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def get_params(cls, instance, ignore=None): """Retrieve the initialization parameters corresponding to a class This helper function retrieves the parameters of function __init__ for class 'cls' and returns the value for these parameters in object 'instance'. When using a composition pattern (e.g. with ...
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import json import base64 def claim_dict(encoded_token): """ This function returns a dictionary of claims from a string JWT. Check the token's signature elsewhere. """ # split the three components _, payload, _ = encoded_token.split('.') # decode the payload in the dictionary of claims ...
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import torch def generate_default_mask(data, dim1=None): """ Returns a default mask which allows the model to attend over all positions. :param data: The data of shape (sequence_len, batch_size) :param dim1: The first dimension of the mask. If none, it is equal to sequence_len. :return: """ ...
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def make_onehot(int_list, one_hot_length): """Convert each int to a one-hot vector. A one-hot vector is 0 everywhere except at the index equal to the encoded value. For example: 5 as a one-hot vector is [0, 0, 0, 0, 0, 1, 0, 0, 0, ...] Args: int_list: A list of ints, each of which will get a one-hot en...
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import math def shannon_index(data: list): """考虑了variety/balance,Shamono & Weaver(1962)。 Shannon指数是生态文献中比较流行的多样性指数, 也叫Shannon Diversity Index、Shannon-Wiener指数、Shannon-Weaver指数和Shannon Entropy。 Args: data(list): 列表中存放不同(物种)分类的出现次数 Returns: float: Shannon Diversity Index """ ...
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def read_data(file_path='data.txt', verbose=False): """ params: - file_path: path to file that contains data (default: 'data.txt') - verbose: whether to print information (default: False) return: a tuple that consists of the following: - n: number of data instances - m: number of features o...
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def get_tapis_abaco_image(base_url): """ Determine the docker image name for a tapis notebook associated with a base_url. """ # designsafe tenant: if 'agave.designsafe-ci.org' in base_url: return 'taccsciapps/jupyteruser-ds-abaco:1.2.14' return None
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def _identify_buffer_measurements(df): """Identify the rows of df where 'Sample ID' column contains "buffer" or "blank". Return a list of indices. """ # first find variations on 'blank' and 'buffer' using boolean indexing buffers = df.loc[ (df["Sample ID"].str.contains("lan")) | (df["S...
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import math def get_phase_law(N, d, wavelength, phi): """Computes a phase law given N (number of elements), d (spacing between elements in m), wavelength (in m) and phi (beam steering angle). """ phase_law = []; for n in range(N): phase_law.append(-2 * math.pi * n * d / wavelength * ma...
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def flatten_dataset(features): """ Flattens a multidimensional dataset down to 1 dimension to feed into SVM. """ nsamples, nx, ny = features.shape reshaped_data = features.reshape((nsamples, nx*ny)) return reshaped_data
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def invertx(x, y, **kwargs): """Multiply x by -1""" return -x, y
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def get_n_most_max_character_counts_tuple(dictionary, n): """Returns a tuple containing the character with the n'th highest count in the dictionary along with its count >>> get_n_most_max_character_counts_tuple(dictionary, 5) ('x', 1234) >>> get_n_most_max_character_counts_tuple(dictionary, 6) ('y'...
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def isclose(mat1, mat2, tol=1e-6): """ check element-wise if two tensors are close within some tolerance. Either tensot can be replaced by a scalar """ return (mat1 - mat2).abs_().lt(tol)
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import random import torch def _get_bert_for_sequence_classification_sample_data_with_random_shapes(device): """Returns sample data with random shape to be used with BertForSequenceClassification model""" x = random.randint(1,100) y = random.randint(1,100) input_ids = torch.randint(0, 100, (x, y), dt...
