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def dont_linkify_urls(attrs, new=False): """Prevent file extensions to convert to links. This is a callback function used by bleach.linkify(). Prevent strings ending with substrings in `file_exts` to be converted to links unless it starts with http or https. """ file_exts = ('.py', '.md', '.sh') txt = attrs['_text'] if txt.startswith(('http://', 'https://')): return attrs if txt.endswith(file_exts): return None return attrs
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def find_pareto_front(population): """Finds a subset of nondominated individuals in a given list :param population: a list of individuals :return: a set of indices corresponding to nondominated individuals """ pareto_front = set(range(len(population))) for i in range(len(population)): if i not in pareto_front: continue ind1 = population[i] for j in range(i + 1, len(population)): ind2 = population[j] # if individuals are equal on all objectives, mark one of them (the first encountered one) as dominated # to prevent excessive growth of the Pareto front if ind2.fitness.dominates(ind1.fitness) or ind1.fitness == ind2.fitness: pareto_front.discard(i) if ind1.fitness.dominates(ind2.fitness): pareto_front.discard(j) return pareto_front
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from pathlib import Path import string import random def make_random_dir_path() -> Path: """ Creates a fully-qualified Path to a fake directory. The directory path is guarantee to begin with / and starts with no special characters other than /. The branch_depth of the path (ie /one/two/three has a depth of 3) is random and lies between 2 and 10 inclusive. Each node in the branch has between 1 and 10 characters, which comprise upper- and lower-case characters and numbers. """ characters = string.ascii_letters + string.digits branch_depth = random.randint(2, 10) dirs = [] for _ in range(branch_depth): string_length = random.randint(1, 10) random_string = ''.join(random.choice(characters) for _ in range(string_length)) dirs.append(random_string) dir_str = '/' + '/'.join(dirs) return Path(dir_str)
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import torch def load_model(filename, model): """Load the model parameters in {filename}.""" model_params = torch.load(str(filename)) model.load_state_dict(model_params) return model
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def aliquot_sum(input_num: int) -> int: """ Finds the aliquot sum of an input integer, where the aliquot sum of a number n is defined as the sum of all natural numbers less than n that divide n evenly. For example, the aliquot sum of 15 is 1 + 3 + 5 = 9. This is a simple O(n) implementation. @param input_num: a positive integer whose aliquot sum is to be found @return: the aliquot sum of input_num, if input_num is positive. Otherwise, raise a ValueError Wikipedia Explanation: https://en.wikipedia.org/wiki/Aliquot_sum >>> aliquot_sum(15) 9 >>> aliquot_sum(6) 6 >>> aliquot_sum(-1) Traceback (most recent call last): ... ValueError: Input must be positive >>> aliquot_sum(0) Traceback (most recent call last): ... ValueError: Input must be positive >>> aliquot_sum(1.6) Traceback (most recent call last): ... ValueError: Input must be an integer >>> aliquot_sum(12) 16 >>> aliquot_sum(1) 0 >>> aliquot_sum(19) 1 """ if not isinstance(input_num, int): raise ValueError("Input must be an integer") if input_num <= 0: raise ValueError("Input must be positive") return sum( divisor for divisor in range(1, input_num // 2 + 1) if input_num % divisor == 0 )
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async def convert_media_format(media_format): """Translates media format names into norwegian""" media_formats = { 'TV': 'TV-Serie', 'TV_SHORT': 'Kort TV-Serie', 'MOVIE': 'Film', 'SPECIAL': 'Ekstramateriale', 'MUSIC': 'Musikk', 'MANGA': 'Manga', 'NOVEL': 'Novelle', 'ONE_SHOT': 'Kort Manga' } try: return media_formats[media_format] except KeyError: return media_format
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def wrap(x, m): """ Mathematical modulo; wraps x so that 0 <= wrap(x,m) < m. x can be negative. """ return (x % m + m) % m
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import json def fluent_list_output(value): """ Return stored json representation as a multilingual dict, if value is already a dict just pass it through. """ if isinstance(value, dict): return value try: result = json.loads(value) return {k: v if isinstance(v, list) else [v] for k, v in list(result.items())} except ValueError: # plain string in the db, return as is so it can be migrated return value
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import requests def is_license_valid(key): """Checking License Key from External API Args: key (str): Serial Key for Raven Restocks Returns: bool: If the key is valid """ r = requests.post( 'https://xserver.boxmarshall.com/api/v2/authorize/validate/no-device', json={"serialkey": key}) return r.json()['success']
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def write_alarm_msg(radar_name, param_name_unit, date_last, target, tol_abs, np_trend, value_trend, tol_trend, nevents, np_last, value_last, fname): """ writes an alarm file Parameters ---------- radar_name : str Name of the radar being controlled param_name_unit : str Parameter and units date_last : datetime object date of the current event target, tol_abs : float Target value and tolerance np_trend : int Total number of points in trend value_trend, tol_trend : float Trend value and tolerance nevents: int Number of events in trend np_last : int Number of points in the current event value_last : float Value of the current event fname : str Name of file where to store the alarm information Returns ------- fname : str the name of the file where data has written """ with open(fname, 'w', newline='') as txtfile: txtfile.write( 'Weather radar polarimetric parameters monitoring alarm\n') if radar_name is not None: txtfile.write('Radar name: '+radar_name+'\n') txtfile.write('Parameter [Unit]: '+param_name_unit+'\n') txtfile.write('Date : '+date_last.strftime('%Y%m%d')+'\n') txtfile.write('Target value: '+str(target)+' +/- '+str(tol_abs)+'\n') if np_trend > 0: txtfile.write( 'Number of points in trend: '+str(np_trend)+' in ' + str(nevents)+' events\n') txtfile.write( 'Trend value: '+str(value_trend)+' (tolerance: +/- ' + str(tol_trend)+')\n') else: txtfile.write('Number of points in trend: NA\n') txtfile.write('Trend value: NA\n') txtfile.write('Number of points: '+str(np_last)+'\n') txtfile.write('Value: '+str(value_last)+'\n') txtfile.close() return fname
