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def convert_datetime_to_timestamp(dt): """Convert pandas datetime to unix timestamp""" return int(dt.timestamp())
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def get_indicator_type_value_pair(field): """ Extracts the type/value pair from a generic field. This is generally used on fields that can become indicators such as objects or email fields. The type/value pairs are used in indicator relationships since indicators are uniquely identified via their ty...
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def doc_arg(name, brief): """argument of doc_string""" return " :param {0}: {1}".format(name, brief)
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def example_project(tmp_path): """ a minimal project """ my_module = tmp_path / "my_module" starter_content = my_module / "starter_content" starter_content.mkdir(parents=True) (tmp_path / "README.md").write_text("# My Module\n") (my_module / "__init__.py").write_text("__version__ = '0.0.0\n...
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def foo(): """ example function documentation an example doctest is included below returns: None >>> x = foo() >>> x 'foo' """ return "foo"
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def string_date(mnthDay, year): """Return a string date as 'mm/dd/yyyy'. Argument format: 'mm/dd' string 'yyyy'""" return(mnthDay + '/' + str(year))
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def check_who_queued(user): """ Returns a function that checks if the song was requested by user """ def pred(song): if song.requested_by and song.requested_by.id == user.id: return True return False return pred
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def _get_lines(filename): """Returns a list of lines from 'filename', joining any line ending in \\ with the following line.""" with open(filename, "r") as f: lines = [] accum = "" for line in f: if line.endswith("\\\n"): accum += line[:-2] els...
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import re def replace_punctuation_and_whitespace(text): """Replace occurrences of punctuation (other than . - _) and any consecutive white space with .""" rx = re.compile(r"[^\w\s\-.]|\s+") return rx.sub(".", text)
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import re def remove_symbols(text): """ Removes all symbols and keep alphanumerics """ whitelist = [] return [re.sub(r'([^a-zA-Z0-9\s]+?)',' ',word) for word in text if word not in whitelist]
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def filter_out_length_of_one(word): """ Filters out all words of length 1 :param word: Input word :return: None if word is of length 1, else the original word """ if len(word) > 1: return True return False
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def bmesh_join(list_of_bmeshes, list_of_matrices, *, normal_update=False, bmesh): """takes as input a list of bm references and outputs a single merged bmesh allows an additional 'normal_update=True' to force _normal_ calculations. """ bm = bmesh.new() add_vert = bm.verts.new add_face = bm.face...
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import json def read_json(jsonfile): """Read a json file into a dictionary Args: jsonfile: the name of the json file to read Returns: the contents of the JSON file as a dictionary >>> from click.testing import CliRunner >>> test = dict(a=1) >>> with CliRunner().isolated_filesyst...
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def zero_float(string): """Try to make a string into a floating point number and make it zero if it cannot be cast. This function is useful because python will throw an error if you try to cast a string to a float and it cannot be. """ try: return float(string) except: return 0
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import re def _special_att_handling(attype, col_args): # noqa: C901 """ laundry list of special handling that sqlalchemy does to convert between a Postgres type and a Sqlalchemy type """ kwargs = {} if attype == 'uuid': kwargs = {'as_uuid': True} args = () elif attype == 'numeri...
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def checksum(data) -> int: """ Found on: http://www.binarytides.com/raw-socket-programming-in-python-linux/. Modified to work in python 3. The checksum is the 16-bit ones's complement of the one's complement sum of the ICMP message starting with the ICMP Type (RFC 792). :param data: data to built ch...
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def _number_convert(match): """ Convert number with an explicit base to a decimal integer value: - 0x0000 -> hexadecimal - 16'h0000 -> hexadecimal - 0b0000 -> binary - 3'b000 -> binary - otherwise -> decimal """ prefix, base, number = match.groups() if prefix is not None: ...
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import requests import sys def get_scientific_name(taxon_id): """Get scientific name for input taxon_id. :param taxon_id: NCBI taxonomy identifier :return scientific_name: scientific name of sample that distinguishes its taxonomy """ # endpoint for scientific name url = 'http://www.ebi.ac.uk/...
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def rating_calc(item, ocurrences, last_ocurrences, total_ocurrences): """ Calculates the rating of the target language. """ rating = ocurrences / total_ocurrences if item in last_ocurrences: rating *= 2 if last_ocurrences and item == last_ocurrences[-1]: rating *= 4 return rating
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import hashlib def makeKey(password, salt): """make master key""" if not hasattr(password, 'decode'): password = password.encode('utf-8') if not hasattr(salt, 'decode'): salt = salt.lower() salt = salt.encode('utf-8') # Here we use 100,000 iterations since that is the default t...
