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import io import zipfile def build_zip_file_in_memory(entries): """ Creates a zip file by writes files and data to a zip file :param entries is compose of MemoryZipFile objects and MemoryZipData :return: File-like object containing a zip file, backed in memory. """ zip_bin = io.BytesIO() ...
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def moments_parser(data, label) -> dict: """ moments are returned from the rest api as a dictionary. The moments parser returns a dictionary that only contains the specified label Parameters ---------- data : dict The complete dictionary label : str The key value of moments to ...
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def fix_samp_id(mystring): """Remove all of the extra ID info from TCGA barcodes.""" if mystring.startswith('TCGA'): return mystring[:12] else: return mystring
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def get_props(obj, prop_names): """ Get multiple attributes of `obj`. Names are given by `prop_names` list. """ return [getattr(obj,p) for p in prop_names]
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def validate_channel_config(channel_config): """ Validates a channel config Args: channel_config (dict): the channel config object Returns: list of str: list of errors or an empty list if no errors """ errors = [] if not channel_config: erro...
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def gaussian_focal_loss(pred, target, alpha=2.0, gamma=4.0): """ Focal Loss introduced in [1] for targets in gaussian distribution. Args: pred (:obj:`torch.Tensor`): The predictions. target (:obj:`torch.Tensor`): The learning targets in gaussian distribution. alpha (floa...
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def parse_args(content): """Gets the command name and arguments from message content""" #Split the message splited = content.split(" ") command_text = splited[0] args = splited[1:] command_text = command_text[1:] command = command_text #If the message is in a group, we need to remove...
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def resolve_parent(previous, parent): """ Figure out the parent to use based on the previous pane or given parent Breadth-based recursion means the previous pane should take precedence over the original parent if one is provided Parameters ---------- previous The previous pane ...
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def trloadchan(dbin, t0, t1, sta, chan): """Load time-series data for a given station, channel, and time-interval into memory""" return dbin.loadchan(t0, t1, sta, chan)
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from typing import List def change_base(number: int, base: int) -> List[int]: """Express an integer in another base. Args: number: The integer to convert. base: The base to which to convert number. Returns: A list of integers, where each integer is a digit in number expressed ...
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from datetime import datetime def validate_timestamp(timestamp): # test """Validates timestamp input for correct format Args: timestamp: datetime string Returns: boolean: if string is in correct format """ try: datetime_input = datetime.strptime(timestamp, '%Y-%m-%d %H:%...
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def normalize_data(x): """Normalize data to values between 0-1 Args: x(NxN float matrix): data to be normalized Returns: x_norm((NxN float matrix): normalized data """ return (x-x.min())/(x.max()-x.min())
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def multiply_regular(data): """ Multiplies all elements in passed sequence. You may assume that all elements in passed argument is numeric. >>> multiply_regular([3, 6, 9]) 162 >>> multiply_regular(range(10)) 0 >>> multiply_regular(range(1, 10)) 362880 >>> multiply_regular((8.2, ...
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import math def to_decibel(value, limit=-70): """ Convert a ratio to decibels. This method will never return less than the specified limit (default -70dB). If value is zero or negative, the limit will be returned as well. """ if value > 0: db = 10 * math.log10(value) if db >= l...
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def min_node(tree): """ Return the minimum node of the tree or raise a ValueError if the tree is empty. """ if tree is None: raise ValueError("Can't take min of empty tree") if tree.left: return min_node(tree.left) return tree
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def byte_pad(data: bytes, block_size: int) -> bytes: """Pad data with 0x00 until its length is a multiple of block_size.""" if remainder := len(data) % block_size: return data + bytes(block_size - remainder) return data
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def init_farthest_distance(far_mat, dist_mat, s): """initialize matrix to keep track of distance from set Parameters: ------------------ far_mat : python list length = dist_mat.shape[0] the minimum distance from solution set to all the points dist_mat : numpy.array (n, n) distanc...
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def get_integer(byte_str): """ Get a integer from byte string :param byte_str: byte string :return: byte string, integer """ integer = int.from_bytes(byte_str[:4], byteorder="little") byte_str = byte_str[4:] return byte_str, integer
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import requests def get_token(code, token_service, client_id, client_secret, redirect_uri, grant_type): """Fetches an OAuth 2 token.""" data = { 'code': code, 'client_id': client_id, 'client_secret': client_secret, 'redirect_uri': redirect_uri, 'grant_type': grant_type,...