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def get_contents(collection_id, collections_referenced): """Return the ``contents`` value of the collection with ``collection_id`` as its ``id`` value. :param int collection_id: the ``id`` value of a collection model. :param dict collections_referenced: the collections (recursively) referenced by a collection. :returns: the contents of a collection, or a warning message. """ return getattr(collections_referenced[collection_id], u'contents', u'Collection %d has no contents.' % collection_id)
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def _ifOnlyWalk(row): """Helper funtion to return True if row only contains Walk mode.""" modes = set(row.split(",")) walkExist = "Mode::Walk" in modes length = len(modes) == 1 return walkExist & length
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def add_header(response): """ Append after request the nessesary headers. """ response.headers['Access-Control-Allow-Headers'] = "accept, content-type" return response
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def sz_to_ind(sz, charge, nsingle): """ Converts :math:`S_{z}` to a list index. Parameters ---------- sz : int Value :math:`S_{z}` of a spin projection in the z direction. charge : int Value of the charge. nsingle : int Number of single particle states. Returns ------- int Value of the list index corresponding to sz. """ szmax = min(charge, nsingle-charge) return int((szmax+sz)/2)
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def load_file(infile): """Read and return text file as a string of lowercase characters.""" with open(infile) as f: loaded_string = f.read().lower() return loaded_string
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def get_inputs(depthdata_str_list): """ Given a list of strings composed of 3 floating pt nbrs x, y, z separated by commas, convert them to floats and return them as 3 individual lists. :param depthdata_str_list: list of floating point string pairs, separated by a comma (think .csv file) :return: lists of x values, y values, and corresponding z values """ assert isinstance(depthdata_str_list, list) assert all([isinstance(s, str) for s in depthdata_str_list]) assert all([3 == len(v.split(",")) for v in depthdata_str_list]) x_list = [] y_list = [] z_list = [] for i, line_str in enumerate(depthdata_str_list): str_list = line_str.split(",") x_str, y_str, z_str = str_list x = float(x_str) y = float(y_str) z = float(z_str) x_list.append(x) y_list.append(y) z_list.append(z) return x_list, y_list, z_list
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def _user_can_edit(user, group_profile): """Can the given user edit the given group profile?""" return user.has_perm("groups.change_groupprofile") or user in group_profile.leaders.all()
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def _set_default_capacitance( subcategory_id: int, style_id: int, ) -> float: """Set the default value of the capacitance. :param subcategory_id: :param style_id: :return: _capacitance :rtype: float :raises: KeyError if passed a subcategory ID outside the bounds. :raises: IndexError if passed a style ID outside the bounds when subcategory ID is equal to three. """ _capacitance = { 1: 0.15e-6, 2: 0.061e-6, 3: [0.027e-6, 0.033e-6], 4: 0.14e-6, 5: 0.33e-6, 6: 0.14e-6, 7: 300e-12, 8: 160e-12, 9: 30e-12, 10: 3300e-12, 11: 81e-12, 12: 1e-6, 13: 20e-6, 14: 1700e-6, 15: 1600e-6, 16: 0.0, 17: 0.0, 18: 0.0, 19: 0.0, }[subcategory_id] if subcategory_id == 3: _capacitance = _capacitance[style_id - 1] return _capacitance
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def test_file(test_dir): """ Returns path to the file with `filename` and `content` at `test_dir`. """ def wrapper(filename: str, content: str): file = test_dir / filename file.write_text(content, encoding="utf-8") return file return wrapper
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def obj_name(obj, oid): """Return name of folder/collection object based on id Args: obj - dict oid - string """ return obj[oid]['name']
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def CompressList(lines, max_length, middle_replacement): """Ensures that |lines| is no longer than |max_length|. If |lines| need to be compressed then the middle items are replaced by |middle_replacement|. """ if len(lines) <= max_length: return lines remove_from_start = max_length / 2 return (lines[:remove_from_start] + [middle_replacement] + lines[len(lines) - (max_length - remove_from_start):])
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def avgCl(lst): """return the average RGB of a RGB list""" c1=c2=c3=0 n = len(lst) for c in lst: c1+=c[0] c2+=c[1] c3+=c[2] c1,c2,c3=c1/n,c2/n,c3/n return [c1,c2,c3]
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def gist_namer(art_title, num): """ Create formatted gist name to help with grouping gists Parameters ---------- art_title : str defaults to the notebook name num: int gist count for this article e.g. first gist of article is 0 """ # lower case and snake_case the whole thing title = art_title.lower().replace(" ", "_") title += str(num) return title
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def retag_from_strings(string_tag) : """ Returns only the final node tag """ valure = string_tag.rfind('+') if valure!= -1 : tag_recal =string_tag [valure+1:] else : tag_recal = string_tag return tag_recal
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def removesuffix(s, suffix): """ Removes suffix a string :param s: string to remove suffix from :param suffix: suffix to remove :type s: str :type suffix: str :return: a copy of the string with the suffix removed :rtype: str """ return s if not s.endswith(suffix) else s[:-len(suffix)]
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def st_rowfreq(row,srate,length): """ for a row in a stockwell transform, give what frequency (Hz) it corresponds to, given the sampling rate srate and the length of the original array """ return row*srate/length
