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#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2013, Cove Schneider
# Copyright: (c) 2014, Joshua Conner <joshua.conner@gmail.com>
# Copyright: (c) 2014, Pavel Antonov <antonov@adwz.ru>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import abso... | mheap/ansible | lib/ansible/modules/cloud/docker/_docker.py | Python | gpl-3.0 | 16,418 | [
"VisIt"
] | dba76ca09fc743b5305e86c39f9d45fba2da75c52ea9cefc1a2371fb94eb5a58 |
from __future__ import division, print_function
import numpy as np
import warnings
import pyprind
import xactcore as xore
import xactlang as lang
# import matplotlib.pyplot as plt
# $$$$$$\ $$$$$$\ $$$$$$$$\ $$\ $$\ $$\ $$\
# $$ __$$\ $$ __$$\\__$$ __|$$ | $$ |$$$\ $$ |
# $$ / \__|$$ / $$ | ... | georglind/humo | humo/xactcotunneling.py | Python | mit | 12,473 | [
"DIRAC"
] | 893d4cc9e64793c5e19fd51b06b9df9b2abbf7b3972908d6934b7883ef92ca49 |
# -*- coding: utf-8 -*-
"""
===========
Spectrum fitter
===========
"""
import numpy
from numpy.ma import median
from numpy import pi, sqrt, log, array, exp
from mpfit import mpfit
from scipy import special, interpolate
from ..analysis.functions import redlaw
"""
The version of mpfit I use can be found here:
http... | Kruehlio/XSspec | utils/fitter.py | Python | mit | 37,890 | [
"Gaussian"
] | f032845f5d4f1c00fd50b5fbea7504647b9acd662277049eb3ff26b84bda860d |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/io/tests/test_registry.py | Python | bsd-3-clause | 63,448 | [
"scikit-bio"
] | 29434f38639e2179016992f94dc9b17bd6a8d1e41b575cf0ec53070a59fec087 |
#!/usr/bin/env python
"""
A test of pymc for ITC.
"""
#=============================================================================================
# IMPORTS
#=============================================================================================
import numpy as np
import pymc
import pint
#=================... | jchodera/assaytools | AssayTools/pymcmodels.py | Python | lgpl-2.1 | 27,554 | [
"Avogadro",
"Gaussian"
] | 42c1909ceba1bdbfc95be4ba5543f470f11bab8d3337cd1765aa007e57cdf592 |
# -*- coding: utf-8 -*-
#
# rayopt - raytracing for optical imaging systems
# Copyright (C) 2012 Robert Jordens <robert@joerdens.org>
#
# This program 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 Found... | jordens/rayopt | rayopt/elements.py | Python | lgpl-3.0 | 19,836 | [
"Gaussian"
] | 9483252d5c2e9ecc48c31568ae6fa7fa3a7b0db4ec2fecefb5361f1019b59d66 |
# Copyright 2013-2015 ARM 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 applicable law or agreed to in w... | Sticklyman1936/workload-automation | wlauto/workloads/facebook/__init__.py | Python | apache-2.0 | 2,815 | [
"VisIt"
] | 4c82969d3b62498f3f41965cfaef543c6ef0cce0b003d7be5dde5c58b4cdee29 |
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library ... | FedoraScientific/salome-hexablock | src/TEST_PY/test_v6/makeRindUni.py | Python | lgpl-2.1 | 1,283 | [
"VTK"
] | dfb9a81777f97e34310f27c0f271275d1c0db7914c7976b821f0acc376e32d97 |
#!/usr/bin/env python
"""
Copyright (c) 2006-2015 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import codecs
import contextlib
import cookielib
import copy
import getpass
import hashlib
import httplib
import inspect
import json
import locale
import logging
import ntpath... | krintoxi/NoobSec-Toolkit | NoobSecToolkit /tools/inject/lib/core/common.py | Python | gpl-2.0 | 132,895 | [
"VisIt"
] | 59bfd8fd1eb9bbb9168cfb6834a5baee484223f3d92c3529fd93000c14daf7dc |
##
# Copyright 2009-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/c/cp2k.py | Python | gpl-2.0 | 35,441 | [
"CP2K"
] | c0c11722938279f9c94959516c55ef04a14f130c5c8188143f79f4e5b38a9dab |
#!/usr/bin/env python3
""" This scripts allows the user to make FEP calculations along a
reaction coordinate with the AMBER and GAUSSIAN software packages"""
# other modules
import argparse
import textwrap
import numpy as np
import decimal
import sys
from collections import OrderedDict
import matplotlib.pyplot as plt... | eduardoftoliveira/oniomMacGyver | omg/dock++/dock_fep.py | Python | gpl-3.0 | 4,030 | [
"Amber",
"Gaussian"
] | f12da101c867b42225daf159cc802582143aaa973e4a2c6bc7cc7dff4dd0cdf2 |
"""Copyright 2008 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.4'
__date__ = 'May 02 2008'
from threading import *
from ... | jantman/tuxostat | fs_backup/home/tuxostat/devel/PhidgetsPython/Phidgets/Devices/Servo.py | Python | gpl-3.0 | 8,066 | [
"VisIt"
] | aa9d65066fcbc59950bae3054f03c43768ed707f5b1ce1983fcd5ccd1933dae4 |
#pylint: disable=missing-docstring
#* 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/... | nuclear-wizard/moose | python/chigger/exodus/ExodusSourceLineSampler.py | Python | lgpl-2.1 | 3,166 | [
"MOOSE",
"VTK"
] | 7b2120a39bb12c2dc189d7d83377f5c571eafb9721763f1dda637b4ddf42a19b |
import time
import numpy as np
from ase import Atoms, units
from ase.optimize import QuasiNewton
from ase.calculators.siesta import Siesta
# Set up a H2O molecule by specifying atomic positions
h2o = Atoms(symbols='H2O',
positions=[( 0.776070, 0.590459, 0.00000),
(-0.776070, 0.59045... | grhawk/ASE | tools/doc/exercises/siesta1/h2o.py | Python | gpl-2.0 | 1,923 | [
"ASE",
"SIESTA"
] | ab223a93a93bcce23232ab0158a64de87b34b2883e178d66ff4b236d02aece15 |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
"""
Backend daemon that conne... | rstreif/rvi_backend | server/utils.py | Python | mpl-2.0 | 2,501 | [
"Jaguar"
] | 218ad501a0d3e07c9c0d2dffddac5d9593a5ff1c485e3fade0f2e27aa85cc5b8 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Martin Hawlisch, Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | pmghalvorsen/gramps_branch | gramps/gen/datehandler/test/datehandler_test.py | Python | gpl-2.0 | 7,511 | [
"Brian"
] | 5aeca9f0157165d00f78db45daf6712f9762f3d38b7f3557ba2dad5c5a3a39eb |
"""
This example shows how to use the VTK postprocessing functions.