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def tidy_dataframe(df, column, sep='|'): """ Given a dataframe with a delimiter-separated string, create a new dataframe with separate rows for each value in each corresponding string. E.g.:: gene score 0 g1|g2 1 1 g3 5 2 g4|g5|g6 9 ...
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def tag_clean(n): """Get tagname without prefix""" if n[0] in u"-~!": return n[1:] return n
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def restrict_common_genes(X1, X2, genes1, genes2): """ Given two expression matrices and two lists of gene identifiers corresponding to the two columns of the matrices, re-configure the matrices to keep only columns for genes that are common between the two datasets. """ gene_to_index1 =...
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def _AddDSATargeting(client, ad_group_id, label_name): """Set custom targeting for the page feed URLs based on a list of labels. Args: client: an AdWordsClient instance. ad_group_id: a str AdGroup ID. label_name: a str label name. Returns: A suds.sudsobject.Object representing the newly created ...
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def unpack_hashtags(hashtag_list): """Takes a list of hashtags and adds a "#" before and a space after each""" hashtags = "" for tag in hashtag_list: hashtags += "#%s " % tag return hashtags
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def normalize_float(v: float, lower_bound: float, upper_bound: float) -> float: """Normalizes ``v`` between ``lower_bound`` and ``upper_bound`` Assumes (and will not check) that `lower_bound <= v <= upper_bound` :param v: the value to be normalized :param lower_bound: the supposedly lowest possible va...
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def escape_latex(value): """Escape a value for Latex """ value = value.replace('\\', '\\textbackslash{}') value = value.replace('{', '\\{') value = value.replace('}', '\\}') value = value.replace('#', '\\#') value = value.replace('$', '\\$') value = value.replace('%', '\\%') value = ...
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def split_table(table_name): """Split a fully-qualified table name into schema and table Args: table_name (string) A table name, either with or without a schema prefix Returns: (tuple) of schema and table name """ table_parts = table_name.split(".") if len(table_parts) == 2: re...
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import wave def get_wav_properties(wav_path): """ Reads sampling rate and duration of an WAV audio file :param wav_path: path to the WAV file :return: sampling rate in Hz, duration in seconds """ with wave.open(wav_path, "rb") as wave_file: fs = wave_file.getframerate() duratio...
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import copy def uniform_crossover(random, mom, dad, args): """Return the offspring of the uniform crossover on the candidate. Based on two candidates (parents) build 2 children: - elements present in both parents will be present in both children; - both children have at least one element; - elemen...
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def encode_intent(encoded_account_identifier: str, currency_code: str, amount: int) -> str: """ Encode account identifier string(encoded), currency code and amount into Diem intent identifier (https://dip.diem.com/dip-5/) """ return "diem://%s?c=%s&am=%d" % (encoded_account_identifier, currency_cod...
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def get_characteristic(input: str | list[str]) -> str: """Return the unique, sorted characters in the string.""" return "".join(sorted(set(input)))
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import math def cos(theNumber): """Returns math.cos(theNumber).""" return math.cos(theNumber)
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def trim_all_columns(df): """ Trim whitespace from ends of each value across all series in dataframe """ trim_strings = lambda x: x.strip() if isinstance(x, str) else x return df.applymap(trim_strings)
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def parametrized(decorator): """ Helper meta-decorator that allows us to provide parameters to a decorator. :param decorator: The decorator that should accept parameters. """ def inner(*args, **kwargs): def g(f): return decorator(f, *args, **kwargs) return g return ...
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def tiddlytag(tg): """Format the tags for tiddlywiki5; when the tag includes white space, it is surrounded by '[[' ']]'. :param str tg: A tag. :return: Decorated tag. """ if ' ' in tg: return '[[' + tg + ']]' else: return tg
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def compute_min_max_variances(variances, n_variances=10): """ Compute the indexes with highest and lowest variances """ max_variances = variances.argsort()[-n_variances:][::-1] min_variances = variances.argsort()[:n_variances] return max_variances, min_variances
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import math def CalcSpeedOfSound(T, Rh=50, P=101.325): """Compute the speed of sound T: temperature in degees C Rh: relative humidity in % (default 50) P: pressure in kPa (default 101.325) adapted from: http://resource.npl.co.uk/acoustics/techguides/speedair/ "This calculation ...
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import urllib3 import certifi def post_json(ctx, path, json): """ Make a POST request with a JSON payload to be sent to a NuvIoT endpoint. Parameters ---------- ctx: Context Object that defines how this method should call the server to include authentication. path: Path u...
