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def write_vcf(lines, vcf): """Create a file from the provided list""" with open(vcf, "w") as vcf_handle: vcf_handle.write('\n'.join(lines)) return vcf
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import random import string def generate_random_filename_safe_text(length: int = 4) -> str: """ Generates a (not cryptographically safe) random filename-safe string. Args: length: Length of the random text. Returns: Generated text. """ return "".join([ ran...
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def reconstruct_path(came_from, start, goal): """Reconstruct a shortest path from a dictionary of back-pointers""" current = goal path = [current] while current != start: current = came_from[current] path.append(current) path.append(start) # optional path.reverse() # optional ...
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import ipaddress import socket def _matches_machine_hostname(host: str) -> bool: """Indicates whether ``host`` matches the hostname of this machine. This function compares ``host`` to the hostname as well as to the IP addresses of this machine. Note that it may return a false negative if this machine...
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def AnyInSet(operator): """ Apply an operator to all elements in a set and check if any of them return true """ return lambda elem, val: any(map(lambda item: operator(item, val), elem))
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import re def extract_jump(message, args, pipeline_data): """ Extracts a jump command from the data, and proceeds to the next step. Jump commands have the same syntax as Go To Anything e.g.: @ to jump to a symbol : to jump to a line # to jump to an instance of the text NOT...
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from typing import Counter def parse(filename): """Parse the input file into Python objects. Input file has lines like this: sdfsjdfk sjdkf lfke ljrl (contains dairy, soy) Parameters: filename (str): the name of the input file to open Returns: candidates (Dict[str, Set[s...
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def standardize_severity_string(severity): """ Returns the severity string in a consistent way. Parameters ---------- severity : str The severity string to standardize. Returns ------- severity : str The standardized severity string. """ return severity.title()
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import copy def get_output_tensors(sub_graph): """ Get all output tensor names of a sub_graph. Args: sub_graph: A SubGraph instance. Returns: A set contains all output tensor names of the sub_graph. """ output_tensors = copy.deepcopy(sub_graph.output_ops) for name in sub_graph.output_subgraphs: ...
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def nmea2deg(nmea): """ convert nmea angle (dddmm.mm) to degree """ w = float(nmea) / 100.0 d = int(w) return d + (w-d) * 100 / 60.0
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from typing import Any def _is_atomic(obj: Any) -> bool: """ Returns True for objects which are iterable but should not be iterated in the context of indexing an OrderedSet. When we index by an iterable, usually that means we're being asked to look up a list of things. However, in the case o...
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def cluster_kubeconfig(name, server, ca_data): """Generate and return a cluster kubeconfig object.""" return { "name": name, "cluster": { "server": server, "certificate-authority-data": ca_data, }, }
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import functools def memoize(f): """Decorator that can be applied to a method to memoize the results. Args: f - The function to decorate with memoization. The first argument of the function should be self - the instance of the class. The function can take an arbitrary amount of additional positio...
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def _partition_products_by_language(products): """ Partitions the given product models into language buckets of product id's. :param products: a list of product models. :returns: a map {language: set of product_id's}. """ products_by_language = {} for product in products.values(): ...
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from tokenize import NEWLINE, INDENT, DEDENT, tokenize import io def get_list_representation(cflow_output): """Return a list object representation of the output from cflow Example: If cflow_output is: main() <int () at main.c:18>: f() <int () at main.c:4>: malloc() pri...
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def numel_(a): """ function which returns the number of elements of a """ return a.size
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import math def is_prime(n): """ Check whether the given number is prime :param n: the given number :type n: int :return: whether the given number is prime :rtype: bool """ for i in range(2, int(math.sqrt(n))): if n % i == 0: return False return n > 1
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from typing import Dict def get_cache(config) -> Dict[str, list]: """Prepare a cache dictionary Args: config (ColocationConfig): configuration file Returns: Dict[str, list]: cache dict """ cache: Dict[str, list] = {} if config.plot_fitness_density: cache['fitnesses']...
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def extract_action_list_from_path(path_list): """ Converts a block idx path to action list. Args path_list: <list> list of block idx from source block to dest block. Returns action_list: <list> list of string discrete action commands (e.g. ['movesouth 1', 'movewest 1', ...] """ ...
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import time def timeit(f): """ time a function by applying a decorator Parameters ---------- f: function Returns ------- a decorated function """ def new_f(*args, **kwargs): bt = time.time() r = f(*args, **kwargs) et = time.time() print("tim...
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from typing import Iterable import itertools def groupby(key, iterable: Iterable): """ Получение словаря, сгруппированного по ключу из неупорядоченной последовательности словарей >>> users = [{'gender': 'female', 'age': 33}, {'gender': 'male', 'age': 20}, {'gender': 'female', 'age': 21}] >>> group...