"""
from __future__ import absolute_import
import os.path as osp
from .linear_homogenization import *
from sfepy.postprocess.utils_vtk import get_vtk_from_mesh,\
get_vtk_by_group, get_vtk_surface, get_vtk_edges, write_vtk_to_file,\
tetrahedral... | rc/sfepy | examples/homogenization/linear_homogenization_postproc.py | Python | bsd-3-clause | 944 | [
"VTK"
] | 3d1edcdcf4d39f7c5804e499aac52c76842ec643411ca0e9d4cc3fc091caad2f |
# Bonnet's thm: d/dm E[f(z)] = E[d/dz f(z)] for z ~ N(m,v)
#Price's thm: d/dv E[f(z)] = 0.5 E[d^2/dz^2 f(z)] for z ~ N(m,v)
# Note that we are taking derivatives wrt the parameters of the sampling distribution
# We rely on the fact that TFP Gaussian samples are reparameterizable
import numpy as np
import jax
import ... | probml/pyprobml | scripts/gradient_expected_value_gaussian.py | Python | mit | 1,299 | [
"Gaussian"
] | 58c559e451a8047ddbb30d7ea5fb9d9918238fb60f7af084a401d4a432e57fff |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | abloomston/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 172,457 | [
"Gaussian"
] | d0ec5fad25baf6c39125fdcc267f2a8f512fa27c238cfba58d8463d3cc803a7d |
from time import time
from collections import namedtuple
import warnings
from scipy import stats
import numpy as np
from ..base import clone
from ..exceptions import ConvergenceWarning
from ..preprocessing import normalize
from ..utils import (check_array, check_random_state, _safe_indexing,
is_... | kevin-intel/scikit-learn | sklearn/impute/_iterative.py | Python | bsd-3-clause | 31,200 | [
"Gaussian"
] | 5121e8aedfe80a33d36a89dd414fe674aaee4bf4693431ea5c2ee22ddbd5fab8 |
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
""" unit testing code for knn models """
from rdkit import RDConfig
import unittest
from rdkit.ML.Data import DataUtils, MLData
from rdkit.ML.KNN import CrossValidate,DistFunctions
from rdkit.ML.KNN import KNNModel,KNNClassificationModel,KNNRegres... | rdkit/rdkit-orig | rdkit/ML/KNN/UnitTestKNN.py | Python | bsd-3-clause | 3,042 | [
"RDKit"
] | 4828769446b0183f55a899d7cc33174b8658d46bc3bff64b8a31283fa62506ec |
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary for... | Nikea/VisTrails | vistrails/packages/vtk/tf_widget.py | Python | bsd-3-clause | 29,698 | [
"VTK"
] | 8c691963546fa846e0a223c5653615b14edc7df8608743433ec6a9cf9c8b8775 |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ 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.
#
""" unit testing code f... | soerendip42/rdkit | rdkit/DataStructs/UnitTestBitVect.py | Python | bsd-3-clause | 8,576 | [
"RDKit"
] | 6c2e9a23a85edc56777614757717ca3ff05d8fabd342f1f3f8a0908767ad5cba |
# Copyright (C) 2012,2013, 2017(H)
# 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... | espressopp/espressopp | testsuite/unittest/testParticle.py | Python | gpl-3.0 | 1,542 | [
"ESPResSo"
] | 9a8a71d6ec00b7e19744bb75e595347cf2969107161a4780cb9a9c3bbd0f708e |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
... | timvideos/HDMI2USB-mode-switch | versioneer.py | Python | apache-2.0 | 68,611 | [
"Brian"
] | c84d9b182b2f629b33debff4aa1373f4606833e32c2e1411a458f5a307733371 |
# Copyright (c) 2014. Mount Sinai School of Medicine
#
# 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 o... | hammerlab/immuno | immuno/mutate.py | Python | apache-2.0 | 8,294 | [
"Biopython"
] | 3329c1fd42e9b885422faef7efe51923d4ff51a39da3c78ec44a24fbf204b883 |
# $Id$
#
# Copyright (C) 2007-2010 Greg Landrum
# All Rights Reserved
#
from rdkit import Chem
class PropertyMol(Chem.Mol):
""" allows rdkit molecules to be pickled with their properties saved.
