text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
import unittest
from django.utils import html
class TestUtilsHtml(unittest.TestCase):
def check_output(self, function, value, output=None):
"""
Check that function(value) equals output. If output is None,
check that function(value) equals value.
"""
if output is None:
... | faun/django_test | tests/regressiontests/utils/html.py | Python | bsd-3-clause | 4,041 | [
"ADF"
] | 7e0dbd3a258eef037434c10613c26f858afd789d60e2bcae171c324d1242a138 |
import unittest
import sys
import re
import logging
sys.path.append('../PyRoute')
from TradeCodes import TradeCodes
from Star import Star
from Galaxy import Sector, Galaxy
class TestTradeCode(unittest.TestCase):
def setUp(self):
self.star1 = Star.parse_line_into_star(
"0103 Irkigkhan ... | makhidkarun/traveller_pyroute | Tests/testTradeCode.py | Python | mit | 5,025 | [
"Galaxy"
] | f18fd9e9cdd96aa9deff563c8ec8eac32ca60be7306876fbd9d435c62a6a684f |
import collections
import numpy
import os
import pandas
import pybedtools
import pysam
from grocsvs import step
from grocsvs import structuralvariants
from grocsvs.stages import final_clustering
from grocsvs.stages import refine_grid_search_breakpoints
pandas.options.display.max_rows = 500
CHUNKSIZE = 10
def nchunks... | grocsvs/grocsvs | src/grocsvs/stages/genotyping.py | Python | mit | 16,435 | [
"pysam"
] | 1f530caa9772f49ab93f2db354575c37ca389d1ba4014706f4401b938aea18a3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
test_django-ai
------------
Tests for `django-ai` models module.
"""
import random
import numpy as np
from bayespy.nodes import Gaussian
from django.test import (TestCase, )
from django.contrib.contenttypes.models import ContentType
from django.core.exceptions impor... | math-a3k/django-ai | tests/apps/bayesian_networks/test_bns.py | Python | lgpl-3.0 | 27,510 | [
"Gaussian"
] | 40089dcebb25093840cac258eee24aa8b4a375f3baf3540a6e64e37e77e2b064 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2013-2014 CRS4.
#
# This file is part of vispa.
#
# vispa is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
#... | crs4/vispa | bl/tiget/mr/blast/__init__.py | Python | gpl-3.0 | 920 | [
"BLAST"
] | aeeb63c9e54c0bf65cc5b825b3afc621fb3c841ca3af5c2750e33b33f1b97a73 |
# $HeadURL$
__RCSID__ = "$Id$"
import socket
import select
import os
try:
import hashlib as md5
except:
import md5
import GSI
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Utilities import List, Network
from DIRAC.Core.DISET.private.Transports.SSL.SocketInfo import SocketInfo
from DIR... | rajanandakumar/DIRAC | Core/DISET/private/Transports/SSL/SocketInfoFactory.py | Python | gpl-3.0 | 6,721 | [
"DIRAC"
] | 5c7683957ac2d8b583c6d75c33b73e49f5a50da9e26d8cd1b533c91e7ac5f364 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This example demonstrates the usage of the vtNamedColor class.
"""
from __future__ import print_function
import vtk
def main():
nc = vtk.vtkNamedColors()
# We can print out the variables.
# The color name and RGBA values are displayed.
print(nc)
... | lorensen/VTKExamples | src/Python/Visualization/NamedColors.py | Python | apache-2.0 | 5,382 | [
"VTK"
] | 4fc7fabc387f420c618097ac68391041d685f3fa175eaf858900f907338816a9 |
# psf.py
import numpy as np
from skimage.util import random_noise
from astropy.io import fits
def add_gaussnoise(img, noise_sigma):
"""
add iid gaussian noise on image
Params
------
img
noise_sigma
Return
------
img
"""
if noise_sigma == 0:
result = img
else:
result = img+random_noise(np.zeros(img... | aileisun/bubbleimg | bubbleimg/imgsim/simtools.py | Python | mit | 1,205 | [
"Gaussian"
] | bbb98c14961bb5679ddbaf5b1cfab574ec545c00623c4b0f93f32d3851cce373 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements input and output processing from Gaussian.
"""
__author__ = 'Shyue Ping Ong, Germain Salvato-Vallverdu, Xin Chen'
__copyright__ = ... | migueldiascosta/pymatgen | pymatgen/io/gaussian.py | Python | mit | 42,348 | [
"Gaussian",
"pymatgen"
] | 06dc104e55879021cd2ca80a887266478929ab2d58d4df50431e0bc4a4a2cd94 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/dependency_check.py | Python | lgpl-3.0 | 1,556 | [
"Psi4"
] | ee4991967ca95c91bfbb73dd8cf9d22d9416307555316aa212bae432d852f4bc |
import networkx as nx
from random import *
import datetime
# Import the Django stuff
import sys
from django.core.management import setup_environ
sys.path.append(('/'.join(__file__.split('/')[:-2])) + '/server')
import settings
setup_environ(settings)
import wiki.models
class Page:
def __init__(self, name, URL):
... | eob/synckit-research | perf/gen_model.py | Python | bsd-3-clause | 6,388 | [
"VisIt"
] | 09f4ebf410f36fabe379444fdbfa184272718d898d5266334f770e5c52dce9f9 |
import ast
from collections import defaultdict
from contextlib import ExitStack, contextmanager
from functools import singledispatch
from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
from breakfast.position import Position
from breakfast.source import Source
from tests import make_source
Qua... | thisfred/breakfast | tests/test_attempt_12.py | Python | bsd-2-clause | 21,250 | [
"VisIt"
] | 689bb2c04344a8c9b67d999ac56c6d1679bba2638eb7d980d53f6ced4d168878 |
# Copyright (c) 2010 - 2014, AllSeen Alliance. All rights reserved.
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PR... | cybertanyellow/alljoyn-core | build_core/tools/scons/javadoc.py | Python | isc | 5,715 | [
"VisIt"
] | 2308ee9a4ac3514c644731ba28ba825a5c86fe8737e521bf5e8f4d1b9e1e6be7 |
# Taking inspiration from https://realpython.com/fastapi-python-web-apis/
# run with
# uvicorn basic:app --reload
# Then visit http://127.0.0.1:8000/docs and http://127.0.0.1:8000/redoc
from fastapi import FastAPI
app = FastAPI()
@app.get("/") # $ routeSetup="/"
async def root(): # $ requestHandler
return {"mes... | github/codeql | python/ql/test/library-tests/frameworks/fastapi/basic.py | Python | mit | 2,541 | [
"VisIt"
] | d3bb314341fb01cd23e3522f631bd4b244e8bad24b71fe71649eec22ec664022 |
'''This module contains models with a few variations on estimating locations
with fitted Gaussian mixture models (GMMs).'''
