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def get_list_of_allowed_websites(): """Fetches list of all the websites the application is allowed to access.""" with open("../tools/tinyproxy/filter", "r") as filter_file: websites = filter_file.read().split("\n") return str(websites[:-1])
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def none_wrapper(value, default=""): """ Pure laziness! Sometimes this ends up being nice syntactic sugar for code readability. """ return value if value is not None else default
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import re def GetBIOSAttrDefaultValues(attr_val_table_data): """ From pldmtool GetBIOSTable of type AttributeValueTable get the dict of attribute handle and its default attribute values. Description of argument(s): attr_val_table_data pldmtool output from GetBIOSTable table type AttributeVal...
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import torch def sqdist(X): """Euclidean distance of coordinates. :param X: sample-coordinates matrix. :type X: torch.FloatTensor :return: Euclidean distance. :rtype: torch.FloatTensor """ x = (X ** 2).sum(dim=1, keepdim=True) sqd = x - 2 * X @ X.t() + x.t() ind = torch.arange(X.s...
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import logging def normalize_bridge_id(bridge_id: str): """Normalize a bridge identifier.""" bridge_id = bridge_id.lower() # zeroconf: properties['id'], field contains semicolons after each 2 char if len(bridge_id) == 17 and bridge_id.count(":") == 5: return bridge_id.replace(":", "") # ...
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import numpy as np def remove_nones(l, return_np_array=False): """ This function removes "None" values from the given list. Importantly, compared to other single-function tests, this uses "is" and avoids strange behavior with data frames, lists of bools, etc. Optionally, the filtered list...
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import itertools def repeatcall(func, *args): """Repeatedly call func(*args) and yield the result. Useful when func(*args) returns different results, esp. randomly. """ return itertools.starmap(func, itertools.repeat(args))
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import json def parse_read_count_tuples(tuple_string): """Parse the string value of one of the CountsOf* ExpansionHunter output fields (CountsOfSpanningReads, CountsOfFlankingReads, or CountsOfInrepeatReads). For example: "CountsOfSpanningReads": "(6, 1), (17, 10), (19, 16)" Return: a list of 2-...
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from io import StringIO def _join(args): """ Join the arguments with spaces, except newlines which don't need to be padded. """ result = StringIO() skipSpace = True for arg in args: if skipSpace: skipSpace = False else: result.write(' ') if a...
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def keep_only_digits(input_string: str) -> str: """This function takes as input a string and returns the same string but only containing digits Args: input_string (str): the input string from which we want to remove non-digit characters Returns: output_string (str): the output string that on...
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def create_files_dict(file_name, metadata_content, bitstream_content): """Create dict of files to upload to S3.""" package_files = [ { "file_name": f"{file_name}.json", "file_content": metadata_content, }, { "file_name": f"{file_name}.pdf", ...
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import pathlib import os def get_name_ext(pathname): """from a complete file name return the last part composed of one or more ext""" #ext_list=path.splitext(pathname)[1:] # work only if not more than 1 .ext ext_list=[] for ext in pathlib.Path(pathname).suffixes : ext_list.append( ext.strip(os.extsep) ) return...
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def fake_get_all_cluster_hosts(*args, **kwargs): """ 返回测试用的集群节点信息 """ return [ {"cluster_id": "BCS-K8S-1001", "inner_ip": "127.0.0.1", "status": "normal"}, {"cluster_id": "BCS-K8S-1001", "inner_ip": "127.0.0.16", "status": "normal"}, ]
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import os def get_filename_from_path(path): """ Returns the filename for a full path. """ return os.path.split(path)[1]
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def supra_adjacency_matrix(net,includeCouplings=True): """Returns the supra-adjacency matrix and a list of node-layer pairs. Parameters ---------- includeCoupings : bool If True, the inter-layer edges are included, if False, only intra-layer edges are included. Returns ------- ...
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import argparse def parse_args(): """ Parse command-line arguments.""" parser = argparse.ArgumentParser() parser.add_argument( '-q','--queries', required = True, help='Input list of query names with column header "query".') parser.add_argument( '-f','--fasta', required = True, ...