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def run_episode(environment, agent, is_training=False): """Run a single episode.""" timestep = environment.reset() while not timestep.last(): action = agent.step(timestep, is_training) new_timestep = environment.step(action) if is_training: agent.update(timestep, action, new_timestep) ti...
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def pandas_df_to_temporary_csv(tmp_path): """Provides a function to write a pandas dataframe to a temporary csv file with function scope.""" def _pandas_df_to_temporary_csv(pandas_df, sep=",", filename="temp.csv"): temporary_csv_path = tmp_path / filename pandas_df.to_csv(temporary_csv_path, se...
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def df(n): """Gives the double factorial of *n*""" return 1.0 if n <= 0 else 1.0 * n * df(n - 2)
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def cli(ctx, job_id): """Resume a job if it is paused. Output: dict containing output dataset associations .. note:: This method is only supported by Galaxy 18.09 or later. """ return ctx.gi.jobs.resume_job(job_id)
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def queue_exists(queue_id): """Returns true if the queue ID belongs to a valid queue.""" return True
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import re def track_num_to_int(track_num_str): """ Convert a track number tag value to an int. This function exists because the track number may be something like 01/12, i.e. first of 12 tracks, so we need to strip off the / and everything after. If the string can't be parsed as a ...
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def elt1(list, context): """return second member""" return list[1]
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def sort_list(player_data_list): """Sort list based on qualifer. Args: player_data_list: player data list Returns: player data list properly sorted """ return sorted(player_data_list, key=lambda x: x[-1])
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def is_alive(worker_dict): """ Test if worker is alive and running | None --> Bool """ return worker_dict['worker'].is_alive()
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def sort(array: list[int]) -> list[int]: """Naive bubble sort implementation. """ for i in range(len(array)): for j in range(len(array) - 1, i, -1): if array[j] < array[j - 1]: array[j], array[j - 1] = array[j - 1], array[j] return array
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def box_teamnames(page): """ A @ H always """ teams = page.find_all("span", {"class": "short-name"}) destinations = page.find_all("span", {"class": "long-name"}) names = [team.text for team in teams] cities = [destination.text for destination in destinations] if not names or not cities: ...
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def _call_bool_filter(context, value): """Pass a value through the 'bool' filter. :param context: Jinja2 Context object. :param value: Value to pass through bool filter. :returns: A boolean. """ return context.environment.call_filter("bool", value, context=context)
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def get_attr(attrs, key): """ Get the attribute that corresponds to the given key""" path = key.split('.') d = attrs for p in path: if p.isdigit(): p = int(p) # Let it raise the appropriate exception d = d[p] return d
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def get_wbo(offmol, dihedrals): """ Returns the specific wbo of the dihedral bonds Parameters ---------- offmol: openforcefield molecule dihedrals: list of atom indices in dihedral Returns ------- bond.fractional_bond_order: wiberg bond order calculated using openforcefield toolkit ...
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import re def _GetLogTag(filename): """Get the tag of a log.""" regex = re.compile(r'\d+\-\d+(:?\-(?P<tag>.+))?.h5') match = regex.search(filename) if match and match.group('tag'): return match.group('tag') elif filename.endswith('.h5'): return filename[:-3] else: return ''
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import numpy def l2_norm(x: numpy.ndarray, y: numpy.ndarray) -> numpy.ndarray: """Euclidean distance between two batches of points stacked across the first dimension.""" return numpy.linalg.norm(x - y, axis=1)
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def ilarisHitProb(at,vt): """ at: AT of attacking character vt: VT of defending character return: probability that attacking character will hit defending character """ # 47.5 is the chance without any bonus # 47.5-((y-41)*y)/8 is the added chance per bonus # (at>vt) is extra if at>vt bec...
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import string import random def random_string() -> str: """Return a random string of characters.""" letters = string.ascii_letters return "".join(random.choice(letters) for i in range(32))
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def bbox_structure_to_square(bbox): """Function to turn from bbox coco struture to square. [x,y,width,height] -> [min_height, min_width, max_height, max_width] """ x,y,width,height = bbox sq = [y,x,y+height,x+width] return sq
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from typing import Pattern def sub_twice(regex: Pattern[str], replacement: str, original: str) -> str: """Replace `regex` with `replacement` twice on `original`. This is used by string normalization to perform replaces on overlapping matches. """ return regex.sub(replacement, regex.sub(replacemen...
