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from pathlib import Path def _setup_filetree_for_priority_test(tmp_path: Path) -> Path: """ root └─ dir_1 └─ dir_1_1 └─ file_1.py Returns: path for file_1.py """ root_dir = tmp_path / 'root' root_dir.mkdir() dir_1 = root_dir / 'dir_1' dir_1.mkdir() dir_1_1 =...
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def simple_incorrect_scan_and_codes(simple_scan): """ Return a scan and error codes, representing a small mesh which produces a couple of known requirement and advisory statements, and the relevant statement codes. Errors as follows: mesh missing cf_role (but identified from datavar) --> R1...
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def key(request) -> int: """Get instance key.""" return request.param
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def derive_table_from(source): """Ease the typical use case /somewhere/TAB.txt -> TAB.json.""" table = source.stem.upper() return table, f'{table}.json'
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def remove_alignments(group, min_length: int=1000, min_coverage: float=0.2): """ Since MUMmer aligns sections of a sequence, it can produce multiple regions of alignment for a given sequence. We filter out low alignments using this function. Args: group: A pandas group_by group. ...
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import functools def require_owner(message=None): """Decorate a function to require the triggering user to be the bot owner. If they are not, `message` will be said if given.""" def actual_decorator(function): @functools.wraps(function) def guarded(bot, trigger, *args, **kwargs): ...
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import socket def ip_sort_key(ip_address): """Get a sort key for an IPv4 or IPv6 address""" if ':' in ip_address: # IPv6 return b'6' + socket.inet_pton(socket.AF_INET6, ip_address) # IPv4 return b'4' + socket.inet_aton(ip_address)
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def lha2scale(lha): """Extract the high scale from a dictionary eturned by pylha from a DSixTools options file.""" return dict(lha['BLOCK']['SCALES']['values'])[1]
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def generate_dot(dc): """ Generates a dot format graph of docker-compose depends_on between services :param dict dc: Docker comppose configuration loaded as a python dict :rtype: string """ lines = [] lines.append("digraph docker {") for service_name, service in dc["services"].items(): ...
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def find_mirror_next(seq, max_window_size, mirror_centre): """Find the next token that will lead to a mirror pattern. Searches in the range of `window_size` tokens to the left from the `mirror_centre` if it's found. E.g., in [a, b, AND, a] the next token should be 'b' to create a mirror pattern. ...
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import requests def exchange_code_for_token(code, token_url, client_id, client_secret, redirect_uri): """exchange a OAuth2 authorization code for an access token https://docs.github.com/en/free-pro-team@latest/developers/apps/authorizing-oauth-apps#2-users-are-redirected-back-to-your-site-by-github Para...
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def query(query_string, data): """ Return a query string for use in HTML links. For example, if query_string is "?page=foo" and data is "date=200807" this function will return "?page=foo&date=200807" while if query_string were "" it would return "?date=200807". """ if query_s...
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def return_item(item, key, silently=False): """Depending of the type of item, return the value corresponding to `key` or the attribute `key` of the object item. Args: item (dict or object): Python object to explore key (str): key to search in the object silently (bool, optional): wh...
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import json def typeforms_embed(url, selector, options={}, mode='widget'): """Embed a typeforms form. Parameters ---------- url : str Typeform share typeform_url. selector : str CSS selector to place typeform_id into. options : dict, str Accepts a dictionary or JSON as...
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def de_dup_and_sort(input): """ Given an input list of strings, return a list in which the duplicates are removed and the items are sorted. """ input = set(input) input = list(input) input.sort() return input
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def get_volume(shade_client, name_or_id, filters=None): """Get a volume by name or ID. :param name_or_id: Name or ID of the volume. :param filters: A dictionary of meta data to use for further filtering. :returns: A volume ``munch.Munch`` or None if no matching volume is found. """ return shad...
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def generate_group_by_range_and_index_str(group_by, data_str, value_str, index_str): """ Generate the range and index string for GROUP BY expression. Args: group_by (str): the column name to be grouped. data_str (str): a string that represents the t...
