> out, " "*indent, name, ":", typeToString(object, flags), "[%d] = %s...%s" % (len(object), object[:50], object[-50:]), else: print >> out, " "*indent, name, ":", typeToString(object, flags), "=", toString(object, flags), ## elif (isinstance(object, float)): ## val = str(object) ## if (len(val) > 17): ## val = val[:17] ## print >> out, " "*indent, name, ":", type(object), "=", val, else: print >> out, " "*indent, name, ":", typeToString(object, flags), "=", toString(object, flags), if (finalNewLine): print >> out return printed
PypiClean
/DeepNN-2020.5.18.11.40.23-py3-none-any.whl/inn/models/FM_2.py
import pandas as pd from tensorflow.python.keras.models import Model from tensorflow.python.keras.layers.normalization import BatchNormalization from tensorflow.python.keras.layers import Input, Embedding, Dense, Flatten, Concatenate, Dot, Reshape, Add, Subtract from tensorflow.keras.optimizers import Adam from tensorflow.python.keras.regularizers import l2 from tensorflow.python.keras.callbacks import EarlyStopping, ModelCheckpoint class KerasFM(object): def __init__(self, k_latent=2, kernel_l2=0.1): self.k_latent = k_latent # TODO: embedding dim 经验值 self.kernel_l2 = kernel_l2 def build_model(self, f_sizes): """ :param f_size: sparse feature nunique :return: """ dim_input = len(f_sizes) # +1 input_x = [Input(shape=(1,)) for i in range(dim_input)] # 多列 sparse feature biases = [self.get_embed(x, size, 1) for (x, size) in zip(input_x, f_sizes)] factors = [self.get_embed(x, size) for (x, size) in zip(input_x, f_sizes)] s = Add()(factors) diffs = [Subtract()([s, x]) for x in factors] dots = [Dot(axes=1)([d, x]) for d, x in zip(diffs, factors)] x = Concatenate()(biases + dots) x = BatchNormalization()(x) output = Dense(1, activation='relu', kernel_regularizer=l2(self.kernel_l2))(x) model = Model(inputs=input_x, outputs=[output]) model.compile(optimizer=Adam(clipnorm=0.5), loss='mean_squared_error') # TODO: radam output_f = factors + biases model_features = Model(inputs=input_x, outputs=output_f) return model, model_features def get_embed(self, x_input, x_size, embedding_l2=0.0002): if x_size > 0: # category embed = Embedding(x_size, self.k_latent, input_length=1, embeddings_regularizer=l2(embedding_l2))(x_input) embed = Flatten()(embed) else: embed = Dense(self.k_latent, kernel_regularizer=l2(embedding_l2))(x_input) return embed def get_factors_biases(self, Xs, feature_names, model_features): """We can now retrieve the factors and the biases""" X_pred = model_features.predict(Xs, 2 ** 10) n = len(X_pred) // 2 factors = X_pred[:n] biases = X_pred[-n:] df = pd.DataFrame() for f, X_p in zip(feature_names, factors): for i in range(self.k_latent): df[f'{f}_fm_factor_{i}'] = X_p[:, i] for f, X_p in zip(feature_names, biases): df[f'{f}_fm_bias'] = X_p[:, 0] return df if __name__ == '__main__': from sklearn.datasets import make_classification from sklearn.preprocessing import LabelEncoder X, y = make_classification(n_samples=1000, n_features=7, random_state=42) Xs = [] f_sizes = [] for i in range(X.shape[1]): X[:, i] = LabelEncoder().fit_transform(X[:, i]) f_sizes.append(int(X[:, i].max() + 1)) Xs.append(X[:, i]) print(f_sizes) fm = KerasFM() model, model_features = fm.build_model(f_sizes) earlystopper = EarlyStopping(patience=0, verbose=1) model.fit(Xs, y.ravel(), epochs=10, batch_size=2 ** 7, verbose=1, shuffle=True, sample_weight=None, callbacks=[earlystopper], ) df_ = fm.get_factors_biases(Xs, range(len(Xs)), model_features) print(df_) print(df_.shape) # n_features * 3 print(model.predict(Xs))
PypiClean
/DendroPy_calver-2023.330.2-py3-none-any.whl/dendropy/legacy/ncbi.py
############################################################################## ## DendroPy Phylogenetic Computing Library. ## ## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder. ## All rights reserved. ## ## See "LICENSE.rst" for terms and conditions of usage. ## ## If you use this work or any portion thereof in published work, ## please cite it as: ## ## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library ## for phylogenetic computing. Bioinformatics 26: 1569-1571. ## ############################################################################## """ Wrappers for interacting with NCBI databases. *** DEPRECATED: use dendropy.interop.genbank.GenBankDna, dendropy.interop.genbank.GenBankRna, or dendropy.interop.genbank.GenBankProtein instead *** """ import warnings from dendropy.utility import messaging from dendropy.utility import textprocessing from dendropy.utility import urlio _LOG = messaging.get_logger(__name__) import sys import dendropy import re from dendropy.utility.error import DataParseError GB_FASTA_DEFLINE_PATTERN = re.compile(r'^gi\|(\d+)\|(\w+)\|([\w\d]+).(\d+)\|(.*)$') def parse_accession_number_and_gi_from_gb(gb_str): accession = re.search(r"ACCESSION\s+(\S+)$", gb_str, flags=re.MULTILINE) if accession is None: raise ValueError("Failed to parse accession number") accession = accession.groups()[0].strip() gi = re.search(r'^VERSION\s+\S+\s+GI:([0-9]+)$', gb_str, flags=re.MULTILINE) if gi is None: raise ValueError("Failed to parse GI number") gi = gi.groups()[0].strip() return accession, gi def parse_ncbi_curation_info_from_defline(gb_defline): m = GB_FASTA_DEFLINE_PATTERN.match(gb_defline) if m is not None: return m.groups()[0], m.groups()[2], m.groups()[2] + '.' + m.groups()[3] else: return None def compose_taxon_label_from_gb_defline(gb_defline, num_desc_components=3, separator='_', gbnum_in_front=True, exclude_gbnum=False): """ If ``gb_defline`` matches a GenBank FASTA-format defline structure, then this returns a label: <GB-ACCESSION-ID><SEPARATOR><DESC_COMPONENT(1)><SEPARATOR><DESC_COMPONENT(2)>...<DESC_COMPONENT(n)> So, for example, given the following FASTA label: gi|158931046|gb|EU105975.1| Homo sapiens Ache non-coding region T1584 genomic sequence the corresponding taxon 3-component (default) label will be: EU105975_Homo_sapiens_Ache If ``gb_defline`` does *not* match a GenBank FASTA-format defline structure, then the string is returned unchanged. """ m = GB_FASTA_DEFLINE_PATTERN.match(gb_defline) if m is not None: groups = m.groups() desc_parts = [s.strip() for s in groups[-1].split() if s] if exclude_gbnum: label_parts = desc_parts[:num_desc_components] elif gbnum_in_front: label_parts = [groups[2]] + desc_parts[:num_desc_components] else: label_parts = desc_parts[:num_desc_components] + [groups[2]] return separator.join(label_parts) else: return gb_defline def relabel_taxa_from_defline(taxon_set, num_desc_components=3, separator='_', gbnum_in_front=True, exclude_gbnum=False): """ Examines the labels of each |Taxon| object in ``taxon_set``, and if conforming to a GenBank pattern, translates the labels to a standard format: <GB-ACCESSION-ID><SEPARATOR><DESC_COMPONENT(1)><SEPARATOR><DESC_COMPONENT(2)>...<DESC_COMPONENT(n)> So, for example, given the following FASTA label: gi|158931046|gb|EU105975.1| Homo sapiens Ache non-coding region T1584 genomic sequence the corresponding taxon 3-component (default) label will be: EU105975_Homo_sapiens_Ache """ for taxon in taxon_set: taxon.label = compose_taxon_label_from_gb_defline( gb_defline=taxon.label, num_desc_components=num_desc_components, separator=separator, gbnum_in_front=gbnum_in_front, exclude_gbnum=exclude_gbnum) return taxon_set class Entrez(object): """ Wraps up all interactions with Entrez. Example usage:: >>> from dendropy.interop import ncbi >>> e = ncbi.Entrez(generate_labels=True, ... label_id_in_front=False, ... sort_taxa_by_label=True) >>> d1 = e.fetch_nucleotide_accessions(['EU105474', 'EU105476']) >>> d2 = e.fetch_nucleotide_accession_range(105474, 106045, prefix="EU") """ BASE_URL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils" DATABASES = [ 'pubmed', 'protein', 'nucleotide', 'nuccore', 'nucgss', 'nucest', 'structure', 'genome', 'biosystems', 'books', 'cancerchromosomes', 'cdd', 'gap', 'dbvar', 'domains', 'epigenomics', 'gene', 'genomeprj', 'gensat', 'geo', 'gds', 'homologene', 'journals', 'mesh', 'ncbisearch', 'nlmcatalog', 'omia', 'omim', 'pepdome', 'pmc', 'popset', 'probe', 'proteinclusters', 'pcassay', 'pccompound', 'pcsubstance', 'seqannot', 'snp', 'sra', 'taxonomy', 'toolkit', 'toolkitall', 'unigene', 'unists', 'linkoutpubmed', 'linkoutseq', 'linkoutother', ] class AccessionFetchError(Exception): def __init__(self, accession_ids): Exception.__init__(self, "Failed to retrieve accessions: %s" % (", ".join([str(s) for s in accession_ids]))) def __init__(self, generate_labels=False, label_num_desc_components=3, label_separator='_', label_id_in_front=True, exclude_gbnum_from_label=False, sort_taxa_by_label=False): """ *** DEPRECATED: use dendropy.interop.genbank.GenBankDna, dendropy.interop.genbank.GenBankRna, or dendropy.interop.genbank.GenBankProtein instead *** Instantiates a broker that queries NCBI and returns data. If ``generate_labels`` is |True|, then appropriate labels for sequences will be automatically composed for each sequence based on the GenBank FASTA defline. ``label_num_desc_components`` specifies the number of components from the defline to use. ``label_separator`` specifies the string used to separate the different label components. ``label_id_in_front`` specifies whether the GenBank accession number should form the beginning (|True|) or tail (|False|) end of the label. ``sort_taxa_by_label`` specifies whether the sequences should be sorted by their final label values. """ warnings.warn("This class (and parent module) has been deprecated. Use the classes provided in 'dendropy.interop.genbak' instead", DeprecationWarning) self.generate_labels = generate_labels self.label_num_desc_components = label_num_desc_components self.label_separator = label_separator self.label_id_in_front = label_id_in_front self.exclude_gbnum_from_label = exclude_gbnum_from_label self.sort_taxa_by_label = sort_taxa_by_label def fetch(self, db, ids, rettype): """ Raw fetch. Returns file-like object opened for reading on string returned by query. """ if textprocessing.is_str_type(ids): id_list = ids else: id_list = ",".join([str(i) for i in set(ids)]) params = {'db': db, 'id': id_list, 'rettype': rettype, 'retmode': 'text'} query_url = Entrez.BASE_URL + "/efetch.fcgi?" + urlio.urlencode(params) return urlio.read_url(query_url) def fetch_gbrecs_as_plaintext_dict(self, db, ids, key_field="accession"): db_name = "nucleotide" gb_recs_str = self.fetch(db=db, ids=ids, rettype="gb") gb_recs_str_list = re.split(r"^//$", gb_recs_str, flags=re.MULTILINE) gb_recs_str_list = [gb_rec for gb_rec in gb_recs_str_list if gb_rec.replace("\n", "")] gb_recs_dict = {} for gb_str in gb_recs_str_list: if not gb_str: continue try: accession, gi = parse_accession_number_and_gi_from_gb(gb_str) except TypeError: print("---") print(gb_str) print("---") raise if key_field == "accession": gb_recs_dict[accession] = gb_str elif key_field == "gi": gb_recs_dict[gi] = gb_str else: raise NotImplementedError("Key field '%s' is not supported" % key_field) return gb_recs_dict def fetch_nucleotide_accessions(self, ids, prefix=None, verify=True, matrix_type=dendropy.DnaCharacterMatrix, **kwargs): """ Returns a DnaCharacterMatrix object (or some other type, if specified by ``matrix_type`` argument) populated with sequences from the Entrez nucleotide database with accession numbers given by ``ids`` (a list of accession numbers). If ``prefix`` is given, it is pre-pended to all values given in the id list. Any other keyword arguments given are passed to the constructor of |DnaCharacterMatrix|. **Note that the order of records is *not* the same as the order of ids!!!** """ if prefix is not None: id_list = ["%s%s" % (prefix,i) for i in ids] else: id_list = [str(i) for i in ids] results_str = self.fetch(db='nucleotide', ids=id_list, rettype='fasta') try: d = matrix_type.get_from_string(results_str, 'fasta', **kwargs) except DataParseError: sys.stderr.write("---\nNCBI Entrez Query returned:\n%s\n---\n" % results_str) raise for taxon in d.taxon_set: taxon.ncbi_defline = taxon.label taxon.ncbi_gi, taxon.ncbi_accession, taxon.ncbi_version = parse_ncbi_curation_info_from_defline(taxon.ncbi_defline) if verify: found_ids = set([t.ncbi_accession for t in d.taxon_set]) missing_ids = set(id_list).difference(found_ids) found_ids = set([t.ncbi_gi for t in d.taxon_set]) missing_ids = set(missing_ids).difference(found_ids) if len(missing_ids) > 0: raise Entrez.AccessionFetchError(missing_ids) if self.generate_labels: relabel_taxa_from_defline(d.taxon_set, num_desc_components=self.label_num_desc_components, separator=self.label_separator, gbnum_in_front=self.label_id_in_front, exclude_gbnum=self.exclude_gbnum_from_label) if self.sort_taxa_by_label: d.taxon_set.sort(key=lambda x: x.label) return d def fetch_nucleotide_accession_range(self, first, last, prefix=None, verify=True, matrix_type=dendropy.DnaCharacterMatrix, **kwargs): """ Returns a DnaCharacterMatrix object (or some other type, if specified by the ``matrix_type`` argument) populated with sequences from the Entrez nucleotide database with accession numbers between ``start`` and, up to and *including* ``end``. If ``prefix`` is given, then it is pre-pended to the ids. Any other keyword arguments given are passed to thee constructor of |DnaCharacterMatrix|. """ ids = range(first, last+1) return self.fetch_nucleotide_accessions(ids=ids, prefix=prefix, verify=verify, matrix_type=matrix_type, **kwargs)
PypiClean
/DJModels-0.0.6-py3-none-any.whl/djmodels/db/backends/mysql/base.py
import re from djmodels.core.exceptions import ImproperlyConfigured from djmodels.db import utils from djmodels.db.backends import utils as backend_utils from djmodels.db.backends.base.base import BaseDatabaseWrapper from djmodels.utils.functional import cached_property try: import MySQLdb as Database except ImportError as err: raise ImproperlyConfigured( 'Error loading MySQLdb module.\n' 'Did you install mysqlclient?' ) from err from MySQLdb.constants import CLIENT, FIELD_TYPE # isort:skip from MySQLdb.converters import conversions # isort:skip # Some of these import MySQLdb, so import them after checking if it's installed. from .client import DatabaseClient # isort:skip from .creation import DatabaseCreation # isort:skip from .features import DatabaseFeatures # isort:skip from .introspection import DatabaseIntrospection # isort:skip from .operations import DatabaseOperations # isort:skip from .schema import DatabaseSchemaEditor # isort:skip from .validation import DatabaseValidation # isort:skip version = Database.version_info if version < (1, 3, 7): raise ImproperlyConfigured('mysqlclient 1.3.7 or newer is required; you have %s.' % Database.__version__) # MySQLdb returns TIME columns as timedelta -- they are more like timedelta in # terms of actual behavior as they are signed and include days -- and Django # expects time. django_conversions = { **conversions, **{FIELD_TYPE.TIME: backend_utils.typecast_time}, } # This should match the numerical portion of the version numbers (we can treat # versions like 5.0.24 and 5.0.24a as the same). server_version_re = re.compile(r'(\d{1,2})\.(\d{1,2})\.(\d{1,2})') class CursorWrapper: """ A thin wrapper around MySQLdb's normal cursor class that catches particular exception instances and reraises them with the correct types. Implemented as a wrapper, rather than a subclass, so that it isn't stuck to the particular underlying representation returned by Connection.cursor(). """ codes_for_integrityerror = ( 1048, # Column cannot be null 1690, # BIGINT UNSIGNED value is out of range ) def __init__(self, cursor): self.cursor = cursor def execute(self, query, args=None): try: # args is None means no string interpolation return self.cursor.execute(query, args) except Database.OperationalError as e: # Map some error codes to IntegrityError, since they seem to be # misclassified and Django would prefer the more logical place. if e.args[0] in self.codes_for_integrityerror: raise utils.IntegrityError(*tuple(e.args)) raise def executemany(self, query, args): try: return self.cursor.executemany(query, args) except Database.OperationalError as e: # Map some error codes to IntegrityError, since they seem to be # misclassified and Django would prefer the more logical place. if e.args[0] in self.codes_for_integrityerror: raise utils.IntegrityError(*tuple(e.args)) raise def __getattr__(self, attr): return getattr(self.cursor, attr) def __iter__(self): return iter(self.cursor) class DatabaseWrapper(BaseDatabaseWrapper): vendor = 'mysql' display_name = 'MySQL' # This dictionary maps Field objects to their associated MySQL column # types, as strings. Column-type strings can contain format strings; they'll # be interpolated against the values of Field.__dict__ before being output. # If a column type is set to None, it won't be included in the output. data_types = { 'AutoField': 'integer AUTO_INCREMENT', 'BigAutoField': 'bigint AUTO_INCREMENT', 'BinaryField': 'longblob', 'BooleanField': 'bool', 'CharField': 'varchar(%(max_length)s)', 'DateField': 'date', 'DateTimeField': 'datetime(6)', 'DecimalField': 'numeric(%(max_digits)s, %(decimal_places)s)', 'DurationField': 'bigint', 'FileField': 'varchar(%(max_length)s)', 'FilePathField': 'varchar(%(max_length)s)', 'FloatField': 'double precision', 'IntegerField': 'integer', 'BigIntegerField': 'bigint', 'IPAddressField': 'char(15)', 'GenericIPAddressField': 'char(39)', 'NullBooleanField': 'bool', 'OneToOneField': 'integer', 'PositiveIntegerField': 'integer UNSIGNED', 'PositiveSmallIntegerField': 'smallint UNSIGNED', 'SlugField': 'varchar(%(max_length)s)', 'SmallIntegerField': 'smallint', 'TextField': 'longtext', 'TimeField': 'time(6)', 'UUIDField': 'char(32)', } # For these columns, MySQL doesn't: # - accept default values and implicitly treats these columns as nullable # - support a database index _limited_data_types = ( 'tinyblob', 'blob', 'mediumblob', 'longblob', 'tinytext', 'text', 'mediumtext', 'longtext', 'json', ) operators = { 'exact': '= %s', 'iexact': 'LIKE %s', 'contains': 'LIKE BINARY %s', 'icontains': 'LIKE %s', 'gt': '> %s', 'gte': '>= %s', 'lt': '< %s', 'lte': '<= %s', 'startswith': 'LIKE BINARY %s', 'endswith': 'LIKE BINARY %s', 'istartswith': 'LIKE %s', 'iendswith': 'LIKE %s', } # The patterns below are used to generate SQL pattern lookup clauses when # the right-hand side of the lookup isn't a raw string (it might be an expression # or the result of a bilateral transformation). # In those cases, special characters for LIKE operators (e.g. \, *, _) should be # escaped on database side. # # Note: we use str.format() here for readability as '%' is used as a wildcard for # the LIKE operator. pattern_esc = r"REPLACE(REPLACE(REPLACE({}, '\\', '\\\\'), '%%', '\%%'), '_', '\_')" pattern_ops = { 'contains': "LIKE BINARY CONCAT('%%', {}, '%%')", 'icontains': "LIKE CONCAT('%%', {}, '%%')", 'startswith': "LIKE BINARY CONCAT({}, '%%')", 'istartswith': "LIKE CONCAT({}, '%%')", 'endswith': "LIKE BINARY CONCAT('%%', {})", 'iendswith': "LIKE CONCAT('%%', {})", } isolation_levels = { 'read uncommitted', 'read committed', 'repeatable read', 'serializable', } Database = Database SchemaEditorClass = DatabaseSchemaEditor # Classes instantiated in __init__(). client_class = DatabaseClient creation_class = DatabaseCreation features_class = DatabaseFeatures introspection_class = DatabaseIntrospection ops_class = DatabaseOperations validation_class = DatabaseValidation def get_connection_params(self): kwargs = { 'conv': django_conversions, 'charset': 'utf8', } settings_dict = self.settings_dict if settings_dict['USER']: kwargs['user'] = settings_dict['USER'] if settings_dict['NAME']: kwargs['db'] = settings_dict['NAME'] if settings_dict['PASSWORD']: kwargs['passwd'] = settings_dict['PASSWORD'] if settings_dict['HOST'].startswith('/'): kwargs['unix_socket'] = settings_dict['HOST'] elif settings_dict['HOST']: kwargs['host'] = settings_dict['HOST'] if settings_dict['PORT']: kwargs['port'] = int(settings_dict['PORT']) # We need the number of potentially affected rows after an # "UPDATE", not the number of changed rows. kwargs['client_flag'] = CLIENT.FOUND_ROWS # Validate the transaction isolation level, if specified. options = settings_dict['OPTIONS'].copy() isolation_level = options.pop('isolation_level', 'read committed') if isolation_level: isolation_level = isolation_level.lower() if isolation_level not in self.isolation_levels: raise ImproperlyConfigured( "Invalid transaction isolation level '%s' specified.\n" "Use one of %s, or None." % ( isolation_level, ', '.join("'%s'" % s for s in sorted(self.isolation_levels)) )) self.isolation_level = isolation_level kwargs.update(options) return kwargs def get_new_connection(self, conn_params): return Database.connect(**conn_params) def init_connection_state(self): assignments = [] if self.features.is_sql_auto_is_null_enabled: # SQL_AUTO_IS_NULL controls whether an AUTO_INCREMENT column on # a recently inserted row will return when the field is tested # for NULL. Disabling this brings this aspect of MySQL in line # with SQL standards. assignments.append('SET SQL_AUTO_IS_NULL = 0') if self.isolation_level: assignments.append('SET SESSION TRANSACTION ISOLATION LEVEL %s' % self.isolation_level.upper()) if assignments: with self.cursor() as cursor: cursor.execute('; '.join(assignments)) def create_cursor(self, name=None): cursor = self.connection.cursor() return CursorWrapper(cursor) def _rollback(self): try: BaseDatabaseWrapper._rollback(self) except Database.NotSupportedError: pass def _set_autocommit(self, autocommit): with self.wrap_database_errors: self.connection.autocommit(autocommit) def disable_constraint_checking(self): """ Disable foreign key checks, primarily for use in adding rows with forward references. Always return True to indicate constraint checks need to be re-enabled. """ self.cursor().execute('SET foreign_key_checks=0') return True def enable_constraint_checking(self): """ Re-enable foreign key checks after they have been disabled. """ # Override needs_rollback in case constraint_checks_disabled is # nested inside transaction.atomic. self.needs_rollback, needs_rollback = False, self.needs_rollback try: self.cursor().execute('SET foreign_key_checks=1') finally: self.needs_rollback = needs_rollback def check_constraints(self, table_names=None): """ Check each table name in `table_names` for rows with invalid foreign key references. This method is intended to be used in conjunction with `disable_constraint_checking()` and `enable_constraint_checking()`, to determine if rows with invalid references were entered while constraint checks were off. """ with self.cursor() as cursor: if table_names is None: table_names = self.introspection.table_names(cursor) for table_name in table_names: primary_key_column_name = self.introspection.get_primary_key_column(cursor, table_name) if not primary_key_column_name: continue key_columns = self.introspection.get_key_columns(cursor, table_name) for column_name, referenced_table_name, referenced_column_name in key_columns: cursor.execute( """ SELECT REFERRING.`%s`, REFERRING.`%s` FROM `%s` as REFERRING LEFT JOIN `%s` as REFERRED ON (REFERRING.`%s` = REFERRED.`%s`) WHERE REFERRING.`%s` IS NOT NULL AND REFERRED.`%s` IS NULL """ % ( primary_key_column_name, column_name, table_name, referenced_table_name, column_name, referenced_column_name, column_name, referenced_column_name, ) ) for bad_row in cursor.fetchall(): raise utils.IntegrityError( "The row in table '%s' with primary key '%s' has an invalid " "foreign key: %s.%s contains a value '%s' that does not " "have a corresponding value in %s.%s." % ( table_name, bad_row[0], table_name, column_name, bad_row[1], referenced_table_name, referenced_column_name, ) ) def is_usable(self): try: self.connection.ping() except Database.Error: return False else: return True @cached_property def mysql_server_info(self): with self.temporary_connection() as cursor: cursor.execute('SELECT VERSION()') return cursor.fetchone()[0] @cached_property def mysql_version(self): match = server_version_re.match(self.mysql_server_info) if not match: raise Exception('Unable to determine MySQL version from version string %r' % self.mysql_server_info) return tuple(int(x) for x in match.groups()) @cached_property def mysql_is_mariadb(self): # MariaDB isn't officially supported. return 'mariadb' in self.mysql_server_info.lower()
PypiClean
/ClueDojo-1.4.3-1.tar.gz/ClueDojo-1.4.3-1/src/cluedojo/static/dojox/data/util/JsonQuery.js
if(!dojo._hasResource["dojox.data.util.JsonQuery"]){ dojo._hasResource["dojox.data.util.JsonQuery"]=true; dojo.provide("dojox.data.util.JsonQuery"); dojo.declare("dojox.data.util.JsonQuery",null,{useFullIdInQueries:false,_toJsonQuery:function(_1,_2){ var _3=true; var _4=this; function _5(_6,_7){ var _8=_7.__id; if(_8){ var _9={}; _9[_4.idAttribute]=_4.useFullIdInQueries?_7.__id:_7[_4.idAttribute]; _7=_9; } for(var i in _7){ var _a=_7[i]; var _b=_6+(/^[a-zA-Z_][\w_]*$/.test(i)?"."+i:"["+dojo._escapeString(i)+"]"); if(_a&&typeof _a=="object"){ _5(_b,_a); }else{ if(_a!="*"){ _c+=(_3?"":"&")+_b+((!_8&&typeof _a=="string"&&_1.queryOptions&&_1.queryOptions.ignoreCase)?"~":"=")+(_4.simplifiedQuery?encodeURIComponent(_a):dojo.toJson(_a)); _3=false; } } } }; if(_1.query&&typeof _1.query=="object"){ var _c="[?("; _5("@",_1.query); if(!_3){ _c+=")]"; }else{ _c=""; } _1.queryStr=_c.replace(/\\"|"/g,function(t){ return t=="\""?"'":t; }); }else{ if(!_1.query||_1.query=="*"){ _1.query=""; } } var _d=_1.sort; if(_d){ _1.queryStr=_1.queryStr||(typeof _1.query=="string"?_1.query:""); _3=true; for(i=0;i<_d.length;i++){ _1.queryStr+=(_3?"[":",")+(_d[i].descending?"\\":"/")+"@["+dojo._escapeString(_d[i].attribute)+"]"; _3=false; } if(!_3){ _1.queryStr+="]"; } } if(_2&&(_1.start||_1.count)){ _1.queryStr=(_1.queryStr||(typeof _1.query=="string"?_1.query:""))+"["+(_1.start||"")+":"+(_1.count?(_1.start||0)+_1.count:"")+"]"; } if(typeof _1.queryStr=="string"){ _1.queryStr=_1.queryStr.replace(/\\"|"/g,function(t){ return t=="\""?"'":t; }); return _1.queryStr; } return _1.query; },jsonQueryPagination:true,fetch:function(_e){ this._toJsonQuery(_e,this.jsonQueryPagination); return this.inherited(arguments); },isUpdateable:function(){ return true; },matchesQuery:function(_f,_10){ _10._jsonQuery=_10._jsonQuery||dojox.json.query(this._toJsonQuery(_10)); return _10._jsonQuery([_f]).length; },clientSideFetch:function(_11,_12){ _11._jsonQuery=_11._jsonQuery||dojox.json.query(this._toJsonQuery(_11)); return this.clientSidePaging(_11,_11._jsonQuery(_12)); },querySuperSet:function(_13,_14){ if(!_13.query){ return _14.query; } return this.inherited(arguments); }}); }
PypiClean
/My-Serializer-For-Json-And-XML-For_Lab3-5-0.1.1.tar.gz/My-Serializer-For-Json-And-XML-For_Lab3-5-0.1.1/Serializators/JSON.py
from Serializators.Core import Serialize from Serializators.Core.functions_for_deserialize import Deserialize class JsonSerializer: data_serializer = Serialize() data_deserializer = Deserialize() def dumps(self, obj): packed = self.data_serializer.serialize(obj) if isinstance(packed, (list, tuple)): return self.__list_n_tuple_to_string_util(packed) if isinstance(packed, dict): return self.__dict_to_string_util(packed) return self.__ser_primitive(obj) def dump(self, obj, file): file.write(self.dumps(obj)) def loads(self, string): result, ind = self.__loads_with_index(string, 0) return self.data_deserializer.deserialize(result) def load(self, file): return self.loads(file.read()) def __list_n_tuple_to_string_util(self, collection): if not collection: return '[]' result = '[' for item in collection: if isinstance(item, dict): result += f'{self.__dict_to_string_util(item)},' elif isinstance(item, (list, tuple)): result += f'{self.__list_n_tuple_to_string_util(item)},' else: result += f'{self.__ser_primitive(item)},' return result[:-1] + ']' def __dict_to_string_util(self, dictionary): if not dictionary: return '{}' result = '{' for key, value in dictionary.items(): if isinstance(value, dict): result += f'"{key}": {self.__dict_to_string_util(value)},' elif isinstance(value, (list, tuple)): result += f'"{key}": {self.__list_n_tuple_to_string_util(value)},' else: result += f'"{key}": {self.__ser_primitive(value)},' return result[:-1] + '}' def __ser_primitive(self,obj): if isinstance(obj,str): obj= f"'{obj}'" return f'"{str(obj)}"' def __deserialize_list(self, string, index): end_index = index + 1 bracket_count = 1 while bracket_count > 0 and end_index < len(string): if string[end_index] == '[': bracket_count += 1 if string[end_index] == ']': bracket_count -= 1 end_index += 1 index += 1 result = [] while index < end_index: if string[index] in (',', ' '): index += 1 continue if end_index - index < 2: break element, index = self.__loads_with_index(string, index) result.append(element) return result, end_index + 1 def __loads_with_index(self, string, index): match string[index]: case '"': if string[index+1] == "'": return self.__deserialize_string(string, index+2) else: return self.__deserialize_primitive(string, index) case '[': return self.__deserialize_list(string, index) case '{': return self.__deserialize_dict(string, index) def __deserialize_dict(self,string,index): end_index=index bracket_count=1 while bracket_count>0 and end_index+1<len(string): end_index+=1 if string[end_index]=='{': bracket_count+=1 if string[end_index]=='}': bracket_count-=1 index+=1 result={} while index<end_index: if string[index] in (',',' '): index+=1 continue key,index = self.__loads_with_index(string,index) while string[index] in (':',' '): index+=1 value,index=self.__loads_with_index(string,index) result[key]=value return result,end_index+1 def __string_catcher(self, string, index): end_index = index while string[end_index] != '"' and end_index < len(string): end_index += 1 data_slice = string[index:end_index] return data_slice, end_index + 3 def __deserialize_string(self, string, index): end_index = index while string[end_index] != "'" and end_index < len(string): end_index += 1 data_slice = string[index:end_index] return data_slice, end_index + 3 def __deserialize_list(self, string, index): end_index = index + 1 bracket_count = 1 while bracket_count > 0 and end_index < len(string): if string[end_index] == '[': bracket_count += 1 if string[end_index] == ']': bracket_count -= 1 end_index += 1 index += 1 result = [] while index < end_index: if string[index] in (',', ' '): index += 1 continue if end_index - index < 2: break element, index = self.__loads_with_index(string, index) result.append(element) return result, end_index + 1 def __deserialize_number(self, string, index): end_index = index while string[end_index] != '"' and end_index < len(string): end_index += 1 data_slice = string[index:end_index] try: if '.' in data_slice: return float(data_slice), end_index + 1 else: return int(data_slice), end_index + 1 except: return self.__string_catcher(string, index) def __deserialize_primitive(self, string, index): index += 1 if string[index] == 'N': return None, index + 5 elif string[index] == 'T': return True, index + 5 elif string[index] == 'F': return False, index + 6 else: return self.__deserialize_number(string, index)
PypiClean
/EDDIE-Tool-1.0.0.tar.gz/EDDIE-Tool-1.0.0/eddietool/arch/Linux/df.py
__version__ = '$Revision: 895 $' __copyright__ = 'Copyright (c) Chris Miles 1999-2005' __author__ = 'Chris Miles' __license__ = ''' This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ''' # Python Modules import re, string # Eddie Modules from eddietool.common import datacollect, log, utils # This fetches data by parsing system calls of common commands. This was done because # it was quick and easy to implement and port to multiple platforms. I know this is # a bit ugly, but will clean it up later with more efficient code that fetches data # directly from /proc or the kernel. CM 19990929 class dfList(datacollect.DataCollect): """dfList provides access to disk usage statistics.""" def __init__(self): apply( datacollect.DataCollect.__init__, (self,) ) ################################################################## # Public, thread-safe, methods def __str__(self): """Create string to display disk usage stats.""" d = self.getHash() rv = "" for item in d.keys(): rv = rv + str(d[item]) + '\n' return(rv) def __getitem__(self, name): """ Extends DataCollect.__getitem__() to search mounthash if default datahash fails. The dfList object can be treated like a dictionary and keyed by either device or mount point. """ try: r = apply( datacollect.DataCollect.__getitem__, (self, name) ) except KeyError: self.data_semaphore.acquire() # thread-safe access to self.data try: r = self.data.mounthash[name] # try to find mount point except KeyError: self.data_semaphore.release() raise KeyError, "Key %s not found in data hashes" % (name) self.data_semaphore.release() return r ################################################################## # Private methods. No thread safety if not using public methods. def collectData(self): """ Collect disk usage data. """ # Get information about all local filesystems from 'df'. rawList = utils.safe_popen('df -l', 'r') rawList.readline() # skip header self.data.datahash = {} self.data.mounthash = {} lines = rawList.read() lines = re.sub( r'\n ', '', lines) lines = string.split(lines, '\n') for line in lines: fields = string.split(line) if len(fields) == 6: p = df(fields) self.data.datahash[fields[0]] = p # dictionary of filesystem devices self.data.mounthash[fields[5]] = p # dictionary of mount points utils.safe_pclose( rawList ) log.log( "<df>dfList.collectData(): filesystem data collected", 7 ) ################################################################## # Define single filesystem information objects. class df: """df object holds stats on disk usage for a file system.""" def __init__(self, *arg): self.raw = arg[0] self.data = {} self.data['fsname'] = self.raw[0] # Filesystem name (device) self.data['size'] = int(self.raw[1]) # Size of filesystem self.data['used'] = int(self.raw[2]) # kb used self.data['avail'] = int(self.raw[3]) # kb free self.data['pctused'] = float(self.raw[4][:-1]) # Percentage Used self.data['mountpt'] = self.raw[5] # Mount point def __str__(self): str = "%-20s %10s %10s %10s %4s %-12s\n" % ("Filesystem","Size","Used","Available","Use%","Mounted on") str = str + "%-20s %10s %10s %10s %4s %-12s" % (self.data['fsname'],self.data['size'],self.data['used'],self.data['avail'],self.data['pctused'],self.data['mountpt']) return(str) def getHash(self): """ Return a copy of the filesystem data dictionary. """ hash_copy = {} hash_copy.update(self.data) return hash_copy ## ## END - df.py ##
PypiClean
/DACBench-0.2.0.tar.gz/DACBench-0.2.0/dacbench/wrappers/policy_progress_wrapper.py
import matplotlib.pyplot as plt import numpy as np from gymnasium import Wrapper class PolicyProgressWrapper(Wrapper): """ Wrapper to track progress towards optimal policy. Can only be used if a way to obtain the optimal policy given an instance can be obtained. """ def __init__(self, env, compute_optimal): """ Initialize wrapper. Parameters ---------- env : gym.Env Environment to wrap compute_optimal : function Function to compute optimal policy """ super(PolicyProgressWrapper, self).__init__(env) self.compute_optimal = compute_optimal self.episode = [] self.policy_progress = [] def __setattr__(self, name, value): """ Set attribute in wrapper if available and in env if not. Parameters ---------- name : str Attribute to set value Value to set attribute to """ if name in [ "compute_optimal", "env", "episode", "policy_progress", "render_policy_progress", ]: object.__setattr__(self, name, value) else: setattr(self.env, name, value) def __getattribute__(self, name): """ Get attribute value of wrapper if available and of env if not. Parameters ---------- name : str Attribute to get Returns ------- value Value of given name """ if name in [ "step", "compute_optimal", "env", "episode", "policy_progress", "render_policy_progress", ]: return object.__getattribute__(self, name) else: return getattr(self.env, name) def step(self, action): """ Execute environment step and record distance. Parameters ---------- action : int action to execute Returns ------- np.array, float, bool, bool, dict state, reward, terminated, truncated, metainfo """ state, reward, terminated, truncated, info = self.env.step(action) self.episode.append(action) if terminated or truncated: optimal = self.compute_optimal(self.env.instance) self.policy_progress.append( np.linalg.norm(np.array(optimal) - np.array(self.episode)) ) self.episode = [] return state, reward, terminated, truncated, info def render_policy_progress(self): """Plot progress.""" plt.figure(figsize=(12, 6)) plt.plot(np.arange(len(self.policy_progress)), self.policy_progress) plt.title("Policy progress over time") plt.xlabel("Episode") plt.ylabel("Distance to optimal policy") plt.show()
PypiClean
/Data-CAT-0.7.2.tar.gz/Data-CAT-0.7.2/LICENSE.md
The data-CAT is an Open Source project supported by the VU University Amsterdam, the Netherlands eScience Center (NLeSC) and Scientific Computing & Modelling NV (SCM). The terms of the [LGPL-3.0 license]* apply. As an exception to the LGPL-3.0 license, you agree to grant SCM a [BSD 3-Clause license]** to the contributions you commit on this Github or provide to SCM in another manner. \* https://opensource.org/licenses/LGPL-3.0 ** https://opensource.org/licenses/BSD-3-Clause [LGPL-3.0 license]: https://opensource.org/licenses/LGPL-3.0 "LGPL-3.0 license" [BSD 3-Clause license]: https://opensource.org/licenses/BSD-3-Clause "BSD 3-Clause license"
PypiClean
/ESMValTool-2.9.0-py3-none-any.whl/esmvaltool/cmorizers/data/formatters/datasets/hwsd.py
import logging import os import iris from cf_units import Unit from iris import NameConstraint from esmvaltool.cmorizers.data import utilities as utils logger = logging.getLogger(__name__) def _extract_variable(short_name, var, cfg, filepath, out_dir): """Extract variable.""" raw_var = var.get('raw', short_name) cube = iris.load_cube(filepath, NameConstraint(var_name=raw_var)) # Sum over levels if short_name in ('cSoil', ): level_coord = iris.coords.DimCoord([0, 1], long_name='level') cube.add_dim_coord(level_coord, 0) cube = cube.collapsed('level', iris.analysis.SUM) # Fix coordinates if var['mip'] != 'fx': cube = iris.util.new_axis(cube) time_dim = iris.coords.DimCoord( [183.0], bounds=[0.0, 366.0], units=Unit('days since 2000-01-01 00:00:00'), standard_name='time', var_name='time', long_name='time') cube.add_dim_coord(time_dim, 0) utils.convert_timeunits(cube, 1950) utils.fix_coords(cube) # Fix units if 'kg C' in cube.units.origin: cube.units = Unit(cube.units.origin.replace('C', '')) cmor_info = cfg['cmor_table'].get_variable(var['mip'], short_name) cube.convert_units(cmor_info.units) # Fix metadata attrs = cfg['attributes'] attrs['mip'] = var['mip'] utils.fix_var_metadata(cube, cmor_info) utils.set_global_atts(cube, attrs) # Save variable utils.save_variable(cube, short_name, out_dir, attrs, unlimited_dimensions=['time']) def cmorization(in_dir, out_dir, cfg, cfg_user, start_date, end_date): """Cmorization func call.""" filepath = os.path.join(in_dir, cfg['filename']) logger.info("Reading file '%s'", filepath) # Run the cmorization for (short_name, var) in cfg['variables'].items(): logger.info("CMORizing variable '%s'", short_name) _extract_variable(short_name, var, cfg, filepath, out_dir)
PypiClean
/GenIce-1.0.11.tar.gz/GenIce-1.0.11/genice/lattices/Struct71.py
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24 51 59 168 71 36 91 62 227 157 4 106 138 178 75 178 197 2 200 202 52 6 197 188 104 84 86 15 50 99 90 99 91 184 70 147 165 186 191 3 211 211 146 175 160 207 40 109 56 32 145 123 64 7 96 135 105 124 55 219 118 137 36 115 181 167 73 187 10 159 215 159 216 190 23 39 52 114 144 172 131 190 111 174 194 208 37 76 93 87 88 63 61 67 68 72 103 203 23 227 17 29 158 92 55 116 225 12 105 27 64 105 17 114 58 24 20 221 196 143 211 162 189 141 42 85 49 160 183 13 100 55 79 148 174 82 94 223 207 190 60 196 11 192 172 201 26 50 173 28 186 217 208 220 191 30 98 217 179 97 8 117 138 149 189 222 49 208 17 112 44 103 89 216 60 139 18 110 151 182 69 160 205 200 19 157 57 137 134 206 217 133 104 139 93 200 145 21 223 140 76 126 64 120 177 201 145 67 31 115 54 152 53 33 166 22 185 148 123 157 226 45 149 80 138 27 127 40 107 206 94 21 46 66 222 86 131 171 222 102 130 153 181 99 65 168 25 169 26 30 4 185 74 15 164 62 125 119 67 209 152 109 172 200 214 181 47 39 77 158 27 102 78 193 205 34 98 32 97 214 73 2 180 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0.625 0.625 0.06989 0.64917 0.5 0.33643 0.7808 0.1875 0.28343 0.50913 0.6875 0.51671 0.5625 0.3125 0.62712 0.18856 0.3125 0.0105 0.6875 0.3125 0.9895 0.3125 0.3125 0.48329 0.4375 0.3125 0.65482 0.81356 0.6875 0.15987 0.33667 0.8125 0.1995 0.6636 0.6875 0.84013 0.66333 0.625 0.42741 0.87394 0.125 0.71287 0.64784 0.5 0.23059 0.79808 0.0 0.23059 0.70192 0.0 0.53342 0.875 0.0 0.51536 0.71814 0.8125 0.34013 0.93511 0.8125 0.0105 0.8125 0.5 0.87037 0.70192 0.125 0.28713 0.35216 0.0 0.76941 0.29808 0.0 0.87037 0.79808 0.3125 0.71657 0.00913 0.3125 0.8005 0.1636 0.6875 0.92537 0.50709 0.3125 0.28343 0.99087 0.8125 0.51671 0.9375 0.1875 0.48059 0.6875 0.5 0.46659 0.375 0.1875 0.48329 0.0625 0.8125 0.51941 0.3125 0.0 0.97525 0.78124 0.6875 0.87512 0.96901 0.3125 0.02 0.0625 0.8125 0.98 0.5625 0.25 0.75115 0.75 0.375 0.71287 0.85216 0.1875 0.37289 0.68856 0.5 0.32208 0.62633 0.6875 0.48329 0.4375 0.6875 0.65482 0.81356 0.3125 0.15987 0.33667 0.1875 0.1995 0.6636 0.3125 0.84013 0.66333 0.875 0.42741 0.62606 0.0 0.46659 0.125 0.5 0.60229 0.62367 0.0 0.72027 0.39784 0.1875 0.62712 0.31144 0.8125 0.48329 0.0625 """ coord= "relative" cages=""" 12 -0.25 -0.43317 -0.25 12 0.5 -0.5 1.0 14 0.0 -0.29673 -0.12212 16 0.0 -0.57224 -0.12744 12 0.5 -0.3541 1.00425 14 0.5 -0.29673 0.62212 15 0.5 0.15756 0.59669 15 -0.5 -0.15756 -0.59669 14 0.0 0.29673 0.12212 15 0.5 0.20097 0.09562 14 0.5 0.06099 -0.12496 12 0.0 0.5 0.5 16 0.5 -0.57224 0.62744 12 0.25 0.43317 0.25 12 0.25 0.71808 0.25 14 0.0 0.06099 0.62496 12 0.25 -0.07999 0.75 16 0.5 0.57224 0.37256 12 -0.25 -0.71808 -0.25 14 0.0 -0.06099 -0.62496 12 0.0 -0.3541 -0.50425 15 0.5 -0.20097 0.90438 12 0.25 -0.71808 0.75 15 0.0 -0.20097 -0.40438 12 -0.25 0.43317 -0.75 15 0.0 0.15756 -0.09669 12 0.25 0.07999 0.25 12 0.25 -0.43317 0.75 12 0.0 0.3541 0.50425 12 0.5 0.0 0.5 15 0.0 0.20097 0.40438 14 0.5 -0.06099 1.12496 14 0.5 0.29673 0.37788 12 0.5 0.3541 -0.00425 16 0.0 0.57224 0.12744 15 0.0 -0.15756 1.09669 12 -0.25 0.07999 -0.75 12 -0.25 -0.07999 -0.25 12 0.0 0.0 0.0 12 -0.25 0.71808 -0.75 """ bondlen = 3 cell = """ 13.48668961126573 49.74996750158407 17.7840545616594 """ density = 0.5711335266668782 from genice.cell import cellvectors cell = cellvectors(a=13.48668961126573, b=49.74996750158407, c=17.7840545616594)
PypiClean
/Flask_AdminLTE3-1.0.9-py3-none-any.whl/flask_adminlte3/static/plugins/moment/locale/ar-tn.js
;(function (global, factory) { typeof exports === 'object' && typeof module !== 'undefined' && typeof require === 'function' ? factory(require('../moment')) : typeof define === 'function' && define.amd ? define(['../moment'], factory) : factory(global.moment) }(this, (function (moment) { 'use strict'; //! moment.js locale configuration var arTn = moment.defineLocale('ar-tn', { months: 'جانفي_فيفري_مارس_أفريل_ماي_جوان_جويلية_أوت_سبتمبر_أكتوبر_نوفمبر_ديسمبر'.split( '_' ), monthsShort: 'جانفي_فيفري_مارس_أفريل_ماي_جوان_جويلية_أوت_سبتمبر_أكتوبر_نوفمبر_ديسمبر'.split( '_' ), weekdays: 'الأحد_الإثنين_الثلاثاء_الأربعاء_الخميس_الجمعة_السبت'.split('_'), weekdaysShort: 'أحد_إثنين_ثلاثاء_أربعاء_خميس_جمعة_سبت'.split('_'), weekdaysMin: 'ح_ن_ث_ر_خ_ج_س'.split('_'), weekdaysParseExact: true, longDateFormat: { LT: 'HH:mm', LTS: 'HH:mm:ss', L: 'DD/MM/YYYY', LL: 'D MMMM YYYY', LLL: 'D MMMM YYYY HH:mm', LLLL: 'dddd D MMMM YYYY HH:mm', }, calendar: { sameDay: '[اليوم على الساعة] LT', nextDay: '[غدا على الساعة] LT', nextWeek: 'dddd [على الساعة] LT', lastDay: '[أمس على الساعة] LT', lastWeek: 'dddd [على الساعة] LT', sameElse: 'L', }, relativeTime: { future: 'في %s', past: 'منذ %s', s: 'ثوان', ss: '%d ثانية', m: 'دقيقة', mm: '%d دقائق', h: 'ساعة', hh: '%d ساعات', d: 'يوم', dd: '%d أيام', M: 'شهر', MM: '%d أشهر', y: 'سنة', yy: '%d سنوات', }, week: { dow: 1, // Monday is the first day of the week. doy: 4, // The week that contains Jan 4th is the first week of the year. }, }); return arTn; })));
PypiClean
/Eddy's%20Memory%20Game-1.0.zip/Eddy's Memory Game-1.0/functions.py
__author__="Edward McKnight (EM-Creations.co.uk)" __date__ ="$05-Jul-2011 09:48:41$" def clearScreen(numlines=100): import os if os.name == "posix": # Unix/Linux/MacOS/BSD/etc os.system('clear') elif os.name in ("nt", "dos", "ce"): # DOS/Windows os.system('CLS') else: # Fallback for other operating systems. print '\n' * numlines return; def displayMainMenu(): print "|=======================================|" print "|============== MAIN MENU ==============|" print "|=======================================|" print "| Option | Description |" print "|---------------------------------------|" print "| 1. | Set up new game |" print "| 2. | Word Database |" print "| 3. | Highscores |" print "| 4. | Credits |" print "| 5. | Exit |" print "|=======================================|" return; def displayWordDBMenu(): print "|=======================================|" print "|============ Word Database ============|" print "|=======================================|" print "| Option | Description |" print "|---------------------------------------|" print "| 1. | View Words |" print "| 2. | Add word |" print "| 3. | Remove Word |" print "| 4. | Return to main menu |" print "|=======================================|" return; def displayHighScores(): print "|==========================================|" print "|============== Highscores ==============|" print "|==========================================|" print "| Rank | Name | Level Reached | Difficulty |" print "|------------------------------------------|" highScores = getHighScores() i = 0; while (i < len(highScores)): print "| "+str(i+1)+" | "+highScores[i][0]+" | "+highScores[i][1]+" | "+highScores[i][2] i += 1; print "|==========================================|" return; def displayCurrentWords(): words = getCurrentWords() print "|========= Current Words =========|" i = 0 while (i < len(words)): print str(i+1)+". "+words[i] i += 1 return; def getCurrentWords(): wordFile = open("words.emg", "r") words = wordFile.read() words = words.split(",") wordFile.close() return words; def getHighScores(): hsFile = open("highscores.emg", "r") highScores = hsFile.read() highScores = highScores.split(";") i = 0 while (i < len(highScores)): highScores[i] = highScores[i].split(",") i += 1; highScores = sorted(highScores, key=lambda k: int(k[1]), reverse=True) # Sort the array so the person with the highest score is listed first hsFile.close() return highScores; def saveHighScore(level, difficulty): print print "|========= Save HighScore =========|" print "Please type in your name." print response = str(raw_input("Your Name: ")) # This is effectively a do while loop response = response.strip() if (len(response) < 3 or len(response) > 29 or not response.isalpha()): print print "Your name must be longer than 2 characters and shorter than 29 characters and must not contain numbers!" while (len(response) < 3 or len(response) > 29 or not response.isalpha()): response = str(raw_input("Your Name: ")) response = response.strip() if (len(response) > 2 and len(response) < 29 and response.isalpha()): break else: print print "Your name must be longer than 2 characters and shorter than 29 characters and must not contain numbers!" name = response.lower() hsFile = open("highscores.emg", "a") hsFile.write(";"+name+","+str(level)+","+str(difficulty)) hsFile.close() print "Your highscore has been saved!" return; def addWord(): print "|========= Add Word =========|" print "Please type in a word which is between 3 and 28 characters that you wish to add to the word database." print response = str(raw_input("New word: ")) # This is effectively a do while loop response = response.strip() if (len(response) < 3 or len(response) > 29 or not response.isalpha()): print print "The word must be longer than 2 characters and shorter than 29 characters and must not contain numbers!" while (len(response) < 3 or len(response) > 29 or not response.isalpha()): response = str(raw_input("New word: ")) response = response.strip() if (len(response) > 2 and len(response) < 29 and response.isalpha()): break else: print print "The word must be longer than 2 characters and shorter than 29 characters and must not contain numbers!" newWord = response.lower() wordFile = open("words.emg", "a") wordFile.write(","+newWord) wordFile.close() print "New word successfully added!" return; def removeWord(): print "|========= Remove Word =========|" print "Please type in the word you want to remove from the word database." print response = str(raw_input("Word to remove: ")) # This is effectively a do while loop response = response.strip() response = response.lower() words = getCurrentWords() wordFound = response in words #Check if the response variable is found within the words list if (wordFound): words.remove(response) wordFile = open("words.emg", "w") wordFile.write(words[0]) i = 1 while (i < len(words)): wordFile.write(","+words[i]) i += 1 wordFile.close() print "\""+response+"\" successfully removed from the word database." else: print "\""+response+"\" is not in the word database." return; def displayCredits(): print "|======================================|" print "|========= Eddy's Memory Game =========|" print "|======================================|" print "| Created by Edward McKnight |" print "| Version 1.0 |" print "| Programmed in Python |" print "| www.EM-Creations.co.uk |" print "|======================================|" return; def playWordGame(difficulty): import random import time if (difficulty == 'easy'): pauseTime = 7 elif (difficulty == 'medium'): pauseTime = 5 elif (difficulty == 'hard'): pauseTime = 3 print print "You are about to play the word version of Eddy's Memory Game.\nYou will be given "+str(pauseTime)+" seconds to remember the sequence of words before having to retype them." print "Note that after the first level you need to include a comma (,) between words!" print raw_input("Press enter when you're ready to begin...") print words = getCurrentWords() wordSequence = "" level = 1 # Set level to 1 while(True): print "Level "+str(level)+":" newWord = random.randrange(0, len(words)) newWord = words[newWord] if (level > 1): wordSequence = wordSequence+","+newWord else: wordSequence = newWord print "Remember this word: "+newWord time.sleep(pauseTime) clearScreen() userSequence = raw_input("Please type in the sequence of words: ") if (userSequence != wordSequence): print "Incorrect! You have lost! You got to level: "+str(level) print "The correct answer was: "+wordSequence print response = str(raw_input("Would you like to save your score? (y/n): ")) # This is effectively a do while loop if (response != 'y' and response != 'n'): print print "Please type either y or n." while (response != 'y' and response != 'n'): response = str(raw_input("Would you like to save your score? (y/n): ")) if (response == 'y' or response == 'n'): break; else: print print "Please type either y or n." if (response == 'y'): saveHighScore(level, difficulty) print raw_input("Press enter to return to the Main Menu...") else: raw_input("Press enter to return to the Main Menu...") break; break; else: print "Correct! Moving onto the next level..." print level+= 1 # Increment level return; def playNumberGame(difficulty): import random import time if (difficulty == 'easy'): pauseTime = 7 elif (difficulty == 'medium'): pauseTime = 5 elif (difficulty == 'hard'): pauseTime = 3 print print "You are about to play the number version of Eddy's Memory Game.\nYou will be given "+str(pauseTime)+" seconds to remember the sequence of numbers before having to retype them." print raw_input("Press enter when you're ready to begin...") numberSequence = "" level = 1 # Set level to 1 while(True): print "Level "+str(level)+":" newNum = random.randrange(0, 9) if (level > 1): numberSequence = numberSequence+str(newNum) else: numberSequence = str(newNum) print "Remember this number: "+str(newNum) time.sleep(pauseTime) clearScreen() userSequence = raw_input("Please type in the sequence of numbers: ") if (userSequence != numberSequence): print "Incorrect! You have lost! You got to level: "+str(level) print "The correct answer was: "+numberSequence print response = str(raw_input("Would you like to save your score? (y/n): ")) # This is effectively a do while loop if (response != 'y' and response != 'n'): print print "Please type either y or n." while (response != 'y' and response != 'n'): response = str(raw_input("Would you like to save your score? (y/n): ")) if (response == 'y' or response == 'n'): break; else: print print "Please type either y or n." if (response == 'y'): saveHighScore(level, difficulty) print raw_input("Press enter to return to the Main Menu...") else: raw_input("Press enter to return to the Main Menu...") break; break; else: print "Correct! Moving onto the next level..." print level+= 1 # Increment level return;
PypiClean
/CircleBlock-1.1.0.tar.gz/CircleBlock-1.1.0/README.md
<div style="display: flex; justify-content: center;"> <img src="images/logo.png" alt="CircleBlock Logo"> </div> <div style="display: flex; justify-content: center;"> <h1>CircleBlock</h1> </div> CircleBlock is a class that monitors the file system in the project root directory. This class detects changes in the file system and automatically updates the exportable functions of each module in each package's `__init__.py` file. [![English](https://img.shields.io/badge/language-English-orange.svg)](README.md) [![Korean](https://img.shields.io/badge/language-Korean-blue.svg)](README.ko.md) ## Features 1. Start/stop file system monitoring 2. Get a list of exportable functions within a module 3. Initialize and update all `__init__.py` files in a directory ## Installation To install CircleBlock, use the following command: ``` pipenv install circleblock ``` ## Usage (CLI) ### Start monitoring To start monitoring the file system, use the following command: ``` ccbk run ``` ### Stop monitoring To stop monitoring the file system, use the following command: ``` ccbk stop ``` ### Initialize and update `__init__.py` files To initialize and update all `__init__.py` files in the project, use the following command: ``` ccbk --init ``` ## Options The options available for the `ccbk` command are as follows: - `--project-root (-p)`: Project root directory path (default: current directory) `--log-level (-l)`: Log level (default: INFO) - `--init (-i)`: Initialize and update all `__init__.py` files in the project (default: False) ## _Example_ Assume you have a project structure like this: ``` my_project/ ├── package1/ │ ├── module1.py │ ├── module2.py │ └── __init__.py └── package2/ ├── module3.py ├── module4.py └── __init__.py ``` If you run `ccbk run` in the `my_project` directory, CircleBlock will start monitoring the file system. Whenever there's a change in any of the modules, CircleBlock will automatically update the `__init__.py` files with the exportable functions. For instance, if `module1.py` has the following content: ``` def func_a(): pass def func_b(): pass ``` The `__init__.py` file in the `package1` directory will be updated with the following content: ``` from .module1 import ( func_a, func_b, ) ``` This way, you can easily import these functions from the package itself: ``` from package1 import func_a, func_b ``` If you want to stop the file system monitoring, simply run the `ccbk stop` command. To initialize and update all `__init__.py` files in the project without starting the file system monitoring, use the `ccbk --init` command.
