text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
#!/usr/bin/env python
"""
This tests the ability to render GPU resident data in VTK.
"""
import sys
import vtk
from vtk.test import Testing
from PistonTestCommon import *
class TestRendering(Testing.vtkTest):
def testRendering(self):
global args
renderer = vtk.vtkRenderer()
renwin = vtk.vtkRenderWind... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Accelerators/Piston/Testing/Python/TestRendering.py | Python | gpl-3.0 | 1,290 | [
"VTK"
] | ba36f1c8e8c780f897e573159a0d516571bd704ae496578fb40bad3885016c29 |
import numpy as np
import ase
from ase.parallel import paropen
cfg_default_fields = np.array( [ 'positions', 'momenta', 'numbers', 'magmoms' ] )
def write_cfg(f, a):
"""Write atomic configuration to a CFG-file (native AtomEye format).
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
if isin... | alexei-matveev/ase-local | ase/io/cfg.py | Python | gpl-2.0 | 6,779 | [
"ASE"
] | 487cf3a2c13d5a6f011bc92d4ef9d3d3c2b0202c9e32652b07ac70ebdf7b68db |
#!/usr/bin/env python
""" Virtual Machine Command Line Interface. """
import pprint
import getpass
from DIRAC.Core.Base.CLI import CLI
from DIRAC.Core.Security.Locations import getProxyLocation
from DIRAC.Core.Utilities.PrettyPrint import printTable
from DIRAC.Resources.Cloud.EndpointFactory import EndpointFactory
f... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/VirtualMachineCLI.py | Python | gpl-3.0 | 7,834 | [
"DIRAC"
] | 89e76c34f873037e1a595fae4573b7ce697e205ae6d33d52c41fd13922ed1f6e |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','desc... | ludolphus/Nimbuslabel | build.py | Python | apache-2.0 | 8,764 | [
"VisIt"
] | e8ecc51bb7e037ddaea95c7749bef8833f71500990b4d4af2f04e31a90c7006b |
########################################################################
# $HeadURL $
# File: FTSAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/31 10:00:13
########################################################################
""" :mod: FTSAgent
==============
.. module: FTSAgent
:syno... | calancha/DIRAC | DataManagementSystem/Agent/FTSAgent.py | Python | gpl-3.0 | 46,590 | [
"DIRAC"
] | 567b980cbedd7cd52412c23e68fc2b2b82ec90558115b8b899f34f55ed390991 |
# a part of cropgui, a graphical front-end for lossless jpeg cropping
# Copyright (C) 2009 Jeff Epler <jepler@unpythonic.net>
# 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; eithe... | jepler/cropgui | cropgui_common.py | Python | gpl-2.0 | 17,507 | [
"FLEUR"
] | 7436506434548cb0149ba02d867e982365e533733c06e9993dee85ba68c0d336 |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | d7415/merlin | Hooks/intel/intel.py | Python | gpl-2.0 | 5,362 | [
"Galaxy"
] | 5918db48bd54eb47d6c3974c12798d15ce9b4f9fba2be500edf6061abe80a018 |
# This file is part of JujuPy, a library for driving the Juju CLI.
# Copyright 2013-2019 Canonical Ltd.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the Lesser GNU General Public License version 3, as
# published by the Free Software Foundation.
#
# This program is di... | wallyworld/juju | acceptancetests/jujupy/k8s_provider/base.py | Python | agpl-3.0 | 9,694 | [
"CDK"
] | a9309b298582da0aeaf95cec66eb9c0c8413ba8d12353c9c5930a13f5a007d0e |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | rvs/gpdb | src/test/tinc/tincrepo/mpp/models/regress/sql_related/regress_sql_perf/regress_sql_perf.py | Python | apache-2.0 | 3,960 | [
"ORCA"
] | 9fd2d8070750def118830adb74af32d2441fa2258316bca2e6d019b356351d52 |
# Copyright (C) 2015-2022: The University of Edinburgh
# Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
#
# This file is part of gprMax.
#
# gprMax 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 Sof... | gprMax/gprMax | tools/Paraview macros/gprMax_info.py | Python | gpl-3.0 | 11,239 | [
"ParaView"
] | bd673b923569d2bd722dfc44a6e8702efdbcbdf0cd6cd0705fb4796ccffd969d |
#!/usr/bin/env python3
import pysam
import sys
import random
def main(f):
with pysam.VariantFile(f) as vcf:
print('''##CADD style randomly generated numbers for testing
#Chrom Pos Ref Alt RawScore PHRED''')
for record in vcf:
for alt in record.alts:
... | gantzgraf/vape | test/utils/generate_cadd_data.py | Python | gpl-3.0 | 930 | [
"pysam"
] | 1bdf8bb0671c934b1c76839804fdcb6f5c21a1829da37b41decb7af1386cbdc5 |
# Lint as: python3
# Copyright 2019 Deepmind Technologies Limited.
#
# 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 ap... | deepmind/deepmind-research | iodine/modules/distributions.py | Python | apache-2.0 | 7,418 | [
"Gaussian"
] | 38173008a29e24ea19798954d774ae776311c8f1c23247faaf479312729d710a |
"""
SymGP - A symbolic algebra library for multivariate Gaussian and Gaussian process probabilistic models
"""
from .mvg import MVG
from .superexpressions import *
from .utils import utils
from .kernels import * | jna29/SymGP | symgp/__init__.py | Python | mit | 216 | [
"Gaussian"
