content stringlengths 35 416k | sha1 stringlengths 40 40 | id int64 0 710k |
|---|---|---|
import argparse
from sys import version
def cmdLineHandler():
"""
Command Line Handler
@param return: Instance of class argparse.Namespace containing all the parsed command line arguments.
"""
parser = argparse.ArgumentParser(description="Run Leo-Babel Tests", usage='%(prog)s [options] tests re... | b672e6b035fae7eb2cca816b6eb6e47b55ecc7d2 | 657,585 |
import math
def entropy(features):
"""
Calculates the entropy of all the categories for every feature.
Parameters
----------
features : dictionary
a dictionary of features with keys as feature name and values as objects of
feature class.
Returns
-------
featu... | 232cee07ca9983c6ba0651dab945a8a08534b33f | 657,586 |
import json
def get_keys_and_secrets():
"""
Function to aggregate all keys and secrets for simplicity and return an easy tuple to parse
"""
## Need to add your own details.json with your keys and secrets ##
credentials = {}
with open("details.json",'r') as file:
credentials = json.load... | 9e557d54e587ad737a6d7cb962ee505cdc885529 | 657,587 |
import re
def get_life_range(source):
"""
Return the birth and death year from _source (as a tuple).
Return empty strings if not available.
"""
years = []
for event in ["from", "to"]:
if source["lifespan"].get(event):
date = source["lifespan"][event].get("date", "")
... | c85e9446ebcf8ed6f8019f84a61c07989ad1c8f0 | 657,589 |
def reverse_and_add(n):
"""Returns n + reversed(n)."""
return n + int(str(n)[::-1]) | 67052b91a66d921dc13e6d481c83180d388a90ca | 657,590 |
def one(s):
"""Get one element of a set"""
return next(iter(s)) | 45ce1607e5d4b6bf2fc53cfc2da5602ccdc83910 | 657,591 |
def empty_string():
"""Return string."""
return '' | 316ebc6dfb4db887397a5655e58fcc90a8944c1f | 657,592 |
def boxes_to_geojson(boxes, class_ids, crs_transformer, class_map,
scores=None):
"""Convert boxes and associated data into a GeoJSON dict.
Args:
boxes: list of Box in pixel row/col format.
class_ids: list of int (one for each box)
crs_transformer: CRSTransformer use... | ddf258d8a25a227ff00b7d036149408e7a2afe59 | 657,593 |
def perturb(x, prn):
"""
Randomly perturb an integer point.
Parameters
----------
x : tuple of int
Point to be perturbed
prn : prng.MRG32k3a object
Returns
-------
tuple of float
The perturbed point
"""
q = len(x)
return tuple(x[i] + 0.3*(prn.random() - ... | ea3156b3b6ca2993d7d6c9c713d9f5ae93b0d9cd | 657,594 |
def create_input(afferetntFiringRate,time):
""" Load previously computed affarent inputs """
afferents = {}
afferents['GM'] = {}
dtUpdateAfferent = 5.
afferents['GM']['Iaf'] = [afferetntFiringRate]*(int(time/dtUpdateAfferent)+1)
afferentsInput = [afferents,dtUpdateAfferent]
return afferentsInput | 09b8b93def996e728182c8ce1c4be3138326546f | 657,595 |
import re
def generate_content_type(type, version=2):
"""
Generate the Content-Type header, including a version number
Content-Types look like: application/vnd.ozp-iwc+json;version=1
"""
try:
version = re.findall(r'version=(\d+)', type)[0]
# version number found already - just use... | 7aa9669f9c567a4526de45da3b57bf952cb22011 | 657,596 |
def dimension_constraint():
""" A helper function to restric dimensions """
def _dim_check(attrs):
if len(attrs['pool_size']) in [1, 2, 3]:
return True
return False
return _dim_check, "Only 1d, 2d, 3d kernel supported." | ce53b088b596bfd4cd9f122ecc80028e35848934 | 657,597 |
def compute_P(new_h, past_observations):
"""Computes weighting factor.
Parameters
----------
new_h : float
Altitude of current observation.
past_observations : list
List of past ``Observation`` objects of the same source.