PypiClean
/Nuitka_fixed-1.1.2-cp310-cp310-win_amd64.whl/nuitka/utils/StaticLibraries.py
import os from nuitka.containers.OrderedSets import OrderedSet from nuitka.PythonFlavors import ( isAnacondaPython, isDebianPackagePython, isNuitkaPython, ) from nuitka.PythonVersions import ( getPythonABI, getSystemPrefixPath, python_version, python_version_str, ) from nuitka.Tracing import general from .FileOperations import getFileContentByLine, getFileList from .Utils import getLinuxDistribution, isDebianBasedLinux, isWin32Windows _ldconf_paths = None _static_lib_cache = {} def locateStaticLinkLibrary(dll_name): if dll_name not in _static_lib_cache: _static_lib_cache[dll_name] = _locateStaticLinkLibrary(dll_name) return _static_lib_cache[dll_name] def _locateStaticLinkLibrary(dll_name): # singleton, pylint: disable=global-statement # global _ldconf_paths if _ldconf_paths is None: _ldconf_paths = OrderedSet() for conf_filemame in getFileList("/etc/ld.so.conf.d", only_suffixes=".conf"): for conf_line in getFileContentByLine(conf_filemame): conf_line = conf_line.split("#", 1)[0] conf_line = conf_line.strip() if os.path.exists(conf_line): _ldconf_paths.add(conf_line) for ld_config_path in _ldconf_paths: candidate = os.path.join(ld_config_path, "lib%s.a" % dll_name) if os.path.exists(candidate): return candidate return None _static_lib_python_path = False def isDebianSuitableForStaticLinking(): dist_name, _base, dist_version = getLinuxDistribution() if dist_name == "Debian": if dist_version is None: return True try: dist_version = tuple(int(x) for x in dist_version.split(".")) except ValueError: # dist_version contains a non-numeric string such as "sid". return True return dist_version >= (10,) else: # TODO: Needs implementing potentially, Mint etc. are based # on something that should be considered. return True def _getSystemStaticLibPythonPath(): # Return driven function with many cases, pylint: disable=too-many-branches,too-many-return-statements sys_prefix = getSystemPrefixPath() python_abi_version = python_version_str + getPythonABI() if isNuitkaPython(): # Nuitka Python has this. if isWin32Windows(): return os.path.join( sys_prefix, "libs", "python" + python_abi_version.replace(".", "") + ".lib", ) else: return os.path.join( sys_prefix, "lib", "libpython" + python_abi_version + ".a", ) if isWin32Windows(): # The gcc used on Windows for Anaconda is far too old for winlibs gcc # to use its library. if isAnacondaPython(): return None candidates = [ # Anaconda has this. os.path.join( sys_prefix, "libs", "libpython" + python_abi_version.replace(".", "") + ".dll.a", ), # MSYS2 mingw64 Python has this. os.path.join( sys_prefix, "lib", "libpython" + python_abi_version + ".dll.a", ), ] for candidate in candidates: if os.path.exists(candidate): return candidate else: candidate = os.path.join( sys_prefix, "lib", "libpython" + python_abi_version + ".a" ) if os.path.exists(candidate): return candidate # For Python2 this works. TODO: Figure out Debian and Python3. if ( python_version < 0x300 and isDebianPackagePython() and isDebianSuitableForStaticLinking() ): candidate = locateStaticLinkLibrary("python" + python_abi_version) else: candidate = None if candidate is not None and os.path.exists(candidate): # Also check libz, can be missing if not locateStaticLinkLibrary("z"): general.warning( "Error, missing 'libz-dev' installation needed for static lib-python." ) return candidate # This is not necessarily only for Python3 on Debian, but maybe others as well, # but that's what's been tested. if python_version >= 0x300 and isDebianPackagePython() and isDebianBasedLinux(): try: import sysconfig candidate = os.path.join( sysconfig.get_config_var("LIBPL"), "libpython" + python_abi_version + "-pic.a", ) if os.path.exists(candidate): return candidate except ImportError: # Cannot detect this properly for Python 2.6, but we don't care much # about that anyway. pass return None def getSystemStaticLibPythonPath(): global _static_lib_python_path # singleton, pylint: disable=global-statement if _static_lib_python_path is False: _static_lib_python_path = _getSystemStaticLibPythonPath() return _static_lib_python_path
PypiClean
/MiWork-2021.2.20.20.8.11-py3-none-any.whl/miwork/exception.py
from __future__ import absolute_import, division, print_function, unicode_literals from six import PY2 if PY2: def implements_to_string(cls): cls.__unicode__ = cls.__str__ cls.__str__ = lambda x: x.__unicode__().encode('utf-8') return cls else: def implements_to_string(x): return x @implements_to_string class OpenLarkException(Exception): def __init__(self, *args, **kwargs): """基本 Exception """ self.code = kwargs.pop('code', None) or getattr(self, 'code', None) or 0 self.msg = kwargs.pop('msg', None) or getattr(self, 'msg', None) self.url = kwargs.pop('url', None) or getattr(self, 'url', None) def __str__(self): if PY2: if self.url: return u'<{} code={} msg="{}" url="{}">'.format(self.__class__.__name__, self.code, self.msg, self.url) else: return u'<{} code={} msg="{}">'.format(self.__class__.__name__, self.code, self.msg) else: if self.url: return '<{} code={} msg="{}" url="{}">'.format(self.__class__.__name__, self.code, self.msg, self.url) else: return '<{} code={} msg="{}">'.format(self.__class__.__name__, self.code, self.msg) # --------- OpenLark SDK 定义的参数错误 class LarkInvalidArguments(OpenLarkException): code = 999901 msg = 'open_lark invalid arguments' class LarkInvalidCallback(OpenLarkException): code = 999902 msg = 'open_lark callback error' class LarkGetAppTicketFail(OpenLarkException): code = 999903 msg = 'get app_ticket fail' class LarkUnknownError(OpenLarkException): code = 999904 msg = 'unknown error' # --------- 机器人和服务端异常 class LarkSendMessageFailException(OpenLarkException): code = 10002 msg = '发送消息失败' class LarkRequestParamsInvalidException(OpenLarkException): code = 10003 msg = '请求参数不合法' class LarkGetUserInfoFailOrUserIDNotExistException(OpenLarkException): code = 10004 msg = '获取用户信息失败或者用户 ID 不存在' class LarkConflictAppIDException(OpenLarkException): code = 10005 msg = '生成 token 的 app_id 和相关 chat、open_id 的 app_id 不一致' class LarkGetOpenChatIDFailException(OpenLarkException): code = 10009 msg = '获取 open_chat_id 失败' class LarkForbiddenSendMessageException(OpenLarkException): code = 10010 msg = '禁止发送消息,请检查 scope 权限,机器人可见性范围' class LarkGetAppAccessTokenFailException(OpenLarkException): code = 10012 msg = '获取 app access token 失败' class LarkGetTenantAccessTokenFailException(OpenLarkException): code = 10013 # 10014 msg = '获取 tenant access token 失败' class LarkWrongAppSecretException(OpenLarkException): code = 10015 msg = 'app_secret 不正确' class LarkSendAppTicketFailException(OpenLarkException): code = 10016 msg = '发送 app_ticket 失败' class LarkUnsupportedUrgentTypeException(OpenLarkException): code = 10019 msg = '加急类型不支持' class LarkWrongMessageIDException(OpenLarkException): code = 10020 msg = '消息 ID 不正确' class LarkForbiddenUrgentException(OpenLarkException): code = 10023 msg = '没有加急 scope 权限' class LarkInvalidOpenChatIDException(OpenLarkException): code = 10029 msg = 'open_chat_id 不合法' class LarkBotNotInChatException(OpenLarkException): code = 10030 msg = '机器人不在群里' class LarkAllOpenIDInvalidException(OpenLarkException): code = 10032 msg = '所有 open_id 都不合法' class LarkUnsupportedCrossTenantException(OpenLarkException): code = 10034 msg = '不支持跨企业操作' class LarkGetMessageIDFailException(OpenLarkException): code = 10037 msg = '获取 message_id 失败' class LarkGetSSOAccessTokenFailException(OpenLarkException): code = 11000 msg = '获取 sso_access_token 失败' class LarkGetCheckSecurityTokenFailException(OpenLarkException): code = 11001 msg = '获取 CheckSecurityToken 失败' class LarkCheckOpenChatIDFailException(OpenLarkException): code = 11100 msg = 'open_chat_id 不合法或者 chat 不存在' class LarkOpenIDNotExistException(OpenLarkException): code = 11101 msg = 'open_id 不存在' class LarkGetOpenIDFailException(OpenLarkException): code = 11102 msg = '查询用户 open_id 失败' class LarkOpenDepartmentIDNotExistException(OpenLarkException): code = 11103 msg = 'open_department_id 不存在' class LarkGetOpenDepartmentIDFailException(OpenLarkException): code = 11104 msg = '查询用户 open_department_id 失败' class LarkEmployeeIDNotExistException(OpenLarkException): code = 11105 msg = 'user_id 不存在' class LarkGetEmployeeIDFailException(OpenLarkException): code = 11106 msg = '查询用户 user_id 失败' class LarkUpdateChatNameFailException(OpenLarkException): code = 11200 msg = '更新群名称失败' class LarkBotNotGroupAdminException(OpenLarkException): code = 11201 # 11208 msg = '机器人不是群主' class LarkOnlyChatAdminCanInviteUserException(OpenLarkException): code = 11202 msg = '只有群主才能拉用户进群' class LarkForbiddenBotBatchSendMessageToUserException(OpenLarkException): code = 11203 msg = '机器人没有给用户批量发送权限' class LarkForbiddenBotBatchSendMessageToDepartmentException(OpenLarkException): code = 11204 msg = '机器人没有给部门批量发送权限' class LarkAppHasNoBotException(OpenLarkException): code = 11205 msg = '应用没有机器人' class LarkUserCannotGrantToChatAdminException(OpenLarkException): code = 11206 msg = '用户不在群中不能被设置为群主' class LarkAppUnavailableException(OpenLarkException): code = 11207 msg = 'app 不可用' class LarkAppNotExistException(OpenLarkException): code = 11209 msg = 'app 不存在' class LarkAppUsageInfoNotExistException(OpenLarkException): code = 11210 msg = 'AppUsageInfo 不存在' class LarkInviteUserToChatInvalidParamsException(OpenLarkException): code = 11211 msg = '拉人进群参数错误' class LarkRemoveUserFromChatInvalidParamsException(OpenLarkException): code = 11212 msg = '踢人出群参数错误' class LarkUpdateChatInvalidParamsException(OpenLarkException): code = 11213 msg = '更新群参数错误' class LarkUploadImageInvalidParamsException(OpenLarkException): code = 11214 msg = '上传图片参数错误' class LarkEmptyChatIDException(OpenLarkException): code = 11215 msg = 'chat_id 为空' class LarkGetChatIDFailException(OpenLarkException): code = 11216 msg = '获取chat_id失败' class LarkInviteBotToChatFailException(OpenLarkException): code = 11217 msg = '拉机器人进群失败' class LarkBotInChatFullException(OpenLarkException): code = 11218 msg = '群机器人已满' class LarkUnsupportedChatCrossTenantException(OpenLarkException): code = 11219 msg = '不支持 chat 跨租户' class LarkForbiddenBotDisbandChatException(OpenLarkException): code = 11220 msg = '禁止机器人解散群' class LarkBotForbiddenToGetImageBelongToThemException(OpenLarkException): code = 11221 msg = '机器人不能获取不属于自己的图片' class LarkOwnerOfBotIsNotInChatException(OpenLarkException): code = 11222 msg = '机器人的 Owner 不在群里' class LarkNotOpenApplicationSendMessagePermissionException(OpenLarkException): code = 11223 msg = '没有打开应用发消息权限' class LarkInvalidMessageIDException(OpenLarkException): code = 11224 msg = 'message_id 参数错误' class LarkAppIsNotVisibleToUserException(OpenLarkException): code = 11225 msg = '你的应用对用户不可见' class LarkInvalidAppIDException(OpenLarkException): code = 11226 msg = 'app_id 参数不对或者没传' class LarkImageKeyNotExistException(OpenLarkException): code = 11227 msg = ' image_key 不存在' class LarkBotIsNotMessageOwnerException(OpenLarkException): code = 11234 msg = 'bot非消息owner' class LarkBanAtALLException(OpenLarkException): code = 11235 msg = '禁止@所有人' class LarkUserNotActiveException(OpenLarkException): code = 11236 msg = '用户已离职' class LarkChatDisbandedException(OpenLarkException): code = 11237 msg = '群聊已解散' class LarkMessageTooOldException(OpenLarkException): code = 11238 msg = '消息过久,不能撤销' class LarkNoPermissionToGotException(OpenLarkException): code = 11239 msg = '无权限获取' class LarkInvalidTenantAccessTokenException(OpenLarkException): code = 99991663 msg = 'tenant access token 无效' class LarkInvalidAppAccessTokenException(OpenLarkException): code = 99991664 msg = 'app access token 无效' class LarkInvalidTenantCodeException(OpenLarkException): code = 99991665 msg = 'tenant code 无效' class LarkInvalidAppTicketException(OpenLarkException): code = 99991666 msg = 'app ticket 无效' class LarkFrequencyLimitException(OpenLarkException): code = 99991400 msg = '发消息频率超过频控限制,目前每个AppID每个接口50/s、1000/min的限制' class LarkInternalException(OpenLarkException): code = 20000 msg = '内部异常' # --------- 审批异常 / 审批错误码 # 40xx 是审批的 v1 接口 class LarkApprovalNotExistException(OpenLarkException): code = 4002 msg = 'approval not exist' class LarkApprovalSubscriptionExistException(OpenLarkException): code = 4007 msg = 'subscription exist' # 600xxx 是审批的 v3 接口 class LarkApprovalInvalidRequestParamsException(OpenLarkException): code = 60001 msg = '请求参数错误' class LarkApprovalApprovalCodeNotFoundException(OpenLarkException): code = 60002 msg = '审批定义 approval_code 找不到' class LarkApprovalInstanceCodeNotFoundException(OpenLarkException): code = 60003 msg = '审批实例 instance_code 找不到' class LarkApprovalUserNotFoundException(OpenLarkException): code = 60004 msg = '用户找不到' class LarkApprovalForbiddenException(OpenLarkException): code = 60009 msg = '权限不足' class LarkApprovalTaskIDNotFoundException(OpenLarkException): code = 60010 msg = '审批任务 task_id 找不到' class LarkApprovalDepartmentValidFailedException(OpenLarkException): code = 60005 msg = '部门验证失败' class LarkApprovalFormValidFailedException(OpenLarkException): code = 60006 msg = '表单验证失败' class LarkApprovalNeedPayException(OpenLarkException): code = 60011 msg = '该审批为付费审批,免费版用户不能发起这个审批' class LarkApprovalInstanceCodeConflictException(OpenLarkException): code = 60012 msg = '审批实例 uuid 冲突' # --------- 审批异常 / 审批错误码 # --------- 云空间 class LarkDriveWrongRequestJsonException(OpenLarkException): code = 90201 msg = '请求体不是一个 json' class LarkDriveWrongRangeException(OpenLarkException): code = 90202 msg = '请求中 range 格式有误' class LarkDriveFailException(OpenLarkException): code = 90203 msg = '不是预期内的 fail' class LarkDriveWrongRequestBodyException(OpenLarkException): code = 90204 msg = '请求体有误' class LarkDriveInvalidUsersException(OpenLarkException): code = 90205 msg = '非法的 user' class LarkDriveEmptySheetIDException(OpenLarkException): code = 90206 msg = 'sheet_id 为空' class LarkDriveEmptySheetTitleException(OpenLarkException): code = 90207 msg = 'sheet 名称为空' class LarkDriveSameSheetIDOrTitleException(OpenLarkException): code = 90208 msg = '请求中有相同的 sheet_id 或 title' class LarkDriveExistSheetIDException(OpenLarkException): code = 90209 msg = 'sheet_id 已经存在' class LarkDriveExistSheetTitleException(OpenLarkException): code = 90210 msg = 'sheet title 已经存在' class LarkDriveWrongSheetIDException(OpenLarkException): code = 90211 msg = '错误的 sheet_id' class LarkDriveWrongRowOrColException(OpenLarkException): code = 90212 msg = '非法的行列' class LarkDrivePermissionFailException(OpenLarkException): code = 90213 msg = '没有文件的权限 forbidden' class LarkDriveSpreadSheetNotFoundException(OpenLarkException): code = 90214 msg = 'sheet 没有找到' class LarkDriveSheetIDNotFoundException(OpenLarkException): code = 90215 msg = 'sheet_id 没有找到' class LarkDriveEmptyValueException(OpenLarkException): code = 90216 msg = '请求中有空值' class LarkDriveTooManyRequestException(OpenLarkException): code = 90217 msg = '请求太频繁' class LarkDriveTimeoutException(OpenLarkException): code = 96402 msg = '超时' class LarkDriveProcessingException(OpenLarkException): code = 96403 msg = '请求正在处理中' class LarkDriveLoginRequiredException(OpenLarkException): code = 91404 msg = '需要登录' class LarkDriveFailedException(OpenLarkException): code = 90301 # 91201 / 96401 msg = '失败' class LarkDriveOutOfLimitException(OpenLarkException): code = 91206 msg = '超过限制' class LarkDriveDuplicateException(OpenLarkException): code = 91207 msg = '重复记录' class LarkDriveForbiddenException(OpenLarkException): code = 91002 # 90303 / 91204 / 91403 msg = '没有权限' class LarkDriveInvalidOperationException(OpenLarkException): code = 91003 msg = '操作异常' class LarkDriveUserNoSharePermissionException(OpenLarkException): code = 91004 msg = '用户没有共享权限' class LarkDriveParamErrorException(OpenLarkException): code = 90302 # 91001 / 91202 / 91401 msg = '参数错误' class LarkDriveMetaDeletedException(OpenLarkException): code = 90304 # 91205 msg = '文件已删除' class LarkDriveMetaNotExistException(OpenLarkException): code = 90305 # 91203 / 91402 msg = '文件不存在' class LarkDriveReviewNotPassException(OpenLarkException): code = 90306 # 91208 msg = '评论内容审核不通过' class LarkDriveInternalErrorException(OpenLarkException): code = 90399 # 95299 / 96201 / 96202 / 96001 / 95201 / 95201—95209 msg = '内部错误' # --------- 云空间 # --------- 会议室 class LarkMeetingRoomInvalidPageTokenException(OpenLarkException): code = 100001 msg = 'page token 格式非法' class LarkMeetingRoomInvalidFieldSelectionException(OpenLarkException): code = 100002 msg = 'fields 中存在非法字段名' class LarkMeetingRoomTimeFormatMustFollowRFC3339StandardException(OpenLarkException): code = 100003 msg = '时间格式未遵循 RFC3339 标准' class LarkMeetingRoomInvalidBuildingIDException(OpenLarkException): code = 100004 msg = 'building ID 非法' class LarkMeetingRoomInvalidRoomIDException(OpenLarkException): code = 100005 msg = 'room ID 非法' class LarkMeetingRoomInternalErrorException(OpenLarkException): code = 105001 msg = '内部错误' # --------- 会议室 def gen_exception(code, url, msg=''): """生成异常 :type code: int :type url: str :type msg: str :rtype: OpenLarkException """ exceptions = { # 自定义 999901: LarkInvalidArguments, 999902: LarkInvalidCallback, 999903: LarkGetAppTicketFail, 999904: LarkUnknownError, # 审批 4002: LarkApprovalNotExistException, 4007: LarkApprovalSubscriptionExistException, 60001: LarkApprovalInvalidRequestParamsException, 60002: LarkApprovalApprovalCodeNotFoundException, 60003: LarkApprovalInstanceCodeNotFoundException, 60004: LarkApprovalUserNotFoundException, 60009: LarkApprovalForbiddenException, 60010: LarkApprovalTaskIDNotFoundException, 60005: LarkApprovalDepartmentValidFailedException, 60006: LarkApprovalFormValidFailedException, 60011: LarkApprovalNeedPayException, 60012: LarkApprovalInstanceCodeConflictException, # 数字超级大的异常, 99991400: LarkFrequencyLimitException, 99991663: LarkInvalidTenantAccessTokenException, 99991664: LarkInvalidAppAccessTokenException, 99991665: LarkInvalidTenantCodeException, 99991666: LarkInvalidAppTicketException, 10002: LarkSendMessageFailException, 10003: LarkRequestParamsInvalidException, 10004: LarkGetUserInfoFailOrUserIDNotExistException, 10005: LarkConflictAppIDException, 10009: LarkGetOpenChatIDFailException, 10010: LarkForbiddenSendMessageException, 10012: LarkGetAppAccessTokenFailException, 10013: LarkGetTenantAccessTokenFailException, 10014: LarkGetTenantAccessTokenFailException, 10015: LarkWrongAppSecretException, 10016: LarkSendAppTicketFailException, 10019: LarkUnsupportedUrgentTypeException, 10020: LarkWrongMessageIDException, 10023: LarkForbiddenUrgentException, 10029: LarkInvalidOpenChatIDException, 10030: LarkBotNotInChatException, 10032: LarkAllOpenIDInvalidException, 10034: LarkUnsupportedCrossTenantException, 10037: LarkGetMessageIDFailException, 11000: LarkGetSSOAccessTokenFailException, 11001: LarkGetCheckSecurityTokenFailException, 11100: LarkCheckOpenChatIDFailException, 11101: LarkOpenIDNotExistException, 11102: LarkGetOpenIDFailException, 11103: LarkOpenDepartmentIDNotExistException, 11104: LarkGetOpenDepartmentIDFailException, 11105: LarkEmployeeIDNotExistException, 11106: LarkGetEmployeeIDFailException, 11200: LarkUpdateChatNameFailException, 11201: LarkBotNotGroupAdminException, 11208: LarkBotNotGroupAdminException, 11202: LarkOnlyChatAdminCanInviteUserException, 11203: LarkForbiddenBotBatchSendMessageToUserException, 11204: LarkForbiddenBotBatchSendMessageToDepartmentException, 11205: LarkAppHasNoBotException, 11206: LarkUserCannotGrantToChatAdminException, 11207: LarkAppUnavailableException, 11209: LarkAppNotExistException, 11210: LarkAppUsageInfoNotExistException, 11211: LarkInviteUserToChatInvalidParamsException, 11212: LarkRemoveUserFromChatInvalidParamsException, 11213: LarkUpdateChatInvalidParamsException, 11214: LarkUploadImageInvalidParamsException, 11215: LarkEmptyChatIDException, 11216: LarkGetChatIDFailException, 11217: LarkInviteBotToChatFailException, 11218: LarkBotInChatFullException, 11219: LarkUnsupportedChatCrossTenantException, 11220: LarkForbiddenBotDisbandChatException, 11221: LarkBotForbiddenToGetImageBelongToThemException, 11222: LarkOwnerOfBotIsNotInChatException, 11223: LarkNotOpenApplicationSendMessagePermissionException, 11224: LarkInvalidMessageIDException, 11225: LarkAppIsNotVisibleToUserException, 11226: LarkInvalidAppIDException, 11227: LarkImageKeyNotExistException, 11234: LarkBotIsNotMessageOwnerException, 11235: LarkBanAtALLException, 11236: LarkUserNotActiveException, 11237: LarkChatDisbandedException, 11238: LarkMessageTooOldException, 11239: LarkNoPermissionToGotException, # 云空间 90201: LarkDriveWrongRequestJsonException, 90202: LarkDriveWrongRangeException, 90203: LarkDriveFailException, 90204: LarkDriveWrongRequestBodyException, 90205: LarkDriveInvalidUsersException, 90206: LarkDriveEmptySheetIDException, 90207: LarkDriveEmptySheetTitleException, 90208: LarkDriveSameSheetIDOrTitleException, 90209: LarkDriveExistSheetIDException, 90210: LarkDriveExistSheetTitleException, 90211: LarkDriveWrongSheetIDException, 90212: LarkDriveWrongRowOrColException, 90213: LarkDrivePermissionFailException, 90214: LarkDriveSpreadSheetNotFoundException, 90215: LarkDriveSheetIDNotFoundException, 90216: LarkDriveEmptyValueException, 90217: LarkDriveTooManyRequestException, 96402: LarkDriveTimeoutException, 96403: LarkDriveProcessingException, 91404: LarkDriveLoginRequiredException, 91206: LarkDriveOutOfLimitException, 91207: LarkDriveDuplicateException, 91003: LarkDriveInvalidOperationException, 91004: LarkDriveUserNoSharePermissionException, # 会议室 100001: LarkMeetingRoomInvalidPageTokenException, 100002: LarkMeetingRoomInvalidFieldSelectionException, 100003: LarkMeetingRoomTimeFormatMustFollowRFC3339StandardException, 100004: LarkMeetingRoomInvalidBuildingIDException, 100005: LarkMeetingRoomInvalidRoomIDException, } if code in exceptions: return exceptions[code](code=code, msg=msg, url=url) if 18000 <= code <= 20000: return LarkInternalException(code=code, msg=msg, url=url) if code in [4002, 60002]: return LarkApprovalNotExistException(code=code, msg=msg, url=url) if code in [90303, 91002, 91204, 91403]: return LarkDriveForbiddenException(code=code, msg=msg, url=url) if code in [90301, 91201, 96401]: return LarkDriveFailedException(code=code, msg=msg, url=url) if code in [90302, 91001, 91202, 91401]: return LarkDriveParamErrorException(code=code, msg=msg, url=url) if code in [90304, 91205]: return LarkDriveMetaDeletedException(code=code, msg=msg, url=url) if code in [90305, 91203, 91402]: return LarkDriveMetaNotExistException(code=code, msg=msg, url=url) if code in [90306, 91208]: return LarkDriveReviewNotPassException(code=code, msg=msg, url=url) if code in [90399, 95201, 95299, 96201, 96202, 96001] or (code >= 95201 and code <= 95209): return LarkDriveInternalErrorException(code=code, msg=msg, url=url) return OpenLarkException(code=code, msg=msg, url=url)
PypiClean
/Flask_AdminLTE3-1.0.9-py3-none-any.whl/flask_adminlte3/static/plugins/jsgrid/jsgrid.min.js
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b.isPlainObject(a)&&(c=a.order,a=a.field),this._clearSortingCss(),this._setSortingParams(a,c),this._setSortingCss(),this._loadStrategy.sort()},_clearSortingCss:function(){this._headerRow.find("th").removeClass(this.sortAscClass).removeClass(this.sortDescClass)},_setSortingParams:function(a,b){a=this._normalizeField(a),b=b||(this._sortField===a?this._reversedSortOrder(this._sortOrder):i),this._sortField=a,this._sortOrder=b},_normalizeField:function(a){return b.isNumeric(a)?this.fields[a]:"string"==typeof a?b.grep(this.fields,function(b){return b.name===a})[0]:a},_reversedSortOrder:function(a){return a===i?j:i},_setSortingCss:function(){var a=this._visibleFieldIndex(this._sortField);this._headerRow.find("th").eq(a).addClass(this._sortOrder===i?this.sortAscClass:this.sortDescClass)},_visibleFieldIndex:function(a){return b.inArray(a,b.grep(this.fields,function(a){return a.visible}))},_sortData:function(){var a=this._sortFactor(),b=this._sortField;b&&this.data.sort(function(c,d){return 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e===l?f=this._createPages():e===k?f=this._createPagerNavButton(this.pageFirstText,1,a>1):e===m?f=this._createPagerNavButton(this.pagePrevText,a-1,a>1):e===n?f=this._createPagerNavButton(this.pageNextText,a+1,c>a):e===o?f=this._createPagerNavButton(this.pageLastText,c,c>a):e===p?f=a:e===q?f=c:e===r&&(f=d),b.isArray(f)?f.concat([" "]):[f," "]},this))},_createPages:function(){var a=this._pagesCount(),b=this.pageButtonCount,c=this._firstDisplayingPage,d=[];c>1&&d.push(this._createPagerPageNavButton(this.pageNavigatorPrevText,this.showPrevPages));for(var e=0,f=c;b>e&&a>=f;e++,f++)d.push(f===this.pageIndex?this._createPagerCurrentPage():this._createPagerPage(f));return a>c+b-1&&d.push(this._createPagerPageNavButton(this.pageNavigatorNextText,this.showNextPages)),d},_createPagerNavButton:function(a,c,d){return this._createPagerButton(a,this.pagerNavButtonClass+(d?"":" "+this.pagerNavButtonInactiveClass),d?function(){this.openPage(c)}:b.noop)},_createPagerPageNavButton:function(a,b){return 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this._resetSorting(),this._resetPager(),this.loadData(a)},loadData:function(a){a=a||(this.filtering?this.getFilter():{}),b.extend(a,this._loadStrategy.loadParams(),this._sortingParams());var c=this._callEventHandler(this.onDataLoading,{filter:a});return this._controllerCall("loadData",a,c.cancel,function(a){a&&(this._loadStrategy.finishLoad(a),this._callEventHandler(this.onDataLoaded,{data:a}))})},getFilter:function(){var a={};return this._eachField(function(b){b.filtering&&this._setItemFieldValue(a,b,b.filterValue())}),a},_sortingParams:function(){return this.sorting&&this._sortField?{sortField:this._sortField.name,sortOrder:this._sortOrder}:{}},getSorting:function(){var a=this._sortingParams();return{field:a.sortField,order:a.sortOrder}},clearFilter:function(){var a=this._createFilterRow();return this._filterRow.replaceWith(a),this._filterRow=a,this.search()},insertItem:function(a){var c=a||this._getValidatedInsertItem();if(!c)return b.Deferred().reject().promise();var d=this._callEventHandler(this.onItemInserting,{item:c});return this._controllerCall("insertItem",c,d.cancel,function(a){a=a||c,this._loadStrategy.finishInsert(a),this._callEventHandler(this.onItemInserted,{item:a})})},_getValidatedInsertItem:function(){var a=this._getInsertItem();return this._validateItem(a,this._insertRow)?a:null},_getInsertItem:function(){var a={};return this._eachField(function(b){b.inserting&&this._setItemFieldValue(a,b,b.insertValue())}),a},_validateItem:function(a,c){var d=[],e={item:a,itemIndex:this._rowIndex(c),row:c};if(this._eachField(function(f){if(f.validate&&(c!==this._insertRow||f.inserting)&&(c!==this._getEditRow()||f.editing)){var g=this._getItemFieldValue(a,f),h=this._validation.validate(b.extend({value:g,rules:f.validate},e));this._setCellValidity(c.children().eq(this._visibleFieldIndex(f)),h),h.length&&d.push.apply(d,b.map(h,function(a){return{field:f,message:a}}))}}),!d.length)return!0;var f=b.extend({errors:d},e);return this._callEventHandler(this.onItemInvalid,f),this.invalidNotify(f),!1},_setCellValidity:function(a,b){a.toggleClass(this.invalidClass,!!b.length).attr("title",b.join("\n"))},clearInsert:function(){var a=this._createInsertRow();this._insertRow.replaceWith(a),this._insertRow=a,this.refresh()},editItem:function(a){var b=this.rowByItem(a);b.length&&this._editRow(b)},rowByItem:function(a){return a.jquery||a.nodeType?b(a):this._content.find("tr").filter(function(){return b.data(this,g)===a})},_editRow:function(a){if(this.editing){var b=a.data(g),c=this._callEventHandler(this.onItemEditing,{row:a,item:b,itemIndex:this._itemIndex(b)});if(!c.cancel){this._editingRow&&this.cancelEdit();var d=this._createEditRow(b);this._editingRow=a,a.hide(),d.insertBefore(a),a.data(h,d)}}},_createEditRow:function(a){if(b.isFunction(this.editRowRenderer))return b(this.renderTemplate(this.editRowRenderer,this,{item:a,itemIndex:this._itemIndex(a)}));var c=b("<tr>").addClass(this.editRowClass);return this._eachField(function(b){var d=this._getItemFieldValue(a,b);this._prepareCell("<td>",b,"editcss").append(this.renderTemplate(b.editTemplate||"",b,{value:d,item:a})).appendTo(c)}),c},updateItem:function(a,b){1===arguments.length&&(b=a);var c=a?this.rowByItem(a):this._editingRow;return(b=b||this._getValidatedEditedItem())?this._updateRow(c,b):void 0},_getValidatedEditedItem:function(){var a=this._getEditedItem();return this._validateItem(a,this._getEditRow())?a:null},_updateRow:function(a,c){var d=a.data(g),e=this._itemIndex(d),f=b.extend(!0,{},d,c),h=this._callEventHandler(this.onItemUpdating,{row:a,item:f,itemIndex:e,previousItem:d});return this._controllerCall("updateItem",f,h.cancel,function(g){var h=b.extend(!0,{},d);f=g||b.extend(!0,d,c);var i=this._finishUpdate(a,f,e);this._callEventHandler(this.onItemUpdated,{row:i,item:f,itemIndex:e,previousItem:h})})},_rowIndex:function(a){return this._content.children().index(b(a))},_itemIndex:function(a){return 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e=b.makeArray(arguments),g=e.slice(1),h=this;return this.each(function(){var e,i=b(this),j=i.data(f);if(j)if("string"==typeof a){if(e=j[a].apply(j,g),e!==c&&e!==j)return h=e,!1}else j._detachWindowResizeCallback(),j._init(a),j.render();else new d(i,a)}),h};var w={},x=function(a){var c;b.isPlainObject(a)?c=d.prototype:(c=w[a].prototype,a=arguments[1]||{}),b.extend(c,a)},y={},z=function(a){var c=b.isPlainObject(a)?a:y[a];if(!c)throw Error("unknown locale "+a);A(jsGrid,c)},A=function(a,c){b.each(c,function(c,d){return b.isPlainObject(d)?void A(a[c]||a[c[0].toUpperCase()+c.slice(1)],d):void(a.hasOwnProperty(c)?a[c]=d:a.prototype[c]=d)})};a.jsGrid={Grid:d,fields:w,setDefaults:x,locales:y,locale:z,version:"1.5.3"}}(window,jQuery),function(a,b){function c(a){this._init(a)}c.prototype={container:"body",message:"Loading...",shading:!0,zIndex:1e3,shaderClass:"jsgrid-load-shader",loadPanelClass:"jsgrid-load-panel",_init:function(a){b.extend(!0,this,a),this._initContainer(),this._initShader(),this._initLoadPanel()},_initContainer:function(){this._container=b(this.container)},_initShader:function(){this.shading&&(this._shader=b("<div>").addClass(this.shaderClass).hide().css({position:"absolute",top:0,right:0,bottom:0,left:0,zIndex:this.zIndex}).appendTo(this._container))},_initLoadPanel:function(){this._loadPanel=b("<div>").addClass(this.loadPanelClass).text(this.message).hide().css({position:"absolute",top:"50%",left:"50%",zIndex:this.zIndex}).appendTo(this._container)},show:function(){var a=this._loadPanel.show(),b=a.outerWidth(),c=a.outerHeight();a.css({marginTop:-c/2,marginLeft:-b/2}),this._shader.show()},hide:function(){this._loadPanel.hide(),this._shader.hide()}},a.LoadIndicator=c}(jsGrid,jQuery),function(a,b){function 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d(a){this._init(a)}d.prototype={_init:function(a){b.extend(!0,this,a)},validate:function(a){var c=[];return b.each(this._normalizeRules(a.rules),function(d,e){if(!e.validator(a.value,a.item,e.param)){var f=b.isFunction(e.message)?e.message(a.value,a.item):e.message;c.push(f)}}),c},_normalizeRules:function(a){return b.isArray(a)||(a=[a]),b.map(a,b.proxy(function(a){return this._normalizeRule(a)},this))},_normalizeRule:function(a){if("string"==typeof a&&(a={validator:a}),b.isFunction(a)&&(a={validator:a}),!b.isPlainObject(a))throw Error("wrong validation config specified");return a=b.extend({},a),b.isFunction(a.validator)?a:this._applyNamedValidator(a,a.validator)},_applyNamedValidator:function(a,c){delete a.validator;var d=e[c];if(!d)throw Error('unknown validator "'+c+'"');return b.isFunction(d)&&(d={validator:d}),b.extend({},d,a)}},a.Validation=d;var e={required:{message:"Field is required",validator:function(a){return a!==c&&null!==a&&""!==a}},rangeLength:{message:"Field value length 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b("<input>").attr("type","number").prop("readonly",!!this.readOnly)}}),a.fields.number=a.NumberField=d}(jsGrid,jQuery),function(a,b){function c(a){d.call(this,a)}var d=a.TextField;c.prototype=new d({insertTemplate:function(){return this.inserting?this.insertControl=this._createTextArea():""},editTemplate:function(a){if(!this.editing)return this.itemTemplate.apply(this,arguments);var b=this.editControl=this._createTextArea();return b.val(a),b},_createTextArea:function(){return b("<textarea>").prop("readonly",!!this.readOnly)}}),a.fields.textarea=a.TextAreaField=c}(jsGrid,jQuery),function(a,b,c){function d(a){if(this.items=[],this.selectedIndex=-1,this.valueField="",this.textField="",a.valueField&&a.items.length){var b=a.items[0][a.valueField];this.valueType=typeof b===f?f:g}this.sorter=this.valueType,e.call(this,a)}var e=a.NumberField,f="number",g="string";d.prototype=new e({align:"center",valueType:f,itemTemplate:function(a){var d,e=this.items,f=this.valueField,g=this.textField;d=f?b.grep(e,function(b){return b[f]===a})[0]||{}:e[a];var h=g?d[g]:d;return h===c||null===h?"":h},filterTemplate:function(){if(!this.filtering)return"";var a=this._grid,b=this.filterControl=this._createSelect();return this.autosearch&&b.on("change",function(){a.search()}),b},insertTemplate:function(){return this.inserting?this.insertControl=this._createSelect():""},editTemplate:function(a){if(!this.editing)return this.itemTemplate.apply(this,arguments);var b=this.editControl=this._createSelect();return a!==c&&b.val(a),b},filterValue:function(){var a=this.filterControl.val();return this.valueType===f?parseInt(a||0,10):a},insertValue:function(){var a=this.insertControl.val();return this.valueType===f?parseInt(a||0,10):a},editValue:function(){var a=this.editControl.val();return this.valueType===f?parseInt(a||0,10):a},_createSelect:function(){var a=b("<select>"),c=this.valueField,d=this.textField,e=this.selectedIndex;return b.each(this.items,function(f,g){var h=c?g[c]:f,i=d?g[d]:g,j=b("<option>").attr("value",h).text(i).appendTo(a);j.prop("selected",e===f)}),a.prop("disabled",!!this.readOnly),a}}),a.fields.select=a.SelectField=d}(jsGrid,jQuery),function(a,b,c){function d(a){e.call(this,a)}var e=a.Field;d.prototype=new e({sorter:"number",align:"center",autosearch:!0,itemTemplate:function(a){return this._createCheckbox().prop({checked:a,disabled:!0})},filterTemplate:function(){if(!this.filtering)return"";var a=this._grid,c=this.filterControl=this._createCheckbox();return c.prop({readOnly:!0,indeterminate:!0}),c.on("click",function(){var a=b(this); a.prop("readOnly")?a.prop({checked:!1,readOnly:!1}):a.prop("checked")||a.prop({readOnly:!0,indeterminate:!0})}),this.autosearch&&c.on("click",function(){a.search()}),c},insertTemplate:function(){return this.inserting?this.insertControl=this._createCheckbox():""},editTemplate:function(a){if(!this.editing)return this.itemTemplate.apply(this,arguments);var b=this.editControl=this._createCheckbox();return b.prop("checked",a),b},filterValue:function(){return this.filterControl.get(0).indeterminate?c:this.filterControl.is(":checked")},insertValue:function(){return this.insertControl.is(":checked")},editValue:function(){return this.editControl.is(":checked")},_createCheckbox:function(){return b("<input>").attr("type","checkbox")}}),a.fields.checkbox=a.CheckboxField=d}(jsGrid,jQuery),function(a,b){function c(a){d.call(this,a),this._configInitialized=!1}var d=a.Field;c.prototype=new d({css:"jsgrid-control-field",align:"center",width:50,filtering:!1,inserting:!1,editing:!1,sorting:!1,buttonClass:"jsgrid-button",modeButtonClass:"jsgrid-mode-button",modeOnButtonClass:"jsgrid-mode-on-button",searchModeButtonClass:"jsgrid-search-mode-button",insertModeButtonClass:"jsgrid-insert-mode-button",editButtonClass:"jsgrid-edit-button",deleteButtonClass:"jsgrid-delete-button",searchButtonClass:"jsgrid-search-button",clearFilterButtonClass:"jsgrid-clear-filter-button",insertButtonClass:"jsgrid-insert-button",updateButtonClass:"jsgrid-update-button",cancelEditButtonClass:"jsgrid-cancel-edit-button",searchModeButtonTooltip:"Switch to searching",insertModeButtonTooltip:"Switch to inserting",editButtonTooltip:"Edit",deleteButtonTooltip:"Delete",searchButtonTooltip:"Search",clearFilterButtonTooltip:"Clear filter",insertButtonTooltip:"Insert",updateButtonTooltip:"Update",cancelEditButtonTooltip:"Cancel edit",editButton:!0,deleteButton:!0,clearFilterButton:!0,modeSwitchButton:!0,_initConfig:function(){this._hasFiltering=this._grid.filtering,this._hasInserting=this._grid.inserting,this._hasInserting&&this.modeSwitchButton&&(this._grid.inserting=!1),this._configInitialized=!0},headerTemplate:function(){this._configInitialized||this._initConfig();var a=this._hasFiltering,b=this._hasInserting;return this.modeSwitchButton&&(a||b)?a&&!b?this._createFilterSwitchButton():b&&!a?this._createInsertSwitchButton():this._createModeSwitchButton():""},itemTemplate:function(a,c){var d=b([]);return this.editButton&&(d=d.add(this._createEditButton(c))),this.deleteButton&&(d=d.add(this._createDeleteButton(c))),d},filterTemplate:function(){var a=this._createSearchButton();return this.clearFilterButton?a.add(this._createClearFilterButton()):a},insertTemplate:function(){return this._createInsertButton()},editTemplate:function(){return this._createUpdateButton().add(this._createCancelEditButton())},_createFilterSwitchButton:function(){return this._createOnOffSwitchButton("filtering",this.searchModeButtonClass,!0)},_createInsertSwitchButton:function(){return this._createOnOffSwitchButton("inserting",this.insertModeButtonClass,!1)},_createOnOffSwitchButton:function(a,c,d){var e=d,f=b.proxy(function(){g.toggleClass(this.modeOnButtonClass,e)},this),g=this._createGridButton(this.modeButtonClass+" "+c,"",function(b){e=!e,b.option(a,e),f()});return f(),g},_createModeSwitchButton:function(){var a=!1,c=b.proxy(function(){d.attr("title",a?this.searchModeButtonTooltip:this.insertModeButtonTooltip).toggleClass(this.insertModeButtonClass,!a).toggleClass(this.searchModeButtonClass,a)},this),d=this._createGridButton(this.modeButtonClass,"",function(b){a=!a,b.option("inserting",a),b.option("filtering",!a),c()});return c(),d},_createEditButton:function(a){return this._createGridButton(this.editButtonClass,this.editButtonTooltip,function(b,c){b.editItem(a),c.stopPropagation()})},_createDeleteButton:function(a){return this._createGridButton(this.deleteButtonClass,this.deleteButtonTooltip,function(b,c){b.deleteItem(a),c.stopPropagation()})},_createSearchButton:function(){return this._createGridButton(this.searchButtonClass,this.searchButtonTooltip,function(a){a.search()})},_createClearFilterButton:function(){return this._createGridButton(this.clearFilterButtonClass,this.clearFilterButtonTooltip,function(a){a.clearFilter()})},_createInsertButton:function(){return this._createGridButton(this.insertButtonClass,this.insertButtonTooltip,function(a){a.insertItem().done(function(){a.clearInsert()})})},_createUpdateButton:function(){return this._createGridButton(this.updateButtonClass,this.updateButtonTooltip,function(a,b){a.updateItem(),b.stopPropagation()})},_createCancelEditButton:function(){return this._createGridButton(this.cancelEditButtonClass,this.cancelEditButtonTooltip,function(a,b){a.cancelEdit(),b.stopPropagation()})},_createGridButton:function(a,c,d){var e=this._grid;return b("<input>").addClass(this.buttonClass).addClass(a).attr({type:"button",title:c}).on("click",function(a){d(e,a)})},editValue:function(){return""}}),a.fields.control=a.ControlField=c}(jsGrid,jQuery);
PypiClean
/Eureqa-1.76.0.tar.gz/Eureqa-1.76.0/eureqa/analysis_templates/execution.py
from progress_update import ProgressUpdate from parameters_values import ParametersValues from parameter_validation_result import ParameterValidationResult from eureqa.utils import Throttle import json from eureqa.utils import utils class Execution: """Represents an analysis template execution on the server. :param dict body: Class metadata as dictionary :param str template_id: The id of the analysis_template the execution belongs to. :param Eureqa eureqa: A eureqa connection. :var str `~eureqa.analysis_templates.execution.Execution.template_id`: The id of the analysis_template the execution belongs to. :var str `~eureqa.analysis_templates.execution.Execution.analysis_id`: The id of the analysis the execution belongs to. :var str state: The current state of the execution. :var list `~eureqa.analysis_templates.execution.Execution.parameters`: The list of parameter values for the execution. :var list `~eureqa.analysis_templates.execution.Execution.progress_updates`: The list of updates for the execution. """ def __init__(self, body, template_id, eureqa): """For internal use only""" self._id = body['id'] self.template_id = template_id self.analysis_id = body['analysis_id'] self.parameters = ParametersValues._from_json(eureqa, body, execution=self).parameters self._add_self_to_data_file_parameters() self._eureqa = eureqa self._body = body @property @Throttle() def state(self): return self._get_updated_self()._body['state'] def _get_updated_self(self): """ Internal. Return a new Execution object representing the current state on the server """ self._eureqa._session.report_progress('Getting details for execution: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) updated_execution = self._eureqa._session.execute('/analysis_templates/%s/executions/%s' % (utils.quote(self.template_id), utils.quote(self._id)), 'GET') return Execution(updated_execution, self.template_id, self._eureqa) def _is_running(self): """Internal (to programatically drive an analysis template). Return true if the execution is currently executing or validating""" the_state = self.state # NB actually makes a RPC return the_state in { 'VALIDATING', 'RUNNING' } def _is_done(self): """Internal (to programatically drive an analysis template). Return true if the execution is currently executing or validating""" the_state = self.state # NB actually makes a RPC return the_state in { 'DONE', 'ERRORED', 'ABORTED' } def _is_waiting_on_confirmation(self): """Internal (to programatically drive an analysis template). Return true if the execution is waiting on the user to accept results of confirmation""" the_state = self.state # NB actually makes a RPC return the_state == 'WAITING_FOR_CONFIRMATION' @property def progress_updates(self): """Get all progress updates for an execution of an analysis template.""" self._eureqa._session.report_progress('Getting progress_updates for execution: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) results = self._eureqa._session.execute('/analysis_templates/%s/executions/%s/progress_updates' % (utils.quote(self.template_id), utils.quote(self._id)), 'GET') return [ProgressUpdate(x) for x in results] @property @Throttle() def validation_results(self): """Get all validation results for the execution of an analysis template.""" def make_parameter(body): r = ParameterValidationResult(type='UNKNOWN') r._from_json(body) return r return [make_parameter(x) for x in self._get_updated_self()._body['validation_results']] def _to_json(self): body = { 'template_id': self.template_id, 'analysis_id': self.analysis_id, 'state': self._body['state'], 'parameter': ParametersValues(self.parameters)._to_json(), 'progress_updates': [x._to_json() for x in self.progress_updates] } return body def _is_running(self): """Internal (to programatically drive an analysis template). Return true if the execution is currently executing or validating""" the_state = self.state # NB actually makes a RPC return the_state in { 'VALIDATING', 'RUNNING' } def __str__(self): return json.dumps(self._to_json(), indent=4) def get_analysis(self): """Retrieves the analysis that belongs to the execution.""" return self._eureqa.get_analysis(self.analysis_id) def get_analysis_template(self): """Retrieves the analysis that belongs to the execution.""" return self._eureqa._get_analysis_template(self.template_id) def update_progress(self, message): """Create a progress update for an execution of an analysis template. :param str message: The progress message """ self._eureqa._session.report_progress('Updating progress of execution: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) self._eureqa._session.execute('/analysis_templates/%s/executions/%s/progress_updates' % (utils.quote(self.template_id), utils.quote(self._id)), 'POST', { 'message': message }) def report_validation_result(self, type, message=None, details=None, parameter_id=None): """ Report an info/warning/error message about the specified parameter to be shown to the user in validation review :param str type: If this result is INFO, WARNING, or ERROR :param str message: The result message :param str details: (optional) Detailed message about the result :param str parameter_id: (optional) the analysis template parameter that this progress update refers to """ self._eureqa._session.report_progress('Reporting validation result for execution: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) validation_result = ParameterValidationResult(type, message, details, parameter_id) self._eureqa._session.execute('/analysis_templates/%s/executions/%s/validation_result' % (utils.quote(self.template_id), utils.quote(self._id)), 'POST', validation_result._to_json()) def report_fatal_error(self, error): """Notifies the server that an error occurred during the execution and terminates the script execution. :param str error: The error that occurred during the execution. """ self._eureqa._session.report_progress('Reporting error in execution: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) self._eureqa._session.execute('/analysis_templates/%s/executions/%s/error' % (utils.quote(self.template_id), utils.quote(self._id)), 'POST', {'message': error}) self._hard_exit() def _report_validation_completion(self): """Notifies the server that the validation portion has completed.""" self._eureqa._session.report_progress('Reporting completion of validation: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) self._eureqa._session.execute('/analysis_templates/%s/executions/%s/validation_completion' % (utils.quote(self.template_id), utils.quote(self._id)), 'POST', {}) def _abort(self): """Notifies the server that something bad happened to the execution.""" self._eureqa._session.report_progress('Aborting execution \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) self._eureqa._session.execute('/analysis_templates/%s/executions/%s/abort' % (utils.quote(self.template_id), utils.quote(self._id)), 'POST', {}) def _report_validation_results_confirmed(self): """Internal (to programatically drive an analysis template). Reports that that the user confirmed validation results""" self._eureqa._session.report_progress('Reporting validation results were confirmed for execution: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) self._eureqa._session.execute('/analysis_templates/%s/executions/%s/validation_results_confirmed' % (utils.quote(self.template_id), utils.quote(self._id)), 'POST', '{}') def _report_completion(self): """Notifies the server that the execution completed and terminates the script execution. """ self._eureqa._session.report_progress('Reporting completion of execution: \'%s\' of analysis_template: \'%s\'.' % (self._id, self.template_id)) self._eureqa._session.execute('/analysis_templates/%s/executions/%s/complete' % (utils.quote(self.template_id), utils.quote(self._id)), 'POST', {}) def _wait_until_finished(self): while not self._is_done(): if self._is_waiting_on_confirmation(): self._report_validation_results_confirmed() def _hard_exit(self): import traceback with open('/tmp/we_are_quitting.txt', 'wb') as fd: fd.write(traceback.format_exc() + '\n') import sys sys.exit() def _add_self_to_data_file_parameters(self): if self.parameters is not None: for p_id in self.parameters: param = self.parameters[p_id] if param._type is "data_file": param._execution = self
PypiClean
/Metamorf-0.4.4.2.tar.gz/Metamorf-0.4.4.2/metamorf/tools/log.py
from metamorf.tools.filecontroller import FileControllerFactory from metamorf.constants import * from datetime import datetime import os class Log: def __init__(self): os.system('') self.file_log = FileControllerFactory().get_file_reader(FILE_TYPE_LOG) self.file_log.set_file_location(ACTUAL_PATH, LOG_FILE_NAME) self.file_log.setup_writer(FILE_WRITER_APPEND) file_controller_properties = FileControllerFactory().get_file_reader(FILE_TYPE_YML) file_controller_properties.set_file_location(os.path.join(PACKAGE_PATH, PROPERTIES_FILE_PATH), PROPERTIES_FILE_NAME) self.properties_file = file_controller_properties.read_file() def log(self, subject: str, message: str, level: int): date_now = datetime.now().strftime("%Y-%m-%d %H:%M:%S") self.file_log.write_file(date_now + " [" + subject + "] " + message + "\n") message = self._get_message_with_color(level, message) if 'options' not in self.properties_file: return if 'log_print' not in self.properties_file['options']: return if level == LOG_LEVEL_ONLY_LOG: return if self.properties_file['options']['print_debug'] == 'N' and level == LOG_LEVEL_DEBUG: return if self.properties_file['options']['log_print'] == "Y": print(COLOR_LIGHT_GRAY + date_now + " " + COLOR_DEFAULT + "[" + COLOR_DARK_GRAY + subject + COLOR_DEFAULT + "]" + "" + COLOR_DEFAULT + ": " + message) def close(self): self.file_log.close() def _get_message_with_color(self, level: int, message: str): result = COLOR_RED + message + COLOR_DEFAULT if level == LOG_LEVEL_DEBUG: result = COLOR_BLUE + message + COLOR_DEFAULT if level == LOG_LEVEL_INFO or level == LOG_LEVEL_ONLY_LOG: result = COLOR_DEFAULT + message + COLOR_DEFAULT if level == LOG_LEVEL_WARNING: result = COLOR_YELLOW + message + COLOR_DEFAULT if level == LOG_LEVEL_ERROR: result = COLOR_LIGHT_RED + message + COLOR_DEFAULT if level == LOG_LEVEL_CRITICAL: result = COLOR_RED + message + COLOR_DEFAULT if level == LOG_LEVEL_OK: result = COLOR_GREEN + message + COLOR_DEFAULT return result
PypiClean
/Astropysics-1.0.tar.gz/Astropysics-1.0/astropysics/coords/coordsys.py
