content stringlengths 35 416k | sha1 stringlengths 40 40 | id int64 0 710k |
|---|---|---|
import json
def jsonDecode(input):
"""
JSON decode.
@param (str) input
@return (mixed)
"""
try:
return json.loads(input)
except: pass | 1200f71a2eab680ac41e4acddd6169f15359e4ee | 673,639 |
def qualify(ns, name):
"""Makes a namespace-qualified name."""
return '{%s}%s' % (ns, name) | 98cc677f4e149d2f515f844fa69e4164442241b1 | 673,640 |
import difflib
def simple_merge(txt1, txt2):
"""Merges two texts"""
differ = difflib.Differ(charjunk=difflib.IS_CHARACTER_JUNK)
diff = differ.compare(txt1.splitlines(1), txt2.splitlines(1))
content = "".join([l[2:] for l in diff])
return content | db353b9fd73a130b8fa6014968546345f66c2aec | 673,641 |
def encoding_fmt(request):
"""
Fixture for all possible string formats of a UTF encoding.
"""
return request.param | 53bc76ee4e5f4188cb5f6bce669d6ea3387a6bca | 673,642 |
import math
def sph2cart(theta, phi, r=1):
"""Converts spherical coords to cartesian"""
x = r * math.sin(theta) * math.cos(phi)
y = r * math.sin(theta) * math.sin(phi)
z = r * math.cos(theta)
vect = [x, y, z]
return vect | cf793f0a81baefa80c96863d1b765fdd8d30b637 | 673,643 |
import base64
def convert_img_to_b64_string(img_path):
""" Converts medical image to b64 string
This function takes the image filepath as an input and outputs it as a b64
string. This string can be sent to the server and then the database.
Args:
img_path (str): the name of the file path contai... | b9d1e2077ae2e7f9c8e027a56c25e79d0262cb27 | 673,644 |
import random
import math
def randomLogGamma(beta,seed=None):
"""
Generate Log-Gamma variates
p(x|beta) = exp(beta*x - x)/gamma(beta)
RNG derived from G. Marsaglia and W. Tsang. A simple method for generating gamma variables. ACM Transactions on Mathematical Software, 26(3):363-372, 2000.
See http... | 3a1afeb59fbb2f6ad969e16de3ca1c58faa747c5 | 673,645 |
def _fmt_cmd_for_err(cmd):
"""
Join a git cmd, quoting individual segments first so that it's
relatively easy to see if there were whitespace issues or not.
"""
return ' '.join(['"%s"' % seg for seg in cmd]) | 4b201ec9ba9f1f27df18913f1104bee4f98dcc49 | 673,647 |
def get_slices_by_indices(str, indices):
"""Given a string and a list of indices, this function returns
a list of the substrings defined by those indices. For example,
given the arguments::
str='antidisestablishmentarianism', indices=[4, 7, 16, 20, 25]
this function returns the list::
['... | e69bd33abfd3f9f423ed33c3b46841ad0ed1a30e | 673,648 |
def cli(ctx, func="download", source="", dbkey="", ncbi_name="", ensembl_dbkey="", url_dbkey="", indexers=""):
"""Download and/or index a genome.
Output:
dict( status: 'ok', job: <job ID> )
If error:
dict( status: 'error', error: <error message> )
"""
return ctx.gi.ge... | 2041a692e2ad81be9841f8cbfd41bd8a65b04c73 | 673,649 |
def _read_pid_file(filename):
"""
Reads a pid file and returns the contents. PID files have 1 or 2 lines;
- first line is always the pid
- optional second line is the port the server is listening on.
:param filename: Path of PID to read
:return: (pid, port): with the PID in the file and the p... | afccae64451ab50c0bb1e179095e4cac23730526 | 673,651 |
def col_variables(datatype):
"""This function provides a key for column names of the two
most widely used battery data collection instruments, Arbin and
MACCOR"""
assert datatype == 'ARBIN' or datatype == 'MACCOR'
if datatype == 'ARBIN':
cycle_ind_col = 'Cycle_Index'
data_point_col =... | 004d851de05c2d0e07ced93a454b6c0377407f31 | 673,652 |
def get_languages(s):
"""
A function to obtain language settings via Accept-Language header.