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import pickle def load_pickle(filename): """ Loads a serialized object Parameters: ----------- filename : string """ return pickle.load(open(filename,'rb'))
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def get_properties(value): """ Converts the specified value into a dict containing the NVPs (name-value pairs) :param value: :return: """ rtnval = None if isinstance(value, dict): # value is already a Python dict, so just return it rtnval = value elif '=' in value: ...
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def get_pdm_terms(site_index, n, adj_sites=4, shift=0): """ inputs: site_index (int): center site index n (int): number of sites in lattice (for enforcing periodic boundary conditions) adj_site (int): how many adjacent sites to collect pop and coherence values from shift (int): r...
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import ast def ast_name_node(**props): """ creates a name ast node with the property names and values as specified in `props` """ node = ast.Name() for name, value in props.items(): setattr(node, name, value) return node
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def buildX(traj_file, t, X): """ Builds the node attribute matrix for a given time step. Inputs: traj_file : string indicating the location of the ground truth trajectory data t : scalar indicating current time step X : empty node attribute matrix in shape [n_nodes, n_features] Outputs: ...
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def move_left(board, row): """Move the given row to one position left""" board[row] = board[row][1:] + board[row][:1] return board
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import re import torch def embed_seq(sequence, tokenizer, prottrans_model, device="cpu"): """ Embed a single sequence from the tokenizer and prottrans model. """ sequences = [sequence] sep_sequences = [] for seq in sequences: sep_sequences.append(" ".join([x for x in seq])) #print(...
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def get_quadrant(x, y): """ Returns the quadrant as an interger in a mathematical positive system: 1 => first quadrant 2 => second quadrant 3 => third quadrant 4 => fourth quadrant None => either one or both coordinates are zero Parameters ---------- x : float x coordina...
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def days_in_month(year, month): """ Inputs: year - an integer between datetime.MINYEAR and datetime.MAXYEAR representing the year month - an integer between 1 and 12 representing the month Returns: The number of days in the input month. """ leapyear=0 if(year%4 ...
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import requests import json def _get_token(user, password, host, port): """ Gets auth token. """ token_url = "{}:{}/api/token/".format(host, port) response = requests.post(token_url, json={ "username": user, "password": password }) if response.ok: return json.loads(response...
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import random def random_point(): """Returns a random point on a 100x100 grid.""" return (random.randrange(100), random.randrange(100))
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def repeat(s, n): """ (str, int) -> str Return s repeated n times; if n is negative, return empty string. >>> repeat('yes', 4) 'yesyesyesyes' >>>repeat('no', 0) '' """ return (s * n)
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def can_translate(user): """Checks if a user translate a product""" return user.permissions['perm_translate']
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def read_xml_file_line_basis(xml_file, element): """ Read the xml file and capture only the elements we need. """ start_tag = f'<{element}>' # 3 end_tag = f'</{element}>' # 2 start_tag_identified = False # 3 captured_records = list() # 4 captured_line = '' with open(xml_file) as f: #...
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def xyz_string(labels, coords): """ .xyz format string for this cartesian geometry :param labels: optional labels for the beginnings of atom lines, by index :type labels: dict """ assert len(labels) == len(coords) dxyz = '\n'.join( '{:s} {:s} {:s} {:s}'.format(asymb, *map(repr, xyz)) ...
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import pandas def Protein_translation_Amb(t, y, data, mRNAData): """ Defines ODE function Conversion of Amb_mRNA to protein p1,p2,p3....: Protein concentrations for all ODEs It will have list of all parameter values for all my ODEs, so 36 values : L, U, D for each mRNA to protein conversion equation ...
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import os def _get_abs_path(path): """Return the absolute path for a given path. :param path: ``str`` $PATH to be created :returns: ``str`` """ return os.path.abspath( os.path.expanduser( path ) )
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def square(num): """ Return the square values of the input number. The input number must be integer. """ return num ** 2
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from typing import OrderedDict def apply_address_fixups(address: OrderedDict[str, str]) -> OrderedDict[str, str]: """Sometimes the usaddress parser makes mistakes. It's an imperfect world. This function applies transformations to the parsed address to correct specific known errors. """ # Fixup: At...
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import torch def mask_finished_scores(score, flag): """ If a sequence is finished, we only allow one alive branch. This function aims to give one branch a zero score and the rest -inf score. Args: score: A real value array with shape [batch_size * beam_size, beam_size]. flag: A bool ar...
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import itertools def args_combinations(*args, **kwargs): """ Given a bunch of arguments that are all a set of types, generate all possible possible combinations of argument type args is list of type or set of types kwargs is a dict whose values are types or set of types """ def asset(v): ...
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import copy def coordinate_tensor(dim): """ :param dim: list of lengths for each dimension :return: a list of every possible coordinate within the dimension system """ # recurrent function def recurrent_dim_filler(dim_current, dim_higher, coordinate_higher, coordinates): # processing...
