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def export_python_string(earth_model, function_name="model"): """ Exports model as a string that evaluates as python code, with no numpy/scipy/sklearn dependencies. :param earth_model: Trained pyearth model :param function_name: string, optional, will be the name of the function in the returned string ...
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import re def clean(string): """Clean string Cleans a string to be a valid Python variable name. It replaces all invalid characters with an underscore. Arguments: string {str} -- string to be formatted Returns: str -- formatted string """ string = re.sub('\W|^(?=\d)', '_...
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import re def parse_braces(sequence): """ Replace all occurrences of ``x{n}`` (where x is any character) with n occurrences of x. Raise ValueError if the expression cannot be parsed. >>> parse_braces('TGA{5}CT') TGAAAAACT """ # Simple DFA with four states, encoded in prev result = '' ...
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import time def timestamp_dir(when=None): """ Returns a directory named after the specified time or the current time, if no specific time is given """ if when is None: when = time.time() return time.strftime("%Y%m%d_%H%M%S", time.localtime(when))
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def points_from_columns(xs): """ Takes a list of rows and converts it into a list of columns. For example, xs = [[1, 2, 3], [4, 5, 6], [1], [2, 4]] will return x = [[1, 4, 1, 2], [2, 5, 4], [3, 6]] xs: list of rows (lists). returns: list of columns (lists). """ x = [] ...
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def l2_norm(x): """ Calculates the l2 norm of the input tensor. Args: x: tensor, any shape tensor to take the l2 norm of. Returns: float, l2 norm of the input """ return x.view(-1).dot(x.view(-1))
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def test_nan(dataframe): """ Test if dataframe contains nan value Parameters ---------- dataframe: pandas dataframe Raises ------ ValueError If contains nan, raise ValueError Returns ------- is_valid: boolean True if did not contain nan, False if contain ...
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import time def most_recent_planet(tree): """Returns planet node that has most recent update date. :param tree: lxml etree :returns: lxml etree """ updates = tree.findall('.//lastupdate') update_time = [time.strptime(date.text,'%y/%m/%d') for date in updates] planet = updates[update_time....
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def is_zero_length(quat): """Checks if a quaternion is zero length. :param numpy.array quat: The quaternion to check. :rtype: boolean. :return: True if the quaternion is zero length, otherwise False. """ return quat[0] == quat[1] == quat[2] == quat[3] == 0.0
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def join_regexes(regexes): """ Utility function, takes in a list of regexes and outputs their OR """ result = r'' for reg in regexes: result = result + '(' result = result + reg result = result + ')|' return result[:-1]
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def strip_query(url): """Remove query string from a url""" return url.split('?', 1)[0]
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def point_avg(points): """ Accepts a list of points, each with the same number of dimensions. NB. points can have more dimensions than 2 Returns a new point which is the center of all the points. """ dimensions = len(points[0]) new_center = [] for dimension in range(dimensions): dim_sum = 0 # dimension ...
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from functools import reduce def fact2(n): """Compute the double factorial as in https://stackoverflow.com/a/4740229/3249688 """ return reduce(int.__mul__, range(n, 0, -2), 1)
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def slice_length(orange): """ Returns the length of the index corresponding to a slice. For example, slice(0,4,2) has a length of two. This is used by some of the methods in message.py. """ t = type(orange) if t is slice: if orange.step: return int((orange.stop-orange.sta...
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def __get_midi_csv(midi_strings): """split comma seperated strings into csv file Arguments: midi_strings {list} -- list of comma separated strings Returns: csv -- midi data in csv format """ midi_csv = [] for row in midi_strings: midi_data = row.split(",") midi_cs...
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def _k_mer_to_index(k_mer): """Converts a k-mer to its numerical index. Args: k_mer (str): The :math:`k`-mer to convert. Returns: int: The index of the :math:`k`-mer. Examples: >>> _k_mer_to_index("A") 0 >>> _k_mer_to_index("T") 3 >>> _k_mer_to_...