] | a21fcd7b510a7857b7de6e09409d5f80472e47b6ffc919720c23fc017cfbab04 |
# -*- coding: utf-8 -*-
#
# Copyright 2018 Ibai Roman
#
# This file is part of GPlib.
#
# GPlib 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 ... | ibaidev/gplib | setup.py | Python | gpl-3.0 | 1,841 | [
"Gaussian"
] | 71d7c231f475452ed475da963c371a1c4afeffe7cb9a11e9a9f00454b7a1819d |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy
node = import_file("../../files/NetCDF/sheared_aSi.nc")
modifier = HistogramModifier()
node.modifiers.append(modifier)
print("Parameter defaults:")
print(" bin_count: {}".format(modifier.bin_count))
modifier.bin_count = 50
print... | srinath-chakravarthy/ovito | tests/scripts/test_suite/histogram_modifier.py | Python | gpl-3.0 | 1,050 | [
"NetCDF",
"OVITO"
] | 784c28072b9808e9aa1c2482c663dc8593cc465e2d48709d01c3d12ccf57eebd |
"""
Functions for extracting information from a repository registry file.
"""
from __future__ import absolute_import
import os
from collections import OrderedDict
import sqlite3
import astropy.time
__all__ = ['find_registry', 'get_visit_mjds', 'get_visits']
def find_registry(data_repo, registry_name='registry.sqlite3... | DarkEnergyScienceCollaboration/pserv | python/desc/pserv/registry_tools.py | Python | bsd-3-clause | 2,529 | [
"VisIt"
] | ef4396f9431b8e437014c9b3d4399f09fe984bb0d0e49b41f6ad54b2049c0ed5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/smartio.py | Python | mit | 580 | [
"pymatgen"
] | 78bcfd06384a25786c1af152a585935e5080adee541358fbc4d438e78beee69a |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | mxm/incubator-beam | sdks/python/apache_beam/runners/portability/fn_api_runner.py | Python | apache-2.0 | 65,525 | [
"VisIt"
] | b75debe6a83ca120e838db0c03d9724944c7b73e7a4c99cb4abf540a5011aa6b |
#!/cluster/home2/mglerner/anaconda3/bin/python
#!/usr/bin/env python
'''
Set up ptraj input files to run a series of H-bond calculations.
'''
import sys, os
from optparse import OptionParser
if __name__ == '__main__':
usage = """%prog [options]
This program sets up ptraj input files to perform a series of H-bon... | LernerLabs/PyPAT | drivers/setup_hbond_ptraj.py | Python | apache-2.0 | 13,851 | [
"Amber"
] | 009031da8b5af0a0c3d585df7c0db15c9dc7edf8ea6ccadaa62f16e41ce864c8 |
# Copyright (C) 2019 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 versio... | fweik/espresso | testsuite/scripts/tutorials/test_electrokinetics.py | Python | gpl-3.0 | 2,546 | [
"ESPResSo"
] | f4d6086b8f868b8879513fbd952cce844965c29eb5662d1121696ebc1a53b89e |
#!/usr/bin/env python
# coding: utf-8
# # Compute Backends Comparison Table
#
# This is an extended version of Table 2 from [Conroy et al. 2020](http://phoebe-project.org/publications/2020Conroy+) and provides an overview of the capabilities and features of the available backends **as implemented by the wrappers**. ... | phoebe-project/phoebe2-docs | development/examples/compute_comparison_table.py | Python | gpl-3.0 | 14,479 | [
"Gaussian"
] | 14c966bd70b75cbb6dcb6281de529fd162f27df8691bfb9a0b40afa9384fff0f |
# -*- coding: utf-8 -*-
#
# mc_neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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
#... | sdiazpier/nest-simulator | pynest/examples/mc_neuron.py | Python | gpl-2.0 | 7,424 | [
"NEURON"
] | f3ed330c4d5ffa32dc8eaf453e5dbde7fd39b57975fa87502d67f370f0c28c02 |
from __future__ import print_function, division
import functools
import nose
import numpy
from scipy import interpolate
sdf_bovy14= None #so we can set this up and then use in other tests
sdft_bovy14= None #so we can set this up and then use in other tests, trailing
# Decorator for expected failure
def expected_failur... | followthesheep/galpy | nose/test_streamdf.py | Python | bsd-3-clause | 67,512 | [
"Gaussian"
] | 85fa590bf11edd0b07fdab20a34da0cb3037a896f5beab62b2ac05604caad54e |
"""
This module contains generic generator functions for traversing tree
(and DAG) structures. It is agnostic to the underlying data structure
and implementation of the tree object. It does this through dependency
injection of the tree's accessor functions: get_parents and
get_children.
The following depth-first tra... | edx-solutions/edx-platform | openedx/core/lib/graph_traversals.py | Python | agpl-3.0 | 12,941 | [
"VisIt"
] | b29c8ba7d1dce0890a35f11a4de0c449f6816e39342d76da95bad82cf720bb96 |
import matplotlib.pyplot as plt
from matplotlib import colors
from matplotlib import patches
import collections
import matplotlib.cm as cm
import pysal.viz.mapclassify as classify
import numpy as np
from ._viz_utils import _classifiers, format_legend
"""
Creating Maps with splot
* Value-by-Alpha maps
* Mapclassify wra... | lixun910/pysal | pysal/viz/splot/_viz_value_by_alpha_mpl.py | Python | bsd-3-clause | 16,986 | [
"COLUMBUS"
] | 4411ed77964345dea605afb24e1914f7b77f4aaca68f7ca04b6e373ccd7b9089 |
#-----------------------------------------------------------------------------
# Purpose:
#
# Adapted from NeuroTools
#
# Licence : GPLv2
#-----------------------------------------------------------------------------
"""
NeuroTools.stgen
================
A collection of tools for stochastic process generation.