>>> from rdkit.six.moves import cPickle
>>> m = Chem.MolFromMolFile('test_data/benzene.mol')
>>> m.GetProp('_Name... | soerendip42/rdkit | rdkit/Chem/PropertyMol.py | Python | bsd-3-clause | 2,784 | [
"RDKit"
] | ae38e728de182892618bdfbbd6ffb97d72a22c6f07d0f6c451dd41476e968e8b |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument('-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument('hwdef', type=str, default=None, help='hardware ... | RedlineResearch/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 31,149 | [
"CRYSTAL"
] | d2a2eb836399d62fdc82b8576c24d574c0cb1f85ed10a0c5fe2859b1cb1d55db |
"""
StructProp
==========
"""
import logging
import os.path as op
import numpy as np
import pandas as pd
from cobra.core import DictList
from collections import defaultdict
import ssbio.protein.sequence.utils.alignment
import ssbio.protein.structure.properties.dssp
import ssbio.protein.structure.properties.msms
impor... | SBRG/ssbio | ssbio/protein/structure/structprop.py | Python | mit | 37,089 | [
"BLAST",
"Biopython"
] | 040d467b6477e254f260209eead42cf71182ce7695c9179b95d2ab50c735f9b4 |
#!/usr/bin/env python
import sys
import time
from launch_instance import launch_instance, get_opt_parser, ssh_command, scp_to_command, run_command
from optparse import OptionParser
if __name__ == "__main__":
start = time.time()
parser = OptionParser()
parser = get_opt_parser(parser=parser)
(opts, args)... | splice/splice-server | ec2/launch_ReportServer.py | Python | gpl-2.0 | 2,165 | [
"VisIt"
] | 54b275738d4c7bbf7b66a3bc8a5238c426e008dbc892e5f28cd5bcf0b1094895 |
#-*- coding:utf-8 -*-
"""
This file is part of OpenSesame.
OpenSesame 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.
OpenSesame is distri... | eort/OpenSesame | openexp/_canvas/legacy.py | Python | gpl-3.0 | 10,944 | [
"Gaussian"
] | c7345cab323cb80ae86df887806bfa154b86202518db3bb1736e8a7d257cbd52 |
"""Examine and query coverage in sequencing experiments.
Provides estimates of coverage intervals based on callable regions
"""
import itertools
import os
import shutil
import yaml
import pybedtools
import pandas as pd
import numpy as np
import pysam
from bcbio.variation.bedutils import clean_file
from bcbio.utils i... | brainstorm/bcbio-nextgen | bcbio/variation/coverage.py | Python | mit | 16,399 | [
"pysam"
] | 32420c3cdb1e7c4ed963075e2932bf7fec8be370154f0456524c649a651d5a85 |
"""Module for working with external libraries.
Portions of this code are adapted from MDTraj and are released under the
following license.
##############################################################################
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Les... | iModels/mbuild | mbuild/utils/io.py | Python | mit | 8,573 | [
"MDTraj",
"Pybel",
"RDKit"
] | b57e9e9cee0669b54ab9e1199d9d8f2405e19201b02f65122bb5473fd9640934 |
"""Helpful utilities for building analysis pipelines.
"""
import gzip
import os
import tempfile
import time
import shutil
import contextlib
import itertools
import functools
import random
import ConfigParser
import collections
import fnmatch
import subprocess
import toolz as tz
import yaml
try:
from concurrent imp... | hjanime/bcbio-nextgen | bcbio/utils.py | Python | mit | 18,266 | [
"Galaxy"
] | 35244fdf9bcc4bb34d6f24751e700c42ff315e1188b1ea807c7d00ce667b32a9 |
#!/bin/env python
"""
tests for InProcessComputingElement module
"""
import os
import shutil
import pytest
from DIRAC.Resources.Computing.test.Test_PoolComputingElement import jobScript, _stopJob
from DIRAC.WorkloadManagementSystem.Utilities.Utils import createJobWrapper
# sut
from DIRAC.Resources.Computing.InProce... | yujikato/DIRAC | src/DIRAC/Resources/Computing/test/Test_InProcessComputingElement.py | Python | gpl-3.0 | 2,136 | [
"DIRAC"
] | 166cc300eb59f9d86f019360649730f11915070a65616bb75d7f0c3f0067bda8 |
""" DRMAA2 Python language binding.
This is a mock implementation for testing purposes.
For further information, please visit drmaa.org.
"""
import drmaa2
# Definition part
job_template_impl_spec = ['mock_testattr']
job_info_impl_spec = []
reservation_template_impl_spec = []
reservation_info_impl_spec = []... | troeger/drmaa2-python | drmaa2/backend/mock.py | Python | apache-2.0 | 3,473 | [
"VisIt"
] | 48ff28c1fbc82a7caa118e9eca056b14e269ff07e1cf9b0b245824be52aef4b9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import collections
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.units import (Energy, Time, Length, unitized, Mass, Memory,
... | migueldiascosta/pymatgen | pymatgen/core/tests/test_units.py | Python | mit | 8,030 | [
"pymatgen"
] | 71787607ed22677345f5398e6c0ce2d9af6e145fd003acdf01be90ca0a079db4 |
# 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 u... | wangsheng1001/incubator-singa | python/singa/optimizer.py | Python | apache-2.0 | 16,090 | [
"Gaussian"
] | de7f29650c9e980f4baf40fc3e59ddebeb65144a9e6ab0146e739f502828eb79 |
from __future__ import division
from collections import defaultdict
import numpy as np
from ._mesh import SphereMesh
from .._util import atoms_to_numpy
from .._atomic_property import GetAtomicNumber, vdw_radii
class SurfaceArea(object):
r"""calculate solvent accessible surface area.
