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import argparse def separator(string): """Parse the separator, possibly raising error""" options = {"tab": "\t", "comma": ","} s = options.get(string, string) if len(s) == 1: return s else: raise argparse.ArgumentTypeError("must be a 1-character string")
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def read_params_Coulomb(fname='in.params.Coulomb'): """ Read in.params.Coulomb. But only for fixed or fixed_bvs charges. """ with open(fname,'r') as f: lines = f.readlines() mode = None chgtype = None chgs = {} coul = {} bvs = {} for line in lines: if line[0] in ...
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import json def mac_entry_info_get(client, vlan_name, port, peer_mac_addr): """based on the input information,found any mac entry is matched. :returns: True if one entry is matched """ status = False # show ethernet-switching table interface xxx command = 'exec cli show ethernet-switching tabl...
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import sys def _catch_thread_exception(fn): """Sets self._worker_exception when fn raises an exception""" def wrapped(self, *args, **kwargs): try: ret = fn(self, *args, **kwargs) except Exception: self._worker_exception = sys.exc_info() else: return ...
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def generate_graph(data, course_to_id): """ Method to read the JSON and build the directed graph of courses (= DAG of course IDs) The graph is represented in an adjacency list format :return: A graph in adjacency list format, with vertices as course IDs and directed edges implying prerequisite relation :rtype: L...
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from typing import Optional import math def round_for_theta( v: float, theta: Optional[float] ) -> float: """ Round a value based on the precision of theta. :param v: Value. :param theta: Theta. :return: Rounded value. """ if theta is None: return v else: ...
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from typing import List def split_badge_list(badges: str, separator: str) -> List[str]: """ Splits a string of badges into a list, removing all empty badges. """ if badges is None: return [] return [badge for badge in badges.split(separator) if badge]
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def get_teams_of_coach(cursor, coach): """gets all the teams a coach has Args: cursor: the cursor coach: the name of the coach Returns: a list of all the teams a coach has """ cursor.execute( "Select team_name from TeamsCoaches where coach_name = '{}'".format(coach...
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import random def seq_generator(): """ Generate each part of sequence. :return: sequence part as str """ return random.choice(["T", "H"])
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import re import html def convert_html_escapes_to_xml(html_text): """Avoid XML parsing errors by converting HTML escape codes to XML.""" html_entities = set( re.findall(r'&(?!quot|lt|gt|amp|apos)[a-zA-Z]{1,30};', html_text) ) for entity in html_entities: html_text = html_text.replace(e...
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def column(matrix, col): """Returns a column from a matrix given the (0-indexed) column number.""" res = [] for r in range(len(matrix)): res.append(matrix[r][col]) return res
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import re def parse_scenario_gtest_name(name): """Parse scenario name to form acceptable by gtest""" # strip name = name.strip() # space and tab to _ name = name.replace(" ", "_").replace("\t", "_") # remove dots. commas name = re.sub('[^a-zA-Z_]+', '', name) # make lower name = na...
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import json def load_json(filepath): """Load a json file. Args: filepath (str): A path to an input json file. Returns: dict: A dictionary data loaded from a json file. """ with open(filepath, 'r') as f: ret = json.load(f) return ret
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def sort_states(state, columns, reverse=True): """ Sort the states according to the list given by prioritize_jobs. prioritize_jobs (or columns in this case) is list of according to which state should be prioritized for job submission. The position in the list indicates the prioritization. columns =...
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def statement(prop, value, source): """ Returns a statement in the QuickStatements experted format """ return "LAST\t{}\t{}\tS854\t\"{}\"".format(prop, value, source)
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import json def get_config_db_json_obj(dut): """ Get config_db content from dut Args: dut (SonicHost): The target device """ config_db_json = dut.shell("sudo sonic-cfggen -d --print-data")["stdout"] return json.loads(config_db_json)
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import argparse def get_arg_parser(parser=None): """Parse the command line arguments for merge using argparse Args: parser (argparse.ArgumentParser or CompliantArgumentParser): an argument parser instance Returns: ArgumentParser: the argument parser instance Notes: i...