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def compute_xi_t(return_t, risk_free_rate, sigma_t): """ Compute innovation xi at time t as a function of return t, rf rate, and sigma t """ return return_t - risk_free_rate + 1/2 * sigma_t
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def _cholesky_solve(M, rhs, dotprodsimp=None): """Solves ``Ax = B`` using Cholesky decomposition, for a general square non-singular matrix. For a non-square matrix with rows > cols, the least squares solution is returned. Parameters ========== dotprodsimp : bool, optional Specifies...
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def rstrip(val: str) -> str: """Remove trailing whitespace.""" return val.rstrip()
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def intprod(xs): """ Product of a sequence of integers """ out = 1 for x in xs: out *= x return out
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def safe_float(val): """ Convert the given value to a float or 0f. """ result = float(0) try: result = float(val) except (ValueError, TypeError): pass return result
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import requests def get_html(url, session_obj=None, headers=None): """ Request to the server and receiving a response, in the form of an html code of a web page. """ try: request = session_obj if session_obj else requests response = request.get(url, timeout = 5, headers=headers) ...
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def _MetadataMessageToDict(metadata_message): """Converts a Metadata message to a dict.""" res = {} if metadata_message: for item in metadata_message.items: res[item.key] = item.value return res
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from pathlib import Path def get_abs_path_from_here(relative_path: str, calling_file_name: str) -> Path: """ return absolute path to file, based on path from the calling location :param calling_file_name: optional name of the calling script that will serce as reference :param relative_path: relative p...
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def lerpv3(a,b,t): """linear interplation (1-t)*a + (t)*b""" return ( (1-t)*a[0] + (t)*b[0], (1-t)*a[1] + (t)*b[1], (1-t)*a[2] + (t)*b[2] )
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def get_venv_name(dockenv_name): """ Helper function to split the user-defined virtual env name out of the full name that includes the dockenv tag :param dockenv_name: The full name to pull the virtual env name out of """ # Format of tage name if dockenv-**NAME**:latest...
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from pathlib import Path from typing import Optional from typing import List import uuid def make_metakernel(kernel_dir: Path, kernels: Optional[List[str]] = None) -> Path: """Create a uniquely-named SPICE metakernel in ``kernel_dir`` and return its path. If ``kernels`` is `None`, this function searches ``ker...
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def _Aij(A, i, j): """Sum of upper-left and lower right blocks of contingency table.""" # See `somersd` References [2] bottom of page 309 return A[:i, :j].sum() + A[i+1:, j+1:].sum()
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from typing import Callable from typing import Any def get_func_name( func: Callable[..., Any], prepend_module: bool = False, repr_fallback: bool = False, ) -> str: """Extract and return the name of **func**. A total of three attempts are performed at retrieving the passed functions name: 1....
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def mimic_case(old_word, new_word): """ >>> print(mimic_case('EtAt', 'état')) ÉtAt """ if len(old_word) != len(new_word): raise ValueError("lengths don't match") return ''.join([ new_word[i].upper() if old_word[i].isupper() else new_word[i].lower() for i in range(len(old_...
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def text_to_word_sequence(text, filters='!"#$%&()*+,-./:;<=>?@[\\]^_`{|}~\t\n', lower=True, split=" ") -> list: """ Convert text to word list :param text: test list :param filters: filter rules, filter all punctuation marks, tabs, newlines, etc. by default :param lower: whether to convert text to lowerc...
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def phase(x): """Returns 1 if the input is even and -1 if it is odd. Mathematically equivalent to (-1)^x""" if x % 2 == 0: return 1 else: return -1
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def calculate_chunk_slices(items_per_chunk, num_items): """Calculate slices for indexing an adapter. Parameters ---------- items_per_chunk: (int) Approximate number of items per chunk. num_items: (int) Total number of items. Returns ------- list of slices """ a...