:type radiuses: np.nda... | mordred-descriptor/mordred | mordred/surface_area/_sasa.py | Python | bsd-3-clause | 3,433 | [
"Biopython",
"RDKit"
] | 83a534206e09682c37ff4696f7c95c93f600986872051adbdc9d43e64817353c |
import itertools
import numpy as np
import mdtraj as md
import msmbuilder as msmb
n_traj = 1
trj0 = md.load("./system.subset.pdb")
pair_indices = np.loadtxt("./AtomPairs.dat", 'int')
metric = msmb.metrics.AtomPairs(atom_pairs=pair_indices)
tica = msmb.reduce.tICA(1, prep_metric=metric)
for filename in ["./Trajector... | hainm/MSMs | attic/src/code/hmsm/save_tica_hmsm_featurizer.py | Python | gpl-2.0 | 730 | [
"MDTraj"
] | 12ec35f08a54844d62b1241cb6edd014c9344e4bf47c88a33af17592d36b202b |
##############################################################################
# Copyright (c) 2013-2017, 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... | lgarren/spack | var/spack/repos/builtin/packages/eccodes/package.py | Python | lgpl-2.1 | 4,223 | [
"NetCDF"
] | b0e7076e97747d5c3be386806fa2d0eb1383ac1630e89dfd3986b964e4f7fcfd |
"""
Perceptron training example
This is example has 3 binary inputs and a single output.
"""
def fire(xVec,wVec):
"""
Implements a single threshold perceptron
xVec is the input vector
wVec is the weight vector of the neuron connections
The size of wVec ... | pauljohnleonard/pod-world | CI_2015/CI_examples/perceptronTraining/simplePerceptronTraining.py | Python | gpl-2.0 | 2,152 | [
"NEURON"
] | 941ce3a5b4f0556ba51402548342d5d09227ede1f1b82d9a5b47e89623f82954 |
"""
typhon.retrieval.qrnn.qrnn
==========================
This module provides the QRNN class, which implements the high-level
functionality of quantile regression neural networks, while the neural
network implementation is left to the model backends implemented in the
``typhon.retrieval.qrnn.models`` submodule.
"""
i... | atmtools/typhon | typhon/retrieval/qrnn/qrnn.py | Python | mit | 23,139 | [
"Gaussian",
"NEURON"
] | fb1b7ba3a1106959c9275fd7f16f94f2a46d8449a9c02fbc5ff73086c353ac22 |
# -*- coding: utf-8 -*-
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. C... | adamcandy/qgis-plugins-meshing-initial | release/mesh_netcdf/ui_meshnetcdf.py | Python | lgpl-2.1 | 14,255 | [
"NetCDF"
] | 351898c80cef1ff96ec4f3cf061544e07881b2909c7956cda4de9b2d0e296bb0 |
""" Module that holds DISET Authorization class for services
"""
from DIRAC.ConfigurationSystem.Client.Config import gConfig
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getGroupsForVO
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Security import CS
from DIRAC.Core.Security i... | arrabito/DIRAC | Core/DISET/AuthManager.py | Python | gpl-3.0 | 10,915 | [
"DIRAC"
] | aaca87eb5b102bd832ef573eded2dab5f929a67e88df90786369f14203df2592 |
import matplotlib as mpl
mpl.use('wxAgg')
import numpy as np
import warnings
import wx
from copy import copy
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
from matplotlib.colors import LinearSegmentedColormap
from matplotlib.figure import Figure, SubplotParams
from numpy import random as r... | theodoregoetz/colormap | cmap-generator.py | Python | gpl-3.0 | 19,669 | [
"Gaussian"
] | 422a922b085b6a6c1903423299bfa0e8bb883e13bae13549b37fbcfbdd2d550d |
import sys,logging,os,time,subprocess,re,hashlib
import xml.dom.minidom, xml.sax.saxutils
#set up logging
logging.root
logging.root.setLevel(logging.ERROR)
formatter = logging.Formatter('%(levelname)s %(message)s')
#with zero args , should go to STD ERR
handler = logging.StreamHandler()
handler.setFormatter(formatter)... | damiendallimore/SplunkModularInputsPythonFramework | implementations/command/bin/command.py | Python | apache-2.0 | 12,832 | [
"VisIt"
] | 024038eafd680fd2c6a5c03ddcda2b33411dfe172f009e692cdb7612b28f534b |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A module for NMR analysis
"""
from collections import namedtuple
import numpy as np
from pymatgen.core.periodic_table import Species
from pymatgen.core.structure import Site
from pymatgen.core.tensors import SquareTenso... | materialsproject/pymatgen | pymatgen/analysis/nmr.py | Python | mit | 8,579 | [
"pymatgen"
] | a07ee5e30880b743ea48dfff23c902696e156dbc764c27f50899c6ac07048c28 |
#!/usr/bin/env python
#
# svnadmin_tests.py: testing the 'svnadmin' tool.
#
# Subversion is a tool for revision control.
# See http://subversion.apache.org for more information.
#
# ====================================================================
# Licensed to the Apache Software Foundation (ASF) under one
#... | YueLinHo/Subversion | subversion/tests/cmdline/svnadmin_tests.py | Python | apache-2.0 | 139,404 | [
"exciting"
] | 0f1ded3506683baec9a971d15f36711b1e88c30a142fa975d201ac4876fc5072 |
# Copyright 2017 the pycolab 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | deepmind/pycolab | pycolab/human_ui.py | Python | apache-2.0 | 21,762 | [
"VisIt"
] | b20bb8594f05d8a6863b7ef9e3c36099f7868ab3b5992290dd00289b50c225f2 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Abstract based class for cclib methods."""
import logging
import sys
class Method(object):
"""Abst... | Schamnad/cclib | src/cclib/method/calculationmethod.py | Python | bsd-3-clause | 1,870 | [
"ADF",
"cclib"
] | 51d3e800994cb53bf92e523c4f3ac1a4b424c079af405de68b416cc0aa0064eb |
##
# Copyright 2009-2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | omula/easybuild-easyblocks | easybuild/easyblocks/o/openfoam.py | Python | gpl-2.0 | 11,997 | [
"ParaView"
] | 458dba931e8a9b318fdd766a93b28bd7e75af673dda40a66d76e125183c5ce33 |
import numpy as np
from scipy import linalg
def log_multivariate_normal_density(X, means, covars, covariance_type='diag'):
"""
Compute the log probability under a multivariate Gaussian distribution.