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from typing import Union from pathlib import Path def expand_wildcards(paths: Union[str, Path]) -> list: """Expand the wildcards that may be present in Paths.""" path = Path(paths).expanduser() parts = path.parts[1:] if path.is_absolute() else path.parts return [f for f in Path(path.root).glob(str(Pat...
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import re import os def get_version(verbose=0): """ Extract version information from source code """ matcher = re.compile('[\t ]*#define[\t ]+OPENQL_VERSION_STRING[\t ]+"(.*)"') with open(os.path.join('..', 'include', 'ql', 'version.h'), 'r') as f: for ln in f: m = matcher.match(ln) ...
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def test_arg_index_attrs() -> None: """Accessing argument index and attributes.""" assert "{0.real}, {0.imag}".format(3 - 5j) == "3.0, -5.0" class Point: """Point with x-y coordinates.""" def __init__(self, x: int, y: int) -> None: self.x = x self.y = y def...
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import torch def validate(model, testloader, criterion): """Validate the model Arguments: model -- The network to validate testloader -- Test data criterion -- Loss function to use """ test_loss = 0 accuracy = 0 for images, targets in testloader: images.resize_...
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def add_integers(*args: int) -> int: """Sum integers. Arguments: *args: One or more integers. Returns: Sum of integers. Raises: TypeError: No argument was passed or a passed argument is not of type `int`. Example: >>> add_integers(3, 4) 7 "...
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def print_dict(data, indent_level=0): """Pretty-print a dict full of key-value metadata pairs""" indent = ' ' * indent_level def _format_key(k): return '{}{}{: <40}{}'.format( indent, '\x1b[36m', k + ':', '\x1b[0m' ) for k, v in sorted(data.items()): if not isinsta...
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def is_valid(s: str) -> bool: """ Time: O(n) Space: O(n) due to the stack we maintain """ stack = [] mapping = {"}": "{", ")": "(", "]": "["} for c in s: if c in mapping: last_elm = stack.pop() if mapping[c] != last_elm: return False el...
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def select_by_year(year, D): """Select year from specification given in dictionary or list of ranges. Examples: >>> spec = {(..., 1990): 'foo', ... 1991: 'bar', ... (1992, 2000): 'foobar', ... (2001, ...): 'blah'} >>> select_by_year(1990, sp...
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import re def md(MD_tag): """ Given MD tag and a sequence, find the number of matched, deletion, and substitution bps Return: 1-level dictionary """ #matchLens = re.sub("\D"," ",MD_tag).split() #replace non-digit chars by blanks #matchLens = map(int, matchLens) #length of the matches before...
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import mmap def matchFilesLine(path, file_name, line, inverted=False): """ This method takes a file system path and a filename and a string to search for, it also takes an option boolean keyword 'inverted', if set it will return True if the string is NOT found. """ file_path = path + '/' + file...
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import hashlib def sqlite_md5(text): """ md5 - Returns the md5 of the text """ if (text!=None): hash = hashlib.md5() hash.update(text.encode("utf-8")) return hash.hexdigest() return None
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def response_error(response, message): """ return a 500: Internal server error message """ if response != message: return "500: Internal server error"
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import random def MERB_config(BIM): """ Rules to identify a HAZUS MERB configuration based on BIM data Parameters ---------- BIM: dictionary Information about the building characteristics. Returns ------- config: str A string that identifies a specific configration wi...
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import torch def hippo_skew_evals(N): """ eigenvalues of (Hippo - Hippo.t()) / 2 (largest imag part first) """ i = torch.arange(N, dtype=torch.float) x = 2*i + 1 Hippo = (x.view(-1,1) * x.view(1,-1)).sqrt().tril(diagonal=-1) # [N N] Skew = (Hippo - Hippo.t()) / 2 ...
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import torch def compute_accuracy(logits, ys_ref, pad): """Compute teacher-forcing accuracy. Args: logits (FloatTensor): `[B, T, vocab]` ys_ref (LongTensor): `[B, T]` pad (int): index for padding Returns: acc (float): teacher-forcing accuracy """ pad_pred = logits...
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import re def bracketify(**kwargs): """ Convert underscores to brackets. """ kw = {} for par in kwargs: m = re.search(r"\_([0-9])\_", par) if m is None: kw[par] = kwargs[par] continue prefix = par.split(m.group(0))[0] ...