#TODO: implement polar motion lookup techniques from __future__ import division,with_statement from ..constants import pi from ..utils import add_docs import numpy as np _twopi = 2*pi _pio2 = pi/2 try: #requires Python 2.6 from abc import ABCMeta from abc import abstractmethod from abc import abstractproperty from collections import Sequence,MutableSequence except ImportError: #support for earlier versions abstractmethod = lambda x:x abstractproperty = property ABCMeta = type class MutableSequence(object): __slots__=('__weakref__',) #support for weakrefs as necessary class Sequence(object): __slots__=('__weakref__',) #support for weakrefs as necessary class AngularCoordinate(object): """ A class representing an angular value. Arithmetic operators can be applied to the coordinate, and will be applied directly to the numerical value in radians. For + and -, two angular coordinates may be used, although for -, an AngularSeparation object will be returned. """ import re as _re __slots__=('_decval','_range') #this disturbingly complex RE matches anything that looks like a standard sexigesimal or similar string __acregex = _re.compile(r'(?:([+-])?(\d+(?:[.]\d*)?)(hours|h|degrees|d|radians|rads|rad|r| |:(?=\d+:\d+[.]?\d*$)))?(?:(\d+(?:[.]\d*)?)(m|\'|[:]| ))?(?:(\d+(?:[.]\d*)?)(s|"|$))?$') #and this one matches all things that look like raw numbers __decregex = _re.compile(r'[+-]?\d+([.]\d*)?$') def __init__(self,inpt=None,sghms=None,range=None,radians=False): """ The input parser is very adaptable, and can be in any of the following forms for `inpt`: * A float value if `radians` is True, this will be interpreted as decimal radians, otherwise, it is in degrees. * An :class:`AngularCoordinate` object A copy of the input object will be created. * None The default of 0 will be used. * A 3-tuple If `sghms` is True, the tuple will be interpreted as (hours,min,sec), otherwise, (degrees,min,sec). * A string of the form ##.## If `radians` is True, this will be cast to a float and used as decimal radians, otherwise, it is in degrees. * A string of the form ##.##d or ##.##degrees The numerical part will be cast to a float and used as degrees. * A string of the form ##.##h or ##.##hours The numerical part will be cast to a float and used as hours. * A string of the form ##.##radians,##.##rads, or ##.##r The numerical part will be cast to a float and used as radians. * A string of the form (+/-)##h##m##.##s The numerical parts will be treated as hours,minutes, and seconds. * A string of the form (+/-)##d##m##.##s or (+/-)##d##'##.##" The numerical parts will be treated as degrees,minutes, and seconds. * A string of the form (+/-)##:##:##.## or (+/-)## ## ##.## Sexigesimal form. If `sghms` is None the presence of a a + or - sign idicates that it should be interpreted as degrees, minutes, and seconds. If the sign is absent, the numerical portions will be treated as hours,min,sec. thewise, if `sghms` evaluates to True, the numerical parts will be treated as hours,minutes, and seconds, and if `sghms` evaluates to False, degrees,minutes, and seconds. :param inpt: The coordinate value -- valid forms are described above. :param sghms: If True, ambiguous sexigesimal inputs should be hours, minutes, and seconds instead of degrees,arcmin, and arcsec :type sghms: boolean :param range: Sets the valid range of coordinates. Either a 2-sequence (lowerdegrees,upperdegrees) or None (for no limit) :param radians: If True, ambiguous inputs are treated as radians rather than degrees. :type radians: boolean **Examples** >>> from math import pi >>> ac = AngularCoordinate(2.5) >>> print ac +2d30'00.00" >>> print AngularCoordinate(ac) +2d30'00.00" >>> print AngularCoordinate(pi,radians=True) +180d00.00" >>> print AngularCoordinate('1.1') +1d6'00.00" >>> print AngularCoordinate('1.1',radians=True) +63d1'31.29" >>> print AngularCoordinate('12d25m12.5s') +12d25'12.50" >>> print AngularCoordinate('3:30:30',sghms=True) +52d37'30.00" >>> print AngularCoordinate('3:30:30',sghms=False) +3d30'30.00" >>> print AngularCoordinate('-3:30:30',sghms=None) -3d30'30.00" >>> print AngularCoordinate('+3:30:30',sghms=None) +3d30'30.00" >>> print AngularCoordinate('3:30:30',sghms=None) +52d37'30.00" """ from operator import isSequenceType self._range = None if isinstance(inpt,AngularCoordinate): self._decval = inpt._decval self._range = inpt._range return elif inpt is None: self._decval = 0 elif isinstance(inpt,basestring): sinpt = inpt.strip() decm = self.__decregex.match(sinpt) if decm: if radians: self.radians = float(decm.group(0)) else: self.degrees = float(decm.group(0)) else: acm = self.__acregex.match(sinpt) if acm: sgn,dec1,mark1,dec2,mark2,dec3,mark3 = acm.group(1,2,3,4,5,6,7) val = (0 if dec1 is None else float(dec1)) + \ (0 if dec2 is None else float(dec2)/60) + \ (0 if dec3 is None else float(dec3)/3600) if sgn == '-': val *= -1 if mark1 == ':' or mark1 == ' ': if sghms is None: if sgn is None: self.hours = val else: #'+' or '-' self.degrees = val elif sghms: self.hours = val else: self.degrees = val elif mark1 == 'hours' or mark1 == 'h': self.hours = val elif mark1 == 'degrees' or mark1 == 'd': self.degrees = val elif mark1 == 'radians' or mark1 == 'rad' or mark1 == 'rads' or mark1=='r': self.radians = val else: try: if radians: self.radians = float(val) else: self.degrees = float(val) except ValueError: raise ValueError('invalid string input for AngularCoordinate') else: raise ValueError('Invalid string input for AngularCoordinate: '+inpt) elif isSequenceType(inpt) and len(inpt)==3: if sghms: self.hrsminsec = inpt else: self.degminsec = inpt elif radians: self._decval = float(inpt) else: from math import radians self._decval = radians(inpt) self.range = range def _setDegminsec(self,dms): if not hasattr(dms, '__iter__') or len(dms)!=3: raise ValueError('Must set degminsec as a length-3 iterator') self.degrees = abs(dms[0])+abs(dms[1])/60.+abs(dms[2])/3600. if dms[0]<0: self._decval*=-1 def _getDegminsec(self): fulldeg = abs(self.degrees) deg = int(fulldeg) fracpart = fulldeg-deg min = int(fracpart*60.) sec = fracpart*3600.-min*60. return -deg if self.degrees < 0 else deg,min,sec degminsec = property(_getDegminsec,_setDegminsec,doc=""" The value of this :class:`AngularCoordinate` as an (degrees,minutes,seconds) tuple, with degrees and minutes as integers and seconds as a float. """) dms = degminsec def _setHrsminsec(self,dms): if not hasattr(dms, '__iter__') or len(dms)!=3: raise ValueError('Must set hrsminsec as a length-3 iterator') self.degrees = 15*(dms[0]+dms[1]/60.+dms[2]/3600.) def _getHrsminsec(self): factorized = self.degrees/15. hrs = int(factorized) mspart = factorized - hrs min = int(mspart*60.) sec = mspart*3600.-min*60. return hrs,min,sec hrsminsec = property(_getHrsminsec,_setHrsminsec,doc=""" The value of this :class:`AngularCoordinate` as an (hours,minutes,seconds) tuple, with hours and minutes as integers and seconds as a float. """) hms = hrsminsec def _setDecdeg(self,deg): rads = deg*pi/180. if self.range is not None: rads = self._checkRange(rads) self._decval = rads def _getDecdeg(self): return self._decval*180/pi degrees = property(_getDecdeg,_setDecdeg,doc=""" The value of this :class:`AngularCoordinate` in decimal degrees. """) d = degrees def _setRad(self,rads): if self.range is not None: rads = self._checkRange(rads) self._decval = rads def _getRad(self): return self._decval radians = property(_getRad,_setRad,doc=""" The value of this :class:`AngularCoordinate` in decimal radians. """) r = radians def _setDechr(self,hr): rads = hr*pi/12 if self.range is not None: rads = self._checkRange(rads) self._decval = rads def _getDechr(self): return self._decval*12/pi hours = property(_getDechr,_setDechr,doc=""" The value of this :class:`AngularCoordinate` in decimal hours. """) h = hours def _checkRange(self,rads): """ Checks if the input value is in range - returns the new value, or raises a :exc:`ValueError`. """ if self._range is not None: low,up,cycle = self._range if cycle is None: if low <= rads <= up: return rads else: raise ValueError('Attempted to set angular coordinate outside range') else: if cycle > 0: #this means use "triangle wave" pattern with the given quarter-period from math import sin,asin offset = low/(low-up)-0.5 return (up-low)*(asin(sin(pi*(2*rads/cycle+offset)))/pi+0.5)+low else: return (rads-low)%(up-low)+low else: return rads def _setRange(self,newrng): oldrange = self._range try: if newrng is None: self._range = None else: from math import radians newrng = tuple(newrng) if len(newrng) == 2: if newrng[1]-newrng[0] == 360: newrng = (newrng[0],newrng[1],0) else: newrng = (newrng[0],newrng[1],None) elif len(newrng)==3: pass else: raise TypeError('range is not a 2 or 3-sequence') if newrng[0] > newrng[1]: raise ValueError('lower edge of range is not <= upper') newrng = ( radians(newrng[0]),radians(newrng[1]), \ None if newrng[2] is None else radians(newrng[2]) ) self._range = newrng self._decval = self._checkRange(self._decval) except ValueError,e: self._range = oldrange if e.args[0] == 'lower edge of range is not <= upper': raise e else: raise ValueError('Attempted to set range when value is out of range') def _getRange(self): if self._range is None: return None else: from math import degrees if self._range[2] is None: return degrees(self._range[0]),degrees(self._range[1]) else: return degrees(self._range[0]),degrees(self._range[1]),degrees(self._range[2]) range = property(_getRange,_setRange,doc=""" The acceptable range of angles for this :class:`AngularCoordinate`. This can be set as a 2-sequence (lower,upper), or as a 3-sequence (lower,upper,cycle), where cycle can be : * 0: Angle values are coerced to lie in the range (default for 2-sequence if upper-lower is 360 degrees) * None: A :exc:`ValueError` will be raised if out-of-range (default for 2-sequence otherwise) * A positive scalar: Values are coerced in a triangle wave scheme, with the scalar specifying the period. e.g. for the latitude, (-90,90,360) would give the correct behavior) """) def __str__(self): return self.getDmsStr(sep=('d',"'",'"')) def __eq__(self,other): if hasattr(other,'_decval'): return self._decval==other._decval else: return self._decval==other def __ne__(self,other): return not self.__eq__(other) def __add__(self,other): if hasattr(other,'_decval'): res = self.__class__() res._decval = self._decval + other._decval else: res = self.__class__() res._decval = self._decval + other return res def __sub__(self,other): if isinstance(other,AngularCoordinate): from math import degrees res = AngularSeparation(degrees(other._decval),degrees(self._decval)) else: res = AngularCoordinate() res._decval = self._decval - other return res def __mul__(self,other): res = self.__class__() res._decval = self._decval*other return res def __div__(self,other): res = self.__class__() res._decval = self._decval/other return res def __truediv__(self,other): res = self.__class__() res._decval = self._decval//other return res def __pow__(self,other): res = self.__class__() res._decval = self._decval**other return res def __float__(self): return self.degrees def getDmsStr(self,secform='%05.2f',sep=(unichr(176),"'",'"'), sign=True, canonical=False, inclzero=True): """ Generates the string representation of this AngularCoordinate as degrees, arcminutes, and arcseconds. :param secform: a formatter for the seconds :type secform: string :param sep: The seperator between components - defaults to degree sign, ' and " symbols. :type sep: string or 3-tuple of strings :param sign: Forces sign to be present before degree component. :type sign: boolean :param canonical: forces [+/-]dd:mm:ss.ss , overriding other arguments :param inclzero: If True, a "0" is included whenever even if the degrees or minutes are 0. Otherise, the "0" and the corresponding separator are omitted from the string. :type inclzero: bool :returns: String representation of this object. """ d,m,s = self.degminsec if canonical: secform = '%05.2f' sep = (':',':','') sign = True s = secform%s if int(float(s))>=60: s = secform%0 m += 1 if m==60: m = 0 d += 1 d,m=str(abs(d)),str(m) if isinstance(sep,basestring): if sep == 'dms': sep = ('d','m','s') sep = (sep,sep) tojoin = [] if sign and self._decval >= 0: tojoin.append('+') if self._decval<0: tojoin.append('-') if inclzero or d is not '0': tojoin.append(d) tojoin.append(sep[0]) if inclzero or m is not '0': tojoin.append(m) tojoin.append(sep[1]) tojoin.append(s) if len(sep)>2: tojoin.append(sep[2]) return ''.join(tojoin) def getHmsStr(self,secform = None,sep = ('h','m','s'), canonical = False, inclzero=True): """ gets the string representation of this AngularCoordinate as hours, minutes, and seconds secform is the formatter for the seconds component sep is the seperator between components - defaults to h, m, and s canonical forces [+/-]dd:mm:ss.ss , overriding other arguments Generates the string representation of this AngularCoordinate as hours, minutes, and seconds. :param secform: a formatter for the seconds component :type secform: string :param sep: The seperator between components - defaults to 'h', 'm', and 's'. :type sep: string or 3-tuple of strings :param canonical: forces [+/-]dd:mm:ss.ss , overriding other arguments :param inclzero: If True, a "0" is included whenever even if the degrees or minutes are 0. Otherise, the "0" and the corresponding separator are omitted from the string. :type inclzero: bool :returns: String representation of this object. """ h,m,s = self.hrsminsec if canonical: secform = '%05.2f' sep = (':',':','') s = str(s) if secform is None else secform % s #this is for the s=60 case if int(float(s))>=60: news = float(s) - 60 s = str(news) if secform is None else secform%news m += 1 if m==60: m = 0 h += 1 if h==24: h = 0 h,m=str(h),str(m) if isinstance(sep,basestring): if sep == 'hms': sep = ('h','m','s') sep = (sep,sep) tojoin = [] if inclzero or h is not '0': tojoin.append(h) tojoin.append(sep[0]) if inclzero or m is not '0': tojoin.append(m) tojoin.append(sep[1]) tojoin.append(s) if len(sep)>2: tojoin.append(sep[2]) return ''.join(tojoin) class AngularSeparation(AngularCoordinate): """ This class represents a separation between two angular coordinates on the unit sphere. A constructor is available, but the most natural way to generate this object is to use the subtraction (-) operator on two :class:`AngularCoordinate` objects or two :class:`LatLongCoordinates` objects. """ def __init__(self,*args): """ Input arguments can be either: * AngularSeparation(:class:`AngularSeparation` object) Generates a copy of the provided object. * AngularSeparation(sep) Generates a separation of the provided distance with no starting point. * AngularSeparation(start,end) Computes the separation from the start and end objects, which must be :class:`AngularCoordinate` objects. """ if len(args) == 1: a = args[0] if a.__class__ == self.__class__: self._decval = args[0]._decval self._range = args[0]._range return sep = a._decval if hasattr(a,'_decval') else a elif len(args) == 2: a0,a1 = args a0 = a0._decval if hasattr(a0,'_decval') else a0 a1 = a1._decval if hasattr(a1,'_decval') else a1 sep = a1 - a0 else: raise ValueError('improper number of inputs to AngularSeparation') AngularCoordinate.__init__(self,sep) def __add__(self,other): if isinstance(other,AngularCoordinate) and not self.__class__ == other.__class__: res = AngularCoordinate() res._decval = self._decval+other._decval return res else: return AngularCoordinate.__add__(self,other) #comparisons def __lt__(self,other): return self._decval < other._decval def __le__(self,other): return self._decval <= other._decval def __gt__(self,other): return self._decval > other._decval def __ge__(self,other): return self._decval >= other._decval def __eq__(self,other): return self._decval == other._decval def __ne__(self,other): return self._decval != other._decval def _getArcsec(self): return self.degrees*3600 def _setArcsec(self,val): self.degrees = val/3600 arcsec = property(_getArcsec,_setArcsec,doc=None) def _getArcmin(self): return self.degrees*60 def _setArcmin(self,val): self.degrees = val/60 arcmin = property(_getArcmin,_setArcmin,doc=None) def projectedSeparation(self,zord,usez=False,**kwargs): """ Computes the physical projected separation assuming a given distance. kwargs are passed into :func:`cosmo_z_to_dist` if `usez` is True. :param zord: Redshift or distance :type zord: scalar number :param usez: If True, the input will be interpreted as a redshift, and kwargs will be passed into the distance calculation. The result will be in pc. Otherwise, `zord` will be interpreted as a distance. :type usez: boolean :returns: a float value for the separation (in pc if redshift is used) """ from .funcs import angular_to_physical_size return angular_to_physical_size(self.arcsec,zord,usez=usez,**kwargs) def separation3d(self,zord1,zord2,usez=False,**kwargs): """ computes the 3d separation assuming the two points at the ends of this :class:`AngularSeparation` are at the distances `zord1` and `zord2`. :param zord1: Redshift or distance for start point :type zord1: scalar number :param zord2: Redshift or distance for end point :type zord2: scalar number :param usez: If True, the inputs will be interpreted as a redshift, and kwargs will be passed into the distance calculation. The result will be in pc. Otherwise, `zord` will be interpreted as a distance. :type usez: boolean :returns: a float value for the separation (in pc if redshift is used) """ from math import sin,cos,sqrt if usez: d1 = cosmo_z_to_dist(zord1,disttype=2,**kwargs)*1e6 #pc d2 = cosmo_z_to_dist(zord1,disttype=2,**kwargs)*1e6 #pc else: if len(kwargs)>0: raise TypeError('if not using redshift, kwargs should not be provided') d1 = zord1 d2 = zord2 costerm = 2*d1*d2*cos(self._decval) return sqrt(d1*d1+d2*d2-costerm) #<-----------------------------Coordinate systems------------------------------> class _CoosysMeta(ABCMeta): """ Metaclass for CoordinateSystem class and subclasses - needed to support :class:`CoordinateSystem.registerTransform` decorator. """ def __init__(cls,name,bases,dct): ABCMeta.__init__(cls,name,bases,dct) import inspect for k,v in inspect.getmembers(cls): if isinstance(v,_TransformerMethodDeco): for vfc,vtc in zip(v.fromclasses,v.toclasses): fromclass = cls if vfc == 'self' else vfc toclass = cls if vtc == 'self' else vtc CoordinateSystem.registerTransform(fromclass,toclass,v.f,v.transtype) setattr(cls,k,staticmethod(v.f)) class _TransformerMethodDeco(object): """ A class representing methods used for registering transforms for the class the are in. """ def __init__(self,f,fromclass,toclass,transtype=None): self.f = f self.fromclasses = [fromclass] self.toclasses = [toclass] self.transtype = transtype #Default for optmizing convert functions - currently false because it's not smart enough _convertoptimizedefault = False class CoordinateSystem(object): """ Base class of all coordinate systems. This class also holds the static methods that manage conversion between coordinate systems. *Subclassing* * Subclasses of :class:`CoordinateSystem` must override :meth:`__init__` to set initial values. * :class:`CoordinateSystem` objects are intended to be quite small, so unless there is a reason to do otherwise, subclasses should have a :attr:`__slots__` class attribute (it should be a sequence of all the valid attribute names for the object - see http://docs.python.org/reference/datamodel.html for an explanation of the `__slots__` mechanism). * The :attr:`transweight` class variable can be set to determine the weighting of this class when computing coordinate transformation pathways. Note that *smaller* weights are preferred paths (e.g. a larger weight is less likely to be visited). See :meth:`CoordinateSystem.getTransformGraph` for more details. """ from collections import defaultdict as _defaultdict __metaclass__ = _CoosysMeta __slots__ = tuple() @abstractmethod def __init__(self): raise NotImplementedError _converters = _defaultdict(dict) #first index is from, second is to _transtypes = dict() @staticmethod def registerTransform(fromclass,toclass,func=None,transtype=None, overwrite=True): """ Register a function to transform coordinates from one system to another. The transformation function is called is func(fromobject) and should return a new object of type `toclass`. If called with no arguments, the function should raise a :exc:`NotImplementedError` or behave in a manner defined in subclasses (see e.g. :class:`LatLongCoordinates`). If `transtype` is not None, the output of the transformation function is filered through the function applied for that type using :meth:`astropysics.CoordinateSystem.addTransType` . If the transformation function `func` is None, the function is taken to be a decorator, and if it is a method of a subclass of :class:`CoordinateSystem`, `fromclass` or `toclass` may be the string 'self' . In this case, the function will use the class itself as the from or to class. The function will then be treated as a static method (e.g. it should not have `self` as the first argument). :param fromclass: The class to transform from. :type fromclass: subclass of :class:`CoordinateSystem` or 'self' :param toclass: The class to transform to. :type toclass: subclass of :class:`CoordinateSystem` or 'self' :param func: the function to perform the transform or None if decorator. :type func: a callable or None :param transtype: A transformation type that will be used to determine how the transform is performed, or None for no transform type. (see :meth:`astropysics.CoordinateSystem.addTransType` for details). :type transtype: string or None :param overwrite: If True, any already existing function will be silently overriden. Otherwise, a ValueError is raised. :type overwrite: boolean **Examples**:: class MyCoordinates(CoordinateSystem): ... class YourCoordinates(CoordinateSystem): ... def transformer(mycooobj): ... return yourcoordobj CoordinateSystem.registerTransform(MyCoordinates,YourCoordinates,transformer) class TheirCoordinates(CoordinateSystem): @CoordinateSystem.registerTransform(MyCoordinates,'self') @classmethod def fromMy(cls,mycoordinates): ... return theircoordobj """ if func is None: if fromclass != 'self': if not issubclass(fromclass,CoordinateSystem): raise TypeError('from class for registerTransform must be a CoordinateSystem') if toclass != 'self': if not issubclass(toclass,CoordinateSystem): raise TypeError('to class for registerTransform must be a CoordinateSystem') def make_or_extend_trans_meth_deco(f): if isinstance(f,_TransformerMethodDeco): f.fromclasses.append(fromclass) f.toclasses.append(toclass) elif callable(f): return _TransformerMethodDeco(f,fromclass,toclass,transtype) else: raise TypeError('Tried to apply registerTransform to a non-callable') return make_or_extend_trans_meth_deco else: if not issubclass(fromclass,CoordinateSystem) or not issubclass(toclass,CoordinateSystem): raise TypeError('to/from classes for registerTransform must be CoordinateSystems') if not overwrite and (toclass in CoordinateSystem._converters[fromclass]): #format requires 2.6 #raise ValueError('function already exists to convert {0} to {1}'.format(fromclass,toclass)) raise ValueError('function already exists to convert %s to %s'%(fromclass,toclass)) if transtype is not None: try: ttf = CoordinateSystem._transtypes[transtype] except KeyError: raise KeyError('coordinate transformation type %s does not exist'%transtype) lfunc = lambda cobj:ttf(func(cobj),cobj,toclass) lfunc.basetrans = func lfunc.transtype = transtype CoordinateSystem._converters[fromclass][toclass] = lfunc else: func.transtype = None CoordinateSystem._converters[fromclass][toclass] = func CoordinateSystem._invalidateTransformCache() @staticmethod def getTransform(fromclass,toclass): """ Returns the transformation function to go from `fromclass` to `toclass`. """ return CoordinateSystem._converters[fromclass][toclass] @staticmethod def listAllTransforms(): """ Returns a list of 2-tuples (fromclass,toclass) of all the coordinate system combinations that have registered transformation functions. """ trlist = [] for fr,l in CoordinateSystem._converters.iteritems(): for li in l: trlist.append((fr,li)) return trlist @staticmethod def listTransformsTo(toclass): """ Returns a list of classes that can be transformed to the supplied class. """ flist = [] for fr,l in CoordinateSystem._converters.iteritems(): for li in l: if li is toclass: flist.append(fr) return flist @staticmethod def listTransformsFrom(fromclass): """ Returns a list of classes that can be transformed from the supplied class. """ if fromclass in CoordinateSystem._converters: return list(CoordinateSystem._converters[fromclass]) else: return [] @staticmethod def delTransform(fromclass,toclass): """ Deletes the transformation function to go from `fromclass` to `toclass`. """ del CoordinateSystem._converters[fromclass][toclass] CoordinateSystem._invalidateTransformCache() @staticmethod def addTransType(funcorname): """ Registers a new transformation type. Transformation types are used to implement particular types of transformations without repeating similar code in each of the actual transformation functions. The transformation type function (`funcorname`) will be called as transfunc(trans,coords,toclass), where trans is the output of the actual registered transformation function, coords is the coordinate object that is being converted, and toclass is the target class. :param funcorname: The function to register as the transfromation type function. If a string, the string is taken to be the name to use for the transformation (intended for use as a function decorator). Otherwise, the transformation type name is taken from the name of the function with any intial _ removed. :type funcorname: callable or string :returns: The function itself, to allow for use as a decorator. Note that this means that if used as a decorator inside a class, the function will be assigned as an *instance* method. Alternative, if `funcorname` is a string, a function to be called on the transformation function will be returned (see second example). **Examples**:: @addTransType def trans1(trans,coord,tocls): return tocls(trans*coord.val) @addTransType('trans1') def _transfunc(trans,coord,tocls): return tocls(trans*coord.val) """ def regtrans(func,typename): if typename in CoordinateSystem._transtypes: #go through and re-assign all existing transes to use the new one for k,v in CoordinateSystem._converters.iteritems(): for k2,v2 in v.items(): if v2.transtype == typename: btfunc = v2.basetrans coof = lambda cobj:func(btfunc(cobj),cobj,k2) coof.transtype = typename coof.basetrans = btfunc CoordinateSystem._converters[k][k2] = coof CoordinateSystem._transtypes[typename] = func return func if isinstance(funcorname,basestring): typename = funcorname return lambda f:regtrans(f,typename) elif callable(funcorname): typename = funcorname.func_name if typename.startswith('_'): typename = typename[1:] return regtrans(funcorname,typename) else: raise TypeError('funcorname is neither a callable nor a string') @staticmethod def getTransformPath(fromsys,tosys): """ Determines the transformation path from one coordinate system to another for use with :meth:`convert`. :param fromsys: The starting coordinate system class :param tosys: The target coordinate system class :returns: A list of coordinate classes with the shortest path from `fromsys` to `tosys` (*including* `fromsys` and `tosys`) or a callable with the transformation if a single-step direct transformation is available :except NotImplementedError: If no path can be found. """ if tosys in CoordinateSystem._converters[fromsys]: return CoordinateSystem._converters[fromsys][tosys] else: failstr = 'cannot convert coordinate system %s to %s'%(fromsys.__name__,tosys.__name__) try: import networkx as nx g = CoordinateSystem.getTransformGraph() if nx.__version__>'1.4': path = nx.shortest_path(g,fromsys,tosys,weight=True) else: path = nx.shortest_path(g,fromsys,tosys,weighted=True) if not path: raise NotImplementedError(failstr+'; no transform path could be found') return path except ImportError,e: if e.args[0] == 'No module named networkx': raise NotImplementedError(failstr+'; networkx not installed') else: raise _transgraph = None @staticmethod def getTransformGraph(): """ Returns a `networkx <http://networkx.lanl.gov/>` :class:`DiGraph` object representing a graph of the registered coordinate systems and the transformations between them. :except ImportError: If networkx is not installed. """ import networkx as nx if CoordinateSystem._transgraph is None: CoordinateSystem._transgraph = g = nx.DiGraph() transes = [] for a,b in CoordinateSystem.listAllTransforms(): avgweight = (getattr(a,'transweight',1) + getattr(b,'transweight',1))/2 transes.append((a,b,dict(weight=avgweight))) g.add_edges_from(transes) return CoordinateSystem._transgraph.copy() _transformcache = _defaultdict(dict) @staticmethod def _invalidateTransformCache(): """ Called when transforms are changed to invalidate the caches """ from collections import defaultdict CoordinateSystem._transformcache = defaultdict(dict) CoordinateSystem._transgraph = None def convert(self,tosys): """ converts the coordinate system from it's current system to a new :class:`CoordinateSystem` object. :param tosys: The new coordinate system class. Should be a subclass of :class:`CoordinateSystem` . :returns: A new object of a class determined by `tosys` :except: raises :exc:`NotImplementedError` if conversion is not present """ convpath = CoordinateSystem.getTransformPath(self.__class__,tosys) if callable(convpath): return convpath(self) else: currobj = self currsys = self.__class__ for intersys in convpath[1:-1]: currobj = CoordinateSystem._converters[currsys][intersys](currobj) currsys = intersys return CoordinateSystem._converters[currsys][tosys](currobj) class EpochalCoordinates(CoordinateSystem): """ A base class for :class:`CoordinateSystem` classes that have *changeable* epochs associated with them. *Subclassing* Subclasses must implement these methods: * :meth:`__init__` from :class:`CoordinateSystem` * :meth:`transformToEpoch` -- see the method's entry for details. Furthermore, subclasses should set :attr:`julianepoch` to determine if they are Julian or Besselian. """ #TODO:figure out if there's a way to put this back in to save space - right #now if two __slots__ classes are mixed together, this is thrown: #TypeError: Error when calling the metaclass bases multiple bases have instance lay-out conflict #__slots__ = ('_epoch',) julianepoch = True """ If True, the epoch is Julian, otherwise, Besselian """ def __getstate__(self): return {'_epoch':self._epoch} def __setstate__(self,d): self._epoch = d['_epoch'] def _getEpoch(self): return self._epoch def _setEpoch(self,val): if val is None: self._epoch = None else: if val == 'now': from ..obstools import jd_to_epoch val = jd_to_epoch(None,self.julianepoch) if not hasattr(self,'_epoch') or self._epoch is None: self._epoch = float(val) else: self.transformToEpoch(float(val)) epoch = property(_getEpoch,_setEpoch,doc=""" Epoch for this coordinate as a float. Setting with the string 'now' will set the epoch to the time at the moment the command is executed. If set, this coordinate will be transformed to the new epoch, unless the current Epoch is None, in which case the epoch will be set with no transformation. If transformation is *not* desired, first set the epoch to None, and then set to the new epoch. Julian vs. Besselian is determined by the :attr:`julianepoch` attribute. """) def _getEpochstr(self): #format requires 2.6 #return '{0}{1}'.format('J' if self.julianepoch else 'B',self._epoch) if self._epoch is None: return '' else: return '%s%s'%('J' if self.julianepoch else 'B',self._epoch) def _setEpochstr(self,val): self.epoch = val epochstr = property(_getEpochstr,_setEpochstr,doc=""" A string representation of the epoch of this object with a J or B prefixed for julian or besselian epochs. """) def _getJdepoch(self): from ..obstools import epoch_to_jd return epoch_to_jd(self._epoch,self.julianepoch) def _setJdepoch(self,val): from ..obstools import jd_to_epoch self._epoch = jd_to_epoch(val,self.julianepoch) jdepoch = property(_getJdepoch,_setJdepoch,doc=""" Julian Date of the epoch for this object. """) def _getMjdepoch(self): from ..obstools import epoch_to_jd return epoch_to_jd(self._epoch,self.julianepoch,mjd=True) def _setMjdepoch(self,val): from ..obstools import jd_to_epoch self._epoch = jd_to_epoch(val,self.julianepoch,mjd=True) mjdepoch = property(_getMjdepoch,_setMjdepoch,doc=""" Modified Julian Date of the epoch for this object. """) @abstractmethod def transformToEpoch(self,newepoch): """ Subclasses should implement this method to transform their coordinates to a new epoch. At the end of this method after the necessary data transformations are performed, subclasses should call ``EpochalCoordinates.transformToEpoch(newepoch)``. """ self._epoch = newepoch class RectangularCoordinates(CoordinateSystem): """ Rectangular/Cartesian Coordinates in three dimensions. Coordinates are accessed via the attributes :attr:`x`, :attr:`y`, and :attr:`z`. """ __slots__ = ('x','y','z') def __init__(self,x,y,z): #: x cartesian coordinate value self.x = x #: y cartesian coordinate value self.y = y #: z cartesian coordinate value self.z = z def __getstate__(self): #TODO: watch if this creates probelms by not being a dict return dict(x=self.x,y=self.y,z=self.z) def __setstate__(self,d): self.x = d['x'] self.y = d['y'] self.z = d['z'] def __str__(self): return '%s: x=%f,y=%f,z=%f'%(self.__class__.__name__,self.x,self.y,self.z) def __add__(self,other): from copy import deepcopy if hasattr(other,'x') and hasattr(other,'y') and hasattr(other,'z'): new = deepcopy(self) new.x = self.x+other.x new.y = self.y+other.y new.z = self.z+other.z return new raise TypeError('Object of type %s does not have x,y, and z for operand +'%other.__class__) def __sub__(self,other): from copy import deepcopy if hasattr(other,'x') and hasattr(other,'y') and hasattr(other,'z'): new = deepcopy(self) new.x = self.x-other.x new.y = self.y-other.y new.z = self.z-other.z return new raise TypeError('Object of type %s does not have x,y, and z for operand -'%other.__class__) def _getLength(self): from math import sqrt return sqrt(self.x**2+self.y**2+self.z**2) def _setLength(self,val): scaling = val/self._getLength() self.x *= scaling self.y *= scaling self.z *= scaling length = property(_getLength,_setLength,doc=""" The Length of this coordinate's vector e.g. distance from the origin. If set, the direction will be preserved but the vector will be scaled to the provided value.""") CartesianCoordinates = RectangularCoordinates class _LatLongMeta(_CoosysMeta): def __init__(cls,name,bases,dct): _CoosysMeta.__init__(cls,name,bases,dct) if cls._longlatnames_[0] is not None: setattr(cls,cls._longlatnames_[0],cls.long) setattr(cls,cls._longlatnames_[0]+'err',cls.longerr) if cls._longlatnames_[1] is not None: setattr(cls,cls._longlatnames_[1],cls.lat) setattr(cls,cls._longlatnames_[1]+'err',cls.laterr) class LatLongCoordinates(CoordinateSystem): """ This object represents an angular location on a sphere as represented in spherical coordinates with a latitude and longitude, and optionally a distance. Subclasses specify details such as transformations or epochs. A :class:`LatLongCoordinate` system is designed to use the transformation type (see :meth:`CoordinateSystem.addTransType`) 'smatrix'. Thus, if the transformation between two :class:`LatLongCoordinate` subclasses can be represented as a unitary matrix operating on position vectors on the unit sphere, the transformation function can be written as:: @CoordinateSystem.registerTransform(InLLCoords,OutLLCoords,transtype='smatrix') def transform(incoord): ... compute the elements of a 3x3 transformation matrix... return np.mat([[a,b,c],[d,e,f],[g,h,i]]) *Subclassing* Subclasses of :class:`LatLongCoordinates` can have the class attribute :attr:`_longlatnames_` as a 2-tuple of strings (longname,latname), with names for the two coordinates, e.g. ('ra','dec'). They can also include the :attr:`_longrange_` attribute, which specifies the range of valid values for the longitude (latitude is always -90 to 90 degrees), or None to place no restriction. See :class:`CoordinateSystem` for additional subclassing information. """ __slots__ = ('_lat','_long','_laterr','_longerr','_dpc') __metaclass__ = _LatLongMeta _longlatnames_ = ('longitude','latitude') _longrange_ = None def __init__(self,long=0,lat=0,longerr=None,laterr=None,distancepc=None): """ See the associated attribute docstrings for the meaning of the inputs. """ self._lat = AngularCoordinate(range=(-90,90,360)) self._long = AngularCoordinate(range=self._longrange_) self.distancepc = distancepc if hasattr(lat,'lat') and hasattr(lat,'long'): if long is 0 and laterr is None and longerr is None: self.lat = lat.lat self.long = lat.long self.laterr = lat.laterr self.longerr = lat.longerr else: raise ValueError("can't provide a LatLongCoordinates as a constructor and set other values simultaneously") else: self.lat = lat self.long = long self.laterr = laterr self.longerr = longerr def __getstate__(self): return dict([(k,getattr(self,k)) for k in LatLongCoordinates.__slots__]) def __setstate__(self,d): for k in LatLongCoordinates.__slots__: setattr(self,k,d[k]) def _getDistancepc(self): if callable(self._dpc): return self._dpc() else: return self._dpc def _setDistancepc(self,val): if val is None: self._dpc = None elif callable(val): self._dpc = val else: try: self._dpc = (float(val[0]),float(val[1])) except (TypeError,IndexError): self._dpc = (float(val),0) distancepc = property(_getDistancepc,_setDistancepc,doc=""" Parallax distance to object in parsecs, or None to assume infinity. Set as either a float, a 2-tuple (distance,distance_error), or a no-argument callable that returns such a tuple. Getter always returns 2-tuple or None. """) def _getDistanceau(self): from ..constants import aupercm,cmperpc auperpc = cmperpc * aupercm if self._dpc is None: return None elif callable(self._dpc): res = self._dpc() else: res = self._dpc return (res[0]*auperpc,res[1]*auperpc) def _setDistanceau(self,val): from ..constants import cmperau,pcpercm pcperau = cmperau * pcpercm if val is None: self._dpc = None elif callable(val): self._dpc = lambda: tuple((v*pcperau for v in val())) else: try: self._dpc = (float(val[0])*pcperau,float(val[1])*pcperau) except (TypeError,IndexError): self._dpc = (float(val)*pcperau,0) distanceau = property(_getDistanceau,_setDistanceau,doc=""" Parallax distance to object in AU, or None to assume infinity. Set as either a float, a 2-tuple (distance,distance_error), or a no-argument callable that returns such a tuple. Getter always returns 2-tuple or None. """) def _getLat(self): return self._lat def _setLat(self,val): if isinstance(val,AngularCoordinate): rads = val.radians%_twopi else: rads = AngularCoordinate(val).radians%_twopi #fix for radian range if rads > 3*pi/2: rads -= _twopi elif rads > pi/2: rads = pi - rads self._lat.radians = rads lat = property(_getLat,_setLat,doc=""" Latitude of this object as a :class:`AngularCoordinate` object. May be set using any valid input form for :class:`AngularCoordinate`. """) def _getLong(self): return self._long def _setLong(self,val): if isinstance(val,AngularCoordinate): self._long.radians = val.radians%_twopi else: self._long.radians = AngularCoordinate(val).radians%_twopi long = property(_getLong,_setLong,doc=""" Longitude of this object as a :class:`AngularCoordinate` object. May be set using any valid input form for :class:`AngularCoordinate`. """) def _getLaterr(self): return self._laterr def _setLaterr(self,val): if val is None: self._laterr = None elif isinstance(val,AngularSeparation): self._laterr = val else: self._laterr = AngularSeparation(val) laterr = property(_getLaterr,_setLaterr,doc=""" Latitude error for this object as a :class:`AngularSeparation` object. May be set using any valid input form for :class:`AngularSeparation`. """) def _getLongerr(self): return self._longerr def _setLongerr(self,val): if val is None: self._longerr = None elif isinstance(val,AngularSeparation): self._longerr = val else: self._longerr = AngularSeparation(val) longerr = property(_getLongerr,_setLongerr,doc=""" Longitude error for this object as a :class:`AngularSeparation` object. May be set using any valid input form for :class:`AngularSeparation`. """) def __str__(self): lat,long = self._lat.d,self._long.d #lat,long = self._lat.getDmsStr(),self._long.getDmsStr() #this requires 2.6 - switch later maybe #return '{0}: {1[0]}={2},{1[1]}={3}'.format(self.__class__.__name__,self._longlatnames_,long,lat) return '%s: %s=%f,%s=%f'%(self.__class__.__name__,self._longlatnames_[0],long,self._longlatnames_[1],lat) def getCoordinateString(self,sep=' ',labels=False,canonical=False,hmslong=False): coords = [] if hmslong: coords.append(self._long.getHmsStr(canonical=canonical,sign=False)) else: coords.append(self._long.getDmsStr(canonical=canonical,sign=False)) coords[-1] = self._longlatnames_[0]+'='+coords[-1] coords.append(self._lat.getDmsStr(canonical=canonical)) coords[-1] = self._longlatnames_[1]+'='+coords[-1] return sep.join(coords) def __eq__(self,other): if hasattr(other,'lat') and hasattr(other,'long'): return self._lat==other.lat and self._long==other.long else: return False def __ne__(self,other): return not self.__eq__(other) def __sub__(self,other): if isinstance(other,LatLongCoordinates) or (hasattr(other,'lat') and hasattr(other,'long')): from math import cos,degrees,acos,asin,sin,sqrt b1 = self._lat.radians b2 = other.lat.radians db = abs(b2 - b1) dl = abs(other.long.radians - self._long.radians) #haversin(theta) = (1-cos(theta))/2 = sin^2(theta/2) #has better numerical accuracy if sin for theta ~ 0, cos ~ pi/2 haversin = lambda t:(1-cos(t))/2 if pi/4 < (t%pi) < 3*pi/4 else sin(t/2)**2 hdb = haversin(db) hdl = haversin(dl) havsep = hdb + cos(b1)*cos(b2)*hdl #archaversin sep = acos(1 - 2*havsep) if 0.25 < havsep <= 0.75 else 2*asin(havsep**0.5) #straightforward definition without the tweaks using haversin - this #is in principal faster, but in practice it ends up only about #10% faster due to the other overhead #sep = acos(sin(b1)*sin(b2)+cos(b1)*cos(b2)*cos(dl)) return AngularSeparation(degrees(sep)) # #small angle version # from math import cos,degrees,sqrt # clat = cos((self._lat.radians+other._lat.radians)/2) # dcorrlong = (self._long.radians - other._long.radians)*clat # dlat = self._lat.radians-other._lat.radians # sep = AngularSeparation(degrees(sqrt(dlat*dlat+dcorrlong*dcorrlong))) # return sep else: raise ValueError("unsupported operand type(s) for -: '%s' and '%s'"%(self.__class__,other.__class__)) @staticmethod @CoordinateSystem.addTransType def _smatrix(m,coord,tocls): newcoord = tocls() newcoord.lat = coord._lat newcoord.laterr = coord._laterr newcoord.long = coord._long newcoord.longerr = coord._longerr newcoord.matrixRotate(m) return newcoord def matrixRotate(self,matrix,apply=True,fixrange=True,unitarycheck=False): """ Applies the supplied unitary rotation matrix to these coordinates. :param matrix: the transformation matrix in cartesian coordinates :type matrix: a 3x3 :class:`numpy.matrix` :param apply: If True, the transform will be applied inplace to the coordinates for this object :type apply: boolean :param fixrange: If True the latitude is autmoatically fixed to be on (-pi/2,pi/2) and the longitude is on (0,2pi). Otherwise the raw coordinate is output. :type fixrange: boolean :param unitarycheck: If True and the matrix is not unitary, a ValueError will be raised. Otherwise no check is performed. :type unitarycheck: boolean :returns: (lat,long) as decimal radians after the transformation matrix is applied or (lat,long,laterr,longerr) if errors are nonzero """ #for single values, math module is much faster than numpy from math import sin,cos,atan2,sqrt m = np.asmatrix(matrix) if unitarycheck: mdagger = m.H rtol = 1e-5 if unitarycheck is True else unitarycheck if not np.allclose(mdagger*m,m*mdagger,rtol): raise ValueError('matrix not unitary') lat = self.lat.radians long = self.long.radians laterr = 0 if self.laterr is None else self.laterr.radians longerr = 0 if self.longerr is None else self.longerr.radians sb = sin(lat) cb = cos(lat) sl = sin(long) cl = cos(long) #spherical w/ r=1 > cartesian x = cb*cl y = cb*sl z = sb #do transform v = np.matrix((x,y,z)).T xp,yp,zp = (m*v).A1 #cartesian > spherical sp = sqrt(xp*xp+yp*yp) #cylindrical radius latp = atan2(zp,sp) longp = atan2(yp,xp) #propogate errors if they are present if laterr != 0 or longerr != 0: #TODO: check formulae #all of these are first order taylor expansions about the value dx = sqrt((laterr*sb*cl)**2+(longerr*cb*sl)**2) dy = sqrt((laterr*sb*sl)**2+(longerr*cb*cl)**2) dz = abs(laterr*cb) dv = np.matrix((dx,dy,dz)) dxp,dyp,dzp = np.sqrt(np.power(m,2)*np.power(dv,2)) #intermediate variables for dlatp - each of the partial derivatives chi = 1/(1+(zp/sp)**2) #common factor chi not included below dbdx = x*z*sp**-3 dbdy = y*z*sp**-3 dbdz = 1/sp dlatp = chi*sqrt((dxp*dbdx)**2 + (dyp*dbdy)**2 + (dzp*dbdz)**2) dlongp = sqrt((dxp*yp*xp**-2)**2 + (dyp/xp)**2)/(1 + (yp/xp)**2) #indep of z else: laterr = None if fixrange: ao = (latp+_pio2)/_twopi latp = _twopi*abs((ao-np.floor(ao+0.5)))-_pio2 longp = longp % _twopi if apply: self.lat.radians = latp self.long.radians = longp if laterr is not None: self.laterr.radians = dlatp self.longerr.radians = dlongp if laterr is None: return latp,longp else: return latp,longp,dlatp,dlongp def convert(self,tosys,optimize=_convertoptimizedefault): """ Converts the coordinate system from it's current system to a new :class:`CoordinateSystem` object possibly with optimizations for matrix-based transformation of :class:`LatLongCoordinates` objects. .. warning:: The transformation optimizations used if `optimize` is True are only correct if the conversion matricies are independent of the coordinate values themselves (e.g. are linear and epoch-independent). Examples that are good for optimization include FK4->FK5->ICRS (all are epoch-independent). In the future, this system will be smarter about knowing when it is safe to optimize, but for now, only use it if you're sure it will work correctly. :param tosys: The new coordinate system class. Should be a subclass of :class:`CoordinateSystem` . :param bool optimize: If True, speed up the transformation by composing matricies where possible. If False, the standard transformation is performed. :returns: A new object of a class determined by `tosys` :except: raises NotImplementedError if converters are not present """ if tosys is self.__class__: return self if optimize: cache = CoordinateSystem._transformcache['smatrix'] #add this object to the cache if its missing if self.__class__ not in cache: cache[self.__class__] = {} if tosys not in cache[self.__class__]: convs = CoordinateSystem.getTransformPath(self.__class__,tosys) if callable(convs): #direct transform convs = [convs] else: convclasses = convs convfuncs = [CoordinateSystem._converters[c1][c2] for c1,c2 in zip(convclasses[:-1],convclasses[1:])] convs = [] #now we populate convs with converter functions that are #either multplied-together matricies if they are smatrix #converters or the actual converter function otherwise combinedmatrix = None lastcls = None for cls,cfunc in zip(convclasses[:-1],convfuncs): #note that cls here is the *previous* conversion's end #class/current conversion's start class... if cfunc.transtype=='smatrix': mt = cfunc.basetrans(self) if hasattr(mt,'nocache') and mt.nocache: cache = None if combinedmatrix is None: combinedmatrix = mt else: combinedmatrix = mt * combinedmatrix else: if combinedmatrix is None: convs.append(cfunc) else: convs.append(_OptimizerSmatrixer(combinedmatrix,cls)) convs.append(cfunc) if combinedmatrix is not None: convs.append(_OptimizerSmatrixer(combinedmatrix,convclasses[-1])) #now cache this transform for future use unless it was banned above if cache is not None: cache[self.__class__][tosys] = convs else: convs = cache[self.__class__][tosys] #now actually do the transforms coord = self for conv in convs: coord = conv(coord) return coord else: return CoordinateSystem.convert(self,tosys) class _OptimizerSmatrixer(object): """ Used internally to do the optimization of :meth`LatLongCoordinates.convert` """ transtype = 'smatrix' def __init__(self,combinedmatrix,tocls): self.combinedmatrix = combinedmatrix self.tocls = tocls def __call__(self,coord): return LatLongCoordinates._smatrix(self.combinedmatrix,coord,self.tocls) def basetrans(self,coords): return self.combinedmatrix class EpochalLatLongCoordinates(LatLongCoordinates,EpochalCoordinates): """ A Coordinate system where the coordinates change as a function of time. The origin and orientation of some coordinate systems are tied to the motion of the Earth and Solar System and hence most be updated as time passes. In general this only accounts for epoch-related changes in its own coordinate system. If (for example) one has a :class:`ITRSCoordinates` coordinate, changing the epoch only updates for polar motion. To properly update all epoch-related such as precession/nutation and earth rotation, the coordinate should be transformed to :class:`ICRSCoordinates` , update the epoch, and transform back to :class:`TIRSCoordinates` . """ __slots__ = tuple() julianepoch = True def __init__(self,long=0,lat=0,longerr=None,laterr=None,epoch=None,distancepc=None): """ See the associated attribute docstrings for the meaning of the inputs. """ LatLongCoordinates.__init__(self,long,lat,longerr,laterr,distancepc) self._epoch = epoch def __getstate__(self): d = LatLongCoordinates.__getstate__(self) d.update(EpochalCoordinates.__getstate__(self)) return d def __setstate__(self,d): LatLongCoordinates.__setstate__(self,d) EpochalCoordinates.__setstate__(self,d) @add_docs(LatLongCoordinates.convert) def convert(self,tosys,optimize=_convertoptimizedefault): '' res = LatLongCoordinates.convert(self,tosys,optimize) if issubclass(tosys,EpochalLatLongCoordinates): res._epoch = self._epoch return res convert.__doc__ = LatLongCoordinates.convert.__doc__ class EquatorialCoordinatesBase(EpochalLatLongCoordinates): """ This object represents an angular location on the unit sphere, specified in right ascension and declination. Some of the subclasses are not strictly speaking equatorial, but they are close, or are tied to the equatorial position of a particular epoch. This is a superclass for all other Equatorial Coordinate systems - particular reference systems implement the :meth:`transformToEpoch` method. See the docstring for :class:`EpochalLatLongCoordinates` for subclassing suggestions. """ __slots__ = tuple() _longlatnames_ = ('ra','dec') _longrange_ = (0,360) def __str__(self): rastr = self.ra.getHmsStr(canonical=True) decstr = self.dec.getDmsStr(canonical=True) #2.6 required for format #return '{3}: {0} {1} ({2})'.format(rastr,decstr,self.epoch,self.__class__.__name__) return '%s: %s %s %s'%(self.__class__.__name__,rastr,decstr,self.epochstr) def __init__(self,*args,**kwargs): """ Input for equatorial coordinates. Can follow any of the following forms: * EquatorialCoordinatesBase() * EquatorialCoordinatesBase(:class:`EquatorialCoordinatesBase`) * EquatorialCoordinatesBase('rastr decstr') * EquatorialCoordinatesBase((ra,dec)) * EquatorialCoordinatesBase(ra,dec) * EquatorialCoordinatesBase(ra,fdec,raerr,decerr) * EquatorialCoordinatesBase(ra,dec,raerr,decerr,epoch) * EquatorialCoordinatesBase(ra,dec,raerr,decerr,epoch,distancepc) Note that the default epoch is 2000 if not otherwise specified. To disable epoch tranformations, set the epoch to None. If scalar values are provided, they are assummed to be degrees. """ posargs = {} if len(args) == 0: pass if len(args) == 1: if isinstance(args[0],EquatorialCoordinatesBase): EpochalLatLongCoordinates.__init__(self, args[0].ra, args[0].dec, args[0].raerr, args[0].decerr, args[0].epoch, args[0].distancepc) return elif isinstance(args[0],basestring): sargs = args[0].split() posargs['ra'] = sargs[0] posargs['dec'] = sargs[1] else: posargs['ra'],posargs['dec'] = args[0] elif len(args) == 2: posargs['ra'] = args[0] posargs['dec'] = args[1] elif len(args) == 4: posargs['ra'] = args[0] posargs['dec'] = args[1] posargs['raerr'] = args[2] posargs['decerr'] = args[3] elif len(args) == 5: posargs['ra'] = args[0] posargs['dec'] = args[1] posargs['raerr'] = args[2] posargs['decerr'] = args[3] posargs['epoch'] = args[4] elif len(args) == 6: posargs['ra'] = args[0] posargs['dec'] = args[1] posargs['raerr'] = args[2] posargs['decerr'] = args[3] posargs['epoch'] = args[4] posargs['distancepc'] = args[5] for k,v in posargs.iteritems(): if k in kwargs: raise ValueError('got multiple values for argument '+k) kwargs[k] = v kwargs.setdefault('ra',0) kwargs.setdefault('dec',0) kwargs.setdefault('raerr',None) kwargs.setdefault('decerr',None) kwargs.setdefault('epoch',2000) EpochalLatLongCoordinates.__init__(self,kwargs['ra'],kwargs['dec'],kwargs['raerr'],kwargs['decerr']) if 'epoch' in kwargs: self.epoch = kwargs['epoch'] if 'distancepc' in kwargs: if 'distanceau' in kwargs: raise TypeError("can't specify distance in both pc and au") self.distancepc = kwargs['distancepc'] elif 'distanceau' in kwargs: self.distanceau = kwargs['distanceau'] else: self._dpc = None @add_docs(EpochalLatLongCoordinates.convert) def convert(self,tosys,optimize=_convertoptimizedefault): '' res = EpochalLatLongCoordinates.convert(self,tosys,optimize) if self._dpc is not None: res._dpc = self._dpc return res convert.__doc__ = EpochalLatLongCoordinates.convert.