"""
langs = [''.join(x.split(';')[:1]) for x in s]
return langs | 92b51de5791aa12ae54826b26f0f4e5cd8b0aea2 | 673,653 |
def make_contribs_dict(tsv_in, ignore=4, initials_col=None, sort_categories=False):
"""
Convert input author contributions .tsv to dict mapping contribution
categories to author initials
"""
with open(tsv_in) as f:
# Read first line of tsv_in to get contribution categories
categs ... | ddc10afb32942055d0c03bcd2a9944b817009162 | 673,654 |
def build_dummy_module_def(group_name, fifo_type, module_in, PE_ids):
"""Build the definition of the dummy module
Parameters
----------
group_name: str
fifo_type: str
module_in: int
PE_ids: list
"""
dir_str = "out" if module_in == 0 else "in"
index_str = ["idx", "idy", "idz"]
... | cb30e32aebc6796a8687f14e67eb5a50de20a080 | 673,655 |
def run(M=10, N=100, D=5, seed=42, maxiter=100, plot=True):
"""
Run deterministic annealing demo for 1-D Gaussian mixture.
"""
raise NotImplementedError("Black box variational inference not yet implemented, sorry")
if seed is not None:
np.random.seed(seed)
# Generate data
data = n... | 3aafb6801c54cbe9f4f0f08ffadcf933d343ddf6 | 673,656 |
def uri_to_id(uri):
""" Utility function to convert entity URIs into numeric identifiers.
"""
_, _, identity = uri.rpartition("/")
return int(identity) | 1578a3a6716e20cede81aeebf04a8da6455413d1 | 673,657 |
from typing import Dict
from typing import Any
from typing import Optional
from typing import List
def find_targets(scene: Dict[str, Any], num_targets: Optional[int] = None) -> List[Dict[str, Any]]:
"""Find 'target' objects in the scene. (IntPhys goals don't really
have them, but they do have objects that may... | b1f05c75785586fcfb6a8e3f00168303ea58a1e4 | 673,658 |
def centimeter2feet(dist):
""" Function that converts cm to ft. """
return dist / 30.48 | f943b322760696d42d45e20da3565cb6e7c20ddb | 673,659 |
def showreporoot(context, mapping):
"""String. The root directory of the current repository."""
repo = context.resource(mapping, 'repo')
return repo.root | 08b84afe2bdb79e3bafeeba408342345577ec796 | 673,660 |
import struct
def char(c):
"""
Input: requires a size 1 string
Output: 1 byte of the ascii encoded char
"""
return struct.pack('=c', c.encode('ascii')) | 355303fdd2bbfbb77ec59e8adb14c6f01841fc90 | 673,661 |
import random
def test_data():
"""Return a pseudo-random string of length between 0 and 5120."""
length = random.randint(0, 5120)
data = [chr(random.randint(0, 255)) for i in range(length)]
return "".join(data) | 739e4112666991b25dd5a62c8c8cb042fc9cefbc | 673,662 |
import torch
def covariance_z_mean(z_mean):
"""Computes the covariance of z_mean.
Borrowed from https://github.com/google-research/disentanglement_lib/
Uses cov(z_mean) = E[z_mean*z_mean^T] - E[z_mean]E[z_mean]^T.
Args:
z_mean: Encoder mean, tensor of size [batch_size, num_latent].
Returns:
... | f9b82a6bb3c08c3ca59381c3f877cfbf0542aeb1 | 673,663 |
import socket
def inet_to_str(inet):
"""Convert inet object to a string
:param inet: inet network address
:type inet: inet struct
:return: str of printable/readable IP address
"""
try:
return socket.inet_ntop(socket.AF_INET, inet)
except ValueError:
return socket.inet_nto... | 313864b214fda7cccf2781fc049381ea998a93b2 | 673,664 |
import torch
def get_idxs(results, test_targets, device):
"""
Args:
results (tensor): predictions
test_targets (tensor): Ground truth labels
Returns:
miss_index: index of misclassifier images
hit_index: index of correctly classifier images
"""
miss_index = torch.where((results.argmax... | 9c194b7b97c19ab5ff05412de7079bd16f5c2eb3 | 673,665 |
def genus_species(tokens):
"""
Input: Brassica oleracea
Output: <taxon genus="Brassica" species="oleracea" sub-prefix=""
sub-species=""><sp>Brassica</sp> <sp>oleracea</sp></taxon>
"""
(genus, species) = (tokens[0], tokens[1])
return f'''<taxon genus="{genus}" species="{species}" sub-prefix=... | 1f492a28a254b07857428f4610f0c700e1f74833 | 673,666 |
def is_redirect(code):
"""Return that further action needs to be taken by the user agent in order to fulfill the request."""