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def update_dict(dict_, **kwargs): """Add keys to a new dictionary. Args: dict_: the dictionary to add to kwargs: the key, value pairs to add Returns: a new dictionary """ return dict(list(dict_.items()) + list(kwargs.items()))
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def convert_byte_dict_to_str_dict(inp: dict) -> dict: """ Convert dictionaries with keys and values as bytes to strings Args: inp: Dictionary with key and values in bytes Returns: Dictionary with key and value as string """ new_dict = dict() for k, v in inp.items(): ...
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from typing import Optional def injection_file_name( science_case: str, num_injs_per_redshift_bin: int, task_id: Optional[int] = None ) -> str: """Returns the file name for the raw injection data without path. Args: science_case: Science case. num_injs_per_redshift_bin: Number of injectio...
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def collection_image_location(instance, filename): """Return the location of a stored media file for a Workflow Collection.""" collection_id = instance.id image_type = instance.type file_extension = filename.rpartition(".")[2] return f"workflow_system/collections/{collection_id}/{image_type}.{file_...
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def find_nearest_power_of_two(a): """return closest power of two number smaller than a i.e. if a = 1025, return 1024 """ i = 0 while a > 1: a = a / 2 i += 1 return 2 ** (i - 1)
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def is_simple_bool(typehint) -> bool: """Check if typehint is bool or Union[None, bool].""" if typehint is bool: return True if hasattr(typehint, "__args__") and bool in typehint.__args__: return True return False
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import hashlib def get_hash_values(file): """ Get MD5/SHA256/SHA512 hash :param file: Path to file :return: MD5/SHA256/SHA512 hash """ blocksize = 65536 hashval_sha256 = hashlib.sha256() hashval_md5 = hashlib.md5() hashval_sha512 = hashlib.sha512() with open(file, 'rb') as file...
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def keys_subset(base_dict, keys): """ Generate a dictionary that contains a subset of the entries of the base dictionary with the given keys """ return dict((k, base_dict[k]) for k in keys if k in base_dict)
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import torch def kl_forward(logu: torch.Tensor) -> torch.Tensor: """ Log-space Csiszar function for forward KL-divergence D_f(p,q) = KL(p||q). Also known as the inclusive KL-divergence, minimizing results in zero-avoiding / mass-covering behavior. Args: logu (torch.Tensor): ``p.log_prob`...
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import six def rev_comp( seq, molecule='dna' ): """ DNA|RNA seq -> reverse complement """ if molecule == 'dna': nuc_dict = { "A":"T", "B":"V", "C":"G", "D":"H", "G":"C", "H":"D", "K":"M", "M":"K", "N":"N", "R":"Y", "S":"S", "T":"A", "V":"B", "W":"W", "Y":"R" } elif molecule == 'rna': nuc_dict = { "A":"U", "...
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def capitalised_string(s): """ Check whether the first letter of a title is uppercase :param s: String containing a title. :return: True if first letter is uppercase else False. """ try: return s[0].isupper() except IndexError: return False
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def get_left_or_right(node_idx, struct): """ Return True if the node is a left child of its parent. o/w return false. """ parent_node = struct[node_idx]['parent'] return struct[parent_node]['left_child'] == node_idx
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def untuple(x): """Untuple a single value that was wrapped in a tuple.""" assert type(x) == type(()), 'Expected tuple.' # safety check assert len(x) == 1, 'Expected tuple singleton.' # safety check return x[0]
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def get_max_rows(worksheet): """ Gets the number of non-empty rows of the current worksheet. :param worksheet: Current worksheet to manipulate. :return: Number of non-empty rows """ return worksheet.max_row
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def get_rebalancing_flow(tnet): """ get rebalancing flow in a supergraph Parameters ---------- tnet: transportation network object Returns ------- float """ return sum([(tnet.G_supergraph[i][j]['flow']-tnet.G_supergraph[i][j]['flowNoRebalancing'])*tnet.G_supergraph[i][j]['len...