__doc__ class ICRSCoordinates(EquatorialCoordinatesBase): """ Equatorial Coordinates tied to the International Celestial Reference System (ICRS). Strictly speaking this is not an Equatorial system, as it is an inertial frame that only aligns with Earth's equator at J2000, but it is nearly an equatorial system at J2000. .. note:: Technically, this is actually the Barycentric Celestial Referense System (BCRS), distringuished from ICRS by having acounted for space motion. In astropysics, instead, space motion is already accounted for by using a :class:`astropysics.coords.ephems.EphemerisObject` object, which yields coordinates (often :class:`ICRSCoordinates`) at the epoch of observation. .. warning:: Abberation of starlight is not yet implemented in transformations to/from ICRS. """ __slots__ = tuple() def transformToEpoch(self,newepoch): """ ICRS is an inertial frame, so no transformation is necessary """ EpochalLatLongCoordinates.transformToEpoch(self,newepoch) #Conversions to/from ICRS are in the other coordinate systems def __makeFrameBias(): from ..utils import rotation_matrix #sing USNO circular 179 for frame bias -- all in milliarcsec da0 = -14.6 xi0 = -16.6170 eta0 = -6.8192 #mas->degrees return rotation_matrix(-eta0/3600000,axis='x') *\ rotation_matrix(xi0/3600000,axis='y') *\ rotation_matrix(da0/3600000,axis='z') frameBiasJ2000 = __makeFrameBias() """ Frame bias matrix such that vJ2000 = B*vICRS . """ #make it a static method just for clarity even though it isn't really visible __makeFrameBias = staticmethod(__makeFrameBias) class RectangularICRSCoordinates(RectangularCoordinates,EpochalCoordinates): """ Rectangular coordinates aligned to the ICRS with origin at the solar system barycenter. The positive z-axis points to the north celestial pole and the positive x-axis is along with the (0,0) point of the equatorial ICRS. .. note:: Units for the coordinates are specified via the :attr:`unit` attribute. When converting *from* :class:`ICRSCoordinates`, distances default to AU if less than 1000 AU, otherwise, pc. If a distance is not present, the default distance is 1 (unspecified unit). """ __slots__ = tuple() julianepoch = True def __init__(self,x,y,z,epoch=None,unit='pc'): RectangularCoordinates.__init__(self,x,y,z) self._epoch = epoch self._unit = None self.unit = unit def __getstate__(self): d = RectangularCoordinates.__getstate__(self) d.update(EpochalCoordinates.__getstate__(self)) return d def __setstate__(self,d): RectangularCoordinates.__setstate__(self,d) EpochalCoordinates.__setstate__(self,d) def __str__(self): if self.epoch is None: epochstr = '' else: epochstr = ' ('+self.epochstr+')' return RectangularCoordinates.__str__(self) + epochstr def transformToEpoch(self,newepoch): EpochalCoordinates.transformToEpoch(self,newepoch) def _getUnit(self): return self._unit def _setUnit(self,val): from ..constants import auperpc if val is None: self._unit = None elif self._unit is None and (val in ('au','pc')): self._unit = val elif val=='au': if self._unit == 'pc': self.x *= auperpc self.y *= auperpc self.z *= auperpc self._unit = val elif val == 'pc': if self._unit == 'au': self.x /= auperpc self.y /= auperpc self.z /= auperpc self._unit = val else: raise ValueError("unit must be 'au' or 'pc' - got %s"%val) unit = property(_getUnit,_setUnit,doc="""The unit for these coordinates. Must be 'au', 'pc', or None - setting to anything else will raise a :exc:`ValueError`. If not None, setting to a new unit will convert the values from AU to pc or vice versa. """) @CoordinateSystem.registerTransform('self',ICRSCoordinates) def _toICRS(ric): from math import asin,atan2,degrees x,y,z = ric.x,ric.y,ric.z r = (x*x+y*y+z*z)**0.5 dec = degrees(asin(z/r)) ra = degrees(atan2(y,x)) if ric.unit is None: return ICRSCoordinates(ra,dec,epoch=ric.epoch) elif ric.unit == 'pc': return ICRSCoordinates(ra,dec,distancepc=r,epoch=ric.epoch) elif ric.unit == 'au': return ICRSCoordinates(ra,dec,distanceau=r,epoch=ric.epoch) else: raise NotImplementedError('Unrecognized unit %s in RectICRS->ICRS'%ric.unit) @CoordinateSystem.registerTransform(ICRSCoordinates,'self') def _fromICRS(ic): from math import sin,cos ra,dec = ic.ra.r,ic.dec.r if ic.distanceau is None: r = 1 unit = None elif ic.distanceau>1000: r = ic.distancepc[0] unit = 'pc' else: r = ic.distanceau[0] unit = 'au' x = r*cos(ra)*cos(dec) y = r*sin(ra)*cos(dec) z = r*sin(dec) return RectangularICRSCoordinates(x,y,z,ic.epoch,unit) class GCRSCoordinates(EquatorialCoordinatesBase): """ Geocentric Celestial Reference System equatorial coordinates. The orientation of this coordinates is fixed to the ICRS orientation, but with origin at the earth geocenter. .. warning:: Abberation of starlight not yet included in transforms. """ __slots__ = tuple() def transformToEpoch(self,newepoch): """ Transforms from the current epoch to a new epoch by converting to ICRS and back again in the new epoch. """ c1 = self.convert(ICRSCoordinates) c1.epoch = newepoch c2 = c1.convert(GCRSCoordinates) self._lat = c2._lat self._long = c2._long self._laterr = c2._laterr self._longerr = c2._longerr self._dpc = c2._dpc EpochalLatLongCoordinates.transformToEpoch(self,newepoch) #TODO:implement direct spherical transformations if needed/wanted for precision # @CoordinateSystem.registerTransform('self',ICRSCoordinates,transtype='smatrix') # def _toICRS(gc): # return np.eye(3).view(np.matrix) # @CoordinateSystem.registerTransform(ICRSCoordinates,'self',transtype='smatrix') # def _fromICRS(ic): # return np.eye(3).view(np.matrix) class RectangularGCRSCoordinates(RectangularCoordinates,EpochalCoordinates): """ Rectangular coordinates aligned to the GCRS with origin at the Earth geocenter. The positive z-axis points to the north celestial pole and the positive x-axis points down the (0,0) point of the equatorial GCRS (and thus, also ICRS). The coordinates at this location are actually an "Astrometric place" - the actual location relative to the geocenter. This is disctinct from :class:`GCRSCoordinates` in that :class:`GCRSCoordinates` *includes* aberration and light deflection, while :class:`RectangularGCRSCoordinates` does not. .. note:: Units for the coordinates are specified via the :attr:`unit` attribute. When converting *from* :class:`GCRSCoordinates`, distances default to AU if less than 1000 AU, otherwise, pc. If a distance is not present, the default distance is 1 (unspecified unit). """ __slots__ = tuple() julianepoch = True def __init__(self,x,y,z,epoch=None,unit='pc'): RectangularCoordinates.__init__(self,x,y,z) self._epoch = epoch self._unit = None self.unit = unit def __getstate__(self): d = RectangularCoordinates.__getstate__(self) d.update(EpochalCoordinates.__getstate__(self)) return d def __setstate__(self,d): RectangularCoordinates.__setstate__(self,d) EpochalCoordinates.__setstate__(self,d) def __str__(self): if self.epoch is None: epochstr = '' else: epochstr = ' ('+self.epochstr+')' return RectangularCoordinates.__str__(self) + epochstr def transformToEpoch(self,newepoch): EpochalCoordinates.transformToEpoch(newepoch) def _getUnit(self): return self._unit def _setUnit(self,val): from ..constants import auperpc if val is None: self._unit = None elif self._unit is None and (val in ('au','pc')): self._unit = val elif val=='au': if self._unit == 'pc': self.x *= auperpc self.y *= auperpc self.z *= auperpc self._unit = val elif val == 'pc': if self._unit == 'au': self.x /= auperpc self.y /= auperpc self.z /= auperpc self._unit = val else: raise ValueError("unit must be 'au' or 'pc' - got %s"%val) unit = property(_getUnit,_setUnit,doc="""The unit for these coordinates. Must be 'au', 'pc', or None - setting to anything else will raise a :exc:`ValueError`. If not None, setting to a new unit will convert the values from AU to pc or vice versa. """) @CoordinateSystem.registerTransform('self',GCRSCoordinates) def _toGCRS(rgc): from math import asin,atan2,degrees #TODO:implement aberration and light deflection x,y,z = rgc.x,rgc.y,rgc.z r = (x*x+y*y+z*z)**0.5 dec = degrees(asin(z/r)) ra = degrees(atan2(y,x)) if rgc.unit is None: return GCRSCoordinates(ra,dec,epoch=rgc.epoch) elif rgc.unit == 'pc': return GCRSCoordinates(ra,dec,distancepc=r,epoch=rgc.epoch) elif rgc.unit == 'au': return GCRSCoordinates(ra,dec,distanceau=r,epoch=rgc.epoch) else: raise NotImplementedError('Unrecognized unit %s in RectGCRS->GCRS'%rgc.unit) @CoordinateSystem.registerTransform(GCRSCoordinates,'self') def _fromGCRS(gc): from math import sin,cos #TODO:implement aberration and light deflection ra,dec = gc.ra.r,gc.dec.r if gc.distanceau is None: r = 1 unit = None elif gc.distanceau>1000: r = gc.distancepc[0] unit = 'pc' else: r = gc.distanceau[0] unit = 'au' x = r*cos(ra)*cos(dec) y = r*sin(ra)*cos(dec) z = r*sin(dec) return RectangularGCRSCoordinates(x,y,z,gc.epoch,unit) @CoordinateSystem.registerTransform('self',RectangularICRSCoordinates) def _toRectICRS(rgc): from .ephems import earth_pos_vel from ..obstools import epoch_to_jd from ..constants import auperpc x = rgc.x y = rgc.y z = rgc.z unit = rgc.unit epoch = rgc.epoch if epoch is None: raise ValueError('cannot transform GCRS to ICRS without an epoch') if unit is None: #infitiely far, so no corrections return RectangularICRSCoordinates(x,y,z,epoch,unit=None) else: #do parallax correction xe,ye,ze = earth_pos_vel(epoch_to_jd(epoch),True)[0] if unit == 'au': xp = x - xe yp = y - ye zp = z - ze elif unit == 'pc': xp = x - xe/auperpc yp = y - ye/auperpc zp = z - ze/auperpc else: raise NotImplementedError('Unit %s not supported by GCRS->ICRS'%unit) return RectangularICRSCoordinates(xp,yp,zp,epoch,unit=unit) @CoordinateSystem.registerTransform(RectangularICRSCoordinates,'self') def _fromRectICRS(ric): from .ephems import earth_pos_vel from ..obstools import epoch_to_jd from ..constants import auperpc x = ric.x y = ric.y z = ric.z unit = ric.unit epoch = ric.epoch if epoch is None: raise ValueError('cannot transform ICRS to GCRS without an epoch') if unit is None: #infitiely far, so no corrections return RectangularGCRSCoordinates(x,y,z,epoch,unit=None) else: #do parallax correction xe,ye,ze = earth_pos_vel(epoch_to_jd(epoch),True)[0] if unit == 'au': xp = x - xe yp = y - ye zp = z - ze elif unit == 'pc': xp = x - xe/auperpc yp = y - ye/auperpc zp = z - ze/auperpc else: raise NotImplementedError('Unit %s not supported by ICRS->GCRS'%unit) return RectangularGCRSCoordinates(xp,yp,zp,epoch,unit=unit) def _precession_matrix_J2000_Capitaine(epoch): """ Computes the precession matrix from J2000 to the given Julian Epoch. Expression from from Capitaine et al. 2003 as written in the USNO Circular 179. This should match the IAU 2006 standard from SOFA (although this has not yet been tested) """ from ..utils import rotation_matrix T = (epoch-2000.0)/100.0 #from USNO circular pzeta = (-0.0000003173,-0.000005971,0.01801828,0.2988499,2306.083227,2.650545) pz = (-0.0000002904,-0.000028596,0.01826837,1.0927348,2306.077181,-2.650545) ptheta = (-0.0000001274,-0.000007089,-0.04182264,-0.4294934,2004.191903,0) zeta = np.polyval(pzeta,T)/3600.0 z = np.polyval(pz,T)/3600.0 theta = np.polyval(ptheta,T)/3600.0 return rotation_matrix(-z,'z') *\ rotation_matrix(theta,'y') *\ rotation_matrix(-zeta,'z') def _load_nutation_data(datafn,seriestype): """ Loads nutation series from saved data files. Seriestype can be 'lunisolar' or 'planetary' """ from ..utils.io import get_package_data if seriestype == 'lunisolar': dtypes = [('nl',int), ('nlp',int), ('nF',int), ('nD',int), ('nOm',int), ('ps',float), ('pst',float), ('pc',float), ('ec',float), ('ect',float), ('es',float)] elif seriestype == 'planetary': dtypes = [('nl',int), ('nF',int), ('nD',int), ('nOm',int), ('nme',int), ('nve',int), ('nea',int), ('nma',int), ('nju',int), ('nsa',int), ('nur',int), ('nne',int), ('npa',int), ('sp',int), ('cp',int), ('se',int), ('ce',int)] else: raise ValueError('requested invalid nutation series type') lines = [l for l in get_package_data(datafn).split('\n') if not l.startswith('#') if not l.strip()==''] lists = [[] for n in dtypes] for l in lines: for i,e in enumerate(l.split(' ')): lists[i].append(dtypes[i][1](e)) return np.rec.fromarrays(lists,names=[e[0] for e in dtypes]) _nut_data_00a_ls = _load_nutation_data('iau00a_nutation_ls.tab','lunisolar') _nut_data_00a_pl = _load_nutation_data('iau00a_nutation_pl.tab','planetary') def _nutation_components20062000A(epoch): """ :returns: eps,dpsi,deps in radians """ from ..obstools import epoch_to_jd from .funcs import obliquity epsa = obliquity(epoch_to_jd(epoch),2006) raise NotImplementedError('2006/2000A nutation model not implemented') return epsa,dpsi,deps _nut_data_00b = _load_nutation_data('iau00b_nutation.tab','lunisolar') def _nutation_components2000B(intime,asepoch=True): """ :param intime: time to compute the nutation components as a JD or epoch :type intime: scalar :param asepoch: if True, `intime` is interpreted as an epoch, otherwise JD :type asepoch: bool :returns: eps,dpsi,deps in radians """ from ..constants import asecperrad from ..obstools import epoch_to_jd,jd2000 from .funcs import obliquity if asepoch: jd = epoch_to_jd(intime) else: jd = intime epsa = np.radians(obliquity(jd,2000)) t = (jd-jd2000)/36525 #Fundamental (Delaunay) arguments from Simon et al. (1994) via SOFA #Mean anomaly of moon el = ((485868.249036 + 1717915923.2178*t)%1296000)/asecperrad #Mean anomaly of sun elp = ((1287104.79305 + 129596581.0481*t)%1296000)/asecperrad #Mean argument of the latitude of Moon F = ((335779.526232 + 1739527262.8478*t)%1296000)/asecperrad #Mean elongation of the Moon from Sun D = ((1072260.70369 + 1602961601.2090*t)%1296000)/asecperrad #Mean longitude of the ascending node of Moon Om = ((450160.398036 + -6962890.5431*t)%1296000)/asecperrad #compute nutation series using array loaded from data directory dat = _nut_data_00b arg = dat.nl*el + dat.nlp*elp + dat.nF*F + dat.nD*D + dat.nOm*Om sarg = np.sin(arg) carg = np.cos(arg) p1uasecperrad = asecperrad*1e7 #0.1 microasrcsecperrad dpsils = np.sum((dat.ps + dat.pst*t)*sarg + dat.pc*carg)/p1uasecperrad depsls = np.sum((dat.ec + dat.ect*t)*carg + dat.es*sarg)/p1uasecperrad #fixed offset in place of planetary tersm masecperrad = asecperrad*1e3 #milliarcsec per rad dpsipl = -0.135/masecperrad depspl = 0.388/masecperrad return epsa,dpsils+dpsipl,depsls+depspl #all in radians def _nutation_matrix(epoch): """ Nutation matrix generated from nutation components. Matrix converts from mean coordinate to true coordinate as r_true = M * r_mean """ from ..utils import rotation_matrix #TODO: implement higher precision 2006/2000A model if requested/needed epsa,dpsi,deps = _nutation_components2000B(epoch) #all in radians return rotation_matrix(-(epsa + deps),'x',False) *\ rotation_matrix(-dpsi,'z',False) *\ rotation_matrix(epsa,'x',False) def _load_CIO_locator_data(datafn): """ Loads CIO locator series terms from saved data files. returns polycoeffs,termsarr (starting with 0th) """ from ..utils.io import get_package_data lines = [l for l in get_package_data(datafn).split('\n') if not l.startswith('#') if not l.strip()==''] coeffs = [] sincs = [] coscs = [] orders = [] inorder = False for l in lines: if 'Polynomial coefficients:' in l: polys = l.replace('Polynomial coefficients:','').split(',') polys = np.array(polys,dtype=float) elif 'order' in l: if inorder: orders.append((np.array(coeffs,dtype=int), np.array(sincs,dtype=float), np.array(coscs,dtype=float))) coeffs = [] sincs = [] coscs = [] inorder = True elif inorder: ls = l.split() coeffs.append(ls[:8]) sincs.append(ls[8]) coscs.append(ls[9]) if inorder: orders.append((np.array(coeffs,dtype=int), np.array(sincs,dtype=float), np.array(coscs,dtype=float))) return polys,orders _CIO_locator_data = _load_CIO_locator_data('iau00_cio_locator.tab') class CIRSCoordinates(EquatorialCoordinatesBase): """ Represents an object as equatorial coordinates in the Celestial Intermediate Reference System. This is the post-2000 IAU system for equatorial coordinates that seperates the coordinate system from the dynamically complicated and somewhat imprecisely-defined ideas of the equinox and ecliptic. This system's fundamental plane is the equator of the Celestial Intermediate Pole (CIP) and the origin of RA is at the Celestial Intermediate Origin (CIO). Changes to the :attr:`epoch` will result in the coordinates being updated for precession nutation. Nutation currently uses the IAU 2000B model that should be good to ~1 mas. If aberration or annual parallax corrections are necessary, convert to :class:`ICRSCoordinates`, change the epoch, and then convert back to :class:`CIRSCoordinates`. To convert from these coordinates to :class:`HorizontalCoordinates` appropriate for observed coordinates, site information is necessary. Hence, the transformations from equatorial to horizontal coordinates are performed by the :class:`~astropysics.obstools.Site` class in the :mod:`~astropysics.obstools` module, and attempting to directly convert will raise an :exc:`TypeError`. """ def transformToEpoch(self,newepoch): """ Transforms these :class:`EquatorialCoordinates` to a new epoch using the IAU 2000 precessions from Capitaine, N. et al. 2003 as written in the USNO Circular 179. """ if self.epoch is not None and newepoch is not None: M = self._CMatrix(self.epoch).T Mn = self._CMatrix(newepoch) self.matrixRotate(Mn*M) #this sets the epoch EpochalLatLongCoordinates.transformToEpoch(self,newepoch) @staticmethod def _CMatrix(epoch): """ The GCRS->CIRS transformation matrix """ B = ICRSCoordinates.frameBiasJ2000 if epoch is None: return B else: from math import sin,cos,atan,atan2,sqrt from ..utils import rotation_matrix P = _precession_matrix_J2000_Capitaine(epoch) N = _nutation_matrix(epoch) x,y,z = (N*P*B).A[2] xsq,ysq = x**2,y**2 bz = 1/(1+z) s = CIRSCoordinates._CIOLocator(epoch) #matrix components - see Circular 179 or IERS Conventions 2003 a,b,c = 1-bz*xsq , -bz*x*y , -x d,e,f = -bz*x*y , 1 - bz*ysq , -y g,h,i = x , y , 1 - bz*(xsq+ysq) #return rotation_matrix(-s,'z',defrees=False)*np.mat([[a,b,c], # [d,e,f], # [g,h,i]]) si = sin(s) co = cos(s) M = [[a*co - d*si,b*co - e*si,c*co - f*si], [a*si + d*co,b*si + e*co,c*si + f*co], [ g, h, i ]] return np.mat(M) # #SOFA implementation using spherical angles - numerically identical # r2 = x*x + y*y # e = atan2(y,x) if r2 != 0 else 0 # d = atan(sqrt(r2/(1-r2))) # return rotation_matrix(-(e+s),'z',False) *\ # rotation_matrix(d,'y',False) *\ # rotation_matrix(e,'z',False) @staticmethod def _CIOLocator(epoch): """ Returns the CIO locator s for the provided epoch. s is the difference in RA between the GCRS and CIP points for the ascending node of the CIP equator. """ #from ..obstools import jd2000,epoch_to_jd from ..constants import asecperrad from .ephems import _mean_anomaly_of_moon,_mean_anomaly_of_sun,\ _mean_long_of_moon_minus_ascnode,_long_earth,\ _mean_elongation_of_moon_from_sun,_long_venus,\ _mean_long_asc_node_moon,_long_prec #first need to find x and y for the CIP, as s+XY/2 is needed B = ICRSCoordinates.frameBiasJ2000 P = _precession_matrix_J2000_Capitaine(epoch) N = _nutation_matrix(epoch) #N*P*B takes GCRS to true, so CIP is bottom row x,y,z = (N*P*B).A[2] #T = (epoch_to_jd(epoch) - jd2000)/36525 T = (epoch-2000)/100 fundargs = [] #fundamental arguments fundargs.append(_mean_anomaly_of_moon(T)) fundargs.append(_mean_anomaly_of_sun(T)) fundargs.append(_mean_long_of_moon_minus_ascnode(T)) fundargs.append(_mean_elongation_of_moon_from_sun(T)) fundargs.append(_mean_long_asc_node_moon(T)) fundargs.append(_long_venus(T)) fundargs.append(_long_earth(T)) fundargs.append(_long_prec(T)) fundargs = np.array(fundargs) polys,orders = _CIO_locator_data newpolys = polys.copy() #copy 0-values to add to for i,o in enumerate(orders): ns,sco,cco = o a = np.dot(ns,fundargs) newpolys[i] += np.sum(sco*np.sin(a) + cco*np.cos(a)) return np.polyval(newpolys[::-1],T)/asecperrad - x*y/2.0 @CoordinateSystem.registerTransform(GCRSCoordinates,'self',transtype='smatrix') def _fromGCRS(gcrsc): return CIRSCoordinates._CMatrix(gcrsc.epoch) @CoordinateSystem.registerTransform('self',GCRSCoordinates,transtype='smatrix') def _toGCRS(cirssys): return CIRSCoordinates._CMatrix(cirssys.epoch).T class EquatorialCoordinatesEquinox(EquatorialCoordinatesBase): """ Represents an object in *mean* geocentric apparent equatorial coordinates, using the pre-IAU2000 systems where the plane of the ecliptic is the fundamental plane and the origin is at the equinox of date (as set by :attr:`epoch`). Changes to the :attr:`epoch` will result in the coordinates being updated for precession, but not nutation, nor annual abberation. Neither are planned by the primary author of this package, as IAU 2000 recommends using only CIO-based systems, but if someone actually wants equinox-based nutation, feel free to implement it and pass it along. To convert from these coordinates to :class:`HorizontalCoordinates` appropriate for observed coordinates, site information is necessary. Hence, the transformations from equatorial to horizontal coordinates are performed by the :class:`~astropysics.obstools.Site` class in the :mod:`astropysics.obstools` module, and attempting to directly convert will raise a :exc:`TypeError`. """ transweight = 1.1 #Equinox-based transforms are to be avoided in favor of CIRS __slots__ = tuple() def transformToEpoch(self,newepoch): """ Transforms these :class:`EquatorialCoordinates` to a new epoch using the IAU 2000 precessions from Capitaine, N. et al. 2003 as written in the USNO Circular 179. """ if self.epoch is not None and newepoch is not None: #convert from current to J2000 B = _nutation_matrix(self.epoch) *\ _precession_matrix_J2000_Capitaine(self.epoch).T #transpose==inv; matrix is real unitary #convert to new epoch A = _nutation_matrix(newepoch) *\ _precession_matrix_J2000_Capitaine(newepoch) self.matrixRotate(A*B) EpochalLatLongCoordinates.transformToEpoch(self,newepoch) @CoordinateSystem.registerTransform(GCRSCoordinates,'self',transtype='smatrix') def _fromGCRS(gcrsc): B = ICRSCoordinates.frameBiasJ2000 if gcrsc.epoch is None: return B else: P = _precession_matrix_J2000_Capitaine(gcrsc.epoch) N = _nutation_matrix(gcrsc.epoch) return N*P*B @CoordinateSystem.registerTransform('self',GCRSCoordinates,transtype='smatrix') def _toGCRS(eqsys): return EquatorialCoordinatesEquinox._fromGCRS(eqsys).T @CoordinateSystem.registerTransform('self',CIRSCoordinates,transtype='smatrix') def _toCIRS(eqsys): if eqsys.epoch is None: return np.eye(3).view(np.matrix) else: from ..obstools import epoch_to_jd from .funcs import equation_of_the_origins from ..utils import rotation_matrix jd = epoch_to_jd(eqsys.epoch) eqo = equation_of_the_origins(jd)*15. #hours>degrees return rotation_matrix(-eqo,'z',True) @CoordinateSystem.registerTransform(CIRSCoordinates,'self',transtype='smatrix') def _fromCIRS(cirssys): return EquatorialCoordinatesEquinox._toCIRS(cirssys).T class ITRSCoordinates(EpochalLatLongCoordinates): """ Coordinates based on the International Terrestrial Reference System. The particular implementation here assumes ITRS matches the WGS84 coordinates (used by GPS) - for astronomical purposes, this is a perfectly good assumption. Epoch transformations in this system only adjust for polar motion - to account for earth rotation, transform back to :class:`CIRSCoordinates` or :class:`EquatorialCoordinatesEquinox`, change the epoch, then transfrom back to :class:`ITRSCoordinates`. Because polar motion is not fully predictable, a number of methods are available for approximating it. To choose a method, set the :attr:`ITRSCoordinates.polarmotion` class attribute -- this will also affect all future transformations to :class:`ITRSCoordinates` from other coordinate systems. The following are valid values: * None Assumes the pole locations are fixed to the CIP at all times, aside from the tiny effect of s' (the TIO-CIO shift). * A 2-tuple of callables (xp,yp) They will be called as xp(epoch) and yp(epoch) and the result will be assumed to give the x and y coordinates of the poles in the CIP frame. .. note:: The transformations from CIRS and Equinox systems to ITRS technically involve converting to TIRS (the Terrestrial Intermediate Reference System), distinguished from ITRS by no polar motion correction. While there is no class explicitly representing TIRS, ITRS with :attr:`epoch` set to None is equivalent to TIRS. """ __slots__ = tuple('_dpc') #_dpc is included for transformation to/from Equatorial-like systems _longrange_ = (-180,180) polarmotion = None """ Technique of computing poles (see :class:`ITRSCoordinates` documentation) """ @staticmethod def _TIOLocator(epoch): """ s-prime, the offset between the0 of longitude for the CIO of CIRS and the TIO of TIRS (Terrestrial Intermediate Reference System) - TIRS and ITRS differ by polar motion. Return value in radians. This is really,really small, and isn't really necessary except for completeness """ from ..constants import asecperrad T = (epoch-2000)/100 return -47e-6*T/asecperrad @staticmethod def _WMatrix(epoch): from ..utils import rotation_matrix sp = ITRSCoordinates._TIOLocator(epoch) if ITRSCoordinates.polarmotion is None: xp = 0 yp = 0 else: #assume 2-sequence (xp,yp) xp,yp = ITRSCoordinates.polarmotion if callable(xp): xp = xp(epoch) if callable(yp): yp = yp(epoch) #TODO: test if the following, linear matrix is good enough to not #bother with the "right" one: #[[1,-sp,-xp], # [sp,1,yp], # [xp,-yp,1]] #can also do sp->0 return rotation_matrix(-yp,'x') *\ rotation_matrix(-xp,'y') *\ rotation_matrix(sp,'z') def transformToEpoch(self,newepoch): """ Transforms these :class:`ITRSCoordinates` to a new epoch, adjusting the coordinate values for polar motion. """ if self.epoch is not None and newepoch is not None: M = self._WMatrix(self.epoch).T Mn = self._WMatrix(newepoch) self.matrixRotate(Mn*M) #this sets the epoch EpochalLatLongCoordinates.transformToEpoch(self,newepoch) @add_docs(EpochalLatLongCoordinates.convert) def convert(self,tosys,optimize=_convertoptimizedefault): '' res = EpochalLatLongCoordinates.convert(self,tosys,optimize) if self._dpc is not None: res._dpc = self._dpc return res @CoordinateSystem.registerTransform(CIRSCoordinates,'self',transtype='smatrix') def _fromEqC(eqc): from .funcs import earth_rotation_angle from ..obstools import epoch_to_jd from ..utils import rotation_matrix epoch = eqc.epoch if epoch is not None: jd = epoch_to_jd(eqc.epoch) era = earth_rotation_angle(jd,degrees=True) W = ITRSCoordinates._WMatrix(eqc.epoch) return W*rotation_matrix(era) else: return np.eye(3).view(np.matrix) @CoordinateSystem.registerTransform(EquatorialCoordinatesEquinox,'self',transtype='smatrix') def _fromEqE(eqe): from .funcs import greenwich_sidereal_time from ..utils import rotation_matrix from ..obstools import epoch_to_jd epoch = eqe.epoch if epoch is not None: jd = epoch_to_jd(eqe.epoch) try: gst = greenwich_sidereal_time(jd,True)*15. #hours -> degrees except Exception,e: from warnings import warn warn('temporarily bypassing problem with greenwich_sidereal_time:%s'%e) gst = greenwich_sidereal_time(jd,'simple')*15. #hours -> degrees W = ITRSCoordinates._WMatrix(eqe.epoch) return W*rotation_matrix(gst) else: return np.eye(3).view(np.matrix) @CoordinateSystem.registerTransform('self',CIRSCoordinates,transtype='smatrix') def _toEqC(itrsc): #really we want inverse, but rotations are unitary -> inv==transpose #we provide itrsc in the call because the epoch is needed return ITRSCoordinates._fromEqC(itrsc).T @CoordinateSystem.registerTransform('self',EquatorialCoordinatesEquinox,transtype='smatrix') def _toEqE(itrsc): #really we want inverse, but rotations are unitary -> inv==transpose #we provide itrsc in the call because the epoch is needed return ITRSCoordinates._fromEqE(itrsc).T class FK5Coordinates(EquatorialCoordinatesEquinox): """ Equatorial Coordinates fixed to the FK5 reference system. """ __slots__ = tuple() @staticmethod def _precessionMatrixJ(epoch1,epoch2): """ Computes the precession matrix from one Julian epoch to another """ from ..utils import rotation_matrix T = (epoch1 - 2000)/100 dt = (epoch2 - epoch1)/100 pzeta = (0.017998,0.000344,0.30188,-0.000139,1.39656,2306.2181) temp = pzeta[5] + T*(pzeta[4]+T*pzeta[3]) zeta = dt*(temp + dt*((pzeta[2]+pzeta[1]*T) + dt*pzeta[0]))/3600 pz = (0.018203,-0.000066,1.09468) z = dt*(temp + dt*((pz[2]+pz[1]*T) + dt*pz[0]))/3600 ptheta = (-0.041833,-0.000217,-0.42665,-0.000217,-0.85330,2004.3109) temp = ptheta[5] + T*(ptheta[4]+T*ptheta[3]) theta = dt*(temp + dt*((ptheta[2]+ptheta[1]*T) + dt*ptheta[0]))/3600 return rotation_matrix(-z,'z') *\ rotation_matrix(theta,'y') *\ rotation_matrix(-zeta,'z') def transformToEpoch(self,newepoch): """ Transforms these :class:`EquatorialCoordinates` to a new epoch. Uses the algorithm resolved by the IAU in 1976 as written in Meeus, as well as Lieske, J.H. 1979. According to SOFA, this for becomes less valid at the following levels: * 1960 CE to 2040 CE < 0.1" * 1640 CE to 2360 CE < 1" * 500 BCE to 3000 CE < 3" * 1200 BCE to 3900 CE > 10" * 4200 BCE to 5600 CE > 100" * 6800 BCE to 8200 CE > 1000" """ if self.epoch is not None and newepoch is not None: self.matrixRotate(self._precessionMatrixJ(self.epoch,newepoch)) EpochalLatLongCoordinates.transformToEpoch(self,newepoch) @CoordinateSystem.registerTransform(ICRSCoordinates,'self',transtype='smatrix') def _fromICRS(icrsc): """ B-matrix from USNO circular 179 """ from ..utils import rotation_matrix eta0 = -19.9/3600000 xi0 = 9.1/3600000 da0 = -22.9/3600000 B = rotation_matrix(-eta0,'x') *\ rotation_matrix(xi0,'y') *\ rotation_matrix(da0,'z') epoch = icrsc.epoch if icrsc.epoch is None: return B else: return FK5Coordinates._precessionMatrixJ(2000,icrsc.epoch)*B @CoordinateSystem.registerTransform('self',ICRSCoordinates,transtype='smatrix') def _toICRS(fk5c): return FK5Coordinates._fromICRS(fk5c).T class FK4Coordinates(EquatorialCoordinatesEquinox): """ Equatorial Coordinates fixed to the FK4 reference system. Note that this implementation does *not* correct for the elliptic terms of aberration as of yet. Epoch is Besselian. """ __slots__ = tuple() julianepoch = False def __init__(self,*args,**kwargs): """ Input for FK4 coordinates. Can follow any of the following forms: * EquatorialCoordinatesBase() * EquatorialCoordinatesBase(:class:`EquatorialCoordinatesBase`) * EquatorialCoordinatesBase('rastr decstr') * EquatorialCoordinatesBase((ra,dec)) * EquatorialCoordinatesBase(ra,dec) * EquatorialCoordinatesBase(ra,fdec,raerr,decerr) * EquatorialCoordinatesBase(ra,dec,raerr,decerr,epoch) * EquatorialCoordinatesBase(ra,dec,raerr,decerr,epoch,distancepc) The epoch of FK4 coordinates defaults to B1950. """ args = list(args) args.insert(0,self) EquatorialCoordinatesEquinox.__init__(*args,**kwargs) if self._epoch==2000.: self._epoch = 1950. def transformToEpoch(self,newepoch): """ Transforms these :class:`EquatorialCoordinates` to a new epoch. Uses the method of Newcomb (pre-IAU1976) to compute precession. """ if self.epoch is not None and newepoch is not None: self.matrixRotate(self._precessionMatrixB(self.epoch,newepoch)) EpochalLatLongCoordinates.transformToEpoch(self,newepoch) @staticmethod def _precessionMatrixB(epoch1,epoch2): """ computes the precession matrix from one Besselian epoch to another using Newcomb's method. """ from ..utils import rotation_matrix #tropical years t1 = (epoch1-1850.0)/1000.0 t2 = (epoch2-1850.0)/1000.0 dt = t2 - t1 zeta1 = 23035.545 + t1*139.720+0.060*t1*t1 zeta2 = 30.240 - 0.27*t1 zeta3 = 17.995 pzeta = (zeta3,zeta2,zeta1,0) zeta = np.polyval(pzeta,dt)/3600 z1 = 23035.545 + t1*139.720 + 0.060*t1*t1 z2 = 109.480 + 0.39*t1 z3 = 18.325 pz = (z3,z2,z1,0) z = np.polyval(pz,dt)/3600 theta1 = 20051.12 - 85.29*t1 - 0.37*t1*t1 theta2 = -42.65 - 0.37*t1 theta3 = -41.8 ptheta = (theta3,theta2,theta1,0) theta = np.polyval(ptheta,dt)/3600 return rotation_matrix(-z,'z') *\ rotation_matrix(theta,'y') *\ rotation_matrix(-zeta,'z') @CoordinateSystem.registerTransform('self',FK5Coordinates,transtype='smatrix') def _toFK5(fk4c): from ..obstools import epoch_to_jd,jd_to_epoch #B1950->J2000 matrix from Murray 1989 A&A 218,325 B = np.mat([[0.9999256794956877,-0.0111814832204662,-0.0048590038153592], [0.0111814832391717,0.9999374848933135,-0.0000271625947142], [0.0048590037723143,-0.0000271702937440,0.9999881946023742]]) if fk4c.epoch is not None and fk4c.epoch != 1950: jd = epoch_to_jd(fk4c.epoch,False) jepoch = jd_to_epoch(jd) T = (jepoch - 1950)/100 #now add in correction terms for FK4 rotating system B[0,0] += -2.6455262e-9*T B[0,1] += -1.1539918689e-6*T B[0,2] += 2.1111346190e-6*T B[1,0] += 1.1540628161e-6*T B[1,1] += -1.29042997e-8*T B[1,2] += 2.36021478e-8*T B[2,0] += -2.1112979048e-6*T B[2,1] += -5.6024448e-9*T B[2,2] += 1.02587734e-8*T PB = FK4Coordinates._precessionMatrixB(fk4c.epoch,1950) return B*PB else: return B @CoordinateSystem.registerTransform(FK5Coordinates,'self',transtype='smatrix') def _fromFK5(fk5c): #need inverse because Murray's matrix is *not* a true rotation matrix return FK4Coordinates._toFK5(fk5c).I class EclipticCoordinatesCIRS(EpochalLatLongCoordinates): """ Ecliptic Coordinates (beta, lambda) such that the fundamental plane passes through the ecliptic at the current epoch. Note that because the concept of the ecliptic can be complicated or even ill-defined, ecliptic coordinates is astropysics are simply defined as tied to a particular set of equatorial coordinates with a given obliquity model. For :class:`EclipticCoordinatesCIRS`, the equatorial coordinates are :class:`CIRSCoordinates` with obliquity given by the IAU 2006 obliquity model (see :func:`obliquity`) """ __slots__ = () _longlatnames_ = ('lamb','beta') _longrange_ = (0,360) obliqyear = 2006 def __init__(self,lamb=0,beta=0,lamberr=None,betaerr=None,epoch=2000, distanceau=None): """ See the associated attribute docstrings for the meaning of the inputs. """ EpochalLatLongCoordinates.__init__(self,lamb,beta,lamberr,betaerr,epoch) self.distanceau = distanceau @CoordinateSystem.registerTransform('self',CIRSCoordinates,transtype='smatrix') def _toEq(eclsc): from .funcs import obliquity from ..utils import rotation_matrix return rotation_matrix(-obliquity(eclsc.jdepoch,EclipticCoordinatesCIRS.obliqyear),'x') @CoordinateSystem.registerTransform(CIRSCoordinates,'self',transtype='smatrix') def _fromEq(eqc): from .funcs import obliquity from ..utils import rotation_matrix return rotation_matrix(obliquity(eqc.jdepoch,EclipticCoordinatesCIRS.obliqyear),'x') def transformToEpoch(self,newepoch): if self.epoch is not None and newepoch is not None: eqc = self.convert(CIRSCoordinates) eqc.epoch = newepoch newval = eqc.convert(self.__class__) self._lat._decval = newval._lat._decval self._long._decval = newval._long._decval self._laterr._decval = newval._lat._decval self._longerr._decval = newval._longerr._decval EpochalLatLongCoordinates.transformToEpoch(self,newepoch) class EclipticCoordinatesEquinox(EpochalLatLongCoordinates): """ Ecliptic Coordinates (beta, lambda) such that the fundamental plane passes through the ecliptic at the current epoch. Note that because the concept of the ecliptic can be complicated or even ill-defined, ecliptic coordinates is astropysics are simply defined as tied to a particular set of equatorial coordinates with a given obliquity model. For :class:`EclipticCoordinatesEquinox`, the equatorial coordinates are :class:`EquatorialCoordinatesEquinox` with obliquity given by the IAU 1980 obliquity model (see :func:`~astropysics.coords.funcs.obliquity`) """ __slots__ = () _longlatnames_ = ('lamb','beta') _longrange_ = (0,360) obliqyear = 1980 def __init__(self,lamb=0,beta=0,lamberr=None,betaerr=None,epoch=2000, distanceau=None): """ See the associated attribute docstrings for the meaning of the inputs. """ EpochalLatLongCoordinates.__init__(self,lamb,beta,lamberr,betaerr,epoch) self.distanceau = distanceau @CoordinateSystem.registerTransform('self',EquatorialCoordinatesEquinox,transtype='smatrix') def _toEq(eclsc): from .funcs import obliquity from ..utils import rotation_matrix return rotation_matrix(-obliquity(eclsc.jdepoch,EclipticCoordinatesEquinox.obliqyear),'x') @CoordinateSystem.registerTransform(EquatorialCoordinatesEquinox,'self',transtype='smatrix') def _fromEq(eqc): from .funcs import obliquity from ..utils import rotation_matrix return rotation_matrix(obliquity(eqc.jdepoch,EclipticCoordinatesEquinox.obliqyear),'x') def transformToEpoch(self,newepoch): if self.epoch is not None and newepoch is not None: eqc = self.convert(EquatorialCoordinatesEquinox) eqc.epoch = newepoch newval = eqc.convert(self.__class__) self._lat._decval = newval._lat._decval self._long._decval = newval._long._decval self._laterr._decval = newval._lat._decval self._longerr._decval = newval._longerr._decval EpochalLatLongCoordinates.transformToEpoch(self,newepoch) class RectangularGeocentricEclipticCoordinates(RectangularCoordinates,EpochalCoordinates): """ Rectangular coordinates oriented so that the x-y plane lies in the plane of the ecliptic at the specified epoch. Distances are in AU. Origin is at the center of mass of the Earth. Note that the epoch should not be set directly - if precession is desired desired, convert to an Ecliptic coordinate system, do the precession, and convert back. """ __slots__ = tuple() julianepoch = True def __init__(self,x,y,z,epoch=None): RectangularCoordinates.__init__(self,x,y,z) self._epoch = epoch def __getstate__(self): d = RectangularCoordinates.__getstate__(self) d.update(EpochalCoordinates.__getstate__(self)) return d def __setstate__(self,d): RectangularCoordinates.__setstate__(self,d) EpochalCoordinates.__setstate__(self,d) def __str__(self): if self.epoch is None: epochstr = '' else: epochstr = ' ('+self.epochstr+')' return RectangularCoordinates.__str__(self) + epochstr def transformToEpoch(self,newepoch): EpochalCoordinates.transformToEpoch(newepoch) @CoordinateSystem.registerTransform('self',EclipticCoordinatesCIRS) def _toEcC(rec): from math import asin,atan2,degrees x,y,z = rec.x,rec.y,rec.z r = (x*x+y*y+z*z)**0.5 beta = degrees(asin(z/r)) lamb = degrees(atan2(y,x)) return EclipticCoordinatesCIRS(lamb,beta,distanceau=r,epoch=rec.epoch) @CoordinateSystem.registerTransform('self',EclipticCoordinatesEquinox) def _toEcQ(rec): from math import asin,atan2,degrees x,y,z = rec.x,rec.y,rec.z r = (x*x+y*y+z*z)**0.5 beta = degrees(asin(z/r)) lamb = degrees(atan2(y,x)) return EclipticCoordinatesEquinox(lamb,beta,distanceau=r,epoch=rec.epoch) @CoordinateSystem.registerTransform(EclipticCoordinatesCIRS,'self') def _fromEcC(ec): from math import sin,cos,degrees l,b = ec.lamb.r,ec.beta.r if ec.distanceau is None: r = 1 else: r = ec.distanceau[0] x = r*cos(l)*cos(b) y = r*sin(l)*cos(b) z = r*sin(b) return RectangularGeocentricEclipticCoordinates(x,y,z,ec.epoch) @CoordinateSystem.registerTransform(EclipticCoordinatesEquinox,'self') def _fromEcQ(ec): from math import sin,cos,degrees l,b = ec.lamb.r,ec.beta.r if ec.distanceau is None: r = 1 else: r = ec.distanceau[0] x = r*cos(l)*cos(b) y = r*sin(l)*cos(b) z = r*sin(b) return RectangularGeocentricEclipticCoordinates(x,y,z,ec.epoch) class GalacticCoordinates(EpochalLatLongCoordinates): __slots__ = tuple() _longlatnames_ = ('l','b') _longrange_ = (0,360) _ngp_J2000 = FK5Coordinates(192.859508, 27.128336,epoch=2000) _long0_J2000 = AngularCoordinate(122.932) _ngp_B1950 = FK4Coordinates(192.25, 27.4,epoch=1950) _long0_B1950 = AngularCoordinate(123) def transformToEpoch(self,newepoch): """ Galactic coordinates are nominally inertial, although the definition is a bit unclear in that regard. """ EpochalLatLongCoordinates.transformToEpoch(self,newepoch) @CoordinateSystem.registerTransform(FK5Coordinates,'self',transtype='smatrix') def _fromFK5(fk5coords): from ..utils import rotation_matrix epoch = 2000 if fk5coords.epoch is None else fk5coords.epoch mat = rotation_matrix(180 - GalacticCoordinates._long0_J2000.d,'z') *\ rotation_matrix(90 - GalacticCoordinates._ngp_J2000.dec.d,'y') *\ rotation_matrix(GalacticCoordinates._ngp_J2000.ra.d,'z') *\ FK5Coordinates._precessionMatrixJ(epoch,2000) mat.nocache = True #can't cache because of the need to get the epoch return mat @CoordinateSystem.registerTransform('self',FK5Coordinates,transtype='smatrix') def _toFK5(galcoords): return GalacticCoordinates._fromFK5(galcoords).T @CoordinateSystem.registerTransform(FK4Coordinates,'self',transtype='smatrix') def _fromFK4(fk4coords): from ..utils import rotation_matrix epoch = 1950 if fk4coords.epoch is None else fk4coords.epoch mat = rotation_matrix(180 - GalacticCoordinates._long0_B1950.d,'z') *\ rotation_matrix(90 - GalacticCoordinates._ngp_B1950.dec.d,'y') *\ rotation_matrix(GalacticCoordinates._ngp_B1950.ra.d,'z') *\ FK4Coordinates._precessionMatrixB(epoch,1950) mat.nocache = True #can't cache because of the need to get the epoch return mat @CoordinateSystem.registerTransform('self',FK4Coordinates,transtype='smatrix') def _toFK4(galcoords): return GalacticCoordinates._fromFK4(galcoords).T class SupergalacticCoordinates(EpochalLatLongCoordinates): __slots__ = tuple() _longlatnames_ = ('sgl','sgb') _longrange_ = (0,360) _nsgp_gal = GalacticCoordinates(47.37,6.32) #glactc is 47.47=WRONG _sg0_gal = GalacticCoordinates(137.37,0) def transformToEpoch(self,newepoch): """ Supergalactic coordinates are nominally inertial, although the definition is a bit unclear in that regard. """ EpochalLatLongCoordinates.transformToEpoch(self,newepoch) @CoordinateSystem.registerTransform('self',GalacticCoordinates,transtype='smatrix') def _toGal(sgalcoords): return SupergalacticCoordinates._fromGal(sgalcoords).T @CoordinateSystem.registerTransform(GalacticCoordinates,'self',transtype='smatrix') def _fromGal(galcoords): from ..utils import rotation_matrix z1r = rotation_matrix(SupergalacticCoordinates._nsgp_gal.l.d,'z') yr = rotation_matrix(90 - SupergalacticCoordinates._nsgp_gal.b.d,'y') z2r = rotation_matrix(180 - SupergalacticCoordinates._sg0_gal.l.d +\ SupergalacticCoordinates._nsgp_gal.l.d,'z') return z2r*yr*z1r class HorizontalCoordinates(LatLongCoordinates): """ This object represents an angular location on the unit sphere, with the north pole of the coordinate position fixed to the local zenith To convert from other :class:`Coordinate` types to horizontal positions, see :class:`astropysics.obstools.Site`, as site information is required for these corrections """ __slots__ = tuple() _longlatnames_ = ('az','alt') _longrange_ = (0,360) def __init__(self,alt=0,az=0,alterr=None,azerr=None,distancepc=None): """ See the associated attribute docstrings for the meaning of the inputs. """ LatLongCoordinates.__init__(self,az,alt,azerr,alterr,distancepc) @CoordinateSystem.registerTransform(EquatorialCoordinatesEquinox,'self') @CoordinateSystem.registerTransform(CIRSCoordinates,'self') def _toHoriz(incoosys=None): raise TypeError('use astropysics.obstools.Site methods to transform celestial to terrestrial coordinates') @CoordinateSystem.registerTransform('self',EquatorialCoordinatesEquinox) @CoordinateSystem.registerTransform('self',CIRSCoordinates) def _fromHoriz(incoosys=None): raise TypeError('use astropysics.obstools.Site methods to transform terrestrial to celestial coordinates') #Now that all the coordinate systems have been made, add the diagram to the docs #That shows the graph of the built-in transforms postbuiltin = """ A similar diagram can be generated after the user has created and registered custom coordinates and transforms:: from networkx import to_agraph,relabel_nodes,draw_networkx from astropysics.coords import CoordinateSystem graph = CoordinateSystem.getTransformGraph() dotgraph = to_agraph(relabel_nodes(graph,lambda n:n.__name__)) dotgraph.graph_attr.update(dict(size='12.0, 12.0',fontsize=12)) dotgraph.write('mygraph.dot') draw_networkx(graph) This will save a graphviz dot file and displaying the graph with matplotlib, showing both builtin and custom-added coordinates and transforms. """ try: from networkx import to_agraph,relabel_nodes graph = to_agraph(relabel_nodes(CoordinateSystem.getTransformGraph(),lambda n:n.__name__)) graph.graph_attr.update(dict(size=r'12.0, 12.0',fontsize=12)) transstr=""" Built-in Transforms ^^^^^^^^^^^^^^^^^^^ A number of coordinate systems are provided built into astropysics. Most of these have pre-defined standard transformations. The built-in coordinate classes with defined transformation are shown in the diagram below. .. graphviz:: """+graph.string().replace('\n','\n ')+postbuiltin __doc__ = __doc__.replace('{transformdiagram}',transstr) del to_agraph,relabel_nodes,graph except ImportError: #if networkx or pygraphviz isn't present, drop the diagram but add a warning that it's missing warningstr = """ Builtin Coordinate System Transforms ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. warning:: A diagram showing the relationships between the pre-defined transformations should be here, but this copy of the documentation was built without `networkx <http://networkx.lanl.gov/>` and `pygraphviz <http://networkx.lanl.gov/pygraphviz/>` available to build the diagram. Please re-build this file after those packages are installed to see the diagram. """+postbuiltin __doc__ = __doc__.replace('{transformdiagram}',warningstr) del warningstr #<--------------------------Convinience Functions------------------------------> def angular_string_to_dec(instr,hms=True,degrees=True): """ Convinience function to convert a angular coordinate string to a decimal value. :param hms: If True, the coordinate will be assumed to be h:m:s, otherwise d:m:s. This will be ignored if the coordinates are specified as ##h##m##s or ##d##m##s, or if the input is not in sexigesimal form. :type hms: boolean :param degrees: If True, the output will be decimal degrees, otherwise radians. :type degrees: boolean :returns: Decimal value in radians or degrees """ ac = AngularCoordinate(instr) if degrees: return ac.degrees else: return ac.radians def objects_to_coordinate_arrays(posobjs,coords='auto',degrees=True): """ converts a sequence of position objects into an array of coordinates. `coords` determines the order of the output coordinates - it can be a comma-seperated list of coordinate names or if 'auto', it will be 'lat,long' for all coordinate systems except for Equatorial, which will use 'ra,dec' if `degrees` is True, returned arrays are in degrees, otherwise radians """ if coords=='auto': coordnames = None else: coordnames = coords.split(',') coords = [] if degrees: for o in posobjs: if coordnames is None: if isinstance(o,EquatorialCoordinates): coords.append((o.ra.d,o.dec.d)) else: coords.append((o.lat.d,o.long.d)) else: coords.append([getattr(o,c).d for c in coordnames]) else: for o in posobjs: if coordnames is None: if isinstance(o,EquatorialCoordinates): coords.append((o.ra.r,o.dec.r)) else: coords.append((o.lat.r,o.long.r)) else: coords.append([getattr(o,c).r for c in coordnames]) return np.array(coords).T
PypiClean
/KnowledgeCore-2.8.10.tar.gz/KnowledgeCore-2.8.10/README.md
KnowledgeCore ============== ![KnowledgeCore icon](icon.png) KnowledgeCore is a RDFlib-backed minimalistic knowledge base, initially designed for robots (in particular human-robot interaction or multi-robot interaction). It features full [ROS](https://www.ros.org) support. It stores triples (like RDF/OWL triples), and provides an [API](doc/api.md) accessible via a simple socket protocol or a [ROS wrapper](#ros-usage). [pykb](https://github.com/severin-lemaignan/pykb) provides an idiomatic Python binding over the socket interface, making easy to integrate the knowledge base in your application. A similar API wrapper exists for ROS as well (see example below). It integrates with the [reasonable](https://github.com/gtfierro/reasonable) OWL2 RL reasoner to provide OWL2 semantics and fast knowledge materialisation. Example ------- This example uses the ROS API (see below), with some Pythonic syntatic sugar: ```python from knowledge_core.api import KB rospy.init_node("test_knowledge_base") kb = KB() def on_robot_entering_antonio_property(evt): print("A robot entered Antonio's %s: %s" (evt[0]["place"], evt[0]["robot"])) kb += "ari rdf:type Robot" kb += ["antonio looksAt ari", "ari isIn kitchen"] kb.subscribe(["?robot isIn ?place", "?place belongsTo antonio", "?robot rdf:type Robot"], onRobotEnteringAntonioProperty) kb += "kitchen belongsTo antonio" # try as well: # kb -= "antonio looksAt ari" to remove facts # kb["* rdf:type Robot"] to query the knowledge base rospy.spin() ``` will print: ``` A robot entered Antonio's kitchen: ari ``` Installation ------------ **KnowledgeCore only supports Python 3** ### Prerequisite `rdflib >= 6.0.0`: ``` $ pip install rdflib ``` For reasoning (optional): ``` $ pip install reasonable ``` ### Installation From `pypi`: ``` $ pip install knowledge_core ``` From source: ``` $ git clone https://github.com/severin-lemaignan/knowledge_core.git $ cd knowledge_core $ python setup.py install $ knowledge_core ``` If using ROS, you can also use your regular catkin workflow. Documentation ------------- ### General usage **If you are a roboticist, [jump to ROS usage](#ros-usage)** You can use `KnowledgeCore` either as a server, accessible from multiple applications (clients), or in *embedded* mode (which does not require to start a server process, but is limited to one single client). Note that the embedded mode is only available for Python applications. In both case, and if your application is written in Python, it is highly recommended to use [pykb](https://github.com/severin-lemaignan/pykb) to interact the knowledge base. #### Server mode To start the knowledge base as a server, simply type: ``` $ knowledge_core ``` (run `knowledge_core --help` for available options) Then: ```python import kb with kb.KB() as kb: #... ``` See usage examples on the [pykb](https://github.com/severin-lemaignan/pykb) page, or in the `KnowledgeCore` [unit-tests](testing). #### Embedded mode No need to start `KnowledgeCore`. Simply use the following code to start using the knowledge base in your code: ```python import kb with kb.KB(embedded=True) as kb: #... ``` #### Interacting with KnowledgeCore from other languages - from C++: check [liboro](https://github.com/severin-lemaignan/liboro) - from any other language: the communication with the server relies on a simply socket-based text protocol. Feel free to get in touch if you need help to add support for your favourite language! #### How do I get that fancy image on top of the README? Check [oro-view](https://github.com/severin-lemaignan/oro-view) ;-) ### ROS usage **Please first read the general [API introduction](doc/api.md), as this applies to the ROS interface as well.** To start the ROS node: ``` rosrun knowledge_core knowledge_core ``` **Note that, in general, you want to use the 'Pythonic' wrapper built on top of the low-level ROS topics/services API. See example above. This Pythonic interface follows the [`pykb`](https://gitlab/interaction/pykb/) API (except in a few corner case that are not supported by the ROS interface).** `knowledge_core` exposes two topics, `/kb/add_facts` and `/kb/remove_facts`, to add/remove triples to the knowledge base. Both topics expect a simple string with 3 tokens separated by spaces (if the object is a literal string, use double quotes to escape it). It also exposes the following services: - `/kb/revise` to add/remove facts using a synchronous interface - `/kb/query` to perform simple queries - `/kb/sparql` to perform complex queries (full SPARQL end-point) - `/kb/events` to subscribe to 'events' by providing a (set of) partially-bound triples. Calling the service returns an event *id*. Subscribe then to `/kb/events/<id>` to be notified everytime a new instance/class match the provided pattern - `/kb/manage` to manage the knowledge base (including eg clearing all the facts) Features -------- ### Server-Client or embedded `KnowledgeCore` can be run as a stand-alone (socket) server, or directly embedded in Python applications. ### Multi-models `KnowledgeCore` is intended for dynamic environments, with possibly several contexts/agents requiring separate knowledge models. New models can be created at any time and each operation (like knowledge addition/retractation/query) can operate on a specific subset of models. Each models are also independently classified by the reasoner. ### Event system `KnowledgeCore` provides a mechanism to *subscribe* to some conditions (like: an instance of a given type is added to the knowledge base, some statement becomes true, etc.) and get notified back. ### Reasoning `KnowledgeCore` provides RDFS/OWL reasoning capabilities via the [reasonable](https://github.com/gtfierro/reasonable) reasoner. See [reasonable README](https://github.com/gtfierro/reasonable#owl-2-rules) for the exact level of support of the different OWL2 RL rules. ### Transient knowledge `KnowledgeCore` allows to attach 'lifespans' to statements: after a given duration, they are automatically collected. **[this functionality is currently disabled. Please open an issue of you need it urgently]** ### Ontology walking `KnowledgeCore` exposes several methods to explore the different ontological models of the knowledge base. It is compatible with the visualization tool [oro-view](https://github.com/severin-lemaignan/oro-view).