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def check_sender(tx: dict, sender: str) -> bool: """ :param tx: transaction dictionary :param sender: string containing sender's address :return: boolean """ if tx["events"][0]["sub"][0]["sender"][0]["account"]["id"] == sender: return True return False
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def is_prime_det(n): """ Returns <True> if <n> is a prime number, returns <False> otherwise. It uses an (optimized) deterministic method to guarantee that the result will be 100% correct. """ # 2 and 3 are prime numbers if (n <= 3): return (n > 1) # Corner cases to speed up the ...
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def count_indents(text): """Takes a string and counts leading white spaces, return int count""" return len(text) - len(text.lstrip(" ")) pass
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def zippify(iterable, len=2, cat=False): """ Zips an iterable with arbitrary length pieces e.g. to create a moving window with len n Example: zippify('abcd',2, cat=False) --> [('a', 'b'), ('b', 'c'), ('c', 'd')] If cat = True, joins the moving windows together ...
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import os def find_paths(directory,stipe): """"" Arguments: directory {str} -- taranmak istenen ust dizin stipe {str} -- taranan uzanti Returns: path_list {list} -- path list for stipe """ if stipe.islower(): stipe_u = stipe.upper() else: ...
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def sanitize_int(value): """ Sanitize an input value to an integer. :param value: Input value to be sanitized to an integer :return: Integer, or None of the value cannot be sanitized :rtype: int or None """ if isinstance(value, str): try: return int(value) except...
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import sys import os def getResourcePath(relative_path): """Get absolute path to resource""" # if cx_freeze attribute found, use frozen resources if getattr(sys, 'frozen', False): base_path = os.path.dirname(sys.executable) else: # use path to development resources base_path = os.path...
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def MeanIoUConfig(argument_parser): """ Set CLI arguments :param argument_parser: argument parser :type argument_parser: ```ArgumentParser``` :returns: argument_parser :rtype: ```ArgumentParser``` """ argument_parser.description = """Computes the mean Intersection-Over-Union metric. M...
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def run_part2(_): """Implmentation for Part 2.""" # Reverse-engineered the input, it simply does: return sum(val for val in range(1, 10551340 + 1) if 10551340 % val == 0)
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def _get_dir_names(param): """Gets the names of the directories for testing the given parameter :param param: The parameter triple to be tested. :returns: A list of directories names to be used to test the given parameter. """ return [ '-'.join([param[0], str(i)]) for i in ...
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def bool_converter(value: str) -> bool: """ :param value: a string to convert to bool. :return: False if lower case value in "0", "n", "no" and "false", otherwise, returns the value returned by the bool builtin function. """ if value.lower() in ['n', '0', 'no', 'false']: return False ...
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def heat_stor(cp, spm, tdif): """ Calculate the heat storage Args: cp: specific heat of layer (J/kg K) spm: layer specific mass (kg/m^2) tdif: temperature change (K) """ return cp * spm * tdif
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from typing import Any from typing import Optional from typing import IO import yaml def dump_yaml(data: Any, stream: Optional[IO[str]] = None) -> Optional[str]: """Dump YAML to stream or return as string.""" if stream is not None: return yaml.safe_dump(data, stream, default_flow_style=False) else...
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def get_link_to_referenced_comment(subreddit_name, user_note): """Extracts the id of the comment referenced by the usernote and formats it as a reddit-internal link""" link_code_segments = user_note['l'].split(',') if len(link_code_segments) == 3: submission_id = link_code_segments[1] commen...
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def _detects_peaks(ecg_integrated, sample_rate): """ Detects peaks from local maximum ---------- Parameters ---------- ecg_integrated : ndarray Array that contains the samples of the integrated signal. sample_rate : int Sampling rate at which the acquisition took place. ...
