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def removecommongaps(s1, s2): """Remove common gap characters between the two sequences. Return s1, s2 with these characters removed. """ if len(s1) != len(s2): raise ValueError('Sequences must be same length') return ( ''.join(b1 for b1, b2 in zip(s1, s2) if b1 != '-' or b2 != '-'),...
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def add_position_clsite(modseq, clpos): """ Adjusts the position of the Cl site with modifications """ # determine the position of the cross-link with modifications in the string add_pos = 0 for modi in modseq: # print (cl_pos1, modi[0]) # -1 is needed since we also subtract it f...
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def warmup_lr(init_lr, step, iter_num): """ Warm up learning rate """ return step/iter_num*init_lr
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import re def escape_html_syntax_characters(string): """ Escape the three HTML syntax characters &, <, >. & becomes &amp; < becomes &lt; > becomes &gt; """ string = re.sub('&', '&amp;', string) string = re.sub('<', '&lt;', string) string = re.sub('>', '&gt;', string) return string
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def Measurement_timeofday_method_diff(self,probe): """ Computes diff between time values and caches last time. """ delta = 0 if hasattr(self,'_last'): delta = probe.microsecondsSinceEpoch - self._last; self._last = probe.microsecondsSinceEpoch return delta
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def read_embeddings(args, graph): """Read embeddings from an external file.""" with open(args.emb_filename) as f: # Ignore the first line (# of nodes, # of dimensions). emb = f.read().splitlines()[1:] emb = [e.split() for e in emb] # Split with whitespace. node_names = list(graph.nod...
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from typing import Tuple def _parse_manifest_file(manifest_file_path: str) -> Tuple[list, list]: """ Parsing manifest file """ audio_paths = list() transcripts = list() with open(manifest_file_path) as f: for idx, line in enumerate(f.readlines()): audio_path, _, transcript = line....
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def makeNgramModel(tokenlist, n, fp={}): """This function generates an N-gram model as a dictionary data-structure. """ for start in range( len(tokenlist) - (n - 1) ): tokenslice = tokenlist[start : start + n] #print("Token-slice:", tokenslice) stringngram = " ".join(tokenslice) #print...
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import re def count(item, string, case_sensitive=False): """Returns the exact number of how many times `item` is found in `string`. :param item: item to count the occurrences of in `string` :param string: string to count occurrences of `item` in. :param case_sensitive: if set to `True`, the search af...
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def as_learning_rate_by_sample(learning_rate_per_minibatch, minibatch_size, momentum=0, momentum_as_unit_gain=False): """ Compute the scale parameter for the learning rate to match the learning rate definition used in other deep learning frameworks. In CNTK, gradients are calculated as follows: ...
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def read_data(data_file): """ Reads in whitespace delimited data points of the form: 2.345 0.87 3.141 6.77 where the last column is the dependent variable and all columns before are indepndent variables. param str data_file: path to training data returns: list of training data insta...
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import importlib def import_modules(modules): """ Utility function to import an iterator of module names as a list. Skips over modules that are not importable. """ module_objects = [] for module_name in modules: try: module_objects.append(importlib.import_module(module_nam...
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def suqeuclidean(x, y): """Square euclidean distance. """ result = 0.0 for i in range(x.shape[0]): result += (x[i] - y[i]) ** 2 return result
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import threading def StrptimeRun(strptime, patched): """Checks the given strptime function runs without raising an Exception. Returns: True on success, False on failure. """ if patched: import _strptime # pylint: disable=unused-import def Target(fn): global error # pylint: disable=global-sta...
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def filter_columns_by_prefix(columns, prefixes): """Filter columns by prefix.""" filtered_columns = {column for column in columns if True in (column.startswith(prefix) for prefix in prefixes)} return filtered_columns
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def non_negative_validation(value): """ Validate if value is negative and raise Validation error """ if isinstance(value, list): if any(v < 0 for v in value): raise ValueError("The Values in the list must not be negative") else: return value else: if ...