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def int_to_vlq(val): """ Converts an integer value into a variable length quantity (list). """ vlq = [] for i in range(21, 0, -7): if val >= (1 << i): vlq.append(((val >> i) & 0x7F) | 0x80) vlq.append(val & 0x7F) return vlq
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def reverse_wave(lst): """ Reverse list of lists :param lst: list of lists :return: reversed list """ return lst[::-1]
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import select def more_data(pipe_out): """Check if there is more data left on the pipe :param pipe_out: The os pipe_out :rtype: bool """ r, _, _ = select.select([pipe_out], [], [], 0) return bool(r)
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def overflow_format(num, overflow): """ Returns string of the given integer. If the integer is large than given overflow, '{overflow}+' is returned :param num: int :param overflow: int :return: str """ if not isinstance(num, int): raise ValueError('Input argument "num" should be int...
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import urllib.request as ur def uniprot2seq(ProteinID): """Get protein sequence from Uniprot ID Parameters ---------- ProteinID : str Uniprot ID Returns ------- str Amino acid sequence of input uniprot ID """ ID = str(ProteinID) localfile = ur.urlopen('http://www.uniprot.org/uniprot/' + ID + ...
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from typing import Any def _get_log_name(var: Any) -> str: """Return var.__name__ if available, 'this object' otherwise.""" try: return str(var.__name__) except AttributeError: return 'this object'
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from typing import Sequence def format_hex(in_bytes: bytes) -> Sequence[str]: """ format an input sequence of bytes into a ordered form with lines of 8 hex-formatted bytes prefixed by the address of the first byte in the line. :param in_bytes: the bytes to format :return: a list of formatted line...
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def camel_to_snake(word: str, depublicize: bool = False): """Convert came case to snake case.""" word = "".join(["_" + i.lower() if i.isupper() else i for i in word]) if not depublicize: word = word.lstrip("_") return word
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def reverse(s: str) -> str: """Reverses the string provided. Example: "Abcd" returns "dcbA". """ return s[::-1]
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def get_threshold_from_DESC(desc_file): """ Parses a family DESC file and returns the gathering threshold desc_file: The path to a valid Rfam family DESC file return: A string which is the corresponding gathering threshold """ threshold = 0 desc_fp = open(desc_file, 'r') for lin...
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def downcase(val: str) -> str: """Make all characters in a string lower case.""" return val.lower()
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import itertools def take(iterable, n): """Return first n items of the iterable as a list.""" return list(itertools.islice(iterable, n))
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from datetime import datetime def data_schema(key, value, url, url_certificado): """ Final data schema input: key: string value: string url: string url_certificado: string return: dict """ return { "key": key, "value": value, "ur...
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def _is_number(val): """ Determine if the value is a number :param val: :return: """ if isinstance(val, list): for v in val: if not _is_number(v): return False return True return isinstance(val, int) or isinstance(val, float)
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def binary_search_iterative(array, target): """ Search target element in the given array by iterative binary search - Worst-case space complexity: O(1) - Worst-case performance: O(log n) :param array: given array :type array: list :param target: target element to search :type target: A...
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def _make_headermap_input_file(namespace, hdrs, flatten_headers): """Create a string representing the mappings from headers to their namespaced include versions. The format is virtual_header_path|real_header_path Note the separator is a pipe character. :param namespace: 'foo' in #include <foo/bar...
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import base64 def file_to_attachment(filename, filehandler=None): """ Convert a file to attachment """ if filehandler: return {'_name': filename, 'content': base64.b64encode(filehandler.read()) } with open(filename, 'rb') as _file: return {'_name': filename,...
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def var_shape(tensor): """Get TensorFlow Tensor shape. Parameters ---------- tensor : tf.Tensor the input tensor Returns ------- list of int the shape """ out = tensor.get_shape().as_list() assert all(isinstance(a, int) for a in out), \ "shape function a...
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def _get_shape_as_list(tensor): """Replaces None with -1 in the tensor shape list representation.""" shape = tensor.get_shape().as_list() for i, v in enumerate(shape): if v is None: shape[i] = -1 return shape
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def convert_extension(filename, extensions=('yaml', 'yml',)): """ Convert YeT extension in filename to .tex :param filename: string of file name. validity not checked. :param extensions: tuple of extensions (without dot) to treat as YeT """ # change YAML extension to .tex if '.' in filename...
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def handle_aligns(aligns): """Converts comma delimited string of alignments to tuple Arguments: aligns: comma delimited string of 'l', 'r', 'c' or empty string Returns: aligns_tuple: tuple of alignments or None """ if not aligns: aligns_tuple = None else: aligns_...