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def RGBStringToList(rgb_string): """Convert string "rgb(red,green,blue)" into a list of ints. The purple air JSON returns a background color based on the air quality as a string. We want the actual values of the components. Args: rgb_string: A string of the form "rgb(0-255, 0-255, 0-255)". Returns: ...
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import six def _metric_value(value_str, metric_type): """ Return a Python-typed metric value from a metric value string. """ if metric_type in (int, float): try: return metric_type(value_str) except ValueError: raise ValueError("Invalid {} metric value: {!r}". ...
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import threading def in_main_thread(): """ True when the current thread is the main thread. """ return threading.current_thread().__class__.__name__ == '_MainThread'
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def fixUnits(object, **kwargs): """Convert output pint units into a proper latex string.""" string = str(object) type = kwargs.get('type', None) unitColor = 'darkBlue' replacements = kwargs.get('replacements', None) if replacements: for old, new in replacements.items(): str...
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def getMDistance(plug): """ Gets the MDistance value from the supplied plug. :type plug: om.MPlug :rtype: om.MDistance """ return plug.asMDistance()
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def get_time_size(rates): """ Get number of time intervals Parameters ---------- Returns ------- out : int Number of time intervals See Also -------- DataStruct """ wgname_keys = list(rates.keys()) mnemo_keys = list(rates[wgname_keys[0]].keys()) return...
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import argparse def arg_parser(): """ """ parser = argparse.ArgumentParser() parser.add_argument("-i", "--input", type=str, dest='input_file', help="Input file with tweets summary information") parser.add_argument("-e", "--input-entities", type=str, dest='input_ent', ...
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def splitFragP(uriref, punct=0): """split a URI reference before the fragment Punctuation is kept. e.g. >>> splitFragP("abc#def") ('abc', '#def') >>> splitFragP("abcdef") ('abcdef', '') """ i = uriref.rfind("#") if i >= 0: return uriref[:i], uriref[i:] else: ...
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def sanitize_name(name): """ Clean-up the given username.""" name = name.strip() # clean up group name = name.replace('- IE', ' -IE') name = name.replace('- MA', ' -MA') for l in [1,2,3,4,5,6,7,8,9]: for g in "AB": name = name.replace(f'IE{l}-{g}', f'IE-{l}{g}') ...
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import os def extensionName(path): """ Function responsible for returning the extension of a file. """ extension = os.path.splitext(path)[1][1:] return extension
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import yaml import re def create_kubeconfig_for_ssh_tunnel(kubeconfig_file, kubeconfig_target_file): """ Creates a kubeconfig in which the Server URL is modified to use a locally set up SSH tunnel. (using 127.0.0.1 as an address) Returns a tuple consisting of: - the original IP/Serve...
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def sse_pack(d): """ Format a map with Server-Sent-Event-meaningful keys into a string for transport. Happily borrowed from: http://taoofmac.com/space/blog/2014/11/16/1940 For reading on web usage: http://www.html5rocks.com/en/tutorials/eventsource/basics For reading on the format: https://...
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import argparse def parse_arguments(): """ Create command-line interface """ desc = "Compute dG, stdDG for different lengths and number of trajectories" parser = argparse.ArgumentParser(description=desc) parser.add_argument("-l", "--lagtime", type=int, default=100, help="Lagtimes to use, d...
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def _touint64(num): """ This is required to convert signed json integers to unsigned. """ return num & 0xffffffffffffffff
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import torch def shuffle(images, targets, global_targets): """ A trick for CAN training """ sample_num = images.shape[1] for i in range(4): indices = torch.randperm(sample_num).to(images.device) images = images.index_select(1, indices) targets = targets.index_select(1, indi...
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def get_lines_from_file(loc): """Reads the file and returns a list with every line. Parameters: loc (str): location of the file. Returns: list: list containing each of the lines of the file. """ f = open(loc) result= [line.replace("\n", "") for line in f] f.clo...
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def GetBuildShortBaseName(target_platform): """Returns the build base directory. Args: target_platform: Target platform. Returns: Build base directory. Raises: RuntimeError: if target_platform is not supported. """ platform_dict = { 'Windows': 'out_win', 'Mac': 'out_mac', 'Li...
