Unnamed: 0
int64
0
389k
code
stringlengths
26
79.6k
docstring
stringlengths
1
46.9k
8,700
def apply_chromatic_adaptation_on_color(color, targ_illum, adaptation=): xyz_x = color.xyz_x xyz_y = color.xyz_y xyz_z = color.xyz_z orig_illum = color.illuminant targ_illum = targ_illum.lower() observer = color.observer adaptation = adaptation.lower() color.xyz_x, color.xyz_y, color.xyz_z = apply_chromatic_adaptation( xyz_x, xyz_y, xyz_z, orig_illum, targ_illum, observer=observer, adaptation=adaptation) color.set_illuminant(targ_illum) return color
Convenience function to apply an adaptation directly to a Color object.
8,701
def generate_apsara_log_config(json_value): input_detail = json_value[] output_detail = json_value[] config_name = json_value[] logSample = json_value.get(, ) logstore_name = output_detail[] endpoint = output_detail.get(, ) log_path = input_detail[] file_pattern = input_detail[] log_begin_regex = input_detail.get(, ) topic_format = input_detail[] filter_keys = input_detail[] filter_keys_reg = input_detail[] config = ApsaraLogConfigDetail(config_name, logstore_name, endpoint, log_path, file_pattern, log_begin_regex, topic_format, filter_keys, filter_keys_reg, logSample) return config
Generate apsara logtail config from loaded json value :param json_value: :return:
8,702
def xmlrpc_task_done(self, result): (task_id, task_results) = result del self.scheduled_tasks[task_id] self.task_store.update_results(task_id, task_results) self.results += 1 return True
Take the results of a computation and put it into the results list.
8,703
def _set_digraph_b(self, char): self.has_digraph_b = True self.active_vowel_ro = di_b_lt[char][0] self.active_dgr_b_info = di_b_lt[char]
Sets the second part of a digraph.
8,704
def aspirate(self, volume: float = None, location: Union[types.Location, Well] = None, rate: float = 1.0) -> : self._log.debug("aspirate {} from {} at {}" .format(volume, location if location else , rate)) if isinstance(location, Well): point, well = location.bottom() loc = types.Location( point + types.Point(0, 0, self.well_bottom_clearance), well) self.move_to(loc) elif isinstance(location, types.Location): loc = location self.move_to(location) elif location is not None: raise TypeError( .format(location)) elif self._ctx.location_cache: loc = self._ctx.location_cache else: raise RuntimeError( "If aspirate is called without an explicit location, another" " method that moves to a location (such as move_to or " "dispense) must previously have been called so the robot " "knows where it is.") cmds.do_publish(self.broker, cmds.aspirate, self.aspirate, , None, None, self, volume, loc, rate) self._hw_manager.hardware.aspirate(self._mount, volume, rate) cmds.do_publish(self.broker, cmds.aspirate, self.aspirate, , self, None, self, volume, loc, rate) return self
Aspirate a volume of liquid (in microliters/uL) using this pipette from the specified location If only a volume is passed, the pipette will aspirate from its current position. If only a location is passed, :py:meth:`aspirate` will default to its :py:attr:`max_volume`. :param volume: The volume to aspirate, in microliters. If not specified, :py:attr:`max_volume`. :type volume: int or float :param location: Where to aspirate from. If `location` is a :py:class:`.Well`, the robot will aspirate from :py:attr:`well_bottom_clearance` mm above the bottom of the well. If `location` is a :py:class:`.Location` (i.e. the result of :py:meth:`.Well.top` or :py:meth:`.Well.bottom`), the robot will aspirate from the exact specified location. If unspecified, the robot will aspirate from the current position. :param rate: The relative plunger speed for this aspirate. During this aspirate, the speed of the plunger will be `rate` * :py:attr:`aspirate_speed`. If not specified, defaults to 1.0 (speed will not be modified). :type rate: float :returns: This instance.
8,705
def update(self, y=None, inplace=False, **kwargs): kwargs.update({: kwargs.pop(, self.k)}) kwargs.update({: kwargs.pop(, self.pct)}) kwargs.update({: kwargs.pop(, self._truncated)}) if inplace: self._update(y, **kwargs) else: new = copy.deepcopy(self) new._update(y, **kwargs) return new
Add data or change classification parameters. Parameters ---------- y : array (n,1) array of data to classify inplace : bool whether to conduct the update in place or to return a copy estimated from the additional specifications. Additional parameters provided in **kwargs are passed to the init function of the class. For documentation, check the class constructor.
8,706
def toto(arch_name, comment=, clear=False, read_comment=False, list_members=False, time_show=False): if comment and clear: clingon.RunnerError("You cannot specify --comment and --clear together") z = None if not os.path.isfile(arch_name): print "Creating archive", arch_name z = zipfile.ZipFile(arch_name, ) for f in [x for x in glob.iglob() if not x.endswith()][:3]: print " Add file %s to %s" % (f, arch_name) z.write(f) if comment: mtime = os.path.getmtime(arch_name) if not z: z = zipfile.ZipFile(arch_name, ) z.comment = comment if z: z.close() if comment: os.utime(arch_name, (time.time(), mtime)) if read_comment: z = zipfile.ZipFile(arch_name, ) print "Comment:", z.comment, len(z.comment) if list_members: z = zipfile.ZipFile(arch_name, ) print "Members:", z.namelist() if time_show: print "Access time:", time.ctime(os.path.getatime(arch_name)) print "Modif time:", time.ctime(os.path.getmtime(arch_name))
Small utility for changing comment in a zip file without changing the file modification datetime.
8,707
def perform_command(self): if self.has_option([u"--list-parameters"]): return self.print_parameters() if len(self.actual_arguments) < 2: return self.print_help() container_path = self.actual_arguments[0] output_directory_path = self.actual_arguments[1] config_string = None if (len(self.actual_arguments)) > 2 and (not self.actual_arguments[2].startswith(u"-")): config_string = self.actual_arguments[2] validate = not self.has_option(u"--skip-validator") if self.has_option(u"--cewsubprocess"): self.rconf[RuntimeConfiguration.CEW_SUBPROCESS_ENABLED] = True if not self.check_input_file_or_directory(container_path): return self.ERROR_EXIT_CODE if not self.check_output_directory(output_directory_path): return self.ERROR_EXIT_CODE if validate: try: self.print_info(u"Validating the container (specify --skip-validator to bypass)...") validator = Validator(rconf=self.rconf, logger=self.logger) result = validator.check_container(container_path, config_string=config_string) if not result.passed: self.print_error(u"The given container is not valid:") self.print_error(result.pretty_print()) return self.ERROR_EXIT_CODE self.print_info(u"Validating the container... done") except Exception as exc: self.print_error(u"An unexpected error occurred while validating the container:") self.print_error(u"%s" % exc) return self.ERROR_EXIT_CODE try: self.print_info(u"Loading job from container...") executor = ExecuteJob(rconf=self.rconf, logger=self.logger) executor.load_job_from_container(container_path, config_string) self.print_info(u"Loading job from container... done") except Exception as exc: self.print_error(u"An unexpected error occurred while loading the job:") self.print_error(u"%s" % exc) return self.ERROR_EXIT_CODE try: self.print_info(u"Executing...") executor.execute() self.print_info(u"Executing... done") except Exception as exc: self.print_error(u"An unexpected error occurred while executing the job:") self.print_error(u"%s" % exc) return self.ERROR_EXIT_CODE try: self.print_info(u"Creating output container...") path = executor.write_output_container(output_directory_path) self.print_info(u"Creating output container... done") self.print_success(u"Created output file " % path) executor.clean(True) return self.NO_ERROR_EXIT_CODE except Exception as exc: self.print_error(u"An unexpected error occurred while writing the output container:") self.print_error(u"%s" % exc) return self.ERROR_EXIT_CODE
Perform command and return the appropriate exit code. :rtype: int
8,708
def add_node(self,node): if not isinstance(node, CondorDAGNode): raise CondorDAGError, "Nodes must be class CondorDAGNode or subclass" if not isinstance(node.job(), CondorDAGManJob): node.set_log_file(self.__log_file_path) self.__nodes.append(node) if self.__integer_node_names: node.set_name(str(self.__node_count)) self.__node_count += 1 if node.job() not in self.__jobs: self.__jobs.append(node.job())
Add a CondorDAGNode to this DAG. The CondorJob that the node uses is also added to the list of Condor jobs in the DAG so that a list of the submit files needed by the DAG can be maintained. Each unique CondorJob will be added once to prevent duplicate submit files being written. @param node: CondorDAGNode to add to the CondorDAG.
8,709
def _api_item_history(self, plugin, item, nb=0): return self._api_itemvalue(plugin, item, history=True, nb=int(nb))
Glances API RESTful implementation. Return the JSON representation of the couple plugin/history of item HTTP/200 if OK HTTP/400 if plugin is not found HTTP/404 if others error
8,710
def withdraw(self, amount): pg = self.usr.getPage("http://www.neopets.com/bank.phtml") try: results = pg.find(text = "Account Type:").parent.parent.parent.find_all("td", align="center") self.balance = results[1].text.replace(" NP", "") except Exception: logging.getLogger("neolib.user").exception("Could not parse userpgtypewithdrawamounts great to see you again" in pg.content: self.__loadDetails(pg) return True else: logging.getLogger("neolib.user").info("Failed to withdraw NPs for unknown reason. User NPs: " + str(self.usr.nps) + ". Amount: " + str(amount), {: pg}) return False
Withdraws specified neopoints from the user's account, returns result Parameters: amount (int) -- Amount of neopoints to withdraw Returns bool - True if successful, False otherwise Raises notEnoughBalance
8,711
def query(self, sql, parameters=None): try: self._cursor.execute(sql, parameters) except psycopg2.Error as err: self._incr_exceptions() raise err finally: self._incr_executions() return results.Results(self._cursor)
A generator to issue a query on the server, mogrifying the parameters against the sql statement. Results are returned as a :py:class:`queries.Results` object which can act as an iterator and has multiple ways to access the result data. :param str sql: The SQL statement :param dict parameters: A dictionary of query parameters :rtype: queries.Results :raises: queries.DataError :raises: queries.DatabaseError :raises: queries.IntegrityError :raises: queries.InternalError :raises: queries.InterfaceError :raises: queries.NotSupportedError :raises: queries.OperationalError :raises: queries.ProgrammingError
8,712
def push(self, value: Union[int, bytes]) -> None: if len(self.values) > 1023: raise FullStack() validate_stack_item(value) self.values.append(value)
Push an item onto the stack.
