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from pathlib import Path import yaml def loadConfigDict(configNames: tuple): # pathLib syntax for windows, max, linux compatibility, see https://realpython.com/python-pathlib/ for an intro """ Generic function to load and open yaml config files :param configNames: Tuple containing names of config fil...
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def is_comment(string): """ Find out if line is a comment or line of code :param string: line to analyze :return: True if line is a comment """ chars = list(string) if len(chars) <= 0: return True if chars[0] == "#": return True else: return False
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import zipfile def un_zip(zip_file, uzip_folder=None): """Uncompression .zip file Args: zip_files: str, zip_file should be file path; uzip_folder: str, uncompression files name. Return: uzip_folder: str, uncompression files name. """ assert zip_file[-4:]==".zip", '`zip...
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def extract_brackets(line): """Splits a scroll 'call line' into identifier + suffix.""" ident, _, enil = line[1:].partition("(") thing, _, _, = enil.rpartition(")") return ident, thing
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def input_output01(input): """ Expects a list of lists as input, outputs each sublist in a line comma delimited. """ return '\n'.join(','.join(map(str,sl)) for sl in input)
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def _str_to_bytes(value: str) -> bytes: """Convert ``str`` to bytes""" return value.encode("utf-8")
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import torch def ordinal_accuracy(logits, levels, device='cpu', tolerance=0, reduction='mean'): """Computes the accuracy with a tolerance for ordinal error. Parameters ---------- logits : torch.tensor, shape(num_examples, num_classes-1) Outputs of the CONDOR layer. levels : torch.tensor,...
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def rho_top_liq(x_aver_top_mass, rho_lc_x_aver_top, rho_hc_x_aver_top): """ Calculates the destiny of liquid at top of column. Parameters ---------- x_aver_top_mass : float The average mass concentration at top of column, [kg/kg] rho_lc_x_aver_top : float The destiny of low-boill...
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def euclidian_distance(ptA, ptB): """ Returns the shortest path distance between the two Points """ if (ptA.X != ptB.X or ptA.Y != ptB.Y): return ( (ptA.X - ptB.X)**2 + (ptA.Y - ptB.Y)**2 ) ** (1/2) return 0.0
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def make_binder_pair( h1, h2 ): """Returns a binder pair from the two hits A pair has the form: ( binder1, binder2, orientation1, orientation2 ) Where the binders are pssm names typically and the orientation describes the strand the pssm binds to (true for positive strand). """ b1...
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from typing import Union from typing import List def get_corresponding( value_or_matrix: Union[int, List[List[int]]], row: int, col: int ) -> int: """If `value_or_matrix` is a matrix, extract the value in cell specified by `row` and `col`. If `value_or_matrix` is a scalar, just return it. """ if i...
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import torch def convert_frequencies_to_mels(f: torch.Tensor) -> torch.Tensor: """ Convert f hertz to m mels https://en.wikipedia.org/wiki/Mel_scale#Formula """ return 2595.0 * torch.log10(1.0 + f / 700.0)
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def strip_line_nums(line): """ Strip line numbers from the start of a line. """ # Find the end of a number at the start of the line, if there is one. pos = 0 line = line.strip() for c in line: if (not c.isdigit()): # Don't delete numeric labels. if (c == ':')...
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def total_count(expression): """ Compute total count library size. :param expression: Expression count matrix with genes as rows and samples as columns :return: integer total count library size per sample """ return expression.sum(axis=0)
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def filename_dist(dist): """ Return the filename of a distribution. """ if hasattr(dist, 'to_filename'): return dist.to_filename() else: return dist
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def calcul_max(l: list) -> int: """ returns the sum of the 2 highest elements of l """ _l = list(l) max1 = max(_l) _l.remove(max1) max2 = max(_l) return max1 + max2
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def _s2_st_to_uv(component: float) -> float: """ Convert S2 ST to UV. This is done using the quadratic projection that is used by default for S2. The C++ and Java S2 libraries use a different definition of the ST cell-space, but the end result in IJ is the same. The below uses the C++ ST definition...
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def delegate(connection, identity_token, whitelist=None): """Returns authentication token and cookies from given X-MSTR- IdentityToken. Args: connection: MicroStrategy REST API connection object identity_token: Identity token whitelist: list of errors for which we skip printing erro...
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def confirm_name(message, name, force=False): """Ask the user to confirm the name. Parameters ---------- message: str The message to be printed. name: str The string that the user must enter. force: bool Override confirmation and return True. Default: False. Returns...