# Copyright (c) Los Alamos National Security, LLC, and others.
from collections import Counter, OrderedDict
import operator
import math
from pprint import pprint
import sys
import time
from... | casmlab/quac | lib/geo/gmm.py | Python | apache-2.0 | 44,885 | [
"Gaussian"
] | 9888cfbc046818eeeeb45b3cef8ca6377be13e25139b655477097341f16fa66d |
# -*- coding: utf-8 -*-
"""
Created on Tue May 12 14:39 2015
@author: Drew Leonard
"""
import numpy as np
from scipy.io.idl import readsav as read
from os.path import expanduser
def gaussian(x, mean=0.0, std=1.0, amp=1.0):
"""Simple function to return a Gaussian distribution"""
if isinstance(x, list):
... | drewleonard42/CoronaTemps | utils.py | Python | bsd-2-clause | 1,130 | [
"Gaussian"
] | a396c6b1aaecd6e887df95e599ac2e802bcc0ae16934059794d7cfeccf0d82e3 |
""" Module for DM Halo calculations
"""
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as np
import pdb
from pkg_resources import resource_filename
from scipy.interpolate import InterpolatedUnivariateSpline as IUS
from scipy.special import hyp2f1
from scipy.interpolat... | FRBs/FRB | frb/halos/models.py | Python | bsd-3-clause | 40,171 | [
"Galaxy",
"Gaussian",
"TINKER"
] | 9bb51b82991041d6d789b940ce4f62ce9dc2e08b0d60efed997e5bcad807f97c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
Module for implementing a CTRL file object class for the Stuttgart
LMTO-ASA code. It will primarily be used to generate a pymatgen
Structure object in the pymatgen.electronic_structure.cohp.py module.
"""
... | gmatteo/pymatgen | pymatgen/io/lmto.py | Python | mit | 15,543 | [
"pymatgen"
] | 07db2421da5b8b6cc0189b682a16ebfa24e621cef03e71bdd6b53d98c6ac922d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Fou... | tiagocardosos/stoq | stoqlib/domain/test/test_views.py | Python | gpl-2.0 | 31,597 | [
"VisIt"
] | ce47b73f3412e56731c6ecc105871642bc329522290a35781f8c2e30e77d84e7 |
#!/usr/bin/env python
################################################################################
# site-alerter.py
# Constructs a XML list of GCNs for a given site and sends alerts
#
# Created by Brian Baughman on 3/4/13.
# Copyright 2013 Brian Baughman. All rights reserved.
##################################... | bbaugh/gcn-parser | site-alerter.py | Python | gpl-2.0 | 12,421 | [
"Brian"
] | e908715ec22f772f173f6722958c735b99d54d6b19d90173b4429a6345dfcf00 |
from lettuce import step, world
# Browse from page to page
@step(r'(?:visit|access|open) the url "([^"]*)"')
def go_to_the_url(step, url):
world.response = world.browser.visit(url)
@step(r'go back(?: a page)?')
def go_back(step):
world.browser.back()
@step(r'go forward(?: a page)?')
def go_forward(step):
... | salad/salad | salad/steps/browser/navigation.py | Python | bsd-3-clause | 438 | [
"VisIt"
] | 104f01b04cf410b3ac5a61730184c6b2e731eead6ca48e891766226edaa4fc3d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
LAYMAN CONFIGURATION
File: config.py
Handles Basic layman configuration
Copyright:
(c) 2005 - 2009 Gunnar Wrobel
(c) 2009 Sebastian Pipping
(c) 2010 - 2011 Brian Dolbec
Distributed under th... | jmesmon/layman | layman/config.py | Python | gpl-2.0 | 13,518 | [
"Brian"
] | ee56f86c3764c033c87012b6f0de9fb692609c09c660a4f9c36be6c25107be92 |
import vtk
import math
import numpy as np
sigmoid_grad = -3.0
def sigmoid(x):
return 1.0 / (1.0 + np.exp(-sigmoid_grad * x))
inner_par_rad = 1/2.0
atp_base = 0.35
sigmoind_domain_min = -2.0
sigmoind_domain_max = 2.0
sigmoid_domain = sigmoind_domain_max - sigmoind_domain_min
scaling_to_sigmoid_domain = sigmoid_d... | BlueFern/DBiharMesher | meshes/c2000f/Generate2000ATPMeshSynCFD.py | Python | gpl-2.0 | 5,498 | [
"VTK"
] | 58e902f0aaf830f40270b4f51da5519de2b1d32c9707648bfd7b2d7480add898 |
#!/usr/bin/python
import tweetproc
import os
