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"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
from avocado.utils import process
from .. import xml_utils
from .. import utils_misc
from ..libvirt_xml import base, accessors, xcepts
from ..libvirt_xml.devices import librarian
class VMXMLDevices(list)... | vipmike007/avocado-vt | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 84,164 | [
"VisIt"
] | 86bd6e6294253a6cd47fb2444a731f140faf9c38531a9d1c31c606f23180de63 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | nuclear-wizard/moose | python/peacock/ExodusViewer/plugins/BlockSelectorWidget.py | Python | lgpl-2.1 | 5,135 | [
"MOOSE",
"VTK"
] | e173a9b2fa36f600c43e49619a9ff151c28e3ed455fdc076d0f9d2fdbcd279f5 |
"""DIRAC Administrator API Class
All administrative functionality is exposed through the DIRAC Admin API. Examples include
site banning and unbanning, WMS proxy uploading etc.
"""
__RCSID__ = "$Id$"
import os
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities.PromptUser import promptUser
from DIRA... | andresailer/DIRAC | Interfaces/API/DiracAdmin.py | Python | gpl-3.0 | 31,519 | [
"DIRAC"
] | 0149cfa5fcd9553b1db629c570ed95fd5266d987c1fe75853b813a1ce08b65e4 |
# -*- coding: utf-8 -*-
"""
E2E tests for the LMS.
"""
from __future__ import absolute_import
from textwrap import dedent
from six.moves import range
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common... | ESOedX/edx-platform | common/test/acceptance/tests/test_annotatable.py | Python | agpl-3.0 | 5,676 | [
"VisIt"
] | fc87e1c8df1c09c76792c045f285dfba360a1225acd4835da0b1781950ac8058 |
#
# @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/psivarrosetta.py | Python | lgpl-3.0 | 18,416 | [
"Psi4"
] | aa6edca5a10059cdd10ea9d440c7d428bba2cb0adc623419de07dbad6b457daf |
from __future__ import print_function
from lasagne.layers import InputLayer as Input, DenseLayer as Dense, flatten as Flatten, DropoutLayer as Dropout, reshape as Reshape
#from keras.layers import Input, Dense, Reshape, Flatten, Dropout, multiply, GaussianNoise
from lasagne.layers import batch_norm as BatchNormalizati... | sofiane87/lasagne-GAN | bigan/bigan.py | Python | mit | 12,651 | [
"Gaussian"
] | 6fa261c74cf0cd5dba5f5581402123cbd1498b6910ebdd2562667d67d002afe4 |
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
class marchingCubes(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self.... | chrisidefix/devide | modules/filters/marchingCubes.py | Python | bsd-3-clause | 1,960 | [
"VTK"
] | cd0b902cfd928639646b45469478f1b2782ba7faa0ae2d35301e0d578a72165a |
#!/usr/bin/env python
## @package fill_missing
# \brief This script solves the Laplace equation as a method of filling holes in map-plane data.
#
# \details The script is an implementation of the SOR method with Chebyshev
# acceleration for the Laplace equation, as described in 'Numerical Recipes in
# Fortran: the art... | talbrecht/pism_pik06 | util/fill_missing.py | Python | gpl-3.0 | 13,695 | [
"NetCDF"
] | ea4c31b951a6f8d0bad433eed84d3bf973b9d39980097144802eecb8c1ac3be2 |
#!/usr/bin/env python3
#
# Script to sum cube files
# by Patrick Melix
# 2018/06/07
#
# You can import the module and then call .main() or use it as a script
from ase.io.cube import read_cube, write_cube
import os, glob
import numpy as np
def main(inList,outFile, subtract=False):
#if output exists mv to .bak
i... | patrickmelix/Python4ChemistryTools | sumCube.py | Python | mit | 1,546 | [
"ASE"
] | fbacf4ee2b15c9332d6b52658acf4b1b19ef2da970e40c06a2a3d262ae6e2913 |
import getpass
import logging
import os
import shutil
import re
import tempfile
from git import Repo
from packaging import version
from kalliope.core.ConfigurationManager import SettingLoader
from kalliope.core.ConfigurationManager.DnaLoader import DnaLoader
from kalliope.core.Models import Neuron
from kalliope.core.... | kalliope-project/kalliope | kalliope/core/ResourcesManager.py | Python | gpl-3.0 | 16,320 | [
"NEURON"
