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def commit_diff(c): """Return the set of changed files. Args: c (git.Commit) Returns: set[str]: a set of file paths (relative to the git repo's root directory). """ changed = set() def add_path(blob): if blob is not None: changed.add(blob.path) prev_c ...
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def sort_donors(donor_dict): """Sort the list of donors by total amount donated. Returns a list of only the donors' names. """ return sorted(list(donor_dict), key=lambda x: -sum(donor_dict[x]))
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from typing import List import ast def get_class_names_in_files(path: str) -> List[str]: """Read all class names in file.""" with open(path) as file: module = ast.parse(file.read()) return [node.name for node in module.body if isinstance(node, ast.ClassDef)]
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import numpy def _encoder_checksum(modes: int) -> numpy.ndarray: """ Helper function for checksum_code that outputs the encoder matrix. Args: modes (int): matrix size is (modes - 1) x modes Returns (numpy.ndarray): encoder matrix """ enc = numpy.zeros(shape=(modes - 1, modes), dtype=int...
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import re def calc_query_pos_from_cigar(cigar, strand): """Uses the CIGAR string to determine the query position of a read The cigar arg is a string like the following: 86M65S The strand arg is a boolean, True for forward strand and False for reverse Returns pair of ints for query start, end pos...
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def mesh_error(mesh1, mesh2): """Error (intersection over union) of the two meshes""" intersection = mesh1.intersection(mesh2) union = mesh1.union(mesh2) error = intersection.volume/union.volume return error
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from typing import List def split_filter(string: str, delim: str) -> List[str]: """Split the given string with the given delimiter. If the given string is empty, an empty list is returned. :param string: String to split. :param delim: Delimiter character. """ if not string: return [...
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from typing import Tuple def index_to_tuple(index: int, size: int) -> Tuple[int, int]: """ Returns a tuple to indicate 2d-array for the given index :param index: :param size: :return: """ assert 0 <= index < size * size, "Out of bound" return int(index / size), int(index % size)
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def find_maxProfit(weights: "list[int]", profits: "list[int]", capacity: "int", greedy_method: "str" = "max") -> float: """Fractional Knapsack Problem Find maximum profit using greedy method Args: weights (List[int]): list/array of weights profits (List[int]): list/array...
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def replace_at(word, line, index): """ Replace the text in-line. The text in line is replaced (not inserted) with the word. The replacement starts at the provided index. The result is cliped to the input length Arguments --------- word : str The text to copy into the line. lin...
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def check_positioners(positioner_ids, command, fps, initialised=False): """Checks if some of the positioners are not connected.""" if any([pid not in fps.positioners for pid in positioner_ids]): command.fail(error="some positioners are not connected.") return False if initialised: ...
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def coverage(comm,edge_attr=None): """ comm: community """ num,den = 0.,0. for e in comm.graph.es: w = 1 if edge_attr: w = e[edge_attr] den += w i = e.source j = e.target if comm.membership[i] == comm.membership[j]: num += w return num/...
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def _normalize_string(text): """Trims the text, removes all the spaces from text and replaces every sequence of lines with a single line. Args: text (str): The schema definition. Returns: str: The normalized text. """ text = text.strip() result = "" whitespaces = [" ", "\t"...
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def load(file, width, height, data_start, colors, color_depth, *, bitmap=None, palette=None): """Loads indexed bitmap data into bitmap and palette objects. :param file file: The open bmp file :param int width: Image width in pixels :param int height: Image height in pixels :param int da...
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import os def get_imu_csv_files(input_dir): """Generates a list of all csv files that start with imu""" imu_files = list() if os.path.exists(input_dir): for path, _, files in os.walk(input_dir): for filename in files: if filename[0:3] == 'imu' and os.path.splitext( ...
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def normalize_rgb(rgb): """ Normalize rgb to 0~1 range :param rgb: the rgb values to be normalized, could be a tuple or list of tuples :return: """ if isinstance(rgb, tuple): return tuple([float(a)/255 for a in rgb]) elif isinstance(rgb, list): norm_rgb = [] for item ...