return 300 <= code <= 399 | 3a02f5a6c7450222c0a4d5217097d4f76a0eff04 | 673,667 |
import torch
def hotflip_attack(averaged_grad,
embedding_matrix,
increase_loss=False,
num_candidates=1,
filter=None):
"""Returns the top candidate replacements."""
with torch.no_grad():
gradient_dot_embedding_matrix = torch.ma... | 24b7ab70c4b8b20be68291d9d9dfed1963228940 | 673,668 |
def calc_g_max(g_cur, g_max):
"""
Calculates g_max
"""
if g_cur > g_max:
g_max = g_cur
return g_max | 6947c053032df30da406c186e0962ba5a4648bb7 | 673,670 |
def osc(last, type):
"""
R=[AG], Y=[CT], K=[GT], M=[AC], S=[GC], W=[AT], and the four-fold
degenerate character N=[ATCG]
"""
if type == "r":
if last == "a": return("g")
if last == "g": return("a")
return("a")
if type == "y":
if last == "c": return("t")
if ... | e46371e9eab32c6f4ebb9f8c31cbb446ac23ea9f | 673,672 |
def trailing_zeros(value: int) -> int:
"""Returns the number of trailing zeros in the binary representation of
the given integer.
"""
num_zeros = 0
while value & 1 == 0:
num_zeros += 1
value >>= 1
return num_zeros | bcb760be12e1b918647a017c04d5b46d87035510 | 673,673 |
def get_health_multiple(obj):
"""
get individual scores for 4 repo components.
"""
branch_count = 0
branch_age = 0
issues = 0
pull_requests = 0
denom = len(obj["repo"])
assert all(isinstance(obj[x], list) for x in obj)
assert all(len(obj[x]) == denom for x in obj)
for brc in ... | 11c85252ddf694dba295d8dd6bd5e117e4d3fff7 | 673,674 |
def getAverageVectorForWords( word_list, model, np ):
"""Calculates average vector for the set of word.
Parameters
----------
word_list : array
Array of words in format [word1, word2, ...].
model : object
Word2Vec model.
np : object
numpy library.
Return... | 5ee60efff539ec1b46728a7c16d1f5b4cf00db1b | 673,675 |
def is_ethiopia_dataset(name):
"""Names with 'TR' at start or Ethiopia"""
return name.upper().startswith('TR') or \
name.lower().find('ethiopia') > -1 | 81f9981a4389f9c9fe7a19f23f8a66541116b04d | 673,676 |
import logging
import sys
def my_custom_logger(logger_name, log_file, level=logging.info):
"""
Method to return a custom logger with the given name and level
"""
logger = logging.getLogger(logger_name)
logger.setLevel(level)
format_string = '%(asctime)s %(message)s'
datefmt_string ='%m/%d/... | 69d0414db2164ee5ba65bf9978f66f473b3d614a | 673,677 |
def format_dependencies(id_to_deps):
"""Format a dependency graph for printing"""
msg = []
for name, deps in id_to_deps.items():
for parent in deps:
msg.append("%s -> %s" % (name, parent))
if len(deps) == 0:
msg.append('%s -> no deps' % name)
return "\n".join(msg) | 70f31b01365f2d1e6cabca5a9c277662c99eef8e | 673,678 |
import win32file
def get_usb_paths_windows():
"""
Credit:
https://stackoverflow.com/questions/4273252/detect-inserted-usb-on-windows
https://mail.python.org/pipermail/python-win32/2006-December/005406.html
"""
path_list = None # []
drivebits = win32file.GetLogicalDrives()
for d in range(1, 26):
mask = 1 <<... | 241eccb8edf4567b0e1f8b8ecffe69f99be5bbbe | 673,679 |
from pathlib import Path
def exhaustive_directory_search(root, filename):
"""Executes an exhaustive, recursive directory search of all downstream
directories, finding directories which contain a file matching the provided
file name query string.