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import math def rotate_point(x,y,theta): """Rotate a point around the origin by an angle theta. Args: x (float): x coordinate of point. y (float): y coordinate of point. theta (float): rotation angle (rad). Returns: list: [x,y] coordinates of rotated point. """ "...
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def iterable(obj): """Utility to check if object is iterable""" try: iter(obj) except: return False else: return True
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import pathlib def zcoord(path:pathlib.Path) -> float: """ Return the putative Z coordinate for a image file path name """ return int(path.name.split(".")[0]) / 10
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from pathlib import Path def can_override(path: Path, override: bool) -> Path: """Check if it's allowed to override a `path`. Args: path: path, where we are going to write override: permission to override flag Returns: The input `path`to facilitate chaining in mapping in code. ...
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def isLarger(ser1, ser2, fractionTrue=1.0, startIdx=0): """ Checks that arr1[startIdx:] > arr2[startIdx:] Parameters ---------- ser1: pd.Series ser2: pd.Series fractionTrue: float in [0, 1] startIdx: int Returns ------- bool """ numTrue = sum(ser1.loc[startIdx:] > s...
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import glob from itertools import chain from typing import Iterable def poly_iglob(filenames_or_patterns: Iterable, *, recursive=True, ignore_case=True): """ Read sequence of file names with or without wildcard characters. Any wildcards are replaced by matching file names using glob.iglob(). :param f...
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from typing import Iterable from typing import Sequence def report_invalid_whitelist_values( whitelist: Iterable[str], items: Sequence[str], item_type: str ) -> str: """Warns the user if there are entries in ``whitelist`` which don't correspond to any item in ``items``. Helps highlight typos. """ ...
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def _count_of_curr_and_next(rule): """Count tokens to be matched and those to follow them in rule.""" return len(rule.tokens) + len(rule.next_tokens or []) + len(rule.next_classes or [])
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def get_charge(lines): """ Searches through file and finds the charge of the molecule. """ for line in lines: if 'ICHRGE' in line: return line.split()[2] return None
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def tvi(b3, b4, b6): """ Transformed Vegetation Index (Broge and Leblanc, 2001). .. math:: TVI = 0.5 * (120 * (b6 - b3) - 200 * (b4 - b3)) :param b3: Green. :type b3: numpy.ndarray or float :param b4: Red. :type b4: numpy.ndarray or float :param b6: Red-edge 2. :type b6: numpy.ndar...
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from typing import Callable def _derive_template_name(view_function: Callable) -> str: """Derive the template name from the view function's module and name.""" # Select segments between `byceps.blueprints.` and `.views`. module_package_name_segments = view_function.__module__.split('.') blueprint_path...
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def count_incident_type(incidents, type): """ Gets total number of incidents of a certain type :param incidents: dictionary -- set of incidents to parse :param type: string -- key to parse within incidents :return: int -- total incidents """ total = 0 for _, incident in incidents.item...
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def load_data(path): """ Load input data from a given path. Data is stored as word,label\nword,label\n ... :param path: path to file :return: (list of words, list of labels) """ words = [] labels = [] with open(path, encoding='utf-8') as f: lines = f.read().splitlines() for ...
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from typing import List def get_clabe_control_digit(clabe: str) -> int: """Generate the checksum digit for a CLABE. :param clabe: CLABE. :return: The CLABE checksum digit. """ factors = [3, 7, 1] products: List[int] = [] for i, digit in enumerate(clabe[:17]): products.append((int...
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def _getcalday(instcal, date): """ Get index of row for current night in instrument calendar table. """ for i in range(len(instcal['date'])): if instcal['date'][i] in date: return i print('\n Date '+date+' not found in instrument configuration calendar.') raise ValueError('Da...
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def comp(DNA: str, pat_len: int) -> list: """Sort all substrings of pat_len length :param DNA: the string to pull substrings from :type DNA: str :param pat_len: the length of substrings to pull :type pat_len: int :returns: all substrings, sorted :rtype: list (of strs) """ if not DN...