] | e1a06f957601cf066f49a1630b29af2c4ee32e61802f18a53da95940e504c9a3 |
# Enthought library imports.
from traits.api import Instance
from tvtk.api import tvtk
# Local imports
from mayavi.filters.filter_base import FilterBase
from mayavi.core.pipeline_info import PipelineInfo
######################################################################
# `DataSetTriangleFilter` class.
#########... | openearth/vtkanim | vtkanim/filters.py | Python | gpl-3.0 | 1,185 | [
"Mayavi"
] | c20402df152b8cebef43df60dca328be66597d9af29a53ade881e6ba58c7cb35 |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following d... | tdsmith/celltool | celltool/numerics/ndimage/fourier.py | Python | gpl-2.0 | 7,162 | [
"Gaussian"
] | 516471cb6eca1b554f02e66d92b31663dc08c7fdecfba827d8d468d27e1fc229 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0026_auto_20150614_1731'),
]
operations = [
migrations.AddField(
model_name='student',
... | koebbe/homeworks | visit/migrations/0027_student_key.py | Python | mit | 429 | [
"VisIt"
] | 599b6b924b9a903aaf9e7be14dfcc74dcd7261ae7e846fc32df0229c4fa644d8 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2009 Nicolas Rougier - INRIA - CORTEX Project
#
# 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... | rougier/dana | examples/dana-attention.py | Python | bsd-3-clause | 4,123 | [
"Gaussian",
"NEURON"
] | 8f179431d4047121d0aa7892339dd6932a25364821426ca2ffb61483318c3b3d |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | liuwenf/moose | python/chigger/tests/graphs/dualx.py | Python | lgpl-2.1 | 1,458 | [
"MOOSE"
] | 75a82acb86ae546cc004c26e59368b4c5549a6b8f4f52bd9dc90365d5779bdc6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: May 2013
"""
import sys,os,commands,threading
import string, math, re
#GUI
import gui.graph as Graph
import gui.md as MD
import gui.gs as GS
import gui.elasticConstant as ElasticConstant
import g... | abinit/abinit | scripts/post_processing/appa/gui/main_frame.py | Python | gpl-3.0 | 11,557 | [
"ABINIT",
"NetCDF"
] | e4c514947c40107ef5757f01f9bebbf4acba64792a3f54cccf828431ec8ae6e0 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'EphysConceptMap.ref_text'
db.alter_column('neuroelectro_ephysconceptmap', 're... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0065_auto__chg_field_ephysconceptmap_ref_text__chg_field_neuronephysdatamap.py | Python | gpl-2.0 | 31,524 | [
"NEURON"
] | 6ce9df38771e2f950ba1919870915c78e690d244375d7870750d033724e2b94b |
"""
A family of function objects for changing a set of weights over time.
Learning functions come in two varieties: LearningFunction, and
CFPLearningFunction. A LearningFunction (e.g. Hebbian) applies to one
set of weights, typically from one ConnectionField. To apply learning
to an entire CFProjection, a LearningFu... | ioam/topographica | topo/learningfn/__init__.py | Python | bsd-3-clause | 5,701 | [
"NEURON"
] | 342bff04411ea078c55ee28d136b1f4524016f3a47f1c69a1a71761b557b3d7a |
"""
Acceptance tests for Studio's Setting pages
"""
import re
import uuid
from nose.plugins.attrib import attr
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest
from common.test.acceptance.pages.lms.create_mode import ModeCreationPage
from common.test.acceptance.pages.studio.settings_c... | louyihua/edx-platform | common/test/acceptance/tests/studio/test_studio_settings_certificates.py | Python | agpl-3.0 | 13,257 | [
"VisIt"
] | 6c74db3d1bc6d5f4bbc282e857fc10bd313b2f55d7115eb98522cb8e6411abb6 |
import numpy as np
import random as rand
import sys, os
import copy
import pickle
#from mpi4py import MPI
from pymatgen import Lattice, Structure, Element, PeriodicSite
from pymatgen.io.vasp import Poscar, VaspInput
from pymatgen.analysis.structure_matcher import StructureMatcher, FrameworkComparator
from pymatgen.app... | skasamatsu/py_mc | examples/zro2_spch/model_setup.py | Python | gpl-3.0 | 10,497 | [
"VASP",
"pymatgen"
] | eb64286f507e2eeaa99884e83f46e16229cbf4b64ebc3373bd4375ca3b700026 |
import pysam
import sys
def Check_Parameters(arg,opts,min,max):
if opts > max or opts < min:
sys.exit('\nArgument %s : expected value in range %s - %s\n' % (arg,str(min),str(max)))
def Check_SimpleRepeatList(arg,opts):
if opts.SimpleRepeatList and not opts.SimpleRepeat:
sys.exit('\nTo use %s please enable -S... | Matteodigg/iEVA | iEVA/iCheck.py | Python | mit | 2,805 | [
"pysam"
] | bb5dcdb2d420c7a3d9be75ba84805290ef074040e9d6b788ced5e5e389e0850f |
# -*- coding: utf-8 -*-
##
##
## This file is part of CDS Indico.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007 CERN.
##
## CDS Indico 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 o... | pferreir/indico-backup | indico/MaKaC/plugins/Collaboration/WebEx/collaboration.py | Python | gpl-3.0 | 34,567 | [
"VisIt"
] | ec1c9e65c6c232abb33ce3456af30dc1315f366656765fae8cb14c8481b175ab |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import sys
import os
class Hdf(AutotoolsPackage):
"""HDF4 (also known as HDF) is a library and multi-object
file... | iulian787/spack | var/spack/repos/builtin/packages/hdf/package.py | Python | lgpl-2.1 | 8,814 | [
"NetCDF"
] | a938e63ea8c699897247c83b6221e889d69b4fbcc51b2b1a4ac1363469658c16 |
#
# @file TestSpeciesType.py
# @brief SpeciesType unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file locate... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestSpeciesType.py | Python | bsd-3-clause | 4,416 | [
"VisIt"
] | 78a9d8a1775fc055c2323179efccee00703e28d9faff43b6cce0f300f116987a |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particles, Meteor"
import pyglet
import summa
from summa.director import ... | shackra/thomas-aquinas | tests/test_particle_meteor.py | Python | bsd-3-clause | 911 | [
"Galaxy"
] | 92b5b2b1668fafa649915514c2f13936593b648a0b1d8bd6f0f62dd75570a77e |
"""
Author: Thomas G. Close (tclose@oist.jp)
Copyright: 2012-2014 Thomas G. Close.
License: This file is part of the "NineLine" package, which is released under
the MIT Licence, see LICENSE for details.
"""
from __future__ import absolute_import
from builtins import next
from builtins import str
from p... | tclose/PyPe9 | pype9/simulate/common/network/base.py | Python | mit | 42,258 | [
"NEURON"
] | 2dbf11f22ae29bd587caf465617e5fe300ae77400661189e4461fdaea193ca5b |
import numpy as np
from ase.atoms import Atom, Atoms
from ase.parallel import paropen
"""Module to read and write atoms in PDB file format"""
def read_pdb(fileobj, index=-1):
"""Read PDB files.