import io
from datetime import *
from tweetproc.sitesdata import *
'''
caseradius=100000
caseradius=50000
campusradius=15000
campusradius=25000
campussites=[
["Tuscarawas",40.467441, -81.407072, campusradius],
["Salem", 40.864983, -80.835811, campusradius],
["Trumbu... | HPCGISLab/TwitterMethods | workflow-sites-to-tic.py | Python | bsd-3-clause | 6,285 | [
"Amber"
] | 9cddce6e32fa273b0978688e36cee3f70aab63205339c2bf15e3f5ae93151a9d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import shutil
import subprocess
import matplotlib.pyplot as plt
import xml.etree.ElementTree as ET
import z2pack
# Edit the paths to your Quantum Espresso and Wannier90 here
qedir = '/home/greschd/software/espresso-5.4.0/bin/'
wandir = '/home/greschd/software/... | Z2PackDev/Z2Pack | examples/fp/espresso/5/Bi/run.py | Python | gpl-3.0 | 2,945 | [
"ESPResSo",
"Quantum ESPRESSO",
"Wannier90"
] | 374a67da1ea6216b6b35dd312b5777fe373d0b01db1b0976a0e29b8fbda16f5c |
#!/usr/bin/env python
try:
from setuptools import setup, Extension
except ImportError:
from distutils.core import setup, Extension
setup(
name="genderator",
version="0.1",
description="Get gender from first name. Uses gender.c file.",
author="Brian Muller",
author_email="bamuller@gmail.com... | bmuller/genderator | setup.py | Python | gpl-3.0 | 482 | [
"Brian"
] | e55b0a6defbb6206ae7773d9ca7a11b34902a8f8b5f3c574e56778b20e673e25 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
#
# Copyright (C) 2001,2003 greg Landrum and Rational Discovery LLC
#
""" unit tests for the QuantTree implementation """
from __future__ import print_function
import unittest
import io
from rdkit import RDConfig
from rdkit.ML.DecTree import BuildQuant... | jandom/rdkit | rdkit/ML/DecTree/UnitTestQuantTree.py | Python | bsd-3-clause | 7,485 | [
"RDKit"
] | 9195f8ce8890cf43e0c5e320804baaafebcded0c86002c21bd7cf368a7a56df9 |
# Author: Gael Varoquaux <gael.varoquaux at normalesup.org>
# Copyright (c) 2007-2015, Enthought, Inc.
# License: BSD Style.
print("!! mayavi.tools.mlab is obsolete and has been replaced by !!")
print("!! mayavi.mlab. Please update your code. !!")
from mayavi.mlab import *
| dmsurti/mayavi | mayavi/tools/mlab.py | Python | bsd-3-clause | 293 | [
"Mayavi"
] | d2636ce08034708f23a4c306276d89da0667052481958ffde2e55db613b0d22b |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import math
# draw a line from pt1 to pt2 with the given color
def drawLine(myscreen, pt1, pt2, lineColor):
myscreen.addActor(ovdvtk.Line(p1=(pt1.x, pt1.y, 0), p2=(pt2.x, pt2.y, 0), color=lineColor))
def drawLinesegs(myscreen, points, lines):
fo... | aewallin/openvoronoi | python_examples/ma-offset/offset2vtk.py | Python | lgpl-2.1 | 10,097 | [
"VTK"
] | 635fb89a56fd49297f7496147befe7b43f2739893908ade99ccd7879bd38b9e1 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/getcurrent.py | Python | gpl-2.0 | 14,438 | [
"VisIt"
] | 5e8c7875f5ee9f4e21238ff523a7395623e4d78badfbc1f12bb08e4effb1160a |
#!/usr/bin/env python
from __future__ import division
import copy
import imp
import os
import traceback
from optparse import OptionParser
import cv2
import rospy
from cv_bridge import CvBridge
from cv_bridge import CvBridgeError
from sensor_msgs.msg import Image
from multi_tracker.msg import DeltaVid
# for basler ... | tom-f-oconnell/multi_tracker | nodes/delta_video_player.py | Python | mit | 9,129 | [
"Firefly"
] | a08bea5b655706e18ae1322e49c326d2128ddd38979128daf6ba17e66fff794c |
#
# Copyright 2014-2015, 2017, 2019-2021 Lars Pastewka (U. Freiburg)
# 2019-2020 Wolfram G. Nöhring (U. Freiburg)
# 2020 Johannes Hoermann (U. Freiburg)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy... | libAtoms/matscipy | tests/test_eam_calculator.py | Python | lgpl-2.1 | 12,830 | [
"ASE",
"LAMMPS",
"Matscipy"