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def min_first(iterable): """Returns the smallest value of all items in the iterable, compared by their zeroth elems.""" return min(iterable, key=lambda element: element[0])
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import json def match_epi_fmaps(bold_pedir, epi_fmap_one, epi_fmap_params_one, epi_fmap_two=None, epi_fmap_params_two=None): """Parse the field map files in the data configuration and determine which ones have the same and opposite phase-encoding directions as the BOLD scan in the curr...
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def mpg(start, end, gal): """This function takes a starting odometer reading, an ending odometer reading, and a volume of gas burned to traverse the difference, and returns mpg.""" return (end-start)/gal
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import io import json def read_from_json(json_file_path): """Function to read json file (annotation file)""" with io.open(json_file_path, "r", encoding="utf-8-sig") as myfile: data = json.load(myfile) return data
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def outline_gcp_project(project_index, project, zone, key_file_path): """Return a summary of a GCP project for logging purpose. Arguments: project_index (int): Project index. project (Resource): GCP Resource object of the project. zone (str): Name of the zone for the project. ke...
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def getRange(xs, ys, xMin, xMax): """ Return the Ys for the range of points where the Xs is at or between the given min/max limits """ rangeYs = [] for i in range(len(ys)): x = xs[i] if(x >= xMin and x <= xMax): rangeYs.append(ys[i]) if len(rangeYs) == 0: ...
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def is_valid_channel_name(name): """ Return True if the given name is a valid channel name. """ # Check channel name length if len(name) == 0 or len(name) > 50: return False # Check if channel name is valid valid = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789`~!@#...
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import re def exclude(images, excludes, verbose): """Return the images that don't match the regexes in the excludes list.""" remaining_images = images.copy() regexes = [re.compile(r) for r in excludes] # pylint: disable=invalid-name for (Id, image) in images.items(): # noqa: N806 for tag ...
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import unittest def requires_attr(obj, attr): """Decorator used to skip tests if an object does not have the required attribute. """ try: getattr(obj, attr) return lambda func: func except AttributeError: return unittest.skip('Required attribute "{}" not found on {}'.forma...
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def Identity(X): """ Identity fuction is the basic activation function It return the same input value as output. Parameters: - X: int ,-Inf to +Inf Returns: X , -Inf to +Inf """ return X
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import socket import fcntl import struct def get_ip(iface='eth0'): """ Use Linux SIOCGIFADDR ioctl to get the IP for the interface. ref http://code.activestate.com/recipes/439094-get-the-ip-address-associated-with-a-network-inter/ """ sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM) re...
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import torch def extract_into_tensor(arr, timesteps, broadcast_shape): """Extract values from a 1-D numpy array for a batch of indices. Args: arr: the 1-D numpy array. timesteps: a tensor of indices into the array to extract. broadcast_shape: a larger shape of K dimensions with the batch dimension ...
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def iscircular(linked_list): """ Determine whether the Linked List is circular or not Args: linked_list(obj): Linked List to be checked Returns: bool: Return True if the linked list is circular, return False otherwise """ if linked_list.head is None: return False slow...
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def default_timeout(variables): """ Default page timeout """ return variables.get('default_timeout', 10)
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def get_fips(geocode): """ Return and array of FIPS6 codes which identify the county regions effected by the weather alert. FIPS6 is a code which uniquely identifies counties in the United States. For more info: https://en.wikipedia.org/wiki/FIPS_county_code FIPS returned by NWS alerts can b...
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def binaryToInt(string): """ Convert binary string to integer """ return int(string[::-1], 2)
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import torch def weighted_mpjpe(predicted, target, w): """ Weighted mean per-joint position error (i.e. mean Euclidean distance) """ assert predicted.shape == target.shape assert w.shape[0] == predicted.shape[0] return torch.mean(w * torch.norm(predicted - target, dim=len(target.shape) - 1))
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def get_E2K_subdict(the_dict, main_key, sub_key): """Returns the subdictionary specified by main_key and sub_key, returning an empty dictionary if any is missing. This is for use in the post-processing functions.""" return the_dict[main_key].get(sub_key, {}) \ if the_dict.get(main_key) else {}
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def solution(A): """ On the face of it this is quite simple, until you factor in negative numbers. Approach is very simple: 1. Sort array in descending order (or ascending if you like) 2. Take the max value in between the sum of the head of the array and the first element of the array c...
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def format_user_results(user: dict): """ Formats and truncates the user result from the Slack API Args: user: The user response retrieved from the Slack API Returns: Formatted and truncated version of the result which is context safe. """ return { 'name': user.get('name'...