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def length(iterable): """ Return number of items in the iterable. Attention: this function consumes the whole iterable and can never return if iterable has infinite number of items. :Example: >>> length(iter([0, 1])) 2 >>> length([0, 1, 2]) 3 """ try: return len(itera...
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def mergeSort(l): """ Algoritem urejanja z zlivanjem seznama l z n elementi. Časovna zahtevnost: O(n log n) """ n = len(l) if n <= 1: return l l1 = mergeSort(l[:n//2]) l2 = mergeSort(l[n//2:]) l = [] i, j = 0, 0 n1, n2 = len(l1), len(l2) while i < n1 and j < n2: ...
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def split_kv(text_pair, sep): """Helper.""" try: key, value = text_pair.split(sep, 1) except TypeError: return None, text_pair except ValueError: return None, text_pair if not key: return None, None return key, value
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def process_dsn(dsn): """ Take a standard DSN-dict and return the args and kwargs that will be passed to the pgdb Connection constructor. """ dsn['password'] = dsn['passwd'] del dsn['passwd'] dsn['database'] = dsn['db'] del dsn['db'] return [], dsn
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import requests def get_request(url: str, headers: dict, path: str)->dict: """ Perform an HTTP GET request :param url: the url to request :param headers: a dict containing the ZT Auth header :param path: the path at the url to request :return: a dict representing the returned JSON object. ...
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from typing import Any def maybestr(value: Any) -> str: """ A "maybified" version of the str() function. """ return str(value)
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def datetime_to_iso_8601(dt): """Format a datetime as an iso 8601 string - YYYY-MM-DDTHH:MM:SS with optional timezone +HH:MM.""" if dt: return dt.replace(microsecond=0).isoformat() else: return None
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def is_rss_data(data): """ This methods gets html data and check if it is content from a rss feed :param data: html object data :return: True if it is content from a rss feed, False otherwise """ data = data.lower() if data.count("<html"): return False return data.count("<rss") ...
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def count_unique_data_points_groupby_point_forall_traffic(reader): """ Process 5-min traffic flow data and execute a breakdown of the data to each different ingress/egress member ASN. Files format: ".avro.point=egress.ipv=4.svln=all.txt.gz" ".avro.point=ingress.ipv=4.svln=all.txt.gz" ingre...
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def format_competition_round_headline(selected_match): """ formats the competition round details match is the match used to create the headline returns the competition round details """ if len(selected_match.competition_round) > 0: round_prefix = (" " if selected_match.competition_r...
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def filtra_lista_request_vars(requestvars,clave): """Sirve para limpiar listas que se forman en request.vars con algunas variables que se ponen en el GEt y en el POST devuelve """ if clave in requestvars: if isinstance(requestvars[clave],(list,tuple)): requestvars[clave]=requestvars...
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def Pa2inH2O(x): """Pa -> inH2O""" return x/249.1
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from typing import Dict from typing import Any from typing import List def get_key_mapping(inverse_mapping: Dict[Any, List[str]]) -> Dict[str, Any]: """Returns the key mapping from the inverse mapping. Args: inverse_mapping: A mapping from the mapped input to the list of keys. Returns: a mapping from ...
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def _qt_list(secondary_dict_ptr, secondary_key_list_ptr, cols, key): """ This sub-function is called by view_utils.qt to add keys to the secondary_key_list and is NOT meant to be called directly. """ if cols[key]: if cols[key] not in secondary_key_list_ptr: secondary_key_list_pt...
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import itertools def combos(indices): """ Return all combinations of indices in a list of index sublists. Arguments: indices: list of int lists List of index lists. """ return list(itertools.product(*indices))
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def setDefaults(configObj={}): """ Return a dictionary of the default parameters which also been updated with the user overrides. """ gain = 7 # Detector gain, e-/ADU grow = 1 # Radius around CR pixel to mask [default=1 for 3x3 for non-NICMOS] ctegrow = 0...
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import subprocess import difflib def get_diffs(files): """ Run clang-format on all `files` and report if it changed anything. Returns a mapping of filename => diff generator """ name_to_diffs = {} for f in files: formatted_text = subprocess.check_output(["clang-format", f]).decode() ...