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def make_wildcard(title, *exts): """Create wildcard string from a single wildcard tuple.""" return "{0} ({1})|{1}".format(title, ";".join(exts))
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from pathlib import Path def dir_files(path, pattern="*"): """ Returns all files in a directory """ if not isinstance(path, Path): raise TypeError("path must be an instance of pathlib.Path") return [f for f in path.glob(pattern) if f.is_file()]
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def myDownsample(y, N) : """ yds = myDownsample(y,N) yds is y sampled at every Nth index, starting with yds[0]=y[0] with y[range(0,len(y),N)]. Implementing Matlab's downsample. Ted Golfinopoulos, 7 June 2012 """ return y[range(0,len(y),N)]
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def _norm_args(norm): """ Returns the proper normalization parameter values. Possible `norm` values are "backward" (alias of None), "ortho", "forward". This function is used by both the builders and the interfaces. """ if norm == "ortho": ortho = True normalise_idft = Fals...
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import torch def all_pair_iou(boxes_a, boxes_b): """ Compute the IoU of all pairs. :param boxes_a: (n, 4) minmax form boxes :param boxes_b: (m, 4) minmax form boxes :return: (n, m) iou of all pairs of two set """ N = boxes_a.size(0) M = boxes_b.size(0) max_xy = torch.min(boxes_a[:...
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def get_empty_theme(): """Create object that contains empty theme.""" return { 'theme': {}, 'background': bytearray() }
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import string def letter_extractor(raws): """letter_ Frequencies of 26 English letters in a given text, case insensitive. Known differences with Writeprints Static feature "letter frequency": None. Args: raws: List of documents. Returns: Frequencies of English letters in the do...
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def crop_frames(frames, speaker): """ frames: (b h w c) """ if speaker == "chem" or speaker == "hs": return frames elif speaker == "chess": return frames[:, 270:460, 770:1130] elif speaker == "dl" or speaker == "eh": return frames[:, int(frames.shape[1] * 3 / 4) :, int(fr...
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def builddict(fin): """ Build a dictionary mapping from username to country for all classes. Takes as input an open csv.reader on the edX supplied file that lists classname, country, and username and returns a dictionary that maps from username to country """ retdict = {} for cours...
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def get_reverse_depends(name, capability_instances): """Gets the reverse dependencies of a given Capability :param name: Name of the Capability which the instances might depend on :type name: str :param capability_instances: list of instances to search for having a dependency on the given Capab...
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import collections def node_degree_counter(g, node, cache=True): """Returns a Counter object with edge_kind tuples as keys and the number of edges with the specified edge_kind incident to the node as counts. """ node_data = g.node[node] if cache and 'degree_counter' in node_data: return no...
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async def get_account_id(db, name): """Get account id from account name.""" return await db.query_one("SELECT find_account_id( (:name)::VARCHAR, True )", name=name)
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def params_to_payload(params, config): """Converts a set of parameters into a payload for a GET or POST request. """ base_payload = {config['param-api-key']: config['api-key']} return dict(base_payload, **params)
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from typing import Any def is_a_string(v: Any) -> bool: """Returns if v is an instance of str. """ return isinstance(v, str)
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def historical(): """" Retrieve stored data from datastore. """ return { 'page': 'historical', }
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import os import re def name_from_cmakelists(cmakelists): """ Get a project name from a CMakeLists.txt file """ if not os.path.exists(cmakelists): return None res = None # capture first word after project(), excluding quotes if any regexp = re.compile(r'^\s*project\s*\("?(\w+).*"?\)',...
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import time import json import requests def catch_distribution(): """抓取行政区域确诊分布数据""" data = dict() url = "https://view.inews.qq.com/g2/getOnsInfo?name=wuwei_ww_area_counts&callback=&_=%d" %int(time.time()*1000) for item in json.loads(requests.get(url=url).json()["data"]): if item["area"] not ...
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import sys def extract_entity_text(text: str, offset: int, length: int) -> str: """ Get entity value. :param text: Full message text :param offset: Entity offset :param length: Entity length :return: Returns required part of the text """ if sys.maxunicode == 0xFFFF: return tex...
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def reconstructTypeFunctionType(typeFunction, args, kwargs): """Reconstruct a type from the values returned by 'isTypeFunctionType'""" #note that our 'key' objects are dict-in-tuple-form, because dicts are #not hashable. So to keyword-call with them, we have to convert back to a dict... return typeFunc...
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def str_to_dict( text: str, /, *keys: str, sep: str = ",", ) -> dict[str, str]: """ Parameters ---------- text: str The text which should be split into multiple values. keys: str The keys for the values. sep: str The separator for the values. Returns ...
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def keyset(): """ Creates a set of numeric keys centered around 0 Provides a comparison function based on numeric closeness of the keys """ class KeySet: extent = 10 def __init__(self): self.key = "0" self.all = [self.key] for i in range(KeyS...
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