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def first(iterable, default=None): """Return the first element of an iterable or the next element of a generator; or default.""" try: return iterable[0] except IndexError: return default except TypeError: return next(iterable, default)
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def recursive_dichotomy(list, value, beginning, end): """ list: array of integers in ascending order value: value to return its position in the list beginning: first index of list (in this case 0) end: last index of list (in this case len(list)) return: False in value not in list, else the position of value...
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def isrange(a, b): """ Return True if the passed tuple `(a,b)` is a valid range (that is, `a` may not be greater than `b`). """ #~ if r[0] is None or r[1] is None: return True #~ if r[0] <= r[1]: return True if a is None or b is None: return True if a <= b: return True ...
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from pathlib import Path from typing import Dict def _get_srcset_st(sources_dir: Path, hinames: Dict[float, Path]): """ Create the srcset string for including on the md line. ie. sources_dir might be /home/sample-proj/source, hinames posix paths to 0: /home/sample-proj/source/plot_types/images/img...
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import torch def l2norm(X): """L2-normalize columns of X """ norm = torch.pow(X, 2).sum(dim=-1, keepdim=True).sqrt() X = torch.div(X, norm+1e-10) return X
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def Median(data): """Returns the median of a time series""" return data.median()
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import re def chop_after_title(source): """Return the source of a document after DocInfo metadata. :param source: Source of RST document :type source: string :returns: All source content after docinfo :rtype: string """ # find the last docinfo element index = re.findall(r'[=-]{3,}\n.*...
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def make_matrix(rows, cols, fill=0.0): """Returns a matrix (list of list of floats) using a default value. :param rows: Number of rows :type rows: int :param cols: Number of columns :type cols: int :param fill: Default value for each element in the matrix :type fill: float """ m...
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def solution(A): # O(N) """ Identify whether four sides (given by four integers) can form a square, a rectangle, or neither. Input: You will receive an array of strings, each containing four space-separated integers, which represent the length of t...
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import re def filter_collection(collection, include=None, exclude=None): """Filter collection based on include and exclude regexps. The regexp patterns are not implicitly anchored at the beginning of strings (i.e. `search` is used, rather than `match`). E.g. 'abc' will match '_abc_' as well as 'abcde...
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def count_digit(value): """Count the number of digits in the number passed into this function""" digit_counter = 0 while value > 0: digit_counter = digit_counter + 1 value = value // 10 return digit_counter
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import re def sanitize(phrase): """Sanitizes words by removing punctuation""" return re.sub('[!-():?.]','',phrase)
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import math def entropy(ps): """Calculates the entropy (log 2) of the distribution given by p """ entropy = 0.0 for p in ps: if not(p == 0): entropy -= p*math.log(p, 2) return entropy
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def H_acceptor_count(mol): """Hydrogen bond acceptor count """ mol.require("Valence") return sum(1 for _, a in mol.atoms_iter() if a.H_acceptor)
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def check_x_lim(x_lim, max_x): """ Checks the specified x_limits are valid and sets default if None. """ if x_lim is None: x_lim = (None, None) if len(x_lim) != 2: raise ValueError("The x_lim parameter must be a list of length 2, or None") try: if x_lim[0] is not None and...
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def _GetReleaseTracks(release_tracks): """Returns a string representation of release tracks. Args: release_tracks: API versions to generate release tracks for. """ release_tracks_normalized = '[{}]'.format(', '.join( [track.upper() for track in sorted(release_tracks)])) return release_tracks_normal...
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def _map_function_arg_pairs(function_list, arg): """Method that maps a list of functions to a list of arguments Args: function_list: List of functions arg: List of single arguments Returns: Map: map of of functions with injected arguments. """ return map(lambda func, arg: f...
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def _find_in_list(key, a, start=None, force=False): """key - object you want to find a - list to search return - index in a """ if start is None: sequence = range(0, len(a)) else: sequence = range(start, len(a)) for i in sequence: if a[i] == key: return i ...