] | 7f275e2674878dc7907a440638ad840b44a45d108652658fa1b3430ebf450131 |
##############################################################################
# Copyright (c) 2017-2018 Mark Olesen, OpenCFD Ltd.
#
# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
# and is released as part of spack under the LGPL license.
# LLNL-CODE-647188
#
# For details, see https://github.com/s... | EmreAtes/spack | var/spack/repos/builtin/packages/openfoam-com/package.py | Python | lgpl-2.1 | 33,458 | [
"ParaView"
] | f0d5a3d50338f022cee5e2c824477882bf832b49cc069f2926717bf61f6da812 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_SO2_high_emissions_n96e_360d.py | Python | gpl-3.0 | 19,293 | [
"NetCDF"
] | 41dea4b978444291e784df3fe32a10cdfff619cd53a98b12340b419fa14ee3e8 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 7 16:21:06 2017
@author: Gerardo A. Rivera Tello
"""
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import matplotlib as mpl
from osgeo import gdal,osr
import numpy as np
import os
#%%
def plot_map(data,lat,lon,band=None,... | DangoMelon0701/PyRemote-Sensing | SPOT Vegetation/combine_files.py | Python | mit | 3,849 | [
"Gaussian"
] | 67cb58df9640fa38e90d8a0b35758e21bcf93e78df176fee0f4b1d957358424f |
#!/usr/bin/env python
# Test Harness Tools
from sklearn import preprocessing
from sklearn import cross_validation
# Classifiers to spot check
from sklearn import linear_model
from sklearn import svm
from sklearn import tree
from sklearn import neural_network
from sklearn import naive_bayes
from sknn import mlp
# Othe... | DonaldWhyte/intro-to-ml | demo/spotcheck_facesvegetables.py | Python | mit | 4,593 | [
"Gaussian"
] | 646787b9e77d88269c8f490b874791782513db1f00c91207b24588f5ce31276f |
ABERRANT_PLURAL_MAP = {
'appendix': 'appendices',
'barracks': 'barracks',
'cactus': 'cacti',
'child': 'children',
'criterion': 'criteria',
'deer': 'deer',
'echo': 'echoes',
'elf': 'elves',
'embargo': 'embargoes',
'focus': 'foci',
'fungus': 'fungi',
'goose': 'geese',
'... | Govexec/django-odd-utilities | odd_utilities/text_utilities.py | Python | mit | 2,465 | [
"CASINO"
] | ebf19f8f5dcd1e50182500e8115b835a84f4a8d402627fe5b5cf1dc518c233b4 |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
####################################################################################
### Copyright (C) 2015-2019 by ABLIFE
####################################################################################
########################################################... | ablifedev/ABLIRC | ABLIRC/bin/public/mapping_distribution_analyse.py | Python | mit | 29,245 | [
"HTSeq"
] | d4b659112fad729c0e2e3a74ae39ce5453b9b50ea55900cc1a25224d03dbda53 |
#!/usr/bin/env python
# Disco-cake
# Copyright (C) 2017 Maugere Lucas
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | Cqfuj/disco-cake | tests/test_shirobako_ost.py | Python | gpl-3.0 | 6,221 | [
"MOE"
] | 42bbddd1ef1730189fb39e2b69bd16eff86f43dc8bad67c0610d2d022fa710e9 |
import logging
from neuro import reshape
import neuro
import numpy
from reikna.algorithms import PureParallel
from reikna.core import Parameter
from reikna.core.signature import Annotation
log = logging.getLogger("classification")
def classification_delta_kernel(ctx, outputs, targets, deltas):
kernel_cache, thr... | schreon/neuronaut | neuro/classification.py | Python | mit | 5,154 | [
"NEURON"
] | 268162bad927419b438572b8c5c784b186e803f2c927123874b3cf7aa0acc0db |
__author__ = 'jiataogu'
import theano
import logging
import copy
import sys
import os.path
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__),os.path.pardir)))
import emolga.basic.objectives as objectives
import emolga.basic.optimizers as optimizers
from theano.compile.nanguardmode import NanGua... | MingyuanXie/CopyNet | emolga/models/covc_encdec.py | Python | mit | 74,715 | [
"Gaussian"
] | 090c43c0c3e09b796e739128bb4d3ed666824fa7da3ac06a9984d9d932f80f39 |
import os
import logging
import tool_shed.repository_types.util as rt_util
from galaxy.model.orm import and_
from galaxy.model.orm import or_
from galaxy.webapps.tool_shed import model
from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import shed_util_common as suc
log ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/repository_registry.py | Python | gpl-3.0 | 27,672 | [
"Galaxy"
] | c37b9eb51e6e64d73c662024da7b6cd1f2bd80650290cb502706c1657ff9c217 |
from unittest import TestCase
from octopus.core import app, initialise
import time, esprit
# switch out the live index for the test index
app.config['ELASTIC_SEARCH_INDEX'] = app.config['ELASTIC_SEARCH_TEST_INDEX']
# if a test on a previous run has totally failed and tearDown has not run, then make sure the index is ... | JiscPER/magnificent-octopus | octopus/modules/es/testindex.py | Python | apache-2.0 | 663 | [
"Octopus"
] | bd5bf211f1f2f6a82a677f0b9e274a0e31e7f93c7736a15a3d838a36ff63a354 |
"""
Computational Neurodynamics
Exercise 2
Simulates the movement of a robot with differential wheels under the
control of a spiking neural network. The simulation runs for a very
long time --- if you get bored, press Ctrl+C a couple of times.
(C) Murray Shanahan et al, 2015
"""
import numpy as np
import numpy.rando... | lawrencejones/neuro | Exercise_2/RobotRun4L.py | Python | gpl-3.0 | 4,878 | [
"DIRAC"
] | 160365767b8818b7513237a36bc2cb2a59ccdc67ebbc4a10dd48777c180e110c |
from vtk import *
from tonic.camera import *
import json, os, math, gzip, shutil
# -----------------------------------------------------------------------------
# Helper function
# -----------------------------------------------------------------------------
def getScalarFromRGB(rgb, scalarRange=[-1.0, 1.0]):
d... | Kitware/tonic-data-generator | python/tonic/paraview/data_converter.py | Python | bsd-3-clause | 11,934 | [
"VTK"
] | dab39c9c80f3f59417122373813b10cf616832bf5fcfe02e2e37dea04812a6c0 |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | jswope00/griffinx | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 53,489 | [
"VisIt"
] | 23909c3b3cdb3a9a3ed02afc7cc14f43a99e8c6cc4c07ef56882972a336d0fc0 |
# -*- coding: utf-8 -*-
"""
pygments.lexers.compiled
~~~~~~~~~~~~~~~~~~~~~~~~
Lexers for compiled languages.
:copyright: Copyright 2006-2012 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
from string import Template
from pygments.lexer import Lexer, Rege... | sergioska/EvernoteSyntaxHighlight | pygments/lexers/compiled.py | Python | apache-2.0 | 123,851 | [
"ASE"
] | 22694aaf9f766a5606adc82a41f7637f3840cccbf8b018219276442bedfcbdca |
"""
Read a single output file and return.
