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"""
Assesment of Generalized Estimating Equations using simulation.
This script checks Gaussian models.
See the generated file "gee_gaussian_simulation_check.txt" for
results.
"""
from statsmodels.compat.python import range, lrange, zip
import scipy
import numpy as np
from itertools import product
from statsmodels.ge... | hlin117/statsmodels | statsmodels/genmod/tests/gee_gaussian_simulation_check.py | Python | bsd-3-clause | 9,914 | [
"Gaussian"
] | e467c1e7a5229c11c6ffc39a8e71ab079c58cc6fa7a9f9e21d06b18256d3ddc8 |
'''Apport package hook for the ubiquity live CD installer.
Copyright (C) 2009 Canonical Ltd.
Authors: Colin Watson <cjwatson@ubuntu.com>,
Brian Murray <brian@ubuntu.com>'''
import apport.hookutils
import os.path
import re
def add_installation_log(report, ident, name):
if os.path.exists('/var/log/install... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/apport/package-hooks/source_ubiquity.py | Python | gpl-3.0 | 4,922 | [
"Brian"
] | 65b9d5cd0eb3019bc58f3b0ff70c7c4d35f8c401ee96b757d511137252bfa582 |
from compliance_checker.base import BaseCheck, TestCtx, Result
from compliance_checker import MemoizedDataset
from compliance_checker.cf.cf_1_7 import CF1_7Check
from netCDF4 import Dataset
from compliance_checker.base import BaseCheck, BaseNCCheck, Result, TestCtx
import requests
from lxml import etree
from shapely.ge... | ioos/compliance-checker | compliance_checker/cf/cf_1_8.py | Python | apache-2.0 | 41,902 | [
"NetCDF"
] | f93c7b806f451845745d5048f1df20856af08fe723e89fca7c1d211049e777e4 |
#!/usr/bin/env python
#
# Copyright (C) 2010-2012 ABINIT Group (Yann Pouillon)
#
# This file is part of the ABINIT software package. For license information,
# please see the COPYING file in the top-level directory of the ABINIT source
# distribution.
#
# FIXME: detect duplicate definitions
from ConfigParser import C... | qsnake/abinit | util/maintainers/check-build-config.py | Python | gpl-3.0 | 5,556 | [
"ABINIT"
] | 360b1ea2aae730e4319c25ecdfa621dcd7a8f08baea661d5c65846409923bd72 |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test 'yank prepare'.
"""
#===========================================================... | andrrizzi/yank | Yank/tests/test_prepare.py | Python | mit | 3,523 | [
"Amber",
"Gromacs"
] | f7375bef3c85dd7f0ed271739319da9022e4da56154938a734a1eb2ccdc39eed |
"""
.. module:: compute_season_stati_score_spatial_distribution.py
:synopsis: This programme is to calculate te various statistical scores
corresponding to each lat-long location,(i.e spatially).
Example:
Let 'TS'(Threat Score) is a statistical score,
we are calculate this spatially.
Writ... | arulalant/mmDiagnosis | diagnosis1/diagnosis/compute_season_stati_score_spatial_distribution.py | Python | gpl-3.0 | 20,517 | [
"NetCDF"
] | 2d90bc4a8bb21d6a09208e804069b5f88086df591d5581ade020cedb7ae17896 |
#!/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.
'''Unit tests for grd_reader package'''
from __future__ import print_function
import os
import sys
if __name__ == '__main__':
s... | endlessm/chromium-browser | tools/grit/grit/grd_reader_unittest.py | Python | bsd-3-clause | 12,542 | [
"xTB"
] | 5171a15018d4c2103aac7fecb4350c59a231bb77fc82b0b05d0bf90dfa17764d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
#
# Project: wb97xdDsC-optim
# FileName: make_input
# Creation: Jul 14, 2015
#
"""Building Gamess input file for single point.
Building Gamess input file for single point used in the wb97x-dDsC optimization.