"""
if len(past_observations) == 0:
P = 1
... | 7cdc27ab3ad917e63ed651a3a6b4c67c177bf79b | 657,598 |
import os
def output_path_concat(path, im_path):
"""Creates a file path of an image
Returns an output file path for the resized images
Parameters
----------
path: a path (str)
a string that lead to an existing file path
im_path: an image path (str)
a string that leads to an e... | 659ae45d30b84dad8e28d18d0840303edfde9132 | 657,599 |
import six
def greedy_max_inden_setcover(candidate_sets_dict, items, max_covers=None):
"""
greedy algorithm for maximum independent set cover
Covers items with sets from candidate sets. Could be made faster.
CommandLine:
python -m utool.util_alg --test-greedy_max_inden_setcover
Example0... | 2545990e0a74102d9137bc37a12e661d0e184a0c | 657,600 |
def LogFiles(log_prefix):
"""Determines the filenames for the instmake log and the make output log
by using an arbitrary prefix. Returns a tuple of the two filenames
(instmake_log, make_log)."""
imlog = log_prefix + ".imlog"
mklog = log_prefix + ".make.out"
return (imlog, mklog) | f96644abdf557a4300226200b130a42093a84add | 657,601 |
import os
def parse_pres_pipes(pres_desc_str):
"""
Parse presentation structure.
This function separates the code of the different slides of the
presentation.
"""
# remove comment lines
pres_desc_lines = pres_desc_str.splitlines()
pres_desc_lines_nocomment = []
for line in pres_des... | fea466d6f0a5945de9f22741927f300041e56c56 | 657,602 |
import json
def to_json(response):
"""" Convert response to JSON """
return json.loads(response.content.decode("utf-8")) | 41e06b184c354b9ea8f7e56dea5ea968529d02ba | 657,603 |
def scalar_ne(x, y):
"""Implement `scalar_ne`."""
return x != y | de68a171645f65d34c32d6c4869c5c219cdf02ed | 657,604 |
def test_apply(plane):
"""Test whether the apply method works with numpy functions."""
def return_array(image):
return image
def return_scalar(image):
return 123
assert plane.apply(return_array) == plane
assert plane.apply(return_scalar) == 123 | 1847b08a9b24e0e4568f6e887a75c3dbf662406c | 657,605 |
import os
def make_local_filename(out_path: str, url: str) -> str:
"""
Choose a local filename for a given URL.
"""
filename = os.path.join(out_path, url).replace(":", "")
if filename.endswith("/") or os.path.isdir(filename):
filename += "index.html"
elif not filename.endswith(".html... | 225f6b38df81920d9b125a7f3089e57fe1170b56 | 657,607 |
def mapVal(inputPos, in_min, in_max, out_min, out_max):
""" This function will linearly scale an incoming value
belonging to a certain range (in_max - in_min) to a new
value in the out range (out_max - out_min). """
scale = ((out_max - out_min) / (in_max - in_min))
return float(((in... | ce360266bd061ed82771e08b2480300b4c64ec8e | 657,608 |
from typing import Union
from typing import AnyStr
from typing import Iterable
def is_blank(obj: Union[AnyStr, Iterable, None]) -> bool:
"""
True if line is empty string, None, string that contains only spaces and
space like characters, or line is iterable that contains only these kinds
of strings/obj... | 9d93ce0eccaa65a10302a13111bcb8ca94d39b1e | 657,609 |
def _convert_to_transformer_inputs(question, answer, tokenizer, max_sequence_length):
"""Converts tokenized input to ids, masks and segments for transformer (including bert)"""
def return_id(str1, str2, truncation_strategy, length):
inputs = tokenizer.encode_plus(str1, str2,
add_specia... | 4d1835b53a10b2fe80db82af60d066576e9261fd | 657,610 |
import re
def parse_requirements(*filenames):
"""
We generate our install_requires from the pip-requires and test-requires
files so that we don't have to maintain the dependency definitions in
two places.