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import random def random_int(from_: int = 0, to: int = 10) -> int: """Generate random int within range from_, to Arguments: from_ {int} -- lower limit, default 0 to {int} -- upper limit Returns: int -- random number """ return random.randint(from_, to)
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def initial_value_count(input_list): """ Args: input_list (list[int]): A non empty list of python integers Returns: Tuple[int, int]: Returns the first value of input_list, and the number of times it consecutively appears in the list from the beginning. """ assert l...
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def head2pres(head, z, rref, grav, psurf): """ Compute pressures from head. Parameters ---------- head : Numpy array One/Two/Three dimensional array of equivalent head values. z0 : float z-variables of model, same dimension as head-array. rref : float Reference den...
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import calendar def datetime_to_timestamp(utc_dt): """Returns UTC datetime as a POSIX timestamp (seconds since epoch). Args: utc_dt: a datetime.datetime object storing a UTC date and time. Returns: The UTC date and time as whole seconds since epoch. Leap seconds (utc_dt.second > 5...
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def crop(im, r, c, sz): """ crop image into a square of size sz, """ return im[r:r + sz, c:c + sz]
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def euclidean_dist(p1, p2): """ Returns the euclidean distance between points (p1, p2) in n-dimensional space. Points must have the same number of dimensions. """ if len(p1) != len(p2): raise ValueError("Points must have the same number of dimensions.") return sum((d1 - d2) ** 2 for...
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def getChapterStatus(dic): """Returns the current status of the relevant chapter. dic -- Dictionary from the JSON with all values. """ return str(dic["content"]["$t"]).split(',')[5].split(':')[1].strip()
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def int_to_smile(array, indices_token, pad_char): """ From an array of int, return a list of molecules in string smile format Note: remove the padding char """ all_mols = [] for seq in array: new_mol = [indices_token[int(x)] for x in seq] all_mols.append(''.join(new_mol).re...
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def custom_score(word, opt): """Make your custom word score. Just put in a dictionary each letter being assigned a score. Args: word: the word to get the score of opt: the options to use. Retuns: The word in the score opt gave. Raises: Exception: if opt is not a dict ...
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import math def next_pow2(value): """Returns next power of 2 for a number""" return float(1 << int(math.ceil(math.log2(value))))
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def check_observing(survey, pick, program): """ Based on programs that have selected a given target, this will figure out which observing method requires the most observing time and then scales other program's costs based on that. Parameters ---------- survey : survey.Survey class o...
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def compose(*values): """ Compose the specified 8-bit *values* into a single integer. """ result = 0 for i, value in enumerate(values): result |= value << (i * 8) return result
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def absmin_diff(current, prevs): """Min of differences between current sample and all previous samples. Given more than one min, use the last one detected which is probably a newer value. Returns (difference, prev used) """ diffs = [abs(current-prev) for prev in prevs] smallest_pos = 0 small...
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import torch def psd_safe_cholesky(A, upper=False, out=None, jitter=None): """Compute the Cholesky decomposition of A. If A is only p.s.d, add a small jitter to the diagonal. Args: :attr:`A` (Tensor): The tensor to compute the Cholesky decomposition of :attr:`upper` (bool, optional...
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from pathlib import Path def non_existing_file(tmp_path): """Returns a path to a non existing file""" return Path(tmp_path).joinpath('usermapping')
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def get_group_policy_names(iam_client, groups): """ Returns the group policy names of the current user Args: iam_client (obj): IAM client obj groups (list): User groups Returns: policy_names (list): List of group policy names the current user has """ policy_names = [] ...
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def eliminate(problem, location, listOfLocations): """ Given a list of locations, eliminate from the problem the number that is present at the `location`. :param list problem: Two-dimensional list of sets :param tuple location: Location with the number to be removed :param list<tuple> listOfLoc...
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def prompt(prompt,valid): """ Returns the choice from a given prompt. This function asks the user a question, and waits for a response. It checks if the response is valid against a list of acceptable answers. If it is not valid, it asks the question again. Otherwise, it returns the player's answe...
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def __get_auto_sample(ndim, gradient): """ Decode which sampling method to use Arguments: ndim: int (dimensionality) gradient: (None or function/true) Returns: sampler string """ if ndim < 10: sample = 'unif' elif 10 <= ndim <= 20: sample = 'rwalk' else: if g...
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import networkx from typing import Counter def make_debruijn_graph(kmers): """Constructs a de Bruijn graph from a list of kmers. Parameters ---------- kmers: list of str Returns ------- dbg: networkx.DiGraph In this graph, multi-edges are collapsed into a single edge....