8,713
def _remove_from_world(self): self.on_remove_from_world() self._extensions = {} self._disable_forum_observation() self._world = None self._id = None
Clear all the internal data the token needed while it was part of the world. Note that this method doesn't actually remove the token from the world. That's what World._remove_token() does. This method is just responsible for setting the internal state of the token being removed.
8,714
def _setAttributes(self, attributes): atd = self.attribute_typecode atd_list = formatted_attribute_list = [] if not attributes: return formatted_attribute_list atd_list.append() idx = 0 while(idx < len(attributes)): a = attributes[idx] idx += 1 if a.isWildCard() and a.isDeclaration(): atd_list.append(\ \ % (atd, SCHEMA.XSD3) ) elif a.isDeclaration(): tdef = a.getTypeDefinition() if tdef is not None: tc = %(NAD.getAlias(tdef.getTargetNamespace()), self.mangle(type_class_name(tdef.getAttributeName())) ) else: t = a.getAttribute() try: tc = BTI.get_typeclass(t[1], t[0]) except: tc = ZSI.TC.String if tc is not None: tc = %tc key = None if a.getAttribute() == : key = % ( a.getTargetNamespace(), a.getAttribute() ) elif a.getAttribute() == : key = % a.getAttribute() else: raise ContainerError, \ \ % a.getAttribute() atd_list.append(\ % (atd, key, tc) ) elif a.isReference() and a.isAttributeGroup(): return formatted_attribute_list
parameters attributes -- a flat list of all attributes, from this list all items in attribute_typecode_dict will be generated into attrComponents. returns a list of strings representing the attribute_typecode_dict.
8,715
def dst_to_src(self, dst_file): for map in self.mappings: src_uri = map.dst_to_src(dst_file) if (src_uri is not None): return(src_uri) raise MapperError( "Unable to translate destination path (%s) " "into a source URI." % (dst_file))
Map destination path to source URI.
8,716
def get_img_tag(self, title=, alt_text=, **kwargs): try: style = [] for key in (, ): if key in kwargs: if isinstance(kwargs[key], (list, tuple, set)): style += list(kwargs[key]) else: style.append(kwargs[key]) if in kwargs: shape = self._get_shape_style(**kwargs) if shape: style.append("shape-outside: url()".format(shape)) attrs = { : alt_text, : title, **self.get_img_attrs(style, **kwargs) } return flask.Markup( self._wrap_link_target( kwargs, utils.make_tag( , attrs, start_end=kwargs.get()), title)) except FileNotFoundError as error: text = .format( html.escape(error.filename)) if in error.filename: text += text += return flask.Markup(text)
Build a <img> tag for the image with the specified options. Returns: an HTML fragment.
8,717
def ContainsKey(self, public_key): return self.ContainsKeyHash(Crypto.ToScriptHash(public_key.encode_point(True), unhex=True))
Test if the wallet contains the supplied public key. Args: public_key (edcsa.Curve.point): a public key to test for its existance. e.g. KeyPair.PublicKey Returns: bool: True if exists, False otherwise.
8,718
def isSelectionPositionValid(self, selPos: tuple): if selPos is None: return False if len(selPos) != 4: return False check1 = self.isPositionValid(*selPos[:2]) check2 = self.isPositionValid(*selPos[2:]) if check1 and check2: return True else: return False
Return **True** if the start- and end position denote valid positions within the document. |Args| * ``selPos`` (**tuple**): tuple with four integers. |Returns| **bool**: **True** if the positions are valid; **False** otherwise. |Raises| * **None**
8,719
def get_health_events(self, recipient): if recipient not in self.addresses_events: self.start_health_check(recipient) return self.addresses_events[recipient]
Starts a healthcheck task for `recipient` and returns a HealthEvents with locks to react on its current state.
8,720
def cached_download(url, name): clean_name = os.path.normpath(name) if clean_name != name: raise ValueError("{} is not normalized.".format(name)) for dir_ in iter_data_dirs(): path = os.path.join(dir_, name) if os.path.exists(path): return path dir_ = next(iter_data_dirs(True)) path = os.path.join(dir_, name) log.info("Downloading {} to {}".format(url, path)) response = urlopen(url) if response.getcode() != 200: raise ValueError("HTTP {}".format(response.getcode())) dir_ = os.path.dirname(path) try: os.makedirs(dir_) except OSError as e: if e.errno != errno.EEXIST: raise tmp_path = path + with open(tmp_path, ) as fh: while True: chunk = response.read(8196) if chunk: fh.write(chunk) else: break os.rename(tmp_path, path) return path
Download the data at a URL, and cache it under the given name. The file is stored under `pyav/test` with the given name in the directory :envvar:`PYAV_TESTDATA_DIR`, or the first that is writeable of: - the current virtualenv - ``/usr/local/share`` - ``/usr/local/lib`` - ``/usr/share`` - ``/usr/lib`` - the user's home
8,721
def _write_error_batch_wait(future, batch, database, measurement, measurements): if not future.done(): ioloop.IOLoop.current().add_timeout( ioloop.IOLoop.current().time() + 0.025, _write_error_batch_wait, future, batch, database, measurement, measurements) return error = future.exception() if isinstance(error, httpclient.HTTPError): if error.code == 400: LOGGER.error( , database, batch, error.code, error.response.body) LOGGER.info(, database, batch, measurement) else: LOGGER.error( , database, batch, error.code) measurements = measurements + [measurement] elif isinstance(error, (TimeoutError, OSError, socket.error, select.error, ssl.socket_error)): LOGGER.error( , database, batch, error) _write_error_batch(batch, database, measurements + [measurement]) measurements = measurements + [measurement] if not measurements: LOGGER.info(, database, batch) return _write_error_batch(batch, database, measurements)
Invoked by the IOLoop, this method checks if the HTTP request future created by :meth:`_write_error_batch` is done. If it's done it will evaluate the result, logging any error and moving on to the next measurement. If there are no measurements left in the `measurements` argument, it will consider the batch complete. :param tornado.concurrent.Future future: The AsyncHTTPClient request future :param str batch: The batch ID :param str database: The database name for the measurements :param str measurement: The measurement the future is for :param list measurements: The measurements that failed to write as a batch
8,722
def _activity_import_doc(self, time_doc, activities): batch_updates = [time_doc] td_start = time_doc[] activities = filter(lambda act: (act[0] < td_start and act[1] in time_doc), activities) creation_field = self.lconfig.get() activities.sort(reverse=True, key=lambda o: o[0]) new_doc = {} for when, field, removed, added in activities: last_doc = batch_updates.pop() if last_doc[] == when: new_doc = deepcopy(last_doc) last_doc = batch_updates.pop() else: new_doc = deepcopy(last_doc) new_doc[] = when new_doc[] = when last_doc[] = when last_val = last_doc[field] new_val, inconsistent = self._activity_backwards(new_doc[field], removed, added) new_doc[field] = new_val if inconsistent: self._log_inconsistency(last_doc, last_val, field, removed, added, when) new_doc[] = {} if not new_doc.get() else new_doc[] return batch_updates
Import activities for a single document into timeline.
8,723
def byteorder_isnative(byteorder): if byteorder in (, sys.byteorder): return True keys = {: , : } return keys.get(byteorder, byteorder) == keys[sys.byteorder]
Return if byteorder matches the system's byteorder. >>> byteorder_isnative('=') True
8,724
def calculate_leaf_paths(self): reverse_xref = {} leaves = set() for v in self.value.values(): if v.leaf: leaves.add(v) for xref in v.value_xref: reverse_xref.setdefault(xref, []).append(v.ident) for leaf in leaves: self.calculate_leaf_path(leaf, reverse_xref)
Build map of reverse xrefs then traverse backwards marking path to leaf for all leaves.
8,725
def update_text(self): self.write() try: newtext = self.text_queue.get_nowait() self._text = newtext except Empty: pass
Write the current text, and check for any new text changes. This also updates the elapsed time.