Class... | inincs/pyNCS | src/pyNCS/pyST/stgen.py | Python | gpl-2.0 | 32,908 | [
"Gaussian"
] | 5172305968696d2fac05a7339c1cab6ea3a93ce9ed0b3194136e8da0275f5478 |
""" Contains the base class for ball devices."""
# ball_device.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
from collections import deque
import time
im... | qcapen/mpf | mpf/devices/ball_device.py | Python | mit | 54,623 | [
"Brian"
] | 3ace602723c36d5c98ad34b12694c25f81d7f34181ecdcf9d2ef71d3b69937e9 |
"""
This a nonuniform sampler with ANGIE sampling scheme. |br|
The modules samples the given signals nonuniformly. |br|
The sampling patterns are generated using ANGIE scheme.
The used ANGIE patterns generator is described further in
"Generation and Analysis of Constrained Random Sampling Patterns",
available in arXi... | JacekPierzchlewski/RxCS | rxcs/acq/nonuniANGIE.py | Python | bsd-2-clause | 25,398 | [
"Gaussian"
] | 60d0db68ccd3e41568b703ec704de20c94f523ae972ef0b8ea4f5c739ae022d2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Mon Jul 14 11:06:54 2014
@author: tg
"""
#%%
from Bio import Restriction
from Bio.Seq import Seq
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from BCBio import GFF
from Bio.Alphabet import generi... | tgbio/RRBS | double_dig.py | Python | apache-2.0 | 27,564 | [
"Biopython"
] | c083aa7f84413796d4e2b6dfc8add5516ac2737263d2ee756bb2fb1f4b21474c |
#!/usr/bin/env python2
import argparse
import sys
import xml.sax
class CLIElement(object):
"""Represents a <clielement> tag.
option_identifier -- str with parameters (e.g. --param), empty if argument.
is_list -- bool whether the element is a list.
"""
def __init__(self, option_identifier='', ma... | bestrauc/seqan | util/ctd2galaxy.py | Python | bsd-3-clause | 7,324 | [
"Galaxy"
] | 08eb5801d457dbd2d0804e412d30c2331dae251828cd1ae3f41a26d110be7770 |
#!/usr/bin/env python
# encoding: utf-8
from ast import literal_eval
import codecs
import io
import pytest
import networkx as nx
from networkx.readwrite.gml import literal_stringizer, literal_destringizer
import os
import tempfile
try:
unicode
except NameError:
unicode = str
try:
unichr
except NameError:
... | sserrot/champion_relationships | venv/Lib/site-packages/networkx/readwrite/tests/test_gml.py | Python | mit | 15,892 | [
"Cytoscape"
] | 1fdb33e61ff191319f6d325ce70676a3af1fb53b52c0fdfc6f2d1767bea8bf0a |
# -*- 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-compute | tests/unit/gapic/compute_v1/test_region_backend_services.py | Python | apache-2.0 | 149,814 | [
"Octopus"
] | c050500397da4ca04e59fc100a37a8bd87fa12798b34f4fc357afd50fd113ca3 |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
import os
import datetime
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit import events
_test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
'test_files', "abinit")
... | xhqu1981/pymatgen | pymatgen/io/abinit/tests/test_events.py | Python | mit | 2,978 | [
"ABINIT",
"pymatgen"
] | c03a724c7ee1b1ff2bece3c4569f917d3ecbc87d6006cead9f86e4354ad79401 |
from dateutil.relativedelta import relativedelta
from datetime import datetime, date
from django.utils import timezone
from edc_constants.constants import SCREENED
from edc_registration.models import RegisteredSubject
from edc_identifier.models import SubjectIdentifier
from edc_constants.constants import FAILED_ELIGIB... | botswana-harvard/tshilo-dikotla | td_infant/tests/test_infant_arv_proph_form.py | Python | gpl-2.0 | 12,781 | [
"VisIt"
] | e06619cf2a238d5b8d226b6cad90eedc594d951e2c388a0386b356579bc299af |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/LBInitPopUniform.py | Python | gpl-3.0 | 2,387 | [
"ESPResSo"
] | 10720d378bff5be44c3911dcca079d9d9e32344770b3d66044bb6c8b27951c3f |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | tobiajo/kubernetes | hack/verify-flags-underscore.py | Python | apache-2.0 | 4,847 | [
"VisIt"
] | 793f33fb707b49f10f603e60735734fadcb0bacac82f1db4a5a710f196fe5d5e |
# -*- coding: utf-8 -*-
"""
***************************************************************************
translate.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
*****************************... | SrNetoChan/QGIS | python/plugins/processing/algs/gdal/gdaladdo.py | Python | gpl-2.0 | 6,902 | [
"Gaussian"
] | d8bde61dcb4d31c2e3db2df2e624f33aa95bc1f2f3f2f0ec688c0e8119186fbf |
# Copyright (C) 2010-2019 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... | KaiSzuttor/espresso | samples/espresso_logo.py | Python | gpl-3.0 | 6,174 | [
"ESPResSo"
] | c7578d2f7b173e1f78988428575893ee9aa2ddbcf0667cf455c38ebfb186cf79 |
# -*- coding: utf-8 -*-
# PEP8 asserts
from copy import deepcopy
import httplib as http
import mock
import time
from nose.tools import * # noqa
from modularodm.exceptions import ValidationValueError
from tests.base import OsfTestCase, fake
from tests.factories import (
UserFactory, NodeFactory, ProjectFactory,... | GageGaskins/osf.io | website/addons/wiki/tests/test_wiki.py | Python | apache-2.0 | 58,299 | [
"VisIt"
] | f2d40ef60f3deff080d0ab52fc7e03c3f5af689a75f6be49b360b2e3a199e6ba |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/io/_warning.py | Python | bsd-3-clause | 602 | [
"scikit-bio"
] | 6e8a561ec36bb624b711540f4f07d55bd6bc860d1ce89af4aa423de17000c630 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/helpers/subtitlehelper.py | Python | gpl-2.0 | 11,356 | [
"VisIt"