"""
requirements = []
for f in filenames:
for line in open(f, 'r').read().spl... | 2b3f95c6f36b09285b3b6a774fa92d2cda12b587 | 657,611 |
from pathlib import Path
import re
from typing import Dict
def find_latest_xml_file(dir_name: Path) -> Path:
"""
Find the latest timestamped xml files, with un-timestamped files as a fallback if no timestamped file is found
:raise FileNotFoundError: if either file can't be found
"""
name_pattern ... | ebfa9496ac46714092fe9b5dd35ea2b5a890197e | 657,612 |
def translate(text, conversion_dict, before=lambda _: _):
""" Translate words from a text using a conversion dictionary
@brief text The text to be translated
@brief conversion_dict The conversion dictionary
@brief before A function to transform the input
"""
# if empty:
if not text: return ... | d597246ed74205e5911d1a2d6a8485546e390c8d | 657,613 |
def prune_by_tum_detect(iqms):
"""Prunes to only contain IQMs for imgs with identifiable tumour
Parameters
----------
iqms : dict
The dict of IQMs for one beamformer
Returns
-------
pruned_iqms : dict
The dict of the IQMs for all images which had an identifiable
tum... | ebddbc482190b420d9ae1fad8be4d3e35b07aaad | 657,614 |
import logging
from datetime import datetime
def log_time(target, message, log_method=None, target_args=None, target_kwargs=None):
"""Execute target and log the start/elapsed time before and after execution"""
logger = logging.info
if log_method is not None:
logger = log_method
start_time = datetime.now()
lo... | 9a7387338fea9c26807ab71f40caebc0b378adbe | 657,615 |
def extract_exposed_seqeunces(sequence, distlist, cutofffreq):
"""(str,[float, str], float) ->[str,str...]
2013-12-02 18:51 WEV this should index the dotbrackets
and then pull the sequences from the components
"""
minimumnumberofbases = 1
#print sequence
#print distlist
listofstartstop =... | 4228316b2b5d2db5781b7dec535bf0b5b1bc3f07 | 657,616 |
def lowercase_f(x):
"""
Returns all strings in a Pandas Series `x` in lowercase.
"""
return x.str.lower() | 6573cc1d0b5d28ea916ff9a4632ed89fa0038456 | 657,617 |
from typing import Any
def invert_results_dict(
results: dict[str, dict[str, dict[str, dict[str, list]]]]
) -> list[dict[str, Any]]:
"""
Flatten the results nested dictionary into a CSV-writable format.
Results has the following nested structure as input:
dict[directory, dict[trial, dict[cut, dict... | 99fdfad9a8d72ee155f2e50168d9e71220c7e85f | 657,618 |
def get_neighbor_verts(vertex):
""" Return the neighbor vertices of a vertex! """
edges = vertex.link_edges[:]
relevant_neighbour_verts = {v for e in edges for v in e.verts[:] if v != vertex}
return relevant_neighbour_verts | 3163e2471d0bc6493cbb5b29a0c14a8e2432f783 | 657,619 |
import os
def read_register_result(resultpath, id1, id2):
"""
Read the registration result of {id1} & {id2} from the resultpath
Return values contain the inlier_number, inlier_ratio, flag(indicating whether this pair is a ground truth match).
"""
# cloud_bin_s = f'Hokuyo_{id1}'
# cloud_bin_t =... | 4765db0fc5746a5aa6c373d20f619658de7a936f | 657,620 |
def _construct_grounding_map(rows):
"""Construct grounding map from rows in a grounding_map csv file
Parameters
----------
rows : list
List of rows from a grounding map csv file. File should contain seven
columns, the first of which is an agent text. The remaining columns
contai... | 54b6dfdba6b2e9dd9ece2bb8c902efc4e0e33aad | 657,621 |
def check_password_format(password, username, email):
"""
Checks that the password adheres to the rules defined by this function.
See `password_requirements`.
:param password:
:param username:
:param email:
:return: True if ok
"""
if not ((any(s.isupper() for s in password)) and (any... | e1de73447fdc55ad978edab75e36e27267d2669f | 657,622 |
from typing import Optional
def get_next_id(current_id: int, size: int, total: int) -> Optional[int]:
"""Get next id.
Assumes a simple list.
Args:
current_id: Current element index.
size: Size of a page.
total: Total elements.
Returns:
``None``, if there is no next p... | bfaf133973f34383e335b85693170905035c3e04 | 657,624 |
def _parse_offset_limit(request):
"""Parse offset and limit values from a given Flask request and return
a tuple containing both.
"""
offset = request.args.get("offset", default=0, type=int)
limit = request.args.get("limit", default=None, type=int)
if limit is not None:
limit = offset + ... | 61ac9d1ed69b82cade39754612d08749a4566d3b | 657,625 |
def calcDailyTravelDistance(self):
"""
:return: Returns daily travel distance per household
"""
dailyDistances = self.data.loc[:, ['hhPersonID', 'tripDistance']].groupby(by=['hhPersonID']).sum()
return dailyDistances.mean() | 4a432bd20dd1ce14514a3d3fd9b07456b9d6dada | 657,626 |
def split_to_sections(text) -> list[str]:
""" "Return the list of text sections.