Parameters
----------
root : os.PathLike
... | cf6ded7ccce0af81190c1337dd511c44d45c3557 | 673,680 |
import math
import struct
def _bytes_to_int(b):
"""Convert bytes to hex integer"""
len_diff = 4 - len(b) % 4 if len(b) % 4 > 0 else 0
b = len_diff * b'\x00' + b # We have to patch leading zeros for using struct.unpack
bytes_num = int(math.floor(len(b) / 4))
ans = 0
items = struct.unpack('>' +... | 67f44fc8a99068aed566ff03a897a23812654949 | 673,681 |
import inspect
def get_commands(inputs: dict, module):
"""Processes the inputs and the given logic module
Returns:
The mapped functions on the module
The command stacked from the inputs
The outputs needed in the view"""
functions = dict(inspect.getmembers(module, inspect.isfunction... | 0f716ce6044238ff2625197e8251b7006c295464 | 673,682 |
def dot(v1,v2):
"""Dot product of two vectors"""
n = len(v1)
prod = 0
if n == len(v2):
for i in range(n):
prod += v1[i]*v2[i]
return prod | 569ad317cf8d875a0c0592a576c3987b02b54f95 | 673,683 |
def has_time_layer(layers):
"""Returns `True` if there is a time/torque layer in `layers.
Returns `False` otherwise"""
return any(layer.time for layer in layers if not layer.is_basemap) | 0351fa97cab084b90e836f624a86baf8922861a1 | 673,684 |
def __plugin_cves(data, db):
"""
Get CVEs of a plugin
:param data: PlecostDatabaseQuery object
:type data: PlecostDatabaseQuery
:return: results of query
:rtype: str
"""
_plugin = data.parameter
_query = ("SELECT DISTINCT(cve) "
"FROM PLUGIN_VULNERABILITIES_CVE as PV... | c71425180fa114119b5016db6b1838124aebc32c | 673,685 |
import secrets
def generate_new_day_key():
"""Returns a fresh random key"""
return secrets.token_bytes(32) | 872e291a49b088be24ec49caf7789df2bf5ec2c2 | 673,686 |
def is_storage(file, storage=None):
"""
Check if file is a local file or a storage file.
Args:
file (str or int): file path, URL or file descriptor.
storage (str): Storage name.
Returns:
bool: return True if file is not local.
"""
if storage:
return True
eli... | 2b4355e4efba38aef2ce5a5961e6013947b3cd94 | 673,687 |
def flatten(x):
"""flatten(sequence) -> list
Return a single, flat list which contains all elements retrieved
from the sequence and all recursively contained sub-sequences
(iterables).
Examples::
>>> [1, 2, [3,4], (5,6)]
[1, 2, [3, 4], (5, 6)]
>>> flatten([[[1,2,3], (42,No... | d435e06613671b1786dcc6de18804ff83d4fa808 | 673,688 |
import argparse
def build_parser(argslist):
"""
_build_parser_
Set up command line parser for the selfupdate command
"""
parser = argparse.ArgumentParser(
description=(
'git cirrus selfupdate command, '
'used to update cirrus itself'
)
)
parser... | 2d45e2f26c8922a171d1c6ab1e5e71533e6df6cb | 673,689 |
def get_strings_section(config, section):
"""
Get config file options from section containing strings.
:param config: ConfigParser object.
:param section: Name of the section to be read.
"""
options = config.options(section)
section_dict = {}
for option in options:
secti... | 65f5ce24464612c8eef8c19fc2253a98bcb026ec | 673,691 |
from typing import Optional
import os
def get_write_path(original_path: str, write_dir_path: Optional[str], n_clusters: int, conducted_iterations: int) -> str:
""" Returns:
altered image file name being extended by n_clusters and conducted_iterations,
prepended either by dir path original ... | 886a7da65ee28346fb04dc1af23d2e37428cd98d | 673,692 |
def minimum_distance(mp, ip, dp, i):
"""
Compares each element from the distance profile with the corresponding element from the matrix profile.
Parameters
----------
mp: numpy.array
Matrix profile.
ip: numpy.array
Index profile.