"""
import logging
import os
import re
import csv
import string
import pandas as pd
from .. import io
from .. import parsing
from .. import util
logger = logging.getLogger(__name__)
class OutputReader(object):
"""
Given a path to an output folder or list of files, ... | jaeddy/bripipetools | bripipetools/postprocessing/reading.py | Python | mit | 3,872 | [
"HTSeq"
] | 5b4b4841ca1912241927491c9a118e6c0b23288c3736e9af302d3b7e184ab913 |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# Denis A. Engemann <d.engemann@fz-juelich.de>
#
# License: BSD 3 clause
from math import log, sqrt
import warnin... | depet/scikit-learn | sklearn/decomposition/pca.py | Python | bsd-3-clause | 20,538 | [
"Gaussian"
] | 6135a9b77771b51dcc5b54a44a69531f9a11103e75a647bb12b9c71bf94e4395 |
#!/usr/bin/env python3
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... | android/tv-samples | ReferenceAppKotlin/scripts/atv-create-media-feed.py | Python | apache-2.0 | 9,780 | [
"VisIt"
] | f4ffc71d12922d6bdd15263b36ca99fe75ac49e5c2dbba61ed05a26aabba2ba5 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import json
import pytz
from datetime import timedelta
from django.conf import settings
from django.core.urlresolvers import reverse
from django.utils import timezone
from mock import patch
from temba.contacts.models import Contact, ContactField, Contact... | ewheeler/rapidpro | temba/msgs/tests.py | Python | agpl-3.0 | 88,157 | [
"VisIt"
] | 3b6e566818bd105aa0fecba9f46a7ba1ad4d762c7259429dcd3c60257c8a4cf1 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/fci/spin_op.py | Python | apache-2.0 | 11,490 | [
"PySCF"
] | a2c5e22a099e5ce19fc4e8e6d4ad243f7ff204ecc8a2e5527dc75ca2b532dda1 |
#!/usr/bin/env python
import vtk
def main():
# Create a graph
graph = vtk.vtkMutableDirectedGraph()
v1 = graph.AddVertex()
v2 = graph.AddVertex()
graph.AddEdge(v1,v2)
# Create an array for the vertex labels
vertexIDs = vtk.vtkIntArray()
vertexIDs.SetNumberOfComponents(1)
... | lorensen/VTKExamples | src/Python/Graphs/ColorVertexLabels.py | Python | apache-2.0 | 1,100 | [
"VTK"
] | 96c982eaf5e0d58547545cf57d44ac2a436e08cca125a2479c29cdc0d05acb48 |
"""
Print out a hierarchical list of changes between two folders' CSV files.
Intended to be used for comparisons of release folders.
Only compares files that are found in both folders.
Sample call when comparing same-year releases:
```
RELEASE_DIR=/fs/ncanda-share/releases/internal/followup_5y
python compare_release... | sibis-platform/ncanda-data-integration | scripts/reporting/compare_releases.py | Python | bsd-3-clause | 7,859 | [
"VisIt"
] | 5a2836a97947ef7582d0dc2f840556821a3b2e71bd71cc1035a1b833514cb70d |
"""
Contains class for gaussian process hyperparameter optimizations.
"""
import os
import logging
import tempfile
from typing import Dict, List, Optional, Tuple, Union
from deepchem.data import Dataset
from deepchem.metrics import Metric
from deepchem.hyper.base_classes import HyperparamOpt
from deepchem.h... | miaecle/deepchem | deepchem/hyper/gaussian_process.py | Python | mit | 12,659 | [
"Gaussian"
] | 0ab7ec2aac5b9a6176462a4e154aeeaabbbd98b955d34b3b0dfde42d9d5a05ce |
from collections import defaultdict
from typing import Dict, List
from libcst import CSTVisitor, MetadataWrapper, Name, parse_module
from libcst.metadata import (
CodeRange,
PositionProvider,
QualifiedNameProvider,
ScopeProvider,
)
from pytest import mark
from breakfast.source import Source
from tests... | thisfred/breakfast | tests/test_libcst_attempt.py | Python | bsd-2-clause | 3,443 | [
"VisIt"
] | 2155b0fe05e3d211d7e9868f31c6235a58b4f070fee32cd0d038ea81b0e4bc14 |
# Open SoundControl for Python
# Copyright (C) 2002 Daniel Holth, Clinton McChesney
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your opti... | inclement/Pyonic-interpreter | pyonic/osc/OSC.py | Python | gpl-3.0 | 13,428 | [
"VisIt"
] | 9c2f15d363e33b0743128fc2884eb6a5f29b80a06a1d14938131f0b9135bcfc0 |
"""
Parse wheel filenames
``wheel-filename`` lets you verify `wheel
<https://www.python.org/dev/peps/pep-0427/>`_ filenames and parse them into
their component fields.
This package adheres strictly to the relevant PEPs, with the following
exceptions:
- Unlike other filename components, version components may contain... | Dallinger/Dallinger | dallinger/docker/wheel_filename.py | Python | mit | 3,657 | [
"VisIt"
] | 3260298762839c4695a58646ff5ebef1c532a7ccb7a5cbfd43a3b7df7dc51d8e |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/chronos/forecaster/lstm_forecaster.py | Python | apache-2.0 | 5,235 | [
"NEURON",
"ORCA"
] | 457648b0079f837e0b2bfc0ac0df7fc20d308e9a014b7b2d6637886a603a51be |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at y... | jat255/hyperspy | hyperspy/docstrings/signal.py | Python | gpl-3.0 | 7,478 | [
"Gaussian"
] | f3d88b59a840fce8c62ee9f0a3f7b5b2df808df56c14bdccbde6ab517be6aa63 |
# Copyright 2011 Nicholas Bray
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | ncbray/pystream | bin/analysis/lifetimeanalysis/__init__.py | Python | apache-2.0 | 17,698 | [
"VisIt"
] | 1e17713602c290f5c87bd67fbf380ab784769ba7cf0265e16ba5c801ed9b5af6 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os
import unittest
from Bio.PopGen import GenePop
from Bio.PopGen... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_PopGen_GenePop_nodepend.py | Python | gpl-2.0 | 5,263 | [
"Biopython"
] | 2cb6c3f17f9cac3a14480ec864211f83796d18123bf258f7940bd77f41880455 |
#!/usr/bin/python
import getopt
import sys
from Bio import SeqIO
import time
import os
import shutil
import pandas
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