The separator of the sections is '--\n' line in the original text
"""
lines = text.split("\n")
sections = []
section_lines = []
for line in lines:
if line == "--":
section = "\n".join(sectio... | 1560105b33fbed329f4812513838e85509152b46 | 657,627 |
import torch
def trans_imu_smooth(trans_params, imu_trans):
"""
:param trans_params:
:param imu_trans:
:return:
"""
trans_diffs = torch.norm(trans_params[:-1,:] - trans_params[1:, :], dim =1)
imu_diffs = torch.norm(torch.tensor(imu_trans[:-1,:] - imu_trans[1:, :], dtype = torch.float, devi... | ff8e549ca3c0c85de39e36a551f0dd0b375e8bd6 | 657,628 |
import numpy
def _sample_over_ranges(rngs, nsamp):
""" randomly sample over several ranges
"""
nrng = len(rngs)
samp_mat = numpy.random.rand(nsamp, nrng)
for i, (start, stop) in enumerate(rngs):
samp_mat[:, i] = samp_mat[:, i] * (stop - start) + start
return tuple(map(tuple, samp_mat)) | b48f2813b51535b1c7d293e69d1dc1a54a4c36be | 657,629 |
def pk_intersection_finder(query_1, query_2):
"""This takes two querysets and finds the intersection between the two
queries pks. One query needs a dog.pk attribute and the other .pk)
Returns a list."""
query_1_pks = set()
for item in query_1:
query_1_pks.add(item.dog.pk)
query_2_pks = ... | 8458b0ea18a93c9fcb396e244a4f9968c760cbaf | 657,630 |
import re
def sectionRecursive(configtree, section):
""" parse configtree recursively and return config with the desired
matches in dict section """
ret = dict()
branchkeys = configtree.keys()
if len(section) == 0:
# no more section matches available, return whole subtree
return co... | 278a08c8b2794d2a09ced638261940099fb1989f | 657,631 |
def decode_core(device, corefile, result_file='', timeout=300):
""" Function to decode the given corefile """
cmd = "/auto/mcp-project1/decoder/decode.py --noemail {cf}".format(
cf=corefile)
decode_output = ''
try:
decode_output = device.api.execute("{command}".format(command=cmd),
... | 213bc526addc2c79550851d7f70653cf894644e0 | 657,632 |
def location(self) -> str:
"""Get the raw location inside the document
:returns: The location inside the document
"""
return self.url.split("#")[1] | 191a0041645ecd4179dd901d111b863daec908ab | 657,633 |
def ucfirst(string):
"""
Convert the first character of a string to uppercase.
"""
return string[:1].upper() + string[1:] | 95b495be087e4a779713626ea22628e558c6c6a7 | 657,634 |
import re
def is_reinstate_line(op):
"""Tell if line is one of the legal lines to exist within entry push."""
# Zeroing.
match = re.match(r'\s*xor.*\s+%(\S+)\s?,.*', op, re.IGNORECASE)
if match:
return True
# Moving labels into registers.
match = re.match(r'\s*mov\w\s+\$[a-zA-Z_]\S*,\s+%\w+$', op, re.... | b6e45a6aa218d284ee0fa9daa31182524d331d1a | 657,635 |
def define_tuner_hparam_space(hparam_space_type):
"""Define tunable hparams for grid search."""
if hparam_space_type != 'ga':
raise ValueError('Hparam space is not valid: "%s"' % hparam_space_type)
return {
'population_size': [10, 25, 50, 100, 500],
'crossover_rate': [0.2, 0.5, 0.7, 0.9, 0.95],
... | ab9d3d11a664d0526945fe16ca9173d80e6454f9 | 657,636 |
def create_demo(ec2):
"""Create EC2 Node Demo
>>> from ec2demo import get_ec2, create_demo
>>> ec2 = get_ec2()
>>> node = create_demo(ec2)
>>> node
<Node: uuid=9d1..., name=i-7b1fa910, state=3, public_ip=[''], ...>
And to destroy the node:
>>> node.destroy()
If you've accidentall... | 7d9fd9fb830cf7b483b452de20828204799b2beb | 657,637 |
def reverse_mac(rmac):
"""Change LE order to BE."""