8,726
def gcm_send_message(registration_id, data, encoding=, **kwargs): messenger = GCMMessenger(registration_id, data, encoding=encoding, **kwargs) return messenger.send_plain()
Standalone method to send a single gcm notification
8,727
def consume(self, data): if not self._started: self.fire(JSONStreamer.DOC_START_EVENT) self._started = True self._file_like.write(data) try: self._parser.parse(self._file_like) except YajlError as ye: raise JSONStreamerException(ye.value)
Takes input that must be parsed Note: Attach all your listeners before calling this method Args: data (str): input json string
8,728
def run_filter_radia(job, bams, radia_file, univ_options, radia_options, chrom): job.fileStore.logToMaster( % (univ_options[], chrom)) work_dir = job.fileStore.getLocalTempDir() input_files = { : bams[], : bams[], : bams[], : bams[], : bams[], : bams[], : radia_file, : radia_options[], : radia_options[] } input_files = get_files_from_filestore(job, input_files, work_dir, docker=True) filterradia_output = .join([, chrom, ]) filterradia_log = .join([work_dir, , chrom, ]) parameters = [univ_options[], chrom.lstrip(), input_files[], , , , , , , , , , , , , , , , , , , , , input_files[], , , docker_path(filterradia_log)] docker_call(tool=, tool_parameters=parameters, work_dir=work_dir, dockerhub=univ_options[]) output_files = defaultdict() output_files[filterradia_output] = \ job.fileStore.writeGlobalFile(.join([work_dir, , univ_options[], , chrom, ])) output_files[os.path.basename(filterradia_log)] = \ job.fileStore.writeGlobalFile(filterradia_log) return output_files
This module will run filterradia on the RNA and DNA bams. ARGUMENTS 1. bams: REFER ARGUMENTS of run_radia() 2. univ_options: REFER ARGUMENTS of run_radia() 3. radia_file: <JSid of vcf generated by run_radia()> 3. radia_options: REFER ARGUMENTS of run_radia() 4. chrom: REFER ARGUMENTS of run_radia() RETURN VALUES 1. Dict of filtered radia output vcf and logfile |- 'radia_filtered_CHROM.vcf': <JSid> +- 'radia_filtered_CHROM_radia.log': <JSid>
8,729
def find_all(self, predicate): for _nid, entry in self._registry.items(): if predicate(entry): yield entry
Returns a generator that produces a sequence of Entry objects for which the predicate returned True. Args: predicate: A callable that returns a value coercible to bool.
8,730
def master_event(type, master=None): event_map = {: , : , : , : } if type == and master is not None: return .format(event_map.get(type), master) return event_map.get(type, None)
Centralized master event function which will return event type based on event_map
8,731
def remove_optional(annotation: type): origin = getattr(annotation, , None) args = getattr(annotation, , ()) if origin == Union and len(args) == 2 and args[1] == type(None): return args[0] else: return annotation
Optional[X] annotations are actually represented as Union[X, NoneType]. For our purposes, the "Optional" part is not interesting, so here we throw it away.
8,732
def node_to_text(self, node, prev_node_hint=None): if node is None: return "" if node.isNodeType(latexwalker.LatexCharsNode): if not self.strict_latex_spaces[] and len(node.chars.strip()) == 0: return "" return node.chars if node.isNodeType(latexwalker.LatexCommentNode): if self.keep_comments: if self.strict_latex_spaces[]: return + node.comment + else: return + node.comment + node.comment_post_space else: if self.strict_latex_spaces[]: return "" else: return node.comment_post_space if node.isNodeType(latexwalker.LatexGroupNode): contents = self._groupnodecontents_to_text(node) if self.keep_braced_groups and len(contents) >= self.keep_braced_groups_minlen: return "{" + contents + "}" return contents def apply_simplify_repl(node, simplify_repl, nodelistargs, what): if callable(simplify_repl): if in getfullargspec(simplify_repl)[0]: return simplify_repl(node, l2tobj=self) return simplify_repl(node) if in simplify_repl: try: return simplify_repl % tuple([self._groupnodecontents_to_text(nn) for nn in nodelistargs]) except (TypeError, ValueError): logger.warning( "WARNING: Error in configuration: {} failed its substitution!".format(what) ) return simplify_repl return simplify_repl if node.isNodeType(latexwalker.LatexMacroNode): macroname = node.macroname.rstrip() if macroname in self.macro_dict: mac = self.macro_dict[macroname] else: mac = self.macro_dict[] def get_macro_str_repl(node, macroname, mac): if mac.simplify_repl: return apply_simplify_repl(node, mac.simplify_repl, node.nodeargs, what="macro "%(macroname)) if mac.discard: return "" a = node.nodeargs if (node.nodeoptarg): a.prepend(node.nodeoptarg) return "".join([self._groupnodecontents_to_text(n) for n in a]) macrostr = get_macro_str_repl(node, macroname, mac) return macrostr if node.isNodeType(latexwalker.LatexEnvironmentNode): envname = node.envname.rstrip() if (envname in self.env_dict): envdef = self.env_dict[envname] else: envdef = self.env_dict[] if envdef.simplify_repl: return apply_simplify_repl(node, envdef.simplify_repl, node.nodelist, what="environment "%(envname)) if envdef.discard: return "" return self._nodelistcontents_to_text(node.nodelist) if node.isNodeType(latexwalker.LatexMathNode): if self.keep_inline_math: return latexwalker.math_node_to_latex(node) else: with _PushEquationContext(self): return self._nodelistcontents_to_text(node.nodelist) logger.warning("LatexNodes2Text.node_to_text(): Unknown node: %r", node) return ""
Return the textual representation of the given `node`. If `prev_node_hint` is specified, then the current node is formatted suitably as following the node given in `prev_node_hint`. This might affect how much space we keep/discard, etc.
8,733
def show_quickref(self): from IPython.core.usage import quick_reference self.main.help.show_plain_text(quick_reference)
Show IPython Cheat Sheet
8,734
def run_opt(self, popsize, numgen, processors, plot=False, log=False, **kwargs): self._params[] = popsize self._params[] = numgen self._params[] = processors self._params[] = plot self._params[] = log self._params.update(**kwargs) self.halloffame = tools.HallOfFame(1) self.stats = tools.Statistics(lambda thing: thing.fitness.values) self.stats.register("avg", numpy.mean) self.stats.register("std", numpy.std) self.stats.register("min", numpy.min) self.stats.register("max", numpy.max) self.logbook = tools.Logbook() self.logbook.header = ["gen", "evals"] + self.stats.fields self._params[] = 0 start_time = datetime.datetime.now() self.initialize_pop() for g in range(self._params[]): self.update_pop() self.halloffame.update(self.population) self.logbook.record(gen=g, evals=self._params[], **self.stats.compile(self.population)) print(self.logbook.stream) end_time = datetime.datetime.now() time_taken = end_time - start_time self._params[] = time_taken print("Evaluated {0} models in total".format( self._params[])) print("Best fitness is {0}".format(self.halloffame[0].fitness)) print("Best parameters are {0}".format(self.parse_individual( self.halloffame[0]))) for i, entry in enumerate(self.halloffame[0]): if entry > 0.95: print( "Warning! Parameter {0} is at or near maximum allowed " "value\n".format(i + 1)) elif entry < -0.95: print( "Warning! Parameter {0} is at or near minimum allowed " "value\n".format(i + 1)) if self._params[]: self.log_results() if self._params[]: print() plt.figure(figsize=(5, 5)) plt.plot(range(len(self.logbook.select())), self.logbook.select()) plt.xlabel(, fontsize=20) plt.ylabel(, fontsize=20)
Runs the optimizer. :param popsize: :param numgen: :param processors: :param plot: :param log: :param kwargs: :return:
8,735
def parse_csv(self, infile, delimiter=",", decimal_sep="."): "Parse template format csv file and create elements dict" keys = (,,,,,,,, ,,,,, ,,, ) self.elements = [] self.pg_no = 0 if not PY3K: f = open(infile, ) else: f = open(infile) for row in csv.reader(f, delimiter=delimiter): kargs = {} for i,v in enumerate(row): if not v.startswith("name'].lower() for v in self.elements]
Parse template format csv file and create elements dict
8,736
def merge(revision, branch_label, message, list_revisions=): alembic_command.merge( config=get_config(), revisions=list_revisions, message=message, branch_label=branch_label, rev_id=revision )
Merge two revision together, create new revision file
8,737
def get_containers(self): images = {} for x in self._docker.images.list(filters={"label": "org.inginious.grading.name"}): try: title = x.labels["org.inginious.grading.name"] created = datetime.strptime(x.attrs[][:-4], "%Y-%m-%dT%H:%M:%S.%f").timestamp() ports = [int(y) for y in x.labels["org.inginious.grading.ports"].split( ",")] if "org.inginious.grading.ports" in x.labels else [] images[x.attrs[]] = {"title": title, "created": created, "ports": ports} except: logging.getLogger("inginious.agent").exception("Container %s is badly formatted", title) latest = {} for img_id, img_c in images.items(): if img_c["title"] not in latest or latest[img_c["title"]]["created"] < img_c["created"]: latest[img_c["title"]] = {"id": img_id, "created": img_c["created"], "ports": img_c["ports"]} return latest
:return: a dict of available containers in the form { "name": { #for example, "default" "id": "container img id", # "sha256:715c5cb5575cdb2641956e42af4a53e69edf763ce701006b2c6e0f4f39b68dd3" "created": 12345678 # create date "ports": [22, 434] # list of ports needed } }
8,738
def _verify_docker_image_size(self, image_name): shell_call([, , image_name]) try: image_size = subprocess.check_output( [, , , image_name]).strip() image_size = int(image_size) except (ValueError, subprocess.CalledProcessError) as e: logging.error(, e) return False logging.info(, image_name, image_size) if image_size > MAX_DOCKER_IMAGE_SIZE: logging.error(, MAX_DOCKER_IMAGE_SIZE) return image_size <= MAX_DOCKER_IMAGE_SIZE
Verifies size of Docker image. Args: image_name: name of the Docker image. Returns: True if image size is within the limits, False otherwise.
