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def rename_bands(img, in_band_names, out_band_names): """Renames image bands. Args: img (object): The image to be renamed. in_band_names (list): The list of of input band names. out_band_names (list): The list of output band names. Returns: object: The output image with the...
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def _decode_message(output: bytes, encoding: str) -> str: """Converts bytes to string, stripping white spaces.""" return output.decode(encoding).strip()
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def lookup_field(line, column): """ Lookup the value of a given (numbered) column in a given Line Returns None if either the column or the line is None """ # During merge, it is not guaranteed that each input file to the # merge has a matching line... if not line: return None ...
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import csv def load_precursors(path): """Loads precursors from file containing SMILES. Precursors must be in a `.csv` file, with the aldehyde in column 1 and the amine in column 2. Args: path: Path to file containing SMILES. Returns: List[List[str]]: List of lists containing SMI...
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def vdot(v1, v2): """ Returns the dot product of v1 and v2 """ return (v1 * v2).sum()
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def load_auth_settings(config): """ Load all the auth configuration settings into a dict auth configuration settings contain an auth_ prefix. Args: config (dict): the global config Returns: (dict): All the auth settings """ auth_config = {} for key, value in config.items()...
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def filter_with_values(df, variable, values): """ Filter dataset for rows containing a specific value in a variable column. Parameters ---------- df : pandas DataFrame dataframe to be filtered variable : str name of variable to be used for filtering values : int/float or...
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from typing import Dict from typing import Set from typing import Any def axis_keys(D: Dict, axis: int) -> Set[Any]: """Return set of keys at given axis. Parameters ------------------------------- D: Dict Dictionary to determine keys of. Axis:int Depth of keys. Returns --...
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import inspect def is_overridden(method_name, obj, parent=None) -> bool: """Check if `method_name` from parent is overridden in `obj`. Args: method_name (str): Name of the method. obj: Instance or class that potentially overrode the method. parent: parent class with which to compare. ...
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from typing import Dict from typing import List def _flatten_dictionary(source_dict: Dict, target_dict: Dict, key: str, flatten_arrays: bool) -> Dict: """Private function to flatten a dictionary representing a JSON Args: source_dict: A Python dictionary containing a JSON representation target...
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from typing import Optional def format_str(value: Optional[str], default_value: str = '?') -> str: """Format an output string. Simply puts single quotes around the value if it contains a space character. If the given argument is none the default value is returned Parameters ---------- value: ...
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def merge_dicts(dict1,dict2): """merge two dictionaries if they have the same keys""" for key, value in dict2.items(): dict1.setdefault(key,[]).extend(value) return dict1
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def combine_dicts(dict1, dict2, which_values_are_key=1): """ Suppose you have two dicts with a common key that you want to 'factor out' to form a new dict where one of the parent's values is the new key and the values are lists of the other dict's values. There is probably a concise name for this op...
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def combinedJunctionDist(dist_0, dist_1): """Computes the combined genomic distance of two splice junction ends from the closest annotated junctions. In essence, it is finding the size indel that could have created the discrepancy between the reference and transcript junctions. Examples ('|' ...
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def function_wrapper(func, arg, kwarg, x): """ Wrapper function for Python functions. To be used with partial: `obj = partial(function_wrapper, func, arg, kwarg)` This allows then calling obj with only the non-masked parameters: `fx = obj(x)` which translates to: `fx = ...
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import networkx as nx def forest_str(graph, use_labels=True, sources=None, write=None): """ Creates a nice utf8 representation of a directed forest Parameters ---------- graph : nx.DiGraph | nx.Graph Graph to represent (must be a tree, forest, or the empty graph) use_labels : bool ...