Parameters
----------
X : array_like, shape (n_samples, n_features)
List of n_features-dim... | hmmlearn/hmmlearn | lib/hmmlearn/stats.py | Python | bsd-3-clause | 3,989 | [
"Gaussian"
] | de3e31250099ac7237a440dee203b8c762e988a2bee67dd0a56c580fc14ec6d7 |
"""
System class: the Lammps Molecular Dynamics main object
"""
from lammps import lammps#neutronstar.DummyLammps import Lammps as lammps
from pylammps import Potential, Computes
from random import randint
import numpy as np
import ctypes as ct
class System(dict):
"""
Any system will be a dictionary with the par... | pabloalcain/lammps-python | pylammps/System.py | Python | gpl-3.0 | 10,621 | [
"Gaussian",
"LAMMPS"
] | 0e2c639ac94e9f3abc01dcacafb4fc9a4ee0132885e8a20b064ee76e943f8d35 |
../../../../share/pyshared/orca/desktop_keyboardmap.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/desktop_keyboardmap.py | Python | gpl-3.0 | 54 | [
"ORCA"
] | cd3d896f7854fd36270a5ae90880763bc672fc226b51686056c03c13c06c39ed |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: LiangTing
2021/12/18 12:06:31
"""
from pylab import *
from ase.io import read
from thermo.gpumd.preproc import add_basis, repeat
from thermo.gpumd.io import create_basis, create_kpoints, ase_atoms_to_gpumd
def read_structure(data_file):
VioletP_unitcell... | brucefan1983/GPUMD | examples/empirical_potentials/phonon_vibration_viewer/create_structure_for_gpumd.py | Python | gpl-3.0 | 2,681 | [
"ASE",
"GPUMD",
"LAMMPS"
] | 277db8b3c7bda1871f646bb5c2ef62ee9ed5c2e6d339ff2de6eb2af89346b82c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible 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... | dmitry-sobolev/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 17,284 | [
"Brian"
] | f479a96f52e6bb7c8b280cf04b791e95ad9873ce97ea188001c49a5b0c3ec4d8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/hh_style/neuron/mm_neuron_alphabeta.py | Python | bsd-2-clause | 6,934 | [
"NEURON"
] | 95de2c6a0ad3eb9f3faa01124d07a8c364d0e7e0cc77ec894450b0d8143852a4 |
from brian.stdunits import *
from brian.units import *
F = 1
N_SUBPOP = 1
INTERCO_RATE = 0
INTERCO_STRENGTH = 0
PARAMETERS = {
'Common':
{'simu_dt' : 0.05*msecond,
'simu_length' : 2000*msecond,
'resample_dt' : 0.5*msecond,
'N_subpop' : N_SUBPOP,
'N_mitral' : N_SUBPOP*100*F,
'inte... | neuro-lyon/multiglom-model | src/paramsets/std_beta_1glom_new.py | Python | mit | 1,535 | [
"Brian"
] | 296e84f3d09dc27e1dc9cf58d5f67c2d6ecc792a2b800c0ef611851e27e67163 |
"""
Functions for working with files
"""
import codecs
import contextlib
import errno
import logging
import os
import re
import shutil
import stat
import subprocess
import tempfile
import time
import urllib.parse
import salt.modules.selinux
import salt.utils.path
import salt.utils.platform
import salt.utils.stringut... | saltstack/salt | salt/utils/files.py | Python | apache-2.0 | 28,263 | [
"VisIt"
] | a90f9ebf915e9f8e0e5cbecb284adc16cf0b3d6bfda79b48ccffc9cb6444fb2f |
##############################################################################
# Copyright (c) 2013-2017, 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... | skosukhin/spack | var/spack/repos/builtin/packages/trilinos/package.py | Python | lgpl-2.1 | 27,647 | [
"NetCDF"
] | 600c61e193c8611f0cc5bd89699f4a44faafb726bb43f63317c619f8cff925b4 |
## NIFTY (Numerical Information Field Theory) has been developed at the
## Max-Planck-Institute for Astrophysics.
##
## Copyright (C) 2013 Max-Planck-Society
##
## Author: Marco Selig
## Project homepage: <http://www.mpa-garching.mpg.de/ift/nifty/>
##
## This program is free software: you can redistribute it and/or mod... | ultimanet/nifty | demos/demo_excaliwir.py | Python | gpl-3.0 | 7,706 | [
"Gaussian"
] | 8629abbcfc5321518b3ce2487571437c172d0d024e3f7415e09f06988be75f64 |
#! /usr/bin/env python
"""
This script fits emission lines on a stacked spectrum
"""
import os
import glob
import numpy as n
import astropy.io.fits as fits
import matplotlib.pyplot as p
# import the fitting routines
import LineFittingLibrary as lineFit
from scipy.interpolate import interp1d
import time
lfit = lineFi... | JohanComparat/pySU | galaxy/bin_LF/magnitude_limit_and_line_detection_limit_deep2.py | Python | cc0-1.0 | 3,293 | [
"Gaussian"
