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def xor(b1, b2): """Expects two bytes objects of equal length, returns their XOR""" assert len(b1) == len(b2) return bytes([x ^ y for x, y in zip(b1, b2)])
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import random import string def random_string(length=1, unicode=False): """ Returns random ascii or unicode string. """ if unicode: def random_fun(): return chr(random.choice((0x300, 0x2000)) + random.randint(0, 0xff)) else: def random_fun(): return random.c...
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import math def probability(ec, en, t): """ Probability function :param ec: current energy :param en: next energy :param t: temperature ratio :return: probability value """ return math.exp((ec - en) / t)
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def add_ext(name, ext, seq=-1): """add_ext constructs file names with a name, sequence number, and extension. Args: name (string) - the filename ext (string) - the file extension seq (int) - the number in a sequence with other files (Default -1) means that it is a standalone file """ #add peri...
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def get_coding_annotation_fasta(seq_record): """ When passed a sequence record object returns an array of FASTA strings for each annotation. :param seq_record: A Biopython sequence record object. :return: A FASTA file string containing all sequences record object CDS sequence features. """ fasta = [] features =...
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from typing import Union def bars_to_atmospheres(bar: float, unit: str) -> Union[float, str]: """ This function converts bar to atm Wikipedia reference: https://en.wikipedia.org/wiki/Standard_atmosphere_(unit) Wikipedia reference: https://en.wikipedia.org/wiki/Bar_(unit) >>> bars_to_atmospheres(3...
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def series(expr, x, point=0, n=6, dir="+"): """Series expansion of expr around point `x=point`. See the doctring of Basic.series() for complete details of this wrapper. """ return expr.series(x, point, n, dir)
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def process_transform_funcs(trans_funcs, func_args=None, func_kwargs=None): """Process input of the apply_transform_funcs function. :param iterable trans_funcs: functions to apply, specified the function or a (function, args, kwargs) tuple :param dict func_args: function positional arguments, specified as ...
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import math def _get_fov(pillow_image) -> float: """Get the horizontal FOV of an image in radians.""" exif_data = pillow_image.getexif() # 41989 is for 'FocalLengthIn35mmFilm'. focal_length = exif_data[41989] # FOV calculation, note 36 is the horizontal frame size for 35mm # film. return ...
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def pieChartInfoPlus(trips): """ Calculates the total distance per activity mode Parameters ---------- trips : dict - Semantic information (nested) Returns ------- list(data): list - labels of the activity modes list(data.values()): list - distance per activity mode """ la...
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def findCharacter(stringList, patternCharacter): """ Find the specific character from the list and return their indices """ return([ind for ind, x in enumerate(list(stringList)) if x == patternCharacter])
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def cell_trap_getter_generator(priv_attr): """ Generates a getter function for the cell_trap property. """ def getter(self): if getattr(self, priv_attr) is None: data =\ ( self.gfpffc_bulb_1 - self.gfpffc_bulb_bg )/self.gfpffc_bulb_bg ...
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def bg_trim(im): """ Function to programmatically crop card to edge. `im` is a PIL Image Object. """ # This initial crop is hacky and stupid (should just be able to set device # options) but scanner isn't 'hearing' those settings. # w,h = im.size im = im.crop((443, 0, 1242, 1200)) # ...
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def get_filtered_query(must_list=None, must_not_list=None): """Get the correct query string for a boolean filter. Accept must and must_not lists. Use MatchList for generating the appropriate lists. """ bool_filter = {} if must_list: bool_filter['must'] = must_list if must_not_list: ...
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def convert_to_letter(grade): """Convert a decimal number to letter grade""" grade = round(grade, 1) if grade >= 82.5: return 'A' elif grade >= 65: return 'B' elif grade >= 55: return 'C' elif grade >= 50: return 'D' else: return 'F'
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def time_coord(cube): """ Return the variable attached to time axis. Examples -------- >>> import iris >>> url = ('http://omgsrv1.meas.ncsu.edu:8080/thredds/dodsC/' ... 'fmrc/us_east/US_East_Forecast_Model_Run_Collection_best.ncd') >>> cube = iris.load_cube(url, 'sea_water_potent...