if len(rmac) != 12:
return None
return (
rmac[10:12]
+ rmac[8:10]
+ rmac[6:8]
+ rmac[4:6]
+ rmac[2:4]
+ rmac[0:2]
) | 83c2be1df99524250f4419aabcbe16ab4bebd94e | 657,638 |
import csv
def read_lun_file(filename):
"""Read lun csv file and return the list."""
lunlist = []
with open(filename, 'r') as cvsfile:
filereader = csv.reader(cvsfile, delimiter=',')
for row in filereader:
lunlist.append(row)
del lunlist[0]
return lunlist | 4ad633dcb673c50fc43d9ee81edb88d34c4b2f89 | 657,639 |
def IC_NIS(ic_cc, ic_ca, ic_pp, ic_pa, p_nis_a, p_nis_c):
"""
Calculates the predicted binding affinity value
based on the IC-NIS model.
"""
return -0.09459*ic_cc + -0.10007*ic_ca + 0.19577*ic_pp + -0.22671*ic_pa \
+ 0.18681*p_nis_a + 0.13810*p_nis_c + -15.9433 | 8b4d549cd2eb9162c33a8f984c295a516cb88ad3 | 657,641 |
import random
def select_j_rand(i, m):
"""
takes 2 values: the index of our first alpha,
and the total number of alphas.
A value is randomly chosen,
as long as it isn't i
"""
j = i
while(j == i):
j = int(random.uniform(0, m))
return j | 1a2c348ba036c9509e84de7e734618ceae5cb2a7 | 657,642 |
def cga(geoact, geoacs, subff2):
"""
GEOACT: GA CENTER POINT
GEOACS: GA AREA C/SUB
0=None
1=Quest
2=<I2
3=<O2
4=<1/2 DA
5=<1DA
6=<2DA
7=>2DA
8=CG
Returns:
0, 1, 88
"""
if geoact == 2 or (geoact == 1 and 2 <= geoacs... | 4cfe79d76f7c7e0fe2e5ebc136b5d772627fba72 | 657,643 |
import re
def omitCommas(row):
"""
Locates data parts with double quotes and removes commas within them.
Parameters:
row (str): The csv string to be searched for double quotes.
Returns:
(str): The same string without double quotes and extra commas.
"""
cases = re.findall('"[^"]+"', row)
replaced = [re.... | 014d90a3d0fa373a58e767a1b8efdb845720737b | 657,645 |
def get_session_workbook(project_path, date_info):
"""
"""
session_path = project_path+"Observations/dss28/%4d/%03d/" % (date_info[1],date_info[4])
wb_name = "%4d-%03d.xlsx" % (date_info[1],date_info[4])
wb_file = session_path+"/"+wb_name
return wb_name, wb_file | 682749ccfe83efb9512a90998e134610a556b5f2 | 657,647 |
def clip(value, minimum=-float("inf"), maximum=float("inf")):
"""Signal hard clipping"""
if value < minimum:
return minimum
if value > maximum:
return maximum
return value | d8171e2660960c99e32f3f91c0654c6ee7fdeeeb | 657,648 |
def extract_property(search_str, str):
"""
This function extracts the first string that matches a given search string from Psi-Mi formatted table's cell
:param search_str: A Psi-Mi property that needs to be extracted from a Psi-Mi cell
:type search_str: string
:param str: A cell of the Psi-Mi format... | 78875bed65c465dd70b557d56d8a80cf94a29897 | 657,649 |
import os
def getFilename(RECORDS_DIR='myo_data'):
"""
Function to allow user to pick filename of CSV to load in the
input records directory. Filename is picked by its
index within the directory which is output to the user
along with the associated filename. If an inval... | 144f2ed40aaa4d9d86aa4ba3a5ad9119313c8bc3 | 657,650 |
def d8n_get_all_images_topic_bag(bag):
"""
Returns the (name, type) of all topics that look like images.