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def justReturn(inval): """ Really, just return the input. Parameters ---------- input : anything Returns ------- input : anything Just return whatever you sent in. """ return inval
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def find_dialogue_event(dialogue_event_name, dialogue_event_defs): """ Find a dialogue event by name in a list of dialogue event definitions. :param dialogue_event_name: the name of the dialogue event to look for. :param dialogue_event_defs: a list of dialogue event definitions. :return: the dialogue_e...
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def split_by_pred(pred, iterable, constructor=list): """Sort elements of `iterable` into two lists based on predicate `pred`. Returns a tuple (l1, l2), where * l1: list of elements in `iterable` for which pred(elem) == True * l2: list of elements in `iterable` for which pred(elem) == False """ ...
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from typing import List def selection_sort(arr: List[int]) -> List[int]: """ sort i items from the end, and decrease i until 1 """ # if [9,7,6,4,1], then i would enumerate as 4,3,2,1 for i in range(len(arr) - 1, 0, -1): # if i = 4, then j would enumerate as 0,1,2,3 largest_j = i for j in range(i...
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def add_size(string): """Helper function for tag creation.""" return str(len(string)) + ':' + string
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from typing import Dict def _map_dtypes(sql_dtypes: Dict[str, str]) -> Dict[str, type]: """ Create mapping from SQL data types to Python data types. :param sql_dtypes: A mapping from the column names in a SQL table to their respective SQL data types. Example: {"ct_id": int(10) unsigned NO...
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def crc16(data): """ Calculate an ISO13239 CRC checksum of the input buffer. """ m_crc = 0xffff for this in data: m_crc ^= ord(this) for _ in range(8): j = m_crc & 1 m_crc >>= 1 if j: m_crc ^= 0x8408 return m_crc
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from typing import Sequence from typing import Any from typing import Counter def sequence_equals(a: Sequence[Any], b: Sequence[Any]) -> bool: # pylint: disable=invalid-name """ Returns a value indicating whether two sequences contain the same elements. More specifically, returns ``True`` if the two seq...
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def _get_gpus_by_instance_type(instances, instance_type): """ Get gpus for the given instance type from the pricing file. :param instances: dictionary conatining the content of the instances file :param instance_type: The instance type to search for :return: the number of GPU for the given instance...
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from bs4 import BeautifulSoup def process_sitemap(s): """ :param s: Sitemap content in xml format :return: A list of URLs of all the web sites listed in site map """ soup = BeautifulSoup(s, features='html.parser') result = [] for loc in soup.findAll('loc'): result.append(loc.text)...
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def backward_cross_entropy_loss(probabilities, labels): """ Compute the gradient of the cross entropy loss with respect to the probabilities. probabilities is of the shape (# classes) labels is of the shape (# classes) The output should be the gradient with respect to the probabilities. Retur...
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def pad_docket_by_year(y): """ year manipulation """ x = str(y) if len(x) == 7: return x # this might be an ought's 2000's case if len(x) == 6: return "0" + x # this might be an exactly 2000 case? if len(x) <= 5: return "00" + x return x
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def add_mixin(klass, *mixins): """ dynamically declare a new class with the name Extended{old_name} and return the inherited class object :param klass: the class to redeclare with mixins :param mixins: the mixins to use :return: object class """ new_name = 'Extended{}'.format(klass.__nam...
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import json def read_class_names(class_names_path: str): """Reads class names from text file. Supports .txt and .json. Args: class_names_path: `str`, path to json/txt file containing classes. Text file should contain one class name per line. Json file should contain only one dictionary, `Map...
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def validate_file_input(file: dict): """This fnx checks if file is correct type for code This fnx tales in a file and if it is not the one needed it returns an error and if it is it returns true. :param file:dictionary file :returns: str and error code or boolean and error code """ if...
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import math def factorial(x): """Returns the factorial of x""" return math.factorial(x)
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def pd_rolling_mean(series, window_size): """ Compute rolling mean on a Series with the given window_size and return only non-None rows, i.e. starning from row number window_size - 1 and until the end. """ rolling_mean = series.rolling(window_size).mean() return rolling_m...