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def parse_encode_biosample(data): """Parse a python dictionary containing ENCODE's biosample metadata into a dictionary with select biosample metadata :param data: python dictionary containing ENCODE' biosample metadata :type s: dict :return: dictionary with parsed ENCODE's biosample meta...
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import json import hashlib def hash_dict(nested_dict): """ Returns hash of nested dict, given that all keys are strings """ dict_string = json.dumps(nested_dict, sort_keys=True) md5_hash = hashlib.md5(dict_string.encode()).hexdigest() return md5_hash
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from typing import Union def milimeter_mercury_to_bars(mm_hg: float, unit: str) -> Union[float, str]: """ This function converts mmHg to bar Wikipedia reference: https://en.wikipedia.org/wiki/Bar_(unit) Wikipedia reference: https://en.wikipedia.org/wiki/Millimetre_of_mercury >>> milimeter_mercury...
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def print_exptree(root): """ Print out an expression tree object via recursion. Args: root: expression tree (object type) """ # Empty tree if root is None: return 0 # Leaf node if root.left is None and root.right is None: return print(f'-- leaf: {root.data}'...
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import click def valid_band(ctx, param, value): """ Check image band validity (band >= 1)""" try: band = int(value) assert band >= 1 except: raise click.BadParameter('Band must be integer above 1') return band
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import socket def get_node_ip_address(address="8.8.8.8:53"): """Determine the IP address of the local node. Args: address (str): The IP address and port of any known live service on the network you care about. Returns: The IP address of the current node. """ ip_address, port = address.split(...
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from typing import Sequence from typing import List def indexify(sequence: Sequence, index_source: Sequence) -> List: """For the given `sequence`, get the index of each item in the `index_source`""" return [index_source.index(item) for item in sequence]
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def _decayed_value_in_linear(x, max_value, padding_center, decay_rate): """ decay from max value to min value with static linear decay rate. """ x_value = max_value - abs(padding_center - x) * decay_rate if x_value < 0: x_value = 1 return x_value
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import json def read_json_file(path: str): """Read a json file into a dict.""" with open(path, 'r') as f: data = json.load(f) return data
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import string import random def generate_session_id(size=32, chars=string.ascii_letters+string.digits): """ Generate session id - 32 length string with ascii letters and digits """ return ''.join(random.choices(chars, k=size))
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def get_chars(path_to_vocab): """ Return the list of all characters found in the vocabulary. """ chars = set() with open(path_to_vocab) as f: for line in f: chars.update(line.rstrip()) return chars
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def fill_nan(df,list): """ Fill nan values with either mean or mode Parameters ---------- df : dataframe dataframe used for checking and filling nan values list: list list of columns to be checked Returns ------- df : dataframe modified dataframe with no nan...
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def cidade_pais(cidade: str, pais: str) -> str: """ -> Devolve o nome da cidade e do seu país formatados de forma elegante. :param cidade: O nome da cidade. :param pais: O nome do país. :return: Retorna a string -> 'Cidade, País' """ return f'{cidade}, {pais}'.title()
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def create_envs(service_component_name, *envs): """Merge all environment variables maps Creates a complete environment variables map that is to be used for creating the container. Args: ----- envs: Arbitrary list of dicts where each dict is of the structure: { <environment...
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def get_underline(string): """ Return an underline string of the same length as `str`. """ return "="*len(string) + "\n"
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def width_multiplier_op(filters: int, width_multiplier: float, min_depth: int = 8) -> int: """Determine the number of channels given width multiplier""" return max(int(filters * width_multiplier), min_depth)
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def get_status(runs): """Get the most recent status of workflow for the current PR. Parameters ---------- runs : list List of comment objects sorted by the time of creation in decreasing order. Returns ------- status : string The most recent status of workflow. Can ...
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from typing import Tuple from typing import Dict def parse_options_header(value: str) -> Tuple[str, Dict[str, str]]: """Like werkzeug.http.parse_options_header(), but ignores the options.""" return value.partition(';')[0].strip(), {}
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def backdoor_examples(xs, backdoor, eps): """ Inject a backdoor into training examples with norm epsilon. """ return xs + backdoor * eps
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from pathlib import Path import re def normalise_nci_symlinks(input_path: Path) -> Path: """ If it's an NCI lustre path, always use the symlink (`/g/data`) rather than specific drives (eg. `/g/data2`). >>> normalise_nci_symlinks(Path('/g/data2/v10/some/dataset.tar')).as_posix() '/g/data/v10/some/data...