] | 3986ba78bc94ff865955ca525869ba79410584d392dd947502a31d47f6e75fbe |
# Copyright (C) 2017-2018 Michael Freitag, Shahin Amiriparian, Sergey Pugachevskiy, Nicholas Cummins, Björn Schuller
#
# This file is part of auDeep.
#
# auDeep 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,... | auDeep/auDeep | audeep/cli/import_data.py | Python | gpl-3.0 | 3,218 | [
"NetCDF"
] | 181f58211e7875dc0fc245ec9263f4945e7451a0ac440e73f465da900e8235b1 |
"""
sendwithus - Python Client
For more information, visit http://www.sendwithus.com
"""
import base64
import logging
import json
import requests
from six import string_types
import warnings
from .encoder import SendwithusJSONEncoder
from .version import version
from .exceptions import APIError, AuthenticationError, ... | mefyl/sendwithus_python | sendwithus/__init__.py | Python | apache-2.0 | 21,845 | [
"VisIt"
] | dfdf4b851091fe76f6eb5859d2c7b7935f18f8663e3b6449778209a76338d8f7 |
import os
import os.path
import shutil
import sys
import unittest
from collections import OrderedDict
from time import sleep
from typing import Union, List, Optional
from unittest import TestCase
from cate.cli import main
from cate.core.ds import DATA_STORE_POOL
from cate.core.op import OP_REGISTRY
from cate.core.type... | CCI-Tools/cate-core | tests/cli/test_main.py | Python | mit | 29,864 | [
"NetCDF"
] | 294b22d87c3d7ea0621af6d0b5f5fea677d50f222ddcbb4cffd21f83798f34a3 |
#
# Copyright Amazon.com, Inc. or its affiliates. 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.
# A copy of the License is located at
#
# http://aws.amazon.com/apache2.0
#
# or in the "license" file accompanyi... | colmmacc/s2n | tests/integration/s2n_test_constants.py | Python | apache-2.0 | 23,450 | [
"Octopus"
] | 9542266baf2e9b2ac4447cff91563f316c09b7fa2afce98bcdd059f7c06a002d |
#
# paws -- provision automated windows and services
# Copyright (C) 2016 Red Hat, Inc.
#
# 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) a... | rhpit/paws | tests/paws_ci_tests.py | Python | gpl-3.0 | 8,926 | [
"Galaxy"
] | 06b348dfb5d7ada2d76fe9ac9eaaf797a75b4c7a2b08c901881a53a275d1f820 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/procrouting/mcscf/mcscf_solver.py | Python | lgpl-3.0 | 13,631 | [
"Psi4"
] | cd762a26512794322c29e3e166c56714318097c33ec5945924359d018714b051 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_plan_deleted.py | Python | apache-2.0 | 9,997 | [
"VisIt"
] | c9f64798761da8007fdab608a981f31b3d9d9354793c5551d5a88421f803d154 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/topology/LAMMPSParser.py | Python | gpl-2.0 | 19,664 | [
"LAMMPS",
"MDAnalysis"
] | 4331ad1721732598e96930e851d0d73e524b15bc270100530484021658f1b3a1 |
# encoding: utf-8
# Copyright 2016 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# The number of lines will be reduced after 2018 update is complete and
# the old stories are removed: https://crbug.com/878390.
# pylint:... | endlessm/chromium-browser | tools/perf/page_sets/system_health/browsing_stories.py | Python | bsd-3-clause | 58,617 | [
"VisIt"
] | ac604abf9fd9244b5bf413afa7f54fd72839ab4ed2364467e85ca794c0ae891a |
"""Functions to plot epochs data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Jaakko Leppakangas <jaeilepp@student.jyu.fi>
# ... | kambysese/mne-python | mne/viz/epochs.py | Python | bsd-3-clause | 43,008 | [
"Gaussian"
] | 6f112c182061e1cfdc5c5145c199ab48aea993e744961647f87ee0f55b445fe8 |
#!/usr/bin/env python
#
# Refine models with explicit-solvent MD simulations
#
# Daniel L. Parton <daniel.parton@choderalab.org> - 21 Mar 2014
#
import MSMSeeder
import MSMSeeder.refinement
# ========
# Parse command-line arguments
# ========
import argparse
argparser = argparse.ArgumentParser(description='Conducts ... | danielparton/MSMSeeder | scripts/RefineExplicitMD.py | Python | gpl-2.0 | 1,444 | [
"OpenMM"
] | 5663a91994708a22a248d82f2c689be367cb6711ac6d1ba09f5c534dbaec350b |
import time
from _MultiNEAT import *
#from concurrent.futures import ProcessPoolExecutor, as_completed
import matplotlib.pyplot as plt
from numpy import array, clip
try:
import cv2
import numpy as np
cvnumpy_installed = True
except:
print ('Tip: install the OpenCV computer vision library (2.0+) with '... | jal278/multineatbranch | MultiNEAT.py | Python | lgpl-3.0 | 16,191 | [
"NEURON"
] | dd5ea20038131713083e813d2166b70d3fe84e10f3cc9f05f18e3560699b21a1 |
import sys
sys.path.insert(1, "../../../")
import h2o
import random
def cv_carsGLM(ip,port):
# read in the dataset and construct training set (and validation set)
cars = h2o.import_file(path=h2o.locate("smalldata/junit/cars_20mpg.csv"))
# choose the type model-building exercise (multinomial classificati... | mrgloom/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_cv_carsGLM.py | Python | apache-2.0 | 6,735 | [
"Gaussian"
] | 7335162f902e2831d88107fdfe55db3e535f67c20a4fa5d318f6f7c84b6bdb75 |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits
from sklearn.cross_validation import cross_val_score
from sklearn.externals.six.moves import zip