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def _recompute_best(results): """_recompute_best. Internal helper function for the AnnealResults class. Computes the best AnnealResult in an AnnealResults object. Parameters ---------- results : AnnealResults object. Returns ------- res : AnnealResult object. The AnnealRes...
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def func_bool(x): """Implementation of `func_bool`.""" return True
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def inv_mod(n: int, p: int): """ Find a inverse of n mod p. :param n: Value of n where nx === 1 (mod p) :param p: Value of p where nx === 1 (mod p) :returns: Value of x where nx === 1 (mod p) """ return pow(n, -1, p)
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import statistics def smooth(data_in, window_size): """Smooths the data, which should be a list, by averaging with the given window size.""" data_in_len = len(data_in) data_out_len = data_in_len - window_size + 1 if data_out_len <= 0: return data_in data_out = [] for i in range(0, dat...
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def groupBy(keyFn, row_data): """Group rows in row_data by the result of keyFn. Arguments: keyFn -- A function that returns the cell data of the column to group by. Needs to be tailored to the structure of row_data. row_data -- A table organized as a list of row data structures. Retur...
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def compose_name(hidden_units, learning_rate, epsilon, lmbda, lr_decay, search_plies=1): """Return name for parameter save file based on the hyperparameters.""" name = f'N{hidden_units:d}' name += f'-alpha{learning_rate:.3f}' name += f'-lambda{lmbda:.2f}' name += f'-epsilon{epsilon:.5f}' name +=...
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def get_down_str(down): """Converts an integer down to a string. :param down: :return: """ if down == 1: return "1st" elif down == 2: return "2nd" elif down == 3: return "3rd" else: return ""
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def drop(num): """Produce a sequence with the same elements as the input sequence, but omitting the first num elements. """ def dropper(input): p = num for elt in input: if p > 0: p -= 1 else: yield elt return dropper
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def build_geometry(self): """Compute the curve (Line) needed to plot the Slot. The ending point of a curve is the starting point of the next curve in the list Parameters ---------- self : SlotW15 A SlotW15 object Returns ------- curve_list: list A list of 6 Segment ...
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def each(xs:list, f) -> list: """each(xs, f) e.g. xs >> each >> f Answers [f(x) for x in xs]""" return [f(x) for x in xs]
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def dict_subset(x, include=[]): """Subset a dict.""" return dict((k, v) for k, v in x.items() if k in include)
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def zscore_normalize_array(array, mean, std_dev): """ Zscore normalize the numpy array based on the genomic mean and standard deviation :param std_dev: :param mean: :param array: Input array of bigwig values :return: Zscore normalized array """ return (array - mean) / std_dev
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def get_final_pop(dict_gen): """ Returns final population of results dict Parameters ---------- dict_gen : dict Dict holding generation number as key and population object as value Returns ------- tup_res : tuple Results tuple (final_pop, list_ann, list_co2) """ ...
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def simplify_logger_name(logger_name: str): """Simple function to reduce the size of the loggers name. Parameters: logger_name (str): Name of the logger to simplify. e.g path.to.my_module Examples: simplify_logger_name('path.to.my_module') = 'p.t.mm' """ modules = [...
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def parse_wire(line): """Parse line to directions with steps creating wire.""" wire = [] for instruction in line.split(','): direction, *steps = instruction wire.append((direction, int(''.join(steps)))) return wire
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def ema(df, n, m): #exponential moving average """ Wrapper function to estimate EMA. :param df: a pandas DataFrame. :return: ema_{t}=(m/n)*a_{t}+((n-m)/n)*ema_{t-1} """ result = df.copy() for i in range(1,len(df)): result.iloc[i]= (m*df.iloc[i-1] + (n-m)*result[i-1]) / n retur...
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import typing import requests import time def get_response( url: str, *, max_attempts=5, **request_kwargs ) -> typing.Union[requests.Response, None]: """Return the response. Tries to get response max_attempts number of times, otherwise return None Args: url (str): url string to be retrieved ...