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def bufsize_type_to_bufsize(bf_type): """ for a given bufsize type, return the actual bufsize we will read. notice that although 1 means "newline-buffered", we're reading a chunk size of 1024. this is because we have to read something. we let a StreamBufferer instance handle splitting our chunk on new...
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import os def PathExists(v): """Verify the path exists, regardless of its type.""" return os.path.exists(v)
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def kida_parser(kida_file): """ KIDA used a fixed format file so we read each line in the chunks they specify and use python built in classes to convert to the necessary types. NOTE KIDA defines some of the same reaction types to UMIST but with different names and coefficients. We fix that by conver...
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import itertools def flatten(iterable): """Flatten the input iterable. >>> list(flatten([[0, 1], [2, 3]])) [0, 1, 2, 3] >>> list(flatten([[0, 1], [2, 3, 4, 5]])) [0, 1, 2, 3, 4, 5] """ return itertools.chain.from_iterable(iterable)
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def build_url(url, store_name, key): """This method combine the different parts of the urls to build the url to acces the REST-API. Parameters ---------- url : str the base url store_name : str the name of the voldemort store key : str the url part which represents t...
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import math def generateParetoScaledVariate(rand, alpha, beta): """ F(x) = 1 - (b/x)^a, x >= b """ return beta / (math.pow((1 - rand), (1/alpha)))
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import os def read_config(fin): """Reads search parameters from file fin""" APP_DATA = os.path.dirname(os.path.abspath(__file__)) res = {} with open(os.path.join(APP_DATA, fin), 'rb') as f: for line in f: line = line.decode('utf-8').lower().strip() if line == '' or line...
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def interpret_numbers(user_range): """ :param user_range: A string specifying a range of numbers. Eg. interpret_numbers('4-6')==[4,5,6] interpret_numbers('4,6')==[4,6] interpret_numbers('4,6-9')==[4,6,7,8,9] :return: A list of integers, or None if the input is not numberic """ ...
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def square_sum(numbers): """ Complete the square sum function so that it squares each number passed into it and then sums the results together. :param numbers: an array of integers. :return: the sum of all the square elements in the array. """ return sum(x ** 2 for x in numbers)
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from typing import Any from typing import Optional from typing import Dict from typing import Iterable def get_attributes( obj: Any, remap: Optional[ Dict[ str, str, ] ] = None, attrs: Optional[Iterable[str]] = None, ) -> Dict[str, Any]: """Extract a list of...
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from datetime import datetime def same_date(date1: datetime, date2: datetime) -> bool: """Check whether two given datetime object are in the same date""" return date1.day == date2.day and date1.month == date2.month and date1.year == date2.year
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import numpy def iplanck(radiance, wavelength=10.25): """ Calculate the inverse of Planck's function for a given thermal radiance and central wavelength Reference: https://ncc.nesdis.noaa.gov/data/planck.html Parameters ---------- wavelength : float Central wavelength used for the cal...
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def find_metadata_end(raw_file): """Extract the metadata from the raw file.""" lines = raw_file.split("\n") start = None end = None for idx, line in enumerate(lines): if "---" in line and start is None: start = idx elif "---" in line and start is not None: re...
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def newton(f, df, x, tol=1e-12, n=0): """ RECURSIVE Parameters ========== f : callable, function df : callable, derivative of f x : initial value tol : tolerance n : number of steps Returns ======= x : root of f n :...
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def cli(ctx, dataset_id, published=False): """Make a dataset publicly available or private. For more fine-grained control (assigning different permissions to specific roles), use the ``update_permissions()`` method. Output: Current roles for all available permission types. .. note:: This me...
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import torch def simple_nms(scores, nms_radius: int): """ Fast Non-maximum suppression to remove nearby points """ assert (nms_radius >= 0) def max_pool(x): return torch.nn.functional.max_pool2d( x, kernel_size=nms_radius * 2 + 1, stride=1, padding=nms_radius) zeros = torch.zeros...
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import numpy def AdamBashforth2Corrector(predicted, calculated, actual, timeStep): """ Implementation of Adam-Bashforth 2 correctorMethod. """ output = numpy.zeros((actual.size, )) summation = output[0] = actual[0] for i in range(1, actual.size): summation += (predicted[i] - calcu...