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.testing import assert_array_equ... | ashhher3/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 12,828 | [
"Gaussian"
] | 8767c87bcddd9761fc75945f0866e1308a7fec209519078df7fee146ca0eab78 |
#!/usr/bin/env python
# boards.txt python builder for esp8266/Arduino
# Copyright (C) 2017 community
# Permission is hereby granted, free of charge, to any person who buy it,
# use it, break it, fix it, trash it, change it, mail - upgrade it, charge
# it, point it, zoom it, press it, snap it, work it, quick - erase it... | Adam5Wu/Arduino | tools/boards.txt.py | Python | lgpl-2.1 | 60,734 | [
"CRYSTAL",
"ESPResSo"
] | 6107ff59d418ddd71079329a095a2862d040da4eb64c0ad8331ac66dc6d0f31c |
from __future__ import division, absolute_import, print_function
import warnings
import numpy as np
from numpy.testing import (
assert_, assert_raises, assert_equal, assert_warns,
assert_no_warnings, assert_array_equal, assert_array_almost_equal,
suppress_warnings
)
from numpy import ra... | Eric89GXL/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 65,228 | [
"Gaussian"
] | 4806ab878e4d865fa3832af0c6e1636f17d7081f81441e5dfe568e6b415b22ad |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
from django.core.exceptions import ImproperlyConfigured, ObjectDoesNotExist
from django.test import TestCase, override_settings
from django.test.client import RequestFactory
from django.views.generic.base import View
from django.... | yephper/django | tests/generic_views/test_detail.py | Python | bsd-3-clause | 9,227 | [
"MOOSE"
] | 5dcb9192dd99717e929e9152fa62286c610c5058e4ea26f05b685675b8970059 |
class Metrics(object):
def __init__(self, master):
self.master = master
def get(self, since=None, until=None, trend=None):
"""general description
Args:
since (int): An optional Unix timestamp to restrict metrics to
those created on or after this time. Formatting ... | meori/delighted-python | delighted/metrics.py | Python | mit | 1,901 | [
"VisIt"
] | aa08f876ac2753e6d62cbf9836e0155a10c0db62b47f334ecb4a124543151b05 |
#
# Physics 1321: Computational Methods in Physics
# University of Pittsburgh
# by Brian R. D'Urso
#
#
# load libraries
#
import math
import numpy as np
import scipy.optimize
def initialize(shell, **kwargs):
shell.interact(kwargs.copy())
clear(**kwargs)
def clear(messages, plot, **kwargs):
plot.cle... | LunarLanding/Pythics | pythics/examples/fitting.py | Python | gpl-3.0 | 2,432 | [
"Brian"
] | 2c81619b37208f70614fcc46afc10c86d1d3cc7d796b7ced655fa7f48c4f4ae1 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageRFFT(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkI... | nagyistoce/devide | modules/vtk_basic/vtkImageRFFT.py | Python | bsd-3-clause | 481 | [
"VTK"
] | 559dd623fc3523b0ce0e0aae565168c6a69b769290fe54991583f594fea6c1ed |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for ... | keflavich/agpy | agpy/mpfit/mpfit.py | Python | mit | 93,253 | [
"Gaussian"
] | df7671844df0e941bfcf3339b962ee193d78ad6442cca14968ed8600e2a5f2be |
"""
The GA4GH data model. Defines all the methods required to translate
data in existing formats into GA4GH protocol types.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import glob
import os
import json
import tempfile
import shutil
import atexit
im... | shajoezhu/server | ga4gh/datamodel/__init__.py | Python | apache-2.0 | 5,990 | [
"pysam"
] | 5ba47605c108685ae1010cb0d1b034b8c9fdf720175a1924e3c627dbaf7227af |
import os
import pytest
import trimesh
import numpy as np
from PIL import Image
import vtk
import pyvista
def test_wrap_none():
# check against the "None" edge case
assert pyvista.wrap(None) is None
def test_wrap_pyvista_ndarray(sphere):
pd = pyvista.wrap(sphere.points)
assert isinstance(pd, pyvist... | akaszynski/vtkInterface | tests/test_helpers.py | Python | mit | 1,542 | [
"VTK"
] | ba92b77a19b8dea58163a75cedb5c19d1c4e3af7fac56cc58c899dd0c50db038 |
"""
example pipelines for running RNA-seq experiments
"""
import yaml
from bipy.utils import nested_lookup
from functools import partial
from bipy.pipeline import AbstractStage
from bipy.toolbox.fastqc import FastQCStage
class AbstractPipeline(object):
def __init__(self, config_file):
with open(config... | roryk/bipy | bipy/pipeline/rnaseq.py | Python | mit | 1,066 | [
"HTSeq"
] | bffaa9c48c12f8776ef7467afe73fbf1b2ee6aaf1effb016c3edc28f8a555eb7 |
#!/usr/bin/env python3
'''Routines for enumerating SMARTS expressions representing fragments of provided molecules'''
import sys,argparse,collections
import numpy as np
from rdkit.Chem import AllChem as Chem
def computepathsmarts(mol, size):
if size <= 0: size = 7 # default to 7 atoms
ret = set()
for len... | dkoes/qsar-tools | createsmartsdescriptors.py | Python | apache-2.0 | 4,321 | [
"RDKit"
] | fd82aa4cfa2f59b62aa5ded0c514a280799edc732a54f0a4506a4f2f03ca7103 |
from twisted.internet import reactor
from octopus.runtime import *
from octopus import runtime as r
from octopus.sequence.util import Tick
def fn1 ():
print "d3 tick."
def fn2 ():
return log("d4 tick...")
e = r._experiment
d1 = Tick(sequence(
log("d1 tick...")