PypiClean
/EC_MS-0.7.5.tar.gz/EC_MS-0.7.5/src/EC_MS/Time_Response.py
from __future__ import division, print_function import os import numpy as np from scipy.optimize import curve_fit from scipy.integrate import odeint from . import Chem from .Molecules import Molecule from .Plotting import plot_operation def fit_exponential(t, y, zero_time_axis=False): """Return (tao, y0, y1) for best fit of y = y0 + (y1-y0) * exp(-t/tao) Args: t (vector): time y (vector): values zero_time_axix (boolean): whether to subtract t[0] from t. False by default """ if zero_time_axis: t = t - t[0] # zero time axis tau_i = t[-1] / 10 # guess at time constant # tau_i = t[-1] #often can't solve with this guess. A smaller tau helps. y0_i = y[-1] # guess at approach value y1_i = y[0] # guess at true initial value pars_i = [tau_i, y0_i, y1_i] def exp_fun(x, tau, y0, y1): z = y0 + (y1 - y0) * np.exp(-x / tau) # print([tau,y0,y1]) #for diagnosing curve_fit problems return z pars, pcov = curve_fit(exp_fun, t, y, p0=pars_i) # pars = [tau, y0, y1] return pars def fit_step(t, y, tpulse=0, step="fall", ax=None, spec="r--", label=None, verbose=1): """ use step='rise' to fit onset and step='fall' to fit tail assumes that data starts from the start of the pulse """ if verbose: print("\n\nfunction 'fit_step' at your service!\n") # zero time axis t0 = t[0] t = t - t0 print("t0 = " + str(t0)) if type(t) is list: t = np.array(t) # 17B02 if step == "fall": I_tail = np.array([I for (I, t_I) in enumerate(t) if tpulse < t_I]) # print(I_tail) t_fit = t[I_tail] - tpulse elif step == "rise": if tpulse == 0: tpulse = t[-1] I_tail = np.array([I for (I, t_I) in enumerate(t) if t_I < tpulse]) t_fit = t[I_tail] else: print("use step='rise' to fit onset and step='fall' to fit tail") pars = fit_exponential(t_fit, y[I_tail]) if ax: tau = pars[0] y0 = pars[1] y1 = pars[2] y_fit = y0 + (y1 - y0) * np.exp(-t_fit / tau) t_fit = t_fit + t0 # put time axis back if step == "fall": t_fit = t_fit + tpulse ax.plot(t_fit, y_fit, spec, label=label) if label: if label == "tau": label = "tau = {0:5.2f} s".format(tau) I_text = int(len(t_fit) / 2) t_text = t_fit[I_text] y_text = y_fit[I_text] ax.text(t_text, y_text, label, color=spec[0]) if verbose: print("tau = " + str(pars[0]) + " s") print("\nfunction 'fit_step' finished!\n\n") return pars def stagnant_diffusion_ode(C, T, pars): # Note that C comes before T here! """ Scott's master p. 52 and appendix C. Z is the new X. returns rate of change dC/dT of concentration profile for non-dimensionalized stagnant sniffer diffusion problem. C = C(X) where X goes from 0 (membrane) to 1 (electrode) T is time non-dimensionalized on the diffusion scale t0 = L²/D pars: [0] alpha = h*L/D is the system parameter. [1] J_fun returns the flux from the electrode as a unction of T. The flux scale J0 is used to define the concentration scale, C0 = J0*L/D #modified 17B02 to enable carrier gas introduction of element using Cg # pars as a list rather than a dict is slightly faster (see fig06.out), # but I like the dict so that I can remember what's what. """ dZ = pars["dZ"] # assigning this here replaces two lookups with one. C_N = C[-1] + pars["J_fun"](T) * dZ # boundary condition dC/dZ = J(T) at electrode C_ = ( C[0] - pars["alpha"] * (C[0] - pars["Cg"]) * dZ ) # boundary condition dC/dZ = -alpha*(C-Cg) at membrane C_up = np.append(C[1:], C_N) C_down = np.append(C_, C[:-1]) d2CdZ2 = (C_up - 2 * C + C_down) * pars["1/dZ**2"] # second derivative of C wrt Z dCdT = d2CdZ2 # Fick's second law return dCdT def solve_stagnant( alpha=1, J_fun=None, Cg=1, Tspan=[0, 10], startstate="zero", N=30, flux=1, verbose=1 ): """solves the stagnant sniffer partial differential equations. pars[0][0] is alpha = h*L/D is the system parameter. pars[0][1] is J_fun. Returns the flux from the electrode as a unction of T. Tspan is [Tstart, Tfinish] on the diffusion timescale t0 = L²/D C0 = C0(X) is start concentration profile. If size(C0) = 1, assumes a uniform concentration. N is descretization (read from C0) flux = 0 to return entire concentration profile (on C0 = J0*L/D scale) flux = 1 to return flux through membrane (on J0 scale) """ if verbose: print("\n\nfunction 'solve_stagnant' at your service!\n") if startstate == "zero": C0 = np.zeros([N]) elif startstate == "steady": C0 = 1 / alpha + np.linspace(0, N) / (N + 1) # Scott's MSc thesis, p. 53 elif startstate == "saturated": C0 = np.ones([N]) * Cg elif np.size(startstate) == 1: C0 = np.ones([N]) * startstate else: C0 = startstate N = np.size() if np.size(Tspan) == 2: Tspan = np.linspace(Tspan[0], Tspan[1], 100) dZ = 1 / N # N+1? N-1? I can never remember what's most 'correct' pars = {"alpha": alpha, "J_fun": J_fun, "Cg": Cg, "dZ": dZ, "1/dZ**2": 1 / dZ ** 2} CC = odeint(stagnant_diffusion_ode, C0, Tspan, args=(pars,)) # 16J18_02h10: this crashes the kernel, I don't know why... 18h56 found it! c before t! J = ( CC[:, 1] - CC[:, 0] ) * N # (positive) J = dC/dX with dC = C0 - C_ and dZ = 1 / N # J is a function of T if verbose: print("solution shape: " + str(np.shape(CC))) print("\nfunction 'solve_stagnant' finished!\n\n") if flux: return Tspan, J else: return Tspan, CC def stagnant_pulse(*args, **kwargs): print( "\n\n'stagnant_pulse' has been renamed 'stagnant_operator'. Remember that next time!" ) return stagnant_operator(*args, **kwargs) def stagnant_operator( tj=None, tpulse=10, tspan=None, j_el=-1, L=100e-6, A=0.196e-4, q0=1.5e15 / Chem.NA, p_m=1e5, mol="H2", p_gas=0, normalize=False, D=None, kH=None, n_el=None, Temp=None, unit="pmol/s", flux_direction="out", verbose=True, ax=None, plot_type=None, startstate="zero", N=30, colormap="plasma", aspect="auto", ): """ Models a pulse of current towards a specified product in our EC-MS setup. Theory in chapter 2 of Scott's masters thesis. all arguments are in pure SI units. The electrode output can either be given as a steady-state square pulse of electrical current (tpulse, j_el, n_el), or as a measured current (tj[1]) as a function of time (tj[0]) #tj[1] should have units A/m^2. 1 mA/cm^2 is 10 A/m^2 #17B02: p_gas is the partial pressure of the analyte in the carrier gas. # this enables, e.g., CO depletion modelling. """ if verbose: print("\n\nfunction 'stagnant_operator' at your service!\n") if type(mol) is str: mol = Molecule(mol) if Temp is not None: mol.set_temperature(Temp) else: Temp = 298.15 # standard temperature in K if D is None: D = mol.D if kH is None: kH = mol.kH if n_el is None and not normalize: n_el = mol.n_el if tspan is None: if tj is None: tspan = [-0.1 * tpulse, 1.2 * tpulse] else: tspan = [tj[0][0], tj[0][-1]] h = kH * Chem.R * Temp * q0 / (p_m * A) # mass transfer coefficeint alpha = L * h / D # system parameter # non-dimensional scales: t0 = L ** 2 / D if tj is None: if normalize: j0 = 1 else: j0 = j_el / (n_el * Chem.Far) else: t = tj[0] if normalize: j0 = 1 j = tj[1] / np.max(np.abs(tj[1])) else: j = tj[1] / (n_el * Chem.Far) # A/m^2 --> mol/(m^2*s) j0 = max(np.abs(j)) c0 = j0 * L / D tau = L ** 2 / (2 * D) + L / h # from the approximate analytical solution, Scott's thesis appendix D Tpulse = tpulse / t0 Tspan = ( np.linspace(tspan[0], tspan[1], 1000) / t0 ) # why do I give so many time points? if tj is None: def J_fun(T): if T < 0: return 0 if T < Tpulse: return 1 return 0 else: T_in = t / t0 J_in = j / max(np.abs(j)) # print('max(J_in) = ' + str(max(J_in))) def J_fun(T): if T < T_in[0]: # assume no current outside of the input tj data return 0 if T < T_in[-1]: return np.interp(T, T_in, J_in) return 0 c_gas = p_gas / (Chem.R * Temp) cg = c_gas / kH # concentration analyte in equilibrium with carrier gas, 17B02 Cg = ( cg / c0 ) # non-dimensionalized concentration analyte at equilibrium with carrier gas, 17B02 # pars = ([alpha, J_fun, Cg],) #odeint needs the tuple. 17A12: Why ?! [T, CC] = solve_stagnant( alpha=alpha, J_fun=J_fun, Cg=Cg, Tspan=Tspan, startstate=startstate, flux=False, N=N, ) cc = CC * c0 t = T * t0 j = h * (cc[:, 0] - cg) # mass transport at the membrane # j1 = D * (cc[:,1] - cc[:,0]) # fick's first law at the membrane gives the same j :) if verbose: print( "q0 = " + str(q0) + " mol/s, h = " + str(h) + " m/s, alpha = " + str(alpha) + ", j0 = " + str(j0) + " mol/(m^2*s), max(j)/j0 = " + str(max(j) / j0) + ", t0 = " + str(t0) + " s, c0 = " + str(c0) + " mol/m^3" + ", tau (analytical) = " + str(tau) + " s" + ", cg = " + str(cg) + " mM" ) # get ready to plot: N = np.shape(cc)[1] z = np.arange(N) / (N - 1) * L # this will only be used for heatmap, so it's okay if dx isn't quite right. if "cm^2" not in unit: j = j * A if unit[0] == "u": j = j * 1e6 elif unit[0] == "n": j = j * 1e9 elif unit[0] == "p": j = j * 1e12 if flux_direction == "in": j = -j if normalize: s_int = np.trapz(j, t) if verbose: print("normalizing from area = " + str(s_int)) j = j / s_int # plotting was moved on 17G30 some legacy code here: if plot_type is not None and ax is not None: print("We recommend you plot seperately, using the function 'plot_operation'.") axes = plot_operation( cc=cc, t=t, z=z, j=j, ax=ax, plot_type=plot_type, colormap=colormap, aspect=aspect, verbose=verbose, ) if verbose: print("\nfunction 'stagnant_operator' finished!\n\n") return t, j, axes results = {"t": t, "z": z, "j": j, "cc": cc, "dimensions": "tz"} return results def flow_diffusion_ode(C, X, pars): """ Scott's master, p. 60. X is the new Y and Z is the new X. """ C_N = C[-1] C_ = C[0] - pars["alpha"] * (C[0] - pars["Cg"]) * pars["dZ"] C_up = np.append(C[1:], C_N) C_down = np.append(C_, C[:-1]) d2CdZ2 = (C_up - 2 * C + C_down) * pars["1/dZ**2"] # I assume multiplication to be faster than division dCdX = d2CdZ2 * pars["1/beta"] return dCdX def solve_flow( alpha=1, beta=1, Cg=0, N=30, flux=False, verbose=True, Xspan=[0, 1], C0="uniform" ): """ This solves the flow ODE and returns either flux through membrane as a function of position (Xspan and J), or the concentration profile (Xspan and CC) It assumes steady state. I think I can use this and then convolute if I need time dependence. """ if verbose: print("\n\nfunction 'solve_flow' at your service!\n") if C0 == "uniform": C0 = np.array([1] * N) # nothing else really makes sense, since c0 defines a scale. if np.size(Xspan) == 2: Xspan = np.linspace(Xspan[0], Xspan[1], 100) dZ = 1 / N # N+1? N-1? I can never remember what's most 'correct' pars = { "alpha": alpha, "1/beta": 1 / beta, "Cg": Cg, "dZ": dZ, "1/dZ**2": 1 / dZ ** 2, } CC = odeint(flow_diffusion_ode, C0, Xspan, args=(pars,)) # 16J18_02h10: this crashes the kernel, I don't know why... 18h56 found it! c before t! J = ( CC[:, 1] - CC[:, 0] ) * N # (positive) J = dC/dZ with dC = C0 - C_ and dX = 1 / N # J is a function of X. if verbose: print("solution shape: " + str(np.shape(CC))) print("\nfunction 'solve_flow' finished!\n\n") if flux: return Xspan, J else: return Xspan, CC pass def flow_operator( mode="steady", # in steady mode it's not really an operator. system="chip", # A_el=0.196e-4, A=0.196e-4, q0=1.5e15 / Chem.NA, Temp=None, # universal pars L=100e-6, w=5e-3, w2=5e-3, F=1e-9, # geometry pars #w and w2 changed from 0.5e-3 to 5e-3 on 17K28. c0=None, j0=None, j_el=-1, # inlet flow pars p_m=1e5, # chip pars phi=0.5, dp=20e-9, Lp=100e-6, # DEMS pars mol="H2", D=None, kH=None, n_el=None, M=None, # mol pars p_gas=0, normalize=False, unit="pmol/s", flux_direction="out", N=100, # solver pars verbose=True, ): """ Follows the recipe in Scott's MSc, page 61, for calculating collection efficiency in a flow system by solving a differential equation. This can be used to compare different types of EC-MS """ if verbose: print("\n\nfunction 'flow_operator' at your service!\n") if type(mol) is str: mol = Molecule(mol) if Temp is not None: mol.set_temperature(Temp) else: Temp = 298.15 # standard temperature in K if D is None: D = mol.D # diffusion constant in electrolyte / [m^2/s] if kH is None: kH = mol.kH # dimensionless henry's law constant if M is None: M = Chem.Mass(mol.name) * 1e-3 # molar mass / [kg/mol] # print(c0) if n_el is None and c0 is None and not normalize: n_el = mol.n_el if c0 is None: if j0 is None: j0 = j_el * A_el / (n_el * Chem.Far) c0 = j0 / F # concentration is production rate over flow rate: [mol/s] / [m^3/s)] = [mol/m^3] ) if system == "chip": h = kH * Chem.R * Temp * q0 / (p_m * A) # Scott's MSc, page 50 elif system == "DEMS": h = ( kH * phi * dp / (3 * Lp) * np.sqrt(8 / np.pi * Chem.R * Temp / M) ) # Scott's MSc, page 49 v0 = F / (L * w2) alpha = h * L / D beta = v0 * L ** 2 / (D * w) # There is a mistake in Scott's MSc page60! # There I got the non-dimensionalization wrong, and wrote beta = v0*w**2/(D*L) # in fact, beta = v0*L**2/(D*w) Xspan = np.linspace(0, 1, 1000) X, CC = solve_flow(alpha=alpha, beta=beta, Xspan=Xspan, N=N, verbose=verbose) x = X * w cc = CC * c0 j = cc[:, 0] * h # mol/m^3 * m/s = mol/(m^2*s) Z = np.linspace(0, 1, N) z = Z * L eta_m = 1 - np.trapz(CC[-1, :], Z) # Scott's MSc, page 61 eta_m_check = ( w2 * np.trapz(j, x) / (c0 * F) ) # m*mol/(m^2*s)*m / ((mol/m^3)*m^3/s) = 1 qm = c0 * F * eta_m if verbose: print("portion not escaped = " + str(eta_m)) print("portion collected = " + str(eta_m_check) + "\n\n") if system == "chip": eta_v = 1 elif system == "DEMS": p_w = Chem.p_vap(mol="H2O", T=Temp, unit="Pa") M_w = Chem.Mass("H2O") * 1e-3 j_w = ( A * p_w / (Chem.R * Temp) * phi * dp / (3 * Lp) * np.sqrt(8 / np.pi * Chem.R * Temp / M_w) ) eta_v = q0 / (qm + j_w) # fixed 17H10 eta = eta_m * eta_v if verbose: print( "q0 = " + str(q0) + " mol/s, h = " + str(h) + " m/s, alpha = " + str(alpha) + ", j0 = " + str(j0) + " mol/s, max(c)/c0 = " + str(np.max(np.max(cc)) / c0) + ", kH = " + str(kH) + ", eta = " + str(eta) + ", mol = " + str(mol.name) + ", system = " + str(system) + "" + ", beta = " + str(beta) + "" + ", v0 = " + str(v0) ) if verbose: print("\nfunction 'flow_operator' at finished!\n\n") results = { "x": x, "z": z, "j": j, "cc": cc, "eta_m": eta_m, "eta_v": eta_v, "eta": eta, "dimensions": "xz", } return results def delta_response( L=100e-6, q0=1e15 / Chem.NA, mol="H2", D=None, kH=None, n_el=None, A=0.196e-4, p_m=1e5, Temp=298.15, verbose=True, tspan="auto", N_t=1000, ): """ Returns the output when a stagnant_operator operates on a delta function. There's probably a much smarter way to do it, but for now I'll just do triangle pulse of width tau/250 """ if D is None or kH is None: if type(mol) is str: mol = Molecule(mol) if D is None: D = mol.D if kH is None: kH = mol.kH if verbose: print("calculating a delta function response.") h = kH * Chem.R * Temp * q0 / (p_m * A) # mass transfer coefficeint tau = L / h + L ** 2 / (2 * D) if tspan == "auto": tspan = [0, 4 * tau] t = np.linspace(tspan[0], tspan[1], N_t) j = np.append(np.array([1]), np.zeros(N_t - 1)) tj = [t, j] print(type(tj)) return stagnant_pulse( tj=tj, normalize=True, tspan=tspan, L=L, A=A, q0=q0, p_m=p_m, D=D, kH=kH, n_el=n_el, Temp=Temp, verbose=True, plot_type=None, ) if __name__ == "__main__": pass ##
PypiClean
/CmlArabicReaderThird-0.1-py3-none-any.whl/ThirdcamelArabicReader/camel_tools/morphology/cachetools/func.py
__all__ = ("fifo_cache", "lfu_cache", "lru_cache", "mru_cache", "rr_cache", "ttl_cache") import collections import functools import math import random import time try: from threading import RLock except ImportError: # pragma: no cover from dummy_threading import RLock from . import FIFOCache, LFUCache, LRUCache, MRUCache, RRCache, TTLCache from . import keys _CacheInfo = collections.namedtuple( "CacheInfo", ["hits", "misses", "maxsize", "currsize"] ) class _UnboundCache(dict): @property def maxsize(self): return None @property def currsize(self): return len(self) class _UnboundTTLCache(TTLCache): def __init__(self, ttl, timer): TTLCache.__init__(self, math.inf, ttl, timer) @property def maxsize(self): return None def _cache(cache, typed): maxsize = cache.maxsize def decorator(func): key = keys.typedkey if typed else keys.hashkey lock = RLock() stats = [0, 0] def wrapper(*args, **kwargs): k = key(*args, **kwargs) with lock: try: v = cache[k] stats[0] += 1 return v except KeyError: stats[1] += 1 v = func(*args, **kwargs) # in case of a race, prefer the item already in the cache try: with lock: return cache.setdefault(k, v) except ValueError: return v # value too large def cache_info(): with lock: hits, misses = stats maxsize = cache.maxsize currsize = cache.currsize return _CacheInfo(hits, misses, maxsize, currsize) def cache_clear(): with lock: try: cache.clear() finally: stats[:] = [0, 0] wrapper.cache_info = cache_info wrapper.cache_clear = cache_clear wrapper.cache_parameters = lambda: {"maxsize": maxsize, "typed": typed} functools.update_wrapper(wrapper, func) return wrapper return decorator def fifo_cache(maxsize=128, typed=False): """Decorator to wrap a function with a memoizing callable that saves up to `maxsize` results based on a First In First Out (FIFO) algorithm. """ if maxsize is None: return _cache(_UnboundCache(), typed) elif callable(maxsize): return _cache(FIFOCache(128), typed)(maxsize) else: return _cache(FIFOCache(maxsize), typed) def lfu_cache(maxsize=128, typed=False): """Decorator to wrap a function with a memoizing callable that saves up to `maxsize` results based on a Least Frequently Used (LFU) algorithm. """ if maxsize is None: return _cache(_UnboundCache(), typed) elif callable(maxsize): return _cache(LFUCache(128), typed)(maxsize) else: return _cache(LFUCache(maxsize), typed) def lru_cache(maxsize=128, typed=False): """Decorator to wrap a function with a memoizing callable that saves up to `maxsize` results based on a Least Recently Used (LRU) algorithm. """ if maxsize is None: return _cache(_UnboundCache(), typed) elif callable(maxsize): return _cache(LRUCache(128), typed)(maxsize) else: return _cache(LRUCache(maxsize), typed) def mru_cache(maxsize=128, typed=False): """Decorator to wrap a function with a memoizing callable that saves up to `maxsize` results based on a Most Recently Used (MRU) algorithm. """ if maxsize is None: return _cache(_UnboundCache(), typed) elif callable(maxsize): return _cache(MRUCache(128), typed)(maxsize) else: return _cache(MRUCache(maxsize), typed) def rr_cache(maxsize=128, choice=random.choice, typed=False): """Decorator to wrap a function with a memoizing callable that saves up to `maxsize` results based on a Random Replacement (RR) algorithm. """ if maxsize is None: return _cache(_UnboundCache(), typed) elif callable(maxsize): return _cache(RRCache(128, choice), typed)(maxsize) else: return _cache(RRCache(maxsize, choice), typed) def ttl_cache(maxsize=128, ttl=600, timer=time.monotonic, typed=False): """Decorator to wrap a function with a memoizing callable that saves up to `maxsize` results based on a Least Recently Used (LRU) algorithm with a per-item time-to-live (TTL) value. """ if maxsize is None: return _cache(_UnboundTTLCache(ttl, timer), typed) elif callable(maxsize): return _cache(TTLCache(128, ttl, timer), typed)(maxsize) else: return _cache(TTLCache(maxsize, ttl, timer), typed)
PypiClean
/IdracRedfishSupport-0.0.8.tar.gz/IdracRedfishSupport-0.0.8/GetIdracServerSlotInformationREDFISH.py
import argparse import getpass import json import logging import os import re import requests import sys import time import warnings from datetime import datetime from pprint import pprint warnings.filterwarnings("ignore") parser=argparse.ArgumentParser(description="Python script using Redfish API with OEM extension to get server slot information. Slot information includes: Fan, CPU, DIMM, PCI, Backplane, PSU") parser.add_argument('-ip',help='iDRAC IP address', required=False) parser.add_argument('-u', help='iDRAC username', required=False) parser.add_argument('-p', help='iDRAC password. If you do not pass in argument -p, script will prompt to enter user password which will not be echoed to the screen.', required=False) parser.add_argument('-x', help='Pass in X-Auth session token for executing Redfish calls. All Redfish calls will use X-Auth token instead of username/password', required=False) parser.add_argument('--ssl', help='SSL cert verification for all Redfish calls, pass in value \"true\" or \"false\". By default, this argument is not required and script ignores validating SSL cert for all Redfish calls.', required=False) parser.add_argument('--script-examples', help='Get executing script examples', action="store_true", dest="script_examples", required=False) parser.add_argument('--get-text', help='Get all server slot information and echo output to the terminal, also redirect output to text file', dest="get_text", action="store_true", required=False) parser.add_argument('--get-xml', help='Get all server slot information and redirect to XML file. NOTE: This argument will not echo slot information to the terminal.', dest="get_xml", action="store_true", required=False) args=vars(parser.parse_args()) logging.basicConfig(format='%(message)s', stream=sys.stdout, level=logging.INFO) def script_examples(): print("""\n- GetIdracServerSlotInformationREDFISH.py -ip 192.168.0.120 -u root -p calvin --get-text, this example will get slot information for all server devices and redirect output to text file. \n- GetIdracServerSlotInformationREDFISH.py -ip 192.168.0.120 -u root -p calvin --get-xml, this example will get slot information for all server devices and redirect output to XML file.""") sys.exit(0) def check_supported_idrac_version(): if args["x"]: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' % idrac_ip, verify=verify_cert, headers={'X-Auth-Token': args["x"]}) else: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' % idrac_ip, verify=verify_cert,auth=(idrac_username, idrac_password)) data = response.json() if response.status_code == 401: logging.warning("\n- WARNING, status code %s returned. Incorrect iDRAC username/password or invalid privilege detected." % response.status_code) sys.exit(0) if response.status_code != 200: logging.warning("\n- WARNING, iDRAC version installed does not support this feature using Redfish API") sys.exit(0) def get_server_slot_info(): try: os.remove(idrac_ip + "_server_slot_info.txt") except: pass open_file = open("%s_server_slot_info.txt" % idrac_ip,"w") get_datetime = datetime.now() current_date_time = "- Data collection timestamp: %s-%s-%s %s:%s:%s\n" % (get_datetime.month, get_datetime.day, get_datetime.year, get_datetime.hour, get_datetime.minute, get_datetime.second) open_file.writelines(current_date_time) open_file.writelines("\n\n") if args["x"]: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' % idrac_ip, verify=verify_cert, headers={'X-Auth-Token': args["x"]}) else: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' % idrac_ip, verify=verify_cert,auth=(idrac_username, idrac_password)) data = response.json() if response.status_code != 200: logging.error("\n- FAIL, GET request failed, status code %s returned. Detailed error results: \n%s" % (response.status_code,data)) sys.exit(0) if data['Members'] == []: logging.error("- FAIL, no data detected for Members property. Manually execute GET on URI 'https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' in browser to check. If no data detected, reboot server and run Collecting Inventory to refresh the configuration database for iDRAC, try GET again." % idrac_ip) sys.exit(0) for i in data['Members']: pprint(i), print("\n") for ii in i.items(): server_slot_entry = ("%s: %s" % (ii[0],ii[1])) open_file.writelines("%s\n" % server_slot_entry) open_file.writelines("\n") number_list = [i for i in range (1,100001) if i % 50 == 0] for seq in number_list: if args["x"]: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection?$skip=%s' % (idrac_ip, seq), verify=verify_cert, headers={'X-Auth-Token': args["x"]}) else: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection?$skip=%s' % (idrac_ip, seq), verify=verify_cert,auth=(idrac_username, idrac_password)) data = response.json() if response.status_code != 200: if "query parameter $skip is out of range" in data["error"]["@Message.ExtendedInfo"][0]["Message"]: open_file.close() logging.info("\n- INFO, iDRAC Server Slot Information also captured in \"%s_server_slot_info.txt\" file" % idrac_ip) sys.exit(0) else: logging.error("\n- FAIL, GET request failed using skip query parameter, status code %s returned. Detailed error results: \n%s" % (response.status_code,data)) sys.exit(0) if "Members" not in data or data["Members"] == [] or response.status_code == 400: break for i in data['Members']: pprint(i), print("\n") for ii in i.items(): server_slot_entry = ("%s: %s" % (ii[0],ii[1])) open_file.writelines("%s\n" % server_slot_entry) open_file.writelines("\n") logging.info("\n- INFO, iDRAC Server Slot Information also captured in \"%s_server_slot_info.txt\" file" % idrac_ip) open_file.close() def get_server_slot_info_xml(): logging.info("\n- INFO, collecting server slot information and converting to XML format, copy to XML file") try: os.remove(idrac_ip+"_server_slot_info.xml") except: pass open_file = open("%s_server_slot_info.xml" % idrac_ip,"a") open_file.writelines("<CIM>\n") if args["x"]: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' % idrac_ip, verify=verify_cert, headers={'X-Auth-Token': args["x"]}) else: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' % idrac_ip, verify=verify_cert,auth=(idrac_username, idrac_password)) data = response.json() if response.status_code != 200: logging.error("\n- FAIL, GET request failed, status code %s returned. Detailed error results: \n%s" % (response.status_code,data)) sys.exit(0) if data['Members'] == []: logging.error("- FAIL, no data detected for Members property. Manually execute GET on URI 'https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' in browser to check. if no data detected, reboot server and run Collecting Inventory to refresh the configuration database for iDRAC" % idrac_ip) sys.exit(0) for i in data['Members']: create_dict = {} for ii in i.items(): if ii[0] == "Id": create_dict[ii[0]] = str(ii[1]) elif ii[0] == "EmptySlot": create_dict[ii[0]] = str(ii[1]) elif ii[0] == "NumberDescription": if ii[1] == "": create_dict["Slot Number"] = "NA" else: create_dict["Slot Number"] = str(ii[1]) create_string = "<VALUE.NAMEDINSTANCE>\n<INSTANCENAME DEVICENAME=\""+create_dict["Id"]+"\">\n<KEYBINDING PROPERTY=\"Slot Number\">\n<VALUE>"+create_dict["Slot Number"]+"</VALUE>\n</KEYBINDING>\n</INSTANCENAME>\n<PROPERTY PROPERTY=\"EmptySlot\">\n<VALUE>"+create_dict["EmptySlot"]+"</VALUE>\n</PROPERTY>\n</VALUE.NAMEDINSTANCE>" open_file.writelines(create_string) number_list = [i for i in range (1,100001) if i % 50 == 0] for seq in number_list: if args["x"]: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection?$skip=%s' % (idrac_ip, seq), verify=verify_cert, headers={'X-Auth-Token': args["x"]}) else: response = requests.get('https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection?$skip=%s' % (idrac_ip, seq), verify=verify_cert,auth=(idrac_username, idrac_password)) data = response.json() if response.status_code != 200: if "query parameter $skip is out of range" in data["error"]["@Message.ExtendedInfo"][0]["Message"]: open_file.writelines("\n</CIM>") open_file.close() logging.info("\n- PASS, iDRAC Server Slot Information captured in \"%s_server_slot_info.xml\" file" % idrac_ip) sys.exit(0) else: logging.error("\n- FAIL, GET request failed using skip query parameter, status code %s returned. Detailed error results: \n%s" % (response.status_code,data)) sys.exit(0) if "Members" not in data or data["Members"] == [] or response.status_code == 400: break if data['Members'] == []: logging.error("- FAIL, no data detected for Members property. Manually execute GET on URI 'https://%s/redfish/v1/Dell/Systems/System.Embedded.1/DellSlotCollection' in browser to check. If no data detected, reboot server and run Collecting Inventory to refresh the configuration database for iDRAC, try GET again." % idrac_ip) sys.exit(0) for i in data['Members']: create_dict = {} for ii in i.items(): if ii[0] == "Id": create_dict[ii[0]] = str(ii[1]) elif ii[0] == "EmptySlot": create_dict[ii[0]] = str(ii[1]) elif ii[0] == "NumberDescription": create_dict["Slot Number"] = str(ii[1]) create_string = "<VALUE.NAMEDINSTANCE>\n<INSTANCENAME DEVICENAME=\""+create_dict["Id"]+"\">\n<KEYBINDING PROPERTY=\"Slot Number\">\n<VALUE>"+create_dict["Slot Number"]+"</VALUE>\n</KEYBINDING>\n</INSTANCENAME>\n<PROPERTY PROPERTY=\"EmptySlot\">\n<VALUE>"+create_dict["EmptySlot"]+"</VALUE>\n</PROPERTY>\n</VALUE.NAMEDINSTANCE>" open_file.writelines(create_string) logging.info("\n- INFO, iDRAC Server Slot Information captured in \"%s_server_slot_info.xml\" file" % idrac_ip) open_file.writelines("\n</CIM>") open_file.close() if __name__ == "__main__": if args["script_examples"]: script_examples() if args["ip"] or args["ssl"] or args["u"] or args["p"] or args["x"]: idrac_ip = args["ip"] idrac_username = args["u"] if args["p"]: idrac_password = args["p"] if not args["p"] and not args["x"] and args["u"]: idrac_password = getpass.getpass("\n- Argument -p not detected, pass in iDRAC user %s password: " % args["u"]) if args["ssl"]: if args["ssl"].lower() == "true": verify_cert = True elif args["ssl"].lower() == "false": verify_cert = False else: verify_cert = False else: verify_cert = False check_supported_idrac_version() else: logging.error("\n- FAIL, invalid argument values or not all required parameters passed in. See help text or argument --script-examples for more details.") sys.exit(0) if args["get_text"]: get_server_slot_info() elif args["get_xml"]: get_server_slot_info_xml() else: logging.error("\n- FAIL, invalid argument values or not all required parameters passed in. See help text or argument --script-examples for more details.")
PypiClean
/DeSide-1.0.2.tar.gz/DeSide-1.0.2/docs/datasets.md
Datasets ======== Datasets used in DeSide *** ## scRNA-seq datasets | Dataset ID | Journal | DOI | Publish Date | Reported cells (total) | Organism | Tissue | Data location | Sequencing method | #patients | |-------------|----------------------|-----------------------------|--------------|------------------|------------------------|----------------------------------|-----------------------------------|-------------------------|-----------| | hnscc_cillo_01 | Immunity | 10.1016/j.immuni.2019.11.014 | 20200107 | 131,224 | Human | Head and Neck Cancer (HNSC) | GSE139324 | 10x Single Cell 3' v2 | 26 | | pdac_pengj_02 | Cell Res | 10.1038/s41422-019-0195-y | 20190704 | 57,530 | Human | Pancreatic Ductal Adenocarcinoma (PDAC)| [Link](https://bigd.big.ac.cn/gsa/browse/CRA001160_) | 10x Single Cell 3' v2 | 22 | | hnscc_puram_03 | Cell | 10.1016/j.cell.2017.10.044 | 20171130 | 5,902 | Human | Head and Neck Cancer (HNSC) | GSE103322 | Smart-seq2 | 16 | | pdac_steele_04 | Nat Cancer | 10.1038/s43018-020-00121-4 | 20201026 | 124,898 | Human | Pancreatic Ductal Adenocarcinoma (PDAC)| GSE155698 | 10x Single Cell 3' v2 | 15 | | luad_kim_05 | Nat Commun | 10.1038/s41467-020-16164-1 | 20200508 | 208,506 | Human | Lung Adenocarcinoma (LUAD) | GSE131907 | 10x Single Cell 3' v2 | 13 | | nsclc_guo_06 | Nature Medicine | 10.1038/s41591-018-0045-3 | 20180625 | 12,346 | Human | Non-Small-Cell Lung Cancer (NSCLC) | GSE99254 | Smart-Seq2 | 13 | | pan_cancer_07 | Nat Genet | 10.1038/s41588-020-00726-6 | 20201030 | 53,513 | Human | Cancer cell lines | GSE157220 | Illumina NextSeq 500 | - | - The number of **reported cells** may include cells that don't originate from solid tumors, which were removed during integrating. ## Merged datasets and Synthetic datasets | Dataset name | #samples | Sampling method | Filtering | #cell types | #genes | Input dataset | GEPs <br/>(type, fortmat) | Dataset type | Notation | |:--------------------------------------:|----------|-----------------|-----------|-------------|--------|--------------------------------|:-------------------------------:|:-----------------------------:|:----------:| | TCGA | 7,699 | - | - | - | 19,712 | - | MCT, `TPM` | Downloaded from TCGA | DA | | merged_7_sc_datasets | 135,049 | - | - | 11 | 12,114 | 7 collected scRNA-seq datasets | Single cell, <br/>`log2(TPM+1)` | Raw dataset from scRNA-seq | S0 | | SCT_POS_N10K | 110,000 | n_base=100 | - | 11 | 12,114 | S0 | SCT, `log2(TPM+1)` | Used to simulate MCT datasets | S1 | | Mixed_N100K_random | 100,000 | Random | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Training set | D0 | | Mixed_N100K_segment | 100,000 | Segment | Yes | 11 | 6,168 | S1 | MCT, `log2(TPM+1)` | Training set | D1 | | Mixed_N100K_segment_<br/>without_filtering | 100,000 | Segment | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Training set | D2 | | Test_set_random | 3,000 | Random | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Test set | T0 | | Test_set1 | 3,000 | Segment | Yes | 11 | 6,168 | S1 | MCT, `log2(TPM+1)` | Test set | T1 | | Test_set2 | 3,000 | Segment | No | 11 | 12,114 | S1 | MCT, `log2(TPM+1)` | Test set | T2 | | SCT_POS_N100 | 1100 | n_base=100 | - | 11 | 12,114 | S0 | SCT, `log2(TPM+1)` | Test set | T3 | - MCT: Bulk gene expression profile with multiple different cell types - SCT: Bulk gene expression profile with single cell type (scGEP) - GEPs: Gene expression profiles ## Download - TCGA: [download link](https://figshare.com/articles/dataset/Merged_gene_expression_profiles_TPM_/23047547) - merged_7_sc_datasets (S0): [download link](https://figshare.com/articles/dataset/Dataset_S0/23283908) - SCT_POS_N10K (S1): [download link](https://figshare.com/articles/dataset/Dataset_S1/23043560) - Mixed_N100K_random (D0): [download link](https://figshare.com/articles/dataset/Dataset_D0/23283932) - Mixed_N100K_segment (D1): [download link](https://figshare.com/articles/dataset/Dataset_D1/23047391) - Mixed_N100K_segment_without_filtering (D2): [download link](https://figshare.com/articles/dataset/Dataset_D2/23284256) - All Test Sets: [download link](https://figshare.com/articles/dataset/All_Test_Sets/23283884) - Test_set_random (T0) - Test_set1 (T1) - Test_set2 (T2) - SCT_POS_N100 (T3) `.h5ad` files can be opened by the function `scanpy.read_h5ad()` in [Scanpy](https://scanpy.readthedocs.io/en/stable/) or the class [`deside.utility.read_file.ReadH5AD`](https://deside.readthedocs.io/en/latest/func/utility.html#deside.utility.read_file.ReadH5AD) in DeSide.
PypiClean
/Choco-1.0.5.tar.gz/Choco-1.0.5/choco/util.py
import re import collections import codecs import os from choco import compat import operator def update_wrapper(decorated, fn): decorated.__wrapped__ = fn decorated.__name__ = fn.__name__ return decorated class PluginLoader(object): def __init__(self, group): self.group = group self.impls = {} def load(self, name): if name in self.impls: return self.impls[name]() else: import pkg_resources for impl in pkg_resources.iter_entry_points( self.group, name): self.impls[name] = impl.load return impl.load() else: from choco import errors raise errors.RuntimeException( "Can't load plugin %s %s" % (self.group, name)) def register(self, name, modulepath, objname): def load(): mod = __import__(modulepath) for token in modulepath.split(".")[1:]: mod = getattr(mod, token) return getattr(mod, objname) self.impls[name] = load def verify_directory(dir): """create and/or verify a filesystem directory.""" tries = 0 while not os.path.exists(dir): try: tries += 1 os.makedirs(dir, compat.octal("0775")) except: if tries > 5: raise def to_list(x, default=None): if x is None: return default if not isinstance(x, (list, tuple)): return [x] else: return x class memoized_property(object): """A read-only @property that is only evaluated once.""" def __init__(self, fget, doc=None): self.fget = fget self.__doc__ = doc or fget.__doc__ self.__name__ = fget.__name__ def __get__(self, obj, cls): if obj is None: return self obj.__dict__[self.__name__] = result = self.fget(obj) return result class memoized_instancemethod(object): """Decorate a method memoize its return value. Best applied to no-arg methods: memoization is not sensitive to argument values, and will always return the same value even when called with different arguments. """ def __init__(self, fget, doc=None): self.fget = fget self.__doc__ = doc or fget.__doc__ self.__name__ = fget.__name__ def __get__(self, obj, cls): if obj is None: return self def oneshot(*args, **kw): result = self.fget(obj, *args, **kw) memo = lambda *a, **kw: result memo.__name__ = self.__name__ memo.__doc__ = self.__doc__ obj.__dict__[self.__name__] = memo return result oneshot.__name__ = self.__name__ oneshot.__doc__ = self.__doc__ return oneshot class SetLikeDict(dict): """a dictionary that has some setlike methods on it""" def union(self, other): """produce a 'union' of this dict and another (at the key level). values in the second dict take precedence over that of the first""" x = SetLikeDict(**self) x.update(other) return x class FastEncodingBuffer(object): """a very rudimentary buffer that is faster than StringIO, but doesn't crash on unicode data like cStringIO.""" def __init__(self, encoding=None, errors='strict', as_unicode=False): self.data = collections.deque() self.encoding = encoding if as_unicode: self.delim = compat.u('') else: self.delim = '' self.as_unicode = as_unicode self.errors = errors self.write = self.data.append def truncate(self): self.data = collections.deque() self.write = self.data.append def getvalue(self): if self.encoding: return self.delim.join(self.data).encode(self.encoding, self.errors) else: return self.delim.join(self.data) class LRUCache(dict): """A dictionary-like object that stores a limited number of items, discarding lesser used items periodically. this is a rewrite of LRUCache from Myghty to use a periodic timestamp-based paradigm so that synchronization is not really needed. the size management is inexact. """ class _Item(object): def __init__(self, key, value): self.key = key self.value = value self.timestamp = compat.time_func() def __repr__(self): return repr(self.value) def __init__(self, capacity, threshold=.5): self.capacity = capacity self.threshold = threshold def __getitem__(self, key): item = dict.__getitem__(self, key) item.timestamp = compat.time_func() return item.value def values(self): return [i.value for i in dict.values(self)] def setdefault(self, key, value): if key in self: return self[key] else: self[key] = value return value def __setitem__(self, key, value): item = dict.get(self, key) if item is None: item = self._Item(key, value) dict.__setitem__(self, key, item) else: item.value = value self._manage_size() def _manage_size(self): while len(self) > self.capacity + self.capacity * self.threshold: bytime = sorted(dict.values(self), key=operator.attrgetter('timestamp'), reverse=True) for item in bytime[self.capacity:]: try: del self[item.key] except KeyError: # if we couldn't find a key, most likely some other thread # broke in on us. loop around and try again break # Regexp to match python magic encoding line _PYTHON_MAGIC_COMMENT_re = re.compile( r'[ \t\f]* \# .* coding[=:][ \t]*([-\w.]+)', re.VERBOSE) def parse_encoding(fp): """Deduce the encoding of a Python source file (binary mode) from magic comment. It does this in the same way as the `Python interpreter`__ .. __: http://docs.python.org/ref/encodings.html The ``fp`` argument should be a seekable file object in binary mode. """ pos = fp.tell() fp.seek(0) try: line1 = fp.readline() has_bom = line1.startswith(codecs.BOM_UTF8) if has_bom: line1 = line1[len(codecs.BOM_UTF8):] m = _PYTHON_MAGIC_COMMENT_re.match(line1.decode('ascii', 'ignore')) if not m: try: import parser parser.suite(line1.decode('ascii', 'ignore')) except (ImportError, SyntaxError): # Either it's a real syntax error, in which case the source # is not valid python source, or line2 is a continuation of # line1, in which case we don't want to scan line2 for a magic # comment. pass else: line2 = fp.readline() m = _PYTHON_MAGIC_COMMENT_re.match( line2.decode('ascii', 'ignore')) if has_bom: if m: raise SyntaxError( "python refuses to compile code with both a UTF8" " byte-order-mark and a magic encoding comment") return 'utf_8' elif m: return m.group(1) else: return None finally: fp.seek(pos) def sorted_dict_repr(d): """repr() a dictionary with the keys in order. Used by the lexer unit test to compare parse trees based on strings. """ keys = list(d.keys()) keys.sort() return "{" + ", ".join(["%r: %r" % (k, d[k]) for k in keys]) + "}" def restore__ast(_ast): """Attempt to restore the required classes to the _ast module if it appears to be missing them """ if hasattr(_ast, 'AST'): return _ast.PyCF_ONLY_AST = 2 << 9 m = compile("""\ def foo(): pass class Bar(object): pass if False: pass baz = 'choco' 1 + 2 - 3 * 4 / 5 6 // 7 % 8 << 9 >> 10 11 & 12 ^ 13 | 14 15 and 16 or 17 -baz + (not +18) - ~17 baz and 'foo' or 'bar' (choco is baz == baz) is not baz != choco choco > baz < choco >= baz <= choco choco in baz not in choco""", '<unknown>', 'exec', _ast.PyCF_ONLY_AST) _ast.Module = type(m) for cls in _ast.Module.__mro__: if cls.__name__ == 'mod': _ast.mod = cls elif cls.__name__ == 'AST': _ast.AST = cls _ast.FunctionDef = type(m.body[0]) _ast.ClassDef = type(m.body[1]) _ast.If = type(m.body[2]) _ast.Name = type(m.body[3].targets[0]) _ast.Store = type(m.body[3].targets[0].ctx) _ast.Str = type(m.body[3].value) _ast.Sub = type(m.body[4].value.op) _ast.Add = type(m.body[4].value.left.op) _ast.Div = type(m.body[4].value.right.op) _ast.Mult = type(m.body[4].value.right.left.op) _ast.RShift = type(m.body[5].value.op) _ast.LShift = type(m.body[5].value.left.op) _ast.Mod = type(m.body[5].value.left.left.op) _ast.FloorDiv = type(m.body[5].value.left.left.left.op) _ast.BitOr = type(m.body[6].value.op) _ast.BitXor = type(m.body[6].value.left.op) _ast.BitAnd = type(m.body[6].value.left.left.op) _ast.Or = type(m.body[7].value.op) _ast.And = type(m.body[7].value.values[0].op) _ast.Invert = type(m.body[8].value.right.op) _ast.Not = type(m.body[8].value.left.right.op) _ast.UAdd = type(m.body[8].value.left.right.operand.op) _ast.USub = type(m.body[8].value.left.left.op) _ast.Or = type(m.body[9].value.op) _ast.And = type(m.body[9].value.values[0].op) _ast.IsNot = type(m.body[10].value.ops[0]) _ast.NotEq = type(m.body[10].value.ops[1]) _ast.Is = type(m.body[10].value.left.ops[0]) _ast.Eq = type(m.body[10].value.left.ops[1]) _ast.Gt = type(m.body[11].value.ops[0]) _ast.Lt = type(m.body[11].value.ops[1]) _ast.GtE = type(m.body[11].value.ops[2]) _ast.LtE = type(m.body[11].value.ops[3]) _ast.In = type(m.body[12].value.ops[0]) _ast.NotIn = type(m.body[12].value.ops[1]) def read_file(path, mode='rb'): fp = open(path, mode) try: data = fp.read() return data finally: fp.close() def read_python_file(path): fp = open(path, "rb") try: encoding = parse_encoding(fp) data = fp.read() if encoding: data = data.decode(encoding) return data finally: fp.close()
PypiClean
/Flask-FlatPages-0.8.1.tar.gz/Flask-FlatPages-0.8.1/README.rst
=============== Flask-FlatPages =============== .. image:: https://github.com/flask-FlatPages/flask-FlatPages/actions/workflows/test.yml/badge.svg?branch=master :target: https://github.com/flask-FlatPages/flask-FlatPages/actions/workflows/test.yml/ .. image:: https://img.shields.io/pypi/v/Flask-FlatPages.svg :target: https://pypi.python.org/pypi/Flask-FlatPages Provides flat static pages to a Flask_ application, based on text files as opposed to a relational database. * Works on Python 2.7 and 3.6+ * BSD licensed * Latest documentation `on Read the Docs`_ * Source, issues and pull requests `on Github`_ * Releases `on PyPI`_ * Install with ``pip install Flask-FlatPages`` .. _Flask: http://flask.pocoo.org/ .. _on Read the Docs: http://flask-flatpages.readthedocs.org/ .. _on Github: https://github.com/SimonSapin/Flask-FlatPages/ .. _on PyPI: http://pypi.python.org/pypi/Flask-FlatPages
PypiClean
/NlvWxPython-4.2.0-cp37-cp37m-win_amd64.whl/wx/lib/popupctl.py
import wx from wx.lib.buttons import GenButtonEvent class PopButton(wx.Control): def __init__(self,*_args,**_kwargs): wx.Control.__init__(self, *_args, **_kwargs) self.up = True self.didDown = False self.Bind(wx.EVT_LEFT_DOWN, self.OnLeftDown) self.Bind(wx.EVT_LEFT_UP, self.OnLeftUp) self.Bind(wx.EVT_MOTION, self.OnMotion) self.Bind(wx.EVT_PAINT, self.OnPaint) def Notify(self): evt = GenButtonEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, self.GetId()) evt.SetIsDown(not self.up) evt.SetButtonObj(self) evt.SetEventObject(self) self.GetEventHandler().ProcessEvent(evt) def OnEraseBackground(self, event): pass def OnLeftDown(self, event): if not self.IsEnabled(): return self.didDown = True self.up = False self.CaptureMouse() self.GetParent().textCtrl.SetFocus() self.Refresh() event.Skip() def OnLeftUp(self, event): if not self.IsEnabled(): return if self.didDown: self.ReleaseMouse() if not self.up: self.Notify() self.up = True self.Refresh() self.didDown = False event.Skip() def OnMotion(self, event): if not self.IsEnabled(): return if event.LeftIsDown(): if self.didDown: x,y = event.GetPosition() w,h = self.GetClientSize() if self.up and x<w and x>=0 and y<h and y>=0: self.up = False self.Refresh() return if not self.up and (x<0 or y<0 or x>=w or y>=h): self.up = True self.Refresh() return event.Skip() def OnPaint(self, event): dc = wx.BufferedPaintDC(self) if self.up: flag = wx.CONTROL_CURRENT else: flag = wx.CONTROL_PRESSED wx.RendererNative.Get().DrawComboBoxDropButton(self, dc, self.GetClientRect(), flag) #--------------------------------------------------------------------------- # Tried to use wxPopupWindow but the control misbehaves on MSW class PopupDialog(wx.Dialog): def __init__(self,parent,content = None): wx.Dialog.__init__(self,parent,-1,'', style = wx.BORDER_SIMPLE|wx.STAY_ON_TOP) self.ctrl = parent self.win = wx.Window(self,-1,pos = (0,0),style = 0) if content: self.SetContent(content) def SetContent(self,content): self.content = content self.content.Reparent(self.win) self.content.Show(True) self.win.SetClientSize(self.content.GetSize()) self.SetSize(self.win.GetSize()) def Display(self): pos = self.ctrl.ClientToScreen( (0,0) ) dSize = wx.GetDisplaySize() selfSize = self.GetSize() tcSize = self.ctrl.GetSize() pos.x -= (selfSize.width - tcSize.width) // 2 if pos.x + selfSize.width > dSize.width: pos.x = dSize.width - selfSize.width if pos.x < 0: pos.x = 0 pos.y += tcSize.height if pos.y + selfSize.height > dSize.height: pos.y = dSize.height - selfSize.height if pos.y < 0: pos.y = 0 self.Move(pos) self.ctrl.FormatContent() self.ShowModal() #--------------------------------------------------------------------------- class PopupControl(wx.Control): def __init__(self,*_args,**_kwargs): wx.Control.__init__(self, *_args, **_kwargs) self.textCtrl = wx.TextCtrl(self, wx.ID_ANY, '', pos = (0,0)) self.bCtrl = PopButton(self, wx.ID_ANY, style=wx.BORDER_NONE) self.pop = None self.content = None self.Bind(wx.EVT_SIZE, self.OnSize) self.bCtrl.Bind(wx.EVT_BUTTON, self.OnButton, self.bCtrl) self.Bind(wx.EVT_SET_FOCUS, self.OnFocus) self.SetInitialSize(_kwargs.get('size', wx.DefaultSize)) self.SendSizeEvent() def OnFocus(self,evt): # embedded control should get focus on TAB keypress self.textCtrl.SetFocus() evt.Skip() def OnSize(self, evt): # layout the child widgets w,h = self.GetClientSize() self.textCtrl.SetSize(0, 0, w - self.marginWidth - self.buttonWidth, h) self.bCtrl.SetSize(w - self.buttonWidth, 0, self.buttonWidth, h) def DoGetBestSize(self): # calculate the best size of the combined control based on the # needs of the child widgets. tbs = self.textCtrl.GetBestSize() return wx.Size(tbs.width + self.marginWidth + self.buttonWidth, tbs.height) def OnButton(self, evt): if not self.pop: if self.content: self.pop = PopupDialog(self,self.content) del self.content else: print('No Content to pop') if self.pop: self.pop.Display() def Enable(self, flag): wx.Control.Enable(self,flag) self.textCtrl.Enable(flag) self.bCtrl.Enable(flag) def SetPopupContent(self, content): if not self.pop: self.content = content self.content.Show(False) else: self.pop.SetContent(content) def FormatContent(self): pass def PopDown(self): if self.pop: self.pop.EndModal(1) def SetValue(self, value): self.textCtrl.SetValue(value) def GetValue(self): return self.textCtrl.GetValue() def SetFont(self, font): self.textCtrl.SetFont(font) def GetFont(self): return self.textCtrl.GetFont() def _get_marginWidth(self): if 'wxMac' in wx.PlatformInfo: return 6 else: return 3 marginWidth = property(_get_marginWidth) def _get_buttonWidth(self): return 20 buttonWidth = property(_get_buttonWidth) # an alias PopupCtrl = PopupControl
PypiClean
/EnergyCapSdk-8.2304.4743.tar.gz/EnergyCapSdk-8.2304.4743/energycap/sdk/models/bill_entry_response.py
from msrest.serialization import Model class BillEntryResponse(Model): """BillEntryResponse. :param bill_id: The bill identifier :type bill_id: int :param account_id: The account identifier :type account_id: int :param vendor_id: The vendor identifier :type vendor_id: int :param needs_to_open_batch: Indicates if a new bill batch needs to be opened to place this bill in :type needs_to_open_batch: bool :param begin_date: The bill's begin date :type begin_date: datetime :param end_date: The bill's end date :type end_date: datetime :param billing_period: The bill's billing period :type billing_period: int :param days: The bill's number of days :type days: int :param total_cost: The bill's total cost :type total_cost: float :param due_date: :type due_date: ~energycap.sdk.models.BillHeaderChild :param statement_date: :type statement_date: ~energycap.sdk.models.BillHeaderChild :param invoice_number: :type invoice_number: ~energycap.sdk.models.BillHeaderChild :param control_code: :type control_code: ~energycap.sdk.models.BillHeaderChild :param next_reading: :type next_reading: ~energycap.sdk.models.BillHeaderChild :param account_period_name: :type account_period_name: ~energycap.sdk.models.BillHeaderChild :param account_period_number: :type account_period_number: ~energycap.sdk.models.BillHeaderChild :param account_period_year: :type account_period_year: ~energycap.sdk.models.BillHeaderChild :param estimated: :type estimated: ~energycap.sdk.models.BillHeaderChild :param bill_note: The bill's note :type bill_note: str :param void: Indicates if the bill has been voided :type void: bool :param from_vendor: Indicates if the bill is from a vendor :type from_vendor: bool :param observation_method: :type observation_method: ~energycap.sdk.models.ObservationMethodChild :param approved: Indicates if the bill has been approved :type approved: bool :param has_been_split: Indicates if the bill has been split :type has_been_split: bool :param export_hold: Indicates if the bill is being withheld from bill exports :type export_hold: bool :param ap_exported: Indicates if the bill has been ap exported :type ap_exported: bool :param gl_exported: Indicates if the bill has been gl exported :type gl_exported: bool :param accrual: Indicates if the bill is an accrual bill :type accrual: bool :param check_number: The number of the check that the bill was paid with :type check_number: str :param check_date: The date and time of the check :type check_date: datetime :param pay_status: The payment status of the bill :type pay_status: str :param cleared_date: The date and time that the check cleared :type cleared_date: datetime :param bill_image_url: The fully qualified url to the bill image :type bill_image_url: str :param general_ledger_code: The general ledger code of the bill's account-level details ("Mixed" if there is more than one) :type general_ledger_code: str :param meters: The billing account's meters :type meters: list[~energycap.sdk.models.BillEntryMeterChild] :param account_body_lines: The bill's account-level details :type account_body_lines: list[~energycap.sdk.models.BillEntryBodyLine] :param vendor_body_lines: The bill's vendor template details :type vendor_body_lines: list[~energycap.sdk.models.BillEntryBodyLine] :param batch: :type batch: ~energycap.sdk.models.BatchChild """ _attribute_map = { 'bill_id': {'key': 'billId', 'type': 'int'}, 'account_id': {'key': 'accountId', 'type': 'int'}, 'vendor_id': {'key': 'vendorId', 'type': 'int'}, 'needs_to_open_batch': {'key': 'needsToOpenBatch', 'type': 'bool'}, 'begin_date': {'key': 'beginDate', 'type': 'iso-8601'}, 'end_date': {'key': 'endDate', 'type': 'iso-8601'}, 'billing_period': {'key': 'billingPeriod', 'type': 'int'}, 'days': {'key': 'days', 'type': 'int'}, 'total_cost': {'key': 'totalCost', 'type': 'float'}, 'due_date': {'key': 'dueDate', 'type': 'BillHeaderChild'}, 'statement_date': {'key': 'statementDate', 'type': 'BillHeaderChild'}, 'invoice_number': {'key': 'invoiceNumber', 'type': 'BillHeaderChild'}, 'control_code': {'key': 'controlCode', 'type': 'BillHeaderChild'}, 'next_reading': {'key': 'nextReading', 'type': 'BillHeaderChild'}, 'account_period_name': {'key': 'accountPeriodName', 'type': 'BillHeaderChild'}, 'account_period_number': {'key': 'accountPeriodNumber', 'type': 'BillHeaderChild'}, 'account_period_year': {'key': 'accountPeriodYear', 'type': 'BillHeaderChild'}, 'estimated': {'key': 'estimated', 'type': 'BillHeaderChild'}, 'bill_note': {'key': 'billNote', 'type': 'str'}, 'void': {'key': 'void', 'type': 'bool'}, 'from_vendor': {'key': 'fromVendor', 'type': 'bool'}, 'observation_method': {'key': 'observationMethod', 'type': 'ObservationMethodChild'}, 'approved': {'key': 'approved', 'type': 'bool'}, 'has_been_split': {'key': 'hasBeenSplit', 'type': 'bool'}, 'export_hold': {'key': 'exportHold', 'type': 'bool'}, 'ap_exported': {'key': 'apExported', 'type': 'bool'}, 'gl_exported': {'key': 'glExported', 'type': 'bool'}, 'accrual': {'key': 'accrual', 'type': 'bool'}, 'check_number': {'key': 'checkNumber', 'type': 'str'}, 'check_date': {'key': 'checkDate', 'type': 'iso-8601'}, 'pay_status': {'key': 'payStatus', 'type': 'str'}, 'cleared_date': {'key': 'clearedDate', 'type': 'iso-8601'}, 'bill_image_url': {'key': 'billImageUrl', 'type': 'str'}, 'general_ledger_code': {'key': 'generalLedgerCode', 'type': 'str'}, 'meters': {'key': 'meters', 'type': '[BillEntryMeterChild]'}, 'account_body_lines': {'key': 'accountBodyLines', 'type': '[BillEntryBodyLine]'}, 'vendor_body_lines': {'key': 'vendorBodyLines', 'type': '[BillEntryBodyLine]'}, 'batch': {'key': 'batch', 'type': 'BatchChild'}, } def __init__(self, **kwargs): super(BillEntryResponse, self).__init__(**kwargs) self.bill_id = kwargs.get('bill_id', None) self.account_id = kwargs.get('account_id', None) self.vendor_id = kwargs.get('vendor_id', None) self.needs_to_open_batch = kwargs.get('needs_to_open_batch', None) self.begin_date = kwargs.get('begin_date', None) self.end_date = kwargs.get('end_date', None) self.billing_period = kwargs.get('billing_period', None) self.days = kwargs.get('days', None) self.total_cost = kwargs.get('total_cost', None) self.due_date = kwargs.get('due_date', None) self.statement_date = kwargs.get('statement_date', None) self.invoice_number = kwargs.get('invoice_number', None) self.control_code = kwargs.get('control_code', None) self.next_reading = kwargs.get('next_reading', None) self.account_period_name = kwargs.get('account_period_name', None) self.account_period_number = kwargs.get('account_period_number', None) self.account_period_year = kwargs.get('account_period_year', None) self.estimated = kwargs.get('estimated', None) self.bill_note = kwargs.get('bill_note', None) self.void = kwargs.get('void', None) self.from_vendor = kwargs.get('from_vendor', None) self.observation_method = kwargs.get('observation_method', None) self.approved = kwargs.get('approved', None) self.has_been_split = kwargs.get('has_been_split', None) self.export_hold = kwargs.get('export_hold', None) self.ap_exported = kwargs.get('ap_exported', None) self.gl_exported = kwargs.get('gl_exported', None) self.accrual = kwargs.get('accrual', None) self.check_number = kwargs.get('check_number', None) self.check_date = kwargs.get('check_date', None) self.pay_status = kwargs.get('pay_status', None) self.cleared_date = kwargs.get('cleared_date', None) self.bill_image_url = kwargs.get('bill_image_url', None) self.general_ledger_code = kwargs.get('general_ledger_code', None) self.meters = kwargs.get('meters', None) self.account_body_lines = kwargs.get('account_body_lines', None) self.vendor_body_lines = kwargs.get('vendor_body_lines', None) self.batch = kwargs.get('batch', None)
PypiClean
/JaqalPaq-1.2.0a1.tar.gz/JaqalPaq-1.2.0a1/examples/HeH+ (Helium Hydride)/JaqalPaq_HeH+_Untapered_Exemplar.ipynb
# Helium Hydride (Untapered HeH+) Exemplar ## Step 0: Import various libraries ``` # Imports for QSCOUT import jaqalpaq from jaqalpaq.core import circuitbuilder from jaqalpaq.run import run_jaqal_circuit from qscout.v1.std.jaqal_gates import ALL_GATES as std from qscout.v1.std import noisy # Imports for basic mathematical functionality from math import pi import numpy as np # Imports for OpenFermion(-PySCF) import openfermion as of from openfermion.chem import MolecularData from openfermionpyscf import run_pyscf # Import for VQE optimizer from scipy import optimize ``` # Step 1: SCF calculation to assmble the second-quantized Hamiltonian ``` # Set the basis set, spin, and charge of the H2 molecule basis = 'sto-3g' multiplicity = 1 charge = 1 #Charge is 1 for HeH+ # Set calculation parameters run_scf = 1 run_fci = 1 delete_input = True delete_output = False # Generate molecule at some bond length (0.8 Angstroms here) geometry = [('He', (0., 0., 0.)), ('H', (0., 0., 0.5))] molecule = MolecularData(geometry, basis, multiplicity, charge, filename='./HeH+_4_sto-3g_single_0.8') #Set file location of data # Run pyscf to generate new molecular data for sto-3g HeH+ molecule = run_pyscf(molecule, run_scf=run_scf, run_fci=run_fci, verbose=False) print("Bond Length in Angstroms: {}".format(0.8)) print("FCI (Exact) energy in Hartrees: {}".format(molecule.fci_energy)) ``` ## Step 2: Convert the fermionic Hamiltonian to a qubit Hamiltonian ``` # Get the fermionic Hamiltonian for HeH+ and map it using the BK encoding hamiltonian = molecule.get_molecular_hamiltonian() hamiltonian_ferm = of.get_fermion_operator(hamiltonian) hamiltonian_bk = of.bravyi_kitaev(hamiltonian_ferm) hamiltonian_jw = of.jordan_wigner(hamiltonian_ferm) terms = [] cs = [] for term in hamiltonian_jw.terms: paulis = [None, None, None, None] for pauli in term: paulis[pauli[0]] = pauli[1] terms += [paulis] cs += [hamiltonian_jw.terms[term]] ``` ## Step 3: Define UCC Ansatz circuit in JaqalPaq ``` def ansatz(theta, term): builder = circuitbuilder.CircuitBuilder(native_gates=std) # Create a qubit register q = builder.register('q', 4) # Define a hadamard macro hadamard = circuitbuilder.SequentialBlockBuilder() hadamard.gate('Sy', 'a') hadamard.gate('Px', 'a') builder.macro('hadamard', ['a'], hadamard) # Define a CNOT macro CNOT = circuitbuilder.SequentialBlockBuilder() CNOT.gate('Sy', 'control') CNOT.gate('MS', 'control', 'target', 0, np.pi/2) Sxd_block = CNOT.block(parallel=True) Sxd_block.gate('Sxd', 'control') Sxd_block.gate('Sxd', 'target') CNOT.gate('Syd', 'control') builder.macro('CNOT', ['control', 'target'], CNOT) # Prepare the Hartree Fock state builder.gate('prepare_all') builder.gate('Px', q[0]) builder.gate('Px', q[1]) # Apply the UCC Ansatz exp[-i*theta(X1 Y0)] builder.gate('hadamard', q[0]) builder.gate('hadamard', q[1]) builder.gate('hadamard', q[2]) builder.gate('Sxd', q[3]) builder.gate('CNOT', q[0], q[1]) builder.gate('CNOT', q[1], q[2]) builder.gate('CNOT', q[2], q[3]) builder.gate('Rz', q[3], theta) builder.gate('CNOT', q[2], q[3]) builder.gate('CNOT', q[1], q[2]) builder.gate('CNOT', q[0], q[1]) builder.gate('hadamard', q[0]) builder.gate('hadamard', q[1]) builder.gate('hadamard', q[2]) builder.gate('Sx', q[3]) # Change basis for measurement depending on term for j, qubit in enumerate(term): if qubit == 'X': builder.gate('hadamard', ('array_item', q, j)), if qubit == 'Y': builder.gate('Sxd', ('array_item', q, j)), builder.gate('measure_all') circuit = builder.build() return circuit ``` ## Step 4: Define functions to calculate energy expectation value of Ansatz state ``` def ansatz_sampling(theta, sample_noise): term_probs = [] for i in range(len(terms)): if sample_noise: probs = np.zeros(16) circuit = ansatz(theta, terms[i]) sim_result = run_jaqal_circuit(circuit) #Run circuit on emulator sim_probs = sim_result.subcircuits[0].probability_by_int sample = np.random.choice(16, size=n_samples, p=sim_probs) #Sample from distribution to get probabilities for count in sample: probs[count] += 1 #Increment state counter probs = probs/n_samples #Determine probabilities from sampling term_probs += [probs] #Combine lists of probs of each term in Hamiltonian else: #Exact solution without sampling circuit = ansatz(theta, terms[i]) sim_result = run_jaqal_circuit(circuit) #Run circuit on emulator sim_probs = sim_result.subcircuits[0].probability_by_int term_probs += [sim_probs] return term_probs # Calculate energy of one term of the Hamiltonian for one possible state def term_energy(term, state, coefficient, prob): parity = 1 for i in range(len(term)): #Change parity if state is occupied and is acted on by a pauli operator if term[i] != None and state[i] == '1': parity = -1*parity return coefficient*prob*parity # Calculate energy of the molecule for a given value of theta def calculate_energy(theta, sample_noise): energy = 0 probs = ansatz_sampling(theta[0], sample_noise) #Convert tuple (from optimization) to float for circuit for i in range(len(terms)): #For each term in the hamiltonian for j in range(len(probs[0])): #For each possible state term = terms[i] state = '{0:04b}'.format(j)[::-1] #convert state to binary (# of qubits) coefficient = cs[i].real prob = probs[i][j] #print(term, state, coefficient, prob) energy += term_energy(term, state, coefficient, prob) return energy ``` ## Step 5: Minimize the energy expectation value in 𝜃 ``` # Minimize the energy using classical optimization n_samples = 10000 optimize.minimize(fun=calculate_energy, x0=[0.01], args=(False), method="COBYLA") ``` ## Step 6: Loop over previous steps to calculate ground state energy at different bond lengths ``` # Set the basis set, spin, and charge of the HeH+ molecule basis = 'sto-3g' multiplicity = 1 charge = 1 # Set calculation parameters run_scf = 1 run_fci = 1 delete_input = True delete_output = False optimized_energies = [[], []] exact_energies = [] # Loop over bond lengths from 0.5 to 1.5 angstroms n_samples = 10000 # Sample circuit n_pts = 11 #Number of points bond_lengths = np.linspace(0.5,1.5,n_pts) for diatomic_bond_length in bond_lengths: # Generate molecule at some bond length geometry = [('He', (0., 0., 0.)), ('H', (0., 0., diatomic_bond_length))] description=str(round(diatomic_bond_length, 2)) molecule = MolecularData( geometry, basis, multiplicity, charge, description=description, filename='./HeH+_4_sto-3g_single_dissociation') # Run pyscf to generate new molecular data for sto-3g HeH+ molecule = run_pyscf(molecule, run_scf=run_scf, run_fci=run_fci, verbose=False) # Get the fermionic Hamiltonian for HeH+ and map it using the BK encoding hamiltonian = molecule.get_molecular_hamiltonian() hamiltonian_ferm = of.get_fermion_operator(hamiltonian) hamiltonian_jw = of.jordan_wigner(hamiltonian_ferm) hamiltonian_bk = of.bravyi_kitaev(hamiltonian_ferm) # Define terms and coefficients of our Hamiltonian terms = [] cs = [] for term in hamiltonian_jw.terms: paulis = [None, None, None, None] for pauli in term: paulis[pauli[0]] = pauli[1] terms += [paulis][::-1] cs += [hamiltonian_jw.terms[term]] # Minimize the expectation value of the energy using a classical optimizer (SPSA) exact_energies.append(molecule.fci_energy) print("R={}\t Exact Energy: {}".format(str(round(diatomic_bond_length, 2)), molecule.fci_energy)) for i in range(2): result = optimize.minimize(fun=calculate_energy, x0=[0.01], args=(i), method="COBYLA") optimized_energies[i].append(result.fun) print("R={}\t Optimized Energy: {}\t Sampling Noise: {}".format(str(round(diatomic_bond_length, 2)), result.fun, bool(i))) print('\n') import matplotlib import matplotlib.pyplot as pyplot # Plot the various energies for different bond lengths fig = pyplot.figure(figsize=(10,7)) pyplot.rcParams['font.size']=18 bkcolor = '#ffffff' ax = fig.add_subplot(1, 1, 1) pyplot.subplots_adjust(left=.2) ax.set_xlabel('R (Angstroms)') ax.set_ylabel(r'E (Hartrees)') ax.set_title(r'HeH+ 4-qubit bond dissociation curve') ax.spines['right'].set_visible(False) ax.spines['top'].set_visible(False) bond_lengths = [float(x) for x in bond_lengths] ax.plot(bond_lengths, optimized_energies[0], 'o', label='UCCSD', color='red') ax.plot(bond_lengths, optimized_energies[1], 'x', label='UCCSD with Sampling Noise', color='blue') ax.plot(bond_lengths, exact_energies, '-', label='Full-CI', color='black') ax.legend(frameon=False) pyplot.show() ```
PypiClean
/EntropyEncoding-0.0.4.tar.gz/EntropyEncoding-0.0.4/README.md
![EntropyEncoding logo](https://mauricelambert.github.io/info/python/security/EntropyEncoding.gif "EntropyEncoding logo") # EntropyEncoding ## Description This package implements an encoding to bypass entropy antivirus check. I have researched about entropy bypass techniques and found people who use adding low-entropy data to bypass entropy check. I think adding data can be optimized and more efficient with a simple entropy encoding to reduce entropy score. Adding low-entropy data: 1. you get a larger file 2. you do not change payload entropy (if the antivirus software splits the file for entropy calculation, it will probably have high entropy on a payload chunk) ## Requirements This package require: - python3 - python3 Standard Library ## Installation ```bash python3 -m pip install EntropyEncoding ``` ```bash git clone "https://github.com/mauricelambert/EntropyEncoding.git" cd "EntropyEncoding" python3 -m pip install . ``` ## Usages ```python from EntropyEncoding import * payload = b"shellcode_payload 0000111122223333444455556666777788889999AAAABBBBCCCCDDDDEEEEFFFF" * 120 key = bytes([0,255,127,55,155,25,225,10,220,40,190,26,100,70,90,45,235,32,64,128,215,28,46,158,123,13,8,5,168,191,69]) encrypted_payload = bytes([key[i % len(key)] ^ x for i, x in enumerate(payload)]) print(shannon_entropy(encrypted_payload)) # 7.753825816757683, good encryption or compression have an entropy score > 7.9 and < 8 # Malicious entropy is detected by antivirus software when entropy score is greater than ~= 7.2 # This encrypted payload will be detected as malicious entropy by antivirus software encoded_shellcode = entropy_encode(encrypted_payload) encoded2_shellcode = entropy_encode2(encrypted_payload) print(encoded_shellcode) print(encoded2_shellcode) assert entropy_decode(encoded_shellcode) == encrypted_payload assert entropy_decode2(encoded2_shellcode) == encrypted_payload print(shannon_entropy(encoded_shellcode)) # 5.770760744294572, entropy score is smaller than 7.2, antivirus software will not detect this payload with entropy checks print(shannon_entropy(encoded2_shellcode)) # 5.767383412620195, entropy score is smaller than 7.2, antivirus software will not detect this payload with entropy checks r""" I get entropy score from Windows executable, average score is ~= 5 (so 5.7 can be a legitimate entropy score): >>> from glob import iglob >>> from statistics import mean >>> from EntropyEncoding import * >>> entropy = [] >>> for a in iglob(r"C:\Windows\System32\*.exe"): entropy.append(shannon_entropy(open(a, "rb").read())) ... >>> max(entropy) 7.932014219115418 >>> min(entropy) 1.6379445326685684 >>> mean(entropy) 5.063622509688209 >>> """ ``` Tests results: ``` ~# python3 EntropyEncoding.py Entropy for non-encoded secrets: 4.521591372417719 Entropy for non-encoded encrypted secrets: 7.951320327821406 Entropy for entropy-encoded encrypted secrets: 5.774096152750044 Entropy for non-encoded exe: 5.22055339277441 Entropy for non-encoded encrypted exe: 7.914685739354301 Entropy for entropy-encoded encrypted exe: 5.759477906043907 ~# ``` ## Links - [Pypi](https://pypi.org/project/EntropyEncoding) - [Github](https://github.com/mauricelambert/EntropyEncoding) - [Documentation](https://mauricelambert.github.io/info/python/security/EntropyEncoding.html) ## License Licensed under the [GPL, version 3](https://www.gnu.org/licenses/).