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import asyncio def create_task(coroutine): """Schedules a coroutine to be run.""" return asyncio.get_event_loop().create_task(coroutine)
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def get_style(format): """Infer style from output format.""" if format == 'simple-html': style = 'html' elif format in ('tex', 'latex', 'pdf'): style = 'markdown_tex' else: style = 'markdown' return style
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def normalise_to_max(xarray,yarray): """Given x and y arrays returns a y array which is normailsed to 100% at the maximum value of the original y array""" ymax=max(yarray) ynorm = (yarray/ymax)*100 return ynorm
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def ProfileCurve(type=0, a=0.25, b=0.25): """ ProfileCurve( type=0, a=0.25, b=0.25 ) Create profile curve Parameters: type - select profile type, L, H, T, U, Z (type=int) a - a scaling parameter (type=float) b - b scaling parameter (type=floa...
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from pathlib import Path def path(s): """ Returns a :class:`Path` object for the given string. :param str s: The string containing the path to parse :returns: A :class:`Path` object representing the path """ i = s.rfind('/') + 1 dirname, basename = s[:i], s[i:] if dirname and dirname ...
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def filter_by_device_name(items, device_names, target_device_name): """Filter a list of items by device name. Args: items: A list of items to be filtered according to their corresponding device names. device_names: A list of the device names. Must have the same legnth as `items`. target_dev...
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import struct def read_crc(file): """Read a crc32 from a file.""" return struct.unpack('<i',file.read(4))[0]
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import math def isPointEqual(point1, point2, tol=1e-4): """Determins if a Point3D is almost-equal to a Point3D in a list Args: point1: (Point3D) The Point to be checked point2: (Point3D) The Points to check agains tol: (float) Tollerance for almost-equality Returns: bool:...
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import time from datetime import datetime def format_date(timestamp, precision=0): """ Construct an ISO 8601 time from a timestamp. There are several possible sources for *timestamp*. - time.time() returns a floating point number of seconds since the UNIX epoch of Jan 1, 1970 UTC. - time....
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def joinf(sep, seq): """sep.join(seq), omitting None, null or so.""" return sep.join([s for s in filter(bool, seq)]) or None
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from datetime import datetime import pytz def now() -> datetime: """ Returns the current datetime with the correct timezone information >>> isinstance(now(), datetime) True """ return datetime.utcnow().replace(tzinfo=pytz.utc)
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def is_file_genpath(genpath): """ Determine whether the genpath is a file (e.g., '/stdout') or not (e.g., 'command') :param genpath: a generalized path :return: a boolean value indicating if the genpath is a file. """ return genpath.startswith('/')
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def filter_interpolations(base: str, *args) -> str: """Filter the interpolations from a string Args: base (str): The text to filter *args: The interpolations (Memory objects) to filter """ for memspace in args: base = str(base).replace(memspace.repr, str(memspace.value)) ret...
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def request_value(request, key, default=None): """ Returns first found value, using this order: POST, GET, default. :param request: :param key: :param default: :return: """ value = request.POST.get(key, None) or request.GET.get(key, None) if value is not None: return value ...
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def get_fitness_score(subject, goal): """ In this case, subject and goal is a list of 5 numbers. Return a score that is the total difference between the subject and the goal. """ total = 0 for i in range(len(subject)): total += abs(goal[i] - subject[i]) return total
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def SearchTFProfNode(node, name): """Search a node in the tree.""" if node.name == name: return node for c in node.children: r = SearchTFProfNode(c, name) if r: return r return None
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import decimal def round(val, digits, mode = decimal.ROUND_HALF_UP): """ Round a decimal value to the given number of decimal places, using the given rounding mode, or the standard ROUND_HALF_UP if not specified """ return val.quantize(decimal.Decimal("10") ** -digits, mode)
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def get_available_resources(threshold, usage, total): """Get a map of the available resource capacity. :param threshold: A threshold on the maximum allowed resource usage. :param usage: A map of hosts to the resource usage. :param total: A map of hosts to the total resource capacity. :return: A map...