8,739
def default(self, statement: Statement) -> Optional[bool]: if self.default_to_shell: if not in self.exclude_from_history: self.history.append(statement) return self.do_shell(statement.command_and_args) else: err_msg = self.default_error.format(statement.command) self.decolorized_write(sys.stderr, "{}\n".format(err_msg))
Executed when the command given isn't a recognized command implemented by a do_* method. :param statement: Statement object with parsed input
8,740
def get_pr_review_status(pr: PullRequestDetails) -> Any: url = ("https://api.github.com/repos/{}/{}/pulls/{}/reviews" "?access_token={}".format(pr.repo.organization, pr.repo.name, pr.pull_id, pr.repo.access_token)) response = requests.get(url) if response.status_code != 200: raise RuntimeError( .format( response.status_code, response.content)) return json.JSONDecoder().decode(response.content.decode())
References: https://developer.github.com/v3/pulls/reviews/#list-reviews-on-a-pull-request
8,741
def submit_combine(basename, readers, job_ids=None, project_name=None): sub = PmidSubmitter(basename, readers, project_name) sub.job_list = job_ids sub.submit_combine() return sub
Submit a batch job to combine the outputs of a reading job. This function is provided for backwards compatibility. You should use the PmidSubmitter and submit_combine methods.
8,742
def patch( target, new=DEFAULT, spec=None, create=False, spec_set=None, autospec=None, new_callable=None, **kwargs ): getter, attribute = _get_target(target) return _patch( getter, attribute, new, spec, create, spec_set, autospec, new_callable, kwargs )
`patch` acts as a function decorator, class decorator or a context manager. Inside the body of the function or with statement, the `target` is patched with a `new` object. When the function/with statement exits the patch is undone. If `new` is omitted, then the target is replaced with a `MagicMock`. If `patch` is used as a decorator and `new` is omitted, the created mock is passed in as an extra argument to the decorated function. If `patch` is used as a context manager the created mock is returned by the context manager. `target` should be a string in the form `'package.module.ClassName'`. The `target` is imported and the specified object replaced with the `new` object, so the `target` must be importable from the environment you are calling `patch` from. The target is imported when the decorated function is executed, not at decoration time. The `spec` and `spec_set` keyword arguments are passed to the `MagicMock` if patch is creating one for you. In addition you can pass `spec=True` or `spec_set=True`, which causes patch to pass in the object being mocked as the spec/spec_set object. `new_callable` allows you to specify a different class, or callable object, that will be called to create the `new` object. By default `MagicMock` is used. A more powerful form of `spec` is `autospec`. If you set `autospec=True` then the mock with be created with a spec from the object being replaced. All attributes of the mock will also have the spec of the corresponding attribute of the object being replaced. Methods and functions being mocked will have their arguments checked and will raise a `TypeError` if they are called with the wrong signature. For mocks replacing a class, their return value (the 'instance') will have the same spec as the class. Instead of `autospec=True` you can pass `autospec=some_object` to use an arbitrary object as the spec instead of the one being replaced. By default `patch` will fail to replace attributes that don't exist. If you pass in `create=True`, and the attribute doesn't exist, patch will create the attribute for you when the patched function is called, and delete it again afterwards. This is useful for writing tests against attributes that your production code creates at runtime. It is off by by default because it can be dangerous. With it switched on you can write passing tests against APIs that don't actually exist! Patch can be used as a `TestCase` class decorator. It works by decorating each test method in the class. This reduces the boilerplate code when your test methods share a common patchings set. `patch` finds tests by looking for method names that start with `patch.TEST_PREFIX`. By default this is `test`, which matches the way `unittest` finds tests. You can specify an alternative prefix by setting `patch.TEST_PREFIX`. Patch can be used as a context manager, with the with statement. Here the patching applies to the indented block after the with statement. If you use "as" then the patched object will be bound to the name after the "as"; very useful if `patch` is creating a mock object for you. `patch` takes arbitrary keyword arguments. These will be passed to the `Mock` (or `new_callable`) on construction. `patch.dict(...)`, `patch.multiple(...)` and `patch.object(...)` are available for alternate use-cases.
8,743
def invert_affine_mat44(mat): inverted = Matrix44() for i in range(3): for j in range(3): inverted.data[i][j] = mat.data[j][i] for row in range(3): inverted.data[3][row] = ( -inverted.data[0][row] * mat.data[3][0] + -inverted.data[1][row] * mat.data[3][1] + -inverted.data[2][row] * mat.data[3][2]) return inverted
Assumes there is only rotate, translate, and uniform scale componenets to the matrix.
8,744
def getReadLengths(reads, gapChars): gapChars = set(gapChars) result = {} for read in reads: result[read.id] = len(read) - sum( character in gapChars for character in read.sequence) return result
Get all read lengths, excluding gap characters. @param reads: A C{Reads} instance. @param gapChars: A C{str} of sequence characters considered to be gaps. @return: A C{dict} keyed by read id, with C{int} length values.
8,745
def codegen(lang, i, schema_metadata, loader ): j = schema.extend_and_specialize(i, loader) gen = None if lang == "python": gen = PythonCodeGen(sys.stdout) elif lang == "java": gen = JavaCodeGen(schema_metadata.get("$base", schema_metadata.get("id"))) else: raise Exception("Unsupported code generation language " % lang) assert gen is not None gen.prologue() document_roots = [] for rec in j: if rec["type"] in ("enum", "record"): gen.type_loader(rec) gen.add_vocab(shortname(rec["name"]), rec["name"]) for rec in j: if rec["type"] == "enum": for symbol in rec["symbols"]: gen.add_vocab(shortname(symbol), symbol) if rec["type"] == "record": if rec.get("documentRoot"): document_roots.append(rec["name"]) field_names = [] for field in rec.get("fields", []): field_names.append(shortname(field["name"])) idfield = "" for field in rec.get("fields", []): if field.get("jsonldPredicate") == "@id": idfield = field.get("name") gen.begin_class(rec["name"], aslist(rec.get("extends", [])), rec.get("doc", ""), rec.get("abstract", False), field_names, idfield) gen.add_vocab(shortname(rec["name"]), rec["name"]) for field in rec.get("fields", []): if field.get("jsonldPredicate") == "@id": fieldpred = field["name"] optional = bool("https://w3id.org/cwl/salad uri_loader = gen.uri_loader(gen.type_loader(field["type"]), True, False, None) gen.declare_id_field(fieldpred, uri_loader, field.get("doc"), optional) break for field in rec.get("fields", []): optional = bool("https://w3id.org/cwl/salad type_loader = gen.type_loader(field["type"]) jld = field.get("jsonldPredicate") fieldpred = field["name"] if isinstance(jld, MutableMapping): ref_scope = jld.get("refScope") if jld.get("typeDSL"): type_loader = gen.typedsl_loader(type_loader, ref_scope) elif jld.get("_type") == "@id": type_loader = gen.uri_loader(type_loader, jld.get("identity", False), False, ref_scope) elif jld.get("_type") == "@vocab": type_loader = gen.uri_loader(type_loader, False, True, ref_scope) map_subject = jld.get("mapSubject") if map_subject: type_loader = gen.idmap_loader( field["name"], type_loader, map_subject, jld.get("mapPredicate")) if "_id" in jld and jld["_id"][0] != "@": fieldpred = jld["_id"] if jld == "@id": continue gen.declare_field(fieldpred, type_loader, field.get("doc"), optional) gen.end_class(rec["name"], field_names) root_type = list(document_roots) root_type.append({ "type": "array", "items": document_roots }) gen.epilogue(gen.type_loader(root_type))
Generate classes with loaders for the given Schema Salad description.
8,746
def _split_generators(self, dl_manager): url = _DL_URLS[self.builder_config.name] data_dirs = dl_manager.download_and_extract(url) path_to_dataset = os.path.join(data_dirs, tf.io.gfile.listdir(data_dirs)[0]) train_a_path = os.path.join(path_to_dataset, "trainA") train_b_path = os.path.join(path_to_dataset, "trainB") test_a_path = os.path.join(path_to_dataset, "testA") test_b_path = os.path.join(path_to_dataset, "testB") return [ tfds.core.SplitGenerator( name="trainA", num_shards=10, gen_kwargs={ "path": train_a_path, "label": "A", }), tfds.core.SplitGenerator( name="trainB", num_shards=10, gen_kwargs={ "path": train_b_path, "label": "B", }), tfds.core.SplitGenerator( name="testA", num_shards=1, gen_kwargs={ "path": test_a_path, "label": "A", }), tfds.core.SplitGenerator( name="testB", num_shards=1, gen_kwargs={ "path": test_b_path, "label": "B", }), ]
Returns SplitGenerators.
8,747
def process_bool_arg(arg): if isinstance(arg, bool): return arg elif isinstance(arg, basestring): if arg.lower() in ["true", "1"]: return True elif arg.lower() in ["false", "0"]: return False
Determine True/False from argument
8,748
def get_var_dict_from_ctx(ctx: commands.Context, prefix: str = ): raw_var_dict = { : ctx.author, : ctx.bot, : ctx.channel, : ctx, : discord.utils.find, : discord.utils.get, : ctx.guild, : ctx.message, : ctx.message } return {f: v for k, v in raw_var_dict.items()}
Returns the dict to be used in REPL for a given Context.
8,749
def exportPreflibFile(self, fileName): elecType = self.getElecType() if elecType != "soc" and elecType != "toc" and elecType != "soi" and elecType != "toi": print("ERROR: printing current type to preflib format is not supported") exit() reverseRankMaps = self.getReverseRankMaps() outfileObj = open(fileName, ) outfileObj.write(str(self.numCands)) for candInt, cand in self.candMap.items(): outfileObj.write("\n" + str(candInt) + "," + cand) preferenceCount = 0 for preference in self.preferences: preferenceCount += preference.count outfileObj.write("\n" + str(self.numVoters) + "," + str(preferenceCount) + "," + str(len(self.preferences))) for i in range(0, len(reverseRankMaps)): outfileObj.write("\n" + str(self.preferences[i].count)) reverseRankMap = reverseRankMaps[i] sortedKeys = sorted(reverseRankMap.keys()) for key in sortedKeys: cands = reverseRankMap[key] if len(cands) == 1: outfileObj.write("," + str(cands[0])) elif len(cands) > 1: outfileObj.write(",{" + str(cands[0])) for j in range(1, len(cands)): outfileObj.write("," + str(cands[j])) outfileObj.write("}") outfileObj.close()
Exports a preflib format file that contains all the information of the current Profile. :ivar str fileName: The name of the output file to be exported.