__author__ = "Andriy Sheremet"
#Helper functions definitions
def genome_shredder(input_dct, shear_val):
shredded = {}
for key, v... | nyirock/mg_blast_wrapper | mg_blast_wrapper_v1.9.py | Python | mit | 19,159 | [
"BLAST"
] | 9030b404dfc9c86afae072a21fa7bfe0c6eb03c16812b45641fce01b46aed497 |
#!/usr/bin/env python
import sys
import gd_util
from Population import Population
################################################################################
if len(sys.argv) != 7:
gd_util.die('Usage')
input, input_type, ind_arg, p1_input, p2_input, output = sys.argv[1:]
p_total = Population()
p_total.fr... | gigascience/galaxy-genome-diversity | tools/offspring_heterozygosity/offspring_heterozygosity.py | Python | gpl-3.0 | 1,458 | [
"Galaxy"
] | 4ad9eb380253940c011c17489227e8c3a4663404a548018af354e88858676642 |
"""
Dashboard view and supporting methods
"""
import datetime
import logging
from collections import defaultdict
from completion.exceptions import UnavailableCompletionData
from completion.utilities import get_key_to_last_completed_course_block
from django.conf import settings
from django.contrib import messages
from... | a-parhom/edx-platform | common/djangoapps/student/views/dashboard.py | Python | agpl-3.0 | 37,336 | [
"VisIt"
] | c92eb87647fe21fab9fec24710e464f9fb14aa282bf025fc5a829ec2e207def3 |
# -*- coding: utf-8 -*-
"""
End-to-end tests related to the cohort management on the LMS Instructor Dashboard
"""
from datetime import datetime
from pytz import UTC, utc
from bok_choy.promise import EmptyPromise
from nose.plugins.attrib import attr
from .helpers import CohortTestMixin
from ..helpers import UniqueCour... | simbs/edx-platform | common/test/acceptance/tests/discussion/test_cohort_management.py | Python | agpl-3.0 | 54,312 | [
"VisIt"
] | 6e3a8b6a2c38955b860cdaa8b0bc4f2f7f9eb5c682d0c3d95e92f205b37d0235 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | chrisjsewell/PyGauss | pygauss/cclib_patch/parser/data.py | Python | gpl-3.0 | 12,144 | [
"Gaussian",
"cclib"
] | a94a3495d3885f91602169be994d376dd6ecb3f55ad004efc2743cd5a179b75f |
#!/usr/bin/python
import subprocess
import re
import argparse
def stripper(fasta):
result = {}
with open(fasta) as f:
for name, seq in fastq_fasta_parser.read_fasta(f):
bases = list(seq)
end1 = bases[-3:]
end1 = ''.join(end1)
if end1 == "CCA":
tmpseq = bases[:-3]
seq = ''.join(tmpseq)
end2... | pdl30/pynoncode | pynoncode/run_bowtie.py | Python | gpl-2.0 | 8,057 | [
"Bowtie"
] | 2d28936a18fafa4d6ef82632c7c19ffc22ecbab33c3c7772c4737861deacb85f |
"""Tests of the makeStr.py module."""
import unittest as ut
import os
import pytest
class TestMakeStructures(ut.TestCase):
"""Tests of the _make_structures subroutine."""
def _compare_files(self,file1,file2):
out1 = []
out2 = []
with open(file1,"r") as o1:
for line in o1:
... | msg-byu/enumlib | aux_src/test_makeStr.py | Python | mit | 3,625 | [
"VASP"
] | b799811170ed90cd38aac91a24c3e2d5fa1a838a01621a7316935106c612dcab |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2010 Tampere University of Technology
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the r... | tema-tut/tema-tg | TemaLib/tema/guidance/stateverifier.py | Python | mit | 3,362 | [
"VisIt"
] | ec3110ee32e2a08b2cc7368496ddb7a69a178ca5f9bac0d264f958f7f021bb49 |
"""
Geckoboard decorators.
"""
import base64
from types import ListType, TupleType
from xml.dom.minidom import Document
try:
from functools import wraps
except ImportError:
from django.utils.functional import wraps # Python 2.4 fallback
from django.conf import settings
from django.http import HttpResponse, ... | geckoboard/django-geckoboard | django_geckoboard/decorators.py | Python | mit | 16,565 | [
"Amber"
] | e0c8bb9fd3f41e62f9de14e4f09481a1cf6de5131f17dfa27f7490338f8dddb7 |
#!/usr/bin/python
# -*- coding:utf-8 -*-
#
#
# Authors: Lester Carballo Pérez <lestcape@gmail.com>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at... | lestcape/Cinnamon-Installer | tools/updater.py | Python | gpl-3.0 | 19,160 | [
"VisIt"
] | ace784c714295793dbb60d3a6f91b6a01fcb5278d87a53045a8e4fd640bc857f |
"""Gradient descent
"""
import numpy as np
from frankenstein.tools.perf_utils import TIMER
from pyscf.lib import logger
""" Helper functions
"""
def get_gHp_fd(get_grad, p, order=1, eps=1.E-4):
""" Compute gradient-Hessian product using finite difference
Inps:
get_grad (callable):
gra... | hongzhouye/frankenstein | sgscf/sgopt.py | Python | bsd-3-clause | 6,925 | [
"PySCF"
] | 51732579a092d5c6cceca4062fd91336486d282e089eb3fac80b6db2a2592d15 |
"""Known matrices related to physics"""
from __future__ import print_function, division
from sympy import Matrix, I, pi, sqrt
from sympy.functions import exp
from sympy.core.compatibility import xrange
def msigma(i):
r"""Returns a Pauli matrix `\sigma_i` with `i=1,2,3`
References
==========
.. [1]... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/sympy/physics/matrices.py | Python | mit | 4,145 | [
"DIRAC"
] | b0cdff8aeea9221b5a6504dfbda3964308e57ef6a0c3b350baefaa20aaac2c2b |
"""URL opener.
Copyright 2004-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt included with the distribution).
"""
import os, urllib2, bisect, httplib, types, tempfile
from _request import ... | ppizarror/korektor | bin/mechanize/_opener.py | Python | gpl-2.0 | 14,892 | [
"VisIt"
] | 5c8bb57e574084d92cef74b2d1eca7e6759280310ca9c98a3081d5c925cffad0 |
# -*- coding: utf-8 -*-
"""
Created on Mon Jul 05 18:55:55 2010
Last changed on : July 2016 by Xueshi
@author: Jonas Neergaard-Nielsen
Tools for calculation of Gaussian beam propagation using ABCD matrix formalism.