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def total_kicks(meta): """ Adds up the total number of kicks from the match metadata. Args: meta: Match metadata (dict). Returns: Number of kicks (int). """ return meta["kicks_red"] + meta["kicks_blue"]
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import re def slugify(value): """ Turns str into slug value :param str value: Regular string to slugify """ value = re.sub(r'[^\w\s-]', '', value.lower()).strip() return re.sub(r'[-\s]+', '-', value)
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def laysin(cols, rows, c): """ Given the center and the amount of rows and columns, return in which bin the axes is in. """ dx, dy = 1.0/cols, 1.0/rows x, y = int(c[0]/dx), int(c[1]/dy) return x + y*cols
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def tokens_to_text(token_list): """Convert a list of binja tokens to plain text Mostly useful for testing """ return ''.join([tok.text for tok in token_list])
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def changeCase(seq): """Change case to capital of a sequence string.""" return seq.replace('a','A').replace('t','T').replace('c','C').replace('g','G').replace('n','N')
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import warnings def _infer_max_treedepth(fit): """Extract max treedepth from a StanFit4Model instance.""" try: return fit.stan_args[0]["ctrl"]["sampling"]["max_treedepth"] except: warnings.warn("Unable to determine max_treedepth. " + "Using value of 10.") return 10
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def triangular_wave(x, period, amplitude): """ Returns a triangular wave evaluated at x, given its period and amplitude. Equation source: https://en.wikipedia.org/wiki/Triangle_wave """ return (4*amplitude/period) * abs(((x - period/4) % period) - period/2) - amplitude
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def rec_getattr(obj, attr, default): """Get object's attribute. May use dot notation. >>> class C(object): pass >>> a = C() >>> a.b = C() >>> a.b.c = 4 >>> rec_getattr(a, 'b.c') 4 """ if obj is None: return default else: if '.' not in attr: return get...
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import requests def _make_request(method: str, url: str, **kwargs) -> requests.Response: """Make a request. Raises an exception if unsuccessful.""" resp = requests.request(method, url, **kwargs) if resp.status_code < 200 or resp.status_code >= 300: resp.raise_for_status() return resp
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import array def round_float32(x_double): """ Uses the array module to retun a (truncated) 32-bit float representation of a python floating point number (double) """ return array.array('f', [x_double])[0]
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import shutil def workdir(_workdir, tmp_path): """Make a fresh copy of the prepared analysis directory""" path = tmp_path / "analysis" shutil.copytree(_workdir, path) return path
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def almost_there(n): """ Given an integer n, return True if n is within 10 of either 100 or 200 :param n:int :return: bool almost_there(90) --> True almost_there(104) --> True almost_there(150) --> False almost_there(209) --> True """ return (abs(100 - n) <= 10) or (abs(200 - n) ...
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async def user_exists(app, username): """Check if a user exists by username. Parameters ---------- app : aiohttp.web.Application The aiohttp application instance username : str The username of the user Returns ------- exists : bool True if the user exists, False ...
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def fmt_app_name(appname): """Format a sysl_pb2.AppName as a syntactically valid string.""" return ' :: '.join(appname.part)
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def bytes_to_kb(num_bytes): """ Converts bytes to kilobytes. Parameters: num_bytes number of bytes Returns: number of kilobytes """ return num_bytes / 1024.0
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def cast(val, typ=int): """Attempts to cast the given value to the given type otherwise None is returned.""" try: val = typ(val) except: val = None return val
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import re def clean_link(link): """Normalize source, this is needed since some source has http, or www. and others doesn't""" if link.startswith('http') or link.startswith('https'): link = re.sub(r'http[s]?://', '', link) if link.startswith('www.'): link = re.sub(r'www\.', '', link) ...
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def pertenece_a_base(ns: str, b: int) -> bool: """Determina si un número pertenece a una base dada. :param ns: Número a evaluar. :type ns: str :param b: Base a evaluar. :type b: int :return: True si pertenece a la base, False en caso contrario. >>> pertenece_a_base('35235', 6) True ...
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def mark_number(number, board): """ Given a number and a board, mark the number on the board if found and return the board """ for r, row in enumerate(board): for c, cell in enumerate(row): if cell == number: # Mark the cell by overwriting it with -1 and return th...
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def datetime(value): """Formats datetime object to a yyyy-mm-dd hh:mm string.""" return value.strftime('%Y-%m-%d %H:%M')
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def join_namespace(namespace, ident): """ Joins a namespace and a bare identifier into a full identifier. >>> join_namespace('a', 'b') 'a:b' >>> join_namespace('', 'b') ':b' """ return ':'.join([namespace, ident])
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def full_serialize(grading_feedback_schema, grading_data): """ Serialize grading_data as a "Grading feedback" JSON schema object and return the resulting JSON string. """ GradingFeedback = grading_feedback_schema["classes"].GradingFeedback schema_object = GradingFeedback(**grading_data) return s...
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import operator def evaluate_slice_index(arg): """ Helper function to convert a slice argument to an integer, and raise TypeError with a suitable message on failure. """ if hasattr(arg, "__index__"): return operator.index(arg) else: raise TypeError( "slice indices ...
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def query_resource_id(manageiq, resource_type, resource_name): """ Query the resource name in ManageIQ. Returns: the resource id if it exists in manageiq, Fail otherwise. """ resource = manageiq.find_collection_resource_by(resource_type, name=resource_name) if resource: return resou...