The format is assumed to follow the description given in
http://www.wwpdb.org/documentation/format32/sect9.h... | slabanja/ase | ase/io/pdb.py | Python | gpl-2.0 | 1,886 | [
"ASE",
"RasMol"
] | de256eb39fed87d2396f71f98ac8133061e110b8d0931ea16b634bfb0d7d78a9 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | Chuban/moose | python/MooseDocs/extensions/sqa.py | Python | lgpl-2.1 | 20,977 | [
"MOOSE"
] | 23ee6293d719399023bdb0c7ee642014054ae0cc5d8230dec403c8ab4cfe34cb |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Tools and helper functions for abinit calculations"""
from __future__ import unicode_literals, division, print_function
import os
import six
import re
import collections
import shutil
import operator
import ... | johnson1228/pymatgen | pymatgen/io/abinit/utils.py | Python | mit | 28,136 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | d87b6e25bd63e3f3e52a1821f91bf6e7d31b1ed71a67ebb47730a9419112f246 |
# 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... | fweik/espresso | testsuite/python/lb_switch.py | Python | gpl-3.0 | 2,788 | [
"ESPResSo"
] | 4dc1f25d2e3f8c4bb672c0668a634c75d48c0d2110a11bbe6e3c95f660c08f95 |
# -*- coding: utf-8 -*-
"""
Spyder Editor
This temporary script file is located here:
/Users/htelg/.spyder2/.temp.py
"""
#ToDo
#- ich denke nicht, dass wir neutral nehen muessen .. unserer laser is polarisiert ...
#- indes of refraction at 405 nm for psl
#- results plotten
# Check using http://omlc.ogi.edu/calc/mie_... | lo-co/atm-py | build/lib/atmPy/for_removal/POPS/mie.py | Python | mit | 51,426 | [
"Gaussian"
] | 8acbe5b3980f0e6c6a0afb354f9e1471657baa9c87b298bd55a63735e73e8ae5 |
# 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/immersed_boundary/addBending.py | Python | gpl-3.0 | 1,453 | [
"ESPResSo"
] | 732ade2ba03c309eddfc012acb21832436b3a518897d572f3728b48c72fc0568 |
# 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... | fedepad/espressopp | src/storage/DomainDecomposition.py | Python | gpl-3.0 | 3,834 | [
"ESPResSo"
] | 21c47313a8899e560e797dd7bedacf47d7bf401486ef854b0d0dcccc3eaea7c5 |
#!/usr/bin/env python
# encoding: utf-8
'''
Generates a Slurm script for running blast against the probes on various fasta files
@author: Andrew Robinson
'''
import sys, argparse, os, subprocess
import common
def main(argv):
''''''
parser = argparse.ArgumentParser(description='Generates a Slurm script fo... | molecularbiodiversity/carlaseq | src/carlaseq_make_blastprobes_job.py | Python | bsd-3-clause | 2,718 | [
"BLAST"
] | d6b2f7c498657ddbb1efec6f2fcccdc1a516196cb29f1c6e29fbd59c970a62a9 |
import os, sys, unittest
import setup_path
from lib.asmlib.linker import *
from lib.asmlib.assembler import *
from lib.asmlib.asm_common_types import *
from lib.commonlib.utils import *
from lib.commonlib.luz_defs import (
USER_MEMORY_START, USER_MEMORY_SIZE)
# Initial offset
IOF = 0x100000
op_call ... | 8l/luz-cpu | luz_asm_sim/tests_unit/test_linker.py | Python | unlicense | 16,362 | [
"MOE"
] | f5ee96d4ab1052697572f0f0b4d94186afdaf93020e250964e06ddeeb08e7215 |
import logging
from logging.config import fileConfig
import os
import re
import sys
import click
import bripipetools
config_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
'config'
)
fileConfig(os.path.join(config_path, 'logging_config.ini'),
disable_existing_loggers=False)
logg... | BenaroyaResearch/bripipetools | bripipetools/__main__.py | Python | mit | 20,134 | [
"Galaxy"
] | 85c24c13f88767efac6e0f5984e90cae190cf7062fe0f73fcad08df4ce9c75ae |
''' Test_RSS_Command_VOBOXAvailabilityCommand
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import mock
import DIRAC.ResourceStatusSystem.Command.VOBOXAvailabilityCommand as moduleTested
from six.moves import reload_module
__RCSID__ ... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Command/test/Test_RSS_Command_VOBOXAvailabilityCommand.py | Python | gpl-3.0 | 3,453 | [
"DIRAC"
] | 3053b39eeabe89dd411c6e70a629112138bde22390205b1897a19a34583adcc4 |
# -*- coding: utf-8 -*-
"""
E2E tests for the LMS.
"""
import time
from .helpers import UniqueCourseTest
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.lms.courseware import CoursewarePage
from ..pages.lms.matlab_problem import MatlabProblemPage
from ..fixtures.course import CourseFixture, XBlockFixtur... | epam-mooc/edx-platform | common/test/acceptance/tests/test_matlab_problem.py | Python | agpl-3.0 | 4,435 | [
"VisIt"
] | eb2294c6eb18c1a7c53a4b184693f51ab0503edb2d79608b5dd6559d77246a4a |
#!/usr/bin/env python3
"""
Template by pypi-mobans
"""
import os
import sys
import codecs
import locale
import platform
from shutil import rmtree
from setuptools import Command, setup, find_packages
# Work around mbcs bug in distutils.
# http://bugs.python.org/issue10945
# This work around is only if a project sup... | chfw/pyexcel-webio | setup.py | Python | bsd-3-clause | 5,880 | [
"VisIt"
] | 25c7d8b1ce3f54ed85e582550ca0d29a3779f334d1696d38c09565270ce4e3f2 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/moosesqa/test/test_LogHelper.py | Python | lgpl-2.1 | 2,100 | [
"MOOSE"