PypiClean
/BitArray2D-2.1.tar.gz/BitArray2D-2.1/BitArray2D.py
__version__ = '2.1' __author__ = "Avinash Kak ([email protected])" __date__ = '2011-March-22' __url__ = 'http://RVL4.ecn.purdue.edu/~kak/dist2d/BitArray2D-2.1.html' __copyright__ = "(C) 2011 Avinash Kak. Python Software Foundation." __doc__ = ''' BitArray2D.py Version: ''' + __version__ + ''' Author: Avinash Kak ([email protected]) Date: ''' + __date__ + ''' @title CHANGE LOG: Version 2.1: BitArray2D is a renamed version of Bit2DArray. This name change was made in response to user requests. BitArray2D is Python 3.x compliant. It should work with both Python 2.x and Python 3.x. @title INSTALLATION: The BitArray2D class was packaged using Distutils. For installation, execute the following command-line in the source directory (this is the directory that contains the setup.py file after you have downloaded and uncompressed the tar archive): python setup.py install You have to have root privileges for this to work. On Linux distributions, this will install the module file at a location that looks like /usr/lib/python2.7/site-packages/ If you do not have root access, you have the option of working directly off the directory in which you downloaded the software by simply placing the following statements at the top of your scripts that use the BitArray2D class import sys sys.path.append( "pathname_to_BitArray2D_directory" ) To uninstall the module, simply delete the source directory, locate where BitArray2D was installed with "locate BitArray2D" and delete those files. As mentioned above, the full pathname to the installed version is likely to look like /usr/lib/python2.6/site-packages/BitArray2D* If you want to carry out a non-standard install of BitArray2D, look up the on-line information on Disutils by pointing your browser to http://docs.python.org/dist/dist.html @title INTRODUCTION: The BitArray2D class is for a memory-efficient packed representation of 2D bit arrays and for logical and other operations (such as blob dilations, erosions, etc.) on such arrays. The implementation of the class takes advantage of the facilities of the BitVector class for the memory representation and for the allowed operations. Operations supported on 2D bit arrays: __str__ __getitem__ __setitem__ __getslice__ __eq__ __ne__ __and__ __or__ __xor__ __invert__ deep_copy size read_bit_array_from_char_file read_bit_array_from_binary_file write_bit_array_to_char_file write_bit_array_to_packed_binary_file shift dilate erode @title CONSTRUCTING 2D BIT ARRAYS: You can construct a 2D bit array in four different ways: (1) You can construct a packed 2D bit array of all zeros by a call like ba = BitArray2D( rows = 20, columns = 10 ) This will create a 2D array of size 20x10. You can then set the individual bits in this array using syntax that is shown later in this documentation. The following call will return an empty BitArray2D instance: ba = BitArray2D( rows=0, columns=0 ) (2) You can construct a 2D bit array from a string in the following manner: ba = BitArray2D( bitstring = "111\n110\n011" ) This will create the following bit array in the memory: 111 110 011 There is no limit on the either the row size or the column size of the bit array created in this manner. However, the rows must all be of exactly the same size. An exception is thrown when that condition is violated. Note that even though you are supplying to the BitArray2D constructor a string made of ASCII 1's and 0's, the 2D bit array that is created is stored in a packed form. So a row with, say, sixteen 1's and/or 0's will be stored as just two bytes in the memory. So a 16x16 bit array will occupy only 32 bytes in the memory. (3) You can create a 2D bit array by reading the bits directly from a text file by calls that look like ba = BitArray2D( filename = "data.txt" ) ba.read_bit_array_from_char_file() You first have to create an empty BitArray2D instance, as in the first statement above, and then call the method read_bit_array_from_char_file() on the instance. Even though the text file supplies ASCII 1's and 0's, the internal representation of the bit array will be packed, as mentioned for the case (2) above. Note that when you create a bit array in this manner, the newline character in the text file is used as a row delimiter. (4) You can create a 2D bit array by reading the bits directly from a binary file through calls like: ba = BitArray2D( filename = "data_binary.dat" ) ba.read_bit_array_from_binary_file(rows = 5, cols = 8) Since you are creating a bit array from a binary file, you cannot designate any particular byte as a row delimiter. That's the reason for why you must now specify the number of rows and the number of columns to the read method in the second statement. If the number of bits in the binary file is less than what you need for the 2D bit array in the second statement above, an exception is thrown. To illustre creating a bit array by reading a file in the binary mode, assume that the file has the characters 'hello' in it and you read this file into a bit array by calling: ba = BitArray2D( filename = "hello_file.dat" ) ba.read_bit_array_from_binary_file(rows = 5, cols = 8) If you now say print ba you will see the following array displayed in your terminal window: 01101000 01100101 01101100 01101100 01101111 These are the ASCII representations of the characters 'h', 'e', 'l', 'l', and 'o'. @title OPERATIONS SUPPORTED BY THE BitArray2D CLASS: @title DISPLAYING BIT ARRAYS: (5) Since the BitArray2D class implements the __str__ method, a bit array can be displayed in a terminal window by print( ba ) where ba is an instance of BitArray2D. This will display in your terminal window the bit array ba, with each row of the array in a separate line. (Obviously, this is not what you would do for very large bit arrays. But, for diagnostic work, such displays can be very helpful.) You can always obtain the string representation of a bit array by str( ba ) In the string representation, the rows are separated by the newline character. @title ACCESSING AND SETTING INDIVIDUAL BITS AND SLICES: (6) You can access any individual bit of a 2D bit array by bit = ba[ godel(i,j) ] The call on the right will return the bit in the i-th row and the j-th column of the BitArray2D ba. This assumes that you have specifically imported the name 'godel' from the BitArray2D module. If that is not the case, the above call will look like bit = ba[ BitArray2D.godel(i,j) ] The function godel(a,b) is used to map a pair of integers a and b into a unique integer with the help of the Godel pairing formula. (7) Any single bit of a bit array ba at row index i and column index j can be set to 1 or 0 by ba[i,j] = 1_or_0 (8) A slice of a bit array, defined by the corner coordinates (i,j) and (k,l), can be retrieved by from BitArray2D import godel ba[ godel(i,j) : godel(k,l) ] In the implementation of the __getslice__ method that handles the above invocation, calls to ungodel(m) are used to recover the components i and j of a pair whose Godel map is m. To demonstrate the working of slice retrieval: ba1 = BitArray2D( bitstring = \ "111111\n110111\n111111\n111111\n111111\n111111" ) ba2 = ba3[godel(2,3) : godel(4,5)] print( ba4 ) yields 11 11 (9) You can also carry out slice assignment by using syntax like from BitArray2D import godel ba1[ godel(i,j) : godel(k,l) ] = ba2 where the 2D bit array ba1 is presumably larger than the 2D bit array ba2. The above call will replace the rectangular region of ba1 that is defined by the corner coordinates (i,j) and (k,l) by the bit array ba2, assuming that that the row width of ba2 is (k-i) and the column width (l-j). So in a call like ba1 = BitArray2D( bitstring = "101\n110\n111" ) # 101 # 110 # 111 ba2 = BitArray2D( rows = 5, columns = 5 ) # 00000 # 00000 # 00000 # 00000 # 00000 ba2[ godel(2, 2+ba2.rows) : godel(2,2+ba2.columns) ] = ba1 print( ba2 ) # 00000 # 00000 # 00101 # 00110 # 00111 (10) You can construct a deep copy of a bit array by ba2 = ba1.deep_copy() The bit array in ba2 will exactly the same as in ba1, except that the two bit arrays will be two different objects in the memory. @title LOGICAL OPERATIONS ON 2D BIT ARRAYS: (11) You can carry out all of the logical operations on 2D bit arrays: result_ba = ba1 & ba2 # for bitwise AND result_ba = ba1 | ba2 # for bitwise OR result_ba = ba1 ^ ba2 # for bitwise XOR result_ba = ~ ba # for bitwise negation @title COMPARING 2D BIT ARRAYS: (12) Given two 2D bit arrays, you can test for equality and inequality through the following boolean comparisons: ba1 == ba2 ba1 != ba2 @title OTHER SUPPORTED OPERATIONS: (13) You can shift a bit array array by ba.shift( rowshift = m, colshift = n ) where m is the number of positions row-wise by which you want to shift the array and the n the same column-wise. The values for m and n are allowed to be negative. A positive value for m will cause a bit array to shift downwards and a positive value for n to shift rightwards. What may make this method confusing at the beginning is the orientation of the positive row direction and the positive column direction. The origin of the array is at the upper left hand corner of your display. Rows are positive going downwards and columns are positive going rightwards: X-----> +ve col direction | | | V +ve row direction So a positive value for rowshift will shift the array downwards and a positive value for colshift will shift it rightwards. Just remember that if you want the shifts to seem more intuitive, use negative values for the rowshift argument. (14) In order to patch small holes, you can dilate the blobs made up of 1's that are connected through neighborhood relationship by calling dilate(): result_ba = ba.dilate( m ) The returned bit array is an OR of the bit arrays obtained by shifting ba by m positions in all four cardinal directions. (15) The opposite of dilate is erode. An erosion operation should shrink the blobs by the deletion of 1's that are at the boundary up to a depth determined by the argument supplied to erode(): result_ba = ba.erode( m ) Logically, the array returned by the above call is an AND of the the bit arrays obtained by shifting ba by m positions in each of the four cardinal directions. (16) You can write a bit array directly to a text file if you want the bits to be written out as ASCII 1's and 0's: ba.write_bit_array_to_char_file("out_file.txt") This can be a useful thing to do when you are playing with small to medium sized bit arrays. This call will deposit the newline character at the end of each row of the bit array. Subsequently, you can re-create the bit array in the memory by reading the file with the calls ba = BitArray2D( filename = "filename.txt" ) ba.read_bit_array_from_char_file() that were mentioned earlier in item (3) above. (17) You can write a bit array in its packed binary representation to a file (that would obviously be a binary file) by calling ba.write_bit_array_to_packed_binary_file("filename.dat") The overall size of bit array ba must be a multiple of 8 for this write function to work. If this condition is not met, the function will throw an exception. When writing an internally generated bit array out to a disk file, the implementation of the write function opens the file in the binary mode. This is particularly important on Windows machines since, if the file were to be opened in the text mode, the bit pattern 00001010 ('\\n') in a bit array will be written out as 0000110100001010 ('\\r\\n'). A binary file created by the above call can be read back into the memory by the calls shown in item (4) above: ba = BitArray2D( filename = "filename.dat" ) ba.read_bit_array_from_binary_file(rows = 5, cols = 8) As mentioned in (4) above, since no bytes can serve as row delimiters for binary files, you have to tell the read function how many rows and columns to read off the file. @title HOW A BIT ARRAY IS STORED: Through the facilities provided by the BitVector class, the bits of a bit array are stored in 16-bit unsigned ints. @title ABOUT THE AUTHOR: Avi Kak is the author of "Programming with Objects: A Comparative Presentation of Object-Oriented Programming with C++ and Java", published by John-Wiley in 2003. This book presents a new approach to the combined learning of two large object-oriented languages, C++ and Java. It is being used as a text in a number of educational programs around the world. This book has also been translated into Chinese. Avi Kak is also the author of "Scripting with Objects: A Comparative Presentation of Object-Oriented Scripting with Perl and Python," published in 2008 by John-Wiley. @title SOME EXAMPLE CODE: import BitArray2D from BitArray2D import godel print("\nConstructing an empty 2D bit array:") ba = BitArray2D.BitArray2D( rows=0, columns=0 ) print(ba) print("\nConstructing a bit array of size 10x10 with zero bits -- ba:") ba = BitArray2D.BitArray2D( rows = 10, columns = 10 ) print(ba) print("\nConstructing a bit array from a bit string -- ba2:") ba2 = BitArray2D.BitArray2D( bitstring = "111\n110\n111" ) print(ba2) print("\nPrint a specific bit in the array -- bit at 1,2 in ba2:") print( ba2[ godel(1,2) ] ) print("\nSet a specific bit in the array --- set bit (0,1) of ba2:") ba2[0,1] = 0 print(ba2) print("\nExperiments in slice getting and setting:") print("Printing an array -- ba3:") ba3 = BitArray2D.BitArray2D( bitstring = "111111\n110111\n111111\n111111\n111111\n111111" ) print(ba3) ba4 = ba3[godel(2,3) : godel(4,5)] print("Printing a slice of the larger array -- slice b4 of ba3:") print(ba4) ba5 = BitArray2D.BitArray2D( rows = 5, columns = 5 ) print("\nPrinting an array for demonstrating slice setting:") print(ba5) ba5[godel(2, 2+ba2.rows) : godel(2,2+ba2.columns)] = ba2 print("\nSetting a slice of the array - setting slice of ba5 to ba2:") print(ba5) print("\nConstructing a deep copy of ba, will call it ba6:") ba6 = ba.deep_copy() ba6[ godel(3,3+ba2.rows) : godel(3,3+ba2.columns) ] = ba2 print("Setting a slice of the larger array -- set slice of ba6 to ba2:") print(ba6) (For a more complete working example, see the example code in the BitArray2DDemo.py file in the Examples sub-directory.) ''' from BitVector import __version__ as bitvector_version if bitvector_version.split('.')[0] < '3': raise ImportError("The imported BitVector module must be of version 3.0 or higher") import BitVector import re class BitArray2D( object ): #(A1) def __init__( self, *args, **kwargs ): #(A2) if args: #(A3) raise ValueError( #(A4) '''BitArray2D constructor can only be called with keyword arguments for the following keywords: rows, columns, filename, bitstring)''') allowed_keys = 'bitstring','filename','rows','columns' #(A5) keywords_used = kwargs.keys() #(A6) for keyword in keywords_used: #(A7) if keyword not in allowed_keys: #(A8) raise ValueError("Wrong keyword used") #(A9) filename = rows = columns = bitstring = None #(A10) if 'filename' in kwargs : filename = kwargs.pop('filename') if 'rows' in kwargs : rows = kwargs.pop('rows') if 'columns' in kwargs : columns = kwargs.pop('columns') if 'bitstring' in kwargs : bitstring = kwargs.pop('bitstring') #(A11 -- A14) self.filename = None #(A15) self.rows = None #(A16) self.columns = None #(A17) self.bitstring = None #(A18) self.FILEIN = None #(A19) if filename: #(A20) if rows or columns or bitstring: #(A21) raise ValueError( '''When filename is specified, you cannot give values to any other constructor args''') #(A22) self.filename = filename #(A23) self.rowVectors = []; self.rows = 0; self.columns = 0 #(A24) import sys #(A25) try: #(A26) if sys.version_info[0] == 3: #(A27) self.FILEIN = open( filename, encoding='utf-8' )#(A28) else: #(A29) self.FILEIN = open( filename, 'rb' ) #(A30) except IOError as e: #(A31) print(e.strerror) #(A32) return #(A33) elif rows is not None and rows >= 0: #(A34) if filename or bitstring: #(A35) raise ValueError( '''When number of rows is specified, you cannot give values to any other constructor args except for columns''') #(A36) if not columns >= 0: #(A37) raise ValueError( '''When number of rows is specified, you must also specify a value for the number of columns''') #(A38) self.rows = rows; self.columns = columns #(A39) self.rowVectors = [ BitVector.BitVector( size = self.columns ) \ for i in range( self.rows ) ] #(A40) return #(A41) elif bitstring or bitstring == '': #(A42) self.rowVectors = [ BitVector.BitVector( bitstring = bits ) \ for bits in re.split( '\n', bitstring ) ] #(A43) self.rows = len( self.rowVectors ) #(A44) self.columns = self.rowVectors[0].length() #(A45) rowVecSizes = [ len(x) for x in self.rowVectors ] #(A46) if max( rowVecSizes ) != min( rowVecSizes ): #(A47) raise AttributeError("Your row sizes do not match") #(A48) def _add_row(self, bitvector): #(B1) if self.columns == 0: #(B2) self.columns = bitvector.length() #(B3) elif self.columns != bitvector.length(): #(B4) raise ValueError("Size wrong for the new row") #(B5) self.rowVectors.append( bitvector ) #(B6) self.rows += 1 #(B7) def __str__( self ): #(C1) 'To create a print representation' if self.rows==0 and self.columns==0: #(C2) return '' #(C3) return '\n'.join( map( str, self.rowVectors ) ) #(C4) def __getitem__( self, pos ): #(D1) 'Get the bit from the designated position' if not isinstance( pos, slice ): #(D2) row,col = ungodel(pos) #(D3) if row >= self.rows or row < -self.rows: #(D4) raise ValueError( "row index range error" ) #(D5) if col >= self.columns or col < -self.columns: #(D6) raise ValueError( "column index range error" ) #(D7) if row < 0: row = self.rows + row #(D8) if col < 0: col = self.columns + col #(D9) return self.rowVectors[row][col] #(D10) else: #(D11) if pos.start is None: #(D12) start = 0,0 #(D13) else: #(D14) start = ungodel(pos.start) #(D15) if pos.stop is None: #(D16) stop = self.rows,self.columns #(D17) else: #(D18) stop = ungodel(pos.stop) #(D19) result = BitArray2D( rows=0, columns=0 ) #(D20) for i in range( start[0], stop[0] ): #(D21) result._add_row( BitVector.BitVector( bitstring = \ str(self.rowVectors[i][start[1]:stop[1]])) ) #(D22) return result #(D23) def __setitem__(self, pos, item): #(E1) ''' This is needed for both slice assignments and for index-based assignments. It checks the type of pos and item to see if the call is for slice assignment. For slice assignment, the second argument must be of type slice '[m:n]' whose two numbers m and n are produced by calling godel() on the two corners of the rectangular regions whose values you want to set by calling this function. So for slice assignments, think of pos as consisting of '[(i,j):(k,l)]' where (i,j) defines one corner of the slice and (k,l) the other slice. As you would expect, for slice assignments, the argument item must of type BitArray2D. For index-based assignment, the pos consists of the tuple (i,j), the point in the array where you want to change the value. Again, for index-based assignment, the last argument will either be 1 or 0. ''' if (not isinstance( item, BitArray2D )): #(E2) if isinstance( pos, slice ): #(E3) raise ValueError("Second arg wrong for assignment") #(E4) i,j = pos #(E5) self.rowVectors[i][j] = item #(E6) # The following section is for slice assignment: if isinstance(pos,slice): #(E7) if (not isinstance( item, BitArray2D )): #(E8) raise TypeError('For slice assignment, \ the right hand side must be a BitArray2D') #(E9) arg1, arg2 = pos.start, pos.stop #(E10) i,j = ungodel(arg1) #(E11) k,l = ungodel(arg2) #(E12) for m in range(i,j): #(E13) self.rowVectors[m][k:l] = item.rowVectors[m-i] #(E14) def __getslice__(self, arg1, arg2): #(F1) ''' A slice of a 2D array is defined as a rectangular region whose one corner is at the (i,j) coordinates, which is represented by the mapped integer arg1 produced by calling godel(i,j). The other corner of the slice is at the coordinates (k,l) that is represented by the integer arg2 produced by calling godel(k,l). The slice is returned as a new BitArray2D instance. ''' i,j = ungodel(arg1) #(F2) k,l = ungodel(arg2) #(F3) sliceArray = BitArray2D( rows=0, columns=0 ) #(F4) if j > self.rows: j = self.rows #(F5) if l > self.columns: l = self.columns #(F6) for x in range(i,k): #(F7) bv = self.rowVectors[x] #(F8) sliceArray._add_row( bv[j:l] ) #(F9) return sliceArray #(F10) def __eq__(self, other): #(G1) if self.size() != other.size(): return False #(G2) if self.rowVectors != other.rowVectors: return False #(G3) return True #(G4) def __ne__(self, other): #(H1) return not self == other #(H2) def __and__(self, other): #(I1) ''' Take a bitwise 'AND' of the bit array on which the method is invoked with the argument bit array. Return the result as a new bit array. ''' if self.rows != other.rows or self.columns != other.columns: #(I2) raise ValueError("Arguments to AND must be of same size")#(I3) resultArray = BitArray2D(rows=0,columns=0) #(I4) list(map(resultArray._add_row, \ [self.rowVectors[i] & other.rowVectors[i] \ for i in range(self.rows)])) #(I5) return resultArray #(I6) def __or__(self, other): #(J1) ''' Take a bitwise 'OR' of the bit array on which the method is invoked with the argument bit array. Return the result as a new bit array. ''' if self.rows != other.rows or self.columns != other.columns: #(J2) raise ValueError("Arguments to OR must be of same size") #(J3) resultArray = BitArray2D(rows=0,columns=0) #(J4) list(map(resultArray._add_row, \ [self.rowVectors[i] | other.rowVectors[i] \ for i in range(self.rows)])) #(J5) return resultArray def __xor__(self, other): #(K1) ''' Take a bitwise 'XOR' of the bit array on which the method is invoked with the argument bit array. Return the result as a new bit array. ''' if self.rows != other.rows or self.columns != other.columns: #(K2) raise ValueError("Arguments to XOR must be of same size")#(K3) resultArray = BitArray2D(rows=0,columns=0) #(K4) list(map(resultArray._add_row, \ [self.rowVectors[i] ^ other.rowVectors[i] \ for i in range(self.rows)])) #(K5) return resultArray #(K6) def __invert__(self): #(L1) ''' Invert the bits in the bit array on which the method is invoked and return the result as a new bit array. ''' resultArray = BitArray2D(rows=0,columns=0) #(L2) list(map(resultArray._add_row, [~self.rowVectors[i] \ for i in range(self.rows)])) #(L3) return resultArray #(L4) def deep_copy(self): #(M1) 'Make a deep copy of a bit array' resultArray = BitArray2D(rows=0,columns=0) #(M2) list(map(resultArray._add_row, [x.deep_copy() \ for x in self.rowVectors])) #(M3) return resultArray #(M4) def size(self): #(N1) return self.rows, self.columns #(N2) def read_bit_array_from_char_file(self): #(P1) ''' This assumes that the bit array is stored in the form of ASCII characters 1 and 0 in a text file. We further assume that the different rows are separated by the newline character. ''' error_str = "You need to first construct a BitArray2D" + \ "instance with a filename as argument" #(P2) if not self.FILEIN: #(P3) raise SyntaxError( error_str ) #(P4) allbits = self.FILEIN.read() #(P5) rows = filter( None, re.split('\n', allbits) ) #(P6) list(map(self._add_row, [BitVector.BitVector( bitstring = x ) \ for x in rows])) #(P7) def write_bit_array_to_char_file(self, file_out): #(Q1) ''' Note that this write function for depositing a bit array into text file uses the newline as the row delimiter. ''' FILEOUT = open( file_out, 'w' ) #(Q2) for bitvec in self.rowVectors: #(Q3) FILEOUT.write( str(bitvec) + "\n" ) #(Q4) def read_bit_array_from_binary_file(self, rows, columns): #(R1) ''' This assumes that the bit array is stored in the form of ASCII characters 1 and 0 in a text file. We further assume that the different rows are separated by the newline character. ''' error_str = "You need to first construct a BitArray2D" + \ "instance with a filename as argument" #(R2) if not self.filename: #(R3) raise SyntaxError( error_str ) #(R4) import os.path #(R5) filesize = os.path.getsize( self.filename ) #(R6) if (rows * columns) % 8 != 0: #(R7) raise ValueError("In binary file input mode, rows*cols must" \ + " be a multiple of 8" ) #(R8) if filesize < int(rows*columns/8): #(R9) raise ValueError("File has insufficient bytes" ) #(R10) bitstring = '' #(R11) i = 0 #(R12) while i < rows*columns/8: #(R13) i += 1 #(R14) byte = self.FILEIN.read(1) #(R15) hexvalue = hex( ord( byte ) ) #(R16) hexvalue = hexvalue[2:] #(R17) if len( hexvalue ) == 1: #(R18) hexvalue = '0' + hexvalue #(R19) bitstring += BitVector._hexdict[ hexvalue[0] ] #(R20) bitstring += BitVector._hexdict[ hexvalue[1] ] #(R21) bv = BitVector.BitVector( bitstring = bitstring ) #(R22) list(map(self._add_row, [ bv[m*columns : m*columns+columns] \ for m in range(rows) ])) #(R23) def write_bit_array_to_packed_binary_file(self, file_out): #(S1) ''' This creates a packed disk storage for your bit array. But for this to work, the total number of bits in your bit array must be a multiple of 8 since all file I/O is byte oriented. Also note that now you cannot use any byte as a row delimiter. So when reading such a file back into a bit array, you have to tell the read function how many rows and columns to create. ''' err_str = '''Only a bit array whose total number of bits is a multiple of 8 can be written to a file.''' #(S2) if self.rows * self.columns % 8: #(S3) raise ValueError( err_str ) #(S4) FILEOUT = open( file_out, 'wb' ) #(S5) bitstring = '' #(S6) for bitvec in self.rowVectors: #(S7) bitstring += str(bitvec) #(S8) compositeBitVec = BitVector.BitVector(bitstring = bitstring) #(S9) compositeBitVec.write_to_file( FILEOUT ) #(S10) def shift( self, rowshift, colshift ): #(T1) ''' What may make this method confusing at the beginning is the orientation of the positive row direction and the positive column direction. The origin of the array is at the upper left hand corner of your display. Rows are positive going downwards and columns are positive going rightwards: X-----> +ve col direction | | | V +ve row direction So a positive value for rowshift will shift the array downwards and a positive value for colshift will shift it rightwards. Just remember that if you want the shifts to seem more intuitive, use negative values for the rowshift argument. ''' if rowshift >= 0: #(T2) self.rowVectors[rowshift : self.rows] = \ self.rowVectors[: self.rows-rowshift] #(T3) self.rowVectors[:rowshift] = \ [BitVector.BitVector(size = self.columns) \ for i in range(rowshift)] #(T4) if colshift >= 0: for bitvec in self.rowVectors[:]: \ bitvec.shift_right(colshift) #(T5) else: for bitvec in self.rowVectors[:]: #(T6) bitvec.shift_left(abs(colshift)) #(T7) else: #(T8) rowshift = abs(rowshift) #(T9) self.rowVectors[:self.rows-rowshift] = \ self.rowVectors[rowshift : self.rows] #(T10) self.rowVectors[self.rows-rowshift:] = \ [BitVector.BitVector(size = self.columns) \ for i in range(rowshift)] #(T11) if colshift >= 0: for bitvec in self.rowVectors[:]: \ bitvec.shift_right(colshift) #(T12) else: #(T13) for bitvec in self.rowVectors[:]: #(T14) bitvec.shift_left(abs(colshift)) #(T15) return self #(T16) def dilate( self, m ): #(U1) accumArray = BitArray2D(rows=self.rows, columns=self.columns)#(U2) for i in range(-m,m+1): #(U3) for j in range(-m,m+1): #(U4) temp = self.deep_copy() #(U5) accumArray |= temp.shift(i,j) #(U6) return accumArray #(U7) def erode( self, m ): #(V1) accumArray = BitArray2D(rows=self.rows, columns=self.columns)#(V2) for i in range(-m,m+1): #(V3) for j in range(-m,m+1): #(V4) temp = self.deep_copy() #(V5) accumArray &= temp.shift(i,j) #(V6) return accumArray #(V7) #------------------------ End of Class Definition ----------------------- #--------------------------- Ancillary Functions ------------------------ def godel(i,j): #(W1) return 2**i*(2*j + 1)-1 #(W2) def ungodel(m): #(X1) i,q = 0,m+1 #(X2) while not q&1: #(X3) q >>= 1 #(X4) i += 1 #(X5) j = ((m+1)/2**i - 1)/2 #(X6) return int(i),int(j) #(X7) #------------------------ Test Code Follows ----------------------- if __name__ == '__main__': print("\nConstructing an empty 2D bit array:") ba = BitArray2D( rows=0, columns=0 ) print(ba) print("\nConstructing a bit array of size 10x10 with zero bits -- ba:") ba = BitArray2D( rows = 10, columns = 10 ) print(ba) print("\nConstructing a bit array from a bit string -- ba2:") ba2 = BitArray2D( bitstring = "111\n110\n111" ) print(ba2) print("\nPrint a specific bit in the array -- bit at 1,2 in ba2:") print( ba2[ godel(1,2) ] ) print("\nSet a specific bit in the array --- set bit (0,1) of ba2:") ba2[0,1] = 0 print(ba2) print("\nExperiments in slice getting and setting:") print("Printing an array -- ba3:") ba3 = BitArray2D( bitstring = "111111\n110111\n111111\n111111\n111111\n111111" ) print(ba3) ba4 = ba3[godel(2,3) : godel(4,5)] print("Printing a slice of the larger array -- slice b4 of ba3:") print(ba4) ba5 = BitArray2D( rows = 5, columns = 5 ) print("\nPrinting an array for demonstrating slice setting:") print(ba5) ba5[godel(2, 2+ba2.rows) : godel(2,2+ba2.columns)] = ba2 print("\nSetting a slice of the array - setting slice of ba5 to ba2:") print(ba5) print("\nConstructing a deep copy of ba, will call it ba6:") ba6 = ba.deep_copy() ba6[ godel(3,3+ba2.rows) : godel(3,3+ba2.columns) ] = ba2 print("Setting a slice of the larger array -- set slice of ba6 to ba2:") print(ba6) print("\nExperiment in bitwise AND:") ba5 = ba.deep_copy() ba7 = ba5 & ba6 print("Displaying bitwise AND of ba5 and ba6 --- ba7:") print(ba7) print("\nExperiment in bitwise OR:") ba7 = ba5 | ba6 print("Displaying bitwise OR of ba5 and ba6 --- ba7:") print(ba7) print("\nExperiment in bitwise XOR:") ba7 = ba5 ^ ba6 print("Displaying bitwise XOR of ba5 and ba6 --- ba7:") print(ba7) print("\nExperiment in bitwise negation:") ba7 = ~ba5 print("Displaying bitwise negation of ba5 --- ba7:") print(ba7) print("\nSanity check (A & ~A => all zeros):") print(ba5 & ~ba5) print("\nConstruct bit array from a char file with ASCII 1's and 0's:" ) ba8 = BitArray2D( filename = "Examples/data.txt" ) ba8.read_bit_array_from_char_file() print("The bit array as read from the file -- ba8:") print(ba8) print("\nConstruct bit array from a packed binary file:") ba9 = BitArray2D( filename = "Examples/data_binary.dat" ) ba9.read_bit_array_from_binary_file(rows = 5, columns = 8) print("The bit array as read from the file -- ba9:") print("size of ba9: " + str(ba9.size())) print(ba9) print("\nTest the equality and inequality operators:") ba10 = BitArray2D( bitstring = "111\n110" ) ba11 = BitArray2D( bitstring = "111\n110" ) print("ba10 is equal to ba11 is: " + str(ba10 == ba11)) ba12 = BitArray2D( bitstring = "111\n111" ) print("ba10 is equal to ba12 is: " + str(ba10 == ba12)) print("\nTest shifting a bit array:") print("printing ba13:") ba13 = ba9.deep_copy() print(ba13) ba13.shift(rowshift=-2, colshift=2) print("The shifted version of ba9:") print(ba13) print("\nTest dilation:") ba14 = BitArray2D( filename = "Examples/data2.txt" ) ba14.read_bit_array_from_char_file() print("Array before dilation:") print(ba14) ba15= ba14.dilate(1) print("Array after dilation:") print(ba15) print("\nTest erosion:") ba16 = BitArray2D( filename = "Examples/data2.txt" ) ba16.read_bit_array_from_char_file() print("Array before erosion:") print(ba16) ba17= ba16.erode(1) print("Array after erosion:") print(ba17) print("\nExperiments with writing array to char file:") ba17.write_bit_array_to_char_file("out1.txt") print("\nExperiments with writing array to packed binary file:") ba9.write_bit_array_to_packed_binary_file("out2.dat")
PypiClean
/HNSC-classifier-1.0.tar.gz/HNSC-classifier-1.0/LICENSE.md
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PypiClean
/CatKit-0.5.4-py3-none-any.whl/catkit/hub/cathubsqlite.py
import sys from ase.db.sqlite import SQLite3Database import sqlite3 import json from past.utils import PY2 from tabulate import tabulate init_commands = [ """ CREATE TABLE publication ( id INTEGER PRIMARY KEY AUTOINCREMENT, pub_id text UNIQUE, title text, authors text, journal text, volume text, number text, pages text, year integer, publisher text, doi text, tags text );""", """CREATE TABLE publication_system ( ase_id text REFERENCES systems(unique_id), pub_id text REFERENCES publication(pub_id), PRIMARY KEY (pub_id, ase_id) );""", """CREATE TABLE reaction ( id INTEGER PRIMARY KEY AUTOINCREMENT, chemical_composition text, surface_composition text, facet text, sites text, coverages text, reactants text, products text, reaction_energy real, activation_energy real, dft_code text, dft_functional text, username text, pub_id text, FOREIGN KEY (pub_id) REFERENCES publication(pub_id) );""", """ CREATE TABLE reaction_system ( name text, energy_correction real, ase_id text, id integer, FOREIGN KEY (ase_id) REFERENCES systems(unique_id), FOREIGN KEY (id) REFERENCES reaction(id) );"""] class CathubSQLite: """Class for managing SQLite3 database for reaction energies, publications and atomic structures. Builds on top of the ASE database for atomic strucutres https://wiki.fysik.dtu.dk/ase/ase/db/db.html with four additional tables: publication: publication info publication_system: one-to-many mapping between publication table and systems table in ASE database reaction: reaction energies for surfaces reaction_system: mamy-to-many mapping between reaction table and systems table in ASE database Connect to a database object: db = CathubSQLite('yourdbfile.db') Set up a connection for several manipulations: with db as CathubSQLite('yourdbfile.db'): Do your work... Parameters ---------- filename : str name of database file """ def __init__(self, filename, stdin=sys.stdin, stdout=sys.stdout): assert filename.endswith('.db'), 'filename should have .db extension' self.filename = filename self.initialized = False self.default = 'NULL' self.connection = None self.stdin = stdin self.stdout = stdout def _connect(self): return sqlite3.connect(self.filename, timeout=600) def __enter__(self): """Set connection upon entry using with statement""" assert self.connection is None self.connection = self._connect() return self def __exit__(self, exc_type, exc_value, tb): """Commit changes upon exit""" if exc_type is None: self.connection.commit() else: self.connection.rollback() self.connection.close() self.connection = None def _initialize(self, con): """Set up tables in SQL""" if self.initialized: return SQLite3Database()._initialize(con) # ASE db initialization cur = con.execute( 'SELECT COUNT(*) FROM sqlite_master WHERE name="reaction"') if cur.fetchone()[0] == 0: # no reaction table for init_command in init_commands: con.execute(init_command) # Create tables con.commit() self.initialized = True def read(self, id, table='reaction'): """ Return an entire row of a table Parameters --------- id: int row integer table: str 'reaction', 'publication', 'publication_system', 'reaction_system' """ con = self.connection or self._connect() self._initialize(con) cur = con.cursor() cur.execute('SELECT * FROM \n {} \n WHERE \n {}.id={}'.format( table, table, id)) row = cur.fetchall() if len(row) == 14: # Old schema row = row.insert(5, 'None') return row def write_publication(self, values): """ Write publication info to db Parameters ---------- values: dict with entries {'pub_id': str (short name for publication), 'authors': list of str () 'journal': str, 'volume': str, 'number': str, 'pages': 'str' 'year': int, 'publisher': str, 'doi': str, 'tags': list of str} """ con = self.connection or self._connect() self._initialize(con) cur = con.cursor() values = (values['pub_id'], values['title'], json.dumps(values['authors']), values['journal'], values['volume'], values['number'], values['pages'], values['year'], values['publisher'], values['doi'], json.dumps(values['tags'])) q = self.default + ',' + ', '.join('?' * len(values)) cur.execute('INSERT OR IGNORE INTO publication VALUES ({})'.format(q), values) pid = self.get_last_id(cur, table='publication') if self.connection is None: con.commit() con.close() return pid def write(self, values, data=None): """ Write reaction info to db file Parameters ---------- values: dict The values dict can include: {'chemical_composition': str (chemical composition on empty slab) , 'surface_composition': str (reduced chemical composition or shortname), 'facet': str 'sites': dict adsorption sites of species. f.ex: {'OH': 'ontop', 'O': 'hollow'} 'coverages': dict coverage of adsorbates relative to the unit cell f.ex. {'OH': 0.25, 'O': 0.5}) 'reactants'/ 'products': dict keys with name of chemical species folloved by phase (gas, *) values are the prefactor in the reaction. For reaction H2Ogas -> 2Hstar + O star you would write: 'reactants': {OHstar: 1, Hstar: 2} 'products': {OHstar: 1, Hstar: 2} 'reaction_energy': float 'activation_energy': float 'dft_code': str 'dft_functional': str 'username': str 'pub_id': str Should match the pub_id of the corresponding publications } """ con = self.connection or self._connect() self._initialize(con) cur = con.cursor() pub_id = values['pub_id'] ase_ids = values['ase_ids'] energy_corrections = values['energy_corrections'] if ase_ids is not None: check_ase_ids(values, ase_ids) else: ase_ids = {} values = (values['chemical_composition'], values['surface_composition'], values['facet'], json.dumps(values['sites']), json.dumps(values['coverages']), json.dumps(values['reactants']), json.dumps(values['products']), values['reaction_energy'], values['activation_energy'], values['dft_code'], values['dft_functional'], values['username'], values['pub_id'] ) """ Write to reaction table""" q = self.default + ',' + ', '.join('?' * len(values)) cur.execute('INSERT INTO reaction VALUES ({})'.format(q), values) id = self.get_last_id(cur) reaction_structure_values = [] """ Write to publication_system and reaction_system tables""" for name, ase_id in ase_ids.items(): if name in energy_corrections: energy_correction = energy_corrections[name] else: energy_correction = 0 reaction_structure_values.append([name, energy_correction, ase_id, id]) insert_statement = """INSERT OR IGNORE INTO publication_system(ase_id, pub_id) VALUES (?, ?)""" cur.execute(insert_statement, [ase_id, pub_id]) cur.executemany('INSERT INTO reaction_system VALUES (?, ?, ?, ?)', reaction_structure_values) if self.connection is None: con.commit() con.close() return id def update(self, id, values, key_names='all'): """ Update reaction info for a selected row Parameters ---------- id: int row integer values: dict See write() method for details key_names: list or 'all' list with name of columns to update. Should match the keys-value pairs in values. default is 'all' """ con = self.connection or self._connect() self._initialize(con) cur = con.cursor() pub_id = values['pub_id'] ase_ids = values['ase_ids'] energy_corrections = values['energy_corrections'] if ase_ids is not None: check_ase_ids(values, ase_ids) else: ase_ids = {} key_list, value_list = get_key_value_list(key_names, values) N_keys = len(key_list) value_strlist = get_value_strlist(value_list) execute_str = ', '.join('{}={}'.format(key_list[i], value_strlist[i]) for i in range(N_keys)) update_command = 'UPDATE reaction SET {} WHERE id = {};'\ .format(execute_str, id) cur.execute(update_command) delete_command = 'DELETE from reaction_system WHERE id = {}'.format(id) cur.execute(delete_command) reaction_structure_values = [] for name, ase_id in ase_ids.items(): reaction_structure_values.append([name, energy_corrections.get(name), ase_id, id]) insert_statement = """INSERT OR IGNORE INTO publication_system(ase_id, pub_id) VALUES (?, ?)""" cur.execute(insert_statement, [ase_id, pub_id]) cur.executemany('INSERT INTO reaction_system VALUES (?, ?, ?, ?)', reaction_structure_values) if self.connection is None: con.commit() con.close() return id def get_last_id(self, cur, table='reaction'): """ Get the id of the last written row in table Parameters ---------- cur: database connection().cursor() object table: str 'reaction', 'publication', 'publication_system', 'reaction_system' Returns: id """ cur.execute("SELECT seq FROM sqlite_sequence WHERE name='{0}'" .format(table)) result = cur.fetchone() if result is not None: id = result[0] else: id = 0 return id def check(self, chemical_composition, reaction_energy): """ Check if entry with same surface and energy is allready written to database file Parameters ---------- chemcial_composition: str reaction_energy: str Returns id or None """ con = self.connection or self._connect() self._initialize(con) cur = con.cursor() statement = """SELECT reaction.id FROM reaction WHERE reaction.chemical_composition=? and reaction.reaction_energy=?""" argument = [chemical_composition, reaction_energy] cur.execute(statement, argument) rows = cur.fetchall() if len(rows) > 0: id = rows[0][0] else: id = None return id def check_reaction_on_surface(self, chemical_composition, reactants, products): """ Check if entry with same surface and reaction is allready written to database file Parameters ---------- chemcial_composition: str reactants: dict products: dict Returns id or None """ con = self.connection or self._connect() self._initialize(con) cur = con.cursor() statement = """SELECT reaction.id FROM reaction WHERE reaction.chemical_composition='{}' and reaction.reactants='{}' and reaction.products='{}';""".format(chemical_composition, json.dumps(reactants), json.dumps(products)) cur.execute(statement) rows = cur.fetchall() if len(rows) > 0: id = rows[0][0] else: id = None return id def check_publication(self, pub_id): con = self.connection or self._connect() self._initialize(con) cur = con.cursor() statement = """ SELECT id FROM publication WHERE publication.pub_id=?""" argument = [pub_id] cur.execute(statement, argument) rows = cur.fetchall() if len(rows) > 0: id = rows[0][0] else: id = None return id def check_publication_structure(self, pub_id, ase_id): con = self.connection or self._connect() self._initialize(con) cur = con.cursor() statement = """ SELECT id FROM publication_system WHERE publication.pub_id=? and publication.ase_id=?""" argument = [pub_id, ase_id] cur.execute(statement, argument) rows = cur.fetchall() if len(rows) > 0: id = rows[0][0] else: id = None return id def print_summary(self): self.stdout.write('------------------------------------------------\n') self.stdout.write('Reaction Summary: \n') self.stdout.write('------------------------------------------------\n') con = self.connection or self._connect() self._initialize(con) cur = con.cursor() cur.execute(""" SELECT surface_composition, reactants, products, reaction_energy, activation_energy, sites FROM reaction;""") rows = cur.fetchall() table = [] for row in rows: equation = get_equation(json.loads(row[1]), json.loads(row[2])) table += [[row[0], equation, row[3], row[4], row[5]]] headers = ['Surface Composition', 'Equation', 'Reaction Energy', 'Activation Energy', 'Sites'] self.stdout.write(tabulate(table, headers) + '\n') def check_ase_ids(values, ase_ids): ase_values = ase_ids.values() assert len(set(ase_values)) == len(ase_values), 'Duplicate ASE ids!' reaction_species = set(list(values['reactants'].keys()) + list(values['products'].keys())) n_split = 0 for spec in ase_ids.keys(): if '_' in spec: n_split += 1 assert len(reaction_species) <= len(ase_values) + n_split, \ 'ASE ids missing!' return def get_key_value_list(key_list, values, table='reaction'): total_keys = {'reaction': ['chemical_composition', 'surface_composition', 'facet', 'sites', 'coverages', 'reactants', 'products', 'reaction_energy', 'activation_energy', 'dft_code', 'dft_functional', 'username', 'pub_id'], 'publication': ['pub_id', 'title', 'authors', 'journal', 'volume', 'number', 'pages', 'year', 'publisher', 'doi', 'tags'], 'reaction_system': ['name', 'energy_correction', 'ase_id', 'id'], 'publication_system': ['ase_id, pub_id']} total_key_list = total_keys[table] if key_list == 'all': key_list = total_key_list else: for key in key_list: assert key in total_key_list value_list = [values[key] for key in key_list] return key_list, value_list def get_value_strlist(value_list): value_strlist = [] for v in value_list: if PY2: # python 2 if isinstance(v, unicode): v = v.encode('ascii', 'ignore') if isinstance(v, dict): v = json.dumps(v) value_strlist.append("'{}'".format(v)) elif isinstance(v, str): value_strlist.append("'{}'".format(v)) elif v is None or v == '': value_strlist.append("{}".format('NULL')) else: value_strlist.append("{}".format(v)) return value_strlist def get_equation(reactants, products): equation = '' arrow = 0 for column in (reactants, products): if arrow == 1: equation += ' -> ' arrow += 1 i = 0 for key in sorted(column, key=len, reverse=True): prefactor = column[key] if 'gas' in key: key = key.replace('gas', '(g)') if 'star' in key: key = key.replace('star', '*') if not i == 0: if prefactor > 0: equation += ' + ' else: equation += ' - ' prefactor *= -1 if prefactor == 1: prefactor = '' equation += str(prefactor) + key i += 1 return equation
PypiClean
/Klampt-0.9.0-cp36-cp36m-win_amd64.whl/klampt/math/symbolic_io.py
from .symbolic import * from .symbolic import _infix_operators,_prefix_operators,_builtin_functions from ..io import loader import json from json import encoder import weakref import sys import warnings VAR_PREFIX = '' USER_DATA_PREFIX = '$' NAMED_EXPRESSION_TAG = '#' NAMED_EXPRESSION_PREFIX = '@' _operator_precedence = {'pow':1, 'mul':2,'div':2.5, 'add':3,'sum':3,'sub':3.5, 'neg':4, 'not':5, 'and':6,'or':6, 'ge':7,'le':7,'eq':7,'ne':7} #just a helper class to do some duck-typing class _Object(object): pass if sys.version_info[0] == 2: def byteify(input): """Helpful for converting unicode values in JSON loaded objects to strings""" if isinstance(input, dict): return {byteify(key): byteify(value) for key, value in input.items()} elif isinstance(input, list): return [byteify(element) for element in input] elif isinstance(input, str): return input.encode('utf-8') else: return input else: def byteify(input): return input class _TaggedExpression(Expression): def __init__(self,name): self.name = name Expression.__init__(self) def indent(s,spaces): if spaces <= 0: return s return s.replace('\n','\n'+' '*spaces) def _prettyPrintExpr(expr,astr,parseCompatible): """Returns a string representing this expression, where astr is a list of strings representing each argument""" if not isinstance(expr,OperatorExpression): return exprToStr(expr,parseCompatible) if len(expr.functionInfo.printers) > 0: if parseCompatible and 'parse' in expr.functionInfo.printers: return expr.functionInfo.printers['parse'](expr,astr) if not parseCompatible and 'str' in expr.functionInfo.printers: return expr.functionInfo.printers['str'](expr,astr) if expr.functionInfo.name in _prefix_operators: prefix = _prefix_operators[expr.functionInfo.name] assert len(expr.args) == 1,"Weird, prefix operator %s has %d arguments? %s"%(expr.functionInfo.name,len(astr),",".join(astr)) return prefix + astr[0] if expr.functionInfo.name in _infix_operators: assert len(expr.args) == 2,"Weird, infix operator %s has %d arguments? %s"%(expr.functionInfo.name,len(astr),",".join(astr)) return astr[0] + _infix_operators[expr.functionInfo.name] + astr[1] if expr.functionInfo.name == 'setitem': vconst = to_const(expr.args[0]) iconst = to_const(expr.args[1]) if vconst is not None and iconst is not None: if hasattr(iconst,'__iter__'): indexset = set(iconst) if parseCompatible: astr[0] = '[' + ','.join(['0' if i in indexset else str(v) for i,v in enumerate(vconst)])+']' else: astr[0] = '[' + ','.join(['*' if i in indexset else str(v) for i,v in enumerate(vconst)])+']' if expr.functionInfo.name == 'getitem': if isinstance(expr.args[0],OperatorExpression) and astr[0][0] != '(' and expr.args[0].functionInfo.name in _infix_operators: astr[0] = '(' + astr[0] + ')' #if expr.functionInfo.name == 'getslice': # if len(astr) <= 2: # astr.append('') # if len(astr) <= 3: # astr.append('') # return astr[0] + '[%s:%s:%s]'%(astr[1],astr[2],astr[3]) if isinstance(expr.args[1],slice): start,stop,step = expr.args[1].start,expr.args[1].stop,expr.args[1].step astr[1] = "%s:%s%s"%(("" if start is None else str(start)), ("" if (stop is None or stop > 900000000000) else str(stop)), ("" if step is None else ":"+str(step))) return astr[0] + '[' +astr[1] + ']' #default if len(astr) > 1 and sum(len(a) for a in astr) > 80-2-len(expr.functionInfo.name): res = expr.functionInfo.name + "(" res += ',\n '.join([indent(a,2) for a in astr]) + ')' else: res = expr.functionInfo.name + "(" res += ','.join(astr) + ')' return res def _make_tagged(expr,prefix="SubExp"): """Creates a copy of expr where each reference to a common subexpression is replaced with a TaggedExpression. If there are no common subexpressions, expr is returned.""" def _refspre(node): if 'refs' in node._cache: node._cache['refs'] += 1 return (False,True,node._cache['refs']) node._cache['refs'] = 1 return (True,True,None) expr._traverse(pre=_refspre,cache=False) #all the cache values are now the number of references to a subexpression def _hassubexpr_pre(node): if node._cache['refs'] > 1: #print "Node",node.functionInfo.name,"is a repeated subexpression" node._cache['hassubexpr'] = True return (False,True,True) return (True,True,None) def _hassubexpr_post(node,cvals): if len(cvals) == 0: return (True,False) res = any(cvals) #print "Child of",node.functionInfo.name,"has repeated subexpression" node._cache['hassubexpr'] = res if res: return (True,True) return (True,False) if not expr._traverse(pre=_hassubexpr_pre,post=_hassubexpr_post,cache=False): #print "***Expression has no subexpressions***" expr._clearCache('refs') expr._clearCache('hassubexpr') return expr assert expr._cache.get('hassubexpr',False) == True expr._clearCache('refs') #print "***Expression has subexpressions***" subexprs = dict() def replace(node): if not node._cache.get('hassubexpr',False): return node if 'refs' in node._cache: if 'id' not in node._cache: #new detected subexpression, not added yet tag = prefix+str(len(subexprs)+1) node._cache['id'] = tag subexprs[tag] = _TaggedExpression(tag) node._cache['refs'] += 1 #print "Reference",node._cache['refs'],"to",node.functionInfo.name return subexprs[node._cache['id']] node._cache['refs'] = 1 if node._children is None: return node else: assert isinstance(node,OperatorExpression) #print "New reference to",node.functionInfo.name creps = [replace(c) for c in node._children] if any(cr is not c for (cr,c) in zip(creps,node._children)): return OperatorExpression(node.functionInfo,creps,node.op) else: return node repl = replace(expr) expr._clearCache('refs') expr._clearCache('hassubexpr') #NEED TO CLEAR 'id' from cache after repl is used return repl def _to_jsonobj(val): if isinstance(val,(bool,int,float)): return val elif isinstance(val,(np.ndarray,np.float64)): return val.tolist() elif isinstance(val,(list,tuple)): return [_to_jsonobj(x) for x in val] else: try: return loader.toJson(val) except: raise ValueError("Unable to convert object "+repr(val)+" to JSON object") return None def _json_complex(jsonval): if isinstance(jsonval,dict): return (len(jsonval) > 0) elif isinstance(jsonval,(list,tuple)): return any(_json_complex(v) for v in jsonval) else: return False def _json_depth(jsonval): if isinstance(jsonval,dict): return 1 + max(_json_depth(v) for v in jsonval.values()) elif isinstance(jsonval,(list,tuple)): return 1 + max(_json_depth(v) for v in jsonval) else: return 1 def exprToStr(expr,parseCompatible=True,expandSubexprs='auto'): """Converts an Expression to a printable or parseable string. Args: expr (Expression): the Expression to convert parseCompatible (bool, optional): if True, the result is readable via exprFromStr() expandSubexprs (str or bool, optional): whether to expand subexpressions. Can be: * 'auto': if parseCompatible, equivalent to False. if parseCompatible=False, equivalent to True. * True: expands all common subexpressions * False: does not expand common subexpressions. * 'show': Internally used. Returns: (str): a printable or parsable string representing expr. """ if isinstance(expr,ConstantExpression): if isinstance(expr.value,slice): start,stop,step = expr.value.start,expr.value.stop,expr.value.step return "%s:%s%s"%(("" if start is None else str(start)), ("" if (stop is None or stop > 900000000000) else str(stop)), ("" if step is None else ":"+str(step))) try: jsonval = _to_jsonobj(expr.value) except: return str(expr.value) if parseCompatible: return json.dumps(jsonval) else: #Note: DOESNT WORK IN Python 3 #original_float_repr = encoder.FLOAT_REPR encoder.FLOAT_REPR = lambda o:format(o,'.14g') try: if _json_complex(jsonval): res = json.dumps(jsonval,sort_keys=True, indent=4, separators=(',', ': ')) else: res = json.dumps(jsonval,sort_keys=True) except Exception: print("Unable to dump constant expression",expr.value,"of type",expr.value.__class__.__name__) def print_recursive(v,indent=0): if hasattr(v,'__iter__'): print(indent*' ',"Sub objects have type",[a.__class__.__name__ for a in v]) for a in v: print_recursive(a,indent+2) print_recursive(expr.value) return "___JSON_ENCODE_ERROR___" #encoder.FLOAT_REPR = original_float_repr return res elif isinstance(expr,VariableExpression): if parseCompatible: return VAR_PREFIX+expr.var.name else: return str(expr.var) elif isinstance(expr,UserDataExpression): return USER_DATA_PREFIX+expr.name elif isinstance(expr,OperatorExpression): if expandSubexprs == 'auto': expandSubexprs = not parseCompatible if expandSubexprs: astr = [] for i,a in enumerate(expr.args): a._parent = (weakref.ref(expr),i) astr.append(exprToStr(a,parseCompatible,expandSubexprs)) if not isinstance(a,OperatorExpression) and expandSubexprs == 'show' and ('id' in a._cache or 'name' in a._cache): #tagged subexprs need parenthesies if astr[-1][-1] != ')': astr[-1] = '('+astr[-1]+')' astr[-1] = astr[-1] + NAMED_EXPRESSION_TAG + a._cache.get('id',a._cache.get('name')) a._parent = None res = _prettyPrintExpr(expr,astr,parseCompatible) if expandSubexprs == 'show' and ('id' in expr._cache or 'name' in expr._cache): #tagged subexprs need parenthesies if res[-1] != ')': res = '('+res+')' return res + NAMED_EXPRESSION_TAG + expr._cache.get('id',expr._cache.get('name')) oldparent = expr._parent iscomplex = expr.depth() >= 0 and (expr.functionInfo.name in _operator_precedence) expr._parent = oldparent if iscomplex and (expr._parent is not None and not isinstance(expr._parent,str)): if parseCompatible: return '(' + res + ')' else: parent = expr._parent[0]() if parent.functionInfo.name in _operator_precedence: expr_precedence = _operator_precedence[expr.functionInfo.name] parent_precedence = _operator_precedence[parent.functionInfo.name] #if - is the first in a summation, don't parenthesize it if expr._parent[1] == 0 and expr.functionInfo.name == 'neg' and parent.functionInfo.name in ['sum','add','sub']: return res if expr_precedence > parent_precedence: return '(' + res + ')' if expr_precedence == parent_precedence: if expr.functionInfo is parent.functionInfo and expr.functionInfo.properties.get('associative',False): return res else: return '(' + res + ')' return res else: if not parseCompatible: taggedexpr = _make_tagged(expr,"") else: taggedexpr = _make_tagged(expr) res = exprToStr(taggedexpr,parseCompatible,'show') if taggedexpr is not expr: expr._clearCache('id',deep=True) return res elif isinstance(expr,_TaggedExpression): return NAMED_EXPRESSION_PREFIX+expr.name elif is_const(expr): return str(expr) else: raise ValueError("Unknown type "+expr.__class__.__name__) def exprFromStr(context,string,fmt=None,add=False): """Returns an Expression from a string. In auto mode, this reads in constants in klampt.loader JSON- compatible format, standard variables in the form "x", user data in the form of strings prepended with $ (e.g., "$x"), and named expression references in the form of strings prepended with @. Args: context (Context): the context containing possible functions in string string (str): the string to parse. fmt (str, optional): specifies a format for the string. Can be None (auto), 'auto', or 'json' add (bool, optional): if true, adds all variables referenced in the string to the context. Otherwise, undefined variables are referred to as user data. An exception is raised on parsing failure. (Parsing is a little slow, so try not to use it in tight inner loops) Returns: (Expression): the expression represented by str. """ if len(string) == 0: raise ValueError("Empty string provided") if fmt == None: if string[0] == '{': fmt = 'json' else: fmt = 'auto' if fmt == 'auto': import re,ast USERDATA_MARKER = '___' EXPR_MARKER = '____' TAGLIST_NAME = '__tagexprlist__' taglist = context.expressions.copy() def __settag__(self,tagname,taglist): assert isinstance(tagname,ConstantExpression) and isinstance(tagname.value,str) taglist[tagname.value] = self return self def __gettag__(tagname,taglist): assert isinstance(tagname,ConstantExpression) and isinstance(tagname.value,str) return taglist[tagname.value] Expression.