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import json def read_config(filename): """Read the JSON configuration file. Parameters ---------- filename : str Path of the configuration file Returns ------- dict Dataset glossary """ with open(filename) as fobj: return json.load(fobj)
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def rotate_tuple(t, k): """ >>> rotate_tuple((1, 2, 3), 0) (1, 2, 3) >>> rotate_tuple((1, 2, 3), 2) (3, 1, 2) """ return t[k:] + t[0:k]
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def count_subset_sum_dp(arr, total): """Count subsets given sum by bottom-up dynamic programming. Time complexity: O(nm). Space complexity: O(nm). """ n = len(arr) - 1 T = [[0] * (total + 1) for _ in range(n + 1)] for a in range(n + 1): T[a][0] = 1 for a in range(n + 1): ...
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def get_neighbor(r, c): """Return the neighbors assuming no diag movement""" return [(r + 1, c), (r - 1, c), (r, c + 1), (r, c - 1)]
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import math def _compute_dcg(s, k): """ A function to compute dcg :param s: sequence of ground truth in the rank order to use for calculating dcg :param k: top k at which to evaluate ndcg :return: dcg for this ordering of ground truth :rtype: numeric """ dcg = 0.0 for i in range(mi...
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from pathlib import Path def getHtml(fileName): """ HTML ファイルを読み込んで中身を返す Parameters ---------- fileName : str 読み込むファイル名 Returns ------- html : str HTML ソース文字列 """ file = Path(Path.cwd()).joinpath('html').joinpath(fileName) html = file.read_text(encoding = 'utf-8') return html
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import torch def one_hot(targets, num_classes, dtype=torch.float32, device=None): """ Encode the targets (an tensor of integers representing a class) as one hot encoding. Support target as N-dimensional data (e.g., 3D segmentation map). Equivalent to torch.nn.functional.one_hot for backward comp...
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def pretty_date(dt): """ Formats a datetime instance, which can be none, in the local TZ """ if not dt: return "<unk date>" return dt.astimezone().strftime("%Y-%m-%d %I:%M%p %Z")
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def slice_data(data, info, split): """Slice data according to the instances belonging to each split.""" if split is None: return data elif split == 'train': return data[:info['train_len']] elif split == 'val': train_n = info['train_len'] val_n = train_n + info['val_len'] ...
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def get_row_col(mouse_x, mouse_y): """ Converts an x, y screen position into a row, col value. """ # Note: the top row is row=0 (bottom row=2), left col is col=0 (right col=2) spacing_x = 86 + 8 spacing_y = 98 + 5 top_y = 50 left_x = 50 return (mouse_y - top_y) // spacing_y, (mouse_x - left_...
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def _get_bc_count(sample_name, bc_count, sample_run): """Retrieve barcode count for a sample :param sample_name: sample name :param bc_count: parsed option passed to application :param sample_run: sample run object :returns: barcode count or None""" if isinstance(bc_count, dict): if sa...
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def groupby_asdf(df, grouped, idx=0): """ Returns pandas DataFrame as a subset from df with given index idx in the grouped Parameters ---------- df: pandas DataFrame grouped: pandas GroupBy object based on df idx: group index in grouped Returns ------- pandas DataFrame as a...
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import re def parse(str_input): """ Parse a string in CEF format and return a dict with the header values and the extension data. """ # Create the empty dict we'll return later values = dict() # This regex separates the string into the CEF header and the extension # data. Once we do...
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import importlib def get_imported_module(module_name): """ import module and return imported module """ return importlib.import_module(module_name)
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def _are_values_different(old_value, new_value): """Checks if the two values are different whilst treating a blank string the same as a None.""" old_value = old_value if old_value != '' else None new_value = new_value if new_value != '' else None return old_value != new_value
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def levenshtein(s: str, t: str) -> int: """Levenshtein distance algorithm, implementation by Sten Helmquist. Copied from https://davejingtian.org/2015/05/02/python-levenshtein-distance-choose-python-package-wisely/""" # degenerate cases if s == t: return 0 if len(s) == 0: return len(...
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def test_lyrics(lyrics): """ Test lyrics downloaded to detect license restrinction string: 'We are not in a position to display these lyrics due to licensing restrictions. Sorry for the inconvinience.' Also test lyrics by looking for multiple new line characters. Returns booleans accordingly """ if no...