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import re def pascal2title(string: str) -> str: """Splits on whitespace between capital and lowercase letters.""" # https://stackoverflow.com/a/29922050 return " ".join(re.findall(r"[A-Z](?:[a-z]+|[A-Z]*(?=[A-Z]|$))", string))
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import copy def flatten_samplesets(samplesets): """ Takes a list of SampleSets (with one or multiple samples in each SampleSet) and returns a list of SampleSets (with one sample in each SampleSet) Parameters ---------- samplesets: list of SampleSets Input list of SampleSets (with one o...
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import torch def center_conv_point(bboxes, kernel_size=3, c_min=0, c_max=1, v3_form=False): """In a parallel manner also keeps the gradient during BP""" #bboxes.clamp_(min=c_min, max=c_max) if v3_form: base = torch.cat([bboxes[:, :2][:, (1, 0)]] * (kernel_size ** 2), dim=1) else: base ...
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def auto_type_convert(value): """Try to convert 'value' to a int, float, or bool. Otherwise leave as a string. This is done recursively with complex values.""" if value is None: return None if isinstance(value, list): return [auto_type_convert(item) for item in value] elif isinstan...
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import itertools def normalise_text(text): """ Removes leading and trailing whitespace from each line of text. Removes leading and trailing blank lines from text. """ stripped = text.strip() stripped_lines = [line.strip() for line in text.split("\n")] # remove leading and trailing empty li...
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def remove_stale_events(data): """ Parse an event dictionary and remove transitions to the same state: .. code:: event_dict = { (entity_id, cohort interval) : [(time, state), ..., (time, state)] (entity_id, cohort interval) : (time, state), ..., (time, state)] } :para...
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import sqlite3 def sqlite3get_table_names(sql_conn: sqlite3.Connection): """For a given sqlite3 database connection object, returns the table names within that database. Examples: >>> db_conn = sqlite3.connect('places.sqlite')\n >>> sqlite3get_table_names(db_conn)\n ['moz_origins', 'm...
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def make_key_frames(): """ make key frames for the regions """ key_frames = {} key_frames[0] = [100, 200, 300] key_frames[1] = [50, 150] return key_frames
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from typing import List from typing import Any def sort(xs: List[Any]) -> List[Any]: """ Sort the list `xs` with the python `sort` function and return the sorted function. The given list is not modified. Parameters ---------- xs A list. Returns ------- xs_sorted ...
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def response_200(result=None): """GET에 대한 반환""" return { 'msg': 'success', 'result': result }, 200
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def limit(): """The number of corpus files to process, e.g ``--limit 100`.""" return '--limit 50'
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def add_pacient(ime, priimek, cepivo=None): """Funkcija v bazo vstavlja novega pacienta za sprejem v bolnišnico.""" return None
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import pickle def read_solver(filename): """ This function reads a .pk1 file. Parameters: filename (str): A file name or path to file excluding file extension. Returns: Content of the loaded .pk1 file. """ try: file = open(filename+'.pk1', 'rb') except IOError: ...
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def sentence_length_feature(sentences): """ List of values from 0 to 1 rating the length of the sentence in comparation with the longest one """ sentence_length_feature_values = [] max_length_sentence = len(sentences[0].original.split(' ')) # Find the longest sentence for sentence in sentences[1:...
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import os def system_terminal_emulator() -> str: """ Goal: find the default terminal emulator """ try: return os.environ["TERM"] except KeyError: raise EnvironmentError("Cannot find default terminal")
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import inspect def get_argument_help_string(param: inspect.Parameter) -> str: """Get a default help string for a parameter :param param: Parameter object :type param: inspect.Parameter :return: String describing the parameter based on the annotation and default value :rtype: str """ help_...