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def token_response(oauth_test_client): """ Return a successful token response. """ oauth_test_client.authorize(data={"confirm": "yes"}) return oauth_test_client.token().response
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def url_add_trailing_slash(uri: str) -> str: """Add trailing slash to url if this is valid Parameters ---------- uri : str Web address to update Returns ------- str uri or updated uri """ if len(uri) == 0 or uri[-1] == "/": return uri split_uri = str.s...
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def add_prefix ( table , prefix = '' ) : """Add certain prefix to each line of the table >>> table = ... >>> table = add_prefix ( table , '# ') """ return prefix + table.replace ( '\n' , '\n' + prefix ) if prefix else table
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def next_card(prize_card, hand, max_card): """ Next-card strategy just picks the next card in the hand (effectively random). """ return hand.cards[0]
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def cross_spectrum(spectrumA, spectrumB): """ Returns a cross-spectrum, ie. spectrum of cross-correlation of two signals. This result does not depend on the order of the arguments. Since we already have the spectra of signals A and B and and want the spectrum of their cross-correlation, we can repla...
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import random def train_test_split_ind(n_sample, test_size, method='random'): """ Return indices splitting n_samples into train and test index lists. :param n_sample: int: number of samples :param test_size: int: number of samples in test set :param method: str: 'first' ('last') to take first (la...
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def filter_by_states(providers, states): """Filter providers by list of states to reduce the quantity of data we're processing.""" return [provider for provider in providers if provider['state'] in states]
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def humanize_join(sequence, separator=',', spacing=' ', conjunction='or', oxford_comma=True): """ Join a list together using the English syntax of inserting a conjunction before the last item. Keyword Arguments: sequence -- The sequence to join together. Convert iterables to sequences ...
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def cat_lump(x, n=5, prop=None, other_level="Other"): """ Lump together least common categories into an "Other" category Parameters ---------- x : pd.Series series to be modified n : int number of levels to preserve prop : float optional instead of n. Choose the minimum pr...
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def roi_is_full(roi, shape): """ Check if ROI covers the entire region. :returns: ``True`` if ``roi`` covers region from ``(0,..) -> shape`` :returns: ``False`` if ``roi`` actually crops an image """ def slice_full(s, n): return s.start in (0, None) and s.stop in (n, None) if isin...
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def replace_input_if_output_is_temp(df, input_column, output_column, output_is_temp): """Replaces the input column in the dataframe if the output was not set This is used with get_temp_col_if_not_set to enable the behavior where a transformer will replace its input column if an output is not specified. ...
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def get_elk_command(line): """Return the 2 character command in the message.""" if len(line) < 4: return "" return line[2:4]
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def _get_latest_raw_pdf(cls): """Given an ETL class, return the latest PDF in the data directory.""" # Get PDF paths for the raw data files dirname = cls.get_data_directory("raw") pdf_files = dirname.glob("*.pdf") # Get the latest latest = sorted(pdf_files)[-1] year, month = map(int, lates...
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import functools import random import time def random_delay(min_delay: float, max_delay: float): """ Decorator to add a random delay before executing the function. :param min_delay: Min delay in seconds. :param max_delay: Max delay in seconds. :return: Decorator. """ assert min_delay >= 0 ...
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def check_member(self, user): """ Check whether a user is in the circle :param (Circle) self: The checked circle :param (User) user: checked user :return (bool): whether the user is in the circle """ return len(list(filter(lambda member: member.id == user.id, self.members))) != 0
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def format_email_address(email: str) -> str: """ Returns a formatted email address. """ return email.lower()
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def is_prime(n): """Returns True is n is prime, False if not""" for i in range(2,n-1): if n%i == 0: return False return True
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from typing import Counter def count_ngram( n: int, target: str) -> Counter: """Count n-gram. Args: n (int): n-gram's n. target: (str): target sentence. Return: Counter: python counter object. """ tokens = target.split(' ') N = len(tokens) counter...