), interval = 2)
d2 = Tick(log("d2 tick"), interval... | rasata/octopus | examples/test_tick.py | Python | mit | 632 | [
"Octopus"
] | 24afee76cdfedbba98e095e7c78c658e90be3f9bf4cab2e66f9a3d06b3fe363b |
""" The guy that takes case of managing sockets
"""
__RCSID__ = "$Id$"
import socket
import select
import os
import hashlib
import GSI
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Utilities import Network
from DIRAC.Core.DISET.private.Transports.SSL.SocketInfo import SocketInfo
from D... | andresailer/DIRAC | Core/DISET/private/Transports/SSL/SocketInfoFactory.py | Python | gpl-3.0 | 6,812 | [
"DIRAC"
] | 5c6c81f36b7592b10d5fc62b8807a65c31c306e142b627a36169a84b391aa46d |
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import ddt
from common.test.acceptance.fixtures.certificates import CertificateConfigFixture
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.p... | edx/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 8,390 | [
"VisIt"
] | 182b1031eb3903b335281a2ce47b1943a4c0bc070b505f6ec0b6eb2adc32d0c2 |
##########################################################################
#
# MRC FGU Computational Genomics Group
#
# $Id$
#
# Copyright (C) 2009 Andreas Heger
#
# 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 ... | CGATOxford/Optic | scripts/gpipe/setup.py | Python | mit | 9,069 | [
"BLAST"
] | 6ad35f16d6bf823aed54e5924259aacea268830a6290d79b3dd0429b28f9a832 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division
from warnings import warn
from six import iteritems
from itertools import product
from multiprocessing import Pool
import pandas as pd
from optlang.interface import OPTIMAL
from numpy import (
nan, abs, arange, dtype, empty, int32, linspace... | zakandrewking/cobrapy | cobra/flux_analysis/phenotype_phase_plane.py | Python | lgpl-2.1 | 23,273 | [
"Mayavi"
] | ab5386b07d68b71a2004c87f3b4446dd34fb716b62f4164c9094f4d8f84421ad |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/molparse/pubchem.py | Python | lgpl-3.0 | 7,591 | [
"Psi4"
] | cd4d065f1a3bbb398f326ffe1ffc0176690d6b891761f2280e1d85ad63fb6c46 |
from __future__ import unicode_literals
from .common import InfoExtractor
class EngadgetIE(InfoExtractor):
_VALID_URL = r'https?://www.engadget.com/video/(?P<id>\d+)'
_TEST = {
'url': 'http://www.engadget.com/video/518153925/',
'md5': 'c6820d4828a5064447a4d9fc73f312c9',
'info_dict': ... | nandhp/youtube-dl | youtube_dl/extractor/engadget.py | Python | unlicense | 612 | [
"Galaxy"
] | 0a1a027144ee70b82d533c8e0d732722b4aebeb7dda47e2c86e9d1709bac31eb |
# SOURCE: https://github.com/txt/mase/blob/0bba5fc5b12bb85dc77c6128ceff721fb7aa31d2/src/a12.py
"""
## Analysis of Experimental Data
This page is about the non-parametric a12 test. It is also a chance for us to discuss a little
statistical theory.
### Standard Header
"""
from __future__ import division
import sys
... | rchakra3/generic-experiment-loop | optimizer/helpers/a12.py | Python | gpl-2.0 | 10,992 | [
"Gaussian"
] | fb3fa613eef28699897b146c6f394aa082821b0c1d86bdcf35ee6950934aa049 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
#"""
#ADF NMR Output Editor
##############################
#Editor class for parsing the NMR data from an ADF calculation
#"""
#from __future__ import absolute_import
#from __future_... | exa-analytics/exatomic | exatomic/adf/nmr/output.py | Python | apache-2.0 | 6,417 | [
"ADF"
] | 24e6f7fcd5dbf66980f8b6dbf8b9f992bafda623076ab35fac2db4020ef3034d |
"""Scraper for United States District Court for the District of Columbia
CourtID: dcd
Court Short Name: D.D.C.