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def _dask_array_fft_has_norm_kwarg(): """returns True if dask.array's fft supports the norm keyword argument """ return False
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def nested_select(d, v, default_selected=True): """ Nestedly select part of the object d with indicator v. If d is a dictionary, it will continue to select the child values. The function will return the selected parts as well as the dropped parts. :param d: The dictionary to be selected :param v: Th...
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import time def timestamp_2_datetime_str(timestamp): """将时间戳转为日期时间字符串""" datetime_tuple = time.localtime(timestamp) return time.strftime("%Y-%m-%d %H:%:%S", datetime_tuple)
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import os import pickle def load_parameters(): """Read the "bridge file to get back the arguments.""" parameter_file_name = os.path.abspath("gdb_driver.params") parameter_file = open(parameter_file_name, "rb") return pickle.loads(parameter_file.read())
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def is_trans(reaction): """Check if a reaction is a transporter.""" return len(reaction.metabolites) == 1
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def format_tile(tile, tile_format, format_str='{x} {y} {z}'): """Convert tile to necessary format. Parameters ---------- tile: pygeotile.tile.Tile Tile object to be formatted. tile_format: str Desired tile format. `google`, `tms`, or `quad_tree` format_str: str String to...
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def percent(a, b): """ Given a and b, this function returns a% of b """ return (a/100)*b
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import math def filter_none(mongo_dict): """Function to filter out Nones and NaN from a dict.""" for key in list(mongo_dict.keys()): val = mongo_dict[key] try: if val is None or math.isnan(val): mongo_dict.pop(key) except Exception: continue ...
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import configparser def read_configfile(): """Read the config file :returns: The ConfigParser object """ c = configparser.ConfigParser() c.read("config.conf") return c
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import csv def read_us_counties_csv(file_name): """ """ # read the data with open(file_name) as csv_file: # convert each row to a list of strings csv_reader = csv.reader(csv_file, delimiter=',') line_count = 0 counties_with_deaths = [] for row in csv_reader...
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def ARGmetric_params_from_row(row): """ Create some ARGmetric params (see ARGmetrics.py) from a row We hack the same polytomy seed as inference seed This stupidly has to be defined at the top level, since it is part of the function passed in to a multiprocessing Pool, and hence needs to be 'pic...
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def argument(*name_or_flags, **kwargs): """Helper function to satisfy argparse.ArgumentParser.add_argument()'s input argument syntax""" return (list(name_or_flags), kwargs)
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import re def fetch_geneid(fn): """ fetch gene id from GTF records gene_id "FBgn0267431"; gene_name "Myo81F"; gene_source "FlyBase"; gene_biotype "protein_coding"; """ assert isinstance(fn, str) ps = fn.split(';') dn = {} for i in fn.split(';'): if len(i) < 8: # shortest field ...
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def fieldsMatch(f0, f1): """ Checks whether any entry in one list appears in a second list. """ for f in f0: if f in f1: return True return False
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def list_to_str(lst): """convert list/tuple to string split by space""" result = " ".join(str(i) for i in lst) return result
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def extract_bias_diagonal(module, S, sum_batch=True): """Extract diagonal of ``(Jᵀ S) (Jᵀ S)ᵀ`` where ``J`` is the bias Jacobian. Args: module (torch.nn.Conv1d or torch.nn.Conv2d or torch.nn.Conv3d): Convolution layer for which the diagonal is extracted w.r.t. the bias. S (torch.Ten...
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import time def read_device(net_connect, sleep=1): """Sleep and read channel.""" time.sleep(sleep) output = net_connect.read_channel() print(output) return output
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import os def __work_mode__(path: str): """Determines the desired mode of operation""" if os.path.isfile(path): # Input is file return "file" if os.path.isdir(path): # Input is dir return "dir" else: return "no"
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def is_numeric_array(x): """ Returns whether an object is a ground numeric array. """ return False
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from gzip import GzipFile from typing import Any import json def gzip_load_var(gzip_file:str) -> Any: """ Load variable from .json.gz file (arbitrary extension!) Parameters ---------- gzip_file : str Filename containing the gzipped JSON variable Returns ------- var : Any ...