] | 0a1706cc14b874e7f58a0b96b82501ab03eaebbaf030ff3415f57753250e8150 |
from django.shortcuts import render
# Create your views here.
from django.http import HttpResponse, HttpResponseRedirect
from rango.models import Category, Page
from rango.forms import CategoryForm, PageForm, UserForm, UserProfileForm
from django.contrib.auth import authenticate, login, logout
from django.core.urlr... | nirajkvinit/django_tango | rango/views.py | Python | mit | 5,455 | [
"VisIt"
] | 5d16035755a07278f1cd1f64065bf77492773f1a24d1fbe019b5c892ea9b7a4b |
# Copyright (c) 2015 Max Zwiessele
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from GPy.models.bayesian_gplvm_minibatch import BayesianGPLVMMiniBatch
from GPy import Parameterized
from nose.tools import assert_list_equal
import numpy as np
from GPy.core.parameterization.observable_array import ObsAr
fr... | mzwiessele/applygpy | applygpy/bgplvmpanama/bgplvmpanama.py | Python | bsd-3-clause | 3,994 | [
"Gaussian"
] | 4793f7ae05e6def1dc82667bc0050362610cf69fd405be9209d67ace5a62ab73 |
#!/usr/bin/env python
# copied and modified from https://github.com/biocore/scikit-bio
from setuptools import find_packages, setup
from glob import glob
__version__ = "0.9.1"
classes = """
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Intended Audience :: Science/Research
Topic ... | gregcaporaso/cual-id | setup.py | Python | bsd-3-clause | 1,316 | [
"scikit-bio"
] | 37aa738a6f87c07e6c7db23d642d1226b4022aef0d19e4278ccb7ab192afea45 |
"""Octopus germline and somatic calling.
https://github.com/luntergroup/octopus
"""
import os
import subprocess
import pysam
import six
from bcbio import utils
from bcbio.distributed.transaction import file_transaction
from bcbio.pipeline import shared
from bcbio.pipeline import datadict as dd
from bcbio.provenance ... | chapmanb/bcbio-nextgen | bcbio/variation/octopus.py | Python | mit | 7,255 | [
"Octopus",
"pysam"
] | ea302197e3f8f2dbbf05f7beeddab8e135360cb879f7ce4abe3b25fddced61eb |
""" This class is a wrap around the rrdtool as it is a command line based tool within this class there are
several methods which take in some parameters required by the corresponding rrd command and executes it.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/private/monitoring/RRDManager.py | Python | gpl-3.0 | 13,023 | [
"DIRAC"
] | a699f55351ee1bd1508c55b147f2bea5bd1f9a9fc0dd9878b0c1d49d930cc812 |
# Copyright 2018 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | brain-research/nngp | nngp.py | Python | apache-2.0 | 15,424 | [
"Gaussian"
] | 839fb69d3a7d7ad2207c8bd3b1aad92b294c96366541690bd6a2b30d0d027505 |
##############################################################################
##############################################################################
# Default settings and helpers for
# Particle filtering and smoothing
#
# Copyright (c) 2016 Johan Dahlin [ johan.dahlin (at) liu.se ]
# Distributed under the MIT... | compops/phd-thesis | python-base/state/smc_helpers.py | Python | gpl-3.0 | 7,200 | [
"Gaussian"
] | 5ee51918ce054e47b2cd41d845697376420a903ed8870c90dc135780577c2764 |
#!/usr/bin/env python
'''
Ground-state and IP/EA-EOM-CCSD for singlet (RHF) and triplet (UHF) O2.
'''
from pyscf import gto, scf, cc
# Singlet
mol = gto.Mole()
mol.verbose = 5
mol.unit = 'A'
mol.atom = 'O 0 0 0; O 0 0 1.2'
mol.basis = 'ccpvdz'
mol.build()
mf = scf.RHF(mol)
mf.verbose = 7
mf.scf()
mycc = cc.RCCSD(... | gkc1000/pyscf | examples/cc/20-ip_ea_eom_ccsd.py | Python | apache-2.0 | 768 | [
"PySCF"
] | 727aeff93691fcae208486aea5ca59590f7c5effd58e3497439f2e6a906c1afb |
#!/usr/bin/env python3
''' Write a program that checks the websites of several web comics and
automatically downloads the images if the comic was updated since the
program’s last visit. Your operating system’s scheduler (Scheduled Tasks
on Windows, launchd on OS X, and cron on Linux) can run your Python
program once a ... | apaksoy/automatetheboringstuff | practice projects/chap 15/swd/scheduledWebDownloader.py | Python | mit | 3,485 | [
"VisIt"
] | 4fa2f56aee266657ddc2c056a41937654dff4c90049a76e28fca38b58fac0bbe |
#!/usr/bin/env python2
import os
import sys
import re
import pandas as pd
import matplotlib.pyplot as plt
import paratemp.energy_histo as eh
from paratemp import cd
from glob import glob
from shutil import copyfile, rmtree
if sys.version_info.major != 2:
raise ImportError(
"Last I checked, paratemp.energ... | theavey/ParaTemp | scripts/check-convergence.py | Python | apache-2.0 | 2,492 | [
"MDAnalysis"
] | efa7b7e5065a205a30a7b0430c89ee64f40ae23da93b50387b4261bd469c4de0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# 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; ... | SNoiraud/gramps | gramps/gen/filters/rules/note/_matchessubstringof.py | Python | gpl-2.0 | 2,000 | [
"Brian"
] | b56fa4cf3bd68e55815caf70ed12e9c68127e6227f10e4edd6d045ac34c6c88e |
"""This module defines an ASE interface to ABINIT.