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def convert_labels(df, columns=['label'], reverse=False): """ Convert labels in provided columns to numeric values (or back to text). Edits the dataframe in place. """ if reverse: labels_vals = { 0: 'Refuted', 1: 'Supported', 2: 'NotEnoughInfo' } else: labels_vals = { 'Refuted': 0, 'Supported': 1, 'NotEnoughInfo': 2 } for col in columns: df[col] = df[col].apply(lambda x: labels_vals[x]) return df
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def select_bboxes_via_score(bboxes_list, scores_list, score_thr): """Select bboxes with scores >= score_thr. Args: bboxes_list (list[ndarray]): List of bboxes. Each element is ndarray of shape (n,8) scores_list (list(list[float])): List of lists of scores. score_thr (float): The score threshold to filter out bboxes. Returns: selected_bboxes (list[ndarray]): List of bboxes. Each element is ndarray of shape (m,8) with m<=n. """ assert isinstance(bboxes_list, list) assert isinstance(scores_list, list) assert isinstance(score_thr, float) assert len(bboxes_list) == len(scores_list) assert 0 <= score_thr <= 1 selected_bboxes = [] for bboxes, scores in zip(bboxes_list, scores_list): if len(scores) > 0: assert len(scores) == bboxes.shape[0] inds = [ iter for iter in range(len(scores)) if scores[iter] >= score_thr ] selected_bboxes.append(bboxes[inds, :]) else: selected_bboxes.append(bboxes) return selected_bboxes
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def fetch_all_views(eng): """ Finds all views. """ tables = eng.execute("SELECT table_name from information_schema.views;") return [table[0] for table in tables if "exp_view_table" in table[0]]
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def add_argument(parser, flag, type=None, **kwargs): """Wrapper to add arguments to an argument parser. Fixes argparse's behavior with type=bool. For a bool flag 'test', this adds options '--test' which by default sets test to on, and additionally supports '--test true', '--test false' and so on. Finally, 'test' can also be turned off by simply specifying '--notest'. """ def str2bool(v): return v.lower() in ('true', 't', '1') if flag.startswith('-'): raise ValueError('Flags should not have the preceeding - symbols, -- will be added automatically.') if type == bool: parser.add_argument('--' + flag, type=str2bool, nargs='?', const=True, **kwargs) parser.add_argument('--no' + flag, action='store_false', dest=flag) else: parser.add_argument('--' + flag, type=type, **kwargs)
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def elevation(location): """Return the elevation field of a location.""" return location[2]
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import math def distance(M, node_1, node_2): """Computes the Euclidean L2 Distance.""" x1, y1 = M.intersections[node_1] x2, y2 = M.intersections[node_2] return math.sqrt(math.pow(x1 - x2, 2) + math.pow(y1 - y2, 2))
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def audit_renamed_col_dict(dct: dict) -> dict: """ Description ----------- Handle edge cases where a col could be renamed back to itself. example: no primary_geo, but country is present. Because it is a protected col name, it would be renamed country_non_primary. Later, it would be set as primary_geo country, and the pair added to renamed_col_dict again: {'country_non_primary' : ['country'], "country": ['country_non_primary'] } Parameters ---------- dct: dict renamed_col_dict of key: new column name, value: list of old columns Output ------ dict: The modified parameter dict. """ remove_these = set() for k, v in dct.items(): vstr = "".join(v) if vstr in dct.keys() and [k] in dct.values(): remove_these.add(vstr) remove_these.add(k) for k in remove_these: dct.pop(k, None) return dct
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def _mangle(cls, name): """ Given a class and a name, apply python name mangling to it :param cls: Class to mangle with :param name: Name to mangle :return: Mangled name """ return f"_{cls.__name__}__{name}"
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import torch def sample_pdf( bins: torch.Tensor, weights: torch.Tensor, N_samples: int, det: bool = False, eps: float = 1e-5, ): """ Samples a probability density functions defined by bin edges `bins` and the non-negative per-bin probabilities `weights`. Note: This is a direct conversion of the TensorFlow function from the original release [1] to PyTorch. Args: bins: Tensor of shape `(..., n_bins+1)` denoting the edges of the sampling bins. weights: Tensor of shape `(..., n_bins)` containing non-negative numbers representing the probability of sampling the corresponding bin. N_samples: The number of samples to draw from each set of bins. det: If `False`, the sampling is random. `True` yields deterministic uniformly-spaced sampling from the inverse cumulative density function. eps: A constant preventing division by zero in case empty bins are present. Returns: samples: Tensor of shape `(..., N_samples)` containing `N_samples` samples drawn from each set probability distribution. Refs: [1] https://github.com/bmild/nerf/blob/55d8b00244d7b5178f4d003526ab6667683c9da9/run_nerf_helpers.py#L183 # noqa E501 """ # Get pdf weights = weights + eps # prevent nans pdf = weights / weights.sum(dim=-1, keepdim=True) cdf = torch.cumsum(pdf, -1) cdf = torch.cat([torch.zeros_like(cdf[..., :1]), cdf], -1) # Take uniform samples if det: u = torch.linspace(0.0, 1.0, N_samples, device=cdf.device, dtype=cdf.dtype) u = u.expand(list(cdf.shape[:-1]) + [N_samples]).contiguous() else: u = torch.rand( list(cdf.shape[:-1]) + [N_samples], device=cdf.device, dtype=cdf.dtype ) # Invert CDF inds = torch.searchsorted(cdf, u, right=True) below = (inds - 1).clamp(0) above = inds.clamp(max=cdf.shape[-1] - 1) inds_g = torch.stack([below, above], -1).view( *below.shape[:-1], below.shape[-1] * 2 ) cdf_g = torch.gather(cdf, -1, inds_g).view(*below.shape, 2) bins_g = torch.gather(bins, -1, inds_g).view(*below.shape, 2) denom = cdf_g[..., 1] - cdf_g[..., 0] denom = torch.where(denom < eps, torch.ones_like(denom), denom) t = (u - cdf_g[..., 0]) / denom samples = bins_g[..., 0] + t * (bins_g[..., 1] - bins_g[..., 0]) return samples