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import torch def _transform_sample( data: torch.Tensor, normalize: bool, transpose: bool ) -> torch.Tensor: """ Optionally normalize and tranpose a torch.Tensor :param data: Input sample :type data: torch.Tensor :param normalize: To normalize sample or not :type normalize: bool...
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from typing import Dict def _init_stats() -> Dict: """Create a statistics data structure. :return: A new statistics data structure. """ return { 'count_scrubbed': 0, 'count_not_found': 0, 'count_partial': 0, }
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def backwards(page_or_revision, data): """Map from three-option tag_filtering to boolean and_filtering. If tag_filtering was "all" (include pages that match all topic tags), set and_filtering to True. Otherwise, set it to False. The backwards field state doesn't support the tag_filtering "none" case. ...
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def buildLine(mesh, matrix, vertex_colors, uv_textures, face_index, idx, verti): """ Returns a list containing a vertex (3 tuple of floats), normal (3 tuple of floats) vertex color (3 tuple of floats) and uv (2 tuple of floats). """ line_data = [] # Append vertex line_data.append((matrix * mesh.vertices...
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def validate_handler_overrides(process_class, handler_overrides, ctx): # pylint: disable=inconsistent-return-statements,unused-argument """Validator for the `handler_overrides` input port of the `BaseRestartWorkChain. The `handler_overrides` should be a dictionary where keys are strings that are the name of a...
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from typing import List from typing import Optional def find_object(objects: List[object], **filters) -> Optional[object]: """ Pass a list of objects and filters as kwargs to get first occurence record. If no filters passed return first object in the list Args: objects: list of objects to ite...
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from functools import reduce def product(arr): """Return the product of a sequence of elements of <arr>.""" return reduce(lambda a,b: a*b, arr)
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def get_frequencies(column): """ The purpose of this function is to get the count for how many times a value appeaars in a given column. Attributes: - column(list): a list of values in a column which will be checked for values and frequencies. Returns: - values, counts(tuple of lists): a tup...
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def count_refs(pileup_base_string): """ Given a pileup string from samtools mpileup output, count the number of reads that support the reference allele in that position. """ ref_count = 0 i = 0 while i < len(pileup_base_string): if pileup_base_string[i] in [".", ","]: ...
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def get_linear_lattice_interpolation_fn(lattice_sizes, monotonicities, output_min, output_max): """Returns function which does lattice interpolation. Returned function matches lattice_layer.LinearInitializer with corresponding parameters. Args: lattice_sizes: list o...
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def s3_key_to_link(region, bucket, key): """generates public link of s3 object""" return "https://s3-{0}.amazonaws.com/{1}/{2}".format( region, bucket, key)
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def sign_non_zero(x): """ returns the sign of the input variable as 1 or -1 arbitrarily sign_non_zero(0) = 1 """ return 2 * (x >= 0) - 1
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def activedb(dbdata, active): """Reduce database to active entries Parameters ---------- dbdata : List[Dict[]] List of database entries active : List List of stems in blacklist directory Returns ------- List[Dict[active entries database schema]] """ out = [e fo...
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import random def take_sample(population, k): """Returns a list of k randomly chosen elements from population.""" result, n, k = [], k, min(k, len(population)) result = random.sample(population, k) while len(result) < n: result += random.sample(population, min(k, n - len(result))) return r...
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def get_interpolation_range(sidelen, n, i): """ Finds the range of indices for interpolation in Robinson Projection Input sidelen: the number of items on both sides of i, including i in the left n: the total number of items i: the index of the largest item smaller than t...