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import re def get_rx(regex, body): """ Return first result of regular expression 'regex' in 'body' """ results = re.compile(regex).findall(body) if not results: return False return results[0]
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import time def song_to_starred_time_struct(song): """ Take a song, return the starred date in the form of a time module 9-tuple. """ try: return time.strptime(song.get('starred', ''), '%Y-%m-%dT%H:%M:%S.%fZ') except ValueError: return time.gmtime(0)
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import re def match_date(date): """Check if a string is a valid date Args: date(str) Returns: bool """ date_pattern = re.compile("^(19|20)\d\d[- /.](0[1-9]|1[012])[- /.](0[1-9]|[12][0-9]|3[01])") if re.match(date_pattern, date): return True return False
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def line_indices(lines, tag): """ :param lines: Must be a list of strings representing each line :param tag: is the tag to find in the list of lines :return: the indices of the lines with that tag """ return [l for l in range(len(lines)) if tag in lines[l]]
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def _lstrip(text: str, chars: str) -> str: """ Given a string `text`, remove the leading `chars` if and only if they appear as the leading characters """ if chars and text[:len(chars)] == chars: text = text[len(chars):] return text
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def safe_index(alist, elem): """ Return index of element e in list l. If e is not present, return the last index """ try: return alist.index(elem) except ValueError: return len(alist) - 1
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def get_mitigations(df, threshold=0.5): """Return number of impact mitigations performed.""" return df[(df['y_prob_1'] > threshold)] \ .groupby(level=['date_time', 'id_blade']) \ .size() \ .size
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import curses def hline_after(prev_win, xstart=0): """ Create a new window on the next row after prev_win. The new window will be for a horizontal line and hence only needs to be 1 line high. To underline the previous window it is 2 cols wider than the pre_win :param prev_win: curses.win :...
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import re def get_largest_blocks(blocking_rule, df, spark, limit=5): """ For a given blocking rule, find out which will be the largest blocks """ parts = re.split(" |=", blocking_rule) parts = [p for p in parts if "l." in p] parts = [p.replace("l.", "") for p in parts] col_expr = ", ".jo...
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def problem_3_6(stack): """ Write a program to sort a stack in ascending order. You should not make any assumptions about how the stack is implemented. The following are the only functions that should be used to write this program: push | pop | peek | isEmpty. Solution #1: use one more stack. ...
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def get_stride_from_chips(chips): """ Stitch up chips into a full array Parameters ---------- chips : dict dictionary of partition indices mapping to actual chips Returns ---------- stride: int number of pixels skipped over to generate adjacent chips """ keys = ...
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def class_as_descriptor(name): """Return the JVM descriptor for the class `name`""" if not name.endswith(';'): return 'L' + name + ';' else: return name
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def find_opposite_axes(axes, ndim): """ Based on the total number of dimensions function finds all axes that are missed in the specified list ``axes``. Parameters ---------- axes : list or tuple Already known axes. ndim : int Total number of dimensions. Returns ...
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def comma_code(a_list): """ Turns a list into a string of elements separated by commas :param a_list: a list of strings :return: a string separated by commas """ a_list[-1] = 'and ' + a_list[-1] stringified = ", ".join(a_list) return stringified
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def feature_to_geojson(json_data: dict) -> dict: """ Converts feature into a GeoJSON, returns output From:: >>> {'geometry': {'type': 'Point', 'coordinates': [30.003755665554, 30.985948744314]}, ... 'id':'506566177256016'} To:: >>> {'type': 'FeatureCollection', 'features': [{...
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def filter_example(ex, use_src_len=True, use_mt_len=True, use_pe_len=True, min_src_len=1, max_src_len=float('inf'), min_mt_len=1, max_mt_len=float("inf"), min_pe_len=1, max_pe_len=float("inf")): """Return whether an example is an acceptable...
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def is_py_file(file_name: str) -> bool: """ Return whether a file is a python file. """ return file_name.endswith(".py")
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def join_string(part1, part2, concatenation_string = 'AND', seperator=' '): """ Join two strings together using a concatenation string Handles the case where either part1 or part2 are an empty string @param part1: First string @param part2: Second string @param concatenation_string: String use...
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def merge_two_dicts(dict_x, dict_y): """ Given two dicts, merge them into a new dict. Uses a shallow copy. """ new_dict = dict_x.copy() new_dict.update(dict_y) return new_dict
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def swap_dict(old_dict): """Returns a new dictionary in wich the keys are all the values of the old dictionary and the values are lists of keys that had that value. Example: d = { 'a':['c','v','b'], 's':['c','v','d']} swap_dict(d) -> {'c': ['a', 's'], 'b': ['a'], 'd': ['s'], 'v': ['a', 's']} ...