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def get_model_config(ckpt_path): """Returns the model configuration to be used with each checkpoint.""" config = { 'audio_backbone': 'resnet50', 'audio_model_kwargs': { 'bn_config': { 'create_offset': True, 'create_scale': True, 'decay_rate': 0.9, ...
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def get_single_value(group, name): """Return single value from attribute or dataset with given name in group. If `name` is an attribute of the HDF5 group `group`, it is returned, otherwise it is interpreted as an HDF5 dataset of `group` and the last value of `name` is returned. This is meant to retriev...
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import typing def lane_offset_width_meters(shape: typing.Sequence[int], poly_evals: typing.Tuple[typing.List[float], typing.List[float]], xm_per_pix: float) -> typing.Tuple[float, float]: """Calculate center-offset of the lane, given polynomial curves for ...
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def z_inverse(x, mean, std): """The inverse of function z_score""" return x * std + mean
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def get_product_images(product): """Return list of product images that will be placed in product gallery.""" return list(product.images.all())
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import random def choose_between_by_p(l1, l2, p, count): """ Choose `count` elements from `l1` (w/ prob `p`) and `l2` (w/ prob `p`-1). """ assert 0 <= p assert p <= 1 return [random.choice(l1) if random.random() <= p else random.choice(l2) for _ in range(count)]
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def mol_file_basename(tag): """Covert a tag into a molecular data file name""" return 'c%06d.' % tag
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def python_trailing(n): """Count the number of trailing zero bits in abs(n).""" if not n: return 0 t = 0 while not n & 1: n >>= 1 t += 1 return t
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import torch def flip_segment(X_spikes, segment): """ Flips the values of a segment in X_spikes format :param X_spikes: spiking input data from spike generator :param segment: segment in X_spikes to be flipped :return: spiking data with flipped segment """ _, (d, t_start, t_end) = segment ...
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def valueFactory(zeroValue, elemValue): """ Return elemValue converted to a value of the same type as zeroValue. If zeroValue is a sequence, return a sequence of the same type and length, with each element set to elemValue. """ val = zeroValue typ = type(val) try: # If the type i...
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def tts_version(version): """Convert a version string to something the TTS will pronounce correctly. Args: version (str): The version string, e.g. '1.1.2' Returns: str: A pronounceable version string, e.g. '1 point 1 point 2' """ return version.replace('.', ' point ')
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def to_sec(d=0, h=0, m=0, s=0): """Convert Day, Hour, minute, seconds to number of seconds.""" secs = d*86400 secs += h*3600 secs += m*60 secs += s return secs ##################
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def alpha_for_N(comps,Influx=10,Outflux=1000): """calculates alpha based on required outflux for given influx""" c=(Outflux/Influx)**(1/float(comps)) alpha_sol= (c-2)/(c-1) return alpha_sol
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def _created_on_to_timestamp_ms(created_on): """ Converts the Message CreatedOn column to a millisecond timestamp value. CreatedOn is number of 100 nanosecond increments since midnight 0000-01-01. Output is number of millisecond increments since midnight 1970-01-01. """ return created_on / 1000...
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from typing import List def left(lst: List[int], idx: int) -> int: """Return left heap child.""" left_idx = idx * 2 + 1 if left_idx < len(lst): return left_idx else: return -1
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from datetime import datetime def outputSPDX(doc, spdxPath): """ Write SPDX doc, package and files content to disk. Arguments: - doc: BuilderDocument - spdxPath: path to write SPDX content Returns: True on success, False on error. """ try: with open(spdxPath, 'w') as f...
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def write_nonequilibrium_trajectory(nonequilibrium_trajectory, trajectory_filename): """ Write the results of a nonequilibrium switching trajectory to a file. The trajectory is written to an mdtraj hdf5 file. Parameters ---------- nonequilibrium_trajectory : md.Trajectory The trajectory...