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def init_comm(base_comm, grid_shape): """Create an MPI communicator with a cartesian topology.""" return base_comm.Create_cart(grid_shape, len(grid_shape) * (False,), reorder=False)
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import re def preprocess(renderer, page): """ Yassg Markdown preprocessor. """ def sub_ref(m): if m.group().startswith('\\'): return m.group()[1:] text, ref = m.groups() if not ref: text, ref = None, text page = renderer.find_page(ref) if not page: return m.group() i...
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def arithmetic_simplify_07(x): """ arithmetic_simplify_07 """ return (x + 1) * 2 * 5
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def create_new_features(df): """ Creates features for price differences: high-low close-open """ df['close-open'] = df['Adj_Close'] - df['Adj_Open'] df['high-low'] = df['Adj_High'] - df['Adj_Low'] # create pct features df['close-open_pct'] = df['close-open'] / df['Adj_Close'] * 100 ...
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def is_test(obj) -> bool: """Is the object a test, i.e. test_func()?""" assert hasattr(obj, "__name__") obj_name = obj.__name__.lower() patterns = ("test", "_test", "__test") return any(obj_name.startswith(pattern) for pattern in patterns)
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import os import fnmatch def dofolderlist(filename, folderlist, envvariable, searchsubfolders, searchpt): """Search for filename in folderlist and return location or "" filename is the file to find. It may be a wildcard expression. folderlist is a possibly empty list of folders to search envvari...
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def keep_aa(attentions): """ Last minute change: transfer over the network is very slow. Need to drop keys from the JSON to make rendering faster """ aa = attentions['aa'] out = {'aa': aa} return out
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def has_shape(data, shape): """Check if the data structure has the given shape.""" # Dict pattern if isinstance(shape, dict): return isinstance(data, dict) and all(has_shape(data.get(key), value) for key, value in shape.items()) # List with known order elif isinstance(shape, list): r...
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import os from subprocess import Popen, PIPE, STDOUT def gitversion(): """Returns `git describe --tags --dirty --always`, or 'unknown' if not a git repo""" origdir = os.getcwd() os.chdir(os.path.dirname(__file__)) try: p = Popen(['git', "describe", "--tags", "--dirty", "--always"], stdout=...
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import argparse def parse_arguments(args): """ Parse the arguments from the user """ parser = argparse.ArgumentParser( description= "HUMAnN Databases\n", formatter_class=argparse.RawTextHelpFormatter) parser.add_argument( "--available", action="store_true", ...
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def harm(x,y): """Harmonic mean of x and y""" return x*y/(x+y)
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import webbrowser def _open_profile_pic(profile_id): """ Input : Profile Id Output : Opens a new tab with profile picture of the username """ try: new_url = "https://graph.facebook.com/" + profile_id + "/picture?width=800" webbrowser.open_new_tab(new_url) return 1 exce...
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def load_stsb_data(filename): """加载数据 单条格式:(文本1, 文本2, 标签) """ D = [] with open(filename, encoding='utf-8') as f: for i, l in enumerate(f): if i > 0: l = l.strip().split('\t') D.append((l[5], l[6], float(l[4]))) return D
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def find_sequencial_nodes(model, Node2nextEntity, Entity2nextNode, search_target=['Conv', 'Add', 'Relu', 'MaxPool'], if_print = False): """ Search Where is Subgroup """ found_nodes = [] for i, node in enumerate(model.graph.node): if if_print: print("\nnode[{}] ...".format(i)) n_idx...
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def qiime_to_maaslin(in_datafile, outfile): """Converts a tsv file from qiime to a maaslin format :param in_datafile: String; file of the qiime tsv format (from biom_to_tsv) :param outfile: String; file of the tsv format for input to maaslin External dependencies - QiimeToMaaslin: https://b...
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import copy def make_state_space(): """Quick and dirty way to generate the state space reference list for v6 agent. Total states: 516097 """ a = [] for i in range(6): for j in range(6): for k in range(6): for l in range(6): for m in rang...
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from pathlib import Path import os def _get_filenames_from_folder(folder): """get the `folder` str, checks and returns children as list of Path instances.""" folder_path = Path(folder) if not folder_path.is_dir(): raise ValueError("'{path}' is not a valid directory".format(path=folder)) f...