__settag__ = __settag__ x = re.sub(r"\$(\w+)", r"___\1",string) x = re.sub(r"\#(\w+)", r'.__settag__("\1",__tagexprlist__)',x) x = re.sub(r"\@(\w+)", r'__gettag__("\1",__tagexprlist__)',x) #print "Substituted string",x tree = ast.parse(x,mode='eval') missing_functions = [] missing_names = [] userdata = {} #hack to easily access functions with the class.attribute syntax allFunctions = _builtin_functions.copy() for name,func in context.customFunctions.items(): path = name.split('.') if len(path) == 1: allFunctions[name] = func else: if path[0] not in allFunctions: allFunctions[path[0]] = _Object() root = allFunctions[path[0]] for n in path[1:-1]: if not hasattr(root,n): setattr(root,n,_Object()) root = getattr(root,n) setattr(root,path[-1],func) allFunctions[TAGLIST_NAME] = taglist allFunctions['__gettag__'] = __gettag__ class RewriteVarNames(ast.NodeTransformer): def __init__(self): self.infunc = False def visit_Call(self,node): self.infunc = True self.generic_visit(node) return node def visit_Name(self, node): if self.infunc: self.infunc = False if node.id not in allFunctions: missing_functions.append(node.id) return node if node.id.startswith(USERDATA_MARKER): basename = node.id[len(USERDATA_MARKER):] userdata[node.id] = expr(basename) else: if node.id in context.variableDict: userdata[node.id] = expr(context.variableDict[node.id]) elif add: userdata[node.id] = expr(context.addVar(node.id,'N')) elif node.id == TAGLIST_NAME: pass else: missing_names.append(node.id) userdata[node.id] = expr(node.id) return node def visit_Num(self, node): return ast.copy_location(ast.Call(func=ast.copy_location(ast.Name(id="_const",ctx=ast.Load()),node),args=[node],keywords=[]),node) def visit_Str(self, node): return ast.copy_location(ast.Call(func=ast.copy_location(ast.Name(id="_const",ctx=ast.Load()),node),args=[node],keywords=[]),node) def visit_List(self, node): args = [] for idx, item in enumerate(node.elts): args.append(self.visit(item)) return ast.copy_location(ast.Call(func=ast.copy_location(ast.Name(id="_convert_list",ctx=ast.Load()),node),args=args,keywords=[]),node) def visit_Tuple(self, node): args = [] for idx, item in enumerate(node.elts): args.append(self.visit(item)) return ast.copy_location(ast.Call(func=ast.copy_location(ast.Name(id="_convert_list",ctx=ast.Load()),node),args=args,keywords=[]),node) #print "old tree:",ast.dump(tree) newtree = RewriteVarNames().visit(tree) #print "new tree:",ast.dump(newtree) if len(missing_functions) > 0: raise ValueError("Undefined functions "+','.join(missing_functions)) if len(missing_names) > 0: raise ValueError("Undefined variable "+','.join(missing_names)) allFunctions['_const'] = const allFunctions['_convert_list'] = lambda *args:array(*args) ctree = compile(newtree, filename="<ast>", mode="eval") res = eval(ctree,allFunctions,userdata) delattr(Expression,'__settag__') return res elif fmt == 'json': import json obj = json.parse(str) return exprFromJson(context,obj) else: raise ValueError("Invalid format "+fmt) def exprToJson(expr): if isinstance(expr,ConstantExpression): return _to_jsonobj(expr.value) elif isinstance(expr,UserDataExpression): return USER_DATA_PREFIX+expr.name elif isinstance(expr,VariableExpression): return VAR_PREFIX+expr.var.name elif isinstance(expr,OperatorExpression): def _tojson(node,childvals): if isinstance(node,OperatorExpression): res = {"type":expr.functionInfo.name} res["args"] = childvals if 'id' in node._cache: res['id'] = node._cache['id'] return True,res else: return True,exprToJson(node) taggedexpr = _make_tagged(expr) res = taggedexpr._traverse(post=_tojson,cacheas='json') if taggedexpr is not expr: expr._clearCache('id',deep=True) return res elif isinstance(expr,_TaggedExpression): return NAMED_EXPRESSION_PREFIX+expr.name def exprFromJson(context,jsonObj,taggedExpressions=None): """Creates an Expression from a JSON object previously saved by expr.toJson()""" #print "exprFromJson:",jsonObj name = str(jsonObj['type']) args = jsonObj['args'] parsedArgs = [] if taggedExpressions is None: taggedExpressions = dict() for a in args: if isinstance(a,str): if a.startswith(USER_DATA_PREFIX): #user data reference plen = len(USER_DATA_PREFIX) parsedArgs.append(context.userData[a[plen:]]) elif a.startswith(NAMED_EXPRESSION_PREFIX): plen = len(NAMED_EXPRESSION_PREFIX) a = a[plen:] if a in taggedExpressions: parsedArgs.append(taggedExpressions[a]) elif a in context.expressions: parsedArgs.append(context.expressions[a]) else: print("exprFromJson(): Valid tags:",list(taggedExpressions.keys()),"(tags)",list(context.expressions.keys()),"(expressions)") raise RuntimeError("Invalid expression tag "+NAMED_EXPRESSION_PREFIX+a) else: #variable reference if a not in context.variableDict: raise RuntimeError("Invalid variable reference "+a) parsedArgs.append(context.variableDict[a]) elif isinstance(a,dict): #assume it's an expression or a loader object try: parsedArgs.append(exprFromJson(context,a,taggedExpressions)) except KeyError: try: parsedArgs.append(loader.fromJson(a)) except Exception: raise ValueError("Error parsing JSON object %s into expression or loader object"%(str(a),)) if 'id' in a: assert a['id'] not in taggedExpressions,"Multiply defined tag "+str(a['id']) taggedExpressions[a['id']] = parsedArgs[-1] else: parsedArgs.append(a) if name in _builtin_functions: return _builtin_functions[name](*parsedArgs) if name in context.customFunctions: return context.customFunctions[name](*parsedArgs) raise RuntimeError("Invalid expression type "+name) def typeToJson(type): res = { 'char':type.char } if type.size is not None: res['size'] = type.size if type.subtype is not None: if isinstance(type.subtype,str): res['subtype'] = type.subtype elif isinstance(type.subtype,list): res['subtype'] = [typeToJson(st) for st in type.subtype] else: res['subtype'] = typeToJson(type.subtype) return res def typeFromJson(jsonObj): assert 'char' in jsonObj st = None if 'subtype' in jsonObj: subtypeobj = jsonObj['subtype'] if isinstance(subtypeobj,list): st = [typeFromJson(stobj) for stobj in subtypeobj] elif isinstance(subtypeobj,str): st = subtypeobj elif isinstance(subtypeobj,dict): st = typeFromJson(subtypeobj) else: raise ValueError("Invalid JSON object specifying Type subtype") return Type(byteify(jsonObj['char']),jsonObj.get('size',None),st) def contextToJson(ctx,saveFunctions=False): """Produces a JSON object from a context. Only the names for userData and customFunctions are saved. If saveFunctions=False, customFunctions are not saved""" res = {} if len(ctx.variables) > 0: varjson = [] for v in ctx.variables: varjson.append({'name':v.name,'type':typeToJson(v.type)}) res['variables'] = varjson if len(ctx.expressions) > 0: exprjson = {} for n,e in ctx.expressions.items(): exprjson[n] = exprToJson(e) res['expressions'] = exprjson if saveFunctions and len(ctx.customFunctions) > 0: res['customFunctions'] = list(ctx.customFunctions.keys()) if len(ctx.userData) > 0: res['userData'] = list(ctx.userData.keys()) return res def contextFromJson(context,jsonObj): """Creates a context from a JSON object previously saved by context.toJson(). userData is not restored and customFunctions are not restored, but rather, userData and customFunctions are assumed to have been set up with exactly the same keys as when toJson was called. Modifies context in-place. """ if 'userData' in jsonObj: for d in jsonObj['userData']: if d not in context.userData: warnings.warn("Context.fromJson(): item {} is not yet in userData".format(d)) if 'customFunctions' in jsonObj: for d in jsonObj['customFunctions']: if d not in context.customFunctions: warnings.warn("Context.fromJson(): item {} is not yet in customFunctions".format(d)) context.variables = [] context.variableDict = dict() context.expressions = dict() if 'variables' in jsonObj: for v in jsonObj['variables']: context.addVar(v['name'],typeFromJson(v['type'])) if 'expressions' in jsonObj: for n,v in jsonObj['expressions'].items(): context.expressions[n] = exprFromJson(context,v) return context def toStr(obj,parseCompatible=True): if not isinstance(obj,Expression): raise ValueError("Can only convert Expressions to strings") return exprToStr(obj,parseCompatible) def toJson(obj): if isinstance(obj,Expression): return exprToJson(obj) elif isinstance(obj,Context): return contextToJson(obj) else: raise ValueError("Argument needs to be an Expression or Context") def latex(expr): """Returns LaTeX code for the Expression expr. Requires Sympy.""" try: import sympy from . import symbolic_sympy except ImportError as e: raise e raise RuntimeError("Sympy is required for conversion to latex") return sympy.latex(symbolic_sympy.exprToSympy(expr)) def pprint(expr): """Pretty-prints the Expression expr. If Sympy is installed it will use the sympy pretty-printer.""" try: import sympy from . import symbolic_sympy sympy.pprint(symbolic_sympy.exprToSympy(expr),use_unicode=False) except ImportError: print(exprToStr(expr,parseCompatible=False)) except TypeError: print(exprToStr(expr,parseCompatible=False)) except ValueError: print(exprToStr(expr,parseCompatible=False)) def codegen(name_expr,language=None,**options): """Similar to sympy.codegen. Generates one or more expressions in the target language. Requires Sympy. Args: name_expr: multiple interpretations: * A single (name, Expression) tuple: generates code for one function * A list of (name, Expression) tuples: generates code for multiple functions * one or more Function objects: generates code for one or more functions, as long as the Function is defined via symbolic Expressions rather than Python functions. * A list of (Variable == Expression) expressions. Generates a function with multiple return values language (str, optional): any language accepted by Sympy. options: other options for sympy.codegen. See the `Sympy codegen documentation <http://docs.sympy.org/latest/modules/utilities/codegen.html>`_ for more information. """ try: import sympy from . import symbolic_sympy from sympy.utilities.codegen import codegen except ImportError: raise RuntimeError("Sympy is required for codegen") def convert(ne): if isinstance(ne,Function): if not isinstance(ne.func,Expression): raise ValueError("Can't do code generation for plain Python function %s"%(ne.name,)) sexpr = symbolic_sympy.exprToSympy(ne.expr) return (ne.name,sexpr) if not isinstance(ne,(list,tuple)) or len(ne)!=2 or not isinstance(ne[0],str): raise ValueError("Input must be a (str,Expression) pair.") name,expr_or_exprs = ne sexpr = None if not isinstance(expr_or_exprs,Expression): if not isinstance(expr_or_exprs,(list,tuple)): raise ValueError("Input must consist of one or more (str,Expression) pairs.") sexpr = [] for expr in expr_or_exprs: sexpr.append(symbolic_sympy.exprToSympy(expr)) else: sexpr = symbolic_sympy.exprToSympy(expr_or_exprs) return name,sexpr if hasattr(name_expr,'__iter__') and isinstance(name_expr[0],(list,tuple)): s_name_expr = [convert(x) for x in name_expr] else: s_name_expr = convert(name_expr) return codegen(s_name_expr,language=language,**options)
PypiClean
/Fom-0.9.10.zip/Fom-0.9.10/fom/db.py
import types import urllib import requests try: import json except ImportError: try: import simplejson as json except ImportError: # For Google AppEngine from django.utils import simplejson as json from errors import raise_error from utils import fom_request_sent, fom_response_received from version import version BASE_URL = 'https://fluiddb.fluidinfo.com' NO_CONTENT = object() PRIMITIVE_CONTENT_TYPE = 'application/vnd.fluiddb.value+json' DESERIALIZABLE_CONTENT_TYPES = set( (PRIMITIVE_CONTENT_TYPE, 'application/json')) ITERABLE_TYPES = set((list, tuple)) SERIALIZABLE_TYPES = set((types.NoneType, bool, int, float, str, unicode, list, tuple)) def _generate_endpoint_url(base, path, urlargs): path_parts = [base] for part in path: if isinstance(part, unicode): part = part.encode('utf-8') path_parts.append(urllib.quote(part, safe='')) url = '/'.join(path_parts) if urlargs: if isinstance(urlargs, dict): # convert the dict to tuple pairs urlargs = tuple(urlargs.items()) # make sure we handle unicode characters as possible values # NOTE: only use UTF-8 unicode for urlargs values. Anything else will # break. clean_urlargs = [] for (tag, value) in urlargs: if isinstance(value, unicode): clean_urlargs.append((tag, value.encode('utf-8'))) else: clean_urlargs.append((tag, value)) urlargs = tuple(clean_urlargs) url = '?'.join([url, urllib.urlencode(urlargs)]) return url def _get_body_and_type(payload, content_type): if content_type: if content_type == 'application/json': return json.dumps(payload), content_type return payload, content_type if payload is NO_CONTENT: return None, None if isinstance(payload, dict): return json.dumps(payload), 'application/json' pt = type(payload) if pt in SERIALIZABLE_TYPES: if pt in ITERABLE_TYPES: if not all(isinstance(x, basestring) for x in payload): raise ValueError('Non-string in list payload %r.' % (payload,)) return json.dumps(payload), PRIMITIVE_CONTENT_TYPE raise ValueError("Can't handle payload %r of type %s" % (payload, pt)) class FluidResponse(object): """A response to a FluidDB request. These are generally created by the API, and returned, and there is little use to create them manually. :param response: A response instance, which is a dict with an additional status attribute. :param content: The body of the HTTP response. :param is_value: A boolean flag to indicate whether the response is from a *value* request. Value requests are not deserialized unless they are of the primitive content type: `application/vnd.fluiddb.value+json` even if they are of a deserializable content type such as `application/json` .. attribute:: content_type The content type of the response. .. attribute:: value The deserialized value of the response body, if it is appropriate for deserialization. .. attribute:: content The raw content of the response body. .. attribute:: request_id The request id of the response. This is only available during errors. .. attribute:: error The error from the response. This is only available during errors. """ def __init__(self, response, content, is_value): self.content_type = response.headers['content-type'] if ((is_value and self.content_type == PRIMITIVE_CONTENT_TYPE) or (self.content_type in DESERIALIZABLE_CONTENT_TYPES)): try: self.value = json.loads(content) except ValueError: self.value = content else: self.value = content self.status = response.status_code self.response = response self.content = content self.request_id = self.response.headers.get('x-fluiddb-request-id') self.error = self.response.headers.get('x-fluiddb-error-class') if self.status >= 400: raise_error(self) def __repr__(self): return '<FluidResponse (%s, %r, %r, %r)>' % (self.status, self.content_type, self.error, self.value) __str__ = __repr__ # XXX Backwards Compatibility layer def __iter__(self): print 'Depravacamated use of status, response' yield self.status yield self.value class FluidDB(object): """HTTP client. Could/Should be swapped out for other implementations. Although is generally synchronous. :param base_url: The base FluidDB url to use. Currently, this can only be either the main FluidDB instance, or the sandbox instance. """ def __init__(self, base_url=BASE_URL): if base_url.endswith('/'): raise ValueError('The domain for FluidDB must *not* end with'\ ' "/". Correct example:'\ ' https://fluiddb.fluidinfo.com') self.base_url = base_url self.headers = { 'User-agent': 'fom/%s' % version, } self.session = requests.session(headers=self.headers) # XXX Backwards compat self.client = self def __call__(self, method, path, payload=NO_CONTENT, urlargs=None, content_type=None, is_value=False): """Make a request and return a response. >>> db = FluidDB() >>> r = db('GET', '/users/aliafshar') >>> print r.value {u'name': u'aliafshar', u'id': u'11e00b96-e346-44e7-af7f-e1a3575ff43e'} :param method: The HTTP method :param path: The path to make the request to :param payload: The body of the request :param urlargs: URL arguments to be applied to the request :param content_type: The content type of the payload :param is_value: A boolean flag to indicate whether the response is from a *value* request. Value requests are not deserialized unless they are of the primitive content type: `application/vnd.fluiddb.value+json` even if they are of a deserializable content type such as `application/json` """ payload, content_type = _get_body_and_type(payload, content_type) urlargs = urlargs or {} headers = self._get_headers(content_type) url = self._get_url(path, urlargs) fom_request_sent.send(self, request=(url, method, payload, headers)) response = self.session.request(method, url, data=payload, headers=headers) fom_response_received.send(self, response=(response.status_code, response.text, None)) return FluidResponse(response, response.text, is_value) def _get_headers(self, content_type): headers = self.headers.copy() if content_type: headers['content-type'] = content_type return headers def _get_url(self, path, urlargs=None): return _generate_endpoint_url(self.base_url, path, urlargs) def login(self, username, password): """Log in to this instance of FluidDB :param username: The username to log in with. :param password: The password to log in with. """ userpass = username + ':' + password auth = 'Basic ' + userpass.encode('base64').strip() self.headers['Authorization'] = auth def login_oauth2(self, token): """Prepare to make OAuth2 calls to Fluidinfo. :param token: The OAuth token to pass in calls to Fluidinfo. """ self.headers['Authorization'] = 'oauth2' self.headers['X-FluidDB-Access-Token'] = token def logout(self): """Log out of this FluidDB instance """ # Use pop here, to avoid catching KeyError if login was never called. self.headers.pop('Authorization', None) self.headers.pop('X-FluidDB-Access-Token', None)
PypiClean
/Nuitka_fixed-1.1.2-cp310-cp310-win_amd64.whl/nuitka/build/inline_copy/yaml_27/yaml/emitter.py
__all__ = ['Emitter', 'EmitterError'] from error import YAMLError from events import * class EmitterError(YAMLError): pass class ScalarAnalysis(object): def __init__(self, scalar, empty, multiline, allow_flow_plain, allow_block_plain, allow_single_quoted, allow_double_quoted, allow_block): self.scalar = scalar self.empty = empty self.multiline = multiline self.allow_flow_plain = allow_flow_plain self.allow_block_plain = allow_block_plain self.allow_single_quoted = allow_single_quoted self.allow_double_quoted = allow_double_quoted self.allow_block = allow_block class Emitter(object): DEFAULT_TAG_PREFIXES = { u'!' : u'!', u'tag:yaml.org,2002:' : u'!!', } def __init__(self, stream, canonical=None, indent=None, width=None, allow_unicode=None, line_break=None): # The stream should have the methods `write` and possibly `flush`. self.stream = stream # Encoding can be overriden by STREAM-START. self.encoding = None # Emitter is a state machine with a stack of states to handle nested # structures. self.states = [] self.state = self.expect_stream_start # Current event and the event queue. self.events = [] self.event = None # The current indentation level and the stack of previous indents. self.indents = [] self.indent = None # Flow level. self.flow_level = 0 # Contexts. self.root_context = False self.sequence_context = False self.mapping_context = False self.simple_key_context = False # Characteristics of the last emitted character: # - current position. # - is it a whitespace? # - is it an indention character # (indentation space, '-', '?', or ':')? self.line = 0 self.column = 0 self.whitespace = True self.indention = True # Whether the document requires an explicit document indicator self.open_ended = False # Formatting details. self.canonical = canonical self.allow_unicode = allow_unicode self.best_indent = 2 if indent and 1 < indent < 10: self.best_indent = indent self.best_width = 80 if width and width > self.best_indent*2: self.best_width = width self.best_line_break = u'\n' if line_break in [u'\r', u'\n', u'\r\n']: self.best_line_break = line_break # Tag prefixes. self.tag_prefixes = None # Prepared anchor and tag. self.prepared_anchor = None self.prepared_tag = None # Scalar analysis and style. self.analysis = None self.style = None def dispose(self): # Reset the state attributes (to clear self-references) self.states = [] self.state = None def emit(self, event): self.events.append(event) while not self.need_more_events(): self.event = self.events.pop(0) self.state() self.event = None # In some cases, we wait for a few next events before emitting. def need_more_events(self): if not self.events: return True event = self.events[0] if isinstance(event, DocumentStartEvent): return self.need_events(1) elif isinstance(event, SequenceStartEvent): return self.need_events(2) elif isinstance(event, MappingStartEvent): return self.need_events(3) else: return False def need_events(self, count): level = 0 for event in self.events[1:]: if isinstance(event, (DocumentStartEvent, CollectionStartEvent)): level += 1 elif isinstance(event, (DocumentEndEvent, CollectionEndEvent)): level -= 1 elif isinstance(event, StreamEndEvent): level = -1 if level < 0: return False return (len(self.events) < count+1) def increase_indent(self, flow=False, indentless=False): self.indents.append(self.indent) if self.indent is None: if flow: self.indent = self.best_indent else: self.indent = 0 elif not indentless: self.indent += self.best_indent # States. # Stream handlers. def expect_stream_start(self): if isinstance(self.event, StreamStartEvent): if self.event.encoding and not getattr(self.stream, 'encoding', None): self.encoding = self.event.encoding self.write_stream_start() self.state = self.expect_first_document_start else: raise EmitterError("expected StreamStartEvent, but got %s" % self.event) def expect_nothing(self): raise EmitterError("expected nothing, but got %s" % self.event) # Document handlers. def expect_first_document_start(self): return self.expect_document_start(first=True) def expect_document_start(self, first=False): if isinstance(self.event, DocumentStartEvent): if (self.event.version or self.event.tags) and self.open_ended: self.write_indicator(u'...', True) self.write_indent() if self.event.version: version_text = self.prepare_version(self.event.version) self.write_version_directive(version_text) self.tag_prefixes = self.DEFAULT_TAG_PREFIXES.copy() if self.event.tags: handles = self.event.tags.keys() handles.sort() for handle in handles: prefix = self.event.tags[handle] self.tag_prefixes[prefix] = handle handle_text = self.prepare_tag_handle(handle) prefix_text = self.prepare_tag_prefix(prefix) self.write_tag_directive(handle_text, prefix_text) implicit = (first and not self.event.explicit and not self.canonical and not self.event.version and not self.event.tags and not self.check_empty_document()) if not implicit: self.write_indent() self.write_indicator(u'---', True) if self.canonical: self.write_indent() self.state = self.expect_document_root elif isinstance(self.event, StreamEndEvent): if self.open_ended: self.write_indicator(u'...', True) self.write_indent() self.write_stream_end() self.state = self.expect_nothing else: raise EmitterError("expected DocumentStartEvent, but got %s" % self.event) def expect_document_end(self): if isinstance(self.event, DocumentEndEvent): self.write_indent() if self.event.explicit: self.write_indicator(u'...', True) self.write_indent() self.flush_stream() self.state = self.expect_document_start else: raise EmitterError("expected DocumentEndEvent, but got %s" % self.event) def expect_document_root(self): self.states.append(self.expect_document_end) self.expect_node(root=True) # Node handlers. def expect_node(self, root=False, sequence=False, mapping=False, simple_key=False): self.root_context = root self.sequence_context = sequence self.mapping_context = mapping self.simple_key_context = simple_key if isinstance(self.event, AliasEvent): self.expect_alias() elif isinstance(self.event, (ScalarEvent, CollectionStartEvent)): self.process_anchor(u'&') self.process_tag() if isinstance(self.event, ScalarEvent): self.expect_scalar() elif isinstance(self.event, SequenceStartEvent): if self.flow_level or self.canonical or self.event.flow_style \ or self.check_empty_sequence(): self.expect_flow_sequence() else: self.expect_block_sequence() elif isinstance(self.event, MappingStartEvent): if self.flow_level or self.canonical or self.event.flow_style \ or self.check_empty_mapping(): self.expect_flow_mapping() else: self.expect_block_mapping() else: raise EmitterError("expected NodeEvent, but got %s" % self.event) def expect_alias(self): if self.event.anchor is None: raise EmitterError("anchor is not specified for alias") self.process_anchor(u'*') self.state = self.states.pop() def expect_scalar(self): self.increase_indent(flow=True) self.process_scalar() self.indent = self.indents.pop() self.state = self.states.pop() # Flow sequence handlers. def expect_flow_sequence(self): self.write_indicator(u'[', True, whitespace=True) self.flow_level += 1 self.increase_indent(flow=True) self.state = self.expect_first_flow_sequence_item def expect_first_flow_sequence_item(self): if isinstance(self.event, SequenceEndEvent): self.indent = self.indents.pop() self.flow_level -= 1 self.write_indicator(u']', False) self.state = self.states.pop() else: if self.canonical or self.column > self.best_width: self.write_indent() self.states.append(self.expect_flow_sequence_item) self.expect_node(sequence=True) def expect_flow_sequence_item(self): if isinstance(self.event, SequenceEndEvent): self.indent = self.indents.pop() self.flow_level -= 1 if self.canonical: self.write_indicator(u',', False) self.write_indent() self.write_indicator(u']', False) self.state = self.states.pop() else: self.write_indicator(u',', False) if self.canonical or self.column > self.best_width: self.write_indent() self.states.append(self.expect_flow_sequence_item) self.expect_node(sequence=True) # Flow mapping handlers. def expect_flow_mapping(self): self.write_indicator(u'{', True, whitespace=True) self.flow_level += 1 self.increase_indent(flow=True) self.state = self.expect_first_flow_mapping_key def expect_first_flow_mapping_key(self): if isinstance(self.event, MappingEndEvent): self.indent = self.indents.pop() self.flow_level -= 1 self.write_indicator(u'}', False) self.state = self.states.pop() else: if self.canonical or self.column > self.best_width: self.write_indent() if not self.canonical and self.check_simple_key(): self.states.append(self.expect_flow_mapping_simple_value) self.expect_node(mapping=True, simple_key=True) else: self.write_indicator(u'?', True) self.states.append(self.expect_flow_mapping_value) self.expect_node(mapping=True) def expect_flow_mapping_key(self): if isinstance(self.event, MappingEndEvent): self.indent = self.indents.pop() self.flow_level -= 1 if self.canonical: self.write_indicator(u',', False) self.write_indent() self.write_indicator(u'}', False) self.state = self.states.pop() else: self.write_indicator(u',', False) if self.canonical or self.column > self.best_width: self.write_indent() if not self.canonical and self.check_simple_key(): self.states.append(self.expect_flow_mapping_simple_value) self.expect_node(mapping=True, simple_key=True) else: self.write_indicator(u'?', True) self.states.append(self.expect_flow_mapping_value) self.expect_node(mapping=True) def expect_flow_mapping_simple_value(self): self.write_indicator(u':', False) self.states.append(self.expect_flow_mapping_key) self.expect_node(mapping=True) def expect_flow_mapping_value(self): if self.canonical or self.column > self.best_width: self.write_indent() self.write_indicator(u':', True) self.states.append(self.expect_flow_mapping_key) self.expect_node(mapping=True) # Block sequence handlers. def expect_block_sequence(self): indentless = (self.mapping_context and not self.indention) self.increase_indent(flow=False, indentless=indentless) self.state = self.expect_first_block_sequence_item def expect_first_block_sequence_item(self): return self.expect_block_sequence_item(first=True) def expect_block_sequence_item(self, first=False): if not first and isinstance(self.event, SequenceEndEvent): self.indent = self.indents.pop() self.state = self.states.pop() else: self.write_indent() self.write_indicator(u'-', True, indention=True) self.states.append(self.expect_block_sequence_item) self.expect_node(sequence=True) # Block mapping handlers. def expect_block_mapping(self): self.increase_indent(flow=False) self.state = self.expect_first_block_mapping_key def expect_first_block_mapping_key(self): return self.expect_block_mapping_key(first=True) def expect_block_mapping_key(self, first=False): if not first and isinstance(self.event, MappingEndEvent): self.indent = self.indents.pop() self.state = self.states.pop() else: self.write_indent() if self.check_simple_key(): self.states.append(self.expect_block_mapping_simple_value) self.expect_node(mapping=True, simple_key=True) else: self.write_indicator(u'?', True, indention=True) self.states.append(self.expect_block_mapping_value) self.expect_node(mapping=True) def expect_block_mapping_simple_value(self): self.write_indicator(u':', False) self.states.append(self.expect_block_mapping_key) self.expect_node(mapping=True) def expect_block_mapping_value(self): self.write_indent() self.write_indicator(u':', True, indention=True) self.states.append(self.expect_block_mapping_key) self.expect_node(mapping=True) # Checkers. def check_empty_sequence(self): return (isinstance(self.event, SequenceStartEvent) and self.events and isinstance(self.events[0], SequenceEndEvent)) def check_empty_mapping(self): return (isinstance(self.event, MappingStartEvent) and self.events and isinstance(self.events[0], MappingEndEvent)) def check_empty_document(self): if not isinstance(self.event, DocumentStartEvent) or not self.events: return False event = self.events[0] return (isinstance(event, ScalarEvent) and event.anchor is None and event.tag is None and event.implicit and event.value == u'') def check_simple_key(self): length = 0 if isinstance(self.event, NodeEvent) and self.event.anchor is not None: if self.prepared_anchor is None: self.prepared_anchor = self.prepare_anchor(self.event.anchor) length += len(self.prepared_anchor) if isinstance(self.event, (ScalarEvent, CollectionStartEvent)) \ and self.event.tag is not None: if self.prepared_tag is None: self.prepared_tag = self.prepare_tag(self.event.tag) length += len(self.prepared_tag) if isinstance(self.event, ScalarEvent): if self.analysis is None: self.analysis = self.analyze_scalar(self.event.value) length += len(self.analysis.scalar) return (length < 128 and (isinstance(self.event, AliasEvent) or (isinstance(self.event, ScalarEvent) and not self.analysis.empty and not self.analysis.multiline) or self.check_empty_sequence() or self.check_empty_mapping())) # Anchor, Tag, and Scalar processors. def process_anchor(self, indicator): if self.event.anchor is None: self.prepared_anchor = None return if self.prepared_anchor is None: self.prepared_anchor = self.prepare_anchor(self.event.anchor) if self.prepared_anchor: self.write_indicator(indicator+self.prepared_anchor, True) self.prepared_anchor = None def process_tag(self): tag = self.event.tag if isinstance(self.event, ScalarEvent): if self.style is None: self.style = self.choose_scalar_style() if ((not self.canonical or tag is None) and ((self.style == '' and self.event.implicit[0]) or (self.style != '' and self.event.implicit[1]))): self.prepared_tag = None return if self.event.implicit[0] and tag is None: tag = u'!' self.prepared_tag = None else: if (not self.canonical or tag is None) and self.event.implicit: self.prepared_tag = None return if tag is None: raise EmitterError("tag is not specified") if self.prepared_tag is None: self.prepared_tag = self.prepare_tag(tag) if self.prepared_tag: self.write_indicator(self.prepared_tag, True) self.prepared_tag = None def choose_scalar_style(self): if self.analysis is None: self.analysis = self.analyze_scalar(self.event.value) if self.event.style == '"' or self.canonical: return '"' if not self.event.style and self.event.implicit[0]: if (not (self.simple_key_context and (self.analysis.empty or self.analysis.multiline)) and (self.flow_level and self.analysis.allow_flow_plain or (not self.flow_level and self.analysis.allow_block_plain))): return '' if self.event.style and self.event.style in '|>': if (not self.flow_level and not self.simple_key_context and self.analysis.allow_block): return self.event.style if not self.event.style or self.event.style == '\'': if (self.analysis.allow_single_quoted and not (self.simple_key_context and self.analysis.multiline)): return '\'' return '"' def process_scalar(self): if self.analysis is None: self.analysis = self.analyze_scalar(self.event.value) if self.style is None: self.style = self.choose_scalar_style() split = (not self.simple_key_context) #if self.analysis.multiline and split \ # and (not self.style or self.style in '\'\"'): # self.write_indent() if self.style == '"': self.write_double_quoted(self.analysis.scalar, split) elif self.style == '\'': self.write_single_quoted(self.analysis.scalar, split) elif self.style == '>': self.write_folded(self.analysis.scalar) elif self.style == '|': self.write_literal(self.analysis.scalar) else: self.write_plain(self.analysis.scalar, split) self.analysis = None self.style = None # Analyzers. def prepare_version(self, version): major, minor = version if major != 1: raise EmitterError("unsupported YAML version: %d.%d" % (major, minor)) return u'%d.%d' % (major, minor) def prepare_tag_handle(self, handle): if not handle: raise EmitterError("tag handle must not be empty") if handle[0] != u'!' or handle[-1] != u'!': raise EmitterError("tag handle must start and end with '!': %r" % (handle.encode('utf-8'))) for ch in handle[1:-1]: if not (u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z' \ or ch in u'-_'): raise EmitterError("invalid character %r in the tag handle: %r" % (ch.encode('utf-8'), handle.encode('utf-8'))) return handle def prepare_tag_prefix(self, prefix): if not prefix: raise EmitterError("tag prefix must not be empty") chunks = [] start = end = 0 if prefix[0] == u'!': end = 1 while end < len(prefix): ch = prefix[end] if u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z' \ or ch in u'-;/?!:@&=+$,_.~*\'()[]': end += 1 else: if start < end: chunks.append(prefix[start:end]) start = end = end+1 data = ch.encode('utf-8') for ch in data: chunks.append(u'%%%02X' % ord(ch)) if start < end: chunks.append(prefix[start:end]) return u''.join(chunks) def prepare_tag(self, tag): if not tag: raise EmitterError("tag must not be empty") if tag == u'!': return tag handle = None suffix = tag prefixes = self.tag_prefixes.keys() prefixes.sort() for prefix in prefixes: if tag.startswith(prefix) \ and (prefix == u'!' or len(prefix) < len(tag)): handle = self.tag_prefixes[prefix] suffix = tag[len(prefix):] chunks = [] start = end = 0 while end < len(suffix): ch = suffix[end] if u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z' \ or ch in u'-;/?:@&=+$,_.~*\'()[]' \ or (ch == u'!' and handle != u'!'): end += 1 else: if start < end: chunks.append(suffix[start:end]) start = end = end+1 data = ch.encode('utf-8') for ch in data: chunks.append(u'%%%02X' % ord(ch)) if start < end: chunks.append(suffix[start:end]) suffix_text = u''.join(chunks) if handle: return u'%s%s' % (handle, suffix_text) else: return u'!<%s>' % suffix_text def prepare_anchor(self, anchor): if not anchor: raise EmitterError("anchor must not be empty") for ch in anchor: if not (u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z' \ or ch in u'-_'): raise EmitterError("invalid character %r in the anchor: %r" % (ch.encode('utf-8'), anchor.encode('utf-8'))) return anchor def analyze_scalar(self, scalar): # Empty scalar is a special case. if not scalar: return ScalarAnalysis(scalar=scalar, empty=True, multiline=False, allow_flow_plain=False, allow_block_plain=True, allow_single_quoted=True, allow_double_quoted=True, allow_block=False) # Indicators and special characters. block_indicators = False flow_indicators = False line_breaks = False special_characters = False # Important whitespace combinations. leading_space = False leading_break = False trailing_space = False trailing_break = False break_space = False space_break = False # Check document indicators. if scalar.startswith(u'---') or scalar.startswith(u'...'): block_indicators = True flow_indicators = True # First character or preceded by a whitespace. preceeded_by_whitespace = True # Last character or followed by a whitespace. followed_by_whitespace = (len(scalar) == 1 or scalar[1] in u'\0 \t\r\n\x85\u2028\u2029') # The previous character is a space. previous_space = False # The previous character is a break. previous_break = False index = 0 while index < len(scalar): ch = scalar[index] # Check for indicators. if index == 0: # Leading indicators are special characters. if ch in u'#,[]{}&*!|>\'\"%@`': flow_indicators = True block_indicators = True if ch in u'?:': flow_indicators = True if followed_by_whitespace: block_indicators = True if ch == u'-' and followed_by_whitespace: flow_indicators = True block_indicators = True else: # Some indicators cannot appear within a scalar as well. if ch in u',?[]{}': flow_indicators = True if ch == u':': flow_indicators = True if followed_by_whitespace: block_indicators = True if ch == u'#' and preceeded_by_whitespace: flow_indicators = True block_indicators = True # Check for line breaks, special, and unicode characters. if ch in u'\n\x85\u2028\u2029': line_breaks = True if not (ch == u'\n' or u'\x20' <= ch <= u'\x7E'): if (ch == u'\x85' or u'\xA0' <= ch <= u'\uD7FF' or u'\uE000' <= ch <= u'\uFFFD') and ch != u'\uFEFF': unicode_characters = True if not self.allow_unicode: special_characters = True else: special_characters = True # Detect important whitespace combinations. if ch == u' ': if index == 0: leading_space = True if index == len(scalar)-1: trailing_space = True if previous_break: break_space = True previous_space = True previous_break = False elif ch in u'\n\x85\u2028\u2029': if index == 0: leading_break = True if index == len(scalar)-1: trailing_break = True if previous_space: space_break = True previous_space = False previous_break = True else: previous_space = False previous_break = False # Prepare for the next character. index += 1 preceeded_by_whitespace = (ch in u'\0 \t\r\n\x85\u2028\u2029') followed_by_whitespace = (index+1 >= len(scalar) or scalar[index+1] in u'\0 \t\r\n\x85\u2028\u2029') # Let's decide what styles are allowed. allow_flow_plain = True allow_block_plain = True allow_single_quoted = True allow_double_quoted = True allow_block = True # Leading and trailing whitespaces are bad for plain scalars. if (leading_space or leading_break or trailing_space or trailing_break): allow_flow_plain = allow_block_plain = False # We do not permit trailing spaces for block scalars. if trailing_space: allow_block = False # Spaces at the beginning of a new line are only acceptable for block # scalars. if break_space: allow_flow_plain = allow_block_plain = allow_single_quoted = False # Spaces followed by breaks, as well as special character are only # allowed for double quoted scalars. if space_break or special_characters: allow_flow_plain = allow_block_plain = \ allow_single_quoted = allow_block = False # Although the plain scalar writer supports breaks, we never emit # multiline plain scalars. if line_breaks: allow_flow_plain = allow_block_plain = False # Flow indicators are forbidden for flow plain scalars. if flow_indicators: allow_flow_plain = False # Block indicators are forbidden for block plain scalars. if block_indicators: allow_block_plain = False return ScalarAnalysis(scalar=scalar, empty=False, multiline=line_breaks, allow_flow_plain=allow_flow_plain, allow_block_plain=allow_block_plain, allow_single_quoted=allow_single_quoted, allow_double_quoted=allow_double_quoted, allow_block=allow_block) # Writers. def flush_stream(self): if hasattr(self.stream, 'flush'): self.stream.flush() def write_stream_start(self): # Write BOM if needed. if self.encoding and self.encoding.startswith('utf-16'): self.stream.write(u'\uFEFF'.encode(self.encoding)) def write_stream_end(self): self.flush_stream() def write_indicator(self, indicator, need_whitespace, whitespace=False, indention=False): if self.whitespace or not need_whitespace: data = indicator else: data = u' '+indicator self.whitespace = whitespace self.indention = self.indention and indention self.column += len(data) self.open_ended = False if self.encoding: data = data.encode(self.encoding) self.stream.write(data) def write_indent(self): indent = self.indent or 0 if not self.indention or self.column > indent \ or (self.column == indent and not self.whitespace): self.write_line_break() if self.column < indent: self.whitespace = True data = u' '*(indent-self.column) self.column = indent if self.encoding: data = data.encode(self.encoding) self.stream.write(data) def write_line_break(self, data=None): if data is None: data = self.best_line_break self.whitespace = True self.indention = True self.line += 1 self.column = 0 if self.encoding: data = data.encode(self.encoding) self.stream.write(data) def write_version_directive(self, version_text): data = u'%%YAML %s' % version_text if self.encoding: data = data.encode(self.encoding) self.stream.write(data) self.write_line_break() def write_tag_directive(self, handle_text, prefix_text): data = u'%%TAG %s %s' % (handle_text, prefix_text) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) self.write_line_break() # Scalar streams. def write_single_quoted(self, text, split=True): self.write_indicator(u'\'', True) spaces = False breaks = False start = end = 0 while end <= len(text): ch = None if end < len(text): ch = text[end] if spaces: if ch is None or ch != u' ': if start+1 == end and self.column > self.best_width and split \ and start != 0 and end != len(text): self.write_indent() else: data = text[start:end] self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end elif breaks: if ch is None or ch not in u'\n\x85\u2028\u2029': if text[start] == u'\n': self.write_line_break() for br in text[start:end]: if br == u'\n': self.write_line_break() else: self.write_line_break(br) self.write_indent() start = end else: if ch is None or ch in u' \n\x85\u2028\u2029' or ch == u'\'': if start < end: data = text[start:end] self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end if ch == u'\'': data = u'\'\'' self.column += 2 if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end + 1 if ch is not None: spaces = (ch == u' ') breaks = (ch in u'\n\x85\u2028\u2029') end += 1 self.write_indicator(u'\'', False) ESCAPE_REPLACEMENTS = { u'\0': u'0', u'\x07': u'a', u'\x08': u'b', u'\x09': u't', u'\x0A': u'n', u'\x0B': u'v', u'\x0C': u'f', u'\x0D': u'r', u'\x1B': u'e', u'\"': u'\"', u'\\': u'\\', u'\x85': u'N', u'\xA0': u'_', u'\u2028': u'L', u'\u2029': u'P', } def write_double_quoted(self, text, split=True): self.write_indicator(u'"', True) start = end = 0 while end <= len(text): ch = None if end < len(text): ch = text[end] if ch is None or ch in u'"\\\x85\u2028\u2029\uFEFF' \ or not (u'\x20' <= ch <= u'\x7E' or (self.allow_unicode and (u'\xA0' <= ch <= u'\uD7FF' or u'\uE000' <= ch <= u'\uFFFD'))): if start < end: data = text[start:end] self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end if ch is not None: if ch in self.ESCAPE_REPLACEMENTS: data = u'\\'+self.ESCAPE_REPLACEMENTS[ch] elif ch <= u'\xFF': data = u'\\x%02X' % ord(ch) elif ch <= u'\uFFFF': data = u'\\u%04X' % ord(ch) else: data = u'\\U%08X' % ord(ch) self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end+1 if 0 < end < len(text)-1 and (ch == u' ' or start >= end) \ and self.column+(end-start) > self.best_width and split: data = text[start:end]+u'\\' if start < end: start = end self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) self.write_indent() self.whitespace = False self.indention = False if text[start] == u' ': data = u'\\' self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) end += 1 self.write_indicator(u'"', False) def determine_block_hints(self, text): hints = u'' if text: if text[0] in u' \n\x85\u2028\u2029': hints += unicode(self.best_indent) if text[-1] not in u'\n\x85\u2028\u2029': hints += u'-' elif len(text) == 1 or text[-2] in u'\n\x85\u2028\u2029': hints += u'+' return hints def write_folded(self, text): hints = self.determine_block_hints(text) self.write_indicator(u'>'+hints, True) if hints[-1:] == u'+': self.open_ended = True self.write_line_break() leading_space = True spaces = False breaks = True start = end = 0 while end <= len(text): ch = None if end < len(text): ch = text[end] if breaks: if ch is None or ch not in u'\n\x85\u2028\u2029': if not leading_space and ch is not None and ch != u' ' \ and text[start] == u'\n': self.write_line_break() leading_space = (ch == u' ') for br in text[start:end]: if br == u'\n': self.write_line_break() else: self.write_line_break(br) if ch is not None: self.write_indent() start = end elif spaces: if ch != u' ': if start+1 == end and self.column > self.best_width: self.write_indent() else: data = text[start:end] self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end else: if ch is None or ch in u' \n\x85\u2028\u2029': data = text[start:end] self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) if ch is None: self.write_line_break() start = end if ch is not None: breaks = (ch in u'\n\x85\u2028\u2029') spaces = (ch == u' ') end += 1 def write_literal(self, text): hints = self.determine_block_hints(text) self.write_indicator(u'|'+hints, True) if hints[-1:] == u'+': self.open_ended = True self.write_line_break() breaks = True start = end = 0 while end <= len(text): ch = None if end < len(text): ch = text[end] if breaks: if ch is None or ch not in u'\n\x85\u2028\u2029': for br in text[start:end]: if br == u'\n': self.write_line_break() else: self.write_line_break(br) if ch is not None: self.write_indent() start = end else: if ch is None or ch in u'\n\x85\u2028\u2029': data = text[start:end] if self.encoding: data = data.encode(self.encoding) self.stream.write(data) if ch is None: self.write_line_break() start = end if ch is not None: breaks = (ch in u'\n\x85\u2028\u2029') end += 1 def write_plain(self, text, split=True): if self.root_context: self.open_ended = True if not text: return if not self.whitespace: data = u' ' self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) self.whitespace = False self.indention = False spaces = False breaks = False start = end = 0 while end <= len(text): ch = None if end < len(text): ch = text[end] if spaces: if ch != u' ': if start+1 == end and self.column > self.best_width and split: self.write_indent() self.whitespace = False self.indention = False else: data = text[start:end] self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end elif breaks: if ch not in u'\n\x85\u2028\u2029': if text[start] == u'\n': self.write_line_break() for br in text[start:end]: if br == u'\n': self.write_line_break() else: self.write_line_break(br) self.write_indent() self.whitespace = False self.indention = False start = end else: if ch is None or ch in u' \n\x85\u2028\u2029': data = text[start:end] self.column += len(data) if self.encoding: data = data.encode(self.encoding) self.stream.write(data) start = end if ch is not None: spaces = (ch == u' ') breaks = (ch in u'\n\x85\u2028\u2029') end += 1
PypiClean
/IBATS_Huobi_Feeder-0.1.3.tar.gz/IBATS_Huobi_Feeder-0.1.3/ibats_huobi_feeder/backend/orm.py
from sqlalchemy import Column, Integer, String, UniqueConstraint, TIMESTAMP, text from sqlalchemy.dialects.mysql import DOUBLE from sqlalchemy.ext.declarative import declarative_base from ibats_common.utils.db import with_db_session from ibats_huobi_feeder.backend import engine_md from ibats_huobi_feeder.config import config import logging logger = logging.getLogger() BaseModel = declarative_base() class SymbolPair(BaseModel): __tablename__ = 'symbol_pair_info' id = Column(Integer, autoincrement=True, unique=True) market = Column(String(10), primary_key=True) base_currency = Column(String(10), primary_key=True) quote_currency = Column(String(10), primary_key=True) price_precision = Column(Integer) amount_precision = Column(Integer) symbol_partition = Column(String(12)) __table_args__ = ( UniqueConstraint('base_currency', 'quote_currency'), ) class MDTick(BaseModel): __tablename__ = 'md_min1_tick_bc' id = Column(Integer, autoincrement=True, unique=True) market = Column(String(10), primary_key=True) symbol = Column(String(10), primary_key=True) ts_start = Column(TIMESTAMP) ts_curr = Column(TIMESTAMP, primary_key=True, server_default=text('CURRENT_TIMESTAMP')) open = Column(DOUBLE) high = Column(DOUBLE) low = Column(DOUBLE) close = Column(DOUBLE) amount = Column(DOUBLE) vol = Column(DOUBLE) count = Column(DOUBLE) class MDMin1(BaseModel): __tablename__ = 'md_min1_bc' market = Column(String(10), primary_key=True) symbol = Column(String(10), primary_key=True) ts_start = Column(TIMESTAMP, primary_key=True, server_default=text('CURRENT_TIMESTAMP')) ts_curr = Column(TIMESTAMP) open = Column(DOUBLE) high = Column(DOUBLE) low = Column(DOUBLE) close = Column(DOUBLE) amount = Column(DOUBLE) vol = Column(DOUBLE) count = Column(DOUBLE) class MDMin1Temp(BaseModel): __tablename__ = 'md_min1_bc_temp' market = Column(String(10), primary_key=True) symbol = Column(String(10), primary_key=True) ts_start = Column(TIMESTAMP, primary_key=True, server_default=text('CURRENT_TIMESTAMP')) ts_curr = Column(TIMESTAMP) open = Column(DOUBLE) high = Column(DOUBLE) low = Column(DOUBLE) close = Column(DOUBLE) amount = Column(DOUBLE) vol = Column(DOUBLE) count = Column(DOUBLE) class MDMin60(BaseModel): __tablename__ = 'md_min60_bc' market = Column(String(10), primary_key=True) symbol = Column(String(10), primary_key=True) ts_start = Column(TIMESTAMP, primary_key=True, server_default=text('CURRENT_TIMESTAMP')) ts_curr = Column(TIMESTAMP) open = Column(DOUBLE) high = Column(DOUBLE) low = Column(DOUBLE) close = Column(DOUBLE) amount = Column(DOUBLE) vol = Column(DOUBLE) count = Column(DOUBLE) class MDMin60Temp(BaseModel): __tablename__ = 'md_min60_bc_temp' market = Column(String(10), primary_key=True) symbol = Column(String(10), primary_key=True) ts_start = Column(TIMESTAMP, primary_key=True, server_default=text('CURRENT_TIMESTAMP')) ts_curr = Column(TIMESTAMP) open = Column(DOUBLE) high = Column(DOUBLE) low = Column(DOUBLE) close = Column(DOUBLE) amount = Column(DOUBLE) vol = Column(DOUBLE) count = Column(DOUBLE) class MDMinDaily(BaseModel): __tablename__ = 'md_daily_bc' market = Column(String(10), primary_key=True) symbol = Column(String(10), primary_key=True) ts_start = Column(TIMESTAMP, primary_key=True, server_default=text('CURRENT_TIMESTAMP')) ts_curr = Column(TIMESTAMP) open = Column(DOUBLE) high = Column(DOUBLE) low = Column(DOUBLE) close = Column(DOUBLE) amount = Column(DOUBLE) vol = Column(DOUBLE) count = Column(DOUBLE) class MDMinDailyTemp(BaseModel): __tablename__ = 'md_daily_bc_temp' market = Column(String(10), primary_key=True) symbol = Column(String(10), primary_key=True) ts_start = Column(TIMESTAMP, primary_key=True, server_default=text('CURRENT_TIMESTAMP')) ts_curr = Column(TIMESTAMP) open = Column(DOUBLE) high = Column(DOUBLE) low = Column(DOUBLE) close = Column(DOUBLE) amount = Column(DOUBLE) vol = Column(DOUBLE) count = Column(DOUBLE) def init(alter_table=False): BaseModel.metadata.create_all(engine_md) if alter_table: with with_db_session(engine=engine_md) as session: show_status_sql_str = f"show table status from {config.DB_SCHEMA_MD} where name=:table_name" for table_name, _ in BaseModel.metadata.tables.items(): row_data = session.execute(show_status_sql_str, params={'table_name': table_name}).first() if row_data is None: continue if row_data[1].lower() == 'myisam': continue logger.info('修改 %s 表引擎为 MyISAM', table_name) sql_str = "ALTER TABLE %s ENGINE = MyISAM" % table_name session.execute(sql_str) sql_str = f"""select table_name from information_schema.columns where table_schema = :table_schema and column_name = 'ts_start' and extra <> ''""" table_name_list = [row_data[0] for row_data in session.execute(sql_str, params={'table_schema': config.DB_SCHEMA_MD})] for table_name in table_name_list: logger.info('修改 %s 表 ts_start 默认值,剔除 on update 默认项', table_name) # TimeStamp 类型的数据会被自动设置 default: 'CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP' # 需要将 “on update CURRENT_TIMESTAMP”剔除,否则在执行更新时可能会引起错误 session.execute(f"ALTER TABLE {table_name} CHANGE COLUMN `ts_start` `ts_start` TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP") # This is an issue https://www.mail-archive.com/[email protected]/msg19744.html session.execute(f"ALTER TABLE {SymbolPair.__tablename__} CHANGE COLUMN `id` `id` INT(11) NULL AUTO_INCREMENT") session.commit() # This is an issue https://www.mail-archive.com/[email protected]/msg19744.html session.execute(f"ALTER TABLE {MDTick.__tablename__} CHANGE COLUMN `id` `id` INT(11) NULL AUTO_INCREMENT") session.commit() logger.info("所有表结构建立完成") if __name__ == "__main__": init()
PypiClean
/graphinate-0.0.9.tar.gz/graphinate-0.0.9/src/graphinate/tools/mutators.py
import dataclasses import inspect from collections.abc import Iterable, Mapping from typing import Any, Callable, Optional def is_strict_iterable(obj: Any) -> bool: return isinstance(obj, Iterable) and not isinstance(obj, (str, bytes, bytearray)) def _process_obj(obj: Any, mapping_handler: Optional[Callable] = None, iterable_handler: Optional[Callable] = None, class_handler: Optional[Callable] = None, *args, **kwargs): if callable(mapping_handler) and isinstance(obj, Mapping): return mapping_handler(obj, *args, **kwargs) if callable(iterable_handler) and is_strict_iterable(obj): return iterable_handler(obj, *args, **kwargs) if callable(class_handler) and inspect.isclass(obj): return class_handler(obj, *args, **kwargs) if (value_converter := kwargs.get('value_converter')) and callable(value_converter): return value_converter(obj) return obj def dictify_mapping(obj: Mapping[Any, Any], key_converter: Optional[Callable[[Any], str]] = None, value_converter: Optional[Callable[[Any], Any]] = None) -> dict: return {(key_converter(k) if key_converter else k): dictify(v, key_converter, value_converter) for k, v in obj.items()} def dictify_iterable(obj: Iterable, key_converter: Optional[Callable[[Any], str]] = None, value_converter: Optional[Callable[[Any], Any]] = None) -> list: return [dictify(v, key_converter, value_converter) for v in obj] def dictify_class(obj, key_converter: Optional[Callable[[Any], str]] = None, value_converter: Optional[Callable[[Any], Any]] = None): if dataclasses.is_dataclass(obj): return {key_converter(k) if key_converter else k: dictify(v, key_converter, value_converter) for k, v in inspect.getmembers(obj) if not k.startswith("_")} return str(obj) def dictify(obj, key_converter: Optional[Callable[[Any], str]] = None, value_converter: Optional[Callable[[Any], Any]] = None): return _process_obj(obj, mapping_handler=dictify_mapping, iterable_handler=dictify_iterable, class_handler=dictify_class, key_converter=key_converter, value_converter=value_converter)
PypiClean
/Bravo-2.0.tar.gz/Bravo-2.0/bravo/plugins/beds.py
from zope.interface import implements from bravo.blocks import blocks, items from bravo.ibravo import IPreBuildHook, IDigHook # Metadata HEAD_PART = 0x8 class Bed(object): """ Make placing/removing beds work correctly. """ implements(IPreBuildHook, IDigHook) def __init__(self, factory): self.factory = factory def deltas(self, orientation): return {'+x': (1, 0), '+z': (0, 1), '-x': (-1, 0), '-z': (0, -1)}[orientation] def pre_build_hook(self, player, builddata): item, metadata, x, y, z, face = builddata if item.slot != items["bed"].slot: return True, builddata, False # Can place only on top of other block if face != "+y": return False, builddata, True # Offset coords for the second block; use facing direction to # set correct bed blocks. orientation = ('-x', '-z', '+x', '+z')[((int(player.location.yaw) \ - 45 + 360) % 360) / 90] dx, dz = self.deltas(orientation) metadata = blocks["bed"].orientation(orientation) y += 1 # Check if there is enough space for the bed. bl = self.factory.world.sync_get_block((x + dx, y, z + dz)) if bl and bl != blocks["snow"].slot: return False, builddata, True # Make sure we can remove it from the inventory. if not player.inventory.consume((item.slot, 0), player.equipped): return False, builddata, False self.factory.world.set_block((x, y, z), blocks["bed-block"].slot) self.factory.world.set_block((x + dx, y, z + dz), blocks["bed-block"].slot) self.factory.world.set_metadata((x, y, z), metadata) self.factory.world.set_metadata((x + dx, y, z + dz), metadata | HEAD_PART) # XXX As we doing all of the building actions manually we cancel at this point. # This is not what we shall do, but now it's the best solution we have. # Please note that post build hooks and automations will be skipped as well as # default run_build() hook. return False, builddata, True def dig_hook(self, chunk, x, y, z, block): if block.slot != blocks["bed-block"].slot: return # Calculate offset for the second block according to the direction. metadata = chunk.get_metadata((x, y, z)) orientation = blocks["bed-block"].face(metadata & 0x3) dx, dz = self.deltas(orientation) # If the head of the bed was digged, look for the second block in # the opposite direction. if metadata & HEAD_PART: dx *= -1 dz *= -1 # Block coordinates for the second block of the bed. x = chunk.x * 16 + x z = chunk.z * 16 + z self.factory.world.destroy((x + dx, y, z + dz)) name = "bed" before = () # plugins that come before this plugin after = tuple()