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def remove_response(stream, pre_filt=(0.01, 0.02, 8.0, 10.0), response_output="DISP"): """ Removes the instrument response. Assumes stream.attach_response has been called before. """ stream.remove_response(pre_filt=pre_filt, output=response_output, ...
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import hashlib def sha256(msg): """ return the hex digest for a givent msg """ return hashlib.sha256(msg).hexdigest()
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def read_messages(message_file): """(file open for reading) -> list of str Read and return the message_file, with each line separated into a different item in a list and the newline character removed. """ returned_message = [] contents = message_file.readlines() for item in contents: ...
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def concatenate_qa(prev_qns_text_list, prev_ans_text_list): """ Concatenates two lists of questions and answers. """ qa = "" for q, a in zip(prev_qns_text_list, prev_ans_text_list): qa += q + " | " + a + " || " return qa
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def is_feat_in_sentence(sentence, features): """ Parameters ---------- sentence: str, One sentence from the info text of a mushroom species features: list of strs List of possible features as in dataset_categories.features_list Return ------ bool, True if sentence contains a...
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import re def add_asic_arg(format_str, cmds_list, asic_num): """ Add ASIC specific arg using the supplied string formatter New commands are added for each ASIC. In case of a regex paramter, new regex is created for each ASIC. """ updated_cmds = [] for cmd in cmds_list: if isinst...
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def set_intersect(variable1, variable2, d): """ Expand both variables, interpret them as lists of strings, and return the intersection as a flattened string. For example: s1 = "a b c" s2 = "b c d" s3 = set_intersect(s1, s2) => s3 = "b c" """ val1 = set(d.getVar(variable1).split(...
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from typing import OrderedDict def read_dat_file(dat_file): """ Read an ASCII ".dat" file from JXP format 'database' Parameters ---------- dat_file : str filename Returns ------- dat_dict : OrderedDict A dict containing the info in the .dat file """ # Define datdic...
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from typing import Tuple def _gray_code_comparator(k1: Tuple[int, ...], k2: Tuple[int, ...], flip: bool = False) -> int: """Compares two Gray-encoded binary numbers. Args: k1: A tuple of ints, representing the bits that are one. For example, 6 would be (1, 2). k2: The second number, represent...
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def reinforce_grad(loss): """ A closure to modify the gradient of a nn module. Use to implement REINFORCE gradient. Gradients will be multiplied by loss. Arguments: - loss: Gradients are multiplied by loss, should be a scalar """ def hook(module, grad_input, grad_output): new_g...
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def build_array(text): """Returns an array of parsed lines from the input text Array elements are in the format: (min, max, character, string) """ array = [] with open(text, 'r') as f: for line in f: _range, char, s = line.strip().split() n, m = _range.split('...
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def transpose(matrix): """ transposes a 2-dimensional list """ return [[matrix[r][c] for r in range(len(matrix))] for c in range(len(matrix[0]))]
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def flip_data_str_signs(data): """Flip the signs of data string, e.g. '1 2 3' --> '-1 -2 -3' """ return ' '.join([str(-float(i)) for i in data.split()])
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def f90float(s): """Convert string repr of Fortran floating point to Python double""" return float(s.lower().replace('d', 'e'))
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import requests import pickle def api_request(file, thresh=0.5): """ Post request to serverless backend api where our model is lcoated Receives a csv with the classes and polygons classified by our model Parameters ---------- file: .tiff file Tiff file to be classified by our model ...
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def dep_parenreduce(mysplit, mypos=0): """Accepts a list of strings, and converts '(' and ')' surrounded items to sub-lists: >>> dep_parenreduce(['']) [''] >>> dep_parenreduce(['1', '2', '3']) ['1', '2', '3'] >>> dep_parenreduce(['1', '(', '2', '3', ')', '4']) ['1', ['2', '3'], '4'] """...