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def get_most_probable_words(wordlist, characters, pattern): """Get a list of most probable words >>> word_list = ["trail", "banana", "frail", "drain"] >>> get_most_probable_words(word_list, "filyar", "+rail") ['frail'] :param wordlist: wordlist to use :param characters: scrambled characters ...
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import torch def rand_uniform(a, b, shape=1): """ sample numbers uniformly between a and b. args: a - lower bound b - upper bound shape - shape of the output tensor returns: torch.Tensor - tensor of shape=shape """ return (b - a) * torch.rand(shape) + a
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from typing import Iterable from typing import Any from typing import List import itertools def flatten(val: Iterable[Iterable[Any]]) -> List[Any]: """ Flatens a list of list into a list >>> flatten( [['abc','def'],[12,34,46],[3.14, 2.22]]) ['abc', 'def', 12, 34, 46, 3.14, 2.22] """ return li...
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def ChiSqStat(ydata, yerr, ymodel): """ Returns the chi-square given arrays of ydata, yerr, and ymodel values. """ chisquared = ((ydata - ymodel)/yerr)**2 stat = chisquared.sum() return stat
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def flattenDict(d): """Reduces the depth of a dictionary to 1, parent keys are ignored. >>> d = {'a': 1, 'c': {'e': 5, 'd': 4}, 'b': 2, 'f': {'g': {'h': 8}}} >>> flattenDict(d) {'a': 1, 'h': 8, 'b': 2, 'e': 5, 'd': 4} """ result = {} for k, v in d.iteritems(): if isinstance(v, dict)...
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import requests def get_drive_time(apiKey, origin, destination): """ Returns the driving time between using the Google Maps Distance Matrix API. API: https://developers.google.com/maps/documentation/distance-matrix/start # INPUT ------------------------------------------------------------------...
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def matrix_to_str(mat): """Convert a 4x4 column-major order matrix into byte string.""" barr = [mat[i%4][i//4] for i in range(16)] return bytes(barr)
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def gcd(*numbers): """Euclid's algorithm for GCD. Arguments are cast to integer.""" def gcd2(a,b): a=abs(int(a)) b=abs(int(b)) a,b = max(a,b), min(a,b) while b>0: a,b=b,a%b return a if len(numbers)==0: return 1 res=numbers[0] for n in numbe...
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def id_from_name(detector, name): """ Jiffy function to get the id of a panel using its name @param detector detector object @param name panel name @return index of panel in detector """ return [p.get_name() for p in detector].index(name)
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def ReversedDomainComponents(s): """Returns a list of domain components in reverse order. Args: s: (str) A string of the form "a.b.c" Returns: list(s) E.g. ['c', 'b', 'a'] """ if not s: return [] parts = s.split('.') parts.reverse() return parts
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def option6(current_person): """The number of children and grandchildren of a person can be printed using this function. Parameters: current_person: The current Person object. Returns: The original Person object for whom the function was called. """ print(f"Number of childr...
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def get_monitors(mon_name): """ Has all the monitors with their specs and returns the one with the specified name. Parameters ---------- mon_name : str name of the requested monitor Returns ------- dict """ test_monitors = { "lab": { "size_cm": (54, ...
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def get_html_header() -> str: """Helper to get a HTML header with some CSS styles for tables."" Returns: A HTML header as string. """ return """<head> <style> table { font-family: arial, sans-serif; border-collapse: colla...
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import json def load_json(file_path): """ Loads json from a file :param file_path: the path to the file :return: dictionary """ try: with open(file_path, "r+") as file: return json.loads(file.read()) except (OSError, IOError): with open(file_path, "r+") as file...