http://www.abinit.org/
"""
import os
from glob import glob
from os.path import join, isfile, islink
import numpy as np
from ase.data import chemical_symbols
from ase.data import atomic_numbers
from ase.units import Bohr, Hartree
class Abinit:
"""Class for doi... | freephys/python_ase | ase/calculators/abinit.py | Python | gpl-3.0 | 21,495 | [
"ABINIT",
"ASE",
"DIRAC"
] | 30a7dcc42fe705e6cbd346e99201d5c94648233e17ee2db63027f402a32a3348 |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
red= (1,0,0)
green= (0,1,0)
blue= (0,0,1)
cyan= (0,1,1)
yellow= (1,1,0)
pink = ( float(255)/255,float(192)/255,float(203)/255)
grey = ( float(127)/255,float(127)/255,float(127)/255)
orange = ( float(255)/255,float(165)/255,float(0)/255... | aewallin/opencamlib | src/attic/oct_test1.py | Python | lgpl-2.1 | 6,427 | [
"VTK"
] | a486707d9f01fcf683fe35333c767681a982fafde8fe6146d7a8e6ff061b31d8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Jan 25, 2012
"""
__author__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Anubhav Jain"
__email__ = "ajain@lbl.g... | dongsenfo/pymatgen | pymatgen/apps/battery/tests/test_insertion_battery.py | Python | mit | 5,761 | [
"pymatgen"
] | 3171b46f6989ee11308d59702451ab8960c2a64f893cbbfc55a2ec018a62958d |
import time
tic=time.time()
import matplotlib
matplotlib.use('Agg')
matplotlib.rcParams.update({'font.size': 32})
import trackeddy
import trackeddy.tracking as ttrack
from trackeddy.geometryfunc import *
from pylab import *
import random
import pdb
import cmocean as cm
import matplotlib.gridspec as gridspec
import tr... | Josue-Martinez-Moreno/trackeddy | validation/random_field.py | Python | mit | 11,468 | [
"Gaussian"
] | 70a6cf445b6b5a74369ee928f9d7059ac16b08d76620923b198ccd977a910a64 |
# The OARN Relief Nursery Database
# Copyright (C) 2015 Oregon Association of Relief Nurseries
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at... | wire-rabbit/oarn-database | oarndb/models/reference_models.py | Python | agpl-3.0 | 15,644 | [
"VisIt"
] | fd9a8767770893c6b7ad3e22a2e936f828d78a26b35f57341b27bd8f20fc50d3 |
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# This program is distr... | xyficu/rts2 | scripts/rts2saf/unittest/test_analyze.py | Python | gpl-2.0 | 6,053 | [
"VisIt"
] | f726c749664881ec3c37794481d3c69cda684b5765f95f732b051e75cd8ee77d |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | marscher/PyEMMA | pyemma/util/tests/statistics_test.py | Python | lgpl-3.0 | 1,917 | [
"Gaussian"
] | 8464d7fa0ccff67265dd6df15ab6223a6315c2a684d177ad69904ad80385d494 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
'''
Plotter
#################
This is supposed to be a collection of classes and functions to aid in plotting
'''
from bokeh.plotting import output_notebook, show, figure
from bokeh.... | exa-analytics/exatomic | exatomic/plotter/plot.py | Python | apache-2.0 | 4,657 | [
"Gaussian"
] | a92729d4c2f27c9bcef1b712aaae65c6de87fedb315068fb93d82159ba1b177d |
""" Contains the ModeController, Mode, and ModeTimers parent classes"""
# modes.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
import logging
import os
f... | jabdoa2/mpf | mpf/system/modes.py | Python | mit | 31,803 | [
"Brian"
] | c8fd581d850199083ab123a63e142b309a37c3239639dbb992bc7b55c28a6ec8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/simulatorbuiltin/sim_builtin_neuron.py | Python | bsd-2-clause | 3,061 | [
"NEURON"
] | 0c41e55ac777dbfb5421b28342fb3ce41ddca26469c2cd6d26ca78b3ddc8feb5 |
#!/usr/bin/env python
"""
The Open GSM Daemon - Python Implementation
(C) 2008-2009 Michael 'Mickey' Lauer <mlauer@vanille-media.de>
(C) 2008 Openmoko, Inc.
(C) 2007-2008 M. Dietrich
GPLv2 or later
Package: ogsmd.modems.ti_calypso
Module: channel
TI Calypso specific modem channels
"""
__version__ = "0.9.10.6"
from... | freesmartphone/framework | framework/subsystems/ogsmd/modems/ti_calypso/channel.py | Python | gpl-2.0 | 13,907 | [
"CRYSTAL"
] | f167d001cb1f1411d8cc44b31b1c050c9528e5b75399de7e6caae43851487278 |
from django.conf import settings
import logging
from django.utils.encoding import smart_unicode
from django.core.urlresolvers import reverse, NoReverseMatch
from splango.models import Subject, Experiment, Enrollment, GoalRecord
SPLANGO_STATE = "SPLANGO_STATE"
SPLANGO_SUBJECT = "SPLANGO_SUBJECT"
SPLANGO_QUEUED_UPDATE... | shimon/Splango | splango/__init__.py | Python | mit | 7,869 | [
"VisIt"
] | 3c8816b208f1684ce5160c05928d09a06764e4645fe196b079bb56a3dc822bdb |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subresultants,
resu... | chaffra/sympy | sympy/polys/tests/test_polytools.py | Python | bsd-3-clause | 108,194 | [
"Gaussian"
] | ea5e00af58905f347f485722a9c1c02c2b3930c75bdd1782838aad701946a076 |
import tempfile
import subprocess
import os
import glob
from subprocess import Popen, PIPE
from multiprocessing import cpu_count
import numpy as np
import montemodes.classes.results as res
def create_tinker_input(molecule):
temp_file_name = tempfile.gettempdir() + '/tinker_temp'+ '_' + str(os.getpid())
ti... | abelcarreras/MonteModes | montemodes/functions/calculate.py | Python | mit | 8,018 | [
"Gaussian",
"TINKER"