Author: V. David Zvenyach
Date created: 2014-02-27
Substantially Revised: Brian W. Carver, 2014-03-28
"""
from juriscraper.opinions.united_states_backscrapers.federal_district import dcd_2013
class Site(dcd_... | Andr3iC/juriscraper | opinions/united_states_backscrapers/federal_district/dcd_2012.py | Python | bsd-2-clause | 540 | [
"Brian"
] | b9b96345c5e8d2bdcf5171667d79bd78a25d73fdcf925d45f318e96b18208879 |
"""
Commands for setting intensities and Ion Chamber gains
"""
import time
def feedback_off():
"""
Turn intensity feedback off
"""
caput('13IDA:efast_pitch_pid.FBON', 0)
caput('13XRM:edb:use_fb', 0)
caput('13IDA:efast_roll_pid.FBON', 0)
#enddef
def feedback_on(roll=True, pitch=True):
"""
... | newville/microprobe_docs | doc/macros/intensity.py | Python | bsd-2-clause | 11,925 | [
"CRYSTAL"
] | b1d76d4a64e35ae605544ec3921fb571ccb20516fdba01bced690ec198088783 |
#!/usr/bin/python
import numpy as np
import scipy.special as spc
import matplotlib.pyplot as plt
'''
Taylor erf(x)/x
C = 2/sqrt(pi)
C +
- x^2/3
+ x^4/5
- x^6/21
+ x^8/108
- x^10/660
+ x^12/4680
- x^14/37800
+ x^16/342720
- x^18/3447360
+ x^20/38102400
- x^22/459043200
+ x^24/5987520000
(Taylo... | ProkopHapala/SimpleSimulationEngine | cpp/sketches_SDL/Molecular/python/erf_approx.py | Python | mit | 7,792 | [
"Gaussian"
] | 76de33a8c186d4f9be531e4f5081ba2ad5224c86031e1e0b4e5d186d5e56a80c |
#!/usr/bin/env python
from __future__ import print_function
from dark.blast import BlastRecords
from dark.blast.records import printBlastRecord
if __name__ == '__main__':
import sys
if len(sys.argv) < 2:
print('Usage: %s BLAST-hitfile...' % sys.argv[0], file=sys.stderr)
else:
blastRecord... | acorg/dark-matter | bin/print-blast-xml.py | Python | mit | 517 | [
"BLAST"
] | 0ed95b071033af9a072311cc5dbe67b2f0d65352b450ef1107d293f3d9e98e69 |
#!/usr/bin/env python
"""Define a snf pipeline workflow in Python and create a makefile
that will execute it"""
import itertools
import json
import os
from os.path import join
class Makefile(object):
def __init__(self, path):
self._file = open(path, 'w')
# keep track of product directories that... | snfactory/pipeline | workflow-test/makemake.py | Python | mit | 3,731 | [
"Gaussian"
] | a14f8fb2828a6323b582348222d48fff43c297292f0408a78f2168c98fe5923b |
import time
import numpy as nm
import scipy.sparse as sp
from sfepy.base.base import Struct, output, assert_
from meshio import MeshIO
##
# 28.05.2007, c
def make_point_cells( indx, dim ):
conn = nm.zeros( (indx.shape[0], dim + 1), dtype = nm.int32 )
for ii in range( 0, dim + 1 ):
conn[:,ii] = indx
... | olivierverdier/sfepy | sfepy/fem/mesh.py | Python | bsd-3-clause | 21,617 | [
"VTK"
] | e48640f0fa6ecd550a77c8a598f23ecf2fdff8fa409fff2a1af3ddc10fa92131 |
#!/usr/bin/python
#
# 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 Licen... | nuigroup/kivy | kivy/lib/osc/OSC.py | Python | lgpl-3.0 | 10,842 | [
"VisIt"
] | ca2fccd5355aa445f7d55458940cc8298838a9fb28e302ad347995923ff5fa8f |
import pysam
import sys
import os
import math
class VCFInfo(object):
def __init__(self, vcf_filename):
self.filename = vcf_filename
self.fh = open(self.filename)
def _get_header(self):
"""
return a list of the header lines for a VCF file.
"""
self.... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/gemini-0.10.0-py2.7.egg/gemini/vcf_info.py | Python | apache-2.0 | 1,637 | [
"pysam"
] | 9dac9bfbef6d012fe454a6aaa7851e83e6d80a2bca43290d65b1d22fbf52fa70 |
# Orca
#
# Copyright (C) 2010 Joanmarie Diggs
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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; eith... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/WebKitGtk/structural_navigation.py | Python | gpl-3.0 | 3,567 | [
"ORCA"
] | 13d8fc43fe7a89e3bbe1ac88a526f6af3eb4eda916659f7aa5b8c142bf424822 |
"""Detect and handle peaks and troughs as well as threshold crossings in data arrays.
## Peak detection
- `detect_peaks()`: detect peaks and troughs using a relative threshold.
- `peak_width()`: compute width of each peak.
- `peak_size_width()`: compute size and width of each peak.
## Threshold crossings
- `thresho... | bendalab/thunderfish | thunderfish/eventdetection.py | Python | gpl-3.0 | 51,072 | [
"Gaussian"
] | 85b80401dfb90e111cf832c61f4e87711010abdf8a8887bf36a6277947d5c1e1 |
#!/usr/bin/env python
"""
Calculates the density of air baed upon the Ideal Gas Law and the Magnus Equation
"""
import argparse
import numpy as np
from scipy.io import netcdf
import math
import os
def calculate_density(pressure, temperature, relative_humidity):
Rl = 287.058 # R for luft (dry air), ... | pgierz/semic | netcdf_interface/echam6_calculate_air_density.py | Python | mit | 1,919 | [
"NetCDF"
] | 2bc90b2e22794f4c2f876e1218cc76fbf338e8662aa7c662da9d181d6fe6e97f |
#!/home/vossj/suncat/bin/python
#above line selects special python interpreter which knows all the paths
#SBATCH -p iric,normal,owners
#################
#set a job name
#SBATCH --job-name=H2_1
#################
#a file for job output, you can check job progress
#SBATCH --output=myjob.out
#################
# a file for ... | brohr/brohr.github.io | ASE/Transition_States/Gaseous_Molecules/N2/opt.py | Python | gpl-2.0 | 2,472 | [
"ASE",
"ESPResSo"
] | 2e2a056aef036e62dd10354625fa18981953fb8ab9b594a63ba7deeea8273321 |
from __future__ import print_function, division
import os,unittest,numpy as np
from pyscf.nao.scf import scf
class KnowValues(unittest.TestCase):
def test_rescf(self):
""" reSCF """
dname = os.path.dirname(os.path.abspath(__file__))
myhf = scf(label='water', cd=dname, verbosity=0, kmat_timing=0.0, ... | gkc1000/pyscf | pyscf/nao/test/test_0041_rescf_scf.py | Python | apache-2.0 | 1,395 | [
"PySCF"
] | 2b727b3c53dfaeea72d1174e60a99542798cda3adacbb76bc4b138583a9ee52d |
#!/usr/bin/python
"""Test of line navigation."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