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def scrape(soup): """ スクレイピングして結果を Dict で返す Parameters ---------- soup : BeautifulSoup BeautifulSoup オブジェクト Returns ------- scrapedDict : dict スクレイピング結果を格納した辞書 """ # 辞書 (Dict) を用意する # 格納順序を保持する場合は 'import collections' し 'collections.OrderedDict()' で初期化する scrapedDict = {} # ...
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def zero_separation(n): """Zero separation in normalized r based on radial order n.""" return 1 / n ** 2
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def process_labels(labels:str): """ Takes a string of phonemes as input and outputs a list of lowercase phonemes """ return labels.lower().split()
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def is_category_malicious(category, reputation_params): """ determine if category is malicious in reputation_params """ return category and category.lower() in reputation_params['malicious_categories']
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def parse_gerber_number(strnumber, frac_digits): """ Parse a single number of Gerber coordinates. :param strnumber: String containing a number in decimal digits from a coordinate data block, possibly with a leading sign. :type strnumber: str :param frac_digits: Number of digits used for the fra...
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def dict_to_lists(d : dict): """ Flattens a dict into keys and values, in the same order :param d: dict to flatten :return: list of keys, list of values """ keys = d.keys() return keys, [d[k] for k in keys]
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def escape_string_killers(msg): """Helper method to fix string escape in teeworlds commands""" return msg.replace('"', '\\"')
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def is_empty_form(form): """ Considered empty if it passes validation but doesn't have data """ if form.is_valid() and not form.cleaned_data: return True else: # form has errors(isn't valid) or # it doesn't have errors and contains data return False
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import pickle def read_pickle(pkl_path): """Returns loaded data from a pickle file.""" with open(pkl_path, 'rb') as f: data = pickle.load(f) return data
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def load_xyz(xyz_fname): """ Load a .xyz file into PySCF mol format """ with open(xyz_fname, "r") as f: lines = f.readlines() # Remove header lines = lines[2:] output = [] for line in lines: elems = line.split() atom = elems[0].capitalize() x = float(e...
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def IF(logical, value1, value2) -> str: """ Creates an IF statement >>> IF(1=1, 0, 1) 'IF(1=1, 0, 1)' """ return "IF({}, {}, {})".format(logical, value1, value2)
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def remove_last_slash(path): """ Remove the last slash in the given path [if any] """ if path.endswith("/"): path = path[:-1] return path
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from typing import List def get_submission_lines(submission_filename: str) -> List[str]: """Returns the lines of a submission file. Args: submission_filename (str): path of the csv submission file. Returns: List[str]: lines of the submission file. """ with open(submission_filenam...
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def __has_methods(obj, *methods): """ For ducktype testers. Tests for methods to exist on objects. :param obj: :param methods: (variadic) :return: """ for method in methods: if not hasattr(obj, method) or not callable(getattr(obj, method)): return False return Tru...
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def has_logs(gerrit_review): """ If a gerrit review exists, create a link to the review """ if gerrit_review: return "https://gerrit.opnfv.org/gerrit/#/c/%s" % gerrit_review return False
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import functools import asyncio def async_test(f): """ Decorator to transform async unittest coroutines into normal test methods """ @functools.wraps(f) def wrapper(*args, **kwargs): loop = asyncio.get_event_loop() loop.run_until_complete(f(*args, **kwargs)) return wrapper
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def split(path): """Parse a full path and return the collection and the resource name If the path ends by a '/' that's a collection :param path: a path in the collection :type path: str :return: a pair with the collection name and the resource/collection name :type: tuple """ if pa...
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def remove(ele, lst): """ remove all occurences of an element from a list """ pops = [] for i in range(len(lst)): if lst[i] == ele: pops.append(i) return [lst[i] for i in range(len(lst)) if i not in pops]
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def parse_subnets_by_tag(subnets, tag_key, tag_value, return_key='id'): """ Args: subnets (list): List of dictionaries of the subnets that were created. tag_key (str): The tag key you are searching by. tag_value (str): The value of the tag you want to search by. Kwargs: retu...
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def _transform_and_shift(affine_transform, col_indices, row_indices, cellxh, cellyh): """ Transforms indices to coordinates and applies a half pixel shift Args: affine_transform (object): The affine transform. col_indices (1d array): The column indices. row_indices (1d array): The ...
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def nested_docfield_unwrapper(field: str, hitdict, value: dict) -> dict: """ Unwraps the JSON for nested fields in a document that was returned from a search """ if isinstance(value, dict): for (sf, sf_v) in value.items(): nested_docfield_unwrapper(field + '.' + sf, hitdict, sf_v) else: ...