... | 62cd66a15a3d3cf526c7eaca1f10fd5f56bde8f5 | 673,693 |
import torch
def conj(self):
"""
Quaternion conjugate
"""
if len(self.shape) > 1:
con = torch.cat([self.a, -self.b, -self.c, -self.d], 1)
else:
con = [self.a, -self.b, -self.c, -self.d]
return self.__class__(con, False) | 866c94b69e0376405b5287f869a8d2b8db30f10b | 673,695 |
def convert_duration(milliseconds):
"""
Convert milliseconds to a timestamp
Format: HH:MM:SS
"""
# it's easier to wrap your head around seconds
seconds = milliseconds / 1000
hrs = seconds // 3600
mins = (seconds % 3600) // 60
s = (seconds % 3600) % 60
return "{:02}:{:02}:{:02}"... | dea6f0d09a0b53e193c1c0cfdf4f844f9da9bb65 | 673,696 |
def rivers_with_station(stations):
"""Returns a set containing all rivers which have a monitoring station.
Params:
Stations - List of all stations. \n.
Returns:
{River 1, River 2, ... }
"""
rivers = set() # set
for station in stations: # iterate and add rivers to set
r... | 9422ecfade5fe19ce162911294abbd00e4444820 | 673,697 |
def place_mld_breakpoints(incompt_pos :list):
"""
Adds an MLD breakpoint in the middle of an incompatible interval.
Parameters:
incompt_pos (list): chop_list() output
Output:
list: indexes of MLD breakpoints in the sequence
"""
return [int(inter[0] + (inter[... | c194c879bc49ebda6bbaf8cadce44852b1ff73aa | 673,698 |
def get_cnn_default_settings(kind):
"""Get default setting for mlp model."""
if kind == 'hidden_sizes':
return [512]
elif kind == 'activation':
return 'relu'
else:
raise KeyError('unknown type: {}'.format(kind)) | e7b11417e1df72c2551eefe521c50fe1912ee4aa | 673,699 |
def random_variable_args():
"""Provide arguments for each random variable."""
# Commented out tests are currently failing and will be fixed
_random_variable_args = (
("Bernoulli", {"probs": 0.5, "sample": 1.0}),
("Beta", {"concentration0": 1, "concentration1": 1}),
("Binomial", {"to... | 70ae6a864f91a0f1ad7bcb79da15c3f89d190ff5 | 673,700 |
def list_drawings_from_document(client, did, wid):
"""List the drawings in a given workspace"""
# Restrict to the application type for drawings
res = client.list_elements(did, wid, element_type='APPLICATION')
res_data = res.json()
drawings = []
for element in res_data:
if element['dataTy... | 1d52169616688dbcde50761d89e7db17cde6a617 | 673,701 |
def read_order(order_file):
"""
Read the order of the API functions from a file.
Comments can be put on lines starting with #
"""
fo = open(order_file, 'r')
order = {}
i = 0
for line in fo:
line = line.strip()
if not line.startswith('#'):
order[line] = i
... | 76d688fb780a3251a027f108127e7314e7c95b69 | 673,702 |
def crop_8x8(img):
"""Crop 8x8 of the input image."""
ori_h = img.shape[0]
ori_w = img.shape[1]
h = (ori_h // 32) * 32
w = (ori_w // 32) * 32
while h > ori_h - 16:
h = h - 32
while w > ori_w - 16:
w = w - 32
y = (ori_h - h) // 2
x = (ori_w - w) // 2
crop_img = img[y:y + h, x:x + w]
retu... | d7e9d4b97d30bc1c12e7b81754769305402400a7 | 673,703 |
def add_spaces_to_fill(text, places):
"""Adds blank spaces to a string so that the length of the final
string is given by 'places'.
"""
return text + (places-len(text))*" " | 26b12e84b90fd331fdc8e1fd97d9680f050c9afe | 673,704 |
from pathlib import Path
def path(file):
"""Test asset path name resolution"""
return Path(__file__).parent / 'assets' / file | 42b3b83836fe3ec8fb9974f3b2884f8c4fb0f4e3 | 673,705 |
import math
def update_global_state(global_params, aggregation_result, global_state):
"""
update global state object
:global_params: global parameters object
:aggregation_result: aggregation result
:global_state: global state object to update
:returns: global_state param
"""
def dist(... | e87aaef58771549bf5bea14acba9dd585905684f | 673,706 |
import time
def _invoke_timed_callback(
reference_time, callback_lambda, callback_period):
"""Invoke callback if a certain amount of time has passed.