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import re def oneliner(s) -> str: """Collapse any whitespace in stringified `s` into a single space. """ return re.sub(r"[\n ]+", " ", str(s).strip())
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from typing import Counter def diff_counts(values : list[int]) -> dict[int, int]: """Count the gaps between ordered elements in a list, by size.""" ordered = [0] + sorted(values) + [max(values) + 3] return Counter(j - i for i, j in zip(ordered, ordered[1:]))
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def convert_netdict_to_pydict(dict_in): """Convert a net dictionary to a Python dictionary. Parameters ---------- dict_in : dict Net dictionary to convert. Returns ------- dict Dictionary converted to Python. """ pydict = {} for key in dict_in.Keys: pyd...
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from typing import List def binary_search(input_array: List[int], target: int): """ Given a sorted input array of integers, the function looks for a target or returns None Returns: Target index or None """ if not input_array or not target: return None left_pointer = 0 ri...
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def is_superuser(view): """Allow access to the view if the requesting user is a superuser.""" return view.request.user.is_superuser
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from typing import Any import torch import numbers def python_scalar_to_tensor(data: Any, device: torch.device = torch.device("cpu")) -> Any: """ Converts a Python scalar number to a torch tensor and places it on the given device. """ if isinstance(data, numbers.Number): data = torch.tensor([data], de...
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def LIGHTNING(conf): """Get Lightning Color code from config""" return conf.get_color("colors", "color_lghtn")
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from typing import Tuple def InterpolateValue(x: float, xy0: Tuple[float, float], xy1: Tuple[float, float]) -> float: """Get the position of x on the line between xy0 and xy1. :type x: float :type xy0: Tuple[float, float] :type xy1: Tuple[float, float] :return: y :rtype: float """ if ...
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def boolean(prompt=None, yes='y', no='n', default=None, sensitive=False, partial=True): """Prompt for a yes/no response. Parameters ---------- prompt : str, optional Use an alternative prompt. yes : str, optional Response corresponding to 'yes'. no : str, optional ...
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import torch def compute_local_cost(pi, a, dx, b, dy, eps, rho, rho2, complete_cost=True): """Compute the local cost by averaging the distortion with the current transport plan. Parameters ---------- pi: torch.Tensor of size [Batch, size_X, size_Y] transport plan used to compute local cost ...
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def electron_binding_energy(charge_number): """Return the electron binding energy for a given number of protons (unit is MeV). Expression is taken from [Lunney D., Pearson J. M., Thibault C., 2003, Rev. Mod. Phys.,75, 1021].""" return 1.44381e-5 * charge_number ** 2.39\ + 1.55468e-12 * char...
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def parse_generic(data, key): """ Returns a list of (potentially disabled) choices from a dictionary. """ choices = [] for k, v in sorted(data[key].iteritems(), key=lambda item: item[1]): choices.append([v, k]) return choices
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def attrs_to_dict(attrs): """ Convert a list of tuples of (name, value) attributes to a single dict of attributes [name] -> value :param attrs: List of attribute tuples :return: Dict of attributes """ out = {} for attr in attrs: if out.get(attr[0]) is None: out[attr[0...
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def count(i): """List or text. Returns the length as an integer.""" return len(i)
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def find_body(view): """ Find first package body declaration. """ return view.find(r'(?im)create\s+(or\s+replace\s+)?package\s+body\s+', 0)
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def get_num_objects(tree): """ Get number of objects in an image. Args: tree: Tree element of xml file. Returns: Number of objects. """ num_obj = 0 for e in tree.iter(): if e.tag == 'object': num_obj = num_obj + 1 return num_obj
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from typing import Union def _get_tol_from_less_precise(check_less_precise: Union[bool, int]) -> float: """ Return the tolerance equivalent to the deprecated `check_less_precise` parameter. Parameters ---------- check_less_precise : bool or int Returns ------- float Toler...
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def get_arg(cmds): """Accepts a split string command and validates its size. Args: cmds: A split command line as a list of strings. Returns: The string argument to the command. Raises: ValueError: If there is no argument. """ if len(cmds) != 2: raise ValueError('%s needs an argument.' % c...