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def imdb_iM_table(imodulon_table, cat_order=None): """ Reformats the iModulon table according Parameters ---------- imodulon_table : ~pandas.DataFrame Table formatted similar to IcaData.imodulon_table cat_order : list, optional List of categories in imodulon_table.category, orde...
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def uint_size(value): """Returns number of bytes (power of two) to represent unsigned value.""" assert value >= 0 n = 8 while not value < (1 << n): n *= 2 return n // 8
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import re def github_to_markdown_body(body: str) -> str: """ Generate a markdown body from the GitHub provided one. :param body: The markdown body provided by the GitHub Releases. :returns: A markdown body. """ body = re.sub( r"#(\d{1,5})", r"[#\1](https://github.com/rucio/rucio/issu...
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def poly_np(x, *coefs): """ f(x) = a * x + b * x**2 + c * x**3 + ... *args = (x, a, b, ...) """ # Add a warning for something potentially incorrect if len(coefs) == 0: raise Exception("You have not provided any polynomial coefficients.") # Calculate using a loop result = x * 0...
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def symbols_gen(N): # генерация списка из символов для красивого вывода матрицы. """ Функция, которая генерирует символы для уравнений :params N: количество переменных :return symbols: сгенерированные символы, список """ symbols = [] for i in range(65, 65 + N): symbols.a...
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def _neighbors(point): """ Get left, right, upper, lower neighbors of this point. """ i, j = point return {(i-1, j), (i+1, j), (i, j-1), (i, j+1)}
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def compute_out_degrees(digraph): """ dict -> dict Takes a directed graph represented as a dictionary, and returns a dictionary in which the keys are the nodes and the values are the nodes' outdegree value. """ out_degrees = {} for node in digraph: out_degrees[node] = len(digraph[nod...
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def overlaps_v(text_proposals, index1, index2): """ Calculate vertical overlap ratio. Args: text_proposals(numpy.array): Text proposlas. index1(int): First text proposal. index2(int): Second text proposal. Return: overlap(float32): vertical overlap. """ h1 = tex...
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def getIstioServiceName(service_name, project_id, zone): """ Returns the Istio service name of a certain service. """ return "ist:{}-zone-{}-cloud-ops-sandbox-default-{}".format(project_id, zone, service_name)
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import torch import math def gaussian(window_size, sigma): """ Generates a list of Tensor values drawn from a gaussian distribution with standard diviation = sigma and sum of all elements = 1. Length of list = window_size """ gauss = torch.Tensor([math.exp(-(x - window_size//2)**2/float(2*sig...
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import random def randBytes(b: int = 2) -> bytes: """ Get a random number of bytes :param b: number of bytes generate :return: random number of bytes requested """ return bytes([random.getrandbits(8) for _ in range(b)])
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from typing import List from typing import Any def sort_file_summary_content(data: List[Any]) -> List[Any]: """sorts the summary file contents""" return sorted( data, key=lambda x: x["branch"] + x["host"] + x["compiler"] + x["c_version"] + x["mpi"] + x["...
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import copy def badmatch(match, badfn): """Make a copy of the given matcher, replacing its bad method with the given one. """ m = copy.copy(match) m.bad = badfn return m
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import yaml def update_config(config, updates): """Modifies the YAML configurations, given a list of YAML updates. """ if isinstance(updates, str): updates = [updates] for update in updates: edits = yaml.safe_load(update) for k, v in edits.items(): node = config ...
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from typing import List from typing import Union from pathlib import Path def cli_args(tmpdir) -> List[Union[Path, str]]: """ Fixture simulating a set of CLI arguments. Returns: List of args. """ in_folder = Path("requirements.in") assert in_folder.exists() out_folder = Path(tmpd...