] | 57598ce9d2f769e4ce04f78180d9daf30338badf97e99ca3cc252deaf0f6fd01 |
# Copyright 2014-2017 The ODL development group
#
# This file is part of ODL.
#
# ODL 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.
#... | bgris/ODL_bgris | odl/operator/fn_ops.py | Python | gpl-3.0 | 17,124 | [
"DIRAC"
] | 68226792fb407753009552fcceb396502d561e5ec46077699e6361bb325c96aa |
# coding: utf-8
# #### this script calculates similarity features, combines them with descriptor data and selects the best features with randomized Lasso
# In[1]:
import pandas as pd
import numpy as np
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import Dat... | dream-olfaction/olfaction-prediction | opc_python/hulab/feature_selection/feature_selection.py | Python | mit | 3,903 | [
"RDKit"
] | 962900a8d7204d8d37f5678bc5cf24b8e657a4998cb21afa7af6916eb84e288f |
# modified mexican hat wavelet test.py
# spectral analysis for RADAR and WRF patterns
# NO plotting - just saving the results: LOG-response spectra for each sigma and max-LOG response numerical spectra
import os, shutil
import time, datetime
import pickle
import numpy as np
from scipy import signal, ndimage
imp... | yaukwankiu/armor | tests/modifiedMexicanHatTest11.py | Python | cc0-1.0 | 7,225 | [
"Gaussian"
] | 3f2700dd3e4b0bbcb5688896e2fc20ccf6453e664072fdcfd28610a5dbf10c64 |
#!/usr/bin/python2
# $HeadURL$
# $Id$
__version__ = "1.0-svn"
__appname__ = "Mirage"
__license__ = """
Mirage, a fast GTK+ Image Viewer
Copyright 2007 Scott Horowitz <stonecrest@gmail.com>
Copyright 2010-2011 Fredric Johansson <fredric.miscmail@gmail.com>
This file is part of Mirage.
Mirage is free software; you can... | kennethryerson/mirage | mirage.py | Python | gpl-3.0 | 209,116 | [
"FLEUR"
] | 3dd76781d7a0a6bb596951586bb941c53e59343c236f13a8f0fe898fe40d492a |
# -*- coding: utf-8 -*-
"""
This modules provides functions to calculate correlations between spike trains.
:copyright: Copyright 2015-2016 by the Elephant team, see `doc/authors.rst`.
:license: Modified BSD, see LICENSE.txt for details.
"""
from __future__ import division, print_function, unicode_literals
import war... | alperyeg/elephant | elephant/spike_train_correlation.py | Python | bsd-3-clause | 40,876 | [
"DIRAC",
"NEURON"
] | 7fbe21f6c8aa9139a5310f7e90484aec75aa33a692e89580a9ecd8989458c6f7 |
# sql/visitors.py
# Copyright (C) 2005-2012 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Visitor/traversal interface and library functions.
SQLAlchemy schema and expressio... | SohKai/ChronoLogger | web/flask/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py | Python | mit | 9,433 | [
"VisIt"
] | 37f2b6f4bda42cb7be8f4e49855fcb7bed99c9801b777df8399551cd8e047c78 |
"""
It is used to test client->db-> service.
It requires the Monitoring service to be running and installed (so discoverable in the .cfg),
and this monitoring service should be connecting to an ElasticSeach instance
"""
# pylint: disable=invalid-name,wrong-import-position
import time
import json
from datetime impo... | DIRACGrid/DIRAC | tests/Integration/Monitoring/Test_MonitoringSystem.py | Python | gpl-3.0 | 8,449 | [
"DIRAC"
] | aef151df8e489a2ce9379703826e99179341a6f453d24f847dd9f845d0307c86 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack import *
TUNE_VARIANTS = (
'none',
'cp2k-lmax-4',
'cp2k-lmax-5',
'cp2k-lmax-6',
... | LLNL/spack | var/spack/repos/builtin/packages/libint/package.py | Python | lgpl-2.1 | 9,050 | [
"CP2K",
"Gaussian"
] | c4550ff152756176f0a22a2c275f74b43dd160d983e967937972de86658666bc |
#!/usr/bin/env python
import argparse
import os
import pickle
import pandas
import requests
from Bio import Entrez, SeqIO
from lxml import html, etree
from tqdm import tqdm
os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'phageAPI.settings')
import django
django.setup()
from util.acc import read_accession_file
fro... | mbonsma/phageParser | populate.py | Python | mit | 6,935 | [
"BLAST"
] | 10420b34a1ab1896e673b3ab6cc8d110f2c6065f1066a944f233ca6469d18cfe |
from ionotomo import *
import numpy as np
import pylab as plt
import h5py
import cmocean
import os
import logging as log
import gpflow as gp
class RationalQuadratic(gp.kernels.Stationary):
def __init__(self, input_dim=1, variance=1.0, alpha=1.0, lengthscales=None, active_dims=[0], ARD=False, alpha_prior=None):... | Joshuaalbert/IonoTomo | src/ionotomo/scripts/rvw_data_analysis/bayes_interp_program.py | Python | apache-2.0 | 21,813 | [
"Gaussian"
] | 9077588e160e09e6f253acc052224e7eecb672a1e79d7eca6e38a783b1291672 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: April 2013
"""
import sys,os
from PyQt4 import Qt,QtGui,QtCore
def main():
import gui.main_frame as mf # GUI
app = QtGui.QApplication(sys.argv)
ex = mf.MainFrame()
try:
s... | jmbeuken/abinit | scripts/post_processing/appa/appa.py | Python | gpl-3.0 | 869 | [
"ABINIT"
] | 9de73608312771feda2a464e452e82f486b614b10d5e89ba64bb728cd9d346e0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | lothian/psi4 | psi4/driver/qcdb/qchem.py | Python | lgpl-3.0 | 18,398 | [
"CFOUR",
"Psi4",
"Q-Chem"
] | 8e391da0b73f9b3905ddb7d2fa3822f3d4bcf222d6f370a3c7a6ec5bad68a8e8 |
'''
Zither pulls raw depths and alt freqs from BAM file(s) based on loci in an
existing VCF; writes a new VCF to stdout.