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def _magnitude_to_marker_size(v_mag): """Calculate the size of a matplotlib plot marker representing an object with a given visual megnitude. A third-degree polynomial was fit to a few hand-curated examples of marker sizes for magnitudes, as follows: >>> x = np.array([-1.44, -0.5, 0., 1., 2., 3., ...
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def upto(limit: str, text: str) -> str: """ return all the text up to the limit string """ return text[0 : text.find(limit)]
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def check_occuring_variables(formula,variables_to_consider,allowed_variables) : """ Checks if the intersection of the variables in <formula> with the variables in <variables_to_consider> is contained in <allowed_variables> Parameters ---------- formula : list of list of integers The formula to cons...
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def _merge_config_dicts(dct1, dct2): """ Return new dict created by merging two dicts, giving dct1 priority over dct2, but giving truthy values in dct2 priority over falsey values in dct1. """ return {str(key): dct1.get(key) or dct2.get(key) for key in set(dct1) | set(dct2)}
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def from_list(*args): """ Input: args - variable number of integers represented as lists, e.g. from_list([1,0,2], [5]) Output: new_lst - a Python array of integers represented as strings, e.g. ['102','5'] """ new_lst = [] for lst in args: new_string = '' for digi...
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def perpetuity_present_value( continuous_cash_payment: float, interest_rate: float, ): """Returns the Present Value of Perpetuity Formula. Parameters ---------- continuous_cash_payment : float Amount of continuous cash payment. interest_rate : float Interest rate, yield or discount r...
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def __avg__(list_): """Return average of all elements in the list.""" return sum(list_) / len(list_)
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import requests def check_hash(h): """ Do the heavy lifting. Take the hash, poll the haveibeenpwned API, and check results. :param h: The sha1 hash to check :return: The number of times the password has been found (0 is good!) """ if len(h) != 40: raise ValueError("A sha1 hash should be 30 characters.") h = ...
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def get_field_hint(config, field): """Get the hint given by __field_hint__ or the field name if not defined.""" return getattr(config, '__{field}_hint__'.format(field=field), field)
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def btc(value): """Format value as BTC.""" return f"{value:,.8f}"
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import time def nagios_from_file(results_file): """Returns a nagios-appropriate string and return code obtained by parsing the desired file on disk. The file on disk should be of format %s|%s % (timestamp, nagios_string) This file is created by various nagios checking cron jobs such as check-rab...
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import math def _width2wing(width, x, min_wing=3): """Convert a fractional or absolute width to integer half-width ("wing"). """ if 0 < width < 1: wing = int(math.ceil(len(x) * width * 0.5)) elif width >= 2 and int(width) == width: # Ensure window width <= len(x) to avoid TypeError ...
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def mb_bl_ind(tr1, tr2): """Returns the baseline index for given track indices. By convention, tr1 < tr2. Otherwise, a warning is printed, and same baseline returned. """ if tr1 == tr2: print("ERROR: no baseline between same tracks") return None if tr1 > tr2: print("WARN...
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def datetime_format_to_js_datetime_format(format): """ Convert a Python datetime format to a time format suitable for use with the datetime picker we use, http://www.malot.fr/bootstrap-datetimepicker/. """ converted = format replacements = { '%Y': 'yyyy', '%y': 'yy', '%m'...
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def make_data(current_data): """ Formats the given data into the required form """ x = [] n = len(current_data) for i in range(n - 1): x.append(current_data[i]) x.append(1) return x, current_data[n - 1]
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def average_over_dictionary(mydict): """ Average over dictionary values. """ ave = sum([x for x in mydict.values()])/len(mydict) return ave
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def treat_category(category: str) -> str: """ Treats a list of string Args: category (str): the category of an url Returns: str: the category treated """ return category.lower().strip()
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def _get_fully_qualified_class_name(obj): """ Obtains the fully qualified class name of the given object. """ return obj.__class__.__module__ + "." + obj.__class__.__name__
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import decimal def new_decimal(value): """Builds a Decimal using the cleaner float `repr`""" if isinstance(value, float): value = repr(value) return decimal.Decimal(value)
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import unicodedata def unidecode(s: str) -> str: """ Return ``s`` with unicode diacritics removed. """ combining = unicodedata.combining return "".join( c for c in unicodedata.normalize("NFD", s) if not combining(c) )
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def AutoUpdateUpgradeRepairMessage(value, flag_name): """Messaging for when auto-upgrades or node auto-repairs. Args: value: bool, value that the flag takes. flag_name: str, the name of the flag. Must be either autoupgrade or autorepair Returns: the formatted message string. """ action =...