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import logging def remediate_iam_policy(sa_iam_policy, sa_resource_name, risky_roles): """Remove risky IAM roles from the service account IAM policy. Args: sa_iam_policy ([dict]): The IAM policy attached to the sa_resource_name. sa_resource_name ([str]): The GCP service account full resource ...
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def _get_test_by_name(tests, name): """ Returns the test with the specified name, or None if none match. """ for test in tests: if test.name == name: return test return None
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def _unpad( s: str, ) -> str: """Unpads a string that was previously padded by _pad(). :param s: The string to unpad :type s: bytes :returns: The unpadded string :rtype: str """ last_character = s[len(s) - 1:] bytes_to_remove = ord(last_character) return s[:-bytes_to_remove]
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def getStats(cm): """Return the usual stats for a confusion matrix.""" measures = {} measures['recall'] = cm['TP'] / (cm['TP'] + cm['FN']) measures['specificity'] = cm['TN'] / (cm['TN'] + cm['FP']) measures['FPR'] = cm['FP'] / (cm['FP'] + cm['TN']) measures['FNR'] = cm['FN'] / (cm['TP'] + cm['...
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def get_frame_from_json(frame): """Get/sanitize raw frame from JSON of frame from `tshark -x -T json ...` Args: frame (dict): A dict of a single packet from tshark. Returns: (str): The ASCII hexdump value of a packet """ if not isinstance(frame, dict): print('frame is type',...
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def get_key_from_val(dict_, val, unknown=None): """ dict_ = {'aa':123} val = 123 get_key_from_val(dict_, val) > 'aa' """ list_vals = list(dict_.values()) if val in list_vals: return list(dict_.keys())[list_vals.index(val)] else: return unknown
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def sklearn_method(estimator): """ A helper to turn a scikit-learn estimator into a spaCy extension. Just in case you *really* wanted to do it manually. ```python import spacy from spacy.tokens import Doc from sklearn.pipeline import make_pipeline from sklearn.feature_extraction.text ...
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def decorate(message: str, symbol: str = '+', line_width: int = 79) -> str: """Вывести текст в обрамлении символов :param message: оригинальное сообщение :param symbol: каким символом написать строки :param line_width: какую ширину заполнить символами :return: оформленное текстовое сообщение в виде...
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def convert(text): """Convert digits to alphanumeric text""" if text.isdigit(): return int(text) else: return text
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def sort_by_to_damage_state_desc(damage_state): """Sort the damage states with the highest first.""" return damage_state.to_state * -1
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def set_policy(crm_service, project_id, policy): """Sets IAM policy for a project.""" policy['version'] = 3 return ( crm_service.projects() .setIamPolicy(resource=project_id, body={"policy": policy}) .execute() )
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def _flatten_cluster_node(obj): """Flatten the structure of the cluster node into a single dict """ data = { 'id': obj.id, 'name': obj.name, 'private_ip': obj.status.private_ip, 'public_ip': obj.status.floating_ip, 'status': obj.status.status, 'flavor': obj.sp...
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def move(position, instruction): """ Take a position and offset it based on instuction, or raise an error on invalid instruction. Keyword arguments: position --- current position as a tuple (x,y) Instruction --- single-character instruction to move in ["^", "v", ">", "<"] """ if instruction == "^": ...
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def list_to_json(source_list): """ Serialise all the items in source_list to json """ result = [] for item in source_list: result.append(item.to_json()) return result
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import random def split_sets(wav_list, split_ratio): """Randomly splits the wav list into training, validation, and test lists. Note that a better approach is to make sure that all the classes have the same proportion of samples (e.g, spk01 should have 80% of samples in training, 10% validation, 10% t...
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def to_flags( supply_mutable: bool, transferable: bool, levy_mutable: bool ) -> int: """Convert 3 binary values to sequential bit flags""" flags: int = 0 if supply_mutable: flags |= 1 if transferable: flags |= 2 if levy_mutable: flags |= 4 return flags
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import re def add_example_ino_library_include(input_text): """Makes sure the example includes the header that loads the library.""" return re.sub(r'#include ', '#include <TensorFlowLite.h>\n\n#include ', input_text, 1)
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def is_relative(s): """Indicate if a given 'from s' import location is a relative import.""" return s.startswith(".")