"""
tat = bag.get_type_and_topic_info()
consider_images = [
'sensor_msgs/Image',
'sensor_msgs/CompressedImage',
]
all_types = set()
found = []
topics = tat.t... | 1093cb8bb13946a170acf2333bcae1617db163d9 | 657,652 |
from typing import Dict
from typing import Any
from pathlib import Path
from typing import Optional
import json
def check_source(pmfpconf: Dict[str, Any], sourcepackdir: Path, template_string: str, env: Optional[str] = None, language: Optional[str] = None) -> Dict[str, Any]:
"""校验组件所在模板库的信息,通过的话返回模板库信息"""
wit... | aeaed36a985803cf58c5865ddd681cbe77d1e127 | 657,653 |
def get_window_content(center, whole_context, windows_size):
"""given whole context, center then return window's content in range windows_size by character
Args:
center(str): center word
whole_context(str): whole context
windows_size(int): window size
Returns:
list: window'... | bcc4dfda2fd7344a92d8315717df339e7784fc4f | 657,654 |
def estimatePublishedYear(authorYearOfBirth, authorYearOfDeath):
"""
@param authorYearOfBirth:
@param authorYearOfDeath:
@return:
@rtype text
"""
estimatedPublishedYear = ''
if authorYearOfBirth > 1800:
estimatedPublishedYear = (authorYearOfBirth + authorYearOfDeath) // 2
... | 21d5db682db4650424474880b424940dcecb4ffd | 657,655 |
from functools import reduce
import operator
def extract_key_paths(d, key_paths, field_naming='full', use_default=False, default_val=None):
"""
getting with a key list or "."-separated string
:param d: dict
:param key_path: list or "."-separated string of keys
:param field_naming: 'full' (default)... | 8a9cf629e5ba6e89943c46a072b2503c147629e7 | 657,656 |
from typing import Optional
from pathlib import Path
import os
def get_access_token(tokenfile=None, log=None) -> Optional[str]:
"""Determine the access token from the mounted configmap (nublado2),
secret (nublado1), or environment (either). Prefer the mounted version
since it can be updated, while the en... | fe9678530bf10fa89ec3ac277f9afcb950235b90 | 657,657 |
from typing import Any
def is_zero_or_mod_zero(mod: int, counter: int, *, ret: Any = True, alt: Any = False) -> Any:
"""
test if mod is zero or if counter % mod is 0
if any of the tests are true return ret
else return alt
:param mod:
:param counter:
:param ret:
:param alt:
:retu... | 338654d073624076093bd9452046d36889d3971e | 657,658 |
from typing import Optional
def validate_text(text: str) -> Optional[int]:
"""
Validate text message.
:param text: text to validate
"""
if text.lower().startswith('sprint '):
sprint, sprint_number = text.split(' ', 1)
try:
sprint_number = int(sprint_number)
exc... | c1dbfafdb90faa1b1eba109edf54b18ce84a2e69 | 657,659 |
import re
def sanitize_filename(filename, allow_spaces=False):
"""Strips invalid characters from a filename.
Considers `POSIX "fully portable filenames"
<http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282>`__
valid. These include:
A-Z a-z 0-9 ._-
Filename... | a239c4488c97a6c1af1a4531a2cec1723353ce1f | 657,661 |
def get_zip_filename(book_id):
""" Get the filename for a zip document with the book identifier. """
return book_id + ".zip" | 2919ca946c887a4c51a98af2d7abea1c74816161 | 657,662 |
def eta1_Vargaftik_and_Yargin(TK):
"""Dynamic viscosity of Li monomers
Dynamic viscosity of the monomers as a function of temperature.
Parameters
----------
TK
K, temperature
Returns
-------
η, Pa s
References
----------
Vargaftik, N B, and V S Yargin.
Ch 7.4:... | f8c08b3f59d9b0ed97ade08f89928e58c0d546a8 | 657,663 |
def _char_police(string):
"""If a string has bad chars, ignore it.
Unclear how a NUL would get in profile data,
but Postgres does not allow them in strings.
"""
if not string:
return None
if string.find('\x00') > -1:
return None
return string | 4125542a797ab5e0f14dc79e64d901366d8200dd | 657,664 |
import logging
import os
import subprocess
def RunPoolStatsR(poolfile_fp, genes_table_fp):
"""
inp_d: (dict) contains
R_fp (str) Path to R script 'PoolStats.R'
output_fp (str) (pool_fp) finished pool file
genes_table_fp (str) genes table file path
nMapped (int)
R_op_fp... | 13a0e975b3cdcc997eebab30c910801b75314832 | 657,666 |
def leap_year(leap):
"""
Help on function leap_year in module a1_akmijares:
leap_year(leap) -> int
leap_year() determines if the year is a leap year
which will return as True or False
e.g: leap_year(2016) -> True
leap_year(2015) -> False
(END)
"""
l_year = leap
if l_yea... | 0b5f9c4aa16e2b5f241fc4ec3af5b3c73f88e88b | 657,667 |
import re
def extract_statuses(raw_html):
"""Given a dump of HTML data, extract the timestamp and return it as a
string value.