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import ast import collections import logging def _get_ground_truth_detections(instances_file, allowlist_file=None, num_images=None): """Processes the annotations JSON file and returns ground truth data corresponding to allowlisted image IDs. Args:...
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def decomp(n): """ Retorna a decomposição em fatores primos de um inteiro em forma de dicionário onde as chaves são as bases e o valores os expoentes. Ex: >>> decomp(12) {2: 2, 3: 1} >>> decomp(72) {2: 3, 3: 2} :param n: number :return: dictionary """ expoente = 0 base...
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import requests def sendRequest(url, type="POST", params=None, headers=None): """ Send a request to a URL ### Input: - `url` (str) | the url to send the request to - `type` (str) | the type of request (GET or POST) - `params` ...
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def get_span_row_count(span): """ Gets the number of rows included in a span Parameters ---------- span : list of lists of int The [row, column] pairs that make up the span Returns ------- rows : int The number of rows included in the span Example ------- C...
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def get_logbook_by_name(logbook_name, conn): """ Get a logbook by name from a persistence backend connection :param str logbook_name: The name of the logbook to get :param obj conn: A persistence backend connection :return obj logbook: The logbook with the specified name """ return next( ...
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from typing import List def get_label_list(labels: List[List[int]]) -> List[int]: """Gets a sorted list of all the unique labels from `labels`. Args: labels: A list of lists, each corresponding to the label-sequence of a text. Returns: All the unique labels the ever appear in `labels`, g...
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def format_message(date_str, node, msg): """Format log message""" message = f"{date_str}: {node.site_name}: {node.location or node.model} ({node.serial}) {msg}" return message
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def _world2fig(ff, x, y): """ Helper function to convert world to figure coordinates. Parameters ---------- ff : `~aplpy.FITSFigure` `~aplpy.FITSFigure` instance. x : ndarray Array of x coordinates. y : ndarray Array of y coordinates. Returns ------- coo...
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def is_palindrome(number): """ Returns True if `number` is a palindrome, False otherwise. """ num_str = str(number) num_comparisons = len(num_str) // 2 for idx in range(num_comparisons): if num_str[idx] != num_str[-1-idx]: return False return True
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from typing import Iterable def flatten_list(li: Iterable): """Flattens a list of lists.""" if isinstance(li, Iterable): return [a for i in li for a in flatten_list(i)] else: return [li]
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import re def remove_unwanted_chars(x: str, *chars: str, to_replace: str = "") -> str: """Remove unwanted characters from a string.""" return re.sub(f"[{''.join(chars)}]", to_replace, x)
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def write_the_species_tree(annotated_species_tree, output_file): """ this function writes the species tree to file args: annotated_species_tree : a string of annotated species tree in .newick format output_file : a file name to write to output: a file containing the annotated sp...
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import functools def compose(*functions): """ A functional helper for dealing with function compositions. It ignores any None functions, and if all are None, it returns None. Parameters ---------- *functions function arguments to compose Returns ------- function or None ...
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def pretty_print_list(lst, name = 'features', repr_format=True): """ Pretty print a list to be readable. """ if not lst or len(lst) < 8: if repr_format: return lst.__repr__() else: return ', '.join(map(str, lst)) else: topk = ', '.join(map(str, lst[:3])) ...
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def _partition(entity, sep): """Python2.4 doesn't have a partition method so we provide our own that mimics str.partition from later releases. Split the string at the first occurrence of sep, and return a 3-tuple containing the part before the separator, the separator itself, and the part after the...