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def format_as_code_block(text_to_wrap: str) -> str: """ Wrap the text in a JIRA code block. Args: text_to_wrap: The text to wrap. Returns: A JIRA formatted code block. """ return "".join(["{code:java}", "{}".format(text_to_wrap), "{code}"])
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def fixupResultForD978(resultStr, output_d978fa): """ For programs that require the strict output format of dump978 or dump978-fa, this routine will edit the result string and return a new string with the desired output. All strings contain the message itself. The 'rs=' reed-solomon errors are printed on...
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import json def insert_organization(cursor, info): """organization情報登録 Args: cursor (mysql.connector.cursor): カーソル info (Dict)): organization情報のJson形式 Returns: int: organization_id """ # insert実行 cursor.execute('INSERT INTO organization ( organization_name, a...
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def isRXCY(s): """ >>> isRXCY('RRCC233') False >>> isRXCY('R22C22') True """ try: idx0 = s.index('R') idx1 = s.index('C') except: return False if idx0 != -1 and idx1 != -1: return any([str(i) in s[idx0+1:idx1] for i in range(10)]) return False
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def apply_mapping(mask, mapping): """Applies the mapping to obtain a frequency aligned mask. Args: mask: Permuted mask with shape (K, F, ...). mapping: Reverse mapping with shape (K, F). >>> np.random.seed(0) >>> K, F, T = 3, 5, 6 >>> reference_mask = np.zeros((K, F, T), dtype=np.i...
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def values_from_syscalls(line): """ Utility method to obtain the system call count values from the relative line in the final analysis output text file. :param line: string from log file :return: int corresponding to system call frequency """ return int(line.strip().split('\t')[1])
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def _calculate_total_dispatchable_mw(case): """ Calculates the total available MW for dispatch. This is equal to the total remaining capacity of all in-service, non-swing generators. :param case: The :class:`Case` that is synchronized with the current loaded case. :type case: :class:`Case` :retu...
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def _check_shape_contain_zero(shp): """Check whether shape contains 0""" if isinstance(shp, int): return shp == 0 if isinstance(shp, (list, tuple)): for s in shp: if s == 0: return True return False
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import math def ray_param(v_int: float, theta: float) -> float: """ Calculates the ray parameter P. :param v_int: Interval velocity :param theta: Angle of incidence (deg) :return: p: Ray parameter """ # Cast inputs to floats theta = float(theta) v = float(v_int) p = ...
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def get_searchpath(golib, mode): """Returns the search path for the given mode""" # The attribute name must match the one assigned in emit_library_actions return getattr(golib, mode+"_searchpath")
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def intorNone(x): """Return int(x) if x is not None.""" return int(x) if x is not None else x
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def tagseq_to_entityseq(tags: list) -> list: """ Convert tags format: [ "B-LOC", "I-LOC", "O", B-PER"] -> [(0, 2, "LOC"), (3, 4, "PER")] """ entity_seq = [] tag_name = "" start, end = 0, 0 for index, tag in enumerate(tags): if tag.startswith("B-"): if tag_name != "": ...
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from typing import Counter def filter_counts(list_of_elements, minimum): """ Filter out elements in a list that are not observed a minimum of times :param list_of_elements: a list of for example positions :param minimum: the miminum number of times an value must be observed :type list_of_element...
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def create_burger(conn, burger): """ Create a new burger within the table :param conn: :param burger: :return burger_id: """ sql_cmd = ''' INSERT INTO burgers(name, availability) VALUES(?,?) ''' cursor = conn.cursor() cursor.execute(sql_cmd, burger) ...
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def shift_by(l, n): """Convenience function to shift a list by a number of steps. If ``n`` is positive it shifts to the left. Args: l (list): list to be shifted n (int): size of the shift """ return l[n:] + l[:n]
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def get_data_mod(data_type, data_name): """Get the pythondata-{}-{} module or raise a useful error message.""" imp = "import pythondata_{}_{} as dm".format(data_type, data_name) try: l = {} exec(imp, {}, l) dm = l['dm'] return dm except ImportError as e: raise Imp...