'''
## Copyright 2014 Bioinformatics Core, University of Michigan
##
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with t... | umich-brcf-bioinf/Zither | zither/zither.py | Python | apache-2.0 | 18,070 | [
"pysam"
] | 81fc6601c1f7acf2f40841f7f967d5adb811fb7bfb6a0ef49db255f5e4a3f303 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# fileio - wrappers to keep file I/O in a single replaceable module
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of t... | heromod/migrid | mig/shared/fileio.py | Python | gpl-2.0 | 16,783 | [
"Brian"
] | bb4ce8809911583034249b9470a68ceab5e5b3b452d90476a194fba8a626e1a6 |
# Copyright 2003-2009 by Bartek Wilczynski. 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.
"""Implementation of sequence motifs (PRIVATE).
"""
from Bio.Seq import Seq
from Bio.S... | bryback/quickseq | genescript/Bio/Motif/_Motif.py | Python | mit | 26,870 | [
"Biopython"
] | 9297b00ded6ba8290d06c82092f58af4ec8eafc3b5c1afbaf99188a141ff1f3f |
#!/usr/bin/env python
from __future__ import print_function
import DIRAC
from DIRAC.Core.Base import Script
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.Core.Utilities import Time
__RCSID__ = "$Id$"
class Params(object):
limited = False
proxyPath = False
proxyLifeTime ... | fstagni/DIRAC | FrameworkSystem/scripts/dirac-admin-users-with-proxy.py | Python | gpl-3.0 | 1,911 | [
"DIRAC"
] | 6d16afd6e7674365d8836ec52353d327155a2a8a5066a7304f5e5f91164bd0f4 |
"""
A buffered iterator for big arrays.
This module solves the problem of iterating over a big file-based array
without having to read it into memory. The `Arrayterator` class wraps
an array object, and when iterated it will return sub-arrays with at most
a user-specified number of elements.
"""
from __future__ impor... | shoyer/numpy | numpy/lib/arrayterator.py | Python | bsd-3-clause | 7,207 | [
"NetCDF"
] | 1535f0c33b39c733f1a546d9984dc9d0286381eb090fd4e2a8103f6c2234e522 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
surface2vtk.py
Generate VTK animations from a NetCDF database of surface wavefield
created by AxiSEM3D (named axisem3d_surface.nc by the solver). Data
are presented on an unstructured mesh.
To see usage, type
python surface2vtk.py -h
'''
################### PAR... | kuangdai/AxiSEM3D | python_tools/surface2vtk.py | Python | mit | 15,530 | [
"NetCDF",
"ParaView",
"VTK"
] | 087df5d64c0483553cad38ef602b42d259727f89cb268812a28a748e07f4cc20 |
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 16 08:47:13 2016
@author: GDM
"""
##### Importing modules #####
import HTSeq
import cPickle as pickle
import pandas as pd
import os
from HaSAPPy.HaSAPPY_time import *
############################################################
class Gene... | gdiminin/HaSAPPy | HaSAPPy/GeneDefinition.py | Python | mit | 10,305 | [
"HTSeq"
] | 166d1e62df3d64322b22663a122c9cb8663b11deffb40555f16ef56d15f266e6 |
# -*- coding: utf-8 -*-
"""
Plot mitoskel network in with various scalar values
"""
import sys
import os
import os.path as op
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.stats as sp
import seaborn as sns
from mayavi import mlab
from tvtk.api import tvtk
from pipeline.make_network... | moosekaka/sweepython | tubule_het/visualize_real_random.py | Python | mit | 5,330 | [
"Mayavi",
"VTK"
] | c63af94c37fac17a109ef4f5244cdf088eff76e2cef18a7d07e3652c7b03bf8a |
from test import support
from test.support import import_helper
from test.support import threading_helper
# Skip tests if _multiprocessing wasn't built.
import_helper.import_module('_multiprocessing')
from test.support import hashlib_helper
from test.support.script_helper import assert_python_ok
import contextlib
im... | brython-dev/brython | www/src/Lib/test/test_concurrent_futures.py | Python | bsd-3-clause | 54,157 | [
"Brian"
] | 191a73e402638f9626cabdf75addf9e2ff90306185edd460921b86ba57c0bfa1 |
# -*- coding: utf-8 -*-
import datetime
import re
"""This module will define/keep all static Xnova data models
and basic classes
"""
class XNCoords:
"""
XNova universe coordinates data model
can parse strings like "[galaxy:solarsystem:planet]"
also holds exact target object type - planet, moon, or de... | minlexx/xnova_galaxy_parser | xnova/xn_data.py | Python | gpl-3.0 | 16,104 | [
"CRYSTAL",
"Galaxy"
] | 4a389db4d335819717a0b326cfd5bd74a1f80aff2214d528051bed6e670e31bc |
# from distutils.core import setup, Extension
import os
from setuptools import setup, Extension, find_packages
here = os.path.abspath(os.path.dirname(__file__))
# Get the long description from the relevant file
with open(os.path.join(here, 'README.rst')) as f:
long_description = f.read()
def get_version(string):... | gatoravi/svviz | setup.py | Python | mit | 2,218 | [
"pysam"
] | aa3561f8ee4129f06bb673b588f2f726d22ceb69d70f0860976c1bda01feda71 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | tdruez/scancode-toolkit | tests/textcode/test_pdf.py | Python | apache-2.0 | 2,545 | [
"VisIt"
] | 35172d5050650ffa602ff60498ce02217947d14b9cb2bca6cc98d00913f0c420 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | SusanJL/iris | lib/iris/tests/test_analysis.py | Python | gpl-3.0 | 46,721 | [
"NetCDF"
] | 237067fc6045c5f07fe91803700d4d42cc3ce0845ade7ca5e98c519bdad0c3d4 |
from argparse import *
from sys import *
from os.path import *
from paraview.simple import *
from paraview.servermanager import *
parser = ArgumentParser(description = 'Process the arguments')
parser.add_argument('inputFile', help = 'Path to the input file (NetCDF compilant)')
parser.add_argument('outputDir', help = 'P... | fercook/SciViz | Voxels/NETCDF_2_VTK_2_Blender/job/dem/paraview/NC2VTKDEM.py | Python | gpl-2.0 | 8,935 | [
"NetCDF",
"ParaView",
"VTK"
] | f337e00c15b79b51372e43b3a4aec9a68bb11e298d34133b05fa0ec6855d1da5 |
"""Handle installation and updates of bcbio-nextgen, third party software and data.