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def insert_user(cursor,username,hash_pw): """ Insert a new user in the database Parameters: ----------- cursor: Psycopg2 cursor Cursor of type RealDict in the postgres database username : Str name of the user hash_pw : Str encrypted password of the user (to be tested against the encrypted password) Returns: -------- id : Int identifier of the inserted user """ SQL = "INSERT INTO users(username, password_hash) VALUES(%s,%s) RETURNING id" cursor.execute(SQL,[username,hash_pw]) res = cursor.fetchone()['id'] return res
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def rectanglesOverlap(r1, r2): """Check whether r1 and r2 overlap.""" if ((r1[0] >= r2[0] + r2[2]) or (r1[0] + r1[2] <= r2[0]) or (r1[1] + r1[3] <= r2[1]) or (r1[1] >= r2[1] + r2[3])): return False else: return True
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def select_shape(input_shape, slice_point, axis=1): """ calculate the output shape of this layer using input shape Args: @input_shape (list of num): a list of number which represents the input shape @slice_point (list): parameter from caffe's Slice layer @axis (int): parameter from caffe's Slice layer Returns: @output_shape (list of num): a list of numbers represent the output shape """ input_shape = list(input_shape) start = slice_point[0] if len(slice_point) == 2: end = slice_point[1] else: end = input_shape[axis] assert end > start, "invalid slice_point with [start:%d, end:%d]"\ % (start, end) output_shape = input_shape output_shape[axis] = end - start return output_shape
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def _dtype_descr(dtype): """ Get a string that describes a numpy datatype. :param dtype: The numpy datatype. :return: A string describing the type. """ if dtype.kind == 'V': return dtype.descr else: return dtype.char
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from typing import Dict def parse_guid(guid: str) -> Dict[str, int]: """ Parse a guid back to its four constituents Args: guid: a valid guid str Returns: A dict with keys 'location', 'work_station', 'sample', and 'time' as integer values """ guid = guid.replace('-', '') components = {} components['sample'] = int(guid[:8], base=16) components['location'] = int(guid[8:10], base=16) components['work_station'] = int(guid[10:16], base=16) components['time'] = int(guid[16:], base=16) return components
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def GetInputs(var, env): """Expands an env substitution variable and returns it as a list of strings.""" return [str(v) for v in env.subst_list(var)[0]]
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def parse_gage(s): """Parse a streamgage key-value pair. Parse a streamgage key-value pair, separated by '='; that's the reverse of ShellArgs. On the command line (argparse) a declaration will typically look like:: foo=hello or foo="hello world" :param s: str :rtype: tuple(key, value) """ # Adapted from: https://gist.github.com/fralau/061a4f6c13251367ef1d9a9a99fb3e8d items = s.split('=') key = items[0].strip() # we remove blanks around keys, as is logical value = '' if len(items) > 1: # rejoin the rest: value = '='.join(items[1:]) return key, value
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def last_support(entry): """Find the last friendly action between the players""" seasons = entry['seasons'] last_support = None for season in seasons[:-1]: if 'support' in season['interaction'].values(): last_support = season['season'] return last_support
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def draw_sure(deck, n, exclusions): """Draw n cards from a deck but skip any cards listed in exclusions. Please note this func always returns a list, unlike native deuces draw function. """ drawn = [] while len(drawn) < n: c = deck.draw() if c in exclusions + drawn: continue drawn.append(c) return drawn
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def getPointRange(iFace, dims): """Return the correct point range for face iFace on a block with dimensions given in dims""" il = dims[0] jl = dims[1] kl = dims[2] if iFace == 0: return [[1, il], [1, jl], [1, 1]] elif iFace == 1: return [[1, il], [1, jl], [kl, kl]] elif iFace == 2: return [[1, 1], [1, jl], [1, kl]] elif iFace == 3: return [[il, il], [1, jl], [1, kl]] elif iFace == 4: return [[1, il], [1, 1], [1, kl]] elif iFace == 5: return [[1, il], [jl, jl], [1, kl]]
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def pypi_link(pkg_filename): """ Given the filename, including md5 fragment, construct the dependency link for PyPI. """ root = 'https://files.pythonhosted.org/packages/source' name, sep, rest = pkg_filename.partition('-') parts = root, name[0], name, pkg_filename return '/'.join(parts)
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def _manifest(package_name): """ Helper function to create an appropriate manifest with a provided package name. :pram package_name The package name used in the manifest file. """ return """ <manifest xmlns:android="http://schemas.android.com/apk/res/android" package="{}" > <uses-sdk android:minSdkVersion="21" android:targetSdkVersion="29"/> </manifest> """.format(package_name)
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import re def avg_word_length(text): """ Averages the word length in `text` :param text: The text to analyze (str) :return: average_word_len (float) """ words = re.sub(r'[\.\?!]', '', text).split() return sum(len(word) for word in words) / len(words)
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def generate_outpath(filepath): """ Generates the output name for an input nii.gz file by appending 'noise' to file name. """ parts = filepath.split('.') prefix = '.'.join(parts[:-2]+['noise']) return prefix
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def sort_012(input_list): """ Given an input array consisting on only 0, 1, and 2, sort the array in a single traversal. The idea is to put 0 and 2 in their correct positions, which will make sure all the 1s are automatically placed in their right positions Args: input_list(list): List to be sorted """ # If list is empty if not input_list: return input_list # initialize pointers for next positions of 0 and 2 next_pos_0 = 0 next_pos_2 = len(input_list) - 1 front_index = 0 while front_index <= next_pos_2: if input_list[front_index] == 0: # If the element is 0, place element at next position input_list[front_index] = input_list[next_pos_0] input_list[next_pos_0] = 0 next_pos_0 += 1 front_index += 1 elif input_list[front_index] == 2: # If the element is 2, place element at next position of 2 input_list[front_index] = input_list[next_pos_2] input_list[next_pos_2] = 2 next_pos_2 -= 1 else: front_index += 1 return input_list