This is a convenience function to standardize update callbacks from the
module.
Args:
reference_time (float): time to base `callback_p... | 44397d5c70d747966c83714a8ed17f9c3109de7c | 673,707 |
def remove_entity_from_list(unique_list, i):
"""
Removes all instances of a particular entity from a list
>>> remove_entity_from_list(['test', 'test', 'three'], 1)
['three']
"""
return [x for x in unique_list if x != unique_list[i]] | ae66405b76842693ab629a8cd8ebc3d7ec145a24 | 673,708 |
import os
import shutil
def new_run_mkdir(directory, username, title):
"""Initialize directories for a new run. Clears out prior uploads with same title."""
os.makedirs(os.path.join(directory, username), exist_ok=True)
try:
shutil.rmtree(os.path.join(directory, username, title))
except OSError... | 14bc8abe394184a8cef0086634ce590845948d23 | 673,709 |
def _tbl_str_width(num, widths):
"""Returns the width-argument for an html table cell using the width from
the list of widths.
Returns width="[some number]" or the empty-string if no width is
specified for this num"""
if num >= len(widths):
return ""
return ' width="%s"' % widths[num] | 3d35c82033ae504eeac143f35653303f1425da60 | 673,710 |
import shutil
def center_text(msg: str, *, pad: str = ' ') -> str:
"""Centers text horizontally for display within the current terminal, optionally padding both sides.
:param msg: message to display in the center
:param pad: if provided, the first character will be used to pad both sides of the message
... | 3ead8c3bce298d779205bf0d6743ec6ac05c4d7a | 673,711 |
def subscription_group(publisher_id):
""" String ACL representation of subscriber permission.
"""
return 'subscription:{}'.format(publisher_id) | 1ae8e3cc7aaf9085cac8809acc1af41855eb55bf | 673,712 |
import typing
def _parse_config_file(content: str) -> typing.Mapping[str, str]:
"""Parses an ini-style config file into a map.
Each line is expected to be a key/value pair, using `=` as a
delimiter. Lines without `=` are silently dropped.
"""
kv = {}
for line in content.splitlines():
if not line or l... | b55a263aaeccb860d9212d35277df0db39893435 | 673,713 |
def get_same_padding_for_kernel_size(kernel_size):
"""
Returns the required padding for "same" style convolutions
"""
if kernel_size % 2 == 0:
raise ValueError(f"Only odd sized kernels are supported, got {kernel_size}")
return (kernel_size - 1) // 2 | 2c0c142d785ea1659f0bb03c22bfa1c972ae2e3d | 673,714 |
import os
def build_vistrails_cmd_line_file(path_to_vistrails, path_to_python,
env_for_vistrails, filename,
version, path_to_figures, pdf=False,
wgraph=False, tree=False):
""" build_vistrails_cmd_line_file(path... | 52d04c39f82ddb76089b356b4f122adbfdc0d8c9 | 673,716 |
def _remove_output_cell(cell):
"""Remove the output of an ipymd cell."""
cell = cell.copy()
if cell['cell_type'] == 'code':
cell['output'] = None
return cell | f4d19cc1c9d9b63988508d4dcc1f70ea68ef6716 | 673,717 |
def sum_loss(loss1, loss2):
"""
Keras only allows multiple losses if multiple outputs exists.
Since only one output exists (because the trace loss is independent
of the prediction output as no target exists), this
loss allows to sum two other losses.
"""
def sum_loss_function(y_true, y_pred)... | 9c2657c7f4a5707aa276694ae1289c7ee6156f64 | 673,718 |
from typing import Tuple
from typing import Optional
def _parse_hp_template(template_name) -> Tuple[str, Optional[int]]:
"""Parses a template name as specified by the user.
Template can versionned:
"my_template@v5" -> Returns (my_template, 5)
or non versionned:
"my_template" -> Returns (my_template, No... | 2225eef7b2f21f5e5180b686261a1f413312b848 | 673,719 |
def construct_mapping(self, node, deep=False) -> dict:
"""
Custom function to override the YAML loader to ensure that keys are
always strings.