Enables automated installation tool and in-place updates to install additional
data and software.
"""
import argparse
import collections
import contextlib
import datetime
import dateutil
from distutils.version import LooseVersion
impor... | hjanime/bcbio-nextgen | bcbio/install.py | Python | mit | 30,685 | [
"BWA",
"Biopython",
"Bowtie",
"Galaxy",
"pysam"
] | 860267e3928403599e896b754ed9f53bfe684ebee0dd892d21f6ca8f631d2573 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | jjdmol/LOFAR | LTA/LTAIngest/SOAPpy-0.12.0/SOAPpy/Client.py | Python | gpl-3.0 | 16,967 | [
"Brian"
] | 9aa30a4e2ea2da78e665ca9f2e85e5a5db1c1d0d26a39e2a063b36f216a7b634 |
from rdkit import RDConfig
import os
import unittest
from rdkit import Chem
from rdkit.Chem import ChemicalForceFields
from rdkit.Chem import rdMolTransforms
class TestCase(unittest.TestCase):
def setUp(self) :
self.molB = """butane
RDKit 3D
butane
17 16 0 0 0 0 0 0 0 0999 V2000
0.0000... | AlexanderSavelyev/rdkit | Code/ForceField/Wrap/testConstraints.py | Python | bsd-3-clause | 9,931 | [
"RDKit"
] | 91e9ac46c210a06f9bfdb562bded56950e8f75d6c17e35fbafef4014fb7e6471 |
#!/usr/bin/env python3
# In many places, falling temperatures get a brief bump after sunset.
# But when, and how much, and for how long?
# This is an attempt to compare post-sunset temperature bumps
# among different locations, using whatever data is available.
# First, abstract fetching temperature as a function of ... | akkana/scripts | weather/evebump.py | Python | gpl-2.0 | 11,622 | [
"NAMD"
] | aeb4e5a30f474d9a6a79fa9c7eb402fa45b4d94a6ec30890d39a01838b198cc1 |
#
# VASP.py
#
# Interface to VASP (https://www.vasp.at)
#
# Copyright (c) 2014-2020 Terumasa Tadano
#
# This file is distributed under the terms of the MIT license.
# Please see the file 'LICENCE.txt' in the root directory
# or http://opensource.org/licenses/mit-license.php for information.
#
from __future__ import pri... | ttadano/alamode | tools/interface/VASP.py | Python | mit | 21,133 | [
"VASP"
] | b67f4c56ede0366af10a6f24a01951ee5c967396391fca410ee294039fe85e88 |
#!/usr/bin/env python
##
## Copyright 2016 SRI International
## See COPYING file distributed along with the package for the copyright and license terms.
##
"""
Baseline cases
This script generates a list of all subject that have a valid baseline and follow-up visit.
"""
import os
import pandas
import redcap
# Firs... | abonil91/ncanda-data-integration | scripts/reporting/baseline_y1_np_cases.py | Python | bsd-3-clause | 1,314 | [
"VisIt"
] | c89a7e733f05971b304a0a32391e43d8288a6efdd1b4d002146d678bb1af414c |
# coding=utf-8
from __future__ import unicode_literals
import json
import pytz
import time
from datetime import datetime, date, timedelta
from django.core.files.base import ContentFile
from django.core.urlresolvers import reverse
from django.conf import settings
from django.utils import timezone
from mock import patc... | reyrodrigues/EU-SMS | temba/contacts/tests.py | Python | agpl-3.0 | 161,357 | [
"VisIt"
] | 147eb9761b4e914540258f7c41bae2b8454952b9b3b78fe10725315693655b87 |
# decay learning rate test
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib.pyplot as plt
import time
for test_num in ... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t21_cartpole_dnn_local.py | Python | mit | 7,348 | [
"NEURON"
] | ba61ccde8269c25d2a3deba845c198ae272a0a244adb35a06684de9bf9ac1eaa |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'Visit.old_survey_sent'
db.delete_column(u'clinics_visit... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0024_auto__del_field_visit_old_survey_sent.py | Python | bsd-2-clause | 13,984 | [
"VisIt"
] | 803e341da59f70174ff9a3469cdabcae93edad7e2b30828cc9b7a9249bead1cb |
###############################################################################
# actionAngle: a Python module to calculate actions, angles, and frequencies
#
# class: actionAngleStaeckel
#
# Use Binney (2012; MNRAS 426, 1324)'s Staeckel approximation for
# calculating the actions
#
# ... | jobovy/galpy | galpy/actionAngle/actionAngleStaeckel.py | Python | bsd-3-clause | 47,912 | [
"Gaussian"