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def calc_mean(values): """Calculates the mean of a list of numbers.""" values_sum = 0 for value in values: values_sum += value return values_sum / len(values)
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from datetime import datetime def datetime_serializer(obj): """Convert a datetime object to its string representation for JSON serialization. :param obj: datetime """ if isinstance(obj, datetime): return obj.isoformat()
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def compute_turbulence_intensity(mean_col, std_col): """ Compute turbulence intensity Args: mean_col(:obj:`array`): array containing the wind speed mean data; units of m/s std_col(:obj:`array`): array containing the wind speed standard deviation data; units of m/s Returns: :ob...
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def set_pairing_bit_on_device_type(pairing_bit: bool, device_type: int): """ Shifts the pairing bit (True = 1, False = 0) 7 bits to the left and adds the device type """ return (pairing_bit << 7) + device_type
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def bits2str(inp): """ Convert a list of bits into a string. If the number of bits is not a multiple of 8, the last group of bits will be padded with zeros. """ bs = [1<<i for i in range(8)] return ''.join(chr(sum(bv if bit else 0 for bv,bit in zip(bs, inp[i:i+8]))) for i in range(0, len(inp), ...
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import random def Ui(lo, hi): """Uniformly distributed integer, inclusive limits.""" return random.randint(lo, hi)
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def get_xpath_for_date_of_available_time_element(day_index: int) -> str: """ The element showing date of the available time is found in the div having the xpath: '/html/body/div[4]/div[2]/div/div[5]/div/div[2]/div[3]/div[N]/span' ^ where N ...
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def applyOrderDic(order, aDic): """ Apply order to aList. An order of the form ["a","b","c"] means that the first element should be aDic["a"], and so on. """ if order==[]: return aDic.value() else: return map(lambda v:aDic[v], order)
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def _get_set_env_var_command(name, value): """Return command to set environment variable on device.""" return ['--env={n}={v}'.format(n=name, v=value)]
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def make_dict(table, key_col): """ Given a 2D table (list of lists) and a column index key_col, return a dictionary whose keys are entries of specified column and whose values are lists consisting of the remaining row entries """ table_dict = {} for key in table: table...
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from typing import Any import json def serialize_json(obj: Any) -> str: """Serialize an object to JSON, removing quotes for special strings.""" return json.dumps(obj).replace('"____', "").replace('____"', "")
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import re def get_index(part): """ check if the part is, e.g [123] return 123 or None """ index = None match = re.match(r'\[(\d+)\]', part) if match: index = int(match.group(1)) return index
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def _vars_dir_for_saved_model( saved_model_path # type: str ): # type: (str) -> str """ Args: saved_model_path: Root directory of a SavedModel on disk Returns the location of the directory where the indicated SavedModel will store its variables checkpoint. """ return saved_model_path + "/va...
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from typing import Set from typing import Callable from typing import Any from typing import Dict def dict_by(keys: Set[str], f: Callable[[str], Any]) -> Dict[str, Any]: """Returns a dictionary with keys equal to the supplied keyset. Each value is the result of applying f to a key in keys. """ return {k: f(k...
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def toX(x, y=None): """ This function is used to load value on Plottable.View :param x: Float value :return: x """ return x
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from pathlib import Path def remove_root(file_path: str) -> str: """Remove the first directory of a path""" full_path = Path(file_path) relative_path = Path(*full_path.parts[1:]) return str(relative_path)
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import torch def swish(x): """ Simple implementation of Swish activation function https://arxiv.org/pdf/1710.05941.pdf """ return x * torch.sigmoid(x)
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from pathlib import Path def get_definitions(base_directory_path): """ For given directory return all *_definition.py files in it and its subdirectories. """ return Path(base_directory_path).glob('**/*_definition.py')
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def overplot_lines(ax, linelabels, lineloc): """ Overplots emission lines on an already existing plot with axes Input: ax: matplolib axis linelabels: list of latex formatted names for the lines lineloc: list of wavelengths of the lines (most likely in Ang) Output: ax2: re...
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import re def remove_chars(text, chars, replace_with=None): """ Removes chars from text or replaces them with the input. Also removes any extra whitespaces which might have been introduced. : param text : text upon which the processing is done : param chars : chars to search fo...
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def myreadlines(self): """Read and return the list of all logical lines using readline.""" lines = [] while True: line = self.readline() if not line: return lines else: lines.append(line)
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def common_superclass_wnid(group_name): """ Get WordNet IDs of common superclasses. Args: group_name (str): Name of group Returns: superclass_wnid (list): List of WordNet IDs of superclasses """ common_groups = { # ancestor_wnid = 'n0000425...