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def sum_first_n_squares(n: int) -> int: """Finds the sum of the squares of the integers from 1 to n.""" return n * (n + 1) * (2 * n + 1) // 6
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def intcode_six(parameter_list, code_list, i): """If first parameter is zero, sets instruction pointer to second parameter. Returns i""" if parameter_list[0] == 0: i = parameter_list[1] return i
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def betamax_parametrized_session(betamax_parametrized_recorder): """Generate a session that has Betamax already installed. See `betamax_parametrized_recorder` fixture. :param betamax_parametrized_recorder: A recorder fixture with a configured request session. :returns: An instantiated ...
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import torch def effective_sample_size(log_weights): """Kish effective sample size; log weights don't have to be normalized""" return torch.exp(2*torch.logsumexp(log_weights, dim=0) - torch.logsumexp(2*log_weights, dim=0))
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import operator def sort_dict_by_value(dict_, reverse=True): """ 按照values排序字典 :param dict_: 待排序字典 :param reverse: 默认从大到小 :return: 排序后的字典 """ return sorted(dict_.items(), key=operator.itemgetter(1), reverse=reverse)
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def set(field, val): """ Set a given field to ``val``. """ def transform(doc): doc[field] = val return transform
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def islist(x): """Is an object a python list""" return type(x) is list
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import re def segment(text): """。や文末記号で文を分割する関数 Args: text (string): テキスト Returns: list of string: 分割されたテキストの配列 """ # 改行削除 text = text.replace("\n", "") # 。!?の後に改行追加 pattern = re.compile(r"(。|!|?|\?|\!)") text = pattern.sub(r"\1\n", text) # 改行で分割 splited =...
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from pathlib import Path def find_files(src_path: Path, glob_pattern: str) -> list[Path]: """ Returns a list of path objects to the files matching the glob pattern. Searches in `src_path` """ files = src_path.glob(glob_pattern) paths = [Path(file) for file in files] return paths
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import re def is_a_number(x): """This function determines if its argument, x, is in the format of a number. It can be number can be in integer, floating point, scientific, or engineering format. The function returns True if the argument is formattted like a number, and False otherwise.""" num...
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def partition_fxn(output_str): """ Parses the MESSPF output file string for the parition function and related information for a single species. :param output_str: string of lines for MESSPF output file :type output_str: str :return temps: List of temperatures :rtype: float(...
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def compare_strings_in_list(list_of_strings): """Compares the list of strings recursively, failing fast when it finds more than 1 non-matching character. :param list_of_strings: The list of strings to iterate through, which gets smaller by one with each loop. :return: The two strings that match. -----...
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from typing import Any def _is_tuple(item: Any) -> bool: """Verifies if item instance is a tuple. Args: item: an item to verify. Returns: `True` if verified, `False` otherwise. """ return isinstance(item, tuple)
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def is_in_element(coords, data_labeled): """ Evaluate if the given coords are in a element. Parameters --------- coords: Tuple Contains the indices to check data_labeled : NdArray Data with elements labeled Returns --------- Boolean True if coords point to a...
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def split_dict(inp, *keyses): """Split an input dict into multiple dicts according to lists of keys Args: ind (dict): input dictionary, usually kwargs *keyses (tuple of lists): Variable length argument list that contains keys to split. That is, keyses itself is a tuple ...
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def region(lat, lon): """ Return the SRTM1 region number of a given lat, lon. Map of regions: http://dds.cr.usgs.gov/srtm/version2_1/SRTM1/Region_definition.jpg """ if 38 <= lat and lat < 50 and -125 <= lon and lon < -111: return 1 if 38 <= lat and lat < 50 and -111 <= ...
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def get_channels_first_permutation(spatial): """Returns a permutation to make a (N, ..., C) array into (N, C, ...).""" return [0, spatial + 1] + list(range(1, spatial + 1))
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def generateDiscretizedValue(value, point_ranges, min_value, max_value): """ Generate discrete symbol based on range This function computes the discrete symbol representation of the value based on the point ranges supplied. The representation will be lowerRange..upperRange. Note: point_ranges must ...
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from typing import Callable def find_first_match(condition: Callable) -> int: """ :param condition: Condition that number needs to match. The condition is assumed to be valid for all integers staring from an initial value. :return: First integer for which condition is valid. """ ...
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def _get_includes(header): """ Returns list of include directives Parameters ---------- header : str CppHeader Returns ------- includes : list List of include directive strings """ includes = [] for inc in header.includes: includes.append(f'#include ...
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import torch def xyxy2xywh(xyxy): """Convert bounding box enconding from [x1, y1, x2, y2] to [x, y, w, h].""" # the input tensor must have four components in the last dimension xywh = torch.zeros_like(xyxy) xywh[:, 0] = (xyxy[:, 0] + xyxy[:, 2]) / 2 xywh[:, 1] = (xyxy[:, 1] + xyxy[:, 3]) / 2 x...