] | 4c452f42d088f91fe8d3414148b182a7c8d6714fbbc0224cbc0225a8e5595d45 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from flask import Blueprint, session, render_template, abort, request, jsonify
import mysql.connector
import secret
from handlers.user import readUser
from handlers.pet import findRelative, searchPets
from handlers.moment import userMoments
users_routes = Blueprint('users_rou... | byn9826/Thousand-Day | api/users.py | Python | bsd-3-clause | 2,588 | [
"VisIt"
] | e0d3e243fe3a513f6e34b74eeaadc82a9ad6b39187c338c70b12fd92111e248d |
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import vtk
class transformVolumeData(NoConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageR... | nagyistoce/devide | modules/filters/transformVolumeData.py | Python | bsd-3-clause | 2,303 | [
"VTK"
] | 0c3a6f9acb60981269d2a5ae8a025cea7296217b6cfb1384c109bedfe3aa772d |
import os.path as osp
work_dir = "/home/salotz/Dropbox/devel/mastic/work/pi_stacking"
ref_ring_path = osp.join(work_dir, "benzene_hex.pdb")
from rdkit import Chem
ref_ring_PDB_rdkit = Chem.MolFromPDBFile(ref_ring_path, removeHs=False, sanitize=False)
from mastic.interfaces.rdkit import RDKitMoleculeWrapper
ring_r... | salotz/mast | work/pi_stacking/make_ringring_systemtype_pkl.py | Python | mit | 2,315 | [
"RDKit"
] | 300d491f007e3372b6dbcbeb59b1288df490a3ebd251f883ab85125aa1a93286 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center ... | molmod/tamkin | tamkin/examples/012_ethyl_ethene_scaling/reaction.py | Python | gpl-3.0 | 3,779 | [
"Gaussian"
] | 667426ee4eca8d6aa005e6c58fe7ba7681470235ef11c58b5981399229e13d54 |
# -*- coding: utf-8 -*-
import numpy as np
import scipy.integrate as sci
import scipy.optimize as opt
import time
import tarfile
import os
import csv
import montagn_classes as mc
######## Constants (USI) ########
b = 2.8977721e-3 #Wien's displacement cst
h = 6.62606957e-34
c = 299792458
kB = 1.3806488e-23
sigma... | lukaltair/MontAGN_V2 | montagn/montagn_utils.py | Python | gpl-3.0 | 29,334 | [
"Gaussian"
] | 5dfa1d5c13f66870f16a74e3f24b872c7a8fddddd83d4b146fd7ab286502f689 |
# -*- coding: utf-8 -*-
# standard
import array
import copy
# local
import popeye
# globals
PIECES = 'KkQqRrBbSsPp'
BLACK = False
WHITE = True
NOTATION = {'K':u'Кр', 'Q':u'Ф', 'R':u'Л', 'B':u'С', 'S':u'К', 'P':u'п'}
NAME = 0
PREV = 1
NEXT = 2
ID = 3
# the main structure to store & manipulate the position
class... | tectronics/olive-gui | legacy/chess.py | Python | gpl-3.0 | 42,642 | [
"VisIt"
] | b41363b97ec6cde5c4cbae676d53fa37586660476c6c9d62879d9c786a98f78d |
import logging
import unittest
import research_papers.logutils as logutils
from research_papers.tools.crossref_resolver import CrossrefResolver
__author__ = 'robodasha'
__email__ = 'damirah@live.com'
class TestCrossrefResolver(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(TestCrossref... | robodasha/research_papers | tests/test_crossref_resolver.py | Python | mit | 1,653 | [
"Galaxy"
] | 6090105784ae293dd8d46dfead47e7747a74e2900fbbdb43ce67bbc0929cb71c |
#
# Copyright (C) 2008 Greg Landrum
# Copyright (C) 2009 Uwe Hoffmann
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import array
import math
i... | bp-kelley/rdkit | rdkit/Chem/Draw/cairoCanvas.py | Python | bsd-3-clause | 14,358 | [
"RDKit"
] | c46e6cc55e9d527cdbac3920c8372ab376178be87158f5583ccebcec70c65c27 |
#! /usr/bin/env python
#
# The purpose of this script is to create a moltemplate lt file for the loplsaa.
# forcefield. This will assist researchers in building complex simulations using
# this LOPLS-UA and the LOPLS-AA forcefields.
__author__="Jason Lambert"
# (some additional corrections by Miguel Gonzalez and Andr... | JE1314/LAMMPS_builder | root/Auxiliary/loplsaa_moltemplateMETAL.py | Python | gpl-3.0 | 19,241 | [
"Gromacs",
"LAMMPS",
"TINKER"
] | 50cb00b1a80551b8d0ac21b0b97d1f6cf0bde9937313330502e535cc4e4c4a63 |
#!/usr/bin/env python
"""
soda.py
Functions for dealing with the soda model for importation into ROMS
Written by Brian Powell on 07/24/15
Copyright (c)2017 University of Hawaii under the MIT-License.