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def area(square): """Get area of a rectangle""" return square.get('width') * square.get('height')
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def inet_ntoa(addr): """ Do the reverse of inet_aton, return the quad notation of 'addr' which is a long containing the network address """ quad = [0,0,0,0] for i in (0,1,2,3): quad[i] = (addr >> (8*(3-i))) & 0xFF return "%u.%u.%u.%u" % tuple(quad)
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def series_sort(elem): """ This is a helper function that will be used in key argument of sorted() in order to sort the list of series by series number """ # return int(elem.split("_")[-1]) # USE THIS IF %SeriesDescription_%SeriesNumber return int(elem.split("_")[0])
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import math def underlined(text, chars='=-'): """Underlines a text with extra chars :param text: The text to underline :param chars: The chars used for underlining. They will be repeated as often as necessary to fit the length of the text. :return: a list containi...
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import torch def stack(tensors, *args, **kwargs): """ Concatenates a sequence of tensors along a new dimension. Examples:: >>> import torch >>> import treetensor.torch as ttorch >>> t1 = torch.randint(10, 30, (2, 3)) >>> t1 tensor([[17, 15, 27], [1...
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import json def get_fluid_path(in_scene): """Extract the path to the fluid model that is used in a SPlisHSPlasH scene file. Args: in_scene: Path to a SPlisHSPlasH scene file Returns: The path to the fluid model file. """ with open(in_scene,"r") as f: scene = json.load(f) ...
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import bisect def takeAdjacent(myList, myNumber, left): """ Assumes myList is sorted. Returns closest value to myNumber on the left or right. """ if left: pos = bisect.bisect_left(myList, myNumber) else: pos = bisect.bisect_right(myList, myNumber) if pos == 0: # first item ...
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def make_gram(summary: str, n: int) -> set: """ Extracts the ngrams of a text Args: summary: A `str` corresponding to a summary we want the ngrams from. n: An `int` giving the length of the ngrams. Returns: A `set` of `str` corresponding to the ngrams of the summary. """ ...
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import math def week_of_month(dt): """ Returns the week of the month for the specified date. """ first_day = dt.replace(day=1) dom = dt.day adjusted_dom = dom + first_day.weekday() return int(math.ceil(adjusted_dom / 7.0))
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def is_xpath_selector(selector): """ A basic method to determine if a selector is an xpath selector. """ if ( selector.startswith("/") or selector.startswith("./") or selector.startswith("(") ): return True return False
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def _read_file(path): """Reads a file into a string. Args: path: The path to a file. Returns: The contents of the file. """ with open(path) as f: return f.read()
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def d2_coords(i, j, width=1): """ given the (i,j) get the coords of the neighbouring cells within `width` """ d2 = [(x, y) for x in range(i - width, i + width + 1) for y in range(j - width, j + width + 1)] return d2
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def retry_argument_spec(spec=None): """Creates an argument spec for working with retrying""" arg_spec = (dict( retries=dict(type='int'), retry_pause=dict(type='float', default=1), )) if spec: arg_spec.update(spec) return arg_spec
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def r2h(rgb): """ Convert an RGB-tuple to a hex string. """ return '#%02x%02x%02x' % tuple(rgb)
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import re def truncate_fastq_to_pair_suffix(fn: str) -> str: """ Turn a XXXBLAFOO_R1.fastq.gz filename into XXXBLAFOO_R1. """ extensions = [ r"_001\.fastq\.gz$", # Default Illumina r"\.fastq\.gz$", # ENA/SRA r"\.fasta\.gz$", # occasionally we get FASTA format reads r...
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def CommaSeparatedList(value_list, is_quoted=False): """Concatenates a list of strings. This turns ['a', 'b', 'c'] into a single string 'a, b and c'. It optionally adds quotes (`a') around each element. Used for logging. """ if is_quoted: value_list = ["`" + value + "'" for value in value_list] if le...
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def lowercase_first_string_letter(v:str): """Transform a string to lowercase first letter. Args: v (str): String value to convert Returns: str: Lowercase first letter of v """ return v[0].lower() + v[1:]
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import re def is_valid_password(password): """ Return if a password is valid or not. A valid password should have its length greater than 8, contain at least one digit, one uppercase letter, one lowercase letter and one special character. """ try: is_valid = True is_valid &= ...
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def introduce(person) -> str: """ Introduces a dictionary representation of a person """ return f'Hello my name is {person["name"]} and I am {person["age"]} years old.'
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def safe_int(num): """Transform a string into int type with safety.""" # this function is mainly designed for elasticsearch # since there are lots of bad int types num = num.strip() if '.' in num: # when the num is something like: `88.` return int(float(num)) return int(num)
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def build(cfg, registry, key='name'): """Build a module from config dict. Args: cfg (dict): Config dict. It should at least contain the key. registry (XXX): The registry to search the type from. key (str): the key. Returns: obj: The constructed object. """ assert isi...
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