:param raw_html: Dump from the ticket page.
"""
re_status = r'<input type="radio" [^<]+name="action" value="([^"]+)'
return re.findall(re_status, raw_html) | 357c8ebe6e90df25e230c2dec23539feaa89a948 | 657,668 |
def ra_dec_prefix(ra_arr, dec_arr, band, prefix):
"""Get the output file name based on (RA, Dec)."""
return [
"{:s}_{:s}_{:s}_{:s}".format(
prefix, "{:8.4f}".format(ra).strip(), "{:8.4f}".format(dec).strip(),
band.lower().strip()
) for (ra, dec) in zip(ra_arr, dec_arr... | 3e9ceee097ad245635b78e0564ad0939ceb88611 | 657,669 |
def composeMap(fun1, fun2, l):
"""
Returns a new list r where each element in r is fun2(fun1(i)) for the
corresponding element i in l
:param fun1: function
:param fun2: function
:param l: list
:return: list
"""
# Fill in
new = []
for i in l:
t = fun2(fun1(i))
... | f063444936dcdf06059cd89a85bbcf69dc0ded4f | 657,671 |
import argparse
def add_atac_args():
"""
Arguments for ATAC-seq pipeline
"""
parser = argparse.ArgumentParser(
description='ATACseq pipeline')
parser.add_argument('-b', '--build-design', dest='build_design',
action='store_true',
help='Create design for fastq files')
par... | f2b50d9703f013f49556a6f19c27707fd4354f90 | 657,672 |
def indented(text, level, indent=2):
"""Take a multiline text and indent it as a block"""
return "\n".join("%s%s" % (level * indent * " ", s) for s in text.splitlines()) | 8de1460106745de2c33fdba4baacb2d0141340ee | 657,673 |
def _test_data(**overrides):
"""Returns a valid set of test data to use during API integration tests
overrides allows the caller to replace one or more items in the returned
dictionary without having to specify the entire thing every time.
"""
test_data = {
'sender': 'someemail@somedomain.c... | 10a8d7eae8547b2d95d4f2baca31a14e1e65e21b | 657,674 |
def get_fixture_or_param_value(request, fixture_or_param_name):
"""
Returns the value associated with parameter or fixture named `fixture_name`, in provided request context.
This is just an easy way to use `getfixturevalue` or `getfuncargvalue` according to whichever is available in
current pytest versi... | 476b267ff7b0c1b7d0f9a1643d3adca8a3223992 | 657,675 |
def list_to_dict(l):
"""Turn a l of tuples into a dictionary."""
return {k: v for v, k in l} | 85ac67fabd89e8ff95ddd833dd85e25722ca276c | 657,676 |
def _denumpy(x):
"""
Try using the numpy.tolist() to convert to native python type.
DBI's can't typically handle numpy vals."""
try:
return x.tolist()
except:
return x | 9c39e3a7f637cd8e9a86d4d7250e69df4eeb6cd8 | 657,677 |
def copy_file(origin, destination):
""" Copy a file from a given origin to a given destination """
return True | 69b6e7472f330ca9a8f343dcc80e6920830d9185 | 657,678 |
def make_range_partition(min_val, max_val):
"""
Returns a new partitioning function that partitions keys in the range
*[min_val:max_val]* into equal sized partitions.
The number of partitions is defined by the *partitions* parameter
"""
r = max_val - min_val
f = "lambda k, n, p: int(round(f... | a86cae26fc79e73974fa05def8a4db531f31a829 | 657,679 |
import os
def get_files(directory):
"""
Get the list of .mhd files in the given directory.
:param directory: Directory to search through for .mhd files.
:return: List of filenames (without directory prefix).
"""
return [os.path.join(directory, f) for f in os.listdir(directory) if f.endswith('... | 3472b630e8e13c1489dcbe8210e83425c247855e | 657,680 |
def load_alist(path):
"""Read `alist`-file [MacKay]_ and return nested list describing the
parity-check matrix of a code.
Many code examples can be found in [UniKL]_.
Input
-----
path:str
Path to file to be loaded.