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def read_clustering(filename): """ Read the clustering in :param filename: The cluster file to read :returns: A list of lists of active site numbers """ clusters = [] cluster = [] with open(filename, 'r') as fp: for line in fp: line = line.strip() ...
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def huffman_decoding(encoded_str, root): """Huffman decoding algorithm Args: sentence: encoded string root: root Node for Huffman Binary Tree Returns: decode_str: string decoded from the sequence """ decoded = [] node = root for e in encoded_str: if e ==...
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import pathlib from typing import Literal import hashlib def _check_file_ready(file: pathlib.Path, md5_checksum: str, open_mode: Literal["r", "rb"]) -> bool: """Checks if the file is ready to use (exists and has the right MD5 checksum) Args: file: path to the file one wants to check md5_check...
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import logging def validateHeartRate(input, patientDict): """ Validates patient hr input, checking that fields are proper and exist :returns: -1 if not successful, 1 if successful """ if(not isinstance(input, type({}))): logging.error("input not type dict") return -1 if "patie...
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def types_args_one_port(port, formatter): """ Extract from a port: 1. a list of "type arg"s 2. a list of args :param port: :param formatter: a string formatter with {0} and/or {1} where {0} is the port name, and {2} is an arg ID. :return: """ types_args = [] args = [] for i ...
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def double_center(mat): """Double center a 2d array. Args: mat (ndarray): 2d numpy array Returns: mat (ndarray): double-centered version of input """ if len(mat.shape) != 2: raise ValueError("Array should be 2d") # keepdims ensures that row/column means are not incor...
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def _cross2d(x, y): """Cross product in 2D.""" return x[:, :, 0] * y[:, :, 1] - x[:, :, 1] * y[:, :, 0]
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def get_file_subset(path_gen, max_number): """ Get a subset of file from a generator :param path_gen: pathlib.Path.glob :param max_number: int :return: list of pathlib.Path objects """ filelist = [] while len(filelist) < max_number: try: next_path = next(path_gen) ...
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from typing import Callable from typing import Tuple from typing import Any def recurse_eval(path: str, data: dict, fn: Callable) -> Tuple[str, Any]: """ Given a `path` such as `a.b.0.split(' ')` this function traverses the `data` dictionary using the path, stopping whenever a key cannot be found in t...
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from typing import List from pathlib import Path def do_single_check(command: str, relevant_files: List[Path], command_check_mapping) -> bool: """Do a single check requested by a command.""" check = dict(command_check_mapping)[command] if command == 'format': success = check(re...
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def format_oauth(oauth_token: str) -> str: """ Format an oauth token for IRC auth. """ return oauth_token if oauth_token.startswith('oauth:') else f'oauth:{oauth_token}'
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def setup_none(lvl): """Set up default, empty smoother.""" def smoother(A, x, b): pass return smoother
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import unicodedata def normalize(tag): """Normalize a single tag: remove non valid chars, lower case all.""" tag_stripped = tag.strip() value = unicodedata.normalize("NFKD", tag_stripped.lower()) value = value.encode('ascii', 'ignore').decode('utf-8') return value
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def formula_has_multi_any_bfunc(formula, bfunc_set): """Returns true if the total times any of the provided basis functions appear in the formula is more than once per per normalization. :formula: str :bfunc_set: list of str :returns: bool """ equivalents=formula.count("+")+1 insta...
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def groups_balanced(arg): """ Match [, {, and ( for balance >>> groups_balanced("(a) and (b)") True >>> groups_balanced("((a) and (b))") True >>> groups_balanced("((a) and (b)") False >>> groups_balanced(" [a] and [b] ") True >>> groups_balanced("((a) and [(b)])") True...
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from io import StringIO import traceback def error2str(e): """returns the formatted stacktrace of the exception `e`. :param BaseException e: an exception to format into str :rtype: str """ out = StringIO() traceback.print_exception(None, e, e.__traceback__, file=out) out.seek(0) retur...