"""
import numpy as np
from datetime import datetime
import netCDF4
from seapy.lib import default_epoch, chu... | ocefpaf/seapy | seapy/model/soda.py | Python | mit | 4,784 | [
"Brian"
] | 96b976c4dd92250ec08855578d830ebd3a2b59c0ca8f8190c753f9b32500d3db |
#!/usr/bin/python
"""Test of line navigation output of Firefox."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(utils.StartRecordingAction())
sequence.append(KeyComboAction("<Control>Home"))
sequence.append(utils.AssertPresentationAction(
"1. Top of file",
["BRAILL... | pvagner/orca | test/keystrokes/firefox/line_nav_bug_577239.py | Python | lgpl-2.1 | 7,773 | [
"ORCA"
] | e5ddb00ba878baf064cc28e772a7a17e95ee1c011080ac60dc2c4a04e986bba3 |
"""
Distance matrices and distance-based statistics (:mod:`skbio.stats.distance`)
=============================================================================
.. currentmodule:: skbio.stats.distance
This subpackage provides functionality for serializing, deserializing, and
manipulating dissimilarity and distance mat... | demis001/scikit-bio | skbio/stats/distance/__init__.py | Python | bsd-3-clause | 5,775 | [
"scikit-bio"
] | 643123d339089b8ee7f511d03321be128ee343ba02ceda2e7e7ac42e56305cee |
""" Test class for JobWrapper
"""
#pylint: disable=protected-access, missing-docstring, invalid-name, line-too-long
# imports
import unittest
import importlib
import os
import shutil
from mock import MagicMock, patch
from DIRAC import gLogger
from DIRAC.DataManagementSystem.Client.test.mock_DM import dm_mock
from ... | hgiemza/DIRAC | WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py | Python | gpl-3.0 | 4,436 | [
"DIRAC"
] | d2ec5d3281214ed18428cc20b4f196d1eb9840cacad4b115b3074db0d56d55b1 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2008,2011 Gary Burton
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011-2012 Paul Franklin
# Copyright (C) 2012 Brian G. Matherly
#
# This program is free software; you can redistribute it and/... | sam-m888/gprime | gprime/plug/report/_options.py | Python | gpl-2.0 | 38,042 | [
"Brian"
] | 4d5a3f627cfc9160523df8ccd49989074406ad8e2dd0f0f1074975c511773e32 |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-gke-hub | scripts/fixup_multiclusteringress_v1_keywords.py | Python | apache-2.0 | 5,937 | [
"VisIt"
] | 1517d3019758c8cab150c7ca34140b16ee340cc9c715922958ce4692e5af04dd |
# -*- coding: utf-8 -*-
#
# brunel_exp_multisynapse_nest.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 o... | hakonsbm/nest-simulator | pynest/examples/brunel_exp_multisynapse_nest.py | Python | gpl-2.0 | 13,970 | [
"NEURON"
] | a015fca375cb9c002f9a9d5188bdc9c8168a845f5569e697736781d18ea2d460 |
# -*- coding: utf-8 -*-
import logging
log = logging.getLogger(__name__)
from enum import Enum
import math
import os
from shutil import copy2
import re
from subprocess import call
import contextlib
import logging
log = logging.getLogger(__name__)
import warnings
import jinja2
import pandas as pd
import numpy as np
... | m3wolf/scimap | scimap/fullprof_refinement.py | Python | gpl-3.0 | 33,866 | [
"Gaussian"
] | 285b9530797d1575bad5a76de0359fa4fd3d156a047a8bfa5db0447fa30bfe6b |
""" A module that allows a user to create one of several standard VTK
poly data sources.
"""
#Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Insta... | dmsurti/mayavi | mayavi/sources/builtin_surface.py | Python | bsd-3-clause | 4,497 | [
"Mayavi",
"VTK"
] | ecd454cad3bf130de5d5649debb1b9125a15f67b9ad032c7f73c79bc1af9d153 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#================================================#
#| |#
#| Minimum-energy two dimensional torsion scans |#
#| Lee-Ping Wang, October 2013 |#
#| |#
#| This script la... | hainm/open-forcefield-group | qm/crank/crank.py | Python | gpl-2.0 | 53,936 | [
"Psi4",
"Q-Chem",
"TINKER"
] | 96309bb212245a8beffeb63e8d8a9cf05a1aecfe37e5f5ed47610635dad38a4e |
#!/usr/bin/python
# Copyright (C) 2012,2013 The ESPResSo project
# Copyright (C) 2011 Olaf Lenz
# Copyright 2008 Marcus D. Hanwell <marcus@cryos.org>
#
# 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 Founda... | roehm/espresso_cpp | maintainer/git2changelog.py | Python | gpl-3.0 | 4,681 | [
"ESPResSo"
] | 8e277f56f1ac938c9af64c2dc6707605f46ae31e59025ef27fec4e0fc28fe304 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
'''Pychemqt, Chemical Engineering Process simulator
Copyright (C) 2009-2017, Juan José Gómez Romera <jjgomera@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 Softwar... | jjgomera/pychemqt | lib/mEoS/EthyOxide.py | Python | gpl-3.0 | 9,459 | [
"Jmol"
] | 8c5ec1850eac3d602352d5d84d4d506dc47cb245e24725c7ab9af8712f5b9fef |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'qt_designer.ui'
#
# Created: Wed Jun 11 11:38:09 2014
# by: PyQt4 UI code generator 4.9.5
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except Att... | AbeJones/obspyck-binaries | qt_designer.py | Python | gpl-2.0 | 60,885 | [
"BLAST"
] | 295bb147c0b680b9d79c4583f7950dd245af003e61a9c7fc2f361c338a8f2fbf |
# -*- coding: UTF-8 -*-
__revision__ = '$Id$'
# Copyright (c) 2005-2012 Vasco Nunes, Piotr Ozarowski
#
# 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, orprint
... | marcin1j/griffith | lib/plugins/movie/PluginMovieAllocine.py | Python | gpl-2.0 | 13,314 | [
"Brian"
] | 68345e08b560464ff03d62d72fce2109ff89ed9b1a718c968cd2d0efd4632620 |
# -*- coding: utf-8 -*-
#
# MDTraj documentation build configuration file, created by
# sphinx-quickstart on Tue Jun 11 21:23:28 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | marscher/mdtraj | docs/conf.py | Python | lgpl-2.1 | 8,953 | [
"MDTraj"
] | 36daedad092f1e1605e47bb8714e1d55087d70e6289eaea1ba97fa96302f30e1 |
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