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from pandas import concat def concatenate_populations(populations, extra_labels={}): """ Write a file containing the set of the populations we want to serialized Args: populations (dict): dictionary of the populations, labeled by the key extra_labels (dict): dictionary of the feature_la...
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def voxel_hash(x, y, z): """ Computes a hash given the int coordinates of a 3D voxel Args: x (np.int64): the x coordinate of a voxel y (np.int64): the y coordinate of a voxel z (np.int64): the z coordinate of a voxel """ return 73856093 * x + 19349669 * y + 83492791 * z
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def remove_dups(lst): """ Inputs: lst - A list object Outputs: Returns a new list with the same elements in lst, in the same order, but without duplicates. Only the first element of each replicated element will appear in the output. """ result = [] dups = set() ...
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import tempfile import os def get_temp_name(suffix='', prefix='tmp', dir=None, unlink=False): """Return temporary file name""" fdesc, fname = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir) os.close(fdesc) if unlink: os.unlink(fname) return fname
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def compute_nodes_overlap_max( graph_1, graph_2, node_match): """ computes a nodes in graph_2 matching with nodes in graph_1 according to node_match Returns - a dictionary of nodes """ nodes_2 = [ filter( lambda n2: node_match( graph_1.node[n1], graph_2.node[n2]), graph_2.nodes()) for n1 in gra...
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def generate_text_using_trigrams(language_model, N_output_words): """ Generate N words using probabilistic language model. Trigrams are used to generate text. """ cprob_2grams, cprob_3grams = language_model # Starting from the end-of-sentence token, generating 2nd token using bigrams, and the re...
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def _WrapAccumulatorCellGradFn(accumulator_layer, cell_grad): """Wrap a cell grad function to disable accumulators.""" def WrappedCellGradFn(theta, state0, inputs, extras, dstate1): """cell_grad wrapped to disable accumulators.""" # Compute the cell grad function with accumulators disabled. accumulator...
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from typing import Dict def get_env_name__value_map(environ_sh_path: str) -> Dict[str, str]: """ 获取environ.sh文件中的k-v值 :param environ_sh_path: :return: """ with open(file=environ_sh_path, mode="r", encoding="utf-8") as environ_sh_reader: lines = environ_sh_reader.readlines() env_n...
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def normalize_service_argument(argument): """ normalize service name and set type: $object, $variable$ Examples: >>> normalize_service_argument('$Mongodb') ['Mongodb', 'object'] >>> normalize_service_argument('%batch_size%') ['batch_size', 'variable'] """ if isinstanc...
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import re def camel_to_snake(camel): """ make a camelcase from a snakecase with a few things thrown in - we had a case where we were parsing a spreadsheet and using the headings as keys in an object one of the headings was "Who Uploads?" """ camel = camel.strip() camel = re.sub(' ', ''...
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from typing import List def format_board(board: List[str]) -> str: """Return the board formatted for output""" out_board = '' for i in range(0, len(board)): if i == 0 or i % 3 == 0: out_board += '\n' + '-------------' + '\n|' tic = board[i] if board[i] in 'XO' else i + 1 ...
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import re def get_bvalue(df): """Return image b-value. Default to 0 if not found. It may also be stored as frame second. Some Siemens scanners have it like this: (0018,0024) SH [*ep_b0] # 6, 1 SequenceName (0018,0024) SH [*ep_b1500t] # 10, 1 SequenceName """ r = None if 'Dif...
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import re def _include_exclude( dictionary: dict, include_pattern: str, exclude_pattern: str, ) -> bool: """ Filters the items of a dictionary based on a include / exclude regexp pair. Returns `True` if the size of the dictionary changed. """ incl, excl = re.compile(include_pattern), r...
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def fruity_file(models_path): """Return fruity sample data file as a Path object.""" return models_path.joinpath("fruity.txt")
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from typing import Sequence from typing import Mapping def _safe_get_any(root, *keys): """ Helper method for getting value from nested dict, special for Gremlin valueMap things where properties can be lists of one or 0. :param root: :param keys: :return: """ current = root for key ...