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import random def random_hero_image(): """Random the image from hero folder and return the location use in static tag""" return f"img/hero/{random.randint(1, 43)}.jpg"
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import math def _cuda_line_ellipsoid_intersection(r0, step, semiaxes): """Calculate the distance from r0 to an axis-aligned ellipsoid centered at origin along step. r0 must be inside the ellipsoid. Parameters ---------- r0 : numba.cuda.cudadrv.devicearray.DeviceNDArray step : numba.cuda.cudad...
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def safe_for_db_retry(f): """Enable db-retry for decorated function, if config option enabled.""" f.__dict__['enable_retry'] = True return f
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def get_targ_pairs(start_cond, end_cond): """Return boolean mask for paired target conditions. This function returns a mask indicating which start/end target conditions in the provided lists come from a paired set. For example, the entry for a a target condition 'T1 -> T5' will have a corresponding va...
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import argparse def make_parser(): """ Build the command line parser for the program. Returns ------- parser: ArgumentParser The parser """ parser = argparse.ArgumentParser(description='Program to compute tangles') parser.add_argument('-t', dest='dataset_name', action='stor...
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def fls(val: int, v6: bool) -> int: """Find last set - returns the index, counting from 0 (from the right) of the most significant set bit in `val`.""" # if b is zero, there is no first set bit if val == 0: return 0 # gradually set all bits right of MSB # this technique is called 'bit s...
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def water_evapotranspiration_flux(evap): """Water evapotranspiration flux ``evspsbl`` [mm]. Computes water evapotranspiration flux ``evspsbl`` from surface evaporation. """ return evap * (-1)
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def _canonize_validator(current_validator): """ Convert current_validator to a new list and return it. If current_validator is None return an empty list. If current_validator is a list, return a copy of it. If current_validator is another type of iterable, return a list version of it. If curre...
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def hexcolor_to_rgbcc(hexcolor): """ Converts an Hex color to its equivalent Red, Green, Blue Converse = hexcolor = (r << 16) + (g << 8) + b """ r = (hexcolor >> 16) & 0x7F g = (hexcolor >> 8) & 0x7F b = hexcolor & 0x7F return r, g, b
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def ra_as_hours(ra_degrees, seconds_decimal_places=2): """ Takes Right Ascension degrees as float, returns RA string. TESTS OK 2020-10-24. :param ra_degrees: Right Ascension in degrees, limited to 0 through 360. [float] :param seconds_decimal_places: number of places at end of RA string (no period if zero)....
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def instrumentState(actor, cmd, user, instrument=None, state="up"): """set the state of an instrument""" if state == "down": actor.instrumentDown[instrument] = True for a in actor.activeAlerts: if instrument in a.instruments: a.disable(user) else: actor.i...
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def str_block(block): # pragma: nocover """ Get title based on block type The default `__str__` methods do not operate within migrations :return: model title """ if block.type == 'static': return '-'.join((block.type, block.node.title)) elif block.type == 'menu': return '-'.join...
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def add(x: int, y: int): """A function to add stuff. :param x: A number, x :param y: A number, y :return: A number, x + y """ return x + y
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def to_title(str): """returns a string formatted as a title""" return str.replace("_", " ").capitalize()
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def _read_count_normalize(X): """Read depth normalization by sample. Assumes samples are columns and guides are rows.""" return (X / X.sum(axis=0)) * 1e6
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def compFirstFivePosInt(iset={1, 2, 3, 4, 5}): """ task 0.5.5 a comprehension over the given set whose value is the set consisting of the squares of the first five positive integers """ return {2**x for x in iset}
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import struct from functools import reduce def fix(d): """Turn mono data into stereo""" line=d n=2 return ''.join([line[i:i+n]*2 for i in range(0, len(line), n)]) shorts = struct.unpack('<' + 'h' * (len(d)/2), d) dbl = reduce(lambda x,y: x+y, zip(shorts, shorts)) return struct.pack('<' + '...