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def ft2m(ft): """feet -> meters""" return 0.3048*ft
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def split_by_unescaped_sep(text, sep=':'): """Split string at sep but only if not escaped.""" def remerge(s): # s is a list of strings. for i in range(len(s) - 1): n_esc = len(s[i]) - len(s[i].rstrip('\\')) if n_esc % 2 == 0: continue else: new_s = s[:i] + [s[i] + sep + s[i + 1]] + s[i + 2:] return remerge(new_s) return s # split by every sep (even unescaped ones) # then re-merge strings that end in an uneven number of escape chars: return remerge(text.split(sep))
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def discretize(pde, geo, time_nsteps=None, space_nsteps=None): """ Discretize PDE and Geometry Parameters: pde (PDE): The partial differential equations. geo (Geometry): The geometry to be discretized. Returns -------- pde_disc: PDE Reserved parameter geo_disc: DiscreteGeometry Discrte Geometry """ # Geometry geo_disc = geo.discretize(time_nsteps, space_nsteps) return pde, geo_disc
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import hmac import hashlib import base64 def sign(message, secret): """Compute a Base64-encoded HMAC-SHA256. Arguments: message (unicode): The value to be signed. secret (unicode): The secret key to use when signing the message. Returns: unicode: The message signature. """ message = message.encode('utf-8') secret = secret.encode('utf-8') # Calculate a message hash (i.e., digest) using the provided secret key digest = hmac.new(secret, msg=message, digestmod=hashlib.sha256).digest() # Base64-encode the message hash signature = base64.b64encode(digest).decode() return signature
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import re def get_flex_counters(module): """ @summary: Parse output of "counterpoll show" command and convert it to the dictionary. Composed dictionary example: {'PG_WATERMARK_STAT': {'Interval': '10000', 'Status': 'enable'}, 'PORT_STAT': {'Interval': '10000', 'Status': 'enable'}, 'QUEUE_STAT': {'Interval': '10000', 'Status': 'enable'}, 'QUEUE_WATERMARK_STAT': {'Interval': '10000', 'Status': 'enable'}} CLI output example: Type Interval (in ms) Status -------------------- ------------------ -------- QUEUE_STAT default (10000) enable PORT_STAT default (1000) enable QUEUE_WATERMARK_STAT default (10000) enable PG_WATERMARK_STAT default (10000) enable @param module: The AnsibleModule object @return: Return dictionary of parsed counters """ result = {} cli_cmd = "counterpoll show" skip_lines = 2 rc, stdout, stderr = module.run_command(cli_cmd) if rc != 0: module.fail_json(msg="Failed to run {}, rc={}, stdout={}, stderr={}".format(cli_cmd, rc, stdout, stderr)) try: for line in stdout.splitlines()[skip_lines:]: if line: key = line.split()[0] matched = re.search("{}.*(enable|disable)".format(key), line) if matched: counter_line = matched.group(0).split() result[key] = {} # Output line will contain 4 columns if default was not changed # And 3 columns if default was changed index = 2 if len(counter_line) % 3 else 1 result[key]["Interval"] = counter_line[index].strip("(|)") result[key]["Status"] = counter_line[-1] except Exception as e: module.fail_json(msg="Failed to parse output of '{}', err={}".format(cli_cmd, str(e))) return result
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def convert_period_into_pandas_freq(period_str): """converts the period into a frequency format used by pandas library. Args: period_str (string): period in string format using m, h and d to represent minutes, hours and days. Returns: string: new value for period according to pandas frequency format. ex: 1m -> 1min, 1h -> 1H and 1d -> 1D """ number = ''.join(filter(str.isdigit, period_str)) letter = ''.join(filter(str.isalpha, period_str)) if letter == 'm': return ''.join([number, 'min']) # return uppercase of period_str for other values of letter return period_str.upper()
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def newline_join(string, line_length): """ Inserts newline into the string. Newline is inserted at first the word boundary after the line_length characters. Parameters ---------- string : str String to insert newlines into. line_length : int Line length threshold after which the new line will be inserted. Returns ------- str with inserted newlines """ array = string.split() count = 0 line = "" for word in array: count = count + len(word) + 1 if count > line_length: line = line + "\n" + word count = len(word) else: line = line + " " + word return(line.strip())
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def Odds(p): """Computes odds for a given probability. Example: p=0.75 means 75 for and 25 against, or 3:1 odds in favor. Note: when p=1, the formula for odds divides by zero, which is normally undefined. But I think it is reasonable to define Odds(1) to be infinity, so that's what this function does. p: float 0-1 Returns: float odds """ if p == 1: return float('inf') return p / (1 - p)
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def seq_to_kmers(seq, k=3): """ Divide a string into a list of kmers strings. Parameters: seq (string) k (int), default 3 Returns: List containing a list of kmers. """ N = len(seq) return [seq[i:i+k] for i in range(N - k + 1)]
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def make_shape_channels_first(shape): """Makes a (N, ..., C) shape into (N, C, ...).""" return shape[:1] + shape[-1:] + shape[1:-1]
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import itertools def flatten(ls): """ flatten a nested list """ flat_ls = list(itertools.chain.from_iterable(ls)) return flat_ls