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def suma_serie(n: int) -> int: """Suma los elementos de la serie E_i = i^3 + 5, desde 1 hasta n. :param n: número de elementos de la serie :n type: int :return: suma de los elementos de la serie :rtype: int """ if n == 1: return 6 else: return (n ** 3 + 5) + suma_ser...
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def NonsfiLoaderArch(target): """Returns the arch for the nonsfi_loader""" arch_map = { 'arm32' : 'arm', 'x8632' : 'x86-32', 'mips32' : 'mips32', } return arch_map[target]
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def tree_unflatten(flat): """Nest depth-1 tree to nested tree {'a.b.c': x} -> {'a': {'b': {'c': x}}} """ def recursion(k, v, out): k, *rest = k.split('.', 1) if rest: recursion(rest[0], v, out.setdefault(k, {})) else: out[k] = v d = {} for k, ...
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def linear_derivative(z): """Linear activation function derivative""" return 1
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def _season_overflow(season, moved_year, now): """Pushes illegal seasons ints into the next/previous year.""" if season > 4: while season > 4: if moved_year is None: moved_year = now.year + 1 else: moved_year += 1 season -= 5 elif ...
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def get_slope(vector_one, vector_two): """Get the slope of a line specified by two vectors""" return(vector_two[1] - vector_one[1])/(vector_two[0] - vector_one[0])
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import itertools def find_anagrams(word, dictionary): """Find all anagrams for a word. This function only runs as fast as the test for membership in the 'dictionary' container. It will be slow if the dictionary is a list and fast if it's a set. Args: word: String of the target word. ...
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def count_on_screen(screen, wanted): """Count occurrences of wanted on the screen.""" return list(screen.values()).count(wanted)
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def googlenet_params(model_name): """ Map VGGNet model name to parameter coefficients. """ params_dict = { # Coefficients: aux_logits, transform_input, blocks, image_size "googlenet": (True, True, None, 224), } return params_dict[model_name]
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import hashlib def make_merkle(blob_name: str) -> str: """Creates a "merkle" by hashing the blob_name to get a unique value. """ m = hashlib.sha256() m.update(blob_name.encode("utf-8")) return m.hexdigest()
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def _get_query_parameters(module_params): """Builds query parameter. :return: dict :example: {"$filter": Name eq 'template name'} """ system_query_param = module_params.get("system_query_options") query_param = {} if system_query_param: query_param = dict([("$" + k, v) for k, v in s...
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def pipes(stream, *transformers): """Pipe several transformers end to end.""" for transformer in transformers: stream = stream.pipe(transformer) return stream
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def pad_sentence_batch(sentence_batch, pad_int): """Pad char seq with <PAD> so that each char sequence of a batch has the same length""" max_seq = max([len(seq) for seq in sentence_batch]) padded_batch=[] for seq in sentence_batch: temp=[] for char in seq: temp.append(char) ...
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def moveIntToBoolList(i): """ Convert an integer in the range [0, 7] to a list of 3 boolean values, corresponding to the binary representation :param i: The integer :return: The list of 3 boolean values """ # not using loops or append because this is faster, and this method only needs to work fo...
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def as_text(value): """Returns the string representation of given value Arguments: value {any} -- Value to get the string representation for Returns: stringified text {String} -- String representation of given value """ return "" if value is None else str(value)
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import random def gen_mac(last_octet=None): """Generate a random MAC address that is in the qemu OUI space and that has the given last octet. """ return "52:54:00:%02x:%02x:%02x" % ( random.randint(0x00, 0xFF), random.randint(0x00, 0xFF), last_octet, )
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def user_privileges(connection): """Get the list of privileges for the authenticated user. The response includes the name, ID, and description of each privilege and specifies which projects the privileges are valid for. Args: connection: MicroStrategy REST API connection object Returns: ...
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def combine_first_last_name(df): """ Combine first and last name if df has those columns. """ if 'first_name' in df.columns and 'last_name' in df.columns: df['full_name'] = df['first_name'] + ' ' + df['last_name'] df.drop(['first_name', 'last_name'], axis=1, inplace=True) return df
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def min_if_exist(n1, n2): """ Returns the minimum between two numbers, or the only defined number (in case the other is `None`) or `None` if none of the numbers are defined. """ if n1 is None and n2 is None: return None elif n1 is None: return n2 elif n2 is None: retu...