:param self: YAML safe loader
:param node: YAML Node
:param deep: Internal argument related to recursive construction
:return:
"""
data = se... | 7dfe372217e92921c4824d12055d9c19d86275af | 673,720 |
def PyUnixTimeConv(some_DT_obj):
""" func to convert DateTime Obj to Unix Epoch time, in SECONDS, hence rounding"""
output_unix_time = some_DT_obj.timestamp()
return round(output_unix_time) | 657f6c34ee9cc9b98681ba2519e843466d1a01b6 | 673,721 |
def get_cigar_sheet(alignment):
""" sift through alignment cigar string for single bp indels
:param pysam.AlignedSegment:
:return: cigar_sheets, # of single bp insertions, # of single bp deletions
"""
aln = alignment
sheets = []
pairs = aln.aligned_pairs
icount = 0
dcount = 0
al... | f2169f5b01683727f4c9e8a630029c228cf47ecc | 673,722 |
import numpy as np
def genTransMat(n):
"""
Generate transition matrix
Arguments: n - dimension of transition matrix
Return: transMat - an n*n transition matrix
"""
transMat = np.random.rand(n,n) #generate a square matrix consisting random numbers
#Normalize transMat to be a tra... | fd31490b0643eeeb8c8455d64b953400dc45baac | 673,723 |
import struct
import socket
def ip2long(ip):
"""Calculate the IP address as a long integer
:param ip: IP address as a dotted-quad string
:return: Long value of the IP address
"""
return struct.unpack('!L', socket.inet_aton(ip))[0] | 22ef65c1b697e851af8b5ffbf1e296214d27ec09 | 673,724 |
import json
def to_json(raw_data):
"""
Pretty-prints JSON data
:param str raw_data: raw JSON data
"""
return json.dumps(raw_data, sort_keys=True,
indent=4, separators=(',', ': ')) | 9faf1a31e2f906e8170226d81160a5523c201566 | 673,725 |
import aiohttp
async def is_online() -> bool:
"""Function for checking if the api is online."""
try:
async with aiohttp.ClientSession() as session:
async with session.get('https://api.github.com') as response:
if not response.status == 200:
raise Excepti... | ef2d1da66bd989708d39684d8260e3154b2b429a | 673,726 |
import re
def get_sleep_awake_folder(s):
"""Get the if animal is sleeping from folder"""
temp = re.split("_|\.|\ |\/", s.lower())
if "sleep" in temp or "sleeping" in temp:
return 1
return 0 | 06c797da20273c3c316fda55db9be142a8a08ad9 | 673,728 |
def make_tuple(str_in):
"""
makes a tuple out of a string of the form "(a,b,c)"
"""
str_in = str_in.strip("()")
l = str_in.split(",")
return tuple(l) | d7ae58a3c618edbff3d2a83b72350d6ad32b1a3a | 673,730 |
def rotate_ccw(str_array: list[str]) -> list[str]:
"""
Rotate a list of strings quarter-turn counter-clock-wise
:param str_array: array as a list of strings
:return: array rotated counter clock-wise
"""
zip_array = list(''.join(c) for c in zip(*str_array))
ccw_rot_array = zip_array[::-1]
... | a8bd4d70856c5c9c48d7b3778f14ceb0a2cbeb20 | 673,731 |
def get_object_name_from_schema(obj: object) -> str:
"""
Returns the name of an object based on type.
This is used to return a userfriendly exception
to the client on bulk update operations.
"""
obj_name = type(obj).__name__
to_remove = ["Base", "Create", "Update"]
for item in to_remove:... | 6e1d33f915ba6265bbea143b3e7c8b64fa06faab | 673,732 |
def normalize_description(description):
"""
Normalizes a docstrings.
Parameters
----------
description : `str` or `Any`
The docstring to clear.
Returns
-------
cleared : `str` or `Any`
The cleared docstring. If `docstring` was given as `None` or is detected as e... | 4ece93902474f53ecce92cb3c902b0157beca733 | 673,733 |
import importlib
def serialize(obj, only=tuple(), exclude=tuple()):
"""
Python object serializer
:param obj: The object to parse into json string
:return: A dictionary
"""
# Read from type name
type_name = type(obj).__name__
try:
# Convert string into actual class object
... | 71911e4dc0d243ac71223588573c63a1474ba788 | 673,734 |
def htheta_function(x, theta_0, theta_1):
"""
Linear function that is to optimized
"""
return theta_0 + theta_1 * x | db1407e423c2ae251fbf6c655981de2b91684dea | 673,735 |
def max_counts(ng1, ng2):
"""
Return a dicitonary of ngram counts such that
each count is the greater of the two individual counts
for each ngram in the input ngram count dictionaries
/ng1/ and /ng2/.