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import random def random_IP() -> str: """ Get random IP """ ip = [] for _ in range(0, 4): ip.append(str(random.randint(1, 255))) return ".".join(ip)
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import hashlib def compute_checksum(path, algorithm: str) -> str: """ Generates a hex digest using specified algorithm for a file. """ buffer_size = 65536 hash_builder = hashlib.new(algorithm) with open(path, 'rb') as f: while True: data = f.read(buffer_size) if not d...
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def rev_bit_str(n: int, bitlen: int) -> int: """ Reverses the bitstring of length bitlen of a number n and returns the bitreverses integer. I.e. rev_bits(3, 4) => "0011" => "1100" => 12 """ bits = bin(n)[2:] # Truncate first 2 characters to avoid '0b' start_pow = bitlen - len(bits) return s...
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def pattern_count(pattern, text): """ The number of times that a pattern appears as a substring of text. Args: pattern (str): the substring pattern to find in the given text. text (str): the string space for looking. Returns: String, number of substring pattern that appears in ...
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def sort_seconds(timestamps): """ Sorts a list of 2-tuples by their first element """ return sorted(timestamps, key=lambda tup: tup[0])
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def all_nums(table): """Returns True if table contains only numbers Precondition: table is a (non-ragged) 2d List""" cnt = 0 number_cnt = 0 for row in table: for item in row: cnt += 1 if type(item) in [int, float]: number_cnt += 1 if cnt != number_...
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def e(parameters, p, r_v): """ Returns an expression for the partial pressure of water vapour from the total pressure and the water vapour mixing ratio. :arg parameters: a CompressibleParameters object. :arg p: the pressure in Pa. :arg r_v: the mixing ratio of water vapour. """ epsilon...
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from typing import Dict from typing import Any def check_is_legacy(sample: Dict[str, Any]) -> bool: """ Check if a sample has legacy read files. :param sample: the sample document :return: legacy boolean """ files = sample["files"] return ( all(file.get("raw", False) is False for...
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def genotype_likelihood_index(allele_indices): """Returns the genotype likelihood index for the given allele indices. Args: allele_indices: list(int). The list of allele indices for a given genotype. E.g. diploid homozygous reference is represented as [0, 0]. Returns: The index into the associated...
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import re def text_area_extractor(text): """ Textbox extractor function to preprocess and extract text Args: text: Raw Extracted Text from the News Article Returns: text: Preprocessed and clean text ready for analysis """ text = text.lower() text = re.sub(r'[^a-zA-Z0-9\s]',...
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import calendar import time def time_string_to_unix(time_string, time_format): """Converts time from string to Unix format. Unix format = seconds since 0000 UTC 1 Jan 1970. :param time_string: Time string. :param time_format: Format of time string (example: "%Y%m%d" or "%Y-%m-%d-%H%M%S"). ...
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import click def read_user_variable(var_name, default_value): """Prompt the user for the given variable and return the entered value or the given default. :param str var_name: Variable of the context to query the user :param default_value: Value that will be returned if no input happens """ #...
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def gvariant(lst): """Turn list of strings to gvariant list.""" assert isinstance(lst, list), "{} is not a list".format(lst) content = ", ".join( "'{}'".format(l) for l in lst ) return '[{}]'.format(content)
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def compss_open(file_name, mode='r'): # type: (str, str) -> object """ Dummy compss_open. Open the given file with the defined mode (see builtin open). :param file_name: The file name to open. :param mode: Open mode. Options = [w, r+ or a , r or empty]. Default=r. :return: An object of 'file' ...
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def can_view_cohorts(user): """To access Cohort views user need to be authenticated and either be an admin, or in a group that has the 'view cohorts' permission.""" return user.is_authenticated and user.has_perm('release.view_releasecohort')
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from typing import Counter import math def conditional_entropy(x, y): """ Calculates the conditional entropy of x given y: S(x|y) Wikipedia: https://en.wikipedia.org/wiki/Conditional_entropy :param x: list / NumPy ndarray / Pandas Series A sequence of measurements :param y: list / NumPy ...