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def flat_cell(cell): """ flat dictionarys in celss """ if isinstance(cell, dict): value_cell = list(cell.values())[0] else: value_cell = cell return value_cell
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def _mock_kwargs_from_env(**kwargs): """ Method to mock docker.utils.kwargs_from_env method. """ return {'base_url': None}
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def assignOrder(order): """ Static method that adds the order attribute to a function. :param order: Order in which the function will be called """ def dstFunc(srcFunc): srcFunc.order = order return srcFunc return dstFunc
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def partial_positionals(func, fix_args, **fix_kwargs): """Like functools.partial, but with positionals as well""" def wrapper(*args, **kwargs): arg = iter(args) return func( *( fix_args[i] if i in fix_args else next(arg) for i in range(len(args) + len...
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import os def load_required(key: str) -> str: """ Load value from env, fails if not found. Args: key: key to lookup Returns: the found value Raises: EnvironmentError: key not found """ value = os.getenv(key, None) if value is None: raise EnvironmentEr...
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def get_key_value_from_tokens(tokens): """ Converts a list of tokens into a single key/value pair. :param tokens: The tokens, as strings. :type tokens: [str] :returns: (key, value) :rtype: (string, string) """ key_tokens = [] value_tokens = [] found_equals_sign = False for token in tokens: # Ma...
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def attributes_present(variables, attr_map): """Returns a list of the relevant attributes present among the variables. """ return [attr for attr in attr_map if any(v.attributes[attr] for v in variables)]
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def is_consecutive(l): """ Determines whether a list contains consecutive numbers. If it does, the sum of the numbers should be the same as n * (min + max) / 2 (where n is num elements) :param l: A set of numbers :return: True or False """ total = sum(l) mathsum = len(l) * (min(l) + max...
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import requests import json def number_of_subscribers(subreddit): """api call to reddit to get the number of subscribers """ base_url = 'https://www.reddit.com/r/' headers = { 'User-Agent': 'Mozilla/5.0 (Windows; U; Windows NT 5.1; de; rv:1.9.2.3) \ Gecko/20100401 Firefox/3.6.3...
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def parse_squad(dataset): """ Parses SQUAD database into more readable format. In this case I only care about question/answers pairs in order to make a seq2seq model that would generate questions out of a paragraph. Inputs: dataset: squad dataset in json format Returns: squad_js...
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import glob import os def get_file_fullname(searching_root, file_name): """ :param searching_root: directory in which file is going to be searched :param file_name: name of a file without extension :return: file name with it's extension """ output = glob.glob(os.path.join(searching_root, file_...
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def get_current(isamAppliance): """ Get permitted features for current user """ return isamAppliance.invoke_get("Get permitted features for current user", "/permissions/v1")
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import os def _get_ssh_config_file(opts): """ :return: Path to the .ssh/config file - usually <home>/.ssh/config """ ssh_config_file = opts.get("ssh_config_file") if not os.path.isfile(ssh_config_file): raise IOError("Cannot find SSH config file") if not os.access(ssh_config_file, os.R...
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def nbi_growth(nbi, nvi, nb, nb0, nv, C, f, R, g, c0, alpha, e, pv, eta): """ Single clone growth rate for bacteria. Inputs: nbi : 1D vector in time of bacteria clone sizes nvi : 1D vector in time of corresponding phage clone sizes nb : 1D vector in time of total bacteria population size nb0...
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def strip_if_first_match(data): """ If we have a keyword and we start with that keyword in the text, remove the match. """ def maybe_strip_match(item): for key, value in item.items(): value_str = str(value).lower() key_str = key.lower() if not value_str.s...
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def write_aed2_eco_configs(config_dict, out_path, config_type): """Write zoo / pathogen / phyto configs""" block_name = '&'+config_dict.keys()[0]+"\n" first_level = config_dict.keys()[0] second_level = config_dict[first_level].keys()[0] real_keys = config_dict[first_level][second_level].keys() ...
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import copy def chain(*renderables): """Chains renderable objects pgmock allows renderable objects (selectors and patches) to be chained to one another like so:: pgmock.statement(0).table('table').patch(...) Sometimes this syntax is undesirable, especially when working with multiple pat...