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import os def verify_directory_layout(project_dir): """ Verifies if directory from path has Maven's "Standard Directory Layout" (src/main/java) :param project_dir: path to the project :raises FileNotFoundError: when a directory is requested but doesn't exist :raises NotADirectoryError: when path ...
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def five_point_derivative(f,x,h): """#5-point function to calaculate 1st derivative""" h = float(h) return (1/(12*h))*(f(x-2*h)-f(x+2*h)- 8*f(x-h)+8*f(x+h))
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def unique_count(value): """Count the number of unique characters in the string representation of a scalar value. Parameters ---------- value: scalar Scalar value in a data stream. Returns ------- int """ unique = set() for c in str(value): unique.add(c) ...
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import os def compare_file_contents(path_a, path_b) -> bool: """ Compares two files and returns whether the files are equal. """ if os.stat(path_a).st_size != os.stat(path_b).st_size: return False with open(path_a, 'rb') as file_a, open(path_b, 'rb') as file_b: while True: ...
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def category_table_build(osm_table_name, categorysql): """ Returns an SQL OSM category table builder Args: osm_table_name (string): a OSM PostGIS table name Returns: sql (string): a sql statement """ sql = ("INSERT INTO category_%s (osm_id, cat) " "SELECT DISTINCT o...
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import time import re def get_uniqueID(idPrefix): """Generates a unique id """ t = time.ctime() uid = '_'.join([idPrefix, t]) return re.sub(r'[: ]', '_', uid)
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def count_helices(d): """Return the helix count from structure freq data.""" return d.get('H', 0) + d.get('G', 0) + d.get('I', 0)
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from datetime import datetime import itertools def satisfies(query, **kwargs): """Check whether a given datetime object satisfies day and time predicates Keyword Args: month: The month predicate (January, February, ...) day: The day of month predicate [1 31) weekday: The day of week p...
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import os import json def check_completeness_single_job(out_file: str, job_no: int, iteration: int) -> bool: """ Check whether an individual inference job has been completed. Args: out_file: n5 file to save inference to. ...
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import requests import json def duckduckgo(search, appName=""): """Gives instant answers from DuckDuckGo (https://duckduckgo.com/). Keyword arguments: search -- <str>; what you are searching for (case sensitive) appName -- <str>; the name of your app Return value: { "...
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def binary_to_decimal(number): """ Calculates the decimal of the given binary number. :param number: decimal number in string or integer format :return integer of the equivalent decimal number """ decimal = [] number = list(str(number)[::-1]) for i in range(len(number)): ...
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def get_dom_attr_value(dom, tag_name, attr_name): """ Return value of a tag's attribute from dom (XML file). Arguments: tag_name -- name of dom tag in which the attribute is found. attr_name -- name of dom attribute for which the value should be returned. """ tag=dom.getElementsByTag...
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def plaintext(): """Test 6: Plaintext""" return b"Hello, World!", {"Content-Type": "text/plain"}
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def EGCD(a, b): """ Extended Euclidean algorithm computes common divisor of integers a and b. a * x + b * y = gcd(a, b) returns gcd, x, y or gcd, y, x. Sorry, I can't remember """ if a == 0: return (b, 0, 1) else: b_div_a, b_mod_a = divmod(b, a) ...
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def filter_attr(the_dict, attr_names): """ Only return the item that in the attr_names list :param the_dict: :param attr_names: comma separated names :return: dict """ if isinstance(the_dict, dict): attrs = attr_names.split(',') return dict((k, v) for k, v in the_dict.items...
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import torch def word_to_one_hot(word, word2idx): """Return the one hot encoding of the word given to this function. Args: word (str): The word for which one hot representation is required. word2idx (Dict): The dictionary mapping from word to indices. Returns: x (torch.Tensor): The on...