The input will be created reading an xyz file where the comm... | grhawk/wb97xdDsC-optim | src/master/make_input.py | Python | gpl-2.0 | 7,794 | [
"GAMESS"
] | 29fd6e2de22fb13c50058b9a38ad29ed6c5520cad126f75ee8ff99e88a3dbb5b |
# Original Author: Travis Oliphant 2002
# Bug-fixes in 2006 by Tim Leslie
from __future__ import division, print_function, absolute_import
import numpy
from numpy import asarray, tan, exp, ones, squeeze, sign, \
all, log, sqrt, pi, shape, array, minimum, where, random
from .optimize import Result, _check_unknown_... | kmspriyatham/symath | scipy/scipy/optimize/anneal.py | Python | apache-2.0 | 23,219 | [
"Gaussian"
] | 9dc531565173e4b48c305ed88d8d9c116a69c07b293f472890581d5938b62eca |
"""Amber Electric Coordinator."""
from __future__ import annotations
from datetime import timedelta
from typing import Any
from amberelectric import ApiException
from amberelectric.api import amber_api
from amberelectric.model.actual_interval import ActualInterval
from amberelectric.model.channel import ChannelType
f... | lukas-hetzenecker/home-assistant | homeassistant/components/amberelectric/coordinator.py | Python | apache-2.0 | 4,238 | [
"Amber"
] | 445b56332a3de6147be8da74a1e3cc99b666a554de373653b25f8139aab4b13a |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010-2013 The Orca Team
#
# 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... | h4ck3rm1k3/orca-sonar | src/orca/guilabels.py | Python | lgpl-2.1 | 38,952 | [
"ORCA"
] | 9dd2a3836c92f0e111b9f019e666cc25879ae2d2c0bc2b97afddf02cb6f4449a |
#!/usr/bin/env python
"""Detector that can be used to experiment with different correlation peak
interpolation methods.
Example usage:
python -m "thrifty.experimental.detect_xcorr_interpol" \
--method autocorr rx.card -o rx.data
"""
from __future__ import print_function
import argparse
from thrifty... | swkrueger/Thrifty | thrifty/experimental/detect_xcorr_interpol.py | Python | gpl-3.0 | 2,795 | [
"Gaussian"
] | 37eb1c8269c2725b8c77b425db6125a6a344a5ed9a68e9f15f70c5e6e0ac76cb |
# FreeCAD TemplatePyMod module
# (c) 2010 Werner Mayer LGPL
"""
The module can be executed with:
FreeCAD -P <path_to_file> Automation.py
FreeCADCmd -P <path_to_file> Automation.py
"""
import FreeCAD, Part
def makeSnapshotWithGui():
from PySide import QtGui
import FreeCADGui
def getMainWindow():
... | marcoitur/FreeCAD | src/Mod/TemplatePyMod/Automation.py | Python | lgpl-2.1 | 2,290 | [
"CRYSTAL"
] | 1b6b407df413362e943190957e3cec819fb685b73da1785f7d74d5b27fed7376 |
#### PATTERN | GRAPH ###############################################################################
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
####################################... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/pattern/graph/__init__.py | Python | gpl-3.0 | 65,664 | [
"VisIt"
] | 9a3e532b78496c6ce22e77b926268c362864eee75f8147bafb940c04e7f3a31e |
from __future__ import annotations
import pytest
import scitbx.matrix
from cctbx import sgtbx
from cctbx.sgtbx import bravais_types
from dxtbx.model import Crystal, Experiment, ExperimentList
from dials.algorithms.indexing import assign_indices, non_primitive_basis
from dials.array_family import flex
@pytest.mark.... | dials/dials | tests/algorithms/indexing/test_non_primitive_basis.py | Python | bsd-3-clause | 1,981 | [
"CRYSTAL"
] | fa04a73e69aef23fe8f3059843d1fbae3502f70b327d16eca9e28a453651c32b |
from modeller import *
from modeller.scripts import complete_pdb
from modeller.optimizers import conjugate_gradients
env = environ()
env.io.atom_files_directory = ['../atom_files']
log.verbose()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
# Read in the model
mdl... | bjornwallner/proq2-server | apps/modeller9v8/examples/python/pseudo_atoms.py | Python | gpl-3.0 | 1,313 | [
"Gaussian"
] | b7fb885d0bc7f020212628979116d0a0f0f0f1d4cebb28a2819337b3c0b0ec66 |