# Work around some new quirk in Gecko that causes this test to fail if
# run via the test harness rather than manually.
sequ... | chrys87/orca-beep | test/keystrokes/firefox/line_nav_wiki_down.py | Python | lgpl-2.1 | 43,149 | [
"ORCA"
] | e930e8fa405076100e30649bd176d994fd72119d792d5443c3257080c2bba060 |
'''
desisim.quicksurvey
===================
Code for quickly simulating the survey results given a mock catalog and
a list of tile epochs to observe.
Directly depends on the following DESI products:
* desitarget.mtl
* :mod:`desisim.quickcat`
* `fiberassign <https://github.com/desihub/fiberassign>`_
'''
from __futur... | desihub/desisim | py/desisim/quicksurvey.py | Python | bsd-3-clause | 15,078 | [
"Galaxy"
] | 07e09b2e858a293551289c18ca438292211b5471d64c1a8c0f71a004cf2d9aaf |
""" ResourceManagementDB:
This module provides definition of the DB tables, and methods to access them.
Written using sqlalchemy declarative_base
For extending the ResourceStatusDB tables:
1) In the extended module, call:
from DIRAC.ResourceStatusSystem.DB.ResourceManagementDB import rmsBase, ... | chaen/DIRAC | ResourceStatusSystem/DB/ResourceManagementDB.py | Python | gpl-3.0 | 18,505 | [
"DIRAC"
] | 603e2362082f2085eb774f660a738893971b5e8fb24a384f81d9ceea79b7048d |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/mefit/package.py | Python | lgpl-2.1 | 1,963 | [
"HTSeq"
] | 77bb46e658735beeb4d1fc811bc181bf8be103f5c146b07451768b15b05ee497 |
# Copyright 2004-2008 by Sebastian Bassi.
# Copyright 2013 by Markus Piotrowski.
# 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.
"""Calculate the melting temperature of nucleot... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SeqUtils/MeltingTemp.py | Python | gpl-2.0 | 43,072 | [
"Biopython"
] | 20bb6de8a5256640758c6a5229553740e50bf008ecd5f5b32e42262571295810 |
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Workflow.Module import *
from DIRAC.Core.Workflow.Step import *
from DIRAC.Core.Workflow.Workflow import *
bodyTestApp = """class TestAppModule:
def __init__(self):
pass
def initialize(self,name,version,parameters):
print( 'Test appl... | DIRACGrid/DIRAC | src/DIRAC/Core/Workflow/test/ModulesSamples.py | Python | gpl-3.0 | 1,671 | [
"DIRAC"
] | 4dc4a64f6ec2556f066d62ef5f9fbe911ff45179279c6a69219f1d1709fab883 |
# 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... | hmenke/espresso | samples/visualization_mmm2d.py | Python | gpl-3.0 | 2,678 | [
"ESPResSo"
] | 9b9f6581c76bd1e058fc111f99de3ac09a786c39a180272d1361044405ed45c9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
from fractions import Fraction
try:
from math import gcd
except ImportError:
from fractions import gcd
from itertools import groupby... | gpetretto/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 47,870 | [
"pymatgen"
] | 04debf3978828bf7d6750254286046fbe879084e4813c5c6fab9169638c81b1c |
"""Undocumented Module"""
__all__ = ['unique', 'indent', 'nonRepeatingRandomList',
'writeFsmTree', 'StackTrace', 'traceFunctionCall', 'traceParentCall',
'printThisCall', 'tron', 'trace', 'troff', 'getClassLineage', 'pdir',
'_pdir', '_is_variadic', '_has_keywordargs', '_varnames', '_getcode',
'Signature', 'doc', 'adju... | silly-wacky-3-town-toon/SOURCE-COD | toontown/toonbase/ToonPythonUtil.py | Python | apache-2.0 | 142,301 | [
"Gaussian"
] | 04261a89973a8ffaa33008ae4a33905bb5b0408e3a28c34c50679c5727b4ea33 |
# 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.
"""Utility functions for working with FDist (DEPRECATED)."""
from Bio.Po... | zjuchenyuan/BioWeb | Lib/Bio/PopGen/FDist/Utils.py | Python | mit | 6,981 | [
"Biopython"
] | 8ca5e0816ea40164461296fb6439c6bebc76320806bb1754b7d9055e7839dc04 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from hashlib import sha256
from abc import abstractmethod
from pathlib import Path
from numbers import Real
import warni... | zerothi/sisl | toolbox/siesta/minimizer/_minimize.py | Python | mpl-2.0 | 13,374 | [
"SIESTA"
] | f48e3269b1d75b1ed5f02027e7fe368bdfb29c3da063294848212206d38ac3e5 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes that define a chemical reaction.
"""
import logging
import re
from itertools import chain, combinations
import numpy as np
from monty.fractions import gcd_float
from monty.json import MontyDe... | vorwerkc/pymatgen | pymatgen/analysis/reaction_calculator.py | Python | mit | 17,423 | [
"pymatgen"
] | 918c0ea5d5da3d741805e9dd16cbbf2ca7b4e25f9617922c4bb8132d8067ccd6 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.