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def get_cut_edge(image, l, r, t, b): """deletes pixels from some sided of an image""" return 0, image[t : image.shape[0] - b, l : image.shape[1] - r]
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def time_offset(ttest, t0): """ Return a string time delta between two datetime objects in seconds formatted to six significant decimal places. :param ttest: :param t0: :return: """ delta = ttest - t0 t = float(delta.seconds) + float(delta.microseconds) / 1000000.0 return "%0.06f...
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from pathlib import Path def _modified_date(f: Path) -> str: """Get the modified date of the file""" return str(f.stat().st_mtime)
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def separate_gradients(gradients, weight_vars, input_vars): """ split the gradient dictionary up into one for input and one for weights. Parameters ---------- gradients: dict: dictionary of gradients. Should be str, list[Objective] key/value pairs. input_vars: list: the input va...
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def insert_sort(unsorted_list): """[Takes in an unsorted list and returns a sorted list] Args: unsorted_list ([list]): [an unsorted list of ints] """ pace = 1 for pace in range(len(unsorted_list)): pace_behind = pace - 1 temp = unsorted_list[pace] while pace_behind >...
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import re def subject_id_of(path) -> str: """ Returns the subject ID closest to the end of the input string or Path. Inputs ------ path : str or Path String or Path containing the subject ID. Returns ------- str Subject ID found in the filename Raises ------ ...
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import logging import inspect def get_file_logger( log_file=None, log_filemode='a', log_level=logging.INFO, log_msg_fmt='%(asctime)s %(levelname)s %(message)s', log_date_fmt='%a, %d %b %Y %H:%M:%S', log_prefix=None ): """ Purpose: Get Logger to file Args: log_level ...
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def class_name(obj): """ Returns the class name of an object""" return obj.__class__.__name__
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def Split(string,n): """Split a string into lines of length n with \n in between them""" N =len(string)//n return '\n'.join([string[i*n:(i+1)*n] for i in range(N)]+[string[N*n:]])
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def molm2_to_molec_cm2(spc_array): """ Convert moles/m2 to molec/cm2 """ avo_num = 6.0221409e23 molec_per_m2 = spc_array * avo_num molec_per_cm2 = molec_per_m2 * 1e4 return molec_per_cm2
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def get_sample_questions(): """ Return a sample of questions. """ questions = { 'CIGOVX1': [ '1', ['SQ001', 'SQ002'], ['SQ001', 'SQ002abc'], ], 'CIGOVX2': [ '1', ['SQ001', 'SQ002'], ['SQ001', 'SQ002'], ...
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def dms2dd(dms): """ DMS to decimal degrees. Args: dms (list). d must be negative for S and W. Return: float. """ d, m, s = dms return d + m/60. + s/3600.
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def br(value): """ Replaces newlines with HTML-style <br>'s """ return value.replace("\n", "<br>")
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def list_count(l): """ count the occurrences of all items in a list and return a dictionary that is of the form {nb_occurence:list_item}, which is the opposite of standard implementation usually found on the web ----------------------------------------------------------------- in python >= 2.7, ...
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import math def binary_entropy(p): """ Uses the binary entropy function denoted H(p) in information theory/statistics Computes the entropy of a Bernoulli process with probability of success p When p = .5, entropy is at its max value (unbiased bit, most common unit of information entropy) @param ...
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import argparse def parse_args(args): """ Parse script arguments. :return: Parsed args for assignment """ parser = argparse.ArgumentParser() parser.add_argument('--build-directory', required=True, help="A directory where box files laid in", ...
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def chat_words_conversion(text, chat_words_list, chat_words_map_dict): """Function to convert the chat words""" new_text = [] for w in text.split(): if w.upper() in chat_words_list: new_text.append(chat_words_map_dict[w.upper()]) else: new_text.append(w) return " ...
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def isosurface(da, coord, target): """ Returns the values of a coordinate in the input array where the input array values equals \ a prescribed target. E.g. returns the depth of the 20 degC isotherm. Returns nans for all \ points in input array where isosurface is not defined...
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def _process_ix(i, idx): """ :param i: :param idx: :return: """ if idx is None: return set(i) if len(idx) > 1: return set( zip([i.get_level_values(l) for l in idx]) ) else: return set( i.get_level_values(idx[0]) )
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