8,750
def get_spot_value(self, assets, field, dt, data_frequency): assets_is_scalar = False if isinstance(assets, (AssetConvertible, PricingDataAssociable)): assets_is_scalar = True else: try: iter(assets) except TypeError: raise TypeError( "Unexpected value of type {}." .format(type(assets)) ) session_label = self.trading_calendar.minute_to_session_label(dt) if assets_is_scalar: return self._get_single_asset_value( session_label, assets, field, dt, data_frequency, ) else: get_single_asset_value = self._get_single_asset_value return [ get_single_asset_value( session_label, asset, field, dt, data_frequency, ) for asset in assets ]
Public API method that returns a scalar value representing the value of the desired asset's field at either the given dt. Parameters ---------- assets : Asset, ContinuousFuture, or iterable of same. The asset or assets whose data is desired. field : {'open', 'high', 'low', 'close', 'volume', 'price', 'last_traded'} The desired field of the asset. dt : pd.Timestamp The timestamp for the desired value. data_frequency : str The frequency of the data to query; i.e. whether the data is 'daily' or 'minute' bars Returns ------- value : float, int, or pd.Timestamp The spot value of ``field`` for ``asset`` The return type is based on the ``field`` requested. If the field is one of 'open', 'high', 'low', 'close', or 'price', the value will be a float. If the ``field`` is 'volume' the value will be a int. If the ``field`` is 'last_traded' the value will be a Timestamp.
8,751
def new_table_graphicFrame(cls, id_, name, rows, cols, x, y, cx, cy): graphicFrame = cls.new_graphicFrame(id_, name, x, y, cx, cy) graphicFrame.graphic.graphicData.uri = GRAPHIC_DATA_URI_TABLE graphicFrame.graphic.graphicData.append( CT_Table.new_tbl(rows, cols, cx, cy) ) return graphicFrame
Return a ``<p:graphicFrame>`` element tree populated with a table element.
8,752
def reply_topic(self, topic_id, content): data = { : content, : self._request.cookies.get() } url = % topic_id r = self.request(url, , data=data) j = r.json() if j[] == 0: return j[][][]
小组回帖 :return: 帖子 id 或 ``None``
8,753
def get_host_health_temperature_sensors(self, data=None): data = self.get_host_health_data(data) d = data[][][] if not isinstance(d, list): d = [d] return d
Get the health Temp Sensor report. :param: the data to retrieve from the server, defaults to None. :returns: the dictionary containing the temperature sensors information. :raises: IloConnectionError if failed connecting to the iLO. :raises: IloError, on an error from iLO.
8,754
def register_actions(self, shortcut_manager): assert isinstance(shortcut_manager, ShortcutManager) self.__shortcut_manager = shortcut_manager for controller in list(self.__child_controllers.values()): if controller not in self.__action_registered_controllers: try: controller.register_actions(shortcut_manager) except Exception as e: logger.error("Error while registering action for {0}: {1}".format(controller.__class__.__name__, e)) self.__action_registered_controllers.append(controller)
Register callback methods for triggered actions in all child controllers. :param rafcon.gui.shortcut_manager.ShortcutManager shortcut_manager: Shortcut Manager Object holding mappings between shortcuts and actions.
8,755
def nmap_discover(): rs = RangeSearch() rs_parser = rs.argparser arg = argparse.ArgumentParser(parents=[rs_parser], conflict_handler=) arg.add_argument(, metavar=, \ help=, \ type=str, choices=[, ]) arguments, nmap_args = arg.parse_known_args() tag = None if arguments.type == : tag = nmap_args.append() nmap_args.append() check_function = include_up_hosts elif arguments.type == : tag = nmap_args.append() check_function = include_hostnames ranges = rs.get_ranges(tags=[.format(tag)]) ranges = [r for r in ranges] ips = [] for r in ranges: ips.append(r.range) print_notification("Running nmap with args: {} on {} range(s)".format(nmap_args, len(ips))) result = nmap(nmap_args, ips) stats = import_nmap(result, tag, check_function) stats[] = len(ips) Logger().log(, "Nmap discover with args: {} on {} range(s)".format(nmap_args, len(ips)), stats) for r in ranges: r.add_tag(tag) r.save()
This function retrieves ranges from jackal Uses two functions of nmap to find hosts: ping: icmp / arp pinging of targets lookup: reverse dns lookup
8,756
def _get_labels_right(self, validate=None): labels = [] for compare_func in self.features: labels = labels + listify(compare_func.labels_right) if not is_label_dataframe(labels, validate): error_msg = "label is not found in the dataframe" raise KeyError(error_msg) return unique(labels)
Get all labels of the right dataframe.
8,757
def post(method, hmc, uri, uri_parms, body, logon_required, wait_for_completion): assert wait_for_completion is True storage_group_oid = uri_parms[0] storage_group_uri = + storage_group_oid try: storage_group = hmc.lookup_by_uri(storage_group_uri) except KeyError: raise InvalidResourceError(method, uri) check_required_fields(method, uri, body, []) candidate_adapter_port_uris = \ storage_group.properties[] for ap_uri in body[]: if ap_uri in candidate_adapter_port_uris: raise ConflictError(method, uri, 483, "Adapter port is already in candidate " "list of storage group %s: %s" % (storage_group.name, ap_uri)) else: candidate_adapter_port_uris.append(ap_uri)
Operation: Add Candidate Adapter Ports to an FCP Storage Group.
8,758
def visit_exec(self, node, parent): newnode = nodes.Exec(node.lineno, node.col_offset, parent) newnode.postinit( self.visit(node.body, newnode), _visit_or_none(node, "globals", self, newnode), _visit_or_none(node, "locals", self, newnode), ) return newnode
visit an Exec node by returning a fresh instance of it
8,759
def is_confusable(string, greedy=False, preferred_aliases=[]): preferred_aliases = [a.upper() for a in preferred_aliases] outputs = [] checked = set() for char in string: if char in checked: continue checked.add(char) char_alias = alias(char) if char_alias in preferred_aliases: } if not greedy: return [output] outputs.append(output) return outputs or False
Checks if ``string`` contains characters which might be confusable with characters from ``preferred_aliases``. If ``greedy=False``, it will only return the first confusable character found without looking at the rest of the string, ``greedy=True`` returns all of them. ``preferred_aliases=[]`` can take an array of unicode block aliases to be considered as your 'base' unicode blocks: - considering ``paρa``, - with ``preferred_aliases=['latin']``, the 3rd character ``ρ`` would be returned because this greek letter can be confused with latin ``p``. - with ``preferred_aliases=['greek']``, the 1st character ``p`` would be returned because this latin letter can be confused with greek ``ρ``. - with ``preferred_aliases=[]`` and ``greedy=True``, you'll discover the 29 characters that can be confused with ``p``, the 23 characters that look like ``a``, and the one that looks like ``ρ`` (which is, of course, *p* aka *LATIN SMALL LETTER P*). >>> confusables.is_confusable('paρa', preferred_aliases=['latin'])[0]['character'] 'ρ' >>> confusables.is_confusable('paρa', preferred_aliases=['greek'])[0]['character'] 'p' >>> confusables.is_confusable('Abç', preferred_aliases=['latin']) False >>> confusables.is_confusable('AlloΓ', preferred_aliases=['latin']) False >>> confusables.is_confusable('ρττ', preferred_aliases=['greek']) False >>> confusables.is_confusable('ρτ.τ', preferred_aliases=['greek', 'common']) False >>> confusables.is_confusable('ρττp') [{'homoglyphs': [{'c': 'p', 'n': 'LATIN SMALL LETTER P'}], 'alias': 'GREEK', 'character': 'ρ'}] :param string: A unicode string :type string: str :param greedy: Don't stop on finding one confusable character - find all of them. :type greedy: bool :param preferred_aliases: Script blocks aliases which we don't want ``string``'s characters to be confused with. :type preferred_aliases: list(str) :return: False if not confusable, all confusable characters and with what they are confusable otherwise. :rtype: bool or list
8,760
def step(self, **args): if self.sequenceType == None: raise AttributeError() if in args: if args[]: self.setContext() del args[] elif self.initContext: self.setContext() if self.initContext == 0: for context in list(self.contextLayers.values()): context.activationSet = 1 for key in args: args[key] = self.replacePatterns( args[key], key ) inputBankNames = [layer.name for layer in self.layers if layer.kind == ] outputBankNames = [layer.name for layer in self.layers if layer.kind == ] inputBankSizes = [layer.size for layer in self.layers if layer.kind == ] inputBankTotalSize = sum(inputBankSizes) inputArgSizes = [len(args[name]) for name in inputBankNames if name in args] inputArgTotalSize = sum(inputArgSizes) sequenceLength = inputArgTotalSize // inputBankTotalSize learning = self.learning totalRetvals = (0.0, 0, 0) totalPCorrect = {} for step in range(sequenceLength): if self.verbosity >= 1 or self.interactive: print("-----------------------------------Step dict = {} dict.update(args) for name in inputBankNames: if name in args: patternLength = self[name].size offset = step * patternLength if (offset + patternLength) >= len(args[name]): dict[name] = args[name][-patternLength:] else: dict[name] = args[name][offset:offset+patternLength] for name in outputBankNames: if name in args: patternLength = self[name].size offset = step * patternLength if (offset + patternLength) >= len(args[name]): dict[name] = args[name][-patternLength:] else: dict[name] = args[name][offset:offset+patternLength] for p in self.prediction: (inName, outName) = p inLayer = self.getLayer(inName) if not inLayer.type == : raise LayerError(Input\, inLayer.type) outLayer = self.getLayer(outName) if not outLayer.type == : raise LayerError(Output\, outLayer.type) if step == sequenceLength - 1: start = 0 if not self._sweeping: raise LayerError("Attempting to predict last item in sequence, but using step(). Use sweep() instead.") else: if self.currentSweepCount == None: pattern = self.getData(self.loadOrder[0]) for key in pattern: pattern[key] = self.replacePatterns( pattern[key], key ) if inName in inputBankNames: if inName in pattern: dict[outName] = pattern[inName][start:start+patternLength] else: pattern = self.getData(self.loadOrder[self.currentSweepCount+1]) for key in pattern: pattern[key] = self.replacePatterns( pattern[key], key ) if inName in inputBankNames: if inName in pattern: dict[outName] = pattern[inName][start:start+patternLength] else: start = (step + 1) * inLayer.size dict[outName] = args[inName][start:start+patternLength] if step < sequenceLength - 1: if not self.learnDuringSequence: self.learning = 0 retvals = self.networkStep(**dict) self.learning = learning totalRetvals = list(map(lambda x,y: x+y, totalRetvals[:3], retvals[:3])) sumMerge(totalPCorrect, retvals[3]) totalRetvals.append( totalPCorrect) return totalRetvals
SRN.step() Extends network step method by automatically copying hidden layer activations to the context layer.