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def get_azfs_url(storage_account, container, blob=''): """Returns the url in the form of https://account.blob.core.windows.net/container/blob-name """ return 'https://' + storage_account + '.blob.core.windows.net/' + \ container + '/' + blob
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import re def regex_strip(text, remove=None): """ Takes a string and performs the same operation as str.strip() This function defaults to removing whitespace, but if the optional remove argument is supplied, the remove value is removed from the text :param str text: source string :param str r...
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def task_catalog_get(task, task_id, is_consumer): """ Get an object from the task catalog @param task: The Celery Task @param task_id: The Celery Task ID @param is_consumer: Boolean @return: scope """ catalog = getattr(task, '_instana_scopes', None) if catalog is None: retur...
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import ipaddress def ip_address(value): """Validate that the value is an IP address""" value = str(value) ipaddress.ip_address(value) return value
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def read_in_list(list_in): """ Convert list file into list object """ file_list = [line.rstrip('\n') for line in open(list_in)] return file_list
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def categorize(df): """ Category Combinations Labels ------- - M = majority winner - P = plurality winner - C = condorcet winner - U = utility winner Categories ---------- - MU = Has majority utility winner - M = Has majority winner that is not utility winner....
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from typing import Sequence def non_english_resource_types() -> Sequence[str]: """All the non-English resource types.""" return ["ulb", "reg", "tn", "tq", "tw"]
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def isinstance_or_subclass(inst, cls): """ Utility for safely checking isinstance and issubclass. """ if isinstance(inst, cls): return True try: if issubclass(inst, cls): return True except TypeError: pass return False
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def rescale_value(value, current_limits, new_limits): """ Given a value and the limits, rescales the value to the new limits input: value : float variable containing the value current_limits : a tuple containing the lower and upper limits of the valu...
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def power(V, R): """Electrical power Watts. V in volts, R in ohms""" return V**2 / R
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def is_valid_kubernetes_resource_name(name: str) -> bool: """ Returns a truthy value indicating whether name meets the kubernetes naming constraints, as outlined in https://kubernetes.io/docs/concepts/overview/working-with-objects/names/#names This implementation is based on https://tools.ietf.org/h...
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def get_windows(src): """ Return a list of all windows composing the entire raster """ return [win for _, win in src.block_windows(1)]
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from typing import List def flatten_list( x: List[list] ) -> list: """ Transform a list of lists into a single flat list. Args: x: A nested list Returns: A flat list """ return [v for sublist in x for v in sublist]
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def read_from_add_translation_dict(address, tdict): """map an original address to x, y coords using the dictionary of unique addresses""" x, y = tdict[address] return x, y
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import colorsys def scale_lightness(rgb, scale_l): """ Scales lightness of color `rgb` https://stackoverflow.com/a/60562502/3413239 """ # convert rgb to hls h, l, s = colorsys.rgb_to_hls(*rgb) # manipulate h, l, s values and return as rgb return colorsys.hls_to_rgb(h, min(1, l * scale_...
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def simple_tokenizer(text: str) -> list[list[str]]: """ Given whitespace/newline tokenized text, return the list of sentences (where each sentence is made of tokens) using whitespaces and newlines """ doc: list[list[str]] = [] if text: for s in text.split("\n"): doc.appe...
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def _name_as_key(name): """Uppercase, stripped, no repeated interior whitespace.""" name = name.upper().strip() while ' ' in name: name = name.replace(' ', ' ') return name
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def mean(items): """Returns the mean of the given items. Example:: >>> mean([5, 3, 7, 1, 9]) 5.0 """ if not items: return 0.0 return sum(items) / len(items)
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from typing import Any def is_empty(data: Any) -> bool: """Checks if argument is empty. Args: data (Any): To check if empty Returns: bool: Returns bool indicating if empty """ if data is None or data == '' or data == 'null': return True return False
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def from_augmented(aug_B): """Convert the augmented matrix back into transformation matrix + tranlsation vector.""" return aug_B[:-1, :-1], aug_B[-1, :-1]
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