"""
ret = ng1.copy()
for k, v in ng2.items():
ret[k] = max(ret.get(k, 0), v)
... | d1c1b78353a1c07070b240b7806b753bd071a122 | 673,736 |
def turn(n):
"""Formula from WIkipedia.
n could be numpy array of integers
"""
return (((n & -n) << 1) & n) != 0 | b37e26fff265be114427fa1657e878eaa1b773a2 | 673,737 |
import torch
def collate_fn(data):
"""批处理，填充同一batch中句子最大的长度"""
x, spans, span_labels, relations, relation_labels, sequence_length = zip(*data)
max_len = max(sequence_length)
x = torch.stack(
[torch.cat([item, torch.zeros(max_len - item.size(0), item.size(1))]) for item in x])
sequence_leng... | 3cbf86ad7edd225243bfe973e771a56bed8bff06 | 673,739 |
import csv
def csv_to_list(plants_csv_path, encode):
"""READ CSV TO LIST"""
plants_list = []
with open(plants_csv_path, newline = "", encoding=encode) as f:
reader = csv.reader(f)
for row in reader:
for i in row:
parameters = i.split(';')
plants_... | 8f55499641f48d4c4e67c0cbc894c200d273d5d5 | 673,740 |
def ratio(x,y):
"""The ratio of 'x' to 'y'."""
return x/y | 70b044627a75dd6fc583a84b87014bbade9b18c1 | 673,742 |
import operator
def sequence_eq(sequence1, sequence2):
"""
Compares two sequences.
Parameters
----------
sequence1 : sequence
The first sequence.
sequence2 : sequence
The second sequence.
Returns
-------
bool
`True` iff `sequence1` equals `sequence2`, othe... | 3e6520602272873f471c808ad14c6d3a90d31972 | 673,743 |
import numpy
import torch
def subsequent_mask(size):
"""
Mask out subsequent positions.
"""
attn_shape = (1, size, size)
mask = numpy.triu(numpy.ones(attn_shape), k=1).astype('uint8')
return torch.from_numpy(mask) == 0 | 278b9c897fc8c8af8be331fdeacc48910307ade1 | 673,744 |
def strFromPositionRow(o):
"""Return string describing an order (for quick review when canceling orders).
As always, 'averageCost' field is for some reason the cost-per-contract field while
'marketPrice' is the cost per share, so we manually convert it into the expected
cost-per-share average cost for ... | 316369d13847ce835d85536506a62b3658de98aa | 673,745 |
def users_are_idiots(string):
"""
splits the input strings and removes any preceeding or trailing whitespaces.
"""
s = string.split(",")
s = [i.strip() for i in s]
return s | c540faab39725990d0c3e94c54354389574b6b93 | 673,746 |
import numpy
def compute_vertex(origin_point, dh, tol=numpy.finfo(float).eps):
"""
Computes the bounding box of a rectangular polygon given its origin points and spacing dh.
Args:
origin_points: list of tuples, where tuple is (x, y)
dh: spacing
tol: used to eliminate overlapping p... | 1be8350f38b452f2c1b4881088e1678233c23958 | 673,747 |
def hello(func):
"""make a func that print hello then execute a func
Examples
-------------
>>> def name():
... print("Alice")
...
>>> hello(name)()
Hello
Alice
>>> @hello
... def name2():
... print("Alice")
...
>>> name2()
Hello
Alice
"""
... | febf5699b6acb4f7d3ce829e81971da3e015c57c | 673,748 |
import re
def fix_tx_name(tx):
"""Remove the .[0-9] at the end of RefSeq IDs."""
if tx.startswith('NM'):
return re.sub('\.[0-9]$', '', tx)
else:
return tx | 68fae9ffd80b47da3d36ac919fa5a4ca2ad9a14f | 673,750 |
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