] | 79949fe3fcbaf1c2bd6268e2d20c248057e4f98f9990cebc2e4149a767884719 |
#
# @file TestKineticLaw_newSetters.py
# @brief KineticLaw unit tests for new set function API
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatic... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestKineticLaw_newSetters.py | Python | bsd-3-clause | 8,990 | [
"VisIt"
] | e62722251fccf7fa7dda752da7ed6a42723a5fa3f947115ef8a33eac5a7d2897 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.4 on 2017-09-04 11:12
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('clients', '0001_initial'),
]
operations = [
migrations.AlterModelOptions(
... | tomp/food_pantry | clients/migrations/0002_auto_20170904_1112.py | Python | mit | 1,627 | [
"VisIt"
] | 1b5ed3cd08d7ab78bf0afe25ca70c1b12c6299eb34d2591b4b6d7ebb42284ae0 |
""" The main modules for the kayu Wood Nondestructive Evaluation Software
"""
# pylint: disable=locally-disabled, W0201, W0401, W0613, W0614, R0901, R0902, R0201, R0914, E1101
from tkinter import *
from tkinter import messagebox, filedialog
import tkinter as tk
import modules
from matplotlib.backends.backend_tkagg im... | mappuji/ugm-kayu-nde | main.py | Python | mit | 26,981 | [
"MOE"
] | e7a136e723191544cef9f2efe8ecb7b884de97246420de4d11a331d2de0aafe3 |
#!/usr/bin/env python
#
# This example introduces 3D widgets. 3D widgets take advantage of the
# event/observer design pattern introduced previously. They typically
# have a particular representation in the scene which can be interactively
# selected and manipulated using the mouse and keyboard. As the widgets
# are ma... | Nikea/VisTrails | examples/vtk_examples/Tutorial/Step6/Cone6.py | Python | bsd-3-clause | 5,066 | [
"VTK"
] | 79b1f0f8a47045c6b2ce6b7101878e95e0848e14648795f007969978bcd36651 |
'''
Script to update locations of stations that failed location quality assurance
and had their location manually corrected.
'''
from twx.db import StationDataDb, build_por_mask, LON, LAT, ELEV
from twx.qa import LocQA
from twx.utils import TwxConfig
import numpy as np
import os
import pandas as pd
if __name__ == '__... | jaredwo/topowx | scripts/step07_update_stn_loc.py | Python | gpl-3.0 | 2,436 | [
"NetCDF"
] | fa10e1c5c2484d3a38aef216a03f6281dd22b63775c24e19d886826b598ea365 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
class TestSynchronizedTemplates3D(Testing.vtkTest):
def testAll(self):
reader = vtk.vtkImageReader()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExte... | timkrentz/SunTracker | IMU/VTK-6.2.0/Filters/Core/Testing/Python/TestSynchronizedTemplates3D.py | Python | mit | 2,261 | [
"VTK"
] | f00cdd1961bd24fa18de6cff315006fc4aa162050dacf9f2b997b61f84032523 |
#!/usr/bin/env python
# Copyright (c) 2012 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.
'''Tool to create a new, empty .grd file with all the basic sections.
'''
from grit.tool import interface
from grit import constan... | hujiajie/chromium-crosswalk | tools/grit/grit/tool/newgrd.py | Python | bsd-3-clause | 2,717 | [
"xTB"
] | e35617decba0f0fe03b274722018e099585b4f58e433dbf575867ca902064215 |
import numpy as np
from tempfile import mktemp
from h5py import tests
import h5py
class GroupBase(tests.HTest):
def setUp(self):
import tempfile
self.name = tempfile.mktemp()
self.f = h5py.File(self.name, 'w')
def tearDown(self):
import os
self.f.close()
os.un... | qsnake/h5py | h5py/tests/high/test_group.py | Python | bsd-3-clause | 8,385 | [
"VisIt"
] | bea2dbaed555dca6c4beb887917d012023062d600b107ff9331bad588b80881f |
from django.test import TestCase, tag
from edc_appointment.models import Appointment
from edc_base import get_utcnow
from edc_facility.import_holidays import import_holidays
from edc_lab.models.panel import Panel
from edc_reference.site import site_reference_configs
from edc_visit_schedule import site_visit_schedules
f... | botswana-harvard/edc-meta-data | edc_metadata/tests/test_handlers.py | Python | gpl-2.0 | 3,888 | [
"VisIt"
] | 0e3e141ad477f7d69dfb3d0ffefd176c7b076acc8c1e5307deb0ffd3a7a1363a |
""" Module for I/O
"""
from __future__ import absolute_import, division, print_function
import numpy as np
import json
import pdb
import ne2001
data_path = ne2001.__path__[0]+'/data/'
def read_galparam(ifile='gal_param.json'):
""" Read Galaxy parameters
Parameters
----------
ifile : str, optional
... | pyigm/NE2001 | ne2001/io.py | Python | bsd-3-clause | 4,214 | [
"Galaxy"
] | a85bf068392545e02dd64286df62648d13cfbbf3c378624acfca376e43026dbb |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The fusion module provides higher-level interfaces to some of the operations
that can be performed with the seg_LabFusion command-line program.
Change directory to provide relative paths for doctests
... | mick-d/nipype | nipype/interfaces/niftyseg/label_fusion.py | Python | bsd-3-clause | 13,683 | [
"Gaussian"
] | 88a41120fee78b178694e77cb37ae9399d17fb9a2a9bb56cb40f06c7654d0a48 |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | testsuite/python/p3m_electrostatic_pressure.py | Python | gpl-3.0 | 5,716 | [
"ESPResSo"
] | 9b4209b40fd3fe17d90fd79bca10ba9ee2eccbcc94ec0635cc9b51c0622063e9 |
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