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import json def load_dict_from_json(filename: str) -> dict: """ Load the given file as a python `dict` Parameters ---------- filename: `str` an absolute path to the json file to be loaded. Returns ------- `dict` The loaded json file as a python dictionary. """ with open(filen...
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def get_n_neighborhood_start_stop_indices_3D(volume_shape, point, n): """ Compute the start and stop indices along the 3 dimensions for the n-neighborhood of the point within the 3D volume. Note that this returns an index range where the end is *non-inclusive*! So for a point at x,y,z with 0-neighborhood (...
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from typing import Dict from typing import Any def add_to_dict_with_swapped_keys(old_dict: Dict[Any, Dict], new_dict: Dict[Any, Dict]) -> Dict[Any, Dict]: """ Swap the keys of two nested dictionaries in a new dictionary. {'Key1': {'Key2': 42}} -> {'Key2': {'Key1': 42}} ...
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import typing import functools def build_simple_validator(func: typing.Callable, *args, **kwargs) -> typing.Callable[[typing.Any], typing.Any]: """Build a ready-to-use simple validator out of a function. Args: - func: callable, the function to be called to validate an input - args: list, args...
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import torch def quat_conjugate(a: torch.Tensor) -> torch.Tensor: """Computes the conjugate of a quaternion. Args: a: quaternion to compute conjugate of, shape (N, 4) Returns: Conjugated `a`, shape (N, 4) """ shape = a.shape a = a.reshape(-1, 4) return torch.cat((-a[:, :3...
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def blank_lines(logical_line, blank_lines, indent_level, line_number, previous_logical): """ Separate top-level function and class definitions with two blank lines. Method definitions inside a class are separated by a single blank line. Extra blank lines may be used (sparingly) to sepa...
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def shiny_gold_in(bag: str, rules: dict) -> bool: """Recursively check for shiny gold bags.""" if "shiny gold" in rules[bag].keys(): return True elif not rules[bag]: # bag holds no others return False else: for inner in rules[bag]: if shiny_gold_in(inner, rules): ...
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def get_position_type(salary_plan): """ Given a salary plan code, map to one of the VIVO position types """ position_dict = { 'CPFI': 'postdoc', 'CTSY': 'courtesy-faculty', 'FA09': 'faculty', 'FA9M': 'clinical-faculty', 'FA10': 'faculty', 'FA12': 'faculty'...
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def str2ms(s): """ Convert the time strings from an SRT file to milliseconds. Arguments: s: A time value in the format HH:MM:SS,mmm where H, M, S and m are digits. Returns: The time string converted to an integer value in milliseconds. """ s = s.strip() time, ms ...
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import torch def get_device(inputs): """ Get used device of a tensor or list of tensors. """ if isinstance(inputs, torch.Tensor): device = inputs.device elif isinstance(inputs, (tuple, list)): device = inputs[0].device else: raise TypeError(f'Inputs can be a tensor or list of t...
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def quick_sort(sequence: list) -> list: """Simple implementation of the quick sort algorithm in Python :param sequence: some mutable ordered collection with heterogeneous comparable items inside :return: the same collection ordered by ascending """ if len(sequence) < 2: return sequence ...
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def score_tup(t): """ Score an ngram tuple returned from a database ngram table. A higher scoring term is more deserving of inclusion in the resulting acrostic :param t: (Term string, initials string, Corpus count, Used count) :return: Fitness score for this term """ term = t[0] inits = ...
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import torch def get_optimizer(parameters, lr, weight_decay): """ Initiate Adam optimizer with fixed parameters Args: parameters: filter, parameters to optimize lr: float, initial learning rate weight_decay: float, between 0.0 and 1.0 Return: a torch.optim.Adam optimizer """ return torch.optim.Adam(p...
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import requests def get_gist(url): """ Get gist contents from gist url. Note the gist url display the raw gist instead of usual gist page. Args: url (str) : url containing the raw gist instead of usual gist page. Returns: (str): output gist str. ""...