#!/usr/bin/env ipython
from pylab import *
import numpy as np
import console_colors as ccl
from scipy.io.netcdf import netcdf_file
import os
import matplotlib.patches as patches
import matplotlib.transforms as transforms
class gral:
def __init__(self):
self.name='name'
#+++++++++++++++++++++++++++++++++++... | jimsrc/seatos | mixed/figs/sheaths.paper/src/splited.py | Python | mit | 8,181 | [
"NetCDF"
] | b4e6b716e33c3c54cd93beb5c1727904db305187add2e09b1b171833507a069b |
# Copyright 2003-2008 by Leighton Pritchard. 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.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# ... | bryback/quickseq | genescript/Bio/Graphics/GenomeDiagram/_Colors.py | Python | mit | 9,024 | [
"Biopython"
] | 7674047cb095e071e658b8a4fe8c802fa76a89fa7ce98230ac288094375bd2e6 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Tim Moore
# Contributors:
#
# MDTraj is free software: you can... | ctk3b/mdtraj | mdtraj/tests/test_hoomdxml.py | Python | lgpl-2.1 | 1,910 | [
"MDTraj"
] | 634760811f057350b55ff43d0405b67b212de40628766113af37c8bcd343b941 |
import urllib
from bs4 import BeautifulSoup
import pafy
import random
import os
import datetime
# import vlc
# import subprocess
# from properties import *
# from sys import executable
# DEFAULT FUNCTIONS
# TODO: Implement DialogFlow API
def getweather(assistant, place):
weather_url = "http://www.bing.com/searc... | SPARC-Auburn/Lab-Assistant | assistant/archived/DefaultSuite-Archived.py | Python | apache-2.0 | 6,593 | [
"exciting"
] | 8cbf191b6ad330b48273b3e5db1f87ffa757915199a4ef9b52b0fe79d1c4e979 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_pca.py | Python | gpl-2.0 | 8,268 | [
"MDAnalysis"
] | 5a2a7c7151f8f9cc8edcb9e3566c9d4e2b36491428e55caf02578312018487d9 |
import os
import sys
import tempfile
import subprocess
from mock import patch
from contextlib import contextmanager
from shutil import rmtree
this_dir = os.path.dirname(__file__)
sys.path.insert(0, os.path.join(this_dir, '..'))
sys.path.insert(0, os.path.join(this_dir, '..', '..'))
BUILD_SCRIPT = os.path.join(this_dir... | Amber-MD/ambertools-conda-build | conda_tools/test/test_build_all.py | Python | mit | 2,194 | [
"Amber"
] | ff2e330e7ee6f79fe583383aeb7091bc4678c41ace44a9ad14cfda411aa7c168 |
"""
Piezo sensitivity analysis module.
"""
import warnings
import numpy as np
from monty.dev import requires
import pymatgen.io.phonopy
from pymatgen.core.tensors import Tensor
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
try:
from phonopy import Phonopy
from phonopy.harmonic import dynm... | vorwerkc/pymatgen | pymatgen/analysis/piezo_sensitivity.py | Python | mit | 27,582 | [
"phonopy",
"pymatgen"
] | 150cf08788da41c6d04972a6640c169f8a7dbc41dc3d9894d2045e71053548aa |
import sys
from time import time, ctime
import numpy as np
from math import sqrt, pi
from datetime import timedelta
from ase.units import Hartree, Bohr
from gpaw import GPAW, extra_parameters
from gpaw.utilities import unpack, devnull
from gpaw.utilities.blas import gemmdot, gemv
from gpaw.mpi import world, rank, size,... | robwarm/gpaw-symm | gpaw/response/base.py | Python | gpl-3.0 | 21,011 | [
"ASE",
"GPAW"
] | 5a4fd6dcc255deecadcf36e370f07d1fd7941bb2132e340aba3783d88059767c |
### This code came from the google sample code ###
### No value added here other than turning on caching. ###
import httplib2
import os
import sys
from googleapiclient.discovery import build
from googleapiclient.errors import HttpError
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file i... | fmoody/playlister | google_auth_code.py | Python | gpl-2.0 | 2,599 | [
"VisIt"
] | ec27785058753e307379b6f008d6c1f6def88aecddd251016245db6c020915ae |
"""
Records who we trust to sign feeds.
Trust is divided up into domains, so that it is possible to trust a key
in some cases and not others.