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def rev_comp(seq: str) -> str: """ Generates the reverse complement of a sequence. """ comp = { "A": "T", "C": "G", "G": "C", "T": "A", "B": "N", "N": "N", "R": "N", "M": "N", "Y": "N", "S": "N", "W": "N", "K...
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def strip_variables(raw_df, targ_hd): """ Some of the ncdf files do not have a <complete> collection of variables (e.g. Rnet, Qg), such that the matrices are different shapes. In order to be able to concatenate all fluxnet datasets together, this function strips out the uncommon variables. """ ...
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def find_nuc_indel(gapped_seq, indel_seq): """ This function finds the entire indel missing in from a gapped sequence compared to the indel_seqeunce. It is assumes that the sequences start with the first position of the gap. """ ref_indel = indel_seq[0] for j in range(1,len(gapped_seq)): ...
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def _match_identifier_re(): """ 匹配BundleId """ return r'^Identifier:\s*([a-zA-Z0-9_\-\.]+)\s*$'
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def get_stats_for_unweighted_hpo_aggregate_metric( hpo_object, metric, date, hpo_name, tables_and_classes_counted, statistics_to_average): """ Function is used once an HPO is found and warrants its own AggregateMetricForHPO because it has a unique set of date and metric parameters. ...
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def codeblock(text): """ Returns text in a Markdown-style code block :param text: Str :return: Str """ return "```\n" + text + "\n```"
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def generate_ensemble(num_layers, *activations): """Given a set of string names and a number of target layers, generate a list of ensemble architectures with those activations Args: num_layers: int the number of hidden layers in the neural network, and also the number of activation fun...
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def regular_graphing_method(): """ This function was created to determine whether the user wants to graph the data on top of each other or on separate graphs. :return boolean regular_ontop: regular_ontop is returned to determine how the data will graph Note: if regular_ontop is true, the non-derivativ...
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def div_to_int(int_numerator, int_denominator, round_away=False): """Integer division with truncation or rounding away. If round_away evaluates as True, the quotient is rounded away from zero, otherwise the quotient is truncated. """ is_numerator_negative = False if int_numerator < 0: int_numerator =...
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import os def dict_to_dir(data, path=str()): """dict_to_dir expects data to be a dictionary with one top-level key.""" dest = os.path.join(os.getcwd(), path) if isinstance(data, dict): for k, v in data.items(): os.makedirs(os.path.join(dest, k)) dict_to_dir(v, os.path.joi...
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import re def get_pids(linesl): """ Required layout lines. Returns dictionary of pid:meaning """ pids = {} foundstartpids = False for line in linesl: # After table if "These PIDs are superseded by PIDs 194, 195, and 196." in line: break # Before table if not foundstartpids and " ...
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def match_server_args_factory(tick_rate: int, realtime: bool, observations_only: bool, env_config_string: str): """ Helper factory to make a argument dictionary for servers with varying ports """ def match_server_args(port): arg_dict = { "tick_rate": tick_rate, "port": port, ...
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from typing import Iterable from typing import Any def parametrize(arg_names: Iterable[str], arg_values: Iterable[Iterable[Any]]): """ Decorator to create parameterized tests. # Parameters arg_names : `Iterable[str]`, required. Argument names to pass to the test function. arg_values : `I...
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def default_colors_to_resets(s): """Hack to make sphinxcontrib.ansi recognized sequences""" return s.replace(b"[39m", b"[0m").replace(b"[49m", b"[0m")
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from typing import List import argparse def get_input() -> List[int]: """ Parse arguments passed to script. Return: Path path to gziped file for this problem. """ parser = argparse.ArgumentParser() msg = "comma separated numbers, i.e '0,3,6'" parser.add_argument("sequence", he...
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def mask_maxipix(mydata, mymask): """Mask the Maxipix frames.""" mydata[:, 255:261] = 0 mydata[255:261, :] = 0 mymask[:, 255:261] = 1 mymask[255:261, :] = 1 return mydata, mymask
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