All lengths are in units of mm.
"""
import numpy as np
from numpy import pi, conj
def wR2q(w, R, lam... | XueshiGuo/Gau-modematching | modematching/abcd.py | Python | mit | 4,366 | [
"Gaussian"
] | 8de78a7fb991ccf7b132ed81d017ba4156c30ba9f96c3bea13c72d308baea180 |
import sys
from os.path import isfile
from collections import defaultdict
import numpy as np
from Bio import AlignIO, SeqIO
from . import config as ttconf
from . import MissingDataError
from .seq_utils import seq2array, guess_alphabet, alphabets
string_types = [str] if sys.version_info[0]==3 else [str, unicode]
def si... | neherlab/treetime | treetime/sequence_data.py | Python | mit | 22,596 | [
"Biopython"
] | a432846b9504686255852220e5ef8b3771fc1f6ed32775f46437058ed6b2fe9d |
# coding=utf-8
# Copyright 2018 The DisentanglementLib Authors. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Un... | google-research/disentanglement_lib | disentanglement_lib/methods/shared/architectures.py | Python | apache-2.0 | 12,624 | [
"Gaussian"
] | 5e3c72f31e12326039522122772e14a7642beab03bac013d01afc77490db8182 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK
from DIRAC.AccountingSystem.Client.Types.WMSHistory import WMSHistory
from DIRAC.AccountingSystem.private.Plotters.BaseReporter import BaseReporter
class WMSHistoryPlotter(BaseReporter)... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/private/Plotters/WMSHistoryPlotter.py | Python | gpl-3.0 | 4,970 | [
"DIRAC"
] | 21a088fe616f3214e5bd859694cadd181368a67b9b73be50e129cb426b63336e |
from __future__ import division
import numpy as np
from astropy.coordinates.distances import Distance
import matplotlib.pyplot as plt
import pyfits
import db
import pyfits
from string import *
from astroML.plotting import hist
from geom import getIncl
def simple_plot(x, y, vel, filename):
fig = plt.figure(figsize=(1... | astrolitterbox/SAMI | utils.py | Python | gpl-2.0 | 6,843 | [
"Galaxy"
] | 5c66dbfcc19e2360f2a7255772de2308306a508717f56d51d1ed0eb50f6a9113 |
"""
Tests for geography support in PostGIS
"""
import os
from django.contrib.gis.db import models
from django.contrib.gis.db.models.functions import Area, Distance
from django.contrib.gis.measure import D
from django.db import NotSupportedError, connection
from django.db.models.functions import Cast
from django.test i... | elena/django | tests/gis_tests/geogapp/tests.py | Python | bsd-3-clause | 6,929 | [
"VisIt"
] | 610aa00bd2d077bd79a42131d6902e9cea13c2198b4691d6814eb3057fbbb795 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-binary-authorization | tests/unit/gapic/binaryauthorization_v1beta1/test_binauthz_management_service_v1_beta1.py | Python | apache-2.0 | 116,500 | [
"Octopus"
] | d52f974fc2ac997e28ccee1ca96b070a68d1bf49cafaada959f8fb1de15cdb3b |
import sqlite3
import pysam
def initialize_database(db):
"""Set up the schema for SQLite3 handle *db*.
"""
db.execute("""
create table sample_group (
id integer primary key,
label text unique,
is_control boolean
)""")
... | madhadron/rnaseq | rnaseq/load.py | Python | gpl-3.0 | 7,679 | [
"Bowtie",
"pysam"
] | 9a86b05f74f128555706b3d99ede8d20609cfa4648f71adb0061274eea3dfe7f |
#!/usr/bin/env python
# encoding: utf-8
import sys
import os
from glob import glob
from metacram import *
''' the actual pipeline '''
args = {}
out = args.get('out', 'out')
reads = glob('data/*')[0]
read_format = args.get('read_format', 'fastq')
# location of databases
db = {
'tc_seed': '~/cram/db/tc_seed.fast... | audy/cram | bin/simple.py | Python | bsd-3-clause | 3,135 | [
"BLAST"
] | b3b8c1e977c9a6fbc29977eeb1020ba0a258350fa2651e79a7f792f70824c3fb |
"""
Downloads feeds, keys, packages and icons.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import os, sys
from zeroinstall import support
from zeroinstall.support import tasks, basedir, portable_rename
from zeroinstall.in... | slovenwd/0install | zeroinstall/injector/fetch.py | Python | lgpl-2.1 | 28,659 | [
"VisIt"
] | 7ad4e15c116b677d0c8ed1e8cd0b175ae460fda480b249a8cdb56727e826a3f5 |
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
config = {
'description': 'LoFi',
'author': 'Desmond Morris',
'author_email': 'hi@desmondmorris.com',
'version': '0.0.1',
'install_requires': ['Flask', 'Flask-MongoEngine', 'nose'],
'packages': ['lofi... | DoSomething/lofi-schools-flask | setup.py | Python | mit | 395 | [
"Desmond"
] | 2cfb06944abcaffaae78d6d63f00cf85e8f0d5f89f856a302163cef33f7914f5 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/field_test.py | Python | gpl-3.0 | 8,115 | [
"ESPResSo"
] | dccb858a0dd5c83556c5053953b76e999a2669588ad28722dee9ef7c9bfb6ea6 |
from django.template import defaultfilters as filters
from django.utils.translation import ugettext_lazy as _
from django.utils.translation import ungettext_lazy
from django import forms
from horizon import forms
from horizon import tables
from models import CrystalProject
from openstack_dashboard import api
from cry... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/projects/projects/tables.py | Python | gpl-3.0 | 4,629 | [
"CRYSTAL"
] | 2213f588367b56cd9553a8adaef338553f0ee7c70a69f6ee5d417d2692310a48 |
#Joe Young
#Sourced from - https://github.com/mrGorman/Python/blob/master/Searching/search_algorithms.py
def linear_search(key, array, index):
""" Function to return index of key in array using
a recursive linear search
"""
if index == len(array):#Checks if the whole list has been checked. If ... | joeyoung658/A-Level_2016-18 | Challenges/Sorting Algorithms/Linear.py | Python | gpl-3.0 | 1,187 | [
"Jaguar"
] | 900478b8b46deb15ecbcb582cfd3c11bafb59626458a10e3f73765311c2da67e |
"""Helpful utilities for building analysis pipelines.