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import re def is_email(addr): """ 判断是否是合法邮箱 :param addr: 邮箱地址 :return: True or False """ re_is_email = re.compile("^[a-z0-9]+([._-]*[a-z0-9])*@([a-z0-9]+[-a-z0-9]*[a-z0-9]+.){1,63}[a-z]+$") if re_is_email.search(addr): return True else: return False
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def merge_unique(a: list, b: list) -> set: """ merges all of the unique values of each list into a new set >>> merge_unique([1, 2, 3], [3, 4, 5]) {1, 2, 3, 4, 5} """ ret = set() a.extend(b) for element in a: ret.add(element) return ret
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def get_wanted_parameter(season_data, names, index_para): """ Take in a list of players' names, a wanted parameter and return :param season_data: a dictionary of players' statistics :param names: a list of players' names :param index_para: index of the wanted parameter depending on the file :return:...
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def DL_ignore(answers): """Return False if any dictionary-learning method was selected. Arguments --------- answers: dict Previous questions answers. Returns ------- bool True if DL verbosity question should be ignored. """ expected = ['ITKrMM', 'wKSVD', 'BPFA'] ...
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def wait(status, timeout=None, *, poll_rate="DEPRECATED"): """(Blocking) wait for the status object to complete Parameters ---------- status: StatusBase A Status object timeout: Union[Number, None], optional Amount of time in seconds to wait. None disables, such that wait() will ...
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import re def find_md_links(md): """Returns dict of links in markdown: 'regular': [foo](some.url) 'footnotes': [foo][3] [3]: some.url """ # https://stackoverflow.com/a/30738268/2755116 INLINE_LINK_RE = re.compile(r'\[([^\]]+)\]\(([^)]+)\)') FOOTNOTE_LINK_TEXT_RE = re.compile(r'\[...
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def epoch_time(start_time, end_time): """ Computes the time for each epoch in minutes and seconds. :param start_time: start of the epoch :param end_time: end of the epoch :return: time in minutes and seconds """ elapsed_time = end_time - start_time elapsed_mins = int(elapsed_time / 60) ...
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def base_prob(phred_score): """ Returns the probabilty that a base is incorrect, given its Phred score. """ prob = 10.0**(-float(phred_score)/10) return prob
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import re def need_format(line: str) -> bool: """ Return true if line as a title declaration followed by content """ return ( ( re.search("\t+e_\w*[-'\w]*\W*=", line) is not None and re.search("\t+e_\w*[-'\w]*\W*=\W*{[\w\t]*\n", line) is None and re.search("...
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def builderFor(action, hypervisor=None, template=None, service=None): """ This decorator is used to supply metadata for functions which is then used to find suitable methods during building just by these properties. :param action: Name of the generic step/action (see planner) that this function impleme...
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def undeployed_value_only_calculator(repository, undeployed_value_tuple, deployed_value_tuple): """ Just return the undeployed value as the value. This calculator can be used when there will be no deployed value. """ return undeployed_value_tuple[2]
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import re def _remove_inner_punctuation(string): """ If two strings are separated by & or -, remove the symbol and join the strings. Example ------- >>> _remove_inner_punctuation("This is AT&T here") 'This is ATT here' >>> _remove_inner_punctuation("A T & T") 'A T T' """ ...
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import random def random_string(length, charset): """ Return a random string of the given length from the given character set. :param int length: The length of string to return :param str charset: A string of characters to choose from :returns: A random string :rtype: str """ n = ...
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def reverse_spline(tck): """Reverse the direction of a spline (parametric or nonparametric), without changing the range of the t (parametric) or x (nonparametric) values.""" t, c, k = tck rt = t[-1] - t[::-1] rc = c[::-1] return rt, rc, k
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import importlib import pkgutil def list_submodules(package, recursive=True): """ Recursively (optional) find the submodules from a module or directory Args: package (str or module): Root module or directory to load submodules from recursive (bool, optional): Recursively find. Defaults to...
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def trainee_already_marked_training_date(trainee, training_date): """Check whether trainee already marked the given training date. If trainee already has training day info it means he/she answered marked the given date. Args: trainee(models.Trainee): trainee instance to check whether already marke...
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