Output
------
alist: list
A nested list containing... | 08579269ae33eb00f6c41b511f201531eb34f9c7 | 657,681 |
import random
def sample_cloud (numpy_cloud, sample_divisor, deterministic_sampling=False ):
"""Samples a numpy cloud by a given divisor. If sample_divisor=4, cloud is 4 times as small after sampling."""
previous_length = numpy_cloud.shape[0]
# deterministic sampling
if (deterministic_sampling ):
... | c06aaec3b88c8a7c3ef92af397c4792db14d4f51 | 657,682 |
import itertools
def jaccard(str1, str2):
"""Implements Jaccard N-Grams metric for n=[2,3].
str1, str2: str
Input values in unicode.
Returns
-------
float
A similarity score normalized in range [0,1].
"""
str1 = " " + str1 + " "
str2 = " " + str2 + " "
a = list(it... | 31a5c31e48362909bcf11ad9ce796244a8bee020 | 657,683 |
from typing import Optional
def set_latest_version_state(version: str, state_file: Optional[str]) -> Optional[int]:
"""
Set version in state file
"""
if not state_file:
return 0
if version:
with open(state_file, "w") as file:
return file.write(version)
raise ValueEr... | 332bd7d522cf1ea579e2ab42426685a34bfd8270 | 657,684 |
def CreateLocalSsdMessage(resources, messages, device_name, interface,
zone=None):
"""Create a message representing a local ssd."""
if zone:
disk_type_ref = resources.Parse('local-ssd',
collection='compute.diskTypes',
... | b7bec14dbdd68314c0b6f1e24663a5130067326c | 657,685 |
def get_fixture_value(request, name):
"""Get the given fixture from the pytest request object.
getfuncargvalue() is deprecated in pytest 3.0, so we need to use
getfixturevalue() there.
"""
try:
getfixturevalue = request.getfixturevalue
except AttributeError:
getfixturevalue = re... | d50ef248dd63d64c0927f80ae5a86928dd975105 | 657,687 |
def put_genomicsCounts(db, counts):
"""
Insert each document in list into 'genomicsCounts' collection.
"""
return db, counts | 45ca251754f151dc30535e75408fc5191cf7f934 | 657,688 |
def hex_to_rgb(color):
"""Convert the color from HEX coordinates to RGB coordinates."""
color = color.lstrip('#')
size = 1 if len(color) == 3 else 2
factor = 2 if len(color) == 3 else 1
return tuple(int(color[i * size:i * size + size] * factor, 16) for i in range(3)) | d17d1144d44fdbb37b26279c22b8bbcac4f3a984 | 657,689 |
def convert(char, counters):
"""Convert counters to graphical chart"""
return "".join(["#" for _ in range(counters.get(char, 0))]) | bd01bd69dba351f8860521f0d9bd45f24840640a | 657,690 |
import torch
def prevent_clip(wav, mode='rescale'):
"""
different strategies for avoiding raw clipping.
"""
assert wav.dtype.is_floating_point, "too late for clipping"
if mode == 'rescale':
wav = wav / max(1.01 * wav.abs().max(), 1)
elif mode == 'clamp':
wav = wav.clamp(-0.99, ... | 67a6d0d4a4c77a0502bafc1ebc6d9687a38884d2 | 657,691 |
def parse_spotify_url(url):
"""
Parse the provided Spotify playlist URL and determine if it is a playlist, track or album.
:param url: URL to be parsed
:return tuple indicating the type and id of the item
"""
if url.startswith("spotify:"):
print("gib meh spotify limk.")
parsed_url =... | 388b6ef45703c392bacb153e725dd69a21855e0a | 657,692 |
def perc_unaligned(n_items, n_aligned, n_targs, **kwargs):
"""
Calculates the percent of items that are unaligned
Args:
n_items: ndarray (same dims as n_targs)
n_aligned: ndarray (same dims as n_targs)
n_targs: ndarray (same dims as n_items)
Returns:
perc: float
... | 7d58aaa8911cc711396f7c282b7d39948875ec8d | 657,693 |
def domain():
"""Provide a domain for the tests."""
return "abc.com" | b686f649670ea5b5450c3865fd98ab75deadf671 | 657,694 |
def str_strip(str_in):
""" strip whitespace at right of string. Wrap string rstrip method into function """
return str(str_in.rstrip()) | 9b2ee0a61fd5351d64b5bd727484114bc38f4418 | 657,695 |
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