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def sentinel(name): """Return a named value to use as a sentinel.""" class Sentinel(object): def __repr__(self): return name return Sentinel()
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import math def event_prediction(alpha, var, r_t): """ predict the total number of retweets :param alpha: a parameter of linear regression (alpha) :param var: a parameter of linear regression (variance) :param r_t: the total number of tweet at the observation time :return: predicted number o...
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def create_snapshot_repo(els, reponame, body, verify=True): """Function: create_snapshot_repo Description: Creates a repository in Elasticsearch cluster. Arguments: (input) els -> ElasticSearch instance. (input) reponame -> Name of repository. (input) body -> Contains arguments ...
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def calculate_dir(start, target): """ Calculate the direction in which to go to get from start to target. start: a tuple representing an (x,y) point target: a tuple representing an (x,y) point as_coord: whether you want a coordinate (-1,0) or a direction (S, NW, etc.) """ dx = target[0] - st...
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def rectified_linear_unit(x): """ Returns the ReLU of x, or the maximum between 0 and x.""" return x*(x > 0)
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def get_meta_value(meta, *keys, default=None): """ Return value from metadata. Given keys can define a path in the document tree. """ try: for key in keys: if not meta: raise KeyError(key) meta = meta[key] return meta except KeyError: ...
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def as_words(string): """Split the string into words >>> as_words('\tfred was here ') == ['fred', 'was', 'here'] True """ return string.strip().split()
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def getChildIndex(parent, toFind): """ Return the index of the given child in the given parent. This performs a linear search. """ count = 0 child = parent.firstChild while child: if child == toFind: return count if child.nodeType == 1: count += 1 ...
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import itertools def pairwise(iterable): """For a list ``s``, return pairs for consecutive entries. For example, a list ``s0``, ``s1``, etc. will produce ``(s0,s1), (s1,s2), ...`` and so on. See: https://docs.python.org/3/library/itertools.html#recipes.""" a, b = itertools.tee(iterable) next(...
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import torch def clip_tensor(x, lb=0., ub=1.): """ Clip a tensor to be within lb and ub :param x: :param lb: lower bound (scalar) :param ub: upper bound (scalar) :return: clipped version of x """ return torch.clamp(x, min=lb, max=ub)
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def between(data, delim1, delim2): """Extracts text between two delimiters. Parameters ---------- data : str Text to analyse delim1 : str First delimiter. delim2 : str Second delimiter. Returns ------- str Text between delimiters. """ return ...
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import getpass def ask_user_password(prompt: str) -> str: """ Read a password from the console. """ return getpass.getpass(prompt + ": ")
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def decode(minterm,n_variables): """ 输入最小项编号,输出最小项的01串 :param minterm: 待转化成string的 :param n_variables: 变元数量 :return: 最小项的01串 :rtype: str """ result=['0']*n_variables for i in reversed(range(n_variables)): result[i]=str(minterm%2) minterm=minterm//2 return ''.join(...
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def lisp_string(python_string): """ Convert a string to a Lisp string literal. """ return '"%s"' % python_string.replace('\\', '\\\\').replace('"', '\\"')
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import bisect def findClosest(a, x): """ Returns index of value closest to `x` in sorted sequence `a`. """ idx = bisect.bisect_left(a, x) if idx == 0: return a[0] if idx == len(a): return a[-1] if a[idx] - x < x - a[idx - 1]: return idx else: return idx ...
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def choose(n, k): """ return the binomial coefficient of n over k """ def rangeprod(k, n): """ returns the product of all the integers in {k,k+1,...,n} """ res = 1 for t in range(k, n+1): res *= t return res if (n < k): ...
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def tsv(infile, comment=None): """ Returns a generator for tab-delmited file. Args: infile: Input file as a file-like object comment (str): Rows beginning with this string will be ignored. Returns: generator: A generator that yields each row in the file as a list. """ if c...
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def fix(s: str) -> str: """ This function capitalise the first letter of the first word of each sentence. """ my_s = [i.capitalize() for i in s.split('. ')] return '. '.join(map(str, my_s))
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