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import json def get_placeholder_value_given_type(value): """Given an a parameter type, return a placeholder value""" # string, array, object, boolean, integer, float, or datetime. if value.lower() == "string": return json.dumps("") elif value.lower() == "array": return [] elif value.lower() == "object": return {} elif value.lower() == "boolean": return "false" elif value.lower() == "integer": return 0 elif value.lower() == "float": return 0 elif value.lower() == "datetime": return "2021-04-01T00:00:00.fffffffZ"
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def is_dos_style_abspath(path): """ Check whether the given path is a DOS/Windows style absolute path. path: A path string """ if len(path) < 3: return False drv = path[0] # drive letter # A:65, B:66, ... Z:90, a:97, b:98, ... z:122 if ord(drv) < 65 or (ord(drv) > 90 and ord(drv) < 97) or ord(drv) > 122: return False return path[1:3] == ":\\"
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def subsample(data_array, subsample_interval): """ Subsample every points_per_sample points """ return data_array[..., 0::subsample_interval]
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def find_next_empty(puzzle): """ Takes a puzzle as parameter Finds the next row, col on the puzzle that's not filled yet (with a value of -1) Returns (row, col) tuple or (None, None) if there is none """ for row in range(9): for col in range(9): if puzzle[row][col] == -1: return row, col return None, None
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def is_defined(value): """Return True IFF `value` is not 'UNDEFINED' or None. >>> is_defined("UNDEFINED") False >>> is_defined(None) False >>> is_defined("FOO") True """ return value not in ["UNDEFINED", None]
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def _mpas_to_netcdf_calendar(calendar): """ Convert from MPAS calendar to NetCDF4 calendar names. """ if calendar == 'gregorian_noleap': calendar = 'noleap' elif calendar != 'gregorian': raise ValueError('Unsupported calendar {}'.format(calendar)) return calendar
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def cut_rod2(p, n, r={}): """Cut rod. Same functionality as the original but implemented as a top-down with memoization. """ q = r.get(n, None) if q: return q else: if n == 0: return 0 else: q = 0 for i in range(n): q = max(q, p[i] + cut_rod2(p, n - (i + 1), r)) r[n] = q return q
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import requests def follow_url(URL): """ Just a wrapper function that automatically raises an error if there's issues requesting. """ r = requests.get(URL) r.raise_for_status() return r.text
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def risk_level(value): """ Returns a string based risk level from a number. 1: Low 2: Medium 3: Medium 4: High """ if value == 1: return 'low' if value == 2 or value == 3: return 'medium' if value == 4: return 'high'
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def _cv_delta(x, eps=1.): """Returns the result of a regularised dirac function of the input value(s). """ return eps / (eps**2 + x**2)
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def bezier_sample(t, params): """Sample points from cubic Bezier curves defined by params at t values.""" A = params.new_tensor([[1, 0, 0, 0], [-3, 3, 0, 0], [3, -6, 3, 0], [-1, 3, -3, 1]]) t = t.pow(t.new_tensor([0, 1, 2, 3])) # [n_samples, 4] points = t @ A @ params # [..., n_samples, 3] return points
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import _warnings def snap_to_lines(fixation_sequence, text_block, method="warp", **kwargs): """ Deprecated in 0.4. Use `eyekit.fixation.FixationSequence.snap_to_lines()`. """ _warnings.warn( "eyekit.tools.snap_to_lines() is deprecated, use FixationSequence.snap_to_lines() instead", FutureWarning, ) return fixation_sequence.snap_to_lines(text_block, method, **kwargs)
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def is_valid_interval(interval): """Checks if the given interval is valid. A valid interval is always a positive, non-zero integer value. """ if not isinstance(interval, int): return False if interval < 0: return False return True
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def get_node_info(node, ws): """ Args: node (Node): ws (list(int)): knowledge weights. [cdscore, rdscore, asscore, stscore] Returns: return node information for a searched tree analysis node information: self node, parent node, depth, score, RDScore, CDScore, STScore, ASScore """ return (f"{id(node)}\t" f"{id(node.parent_node)}\t" f"{node.depth}\t" f"{node.total_scores / node.visits}\t" f"{node.state.rdscore}\t" f"{node.state.cdscore * ws[0]}\t" f"{node.state.stscore * ws[3]}\t" f"{node.state.asscore * ws[2]}")
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import ipaddress def is_ipv4(ip: str): """Return True if given address is a valid IPv4 address, otherwise return False""" try: ipaddress.IPv4Address(ip) except ipaddress.AddressValueError: return False return True
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def mutate_string(string, pos, change_to): """ Fastest way I've found to mutate a string @ 736 ns >>> mutate_string('anthony', 0, 'A') 'Anthony' :param string: :param pos: :param change_to: :return: """ string_array = list(string) string_array[pos] = change_to return ''.join(string_array)
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def create_minio_dispatcher_node(name): """ Args: name(str): Name of the minio node Returns: dict: A dictionnary with the minio node configuration """ return { "endpoint_url": "http://{:s}:9000/".format(name), "aws_access_key_id": "playcloud", "aws_secret_access_key": "playcloud", "type": "s3", }
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def activeTT_init(M): """ Initialize list of tour types that can be used in this problem instance :param M: Model :return: list of tour type indexes """ return [t for t in M.TTYPES if M.tt_ub[t] > 0]
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def get_other_person_from_match(user_id, match): """given a Match, return the Person corresponding to the user who is NOT the passed user ID (i.e. the other Person) """ if match.person_1.user_id == user_id: return match.person_2 elif match.person_2.user_id == user_id: return match.person_1 else: raise Exception(f"Person with user ID \"{user_id}\" is not part of " f"the passed match ({match}).")