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def evaluate_error(model, test_gen, no_test_sam): """ DESCRIPTION: Evaluate the network performance INPUT: The trained model, the test set generator, number of testing images OUTPUT: List of statistics about the performance of the model """ stats = model.evaluate_generator(test_gen, no_test_...
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import torch def get_valid_negative_mask(labels): """ To be a valid negative pair (a,n), - a and n are different embeddings - a and n have the different label """ indices_equal = torch.eye(labels.size(0)).byte() indices_not_equal = ~indices_equal label_not_equal = torch.ne(labels.unsqueeze(1), labels.unsqu...
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def compoundInterestFutureValue(p, r, c, n): """Compound interest future value Returns: future value Input values: p : principal r : interest rate c : number of compounding periods in a year n : (c * t) , total number of compounding periods """ fv = (p * (1 + (r / c))) **...
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def signature(self): """ Returns the signature of the quadratic form, defined as: number of positive eigenvalues - number of negative eigenvalues of the matrix of the quadratic form. INPUT: None OUTPUT: an integer EXAMPLES: sage: Q = DiagonalQuadraticForm(Z...
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def rgb_to_hex(r, g, b): """ Convert RGB color to an Hexadecimal representation """ return "%02x%02x%02x" % (r, g, b)
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def binary_lookup(index, offsets): """ Given a character index, look up the index of it in the offsets. This will be the number at which the next index is greater """ bottom = 0 top = len(offsets) - 1 if index > offsets[top]: return top while top - bottom > 1: mid = ...
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import random def snp(sequence): """ Function takes a sequence string and introduces a single nucleotide polymorphism (SNP) Randomly finds an index in the string and replaces the value at the index with a new letter from the given alphabet. If the value is the same as the previous value, the funct...
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import csv def load_training3(infile): """Load training data with normalized unigram count, hamming distance, and query length. Args: infile: file name to load data from """ X = [] Y = [] with open(infile, 'r') as f: reader = csv.reader(f) for row in reader: if reader.line_num == ...
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def compute_whitespace(d): """Calculates the percentage of empty strings in a two-dimensional list. Parameters ---------- d : list Returns ------- whitespace : float Percentage of empty cells. """ whitespace = 0 r_nempty_cells, c_nempty_cells = [], [] for i in ...
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import time import torch from typing import OrderedDict def load_model(model, model_file, is_restore=False): """Load model. :param model: created model. :param model_file: pretrained model file. :param is_restore: set true to load from model_file. """ t_start = time.time() if isinstance(m...
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import re def camel_case(words): """Convert a noun phrase to a CamelCase identifier.""" result = '' for word in re.split(r'(?:\W|_)+', words): if word: if word[:1].islower(): word = word.capitalize() result += word return result
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def key(profile): """Get a sorting key based on the lower case last name, then firstname""" components = profile["name"].lower().split(" ") return " ".join([components[-1]] + components[:-1])
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def insertion_sort(A, reverse = False): """Assumes A is a list of integers, by default reverse = False Returns the sorted A in non-decreasing order if reverse = False, and in non-increasing order if reverse = True. **************************************** The complexity of the algorithm...
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import random import json def _retrieve_quote(json_filename): """ Retrieve a random quote entry from json_filename, very quickly, without loading the entire file into memory :param str json_filename: Name of .json file to open :return: Tuple of the form: (str(quote_text), str(quote_author)) ...
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def compute_overdose_deaths(run, start_year, end_year, config, intervention): """Compute number of opioid overdose deaths from start_year to end_year. Parameters ---------- run: whynot.dynamics.Run Run object produced by running simulate for the opioid simulator start_year: int ...
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def sequential_search(target, lyst): """ in() 顺序搜索 Returns the position of the target item if found, or -1 otherwise. :param target: :param lyst: :return: """ position = 0 while position < len(lyst): if target == lyst[position]: return position positio...
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def check_obs(idx, obs): """Check every term in every sequence of obs and see if any term is >= idx or < 0. If true, return false. Otherwise return true. """ for o in obs: for term in o: if (term >= idx) or (term < 0): return False return True
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