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def create_uniform_grid(low, high, bins=(10, 10)): """Define a uniformly-spaced grid that can be used to discretize a space. Parameters ---------- low : array_like Lower bounds for each dimension of the continuous space. high : array_like Upper bounds for each dimension of the c...
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def url_path_param_quoting(param): """Quote URL path parameters Convert '/' to _FORWARDSLASH_ - otherwise is interpreted as additional path parameter gunicorn processes the path prior to Falcon and interprets the correct quoting of %2F into a slash """ return param.replace("/", "_FORWAR...
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def listify(llist): """Encapsulate l with list[] if not.""" return [llist] if not isinstance(llist, list) else llist
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def fibonacci(n): """ >>> fibonacci(0) 0 >>> fibonacci(1) 1 >>> fibonacci(10) 55 """ if n < 2: return n else: return fibonacci(n - 1) + fibonacci(n - 2)
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def elem_resolution(elem): """formatting of element name to remove resolution for ELEMENT2 instrument""" elem = elem.replace('(LR)', '').replace('(MR)', '').replace('(HR)', '') return elem
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import json def recv(fh): """ Receive a JSON-encoded message from the given file object. """ s = fh.readline() return json.loads(s)
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def certificate_signing_status_get(handle): """ This api checks the status of the certificate generation request submitted previously Args: handle (Imchandle) Returns: Status of the certificate generation activity (string) """ mo = handle.query_classid("GenerateCertificate...
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def brg_to_rgb(brg_colour): """Reorders RGB colour value used by DAWN's LED strip to standard RGB order""" return ( brg_colour[1], brg_colour[2], brg_colour[0] )
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async def rollover(es, params): """ Runs a rollover operation against Elasticsearch. It expects the parameter hash to contain a key "alias" specifying the alias to rollover as well as a key "body" containing the actual rollover request and associated conditions. """ await es.indices.rollover(a...
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import importlib def _load_player(modulename, package='.'): """ Load a Player class given the name of a module. :param modulename: where to look for the Player class (name of a module) :param package: where to look for the module (relative package) :return: the Player class (a class object) ...
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def to_domain(pre, org): """Appends pre to org to create a domain name""" return pre + "." + org["Domain"]
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def shift_tier(vector, base_name, left_orders, right_orders, oob="∅"): """ Compute shifted versions of a vector. Parameters ---------- vector : list Vector to be shifted. base_name : str Base name of the tier. left_orders: list of int List of left contexts to include...
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def _new_versions(quay, conda): """Calculate the versions that are in conda but not on quay.io.""" sconda = set(conda) squay = set(quay) if quay else set() return sconda - squay
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from bs4 import BeautifulSoup def extract_text(html: str) -> str: """Extract plaintext from HTML.""" soup = BeautifulSoup(html, 'html.parser') plaintexts = [p.text for p in soup.find_all(['h1', 'h2', 'h3', 'p'])] return ' '.join(plaintexts)
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def RotInv(R): """Inverts a rotation matrix :param R: A rotation matrix :return: The inverse of R Example Input: R = np.array([[0, 0, 1], [1, 0, 0], [0, 1, 0]]) Output: np.array([[0, 1, 0], [0, 0, 1], [1,...
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def valid_sec(string): """Check if string is a valid IP address section""" if len(string) == 0: return False num = int(string) if string != str(num): # invalid string like "000" -- only one "0" is okay return False return num >= 0 and num <= 255
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def head_compose(*decomposition_functions): """Compose the first function with all the remaining functions.""" main_decomposition_function = decomposition_functions[0] argument_decomposition_functions = [f for f in decomposition_functions[1:]] def head_composition(in_graph_component): graph_com...
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def previous_series_is_sbref(seqinfo, index): """ Checks if the previous series is a SBRef image seqinfo: list with the sequences information index: index of the series, so the previous series would be index-1 """ return ( index > 0 and seqinfo[index - 1].series_description.lower...
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def deps(dict_1040): """ A function to calculate no. of dependents. This currently goes up to 4 dependents. """ dep_count = 0 #while counter = 1 while counter <= 4 and dict_1040["Dep" + str(counter)]["FN_LN"] != "": counter += 1 dep_count += 1 return dep_count
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def isstream(stream): """Check that the term passed as an argument is a stream-term. A stream-term is a compound term of the form '$stream'(N), where N is an integer that uniquely identify the stream.""" return ((stream.name == "$stream") and stream.arity == 1 and isinstance(st...
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