8,761
def find(entity, **kwargs): try: typedfields = entity.typed_fields() except AttributeError: typedfields = iterfields(entity.__class__) matching = [x for x in typedfields if _matches(x, kwargs)] return matching
Return all TypedFields found on the input `Entity` that were initialized with the input **kwargs. Example: >>> find(myentity, multiple=True, type_=Foo) Note: TypedFields.__init__() can accept a string or a class as a type_ argument, but this method expects a class. Args: **kwargs: TypedField __init__ **kwargs to search on. Returns: A list of TypedFields with matching **kwarg values.
8,762
def arraymax(X,Y): Z = np.zeros((len(X),), int) A = X <= Y B = Y < X Z[A] = Y[A] Z[B] = X[B] return Z
Fast "vectorized" max function for element-wise comparison of two numpy arrays. For two numpy arrays `X` and `Y` of equal length, return numpy array `Z` such that:: Z[i] = max(X[i],Y[i]) **Parameters** **X** : numpy array Numpy array; `len(X) = len(Y)`. **Y** : numpy array Numpy array; `len(Y) = len(X)`. **Returns** **Z** : numpy array Numpy array such that `Z[i] = max(X[i],Y[i])`. **See Also** :func:`tabular.fast.arraymin`
8,763
def server_extensions_handshake(requested, supported): accepts = {} for offer in requested: name = offer.split(";", 1)[0].strip() for extension in supported: if extension.name == name: accept = extension.accept(offer) if accept is True: accepts[extension.name] = True elif accept is not False and accept is not None: accepts[extension.name] = accept.encode("ascii") if accepts: extensions = [] for name, params in accepts.items(): if params is True: extensions.append(name.encode("ascii")) else: params = params.decode("ascii") if params == "": extensions.append(("%s" % (name)).encode("ascii")) else: extensions.append(("%s; %s" % (name, params)).encode("ascii")) return b", ".join(extensions) return None
Agree on the extensions to use returning an appropriate header value. This returns None if there are no agreed extensions
8,764
def rpc(ctx, call, arguments, api): try: data = list(eval(d) for d in arguments) except: data = arguments ret = getattr(ctx.bitshares.rpc, call)(*data, api=api) print_dict(ret)
Construct RPC call directly \b You can specify which API to send the call to: uptick rpc --api assets You can also specify lists using uptick rpc get_objects "['2.0.0', '2.1.0']"
8,765
def shell_context_processor(self, func: Callable) -> Callable: self.shell_context_processors.append(func) return func
Add a shell context processor. This is designed to be used as a decorator. An example usage, .. code-block:: python @app.shell_context_processor def additional_context(): return context
8,766
def exception(self, message, *args, **kwargs): self.logger.exception(message, *args, **kwargs)
Handle exception
8,767
def analysis_download(self, webid, type, run=None, file=None): if file is None: _file = io.BytesIO() else: _file = file data = { : self.apikey, : webid, : type, : run, } response = self._post(self.apiurl + "/v2/analysis/download", data=data, stream=True) try: filename = response.headers["Content-Disposition"].split("filename=")[1][1:-2] except Exception as e: filename = type if not response.ok: self._raise_or_extract(response) raise RuntimeError("Unreachable because statement above should raise.") try: for chunk in response.iter_content(1024): _file.write(chunk) except requests.exceptions.RequestException as e: raise ConnectionError(e) if file is None: return (filename, _file.getvalue()) else: return filename
Download a resource for an analysis. E.g. the full report, binaries, screenshots. The full list of resources can be found in our API documentation. When `file` is given, the return value is the filename specified by the server, otherwise it's a tuple of (filename, bytes). Parameters: webid: the webid of the analysis type: the report type, e.g. 'html', 'bins' run: specify the run. If it is None, let Joe Sandbox pick one file: a writeable file-like object (When obmitted, the method returns the data as a bytes object.) Example: json_report, name = joe.analysis_download(123456, 'jsonfixed') Example: with open("full_report.html", "wb") as f: name = joe.analysis_download(123456, "html", file=f)
8,768
def limit(self, limit): if limit is None: raise ValueError("Invalid value for `limit`, must not be `None`") if limit > 200: raise ValueError("Invalid value for `limit`, must be a value less than or equal to `200`") if limit < 1: raise ValueError("Invalid value for `limit`, must be a value greater than or equal to `1`") self._limit = limit
Sets the limit of this ListEmployeeWagesRequest. Maximum number of Employee Wages to return per page. Can range between 1 and 200. The default is the maximum at 200. :param limit: The limit of this ListEmployeeWagesRequest. :type: int
8,769
def _go_to_line(editor, line): b = editor.application.current_buffer b.cursor_position = b.document.translate_row_col_to_index(max(0, int(line) - 1), 0)
Move cursor to this line in the current buffer.
8,770
def get_json(self, path: str, params: Dict[str, Any], host: str = , session: Optional[requests.Session] = None, _attempt=1) -> Dict[str, Any]: is_graphql_query = in params and in path sess = session if session else self._session try: self.do_sleep() if is_graphql_query: self._ratecontrol_graphql_query(params[]) resp = sess.get(.format(host, path), params=params, allow_redirects=False) while resp.is_redirect: redirect_url = resp.headers[] self.log(.format(host, path, redirect_url)) if redirect_url.startswith(.format(host)): resp = sess.get(redirect_url if redirect_url.endswith() else redirect_url + , params=params, allow_redirects=False) else: break if resp.status_code == 400: raise QueryReturnedBadRequestException("400 Bad Request") if resp.status_code == 404: raise QueryReturnedNotFoundException("404 Not Found") if resp.status_code == 429: raise TooManyRequestsException("429 Too Many Requests") if resp.status_code != 200: raise ConnectionException("HTTP error code {}.".format(resp.status_code)) is_html_query = not is_graphql_query and not "__a" in params and host == "www.instagram.com" if is_html_query: match = re.search(r, resp.text) if match is None: raise ConnectionException("Could not find \"window._sharedData\" in html response.") return json.loads(match.group(1)) else: resp_json = resp.json() if in resp_json and resp_json[] != "ok": if in resp_json: raise ConnectionException("Returned \"{}\" status, message \"{}\".".format(resp_json[], resp_json[])) else: raise ConnectionException("Returned \"{}\" status.".format(resp_json[])) return resp_json except (ConnectionException, json.decoder.JSONDecodeError, requests.exceptions.RequestException) as err: error_string = "JSON Query to {}: {}".format(path, err) if _attempt == self.max_connection_attempts: raise ConnectionException(error_string) from err self.error(error_string + " [retrying; skip with ^C]", repeat_at_end=False) try: if isinstance(err, TooManyRequestsException): self._ratecontrol_graphql_query(params[], untracked_queries=True) return self.get_json(path=path, params=params, host=host, session=sess, _attempt=_attempt + 1) except KeyboardInterrupt: self.error("[skipped by user]", repeat_at_end=False) raise ConnectionException(error_string) from err
JSON request to Instagram. :param path: URL, relative to the given domain which defaults to www.instagram.com/ :param params: GET parameters :param host: Domain part of the URL from where to download the requested JSON; defaults to www.instagram.com :param session: Session to use, or None to use self.session :return: Decoded response dictionary :raises QueryReturnedBadRequestException: When the server responds with a 400. :raises QueryReturnedNotFoundException: When the server responds with a 404. :raises ConnectionException: When query repeatedly failed.
8,771
def match_hostname(cert, hostname): if not cert: raise ValueError("empty or no certificate, match_hostname needs a " "SSL socket or SSL context with either " "CERT_OPTIONAL or CERT_REQUIRED") try: host_ip = ipaddress.ip_address(six.text_type(hostname)) except ValueError: host_ip = None dnsnames = [] san = cert.get(, ()) for key, value in san: if key == : if host_ip is None and _dnsname_match(value, hostname): return dnsnames.append(value) elif key == : if host_ip is not None and _ipaddress_match(value, host_ip): return dnsnames.append(value) if not dnsnames: for sub in cert.get(, ()): for key, value in sub: if key == : if _dnsname_match(value, hostname): return dnsnames.append(value) if len(dnsnames) > 1: raise CertificateError( "hostname %r doesn, t match %r" % (hostname, dnsnames[0]) ) else: raise CertificateError( "no appropriate commonName or " "subjectAltName fields were found" )
Verify that *cert* (in decoded format as returned by SSLSocket.getpeercert()) matches the *hostname*. RFC 2818 and RFC 6125 rules are followed, but IP addresses are not accepted for *hostname*. CertificateError is raised on failure. On success, the function returns nothing.