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import json def load_ee_params(filepath): """ Loads parameters for a posteriori error estimation for the PINN from the json file provided via param filepath. returns - K: as used for trapezoidal rule - mu: smoothing parameter for delta function - L_f: Lipschitz constant or spectral abscissa ...
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import math def euclidean_distance(xyz1, xyz2): """ Simple function for calculating euclidean distance between two points. """ dist = [(a - b)**2 for a,b in zip(xyz1, xyz2)] return math.sqrt(sum(dist))
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def contenttypes_uuid(obj): """ function for Issue models to generate the content_str by models app label + model name and object primary key easy to filter in queryset """ return f"{obj._meta.app_label}|{obj._meta.model_name}|{obj.pk}"
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import functools import traceback def wrap_exceptions(target_exception): """ Wrap exceptions into generic exception (for RPC transport) """ # def _decorator(func): _target_exception = target_exception # @functools.wraps(func) def _decorated(*_args, **_kvargs): t...
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import fnmatch import click def _match_pattern(what, items, pattern): """ Match given pattern against given items. Parameters ---------- what: str Describes what is filterd. items: Iterable[str] Items to be filtered include_pattern: str Comma separated items which ...
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def move_row_to_bottom(i,arrayIn): """" Moves a specified row (just one) to the bottom of the matrix, then rotates the rows at the bottom up. For example, if we had a matrix with 5 rows, and we wanted to push row 2 to the bottom, then the resulting row order would be: 1,3,4,5,2 """ arrayOut = arrayIn.c...
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def n_gal(zc, params): """ Number density of detected HI galaxies in a given redshift bin, n ~ Mpc^-3. """ return 1e-4
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def get_shipping_voucher_discount(voucher, total_price, shipping_price): """Calculate discount value for a voucher of shipping type.""" voucher.validate_min_amount_spent(total_price) return voucher.get_discount_amount_for(shipping_price)
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def _define_tabledict_keys(header, fields, separator): """ Define the keys for the tabledict dictionary. Note: this function is only used by parse_table_from_file(). :param header: header string. :param fields: header content string. :param separator: separator character (char). :return: ta...
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import math def _calc_degrees(opposite, adjacent): """ Calculates angle in degrees with inverse tangens based on length of opposite and adjacent sides """ return math.degrees(math.atan(abs(opposite) / abs(adjacent)))
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def read_gene_subsets2(fns): """Read gene names from a single txt file or multiple files. Only unique gene names are kept""" names=[] for fn in fns: name=[] for line in open(fn,'r'): try: name.append(line.strip().split()[0]) except IndexError: ...
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def pv_efficiency(eta_PVref, beta, NOCT, NOCT_ref, NOCT_sol, T_amb, I): """ Calculates time resolved PV efficiency [-] :param eta_PVref: Reference PV efficiency under NOCT [-] :param beta: Temperature coefficient [-] :param NOCT: Nominal operating cell temperature [deg C] :param NOCT_ref: Refere...
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def is_tonghao(num1, num2): """用于判断两个数是否同号""" is_both_positive = num1 > 0 and num2 > 0 is_both_negative = num1 < 0 and num2 < 0 return is_both_positive or is_both_negative
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def getSectionByName(sections, name, key="name", default=None): """identify the first section with matching key among 'sections'""" for s in sections: if name == s.get(key): return s return default
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def ip_exists(ip_address, client): """Determines whether an IP address already exists in database Args: ip_address client: pymongo client used to connect to mongodb database Return: exists: boolean indicating whether an IP address exists in database """ user_collection = c...
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from typing import List def ibo1_to_bio(sequence_label: List[str]) -> List[str]: """ IBO1 的序列标签格式转换成 bio 格式。ibo1格式是指 "I-Label" 作为一个序列的开始, 直到遇到 O。 "B-Label" 是指连续 "I-Label" 是多个 span 的时候,除了第一个span,其他都是 "B-Label"。 另外 BIO 的格式也兼容,比如 "B-Lable", "I-Label" 这种BIO格式也是正确的。 例子如下: "I-Label1 I-Label1 O I-Lab...
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