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def evaluate(h,x): """evaluate an instance x with an hypothesis h, that is a function X->{Yes,No}""" for i,feature in enumerate(h): if feature=="0": return "No" if feature!="?" and feature!=x[i]: return "No" return "Yes"
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def has_resected_pair(unresected_idx, resected_imgs, img_adjacency): """Return true if unresected_idx image has matches to >= 1 currently resected image(s) """ for idx in resected_imgs: if img_adjacency[unresected_idx][idx] == 1 or img_adjacency[idx][unresected_idx] == 1: return True ret...
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def inhg_to_mb(val): """ Converts inches of mercury to millibars; accepts numeric or string """ try: return float(val) * 33.8639 except (TypeError, ValueError): return val * 33.8639
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def _populate_wf_data(wf_def, wf_data): """ Populate the workflow data in the workflow definition Args: wf_def (dict): workflow definition wf_data (dict): workflow data to be populated into workflow definition Returns: dict: workflow definition with the workflow data populated ...
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def search(value, node): """ Search for element in the linked list :param value: value to look for :param node: value of head node, start of list :return: bool: weather or not element is in the list """ if node is not None: # iterate through while valid nodes if node.value == value...
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def connect(endpoint=None): """Generate connect packet. `endpoint` Optional endpoint name """ return u'1::%s' % ( endpoint or '' )
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def _mk_key(srev_info): """Returns the key for a SignedRevInfo object.""" return (srev_info.rev_info().isd_as(), srev_info.rev_info().p.ifID)
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def is_free(board: list, pos: int) -> bool: """checks if pos is free or filled""" return board[pos] == " "
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def process_spatial(geo): """Process time range so it can be added to the dates metadata Parameters ---------- geo : list [minLon, maxLon, minLat, maxLat] Returns ------- polygon : dict(list(list)) Dictionary following GeoJSON polygon format """ polygon = { "type"...
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from typing import OrderedDict def flatten_json(dictionary): """Recursively flattens a nested json. :param dictionary: dict object to flatten :return: dict object containing flat json. """ out = {} def flatten(element, name=''): if type(element) is dict: for a in element:...
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def ioc_restart_pending(ioc_pv, channel_access): """Check if a particular IOC is restarting. Assumes it has suitable restart PV Args: ioc_pv: The base PV for the IOC with instrument PV prefix channel_access (ChannelAccess): The channel access object to be used for accessing PVs Return ...
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def dictincr(dictionary, element): """ Increments `element` in `dictionary`, setting it to one if it doesn't exist. """ dictionary.setdefault(element, 0) dictionary[element] += 1 return dictionary[element]
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def mc_eta_to_m12(mc, eta): """ Convert chirp mass and symmetric mass ratio to component masses. Input: mc - chirp mass eta - symmetric mass ratio Return: m1, m2 - primary and secondary masses, m1>m2 """ m1 = mc / eta ** 0.6 * (1 + (1 - 4 * eta) ** 0.5) / 2 m2 = mc / eta ** 0.6 * (1 - (...
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def read_first_line(path: str) -> str: """Read the first line from the given file.""" with open(path, encoding='utf8') as f: return f.readline()
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import logging import json def extract_initial_data(html): """Extract and parse the JSON string from the HTML of a playlist webpage. Parameters ---------- html : str HTML to extract the string from. Returns ------- Dict Parsed JSON data. """ logging.info("Extract...
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def sign (x): """Return `-1` if `x < 0`, `0` if `x == 0` and `1` if `x > 0`.""" return 0 if x == 0 else (1 if x > 0 else -1)
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def list_strip_eos(list_, eos_token): """Strips EOS token from a list of lists of tokens. """ list_strip = [] for elem in list_: if eos_token in elem: elem = elem[:elem.index(eos_token)] list_strip.append(elem) return list_strip
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def diff_sec(time1, time2): """Calculate the difference between two times in seconds.""" # return (as_utc(time1) - as_utc(time2)).total_seconds() return (time1 - time2).total_seconds()
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def order_by_length(*items): """Orders items by length, breaking ties alphabetically.""" sorted_items = sorted(items, key=lambda item: (len(str(item)), str(item))) return ' '.join(sorted_items)
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