8,772
def update_metric_by_name(self, metric_name, metric_type, description=None, custom_properties=None, tags=None, **kwargs): data = {: metric_type.upper(), : description or , : custom_properties or {}, : tags or []} resp = self._put(self._u(self._METRIC_ENDPOINT_SUFFIX, str(metric_name)), data=data, **kwargs) resp.raise_for_status() return resp.json()
Create or update a metric object Args: metric_name (string): name of metric type (string): metric type, must be one of 'gauge', 'counter', 'cumulative_counter' description (optional[string]): a description custom_properties (optional[dict]): dictionary of custom properties tags (optional[list of strings]): list of tags associated with metric
8,773
def write_state_file(self): fh = open(, ) state = {} state[] = self.vpc_id state[] = self.sg_id state[] = self.sn_ids state[] = self.instances state["instanceState"] = self.instance_states fh.write(json.dumps(state, indent=4))
Save information that must persist to a file. We do not want to create a new VPC and new identical security groups, so we save information about them in a file between runs.
8,774
def add_node(self, node, weight=1): self._nodes.add(node) self._weights[node] = weight self._hashring = dict() self._sorted_keys = [] self._build_circle()
Adds node to circle and rebuild it.
8,775
def _append_instruction(self, obj, qargs=None): if isinstance(obj, Instruction): chan = None if obj.name == : chan = SuperOp( np.array([[1, 0, 0, 1], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]])) if obj.name == : kraus = obj.params dim = len(kraus[0]) chan = SuperOp(_to_superop(, (kraus, None), dim, dim)) elif hasattr(obj, ): try: kraus = [obj.to_matrix()] dim = len(kraus[0]) chan = SuperOp( _to_superop(, (kraus, None), dim, dim)) except QiskitError: pass if chan is not None: op = self.compose(chan, qargs=qargs) self._data = op.data else:
Update the current Operator by apply an instruction.
8,776
def respond_to_SIGHUP(signal_number, frame, logger=None): global restart restart = True if logger: logger.info() raise KeyboardInterrupt
raise the KeyboardInterrupt which will cause the app to effectively shutdown, closing all it resources. Then, because it sets 'restart' to True, the app will reread all the configuration information, rebuild all of its structures and resources and start running again
8,777
def calc_asymptotic_covariance(hessian, fisher_info_matrix): hess_inv = scipy.linalg.inv(hessian) return np.dot(hess_inv, np.dot(fisher_info_matrix, hess_inv))
Parameters ---------- hessian : 2D ndarray. It should have shape `(num_vars, num_vars)`. It is the matrix of second derivatives of the total loss across the dataset, with respect to each pair of coefficients being estimated. fisher_info_matrix : 2D ndarray. It should have a shape of `(num_vars, num_vars)`. It is the approximation of the negative of the expected hessian formed by taking the outer product of (each observation's gradient of the loss function) with itself, and then summing across all observations. Returns ------- huber_white_matrix : 2D ndarray. Will have shape `(num_vars, num_vars)`. The entries in the returned matrix are calculated by the following formula: `hess_inverse * fisher_info_matrix * hess_inverse`.
8,778
def _comparison_functions(cls, partial=False): def prerelease_cmp(a, b): if a and b: return identifier_list_cmp(a, b) elif a: return -1 elif b: return 1 else: return 0 def build_cmp(a, b): if a == b: return 0 else: return NotImplemented def make_optional(orig_cmp_fun): @functools.wraps(orig_cmp_fun) def alt_cmp_fun(a, b): if a is None or b is None: return 0 return orig_cmp_fun(a, b) return alt_cmp_fun if partial: return [ base_cmp, make_optional(base_cmp), make_optional(base_cmp), make_optional(prerelease_cmp), make_optional(build_cmp), ] else: return [ base_cmp, base_cmp, base_cmp, prerelease_cmp, build_cmp, ]
Retrieve comparison methods to apply on version components. This is a private API. Args: partial (bool): whether to provide 'partial' or 'strict' matching. Returns: 5-tuple of cmp-like functions.
8,779
def follow(user, obj): follow, created = Follow.objects.get_or_create(user, obj) return follow
Make a user follow an object
8,780
def has_plugin(self, name=None, plugin_type=None): if name is None and plugin_type is None: return len(self.plugins) > 0 return name in self.plugins
Check if the manager has a plugin / plugin(s), either by its name, type, or simply checking if the manager has any plugins registered in it. Utilizing the name argument will check if a plugin with that name exists in the manager. Using both the name and plugin_type arguments will check if a plugin with that name, and type, exists. Using only the plugin_type argument will check if any plugins matching the type specified are registered in the plugin manager. :param name: Name of the plugin to check for. :param plugin_type: Plugin Type to check for. :return:
8,781
def predict(self, X): check_rdd(X, (np.ndarray, sp.spmatrix)) if hasattr(self, ): if isinstance(X, ArrayRDD): X = X.unblock() return X.map(lambda x: self._mllib_model.predict(x)) else: rdd = X.map(lambda X: super(SparkKMeans, self).predict(X)) return ArrayRDD(rdd)
Predict the closest cluster each sample in X belongs to. In the vector quantization literature, `cluster_centers_` is called the code book and each value returned by `predict` is the index of the closest code in the code book. Parameters ---------- X : ArrayRDD containing array-like, sparse matrix New data to predict. Returns ------- labels : ArrayRDD with predictions Index of the cluster each sample belongs to.
8,782
def initialize(self): if not in self._vim.vars: self._vim.vars[] = self._vim.command()
Sets up initial ensime-vim editor settings.
8,783
def _get_cache(self): if not self._cache: self._cache = get_cache(self.app) return self._cache
Return the cache to use for thundering herd protection, etc.
8,784
def resize(self, size=None): if not self.operation.israw(): return size = size or tty.size(self.operation.stdout) if size is not None: rows, cols = size try: self.operation.resize(height=rows, width=cols) except IOError: pass
Resize the container's PTY. If `size` is not None, it must be a tuple of (height,width), otherwise it will be determined by the size of the current TTY.
8,785
def _db_upgrade(self, db_name): current_db_version = self._get_db_version() self._execute(db_schema.functions) for i in range(current_db_version, nipap.__db_version__): self._logger.info("Upgrading DB schema:", i, "to", i+1) upgrade_sql = db_schema.upgrade[i-1] self._execute(upgrade_sql % (db_name)) self._execute(db_schema.triggers)
Upgrade nipap database schema
8,786
def transformFromNative(obj): obj.isNative = False obj.value = serializeFields(obj.value, NAME_ORDER) return obj
Replace the Name in obj.value with a string.
8,787
def pivot_pandas_to_excel(soup, show_intermediate_breakdown=False, show_total_breakdown=False): col1col2col3indexcol4sumcol4COL1COL2AllROW1ROW2ALL tables = soup.findAll() for table in tables: table.thead.findChildren()[1].decompose() new_body = Tag(name=) bc = 0 num_columns_max = max(len(row.findAll()) for row in table.tbody.findAll()) num_headers_max = max(len(row.findAll()) for row in table.tbody.findAll()) last = False for row in table.tbody.findChildren(): headers = list(row.findChildren()) data = list(row.findChildren()) if len(headers) > 1: if in headers[0].contents: last = True indent = 0 first_header = (len(headers) == num_headers_max) if not last: for header in headers[:-1]: new_row = Tag(name=, attrs={: }) if first_header else Tag(name=, attrs={: }) if not header.contents: continue new_header = Tag(name=, attrs={: , : + str(10*(num_headers_max - len(headers) + indent)) + }) if first_header else \ Tag(name=, attrs={: , : + str(10*(num_headers_max - len(headers) + indent)) + }) new_header.contents = header.contents new_row.insert(0, new_header) for j in range(num_columns_max-1): new_row.insert(j+1, Tag(name=, attrs={: })) if first_header else new_row.insert(j+1, Tag(name=, attrs={: })) new_body.insert(bc, new_row) bc += 1 indent += 1 first_header = False new_row = Tag(name=) new_header = Tag(name=, attrs={: , : + str(10*(num_headers_max-1)) + }) new_header.contents = headers[-1].contents if in headers[-1].contents: if not show_intermediate_breakdown and not last: continue elif not show_intermediate_breakdown: last = False new_row = Tag(name=, attrs={: }) new_header = Tag(name=, attrs={: }) new_header.contents = [NavigableString()] elif not last: pass if last: continue new_row.insert(0, new_header) cc = 1 for _ in range(num_columns_max - len(data) - 1): new_header = Tag(name=, attrs={: }) if in headers[-1].contents else Tag(name=) new_row.insert(cc, new_header) cc += 1 for dat in data: new_data = Tag(name=) if not in headers[-1].contents else Tag(name=, attrs={: }) new_data.contents = dat.contents new_row.insert(cc, new_data) cc += 1 new_body.insert(bc, new_row) bc += 1 table.tbody.replaceWith(new_body) return soup
pandas style pivot to excel style pivot formatting for outlook/html This function is meant to be provided to the email functionality as a postprocessor. It expects a jupyter or pandas exported html table of a dataframe with the following index: example: # a single pivot pt1 = pd.pivot_table(data, value=['col1', 'col2', 'col3'], index=['index'], columns=['col4'], aggfunc='sum', margins=True).stack('col4') # here we reindex the table to have the appropriate row ordering pt1 = pt1.reindex( pd.MultiIndex( levels=[['COL1', 'COL2', 'All'], ['ROW1', 'ROW2', 'ALL']], labels=[[0, 0, 0, 1, 1, 1, 2], # This is the key, changing the label order (2-ALL) [2, 0, 1, 2, 0, 1, 2]], names=['', ''], sortorder=0) ).fillna(0) show_intermediate_breakdown --> intermediate sumations to be shown? show_total_breakdown --> total sumations to be shown?