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import hashlib def generate_identifier(metadata: str) -> str: """Generate a (hopefully) unique identifier.""" obj = hashlib.md5(metadata.encode()) dig = obj.hexdigest() return str(int(dig[:6], 16))
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import re def check_global_attr_against_regex(ds, attr, regex): """ Returns 0 if attribute `attr` not found, 1 if found but doesn't match and 2 if found and matches `regex`. :param ds: netCDF4 Dataset object :param attr: global attribute name [string] :regex: a regular expression definition [...
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def ordinal(n, combine=False): """ Return the ordinal of the number n. If combine then return the number concatenated with the ordinal """ number_string = str(n) if combine else "" special_cases = {1: "st", 2: "nd", 3: "rd"} if not 10 <= n % 100 <= 20 and n % 10 in special_cases: re...
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def npieces(request): """Number of collocation pieces.""" return request.param
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def apply_op(input_layer, operation, *op_args, **op_kwargs): """Applies the given operation to this before without adding any summaries. Args: input_layer: The input layer for this op. operation: An operation that takes a tensor and the supplied args. *op_args: Extra arguments for operation. **op_k...
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def extract_job_fields(tags): """Extracts common job's metric fields from TaskResultSummary. Args: tags (list of str): list of 'key:value' strings. """ tags_dict = {} for tag in tags: try: key, value = tag.split(':', 1) tags_dict[key] = value except ValueError: pass spec_name...
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def replace_string(text, replacements=None, whitespace=True): """A wrapper around str.replace where replacements is a dictionary: original_string -> replacement_string whitespace=True surounds the replacement with whitespaces. """ if not replacements: return text for ori, rpl in repl...
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def get_domain(url: str, /) -> str: """Get domain from an url""" return url.split('//')[-1].split('/')[0].split('?')[0]
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def rectangles_intersect(rect1, rect2): """Returns True if two rectangles intersect.""" return all([(rect1[1][i] >= rect2[0][i]) and (rect2[1][i] >= rect1[0][i]) for i in range(2)])
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from typing import Any def typename(o: Any) -> str: """Return the full name (including module) of the type of o. >>> typename(5) 'int' >>> typename('text') 'str' >>> typename(np.array([1])) 'numpy.ndarray' """ # https://stackoverflow.com/a/2020083 name: str = o.__class__.__qualname__ module =...
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def null_count(df): """ Check a dataframe for nulls and return the number of missing values """ # Example Input (df = pd.DataFrame): # > | column 0 | column 1 | column 2 | # > | ----------- | ----------- | ----------- | # > | NaN | 9 | 10 | # > | 4 ...
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def round(addr: int, align: int, up: bool = False) -> int: """Round an address up or down based on an alignment. Args: addr: the address align: the alignment value up: Whether to round up or not Returns: The aligned address """ if addr % align == 0: return ...
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def is_group(message) -> bool: """Whether message was sent at a group.""" # See "type" at https://core.telegram.org/bots/api#chat. return 'group' in message.chat.type
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def is_not_excluded_type(file, exclude_types): """Return False if file type excluded, else True""" if exclude_types: for exclude_type in exclude_types: if file.lower().endswith(exclude_type.lower()): return False return True
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from functools import wraps def consumer(func): """A decorator, advances func to its first yield point when called. """ @wraps(func) def wrapper(*args, **kw): gen = func(*args, **kw) gen.next() return gen return wrapper
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def excel_to_python(command_string): """ Returns the python equivalent of many excel formula names """ d = { 'SUM' : 'np.sum', 'AVERAGE' : 'np.mean', 'MAX' : 'np.max', 'MIN' : 'np.min', 'MEDIAN' : 'np.median', 'MODE' :...
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def get_end_pos(cls, start_pos, dimensions, left=False, up=False): """ calculate the end position if were to build an array of items :param cls: Type :param start_pos: (int, int) :param dimensions: (int, int) :param left: bool: default builds rightward :param up: bool: default builds downwar...
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def find_out_of_order_packet_indices(packet_ns): """ Return indices of packets which have apparently arrived out-of-order. Specifically: return indices of any packet number which was less than the previous packet number. For example, for the list of packet numbers: 0, 1, 2, 3, 5, 4, 6, 7. re...
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import base64 def base64_encode(s): """Encode a URL-safe string. :type s: six.text_type :rtype: six.text_type """ # urlsafe_b64encode() returns six.binary_type so need to convert to # six.text_type, might as well do it before stripping. return base64.urlsafe_b64encode(s).decode('utf-8')....
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def resultIsSuccess(res): """ JSON-decoded stake pool responses have a common base structure that enables a universal success check. Args: res (dict): The freshly-decoded-from-JSON response. Returns: bool: True if result fields indicate success. """ try: return res[...
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