"""
import gzip
import os
import tempfile
import time
import shutil
import contextlib
import itertools
import functools
import random
import ConfigParser
import collections
import fnmatch
import subprocess
import sys
import subprocess
import toolz as tz
import yaml... | gifford-lab/bcbio-nextgen | bcbio/utils.py | Python | mit | 21,875 | [
"Galaxy"
] | 663d51ee751f679403352be2c7a4228ad7456e687a06b1b19a0a30e419703c2c |
#!/usr/bin/env python
from brian import *
duration = 0.1*second
N_sims = 1
lif_eq = ['dV/dt = (V_rest-V)/tau_mem : volt']
V_rest = 0*mV
V_reset = 0*mV
V_th = 15*mV
t_refr = 2*ms
tau_mem = 10*msecond
N_in = 100
f_in = 20*Hz
DV_s = 1*mV
inp = PoissonGroup(N_in,f_in)
nrns = NeuronGroup(N_sims,lif_eq,threshold=V_th,rese... | achilleas-k/brian-scripts | lif.py | Python | apache-2.0 | 943 | [
"Brian",
"NEURON"
] | eddae70b90e70111b32431df324e7308ca9b2623e59e05196bc7b1e1c7195c33 |
#Author : Lewis Mervin lhm30@cam.ac.uk
#Supervisor : Dr. A. Bender
#All rights reserved 2014
#Protein Target Prediction Tool trained on SARs from PubChem (Mined 08/04/14) and ChEMBL18
#Molecular Descriptors : 2048bit Morgan Binary Fingerprints (Rdkit) - ECFP4
#Dependencies : rdkit, sklearn, numpy
#libraries
from rdkit... | lhm30/PIDGIN | predict_enriched_two_libraries.py | Python | mit | 4,150 | [
"RDKit"
] | b1e83473004bf9de74fef3991d0383d49d5e5f36a6a49a2bc9a8c2f5fbaafb2e |
# Copyright (c), Michael DeHaan <michael.dehaan@gmail.com>, 2012-2013
# Copyright (c), Toshio Kuratomi <tkuratomi@ansible.com> 2016
# Simplified BSD License (see licenses/simplified_bsd.txt or https://opensource.org/licenses/BSD-2-Clause)
SIZE_RANGES = {
'Y': 1 << 80,
'Z': 1 << 70,
'E': 1 << 60,
'P': 1... | schlueter/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 114,268 | [
"VisIt"
] | 02cc434a72206930df49e5c79056fb58d37bef9a8b3f0aa561cf40fa3876b65a |
from __future__ import absolute_import, division, print_function
import numbers
import os
import re
import subprocess
import sys
import decimal
import warnings
from functools import partial
from operator import attrgetter
from itertools import chain
from collections import Iterator
from datetime import datetime, date... | ContinuumIO/odo | odo/backends/sql.py | Python | bsd-3-clause | 34,291 | [
"VisIt"
] | 548881348d75fef2aad9514b979cd0457e08ee83785b3affecdfbf978fb9259a |
# Copyright 2020 Tensorforce Team. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable la... | reinforceio/tensorforce | tensorforce/agents/a2c.py | Python | apache-2.0 | 13,157 | [
"Gaussian"
] | 8a2a0088ee1098bcadeaba57ed2a8ec102733431427fb30a411eebc35b0a31e9 |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import json
import os.path
import random
import re
import time
import traceback
from .common import InfoExtractor, SearchInfoExtractor
from ..jsinterp import JSInterpreter
from ..swfinterp import SWFInterpreter
from ..compat import (
compa... | Orochimarufan/youtube-dl | youtube_dl/extractor/youtube.py | Python | unlicense | 155,314 | [
"ADF"
] | 66cfa919d8c3ce0cf1dea174d0dbe296bf03f6e620715a1d45ab478ab994e7dc |
#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Test the different representations of Genes.
This exercises the Motif, Schema and Signature methods of representing
genes, a... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_NNGene.py | Python | gpl-2.0 | 24,146 | [
"Biopython"
] | 474114214bfe5feee44a7ee545a3401c9230e143f06db0f056dd38447220235a |
# Copyright 2020 The LUCI Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0
# that can be found in the LICENSE file.
"""Utilities to work with realms_pb2 messages."""
from .proto import realms_pb2
# Currently acceptable version of Realms API. See api_version i... | luci/luci-py | appengine/components/components/auth/realms.py | Python | apache-2.0 | 4,222 | [
"VisIt"
] | f93289812b91ba06268c2a2e952d5d8eb4c4a4b083125525ad661f3ddca391b9 |
""" :mod: RequestTaskTests
=======================
.. module: RequestTaskTests
:synopsis: test cases for RequestTask class
test cases for RequestTask class
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id $"
# #
# @file ... | yujikato/DIRAC | src/DIRAC/RequestManagementSystem/private/test/RequestTaskTests.py | Python | gpl-3.0 | 3,237 | [
"DIRAC"
] | 141eb7a66f38efe2c14199b58ebafc8261f4b9bb2fe2fec603d6b27e5edba9d4 |
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# This program is distr... | RTS2/rts2 | scripts/rts2saf/unittest/test_executables.py | Python | lgpl-3.0 | 9,130 | [
"VisIt"
] | c2139346573b6fa9985fec58d57165bc913f31f8ddb14c57ec14f80ae53eb3d5 |
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