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def partition_from_ragged_tensor_by_name(ragged_tensor, partition_type: str): """Extract row partition tensor from ragged tensor defined by string identifier of the partition scheme. Args: ragged_tensor (tf.RaggedTensor): Ragged tensor to extract row partition from. partition_type (str): String identifier of the partition scheme. Either `row_splits`, `row_limits` etc. Returns: tf.Tensor: Row partition defined by partition_type. """ # Not for nested ragged definition flat_tens = ragged_tensor.values if partition_type in ["row_length", "row_lengths"]: out_part = ragged_tensor.row_lengths() elif partition_type in ["row_split", "row_splits"]: out_part = ragged_tensor.row_splits elif partition_type == "value_rowids": out_part = ragged_tensor.value_rowids() elif partition_type in ["row_limit", "row_limits"]: out_part = ragged_tensor.row_limits() elif partition_type in ["row_start", "row_starts"]: out_part = ragged_tensor.row_starts() else: raise TypeError("Unknown partition scheme, use: 'row_lengths', 'row_splits', ...") return [flat_tens, out_part]
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def lerp(value1=0.0, value2=1.0, parameter=0.5): """ Linearly interpolates between value1 and value2 according to a parameter. Args: value1: First interpolation value value2: Second interpolation value parameter: Parameter of interpolation Returns: The linear intepolation between value 1 and value 2 """ return value1 + parameter * (value2 - value1)
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def trim_variant_fields(location, ref, alt): """ Trims common prefixes from the ref and alt sequences Parameters ---------- location : int Position (starting from 1) on some chromosome ref : str Reference nucleotides alt : str Alternate (mutant) nucleotide Returns adjusted triplet (location, ref, alt) """ if len(alt) > 0 and ref.startswith(alt): # if alt is a prefix of the ref sequence then we actually have a # deletion like: # g.10 GTT > GT # which can be trimmed to # g.12 'T'>'' ref = ref[len(alt):] location += len(alt) alt = "" if len(ref) > 0 and alt.startswith(ref): # if ref sequence is a prefix of the alt sequence then we actually have # an insertion like: # g.10 GT>GTT # which can be trimmed to # g.11 ''>'T' # Note that we are selecting the position *before* the insertion # (as an arbitrary convention) alt = alt[len(ref):] location += len(ref) - 1 ref = "" return location, ref, alt
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def ensure_quotes(s: str) -> str: """Quote a string that isn't solely alphanumeric.""" return '"{}"'.format(s) if not s.isalnum() else s
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import math def keep_top_genes(counts, num_genes_discard, criteria="Variance"): """ This function takes a matrix of counts (Genes as columns and spots as rows) and returns a new matrix of counts where a number of genesa re kept using the variance or the total count as filtering criterias. :param counts: a matrix of counts :param num_genes_discard: the % (1-100) of genes to keep :param criteria: the criteria used to select ("Variance or "TopRanked") :return: a new matrix of counts with only the top ranked genes. """ if num_genes_discard <= 0: return counts # Spots as columns and genes as rows counts = counts.transpose() # Keep only the genes with higher over-all variance num_genes = len(counts.index) print("Removing {}% of genes based on the {}".format(num_genes_discard * 100, criteria)) if criteria == "Variance": var = counts.var(axis=1) min_genes_spot_var = var.quantile(num_genes_discard) if math.isnan(min_genes_spot_var): print("Computed variance is NaN! Check your input data.") else: print("Min normalized variance a gene must have over all spots " "to be kept ({0}% of total) {1}".format(num_genes_discard, min_genes_spot_var)) counts = counts[var >= min_genes_spot_var] elif criteria == "TopRanked": sum = counts.sum(axis=1) min_genes_spot_sum = sum.quantile(num_genes_discard) if math.isnan(min_genes_spot_sum): print("Computed sum is NaN! Check your input data.") else: print("Min normalized total count a gene must have over all spots " "to be kept ({0}% of total) {1}".format(num_genes_discard, min_genes_spot_sum)) counts = counts[sum >= min_genes_spot_sum] else: raise RuntimeError("Error, incorrect criteria method\n") print("Dropped {} genes".format(num_genes - len(counts.index))) return counts.transpose()
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import re def fixSlashes(url): """ Removes double slashes in URLs, and ensures the protocol is doubleslahed """ # insert missing protocol slashes p = re.compile( '(:/)([^/])' ) url = p.subn( r'\1/\2', url)[0] # strip any double slashes excluding :// p = re.compile( '([^:])//' ) return p.subn( r'\1/', url)[0]
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import math def days_to_hmsm(days): """ Convert fractional days to hours, minutes, seconds, and microseconds. Precision beyond microseconds is rounded to the nearest microsecond. Parameters ---------- days : float A fractional number of days. Must be less than 1. Returns ------- hour : int Hour number. min : int Minute number. sec : int Second number. micro : int Microsecond number. Raises ------ ValueError If `days` is >= 1. Examples -------- >>> days_to_hmsm(0.1) (2, 24, 0, 0) """ hours = days * 24. hours, hour = math.modf(hours) mins = hours * 60. mins, min = math.modf(mins) secs = mins * 60. secs, sec = math.modf(secs) micro = round(secs * 1.e6) return int(hour), int(min), int(sec), int(micro)
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def filter_resources(resource, filter_name, filter_value): """Filter AWS resources Args: resource (object): EC2 resource filter_name (string): Filter name filter_value (string/list): Filter value(s) Returns: List: Filtered AWS resources """ values = [filter_value] if type(filter_value) is list: values = filter_value filters = [{ "Name": filter_name, "Values": values }] return list(resource.filter(Filters=filters))