@var trust_db: Singleton trust database instance.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall i... | rammstein/0install | zeroinstall/injector/trust.py | Python | lgpl-2.1 | 9,330 | [
"VisIt"
] | 40556d4c9b31439205eb2fa599c52c642c79259f69ffcd8375eeed8ff63f3122 |
from proteus import *
from proteus.default_p import *
from math import *
"""
2D, Linear advection of a guassian
"""
## \page Tests Test Problems
# \ref la_gauss_2d_p.py "Linear advection of a Gaussian"
# \addtogroup test
#
# \file la_gauss_2d_p.py
# @{
#
##\ingroup test
# \brief Conservative linear advection of... | erdc/proteus | proteus/tests/dg/la_gauss_2d_p.py | Python | mit | 3,312 | [
"Gaussian"
] | 25cf8bbf7ba984da0e2701b2275325641733d1d27404806e18b9c4eaf9e92736 |
"""
Set of utilities to retrieve Information from proxy
"""
import base64
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.X509Chain import X509Chain # pylint: disable=import-error
from DIRAC.Core.Security.VOMS import VOMS
from DIRAC.Core.Security import Locations
fr... | fstagni/DIRAC | Core/Security/ProxyInfo.py | Python | gpl-3.0 | 5,830 | [
"DIRAC"
] | b4249ef6018e51fc6f2f26ca33fca30ceaf50fdf80f4f8021df24862548bf182 |
import cPickle as pickle
import contextlib
import os.path
import tempfile
from cStringIO import StringIO
import numpy as np
import pandas as pd
from xray import Dataset, open_dataset, backends
from . import TestCase, requires_scipy, requires_netCDF4, requires_pydap
from test_dataset import create_test_data
try:
... | takluyver/xray | test/test_backends.py | Python | apache-2.0 | 9,719 | [
"NetCDF"
] | bdc5686d212c4c54dd913aa689563f93e4eb943d3f73ece5b7ba1e3069d6e8bd |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Module to test fitting routines
"""
from __future__ import (absolute_import, unicode_literals, division,
print_function)
import os.path
import numpy as np
from numpy import linalg
from numpy.testing.utils import assert_raise... | tbabej/astropy | astropy/modeling/tests/test_fitters.py | Python | bsd-3-clause | 24,041 | [
"Gaussian"
] | bfa6e594c186fba4f810d7e27c3b46522ef7b1d8c6af4358a1ca9bf44578e3b4 |
#!/bin/env python
#
# Copyright 2007-2009 Fedora Unity Project (http://fedoraunity.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 Foundation; version 2, or (at your option) any
# later version.
#
# ... | sanjayankur31/pyjigdo | pyjigdo_interface.py | Python | gpl-2.0 | 15,194 | [
"VisIt"
] | 8ffbf54c917a9d22c0aae6c2fdc910d084dd148160036c52740217d3fe7d239d |
""" This is a test of the chain
ReportsClient -> ReportsGeneratorHandler -> AccountingDB
It supposes that the DB is present, and that the service is running.
Also the service DataStore has to be up and running.
this is pytest!
"""
# pylint: disable=invalid-name,wrong-import-position
import datetime
... | andresailer/DIRAC | tests/Integration/AccountingSystem/Test_ReportsClient.py | Python | gpl-3.0 | 2,062 | [
"DIRAC"
] | 7bdfeb18a37d946caceb48074828a762ad86672c4093f80e89a533086d99643f |
## Description: utility functions used while loading NeuroML L1,2,3 files.
## Version 1.0 by Aditya Gilra, NCBS, Bangalore, India, 2011 for serial MOOSE
## Version 1.5 by Niraj Dudani, NCBS, Bangalore, India, 2012, modified for parallel MOOSE
## Version 1.6 by Aditya Gilra, NCBS, Bangalore, India, 2012, minor changes f... | subhacom/moose-core | python/moose/neuroml/utils.py | Python | gpl-3.0 | 13,912 | [
"MOOSE"
] | 7562cb362440e51e4de8abc1d0109bc6f870e9fb697a269f43e5a2c045f65a89 |
# copyright 2003-2013 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of logilab-astng.
#
# logilab-astng is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as publis... | tlksio/tlksio | env/lib/python3.4/site-packages/logilab/astng/utils.