8,788
def load_plugins(self, plugin_path): self.logger.debug(.format(plugin_path)) plugins = {} plugin_dir = os.path.realpath(plugin_path) sys.path.append(plugin_dir) for f in os.listdir(plugin_dir): if f.endswith(".py"): name = f[:-3] elif f.endswith(".pyc"): name = f[:-4] else: continue try: self.logger.debug(.format(f)) mod = __import__(name, globals(), locals(), [], 0) for plugin_class in inspect.getmembers(mod): if plugin_class[0][0:2] == : continue if hasattr(plugin_class[1], ): if plugin_class[1].config_name is not None: plugins[plugin_class[1].config_name] = plugin_class[1] self.logger.debug(.format(plugin_class[1].config_name)) except ImportError as e: self.logger.error(e) pass self.logger.debug() return plugins
Loads plugins from modules in plugin_path. Looks for the config_name property in each object that's found. If so, adds that to the dictionary with the config_name as the key. config_name should be unique between different plugins. :param plugin_path: Path to load plugins from :return: dictionary of plugins by config_name
8,789
def execute_code_block(elem, doc): command = select_executor(elem, doc).split() code = elem.text if in elem.attributes or in elem.classes: code = save_plot(code, elem) command.append(code) if in elem.attributes: for arg in elem.attributes[].split(): command.append(arg) cwd = elem.attributes[] if in elem.attributes else None return subprocess.run(command, encoding=, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=cwd).stdout
Executes a code block by passing it to the executor. Args: elem The AST element. doc The document. Returns: The output of the command.
8,790
async def subscribe( schema: GraphQLSchema, document: DocumentNode, root_value: Any = None, context_value: Any = None, variable_values: Dict[str, Any] = None, operation_name: str = None, field_resolver: GraphQLFieldResolver = None, subscribe_field_resolver: GraphQLFieldResolver = None, ) -> Union[AsyncIterator[ExecutionResult], ExecutionResult]: try: result_or_stream = await create_source_event_stream( schema, document, root_value, context_value, variable_values, operation_name, subscribe_field_resolver, ) except GraphQLError as error: return ExecutionResult(data=None, errors=[error]) if isinstance(result_or_stream, ExecutionResult): return result_or_stream result_or_stream = cast(AsyncIterable, result_or_stream) async def map_source_to_response(payload): result = execute( schema, document, payload, context_value, variable_values, operation_name, field_resolver, ) return await result if isawaitable(result) else result return MapAsyncIterator(result_or_stream, map_source_to_response)
Create a GraphQL subscription. Implements the "Subscribe" algorithm described in the GraphQL spec. Returns a coroutine object which yields either an AsyncIterator (if successful) or an ExecutionResult (client error). The coroutine will raise an exception if a server error occurs. If the client-provided arguments to this function do not result in a compliant subscription, a GraphQL Response (ExecutionResult) with descriptive errors and no data will be returned. If the source stream could not be created due to faulty subscription resolver logic or underlying systems, the coroutine object will yield a single ExecutionResult containing `errors` and no `data`. If the operation succeeded, the coroutine will yield an AsyncIterator, which yields a stream of ExecutionResults representing the response stream.
8,791
def set_password(username, password, encrypted=False, role=None, crypt_salt=None, algorithm=, **kwargs): t save configuration commands to startup configuration. If False, save configuration to startup configuration. Default: False .. code-block:: bash salt nxos.cmd set_password admin TestPass salt nxos.cmd set_password admin \\ password= \\ encrypted=True username {0} password 5 {1} role {0}'.format(role) return config(password_line, **kwargs)
Set users password on switch. username Username to configure password Password to configure for username encrypted Whether or not to encrypt the password Default: False role Configure role for the username Default: None crypt_salt Configure crypt_salt setting Default: None alogrithm Encryption algorithm Default: sha256 no_save_config If True, don't save configuration commands to startup configuration. If False, save configuration to startup configuration. Default: False .. code-block:: bash salt '*' nxos.cmd set_password admin TestPass salt '*' nxos.cmd set_password admin \\ password='$5$2fWwO2vK$s7.Hr3YltMNHuhywQQ3nfOd.gAPHgs3SOBYYdGT3E.A' \\ encrypted=True
8,792
def sort_projects( self, workflowTags): self.refresh if not isinstance(workflowTags, list): workflowTagsLists = workflowTags.strip().replace(",", "").replace("@", "") workflowTagsLists = workflowTagsLists.split(" ") else: workflowTagsLists = [] workflowTagsLists[:] = [l.replace("@", "") for l in workflowTags] matchedProjects = collections.OrderedDict() unmatchedProjects = [] for wt in workflowTagsLists: matchedProjects[wt.lower()] = [] for p in self.projects: matched = False for pt in p.tags: if matched: break for wt in workflowTagsLists: thisTag = pt.lower() if "(" not in wt: thisTag = pt.split("(")[0].lower() if thisTag == wt.lower() and matched == False: matchedProjects[wt.lower()].append(p) matched = True break if matched == False: unmatchedProjects.append(p) sortedProjects = [] for k, v in matchedProjects.iteritems(): sortedProjects += v sortedProjects += unmatchedProjects self.projects = sortedProjects self.content = self.to_string( title=False, projects=sortedProjects, indentLevel=0) for p in self.projects: p.projects = p.sort_projects(workflowTags) oldContent = self.to_string(indentLevel=1) newContent = self.to_string( indentLevel=1, projects=sortedProjects) if self.parent: self.parent._update_document_tree( oldContent=oldContent, newContent=newContent ) self.content = self.content.replace(self.to_string(indentLevel=0, title=False), self.to_string( indentLevel=0, title=False, projects=sortedProjects)) self.refresh return sortedProjects
*order the projects within this taskpaper object via a list of tags* The order of the tags in the list dictates the order of the sort - first comes first* **Key Arguments:** - ``workflowTags`` -- a string of space/comma seperated tags. **Return:** - ``None`` **Usage:** To recursively sort the projects within a taskpaper document with the following order: 1. *@due* 2. *@flag* 3. *@hold* 4. *@next* 5. *@someday* 6. *@wait* use the following: .. code-block:: python doc.sort_projects("@due, @flag, @hold, @next, @someday, @wait")
8,793
def iter_subclasses(class_): ensure_class(class_) classes = set() def descend(class_): subclasses = set(class_.__subclasses__()) - classes classes.update(subclasses) return subclasses result = breadth_first(class_, descend) next(result) return result
Iterate over all the subclasses (and subclasses thereof, etc.) of given class. :param class_: Class to yield the subclasses of :return: Iterable of subclasses, sub-subclasses, etc. of ``class_``
8,794
def get_update_status_brok(self): data = {: self.uuid} self.fill_data_brok_from(data, ) return Brok({: + self.my_type + , : data})
Create an update item brok :return: Brok object :rtype: alignak.Brok
8,795
def knx_to_date(knxdata): if len(knxdata) != 3: raise KNXException("Can only convert a 3 Byte object to date") year = knxdata[2] if year >= 90: year += 1900 else: year += 2000 return date(year, knxdata[1], knxdata[0])
Convert a 3 byte KNX data object to a date
8,796
def bowtie_alignment_plot (self): keys = OrderedDict() keys[] = { : , : } keys[] = { : , : } keys[] = { : , : } config = { : , : , : , : } self.add_section( description = , helptext = , plot = bargraph.plot(self.bowtie_data, keys, config) )
Make the HighCharts HTML to plot the alignment rates
8,797
def _get_path(self, file): dir = self._cache_directory() if not os.path.exists(dir): os.makedirs(dir) return os.path.join(dir, file)
Creates the cache directory if it doesn't already exist. Returns the full path to the specified file inside the cache directory.
8,798
def decompressBWT(inputDir, outputDir, numProcs, logger): s original form. While unusual to do, itt care @param numProcs - number of processes we msbwt = MultiStringBWT.CompressedMSBWT() msbwt.loadMsbwt(inputDir, logger) outputFile = np.lib.format.open_memmap(outputDir+, , , (msbwt.getTotalSize(),)) del outputFile worksize = 1000000 tups = [None]*(msbwt.getTotalSize()/worksize+1) x = 0 if msbwt.getTotalSize() > worksize: for x in xrange(0, msbwt.getTotalSize()/worksize): tups[x] = (inputDir, outputDir, x*worksize, (x+1)*worksize) tups[-1] = (inputDir, outputDir, (x+1)*worksize, msbwt.getTotalSize()) else: tups[0] = (inputDir, outputDir, 0, msbwt.getTotalSize()) if numProcs > 1: myPool = multiprocessing.Pool(numProcs) rets = myPool.map(decompressBWTPoolProcess, tups) else: rets = [] for tup in tups: rets.append(decompressBWTPoolProcess(tup))
This is called for taking a BWT and decompressing it back out to it's original form. While unusual to do, it's included in this package for completion purposes. @param inputDir - the directory of the compressed BWT we plan on decompressing @param outputFN - the directory for the output decompressed BWT, it can be the same, we don't care @param numProcs - number of processes we're allowed to use @param logger - log all the things!
8,799
def set_scan_option(self, scan_id, name, value): return self.scan_collection.set_option(scan_id, name, value)
Sets a scan's option to a provided value.