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def read_prophage_table(infile): """ Reads tab-delimited table with columns for: 1 - path to GenBank file, 2 - replicon id, 3 - prophage start coordinate, 4 - prophage end coordinate, 5 (optional) - prophage name (if not provided pp1, pp2, etc. will be assigned for each file) :param infile: path to the file :return prophages: dictionary of GenBank file(s) paths, replicons and prophages coordinates """ prophages = {} with open(infile) as inf: for line in inf: if line.startswith('#'): continue line = line.strip().split('\t') file_path, replicon_id, start, end = line[:4] # adjust coords to Python's indexing coords = (int(start) - 1, int(end) - 1) if start > end: start, end = end, start if file_path in prophages: pp_cnt = len(prophages[file_path]) + 1 else: pp_cnt = 1 pp = line[4] if len(line) == 5 else f"pp{pp_cnt}" try: prophages[file_path][replicon_id][coords] = pp except KeyError: try: prophages[file_path][replicon_id] = {coords: pp} except KeyError: prophages[file_path] = {replicon_id: {coords: pp}} return prophages
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import struct def read_uint(buf, endianness=""): """ Reads an unsigned integer from `buf`. """ return struct.unpack(endianness + "H", buf.read(2))[0]
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def _is_A_list_company_symbol(code: str) -> bool: """测试code是否是符合A股代码要求的字符串 Precondition ======================================================================================= :param code: A股代码 Post condition ======================================================================================= :return: True or False Examples: ======================================================================================= >>> _is_A_list_company_symbol('300072') True >>> _is_A_list_company_symbol(300072) Traceback (most recent call last): ... AssertionError >>> _is_A_list_company_symbol('300072.SZ') False >>> _is_A_list_company_symbol('700072.SZ') False """ assert isinstance(code, str) return code.isdigit() \ and len(code) == 6 \ and code[:3] in ('000', '002', '300', '600', '601', '603', '608', '688')
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import requests def url_exists(url): """Check if a given url exists.""" codes = [200, 302] # 200 OK, 302 Found return True if requests.head(url).status_code in codes else False
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def get_text(soup): """ Extracts text from the page source PARAMS: soup:BeautifulSoup object - page source converted to BeautifulSoup object RETURNS: text:str - text contents of the page """ text = "" lead = soup.find("div", {"class": "delfi-article-lead"}).text text += lead p_tags = soup.find_all("p") for p in p_tags: if not p.text.endswith("..."): text += p.text + "\n " return text
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def fraction_str(numerator, denominator) -> str: """ Formats a fraction to the format %.5f [numerator/deniminator] :param numerator: :param denominator: :return: Formatted string """ if denominator > 0: return "%.5f [%.5f/%d]" % (float(numerator)/denominator, numerator, denominator) else: return "No Data"
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import typing def first_non_null(iterable: list) -> typing.Optional[str]: """Takes in an iterable, returns the first item that is not equal to '', if not found then None. :parameter iterable: A list that a for loop can iterate over :type iterable: list :return: The first item that is not equal to '' in the list or None if none is found :rtype: str or None """ for i in iterable: if i != '': return str(i) return None
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def ndvire3(b7, b8): """ Normalized Difference Vegetation Index Red-edge 3 \ (Gitelson and Merzlyak, 1994). .. math:: NDVIRE3 = (b8 - b7) / (b8 + b7) :param b7: Red-edge 3. :type b7: numpy.ndarray or float :param b8: NIR. :type b8: numpy.ndarray or float :returns NDVIRE3: Index value .. Tip:: Gitelson, A., Merzlyak, M. N. 1994. Spectral reflectance changes \ associated with autumn senescence of Aesculus hippocastanum L. and \ Acer platanoides L. leaves. Spectral features and relation to \ chlorophyll estimation. Journal of Plant Physiology 143(3), 286-292. \ doi:10.1016/S0176-1617(11)81633-0. """ NDVIRE3 = (b8 - b7) / (b8 + b7) return NDVIRE3
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def FormatDiffHunks(hunks): """Re-serialize a list of DiffHunks.""" r = [] last_header = None for hunk in hunks: this_header = hunk.header[0:2] if last_header != this_header: r.extend(hunk.header) last_header = this_header else: r.extend(hunk.header[2]) r.extend(hunk.lines) r.append("\n") return "".join(r)
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def _parse_r_line(line, *_): """ Parse router info line. :param line: the line :return: dict with router info """ split_line = line.split(' ') return { 'nickname': split_line[0], 'ip': split_line[5], 'dir_port': int(split_line[7]), 'tor_port': int(split_line[6]), '_fingerprint': split_line[1], }
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def _conditional_field_block(if_keyword, expression, colon, comment, newline, indent, fields, dedent): """Applies an existence_condition to each element of fields.""" del if_keyword, newline, colon, comment, indent, dedent # Unused. for field in fields.list: condition = field.field.existence_condition condition.CopyFrom(expression) condition.source_location.is_disjoint_from_parent = True return fields
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def convert_bool_args(args: dict) -> dict: """Convert boolean CLI arguments from string to bool. Args: args: a mapping from CLI argument names to values Returns: copy of args with boolean string values convert to bool """ new_args = {} for k, v in args.items(): if v.lower() == 'true': v = True elif v.lower() == 'false': v = False new_args[k] = v return new_args
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