PypiClean
/DjangoDjangoAppCenter-0.0.11-py3-none-any.whl/AppCenter/simpleui/static/admin/simpleui-x/elementui/link.js
module.exports = /******/ (function (modules) { // webpackBootstrap /******/ // The module cache /******/ var installedModules = {}; /******/ /******/ // The require function /******/ function __webpack_require__(moduleId) { /******/ /******/ // Check if module is in cache /******/ if (installedModules[moduleId]) { /******/ return installedModules[moduleId].exports; /******/ } /******/ // Create a new module (and put it into the cache) /******/ var module = installedModules[moduleId] = { /******/ i: moduleId, /******/ l: false, /******/ exports: {} /******/ }; /******/ /******/ // Execute the module function /******/ modules[moduleId].call(module.exports, module, module.exports, __webpack_require__); /******/ /******/ // Flag the module as loaded /******/ module.l = true; /******/ /******/ // Return the exports of the module /******/ return module.exports; /******/ } /******/ /******/ /******/ // expose the modules object (__webpack_modules__) /******/ __webpack_require__.m = modules; /******/ /******/ // expose the module cache /******/ __webpack_require__.c = installedModules; /******/ /******/ // define getter function for harmony exports /******/ __webpack_require__.d = function (exports, name, getter) { /******/ if (!__webpack_require__.o(exports, name)) { /******/ Object.defineProperty(exports, name, {enumerable: true, get: getter}); /******/ } /******/ }; /******/ /******/ // define __esModule on exports /******/ __webpack_require__.r = function (exports) { /******/ if (typeof Symbol !== 'undefined' && Symbol.toStringTag) { /******/ Object.defineProperty(exports, Symbol.toStringTag, {value: 'Module'}); /******/ } /******/ Object.defineProperty(exports, '__esModule', {value: true}); /******/ }; /******/ /******/ // create a fake namespace object /******/ // mode & 1: value is a module id, require it /******/ // mode & 2: merge all properties of value into the ns /******/ // mode & 4: return value when already ns object /******/ // mode & 8|1: behave like require /******/ __webpack_require__.t = function (value, mode) { /******/ if (mode & 1) value = __webpack_require__(value); /******/ if (mode & 8) return value; /******/ if ((mode & 4) && typeof value === 'object' && value && value.__esModule) return value; /******/ var ns = Object.create(null); /******/ __webpack_require__.r(ns); /******/ Object.defineProperty(ns, 'default', {enumerable: true, value: value}); /******/ if (mode & 2 && typeof value != 'string') for (var key in value) __webpack_require__.d(ns, key, function (key) { return value[key]; }.bind(null, key)); /******/ return ns; /******/ }; /******/ /******/ // getDefaultExport function for compatibility with non-harmony modules /******/ __webpack_require__.n = function (module) { /******/ var getter = module && module.__esModule ? /******/ function getDefault() { return module['default']; } : /******/ function getModuleExports() { return module; }; /******/ __webpack_require__.d(getter, 'a', getter); /******/ return getter; /******/ }; /******/ /******/ // Object.prototype.hasOwnProperty.call /******/ __webpack_require__.o = function (object, property) { return Object.prototype.hasOwnProperty.call(object, property); }; /******/ /******/ // __webpack_public_path__ /******/ __webpack_require__.p = "/dist/"; /******/ /******/ /******/ // Load entry module and return exports /******/ return __webpack_require__(__webpack_require__.s = 117); /******/ }) /************************************************************************/ /******/({ /***/ 0: /***/ (function (module, __webpack_exports__, __webpack_require__) { "use strict"; /* harmony export (binding) */ __webpack_require__.d(__webpack_exports__, "a", function () { return normalizeComponent; }); /* globals __VUE_SSR_CONTEXT__ */ // IMPORTANT: Do NOT use ES2015 features in this file (except for modules). // This module is a runtime utility for cleaner component module output and will // be included in the final webpack user bundle. function normalizeComponent( scriptExports, render, staticRenderFns, functionalTemplate, injectStyles, scopeId, moduleIdentifier, /* server only */ shadowMode /* vue-cli only */ ) { // Vue.extend constructor export interop var options = typeof scriptExports === 'function' ? scriptExports.options : scriptExports // render functions if (render) { options.render = render options.staticRenderFns = staticRenderFns options._compiled = true } // functional template if (functionalTemplate) { options.functional = true } // scopedId if (scopeId) { options._scopeId = 'data-v-' + scopeId } var hook if (moduleIdentifier) { // server build hook = function (context) { // 2.3 injection context = context || // cached call (this.$vnode && this.$vnode.ssrContext) || // stateful (this.parent && this.parent.$vnode && this.parent.$vnode.ssrContext) // functional // 2.2 with runInNewContext: true if (!context && typeof __VUE_SSR_CONTEXT__ !== 'undefined') { context = __VUE_SSR_CONTEXT__ } // inject component styles if (injectStyles) { injectStyles.call(this, context) } // register component module identifier for async chunk inferrence if (context && context._registeredComponents) { context._registeredComponents.add(moduleIdentifier) } } // used by ssr in case component is cached and beforeCreate // never gets called options._ssrRegister = hook } else if (injectStyles) { hook = shadowMode ? function () { injectStyles.call(this, this.$root.$options.shadowRoot) } : injectStyles } if (hook) { if (options.functional) { // for template-only hot-reload because in that case the render fn doesn't // go through the normalizer options._injectStyles = hook // register for functioal component in vue file var originalRender = options.render options.render = function renderWithStyleInjection(h, context) { hook.call(context) return originalRender(h, context) } } else { // inject component registration as beforeCreate hook var existing = options.beforeCreate options.beforeCreate = existing ? [].concat(existing, hook) : [hook] } } return { exports: scriptExports, options: options } } /***/ }), /***/ 117: /***/ (function (module, __webpack_exports__, __webpack_require__) { "use strict"; __webpack_require__.r(__webpack_exports__); // CONCATENATED MODULE: ./node_modules/[email protected]@vue-loader/lib/loaders/templateLoader.js??vue-loader-options!./node_modules/[email protected]@vue-loader/lib??vue-loader-options!./packages/link/src/main.vue?vue&type=template&id=01cf3b65& var render = function () { var _vm = this var _h = _vm.$createElement var _c = _vm._self._c || _h return _c( "a", _vm._b( { class: [ "el-link", _vm.type ? "el-link--" + _vm.type : "", _vm.disabled && "is-disabled", _vm.underline && !_vm.disabled && "is-underline" ], attrs: {href: _vm.disabled ? null : _vm.href}, on: {click: _vm.handleClick} }, "a", _vm.$attrs, false ), [ _vm.icon ? _c("i", {class: _vm.icon}) : _vm._e(), _vm.$slots.default ? _c("span", {staticClass: "el-link--inner"}, [_vm._t("default")], 2) : _vm._e(), _vm.$slots.icon ? [_vm.$slots.icon ? _vm._t("icon") : _vm._e()] : _vm._e() ], 2 ) } var staticRenderFns = [] render._withStripped = true // CONCATENATED MODULE: ./packages/link/src/main.vue?vue&type=template&id=01cf3b65& // CONCATENATED MODULE: ./node_modules/[email protected]@babel-loader/lib!./node_modules/[email protected]@vue-loader/lib??vue-loader-options!./packages/link/src/main.vue?vue&type=script&lang=js& // // // // // // // // // // // // // // // // // // // // // // // /* harmony default export */ var mainvue_type_script_lang_js_ = ({ name: 'ElLink', props: { type: { type: String, default: 'default' }, underline: { type: Boolean, default: true }, disabled: Boolean, href: String, icon: String }, methods: { handleClick: function handleClick(event) { if (!this.disabled) { if (!this.href) { this.$emit('click', event); } } } } }); // CONCATENATED MODULE: ./packages/link/src/main.vue?vue&type=script&lang=js& /* harmony default export */ var src_mainvue_type_script_lang_js_ = (mainvue_type_script_lang_js_); // EXTERNAL MODULE: ./node_modules/[email protected]@vue-loader/lib/runtime/componentNormalizer.js var componentNormalizer = __webpack_require__(0); // CONCATENATED MODULE: ./packages/link/src/main.vue /* normalize component */ var component = Object(componentNormalizer["a" /* default */])( src_mainvue_type_script_lang_js_, render, staticRenderFns, false, null, null, null ) /* hot reload */ if (false) { var api; } component.options.__file = "packages/link/src/main.vue" /* harmony default export */ var main = (component.exports); // CONCATENATED MODULE: ./packages/link/index.js /* istanbul ignore next */ main.install = function (Vue) { Vue.component(main.name, main); }; /* harmony default export */ var packages_link = __webpack_exports__["default"] = (main); /***/ }) /******/ });
PypiClean
/ARGs_OAP-2.3.2.tar.gz/ARGs_OAP-2.3.2/ARGs_OAP/bin/bbmap/postfilter.sh
usage(){ echo " Written by Brian Bushnell Last modified July 27, 2015 Description: Maps reads, then filters an assembly by contig coverage. Intended to reduce misassembly rate of SPAdes by removing suspicious contigs. Usage: postfilter.sh in=<reads> ref=<contigs> out=<filtered contigs> Standard Parameters: in=<file> File containing input reads. in2=<file> Optional file containing read mates. ref=<file> File containing input assembly. cov=covstats.txt File to write coverage stats generated by pileup. out=filtered.fa Destination of clean output assembly. outdirty=<file> (outd) Destination of removed contigs; optional. ow=f (overwrite) Overwrites files that already exist. app=f (append) Append to files that already exist. zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max). int=f (interleaved) Determines whether input reads are considered interleaved. Filtering Parameters: minc=2 (mincov) Discard contigs with lower average coverage. minp=95 (minpercent) Discard contigs with a lower percent covered bases. minr=6 (minreads) Discard contigs with fewer mapped reads. minl=400 (minlength) Discard shorter contigs. trim=0 (trimends) Trim the first and last X bases of each sequence. Mapping Parameters (unlisted params will use BBMap defaults) minhits=2 maxindel=0 tipsearch=0 bw=20 rescue=f Java Parameters: -Xmx This will set Java's memory usage, overriding autodetection. -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. The max is typically 85% of physical memory. -eoom This flag will cause the process to exit if an out-of-memory exception occurs. Requires Java 8u92+. -da Disable assertions. Other parameters will be passed directly to BBMap. Please contact Brian Bushnell at [email protected] if you encounter any problems. " } #This block allows symlinked shellscripts to correctly set classpath. pushd . > /dev/null DIR="${BASH_SOURCE[0]}" while [ -h "$DIR" ]; do cd "$(dirname "$DIR")" DIR="$(readlink "$(basename "$DIR")")" done cd "$(dirname "$DIR")" DIR="$(pwd)/" popd > /dev/null #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" CP="$DIR""current/" z="-Xmx800m" set=0 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then usage exit fi calcXmx () { source "$DIR""/calcmem.sh" setEnvironment parseXmx "$@" if [[ $set == 1 ]]; then return fi freeRam 800m 84 z="-Xmx${RAM}m" z2="-Xms${RAM}m" } calcXmx "$@" function postfilter() { local CMD="java $EA $EOOM $z -cp $CP assemble.Postfilter $@" echo $CMD >&2 eval $CMD } postfilter "$@"
PypiClean
/GNUIndentBear-0.10.0.tar.gz/GNUIndentBear-0.10.0/coalaGNUIndentBear/GNUIndentBear.py
import platform import shlex from coalib.bearlib import deprecate_settings from coalib.bearlib.abstractions.Linter import linter from coalib.bearlib.spacing.SpacingHelper import SpacingHelper from dependency_management.requirements.DistributionRequirement import ( DistributionRequirement) @linter(executable='indent' if platform.system() != 'Darwin' else 'gindent', use_stdin=True, output_format='corrected', result_message='Indentation can be improved.') class GNUIndentBear: """ This bear checks and corrects spacing and indentation via the well known Indent utility. C++ support is considered experimental. """ LANGUAGES = {'C', 'C++'} REQUIREMENTS = {DistributionRequirement(apt_get='indent')} AUTHORS = {'The coala developers'} AUTHORS_EMAILS = {'[email protected]'} LICENSE = 'AGPL-3.0' CAN_FIX = {'Formatting'} @staticmethod @deprecate_settings(indent_size='tab_width') def create_arguments(filename, file, config_file, max_line_length: int=79, use_spaces: bool=True, blank_lines_after_declarations: bool=False, blank_lines_after_procedures: bool=False, blank_lines_after_commas: bool=False, braces_on_if_line: bool=False, braces_on_func_def_line: bool=False, cuddle_else: bool=False, while_and_brace_on_same_line: bool=False, case_indentation: int=0, space_before_semicolon_after_empty_loop: bool=True, delete_optional_blank_lines: bool=True, declaration_indent: int=0, brace_indent: int=2, gnu_style: bool=False, k_and_r_style: bool=False, linux_style: bool=False, indent_size: int=SpacingHelper.DEFAULT_TAB_WIDTH, indent_cli_options: str=''): """ :param max_line_length: Maximum number of characters for a line. :param use_spaces: True if spaces are to be used, else tabs. :param blank_lines_after_declarations: Forces blank lines after the declarations. Example: If ``blank_lines_after_declarations = True`` then ``` int a; return ...; ``` changes to ``` int a; return ...; ``` :param blank_lines_after_procedures: Force blank lines after procedure bodies. :param blank_lines_after_commas: Forces newline after comma in declaration. Example: If ``blank_lines_after_commas = True`` then ``` int a, b; ``` changes to ``` int a, b; ``` :param braces_on_if_line: Puts the brace ``{`` on same line with if. Example: If ``braces_on_if_line = True`` then ``` if (x > 0) { ``` changes to ``` if (x > 0) { ``` :param braces_on_func_def_line: Puts the brace `{` on same line with the function declaration. :param cuddle_else: Cuddle else and preceding ``}``. Example: If ``cuddle_else = True`` then ``` if (...) { .... } else { ``` changes to ``` if (...) { .... } else { ``` :param while_and_brace_on_same_line: Cuddles while of ``do {} while``; and preceding ``}``. :param case_indentation: Specifies the number of spaces by which ``case`` in the ``switch`` are indented. :param space_before_semicolon_after_empty_loop: Forces a blank before the semicolon ``;`` on one-line ``for`` and ``while`` statements. :param delete_optional_blank_lines: Deletes blank lines that are not needed. An example of needed blank line, is the blank line following a declaration when ``blank_line_after_declaration=True``. :param declaration_indent: Forces variables names to be aligned in column ``n`` with ``n = declaration_indent`` in declaration. Example: If ``declaration_indent = 8`` then, ``` int a; float b; ``` changes to ``` int a; float b; ``` :param brace_indent: Specifies the number of spaces by which braces are indented. Its default value is 2. :param gnu_style: Uses GNU coding style. :param k_and_r_style: Uses Kernighan & Ritchie coding style. :param linux_style: Uses Linux coding style. :param indent_size: Number of spaces per indentation level. :param indent_cli_options: Any command line options the indent binary understands. They will be simply passed through. """ indent_options = ('--no-tabs' if use_spaces else '--use-tabs', '--line-length', str(max_line_length), '--indent-level', str(indent_size), '--tab-size', str(indent_size), ) indent_options += (('--cuddle-do-while',) if while_and_brace_on_same_line else ('--dont-cuddle-do-while',)) indent_options += (('--swallow-optional-blank-lines',) if delete_optional_blank_lines else ('-nsob',)) indent_options += (('--blank-lines-after-declarations',) if blank_lines_after_declarations else ('-nbad',)) indent_options += (('--blank-lines-after-commas',) if blank_lines_after_commas else ('-nbc',)) indent_options += (('--blank-lines-after-procedures',) if blank_lines_after_procedures else ('-nbap',)) indent_options += (('-di' + str(declaration_indent),) if declaration_indent != 0 else ()) indent_options += (('--case-indentation'+str(case_indentation),) if case_indentation != 0 else ()) indent_options += (('--space-special-semicolon',) if space_before_semicolon_after_empty_loop else ('-nss',)) indent_options += ('--brace-indent'+str(brace_indent),) indent_options += (('--braces-on-func-def-line',) if braces_on_func_def_line else ('-blf',)) indent_options += ((('-ce',) if cuddle_else else ('-nce',)) + ('-br',)) if braces_on_if_line else ('-bl',) indent_style_option = () indent_style_option += ('--gnu-style',) if gnu_style else () indent_style_option += (('--k-and-r-style',) if k_and_r_style and indent_style_option is () else ()) indent_style_option += (('--linux-style',) if linux_style and indent_style_option is () else ()) # If a style is chosen the other configs aren't passed to `indent` return (indent_style_option if indent_style_option is not () else indent_options) + tuple(shlex.split(indent_cli_options))
PypiClean
/Django-MobilityHelpers-0.3.0.tar.gz/Django-MobilityHelpers-0.3.0/mobilityhelpers/middleware/__init__.py
import re from mobilityhelpers import detect_flavour, disable_helper from django.utils.deprecation import MiddlewareMixin class MobileDetectionMiddleware(MiddlewareMixin): """ """ def process_request(self, request): is_mobile = False if 'HTTP_USER_AGENT' in request.META: user_agent = request.META['HTTP_USER_AGENT'] if 'Nexus 7' in user_agent: setattr(request, 'mobile_flavour', 'tablet') request.is_mobile = True return # Test common mobile values. pattern = "(up.browser|up.link|mmp|symbian|smartphone|midp|wap|phone|windows ce|pda|mobile|mini|palm|netfront)" prog = re.compile(pattern, re.IGNORECASE) match = prog.search(user_agent) if match: is_mobile = True else: # Nokia like test for WAP browsers. # http://www.developershome.com/wap/xhtmlmp/xhtml_mp_tutorial.asp?page=mimeTypesFileExtension if 'HTTP_ACCEPT' in request.META: http_accept = request.META['HTTP_ACCEPT'] pattern = "application/vnd\.wap\.xhtml\+xml" prog = re.compile(pattern, re.IGNORECASE) match = prog.search(http_accept) if match: is_mobile = True if not is_mobile: # Now we test the user_agent from a big list. user_agents_test = ("w3c ", "acs-", "alav", "alca", "amoi", "audi", "avan", "benq", "bird", "blac", "blaz", "brew", "cell", "cldc", "cmd-", "dang", "doco", "eric", "hipt", "inno", "ipaq", "java", "jigs", "kddi", "keji", "leno", "lg-c", "lg-d", "lg-g", "lge-", "maui", "maxo", "midp", "mits", "mmef", "mobi", "mot-", "moto", "mwbp", "nec-", "newt", "noki", "xda", "palm", "pana", "pant", "phil", "play", "port", "prox", "qwap", "sage", "sams", "sany", "sch-", "sec-", "send", "seri", "sgh-", "shar", "sie-", "siem", "smal", "smar", "sony", "sph-", "symb", "t-mo", "teli", "tim-", "tosh", "tsm-", "upg1", "upsi", "vk-v", "voda", "wap-", "wapa", "wapi", "wapp", "wapr", "webc", "winw", "winw", "xda-",) test = user_agent[0:4].lower() if test in user_agents_test: is_mobile = True if is_mobile: if detect_flavour and 'ipad' in user_agent.lower(): setattr(request, 'mobile_flavour', 'ipad') else: setattr(request, 'mobile_flavour', 'mobile') else: setattr(request, 'mobile_flavour', None) request.is_mobile = is_mobile
PypiClean
/DuHast-1.0.7-py3-none-any.whl/duHast/APISamples/RevitFamilyCategoryDataUtils.py
from collections import namedtuple import Utility as util # tuples containing change family category data read from file changeFamilyCategory = namedtuple('changeFamilyCategory', 'filePath newCategoryName') # tuples containing change family subcategory data read from file changeFamilySubCategory = namedtuple('changeFamilySubCategory', 'familyCategory oldSubCategoryName newSubCategoryName') # tuples used to build category data graphicPropertyRGB = namedtuple('graphicPropertyRGB', 'red green blue') graphicPropertyLineWeight = namedtuple('graphicPropertyLineWeight', 'cut projection') graphicPropertyMaterial = namedtuple('graphicPropertyMaterial', 'id name') graphicPropertyThreeDCutProjection = namedtuple('graphicProperty', 'threeD cut projection') # container for category properties subCategoryPropertiesContainer = namedtuple('subCategoryProperties', 'rgb lineWeight material graphic') # the actual subcategory representing single row in report subCategory = namedtuple('subCategory', 'parentCategoryName subCategoryName subCategoryId usageCounter usedBy subCategoryProperties ') # a root family rootFamily = namedtuple('rootFamily', 'name category filePath parent child subcategories') # a nested family nestedFamily = namedtuple('nestedFamily', 'name category filePath rootPath categoryPath hostFamily subcategories') # row structure of family change category directive file _CATEGORY_CHANGE_DATA_LIST_INDEX_FAMILY_FILE_PATH = 0 _CATEGORY_CHANGE_DATA_LIST_INDEX_NEW_FAMILY_CATEGORY = 1 # row structure of family change subcategory directive file _SUBCATEGORY_CHANGE_DATA_LIST_INDEX_FAMILY_CATEGORY = 0 _SUBCATEGORY_CHANGE_DATA_LIST_INDEX_OLD_SUBCATEGORY_NAME = 1 _SUBCATEGORY_CHANGE_DATA_LIST_INDEX_NEW_SUBCATEGORY_NAME = 2 # row structure of family category data file _CATEGORY_DATA_LIST_INDEX_ROOT_PATH = 0 _CATEGORY_DATA_LIST_INDEX_ROOT_CATEGORY_PATH = 1 _CATEGORY_DATA_LIST_INDEX_FAMILY_NAME = 2 _CATEGORY_DATA_LIST_INDEX_FAMILY_FILE_PATH = 3 _CATEGORY_DATA_LIST_INDEX_USAGE_COUNTER = 4 _CATEGORY_DATA_LIST_INDEX_USED_BY = 5 _CATEGORY_DATA_LIST_INDEX_CATEGORY_NAME = 6 _CATEGORY_DATA_LIST_INDEX_SUBCATEGORY_NAME = 7 _CATEGORY_DATA_LIST_INDEX_SUBCATEGORY_ID = 8 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_3D = 9 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_CUT = 10 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_PROJECTION = 11 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_MATERIAL_NAME = 12 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_MATERIAL_ID = 13 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_LINE_WEIGHT_CUT = 14 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_LINE_WEIGHT_PROJECTION = 15 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_RGB_RED = 16 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_RGB_GREEN = 17 _CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_RGB_BLUE = 18 # file name identifiers for family base data _FAMILY_CATEGORY_DATA_FILE_NAME_PREFIX = 'FamilyCategories' _FAMILY_CATEGORY_DATA_FILE_EXTENSION = '.csv' # file name identifiers for category change directives _CATEGORY_CHANGE_DIRECTIVE_FILE_NAME_PREFIX = 'CategoryChangeDirective' _CATEGORY_CHANGE_DIRECTIVE_FILE_EXTENSION = '.csv' # file name identifiers for subcategory change directives _SUBCATEGORY_CHANGE_DIRECTIVE_FILE_NAME_PREFIX = 'SubCategoryChangeDirective' _SUBCATEGORY_CHANGE_DIRECTIVE_FILE_EXTENSION = '.csv' # exceptions _EXCEPTION_NO_FAMILY_CHANGE_DIRECTIVE_DATA_FILES = 'Families change directive list files do not exist.' _EXCEPTION_EMPTY_CHANGE_DIRECTIVE_DATA_FILES = 'Empty Families change directive data file(s)!' _EXCEPTION_NO_FAMILY_CATEGORY_DATA_FILES = 'Families category data list files do not exist.' _EXCEPTION_EMPTY_FAMILY_CATEGORY_DATA_FILES = 'Empty Families category data list file!' _EXCEPTION_NO_FAMILY_SUBCATEGORY_DATA_FILES = 'Families subcategory data list files do not exist.' _EXCEPTION_EMPTY_FAMILY_SUBCATEGORY_DATA_FILES = 'Empty Families subcategory data list file!' # -------------------------------- read category data set ---------------------------------------------------------------- # sample root and nested family tuple usage / set up # set up subcategory properties ''' dataRGB = graphicPropertyRGB(120,120,120) dataLineWeight = graphicPropertyLineWeight(3,6) dataMaterial = graphicPropertyMaterial(-1,'') dataGraphic = graphicPropertyThreeDCutProjection(None,None,None) # combine into a container dataSubPropertiesContainer = subCategoryPropertiesContainer (dataRGB, dataLineWeight, dataMaterial, dataGraphic) # set up the actual sub category ( single row in report ) dataSubCatSample = subCategory('Parent Cat Name', 'subCat name', 1234, dataSubPropertiesContainer) # set up a root family tuple dataRootFam = rootFamily('root family name', 'root family category', 'file path', [], [], [dataSubCatSample]) # set up a nested family tuple dataNestedFam = nestedFamily('nested family name', 'nested family category', 'file path', 'root Path', 'category Path','host Family data', [dataSubCatSample]) ''' #end samples def _createRootFamilyFromData(dataRow): ''' Sets up a root family tuple from data row past in. :param dataRow: A row from the category report. :type dataRow: [str] :return: a rootFamily tuple :rtype: named tuple :rootFamily ''' # need to check if this is a category belonging to the current family or a new family?? fam = rootFamily( dataRow[_CATEGORY_DATA_LIST_INDEX_FAMILY_NAME], dataRow[_CATEGORY_DATA_LIST_INDEX_CATEGORY_NAME], dataRow[_CATEGORY_DATA_LIST_INDEX_FAMILY_FILE_PATH], [], # set up an empty list for parent families [], # set up an empty list for child families [] # set up empty list for sub-categories ) return fam def _createNestedFamilyFromData(dataRow): ''' Sets up a nested family tuple from data row past in. :param dataRow: A row from the category report. :type dataRow: [str] :return: a nested family tuple :rtype: named tuple :nestedFamily ''' # found a child family fam = nestedFamily ( dataRow[_CATEGORY_DATA_LIST_INDEX_FAMILY_NAME], dataRow[_CATEGORY_DATA_LIST_INDEX_CATEGORY_NAME], dataRow[_CATEGORY_DATA_LIST_INDEX_FAMILY_FILE_PATH], dataRow[_CATEGORY_DATA_LIST_INDEX_ROOT_PATH].split(' :: '), # split root path into list for ease of searching dataRow[_CATEGORY_DATA_LIST_INDEX_ROOT_CATEGORY_PATH].split(' :: '), # split category path into list for ease of searching [], # set up an empty list for host families [] # set up empty list for sub-categories ) return fam def _setupFamilyFromData(dataRow): ''' Creates a nested family or root family tuple from data row past in. :param dataRow: A row from the category report. :type dataRow: [str] :return: A nested or root family tuple. :rtype: named tuple ''' fam = None if( '::' not in dataRow[_CATEGORY_DATA_LIST_INDEX_ROOT_PATH]): fam = _createRootFamilyFromData(dataRow) else: # found a child family fam = _createNestedFamilyFromData(dataRow) return fam def _buildSubCategoryPropertiesFromData(dataRow): ''' Generates a subcategory tuple based on data row past in. :param dataRow: A row from the category report. :type dataRow: [str] :return: A subCategory tuple. :rtype: named tuple ''' # read category data first # get colour RGB values dataRGB = graphicPropertyRGB( dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_RGB_RED], dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_RGB_GREEN], dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_RGB_BLUE] ) # get line weight values dataLineWeight = graphicPropertyLineWeight( dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_LINE_WEIGHT_CUT], dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_LINE_WEIGHT_PROJECTION] ) # get material values dataMaterial = graphicPropertyMaterial( dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_MATERIAL_ID], dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_MATERIAL_NAME] ) # get graphic properties dataGraphic = graphicPropertyThreeDCutProjection( dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_3D], dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_CUT], dataRow[_CATEGORY_DATA_LIST_INDEX_GRAPHIC_PROPERTY_PROJECTION] ) # put all of the above together dataSubPropertiesContainer = subCategoryPropertiesContainer ( dataRGB, dataLineWeight, dataMaterial, dataGraphic ) # set up the actual sub category ( single row in report ) dataSubCatSample = subCategory( dataRow[_CATEGORY_DATA_LIST_INDEX_CATEGORY_NAME], dataRow[_CATEGORY_DATA_LIST_INDEX_SUBCATEGORY_NAME], dataRow[_CATEGORY_DATA_LIST_INDEX_SUBCATEGORY_ID], dataRow[_CATEGORY_DATA_LIST_INDEX_USAGE_COUNTER], dataRow[_CATEGORY_DATA_LIST_INDEX_USED_BY], dataSubPropertiesContainer ) return dataSubCatSample def _getCategoryDataFileName(directoryPath): ''' Gets the first family base data file in provided directory or any of it's sub directories. :param directoryPath: Fully qualified directory path. :type directoryPath: str :raises Exception: EXCEPTION_NO_FAMILY_BASE_DATA_FILES :return: Fully qualified file path to family base data file. :rtype: str ''' # get all base data files in folder files = util.GetFilesFromDirectoryWalkerWithFilters( directoryPath, _FAMILY_CATEGORY_DATA_FILE_NAME_PREFIX, '', _FAMILY_CATEGORY_DATA_FILE_EXTENSION ) if( len(files) > 0): return files[0] else: raise Exception(_EXCEPTION_NO_FAMILY_CATEGORY_DATA_FILES) def ReadOverallFamilyDataList(filePath): ''' Reads list of families from family category data report file into named tuples. :param filePath: Fully qualified file path to family category data report file. :type filePath: str :raises Exception: "Families category data list files does not exist." :raises Exception: "Empty Families category data list file!" :return: Two lists: first list of named tuples contain family root data, second list contains family nested data. :rtype: [rootFamily], [nestedFamily] ''' rows = [] if(util.FileExist(filePath)): rows = util.ReadCSVfile(filePath) else: raise Exception(_EXCEPTION_NO_FAMILY_CATEGORY_DATA_FILES) if(len(rows) > 0): pass else: raise Exception(_EXCEPTION_EMPTY_FAMILY_CATEGORY_DATA_FILES) returnValueRootFamily = [] returnValueNestedFamily = [] # pointer to the current family currentFam = None for i in range(1, len(rows)): # set up the actual sub category ( single row in report ) dataSubCatSample = _buildSubCategoryPropertiesFromData(rows[i]) # get name and category as unique identifier famId = rows[i][_CATEGORY_DATA_LIST_INDEX_FAMILY_NAME] + rows[i][_CATEGORY_DATA_LIST_INDEX_CATEGORY_NAME] # check if this is the current family ... # this assumes family category data in report file is ordered by family!!! if(currentFam == None): # and set up a new one: currentFam = _setupFamilyFromData(rows[i]) # append category data to new family currentFam.subcategories.append(dataSubCatSample) elif (currentFam.name + currentFam.category == famId): # append category data to existing family currentFam.subcategories.append(dataSubCatSample) else: # if not: # append family to one of the list to be returned if(isinstance(currentFam,rootFamily)): returnValueRootFamily.append(currentFam) else: returnValueNestedFamily.append(currentFam) # and set up a new one: currentFam = _setupFamilyFromData(rows[i]) # append category data to new family currentFam.subcategories.append(dataSubCatSample) return returnValueRootFamily, returnValueNestedFamily def ReadOverallFamilyCategoryDataFromDirectory(directoryPath): ''' Reads the first family category data file it finds in a folder. Note: This method calls ReadOverallFamilyDataList(filePath) which will raise exceptions if files are empty or dont exist in specified folder. :param directoryPath: A fully qualified directory path containing family category data file(s) :type directoryPath: _str :return: Two lists: first list of named tuples contain family root data, second list contains family nested data. :rtype: [rootFamily], [nestedFamily] ''' fileName = _getCategoryDataFileName(directoryPath) return ReadOverallFamilyDataList(fileName) # -------------------------------- read family category change directives ---------------------------------------------------------------- def ReadOverallChangeCategoryDirectivesList(filePaths): ''' Reads list of family change category directives from files into named tuples. :param filePath: List of fully qualified file path to family change category directive file. :type filePath: [str] :raises Exception: "Families change directive list files do not exist." :raises Exception: "Empty Families category data list file!" :return: List of named tuples contain family category change directive. :rtype: [changeFamilyCategory] ''' rows = [] matchAnyFile = False for filePath in filePaths: if(util.FileExist(filePath)): # set flag that we at least found one file matchAnyFile = True rowsFile = util.ReadCSVfile(filePath) result = list(rows) result.extend(item for item in rowsFile if item not in result) rows = result # check if any files found if(matchAnyFile == False): raise Exception(_EXCEPTION_NO_FAMILY_CHANGE_DIRECTIVE_DATA_FILES) # check if files contained any data if(len(rows) > 0): # populate change directive tuples returnValueChangeDirectives = [] for row in rows: changeDirective = changeFamilyCategory( row[_CATEGORY_CHANGE_DATA_LIST_INDEX_FAMILY_FILE_PATH], row[_CATEGORY_CHANGE_DATA_LIST_INDEX_NEW_FAMILY_CATEGORY] ) returnValueChangeDirectives.append(changeDirective) else: raise Exception(_EXCEPTION_EMPTY_CHANGE_DIRECTIVE_DATA_FILES) return returnValueChangeDirectives def _getCategoryChangeDirectiveFileNames(directoryPath): ''' Gets change category directive file in provided directory or any of it's sub directories. :param directoryPath: Fully qualified directory path. :type directoryPath: str :raises Exception: _EXCEPTION_NO_FAMILY_CHANGE_DIRECTIVE_DATA_FILES :return: List of fully qualified file path to family change category directive files. :rtype: [str] ''' # get all base data files in folder files = util.GetFilesFromDirectoryWalkerWithFilters( directoryPath, _CATEGORY_CHANGE_DIRECTIVE_FILE_NAME_PREFIX, '', _CATEGORY_CHANGE_DIRECTIVE_FILE_EXTENSION ) if( len(files) > 0): return files else: raise Exception(_EXCEPTION_NO_FAMILY_CHANGE_DIRECTIVE_DATA_FILES) def ReadOverallFamilyCategoryChangeDirectivesFromDirectory(directoryPath): ''' Reads all category change directive file it finds in a folder. Note: This method calls ReadOverallFamilyDataList(filePath) which will raise exceptions if files are empty or dont exist in specified folder. :param directoryPath: A fully qualified directory path containing family category change directive file(s) :type directoryPath: _str :return: list of named tuples contain family category change directives. :rtype: [changeFamilyCategory] ''' fileNames = _getCategoryChangeDirectiveFileNames(directoryPath) return ReadOverallChangeCategoryDirectivesList(fileNames) # -------------------------------- read family subcategory change directives ---------------------------------------------------------------- def ReadOverallFamilySubCategoryChangeDirectivesFromDirectory(directoryPath): ''' Reads all subcategory change directive file it finds in a folder. Note: This method calls ReadOverallFamilyDataList(filePath) which will raise exceptions if files are empty or dont exist in specified folder. :param directoryPath: A fully qualified directory path containing family category change directive file(s) :type directoryPath: _str :return: list of named tuples contain family sub category change directives. :rtype: [changeFamilySubCategory] ''' fileNames = _getSubCategoryChangeDirectiveFileNames(directoryPath) return ReadOverallChangeSubCategoryDirectivesList(fileNames) def _getSubCategoryChangeDirectiveFileNames(directoryPath): ''' Gets change subcategory directive file in provided directory or any of it's sub directories. :param directoryPath: Fully qualified directory path. :type directoryPath: str :raises Exception: _EXCEPTION_NO_FAMILY_CHANGE_DIRECTIVE_DATA_FILES :return: List of fully qualified file path to family change sub category directive files. :rtype: [str] ''' # get all base data files in folder files = util.GetFilesFromDirectoryWalkerWithFilters( directoryPath, _SUBCATEGORY_CHANGE_DIRECTIVE_FILE_NAME_PREFIX, '', _SUBCATEGORY_CHANGE_DIRECTIVE_FILE_EXTENSION ) if( len(files) > 0): return files else: raise Exception(_EXCEPTION_NO_FAMILY_CHANGE_DIRECTIVE_DATA_FILES) def ReadOverallChangeSubCategoryDirectivesList(filePaths): ''' Reads list of family change subcategory directives from files into named tuples. :param filePath: List of fully qualified file path to family change category directive file. :type filePath: [str] :raises Exception: _EXCEPTION_NO_FAMILY_SUBCATEGORY_DATA_FILES :raises Exception: _EXCEPTION_EMPTY_FAMILY_SUBCATEGORY_DATA_FILES :return: List of named tuples containing family subcategory change directive. :rtype: [changeFamilySubCategory] ''' rows = [] matchAnyFile = False for filePath in filePaths: if(util.FileExist(filePath)): # set flag that we at least found one file matchAnyFile = True rowsFile = util.ReadCSVfile(filePath) result = list(rows) result.extend(item for item in rowsFile if item not in result) rows = result # check if any files found if(matchAnyFile == False): raise Exception(_EXCEPTION_NO_FAMILY_SUBCATEGORY_DATA_FILES) # check if files contained any data if(len(rows) > 0): # populate change directive tuples returnValueChangeDirectives = [] for row in rows: changeDirective = changeFamilySubCategory( row[_SUBCATEGORY_CHANGE_DATA_LIST_INDEX_FAMILY_CATEGORY], row[_SUBCATEGORY_CHANGE_DATA_LIST_INDEX_OLD_SUBCATEGORY_NAME], row[_SUBCATEGORY_CHANGE_DATA_LIST_INDEX_NEW_SUBCATEGORY_NAME], ) returnValueChangeDirectives.append(changeDirective) else: raise Exception(_EXCEPTION_EMPTY_FAMILY_SUBCATEGORY_DATA_FILES) return returnValueChangeDirectives def GetFamiliesRequiringSubCategoryChange(rootFamilies, subCatChangeDirectives): ''' Returns a list of file path of root families containing subcategories requiring a rename. Note: list of file path returned is unique: i.e. if a family has multiple matches for rename subcategory directives it will still only appear once in the list. :param rootFamilies: List of tuples of root families. :type rootFamilies: [rootFamily] :param subCatChangeDirectives: List of subcategory change directives. :type subCatChangeDirectives: [changeFamilySubCategory] :return: List of family file path. :rtype: [str] ''' rootFamiliesNeedingChange = [] # check each root family for rootFam in rootFamilies: # against each subcategory change directive for changeD in subCatChangeDirectives: # check if match family category if(rootFam.category == changeD.familyCategory): # loop over subcategories in family and check if any of them needs renaming for subCatRoot in rootFam.subcategories: if(subCatRoot.subCategoryName == changeD.oldSubCategoryName): # found a match if (rootFam.filePath not in rootFamiliesNeedingChange): rootFamiliesNeedingChange.append(rootFam.filePath) break return rootFamiliesNeedingChange
PypiClean
/Firefly%20III%20API%20Python%20Client-1.5.6.post2.tar.gz/Firefly III API Python Client-1.5.6.post2/firefly_iii_client/model/rule_trigger_type.py
import re # noqa: F401 import sys # noqa: F401 from firefly_iii_client.model_utils import ( # noqa: F401 ApiTypeError, ModelComposed, ModelNormal, ModelSimple, cached_property, change_keys_js_to_python, convert_js_args_to_python_args, date, datetime, file_type, none_type, validate_get_composed_info, ) from ..model_utils import OpenApiModel from firefly_iii_client.exceptions import ApiAttributeError class RuleTriggerType(ModelSimple): """NOTE: This class is auto generated by OpenAPI Generator. Ref: https://openapi-generator.tech Do not edit the class manually. Attributes: allowed_values (dict): The key is the tuple path to the attribute and the for var_name this is (var_name,). The value is a dict with a capitalized key describing the allowed value and an allowed value. These dicts store the allowed enum values. validations (dict): The key is the tuple path to the attribute and the for var_name this is (var_name,). The value is a dict that stores validations for max_length, min_length, max_items, min_items, exclusive_maximum, inclusive_maximum, exclusive_minimum, inclusive_minimum, and regex. additional_properties_type (tuple): A tuple of classes accepted as additional properties values. """ allowed_values = { ('value',): { 'STORE-JOURNAL': "store-journal", 'UPDATE-JOURNAL': "update-journal", }, } validations = { } additional_properties_type = None _nullable = False @cached_property def openapi_types(): """ This must be a method because a model may have properties that are of type self, this must run after the class is loaded Returns openapi_types (dict): The key is attribute name and the value is attribute type. """ return { 'value': (str,), } @cached_property def discriminator(): return None attribute_map = {} read_only_vars = set() _composed_schemas = None required_properties = set([ '_data_store', '_check_type', '_spec_property_naming', '_path_to_item', '_configuration', '_visited_composed_classes', ]) @convert_js_args_to_python_args def __init__(self, *args, **kwargs): """RuleTriggerType - a model defined in OpenAPI Note that value can be passed either in args or in kwargs, but not in both. Args: args[0] (str): Which action is necessary for the rule to fire? Use either store-journal or update-journal.., must be one of ["store-journal", "update-journal", ] # noqa: E501 Keyword Args: value (str): Which action is necessary for the rule to fire? Use either store-journal or update-journal.., must be one of ["store-journal", "update-journal", ] # noqa: E501 _check_type (bool): if True, values for parameters in openapi_types will be type checked and a TypeError will be raised if the wrong type is input. Defaults to True _path_to_item (tuple/list): This is a list of keys or values to drill down to the model in received_data when deserializing a response _spec_property_naming (bool): True if the variable names in the input data are serialized names, as specified in the OpenAPI document. False if the variable names in the input data are pythonic names, e.g. snake case (default) _configuration (Configuration): the instance to use when deserializing a file_type parameter. If passed, type conversion is attempted If omitted no type conversion is done. _visited_composed_classes (tuple): This stores a tuple of classes that we have traveled through so that if we see that class again we will not use its discriminator again. When traveling through a discriminator, the composed schema that is is traveled through is added to this set. For example if Animal has a discriminator petType and we pass in "Dog", and the class Dog allOf includes Animal, we move through Animal once using the discriminator, and pick Dog. Then in Dog, we will make an instance of the Animal class but this time we won't travel through its discriminator because we passed in _visited_composed_classes = (Animal,) """ # required up here when default value is not given _path_to_item = kwargs.pop('_path_to_item', ()) if 'value' in kwargs: value = kwargs.pop('value') elif args: args = list(args) value = args.pop(0) else: raise ApiTypeError( "value is required, but not passed in args or kwargs and doesn't have default", path_to_item=_path_to_item, valid_classes=(self.__class__,), ) _check_type = kwargs.pop('_check_type', True) _spec_property_naming = kwargs.pop('_spec_property_naming', False) _configuration = kwargs.pop('_configuration', None) _visited_composed_classes = kwargs.pop('_visited_composed_classes', ()) if args: raise ApiTypeError( "Invalid positional arguments=%s passed to %s. Remove those invalid positional arguments." % ( args, self.__class__.__name__, ), path_to_item=_path_to_item, valid_classes=(self.__class__,), ) self._data_store = {} self._check_type = _check_type self._spec_property_naming = _spec_property_naming self._path_to_item = _path_to_item self._configuration = _configuration self._visited_composed_classes = _visited_composed_classes + (self.__class__,) self.value = value if kwargs: raise ApiTypeError( "Invalid named arguments=%s passed to %s. Remove those invalid named arguments." % ( kwargs, self.__class__.__name__, ), path_to_item=_path_to_item, valid_classes=(self.__class__,), ) @classmethod @convert_js_args_to_python_args def _from_openapi_data(cls, *args, **kwargs): """RuleTriggerType - a model defined in OpenAPI Note that value can be passed either in args or in kwargs, but not in both. Args: args[0] (str): Which action is necessary for the rule to fire? Use either store-journal or update-journal.., must be one of ["store-journal", "update-journal", ] # noqa: E501 Keyword Args: value (str): Which action is necessary for the rule to fire? Use either store-journal or update-journal.., must be one of ["store-journal", "update-journal", ] # noqa: E501 _check_type (bool): if True, values for parameters in openapi_types will be type checked and a TypeError will be raised if the wrong type is input. Defaults to True _path_to_item (tuple/list): This is a list of keys or values to drill down to the model in received_data when deserializing a response _spec_property_naming (bool): True if the variable names in the input data are serialized names, as specified in the OpenAPI document. False if the variable names in the input data are pythonic names, e.g. snake case (default) _configuration (Configuration): the instance to use when deserializing a file_type parameter. If passed, type conversion is attempted If omitted no type conversion is done. _visited_composed_classes (tuple): This stores a tuple of classes that we have traveled through so that if we see that class again we will not use its discriminator again. When traveling through a discriminator, the composed schema that is is traveled through is added to this set. For example if Animal has a discriminator petType and we pass in "Dog", and the class Dog allOf includes Animal, we move through Animal once using the discriminator, and pick Dog. Then in Dog, we will make an instance of the Animal class but this time we won't travel through its discriminator because we passed in _visited_composed_classes = (Animal,) """ # required up here when default value is not given _path_to_item = kwargs.pop('_path_to_item', ()) self = super(OpenApiModel, cls).__new__(cls) if 'value' in kwargs: value = kwargs.pop('value') elif args: args = list(args) value = args.pop(0) else: raise ApiTypeError( "value is required, but not passed in args or kwargs and doesn't have default", path_to_item=_path_to_item, valid_classes=(self.__class__,), ) _check_type = kwargs.pop('_check_type', True) _spec_property_naming = kwargs.pop('_spec_property_naming', False) _configuration = kwargs.pop('_configuration', None) _visited_composed_classes = kwargs.pop('_visited_composed_classes', ()) if args: raise ApiTypeError( "Invalid positional arguments=%s passed to %s. Remove those invalid positional arguments." % ( args, self.__class__.__name__, ), path_to_item=_path_to_item, valid_classes=(self.__class__,), ) self._data_store = {} self._check_type = _check_type self._spec_property_naming = _spec_property_naming self._path_to_item = _path_to_item self._configuration = _configuration self._visited_composed_classes = _visited_composed_classes + (self.__class__,) self.value = value if kwargs: raise ApiTypeError( "Invalid named arguments=%s passed to %s. Remove those invalid named arguments." % ( kwargs, self.__class__.__name__, ), path_to_item=_path_to_item, valid_classes=(self.__class__,), ) return self
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/BinTools-0.2.0.zip/BinTools-0.2.0/README.txt
=========== Python modules for Software Development Tools =========== PyDevTools is a suite of python modules for the rapid prototyping of software development tools. Currently, the project include modules for: * ELF handling * DWARF handling Next, we are planning to add a GDB module containing : * `RSP <http://sourceware.org/gdb/current/onlinedocs/gdb/Remote-Protocol.html>` * `MI <http://sourceware.org/gdb/current/onlinedocs/gdb/GDB_002fMI.html>` protocols implementation, this will allow to drive gdbserver and gdb from python scripts. Please, report a new issue for bugs, or desired features. (possibly, attaching the target ELF file to reproduce the issue). 'E-mail <mailto:[email protected]>`the project owner for any feedback, or for joining the project.
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/KratosDelaunayMeshingApplication-9.1.3-1-cp37-cp37m-win_amd64.whl/KratosMultiphysics/DelaunayMeshingApplication/mesher.py
from __future__ import print_function, absolute_import, division # makes KratosMultiphysics backward compatible with python 2.6 and 2.7 #import kratos core and applications import KratosMultiphysics import KratosMultiphysics.DelaunayMeshingApplication as KratosDelaunay def CreateMesher(main_model_part, meshing_parameters): return Mesher(main_model_part, meshing_parameters) class Mesher(object): # def __init__(self, main_model_part, meshing_parameters): self.echo_level = 1 self.main_model_part = main_model_part self.MeshingParameters = meshing_parameters self.model_part = self.main_model_part if( self.main_model_part.Name != self.MeshingParameters.GetSubModelPartName() ): self.model_part = self.main_model_part.GetSubModelPart(self.MeshingParameters.GetSubModelPartName()) # def Initialize(self, dimension): self.dimension = dimension # set mesher if(self.dimension == 2): self.mesher = KratosDelaunay.TriangularMesh2DMesher() elif(self.dimension == 3): self.mesher = KratosDelaunay.TetrahedralMesh3DMesher() self.mesher.SetEchoLevel(self.echo_level) self.mesher.SetMeshingParameters(self.MeshingParameters) self.SetPreMeshingProcesses() self.SetPostMeshingProcesses() self.mesher.Initialize() # def InitializeMeshing(self): self.MeshingParameters.InitializeMeshing() # set execution flags: to set the options to be executed in methods and processes execution_options = KratosMultiphysics.Flags() execution_options.Set(KratosDelaunay.MesherUtilities.INITIALIZE_MESHER_INPUT, False) execution_options.Set(KratosDelaunay.MesherUtilities.FINALIZE_MESHER_INPUT, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_NODES_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_ELEMENTS_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_NEIGHBOURS_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_FACES_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.SELECT_TESSELLATION_ELEMENTS, False) execution_options.Set(KratosDelaunay.MesherUtilities.KEEP_ISOLATED_NODES, False) self.MeshingParameters.SetExecutionOptions(execution_options) # set mesher flags: to set options for the mesher (triangle 2D, tetgen 3D) if( self.dimension == 2 ): pass #REFINE #ADD NODES #to add_nodes automatically and refine the mesh ("q"-quality mesh and "a"-area constraint switches) # "YYJaqrn" "YJq1.4arn" "Jq1.4arn" #refine #mesher_flags = "YJq1.4arnQ" #refine constrained #mesher_flags = "pYJq1.4arnCQ" #INSERT NODES #to insert a set of given points and refine the mesh # "rinYYJQ" "rinYYJQ" "rinJQ" "rinQ" #refine #mesher_flags = "rinJQ" #refine constrained #mesher_flags = "rinYYJQ" #refine without adding nodes #mesher_flags = "YJrnQ" #RECONNECT #to reconnect a set of points only #mesher_flags = "nQP" #constrained #mesher_flags = "pnBYYQ" #BOUNDARY SEARCH #to get conectivities, boundaries and neighbours only #mesher_flags = "ncEBQ" if( self.dimension == 3 ): #other flags pass # def SetPreMeshingProcesses(self): # The order set is the order of execution: # process to refine elements / refine boundary refine_mesh_elements = KratosDelaunay.RefineElementsOnThreshold(self.model_part, self.MeshingParameters, self.echo_level) self.mesher.SetPreMeshingProcess(refine_mesh_elements) # process to refine boundary / contact boundary refine_mesh_boundary = RefineConditions(self.model_part, self.RefiningParameters, self.echo_level) self.mesher.SetPreMeshingProcess(refine_mesh_boundary) # process to remove nodes / remove boundary remove_mesh_nodes = KratosDelaunay.RemoveNodes(self.model_part, self.MeshingParameters, self.echo_level) self.mesher.SetPreMeshingProcess(remove_mesh_nodes) # def SetPostMeshingProcesses(self): # The order set is the order of execution: #generate new particles generate_particles = KratosDelaunay.GenerateNewNodes(self.model_part, self.MeshingParameters, self.echo_level) self.mesher.SetPostMeshingProcess(generate_particles) #select mesh elements select_mesh_elements = KratosDelaunay.SelectElements(self.model_part, self.MeshingParameters, self.echo_level) self.mesher.SetPostMeshingProcess(select_mesh_elements) #rebuild elements rebuild_mesh_elements = KratosDelaunay.GenerateNewElements(self.model_part, self.MeshingParameters, self.echo_level) self.mesher.SetPostMeshingProcess(rebuild_mesh_elements) #rebuild boundary rebuild_mesh_boundary = KratosDelaunay.GenerateNewConditions(self.model_part, self.MeshingParameters, self.echo_level) self.mesher.SetPostMeshingProcess(rebuild_mesh_boundary) # def FinalizeMeshing(self): # reset execution flags: to unset the options to be executed in methods and processes execution_options = KratosMultiphysics.Flags() # all flags execution_options.Set(KratosDelaunay.MesherUtilities.INITIALIZE_MESHER_INPUT, False) execution_options.Set(KratosDelaunay.MesherUtilities.FINALIZE_MESHER_INPUT, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_NODES_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_ELEMENTS_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_NEIGHBOURS_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.TRANSFER_KRATOS_FACES_TO_MESHER, False) execution_options.Set(KratosDelaunay.MesherUtilities.SELECT_TESSELLATION_ELEMENTS, False) execution_options.Set(KratosDelaunay.MesherUtilities.KEEP_ISOLATED_NODES, False) self.MeshingParameters.SetExecutionOptions(execution_options) self.MeshingParameters.FinalizeMeshing() # def ExecuteMeshing(self): self.InitializeMeshing() #set execution flags and mesher flags self.mesher.ExecuteMeshing(self.model_part) self.FinalizeMeshing() #set execution flags and mesher flags # def SetEchoLevel(self, echo_level): self.echo_level = echo_level # @classmethod def _class_prefix(self): header = "::[-------Mesher------]::" return header
PypiClean
/LeanSim-0.1.tar.gz/LeanSim-0.1/leansim/workflow.py
from __future__ import print_function from time import sleep import os from .worker import Worker import sys class Workflow: def __init__(self, workers): self.workers = workers self.work_done = 0 @property def total_work(self): return sum(w.wip + w.done for w in self.workers) - self.workers[-1].done @property def wip(self): return self.total_work - self.workers[0].todo def step(self): for worker in self.workers[::-1]: work_done = worker.work() worker.push() self.work_done += work_done def process(self, work, verbose=False, sleep_time=0, start_delay=1.5): """Returns number of steps to process some piece of work.""" self.workers[0].todo = work if verbose: os.system('cls' if os.name == 'nt' else 'clear') print(self) sleep(start_delay) steps = 0 while self.total_work: steps += 1 self.step() if verbose: os.system('cls' if os.name == 'nt' else ' clear') print(self) print('Steps: {}'.format(steps), end='\n\n') sys.stdout.flush() if sleep_time: sleep(sleep_time) return steps def __repr__(self): rep = '------------------------- LEAN SIM --------------------------------\n\n' for attr in ['task_duration', 'capacity', 'batch_size', 'max_todo', '', 'todo', 'doing', 'done', '', 'wip']: rep += '{:>15}:'.format(attr) for w in self.workers: if attr: val = getattr(w, attr) val = len(val) if hasattr(val, '__iter__') else val rep += '\t {}'.format(val if val else ' ') else: rep += '\t---' rep += '\n' rep += '\n-------------------------------------------------------------------\n' for attr in ['total_work', 'wip']: rep += '{}: {} '.format(attr, getattr(self, attr)) return rep @classmethod def run_chained_process(cls, work=20, workers=4, verbose=False, sleep_time=0.2, bottleneck_worker=None, **worker_kwargs): queue = [Worker(**worker_kwargs) for _ in range(workers)] for w1, w2 in zip(queue[:-1], queue[1:]): w1.target = w2 workflow = cls(workers=queue) if bottleneck_worker: workflow.workers[bottleneck_worker - 1].task_duration = workflow.workers[0].task_duration * 4 steps = workflow.process(work=work, verbose=verbose, sleep_time=sleep_time) return steps
PypiClean