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def brzycki(w, r): """ Realistic for low reps. Conservative for high reps. 1RM estimate based on weight and reps of a set. """ return w * 36 / (37 - r)
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def _get_author_weight(authors_in_paper): """ Method that returns the weight of a single author in a paper""" #I check if there is at least 1 author otherwise the weight is 0 if len(authors_in_paper) > 0: return 1./len(authors_in_paper) else: return 0
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def last_but_one_word(string): """Function to get the last but one word of a sentence in lower case""" try: return (string.rsplit(None, 2)[-2]).lower() except: return None
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def summation(numbers): """ Summation of a list of numbers Args: numbers: int, float Returns: sum of numbers, int, float """ return sum(numbers)
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def sorted_squares_brute_force(nums: list[int]) -> list[int]: """Returns a (non-decreasing) sorted array of the squares of each element in nums Naively squares each element and sorts the array Complexity: n = len(nums) Time: O(nlogn) Space: O(n) (for the sorted array) N...
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import torch def brownian_motion_sample(num_steps, num_samples, dim, t, init_point, model): """Returns the points of a discretized Brownian motion (BM) on a manifold (a.k.a. latent space). params: num_steps: int - the number of time steps for which the BM will run ...
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def fibonacci(end=None, start=0, inclusive=True, length=None): """This function returns a Fibonacci series list: - either upto an end number - or with a length argument which defines the length of the list start number is default to 0 and optinal to change for both. All items in the returnin...
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def afficher_graine(graine): """ Formate un texte avec la graine donnée ou ne donner rien si cette dernière est None :param graine: La graine à afficher :return: Un texte sous la forme ". Graine aléatoire: <graine>" si seed différent de None sinon "" """ if graine is None: return "" ...
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def invert_items(df): """This function inverts the scale of some items of LoC so that for all items higher numbers reflect greater feelings of control.""" inverted_items = [ "LOC_ACHIEVED_DESERVE", "LOC_LUCK", "LOC_OTHERS", "LOC_DOUBT", "LOC_POSSIBILITIES", "L...
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def _all_close(values, other_value, threshold): """Return true if all values are within threshold distance of other_value.""" for value in values: if abs(value - other_value) > threshold: return False return True
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def key_value(tree): """Returns the key value of given tree""" return tree[1]
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import re def unmangle_columns(columns: list[str]) -> list[str]: """Utility function to convert "X.1...X.N" into "X...X", reversing the normal column name mangle ref: https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html :param columns: Original mangled column names :type columns: list[st...
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def is_id_selector(selector): """ A basic method to determine whether a ID selector or not """ if ":id" in selector: return True return False
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from datetime import datetime def convert_to_milliseconds(date_time: datetime) -> int: """takes datetime and returns milliseconds""" return round(date_time.timestamp() * 1000)
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from typing import List import warnings def get_expression_blocks(expression: str) -> List[str]: """Split expression in blocks. Args: expression (str): band math/combination expression. Returns: list: expression blocks (str). Examples: >>> parse_expression("b1/b2,b2+b1") ...
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def has_flag(flag, content): """Determines if a command's content contains a flag. Arguments: flag -- the flag for which to search content -- the content of the command """ return "-" + flag in content.split()
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def greeting(name: str = 'World') -> str: """Returns greeting message.""" return f'Hello {name}'
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def extrapolate_wind_speed(height_in, height_out, wind_speed): """ :param height_in: m, Height data was recorded at :param height_out: m, Height desired :param wind_speed: m/s, Array of wind speeds recorded at height_in :return: """ shear_exponent = .144444 extrapolated_wind_speed = [x ...
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def get_report(analytics, query): """Queries the Analytics Reporting API V4. Args: analytics: An authorized Analytics Reporting API V4 service object. Returns: The Analytics Reporting API V4 response. """ return analytics.reports().batchGet(body=query).execute()
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def deprel(args, premise): """Return dependency relation to head.""" return args[0].deprel
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def getCisDist(df): """Calcualtes percentage of reads at certain distance""" result = {} for dist in [ "cis_1kb+", "cis_2kb+", "cis_4kb+", "cis_10kb+", "cis_20kb+", "cis_40kb+", ]: result[dist] = ( df.loc[df[0] == dist, 1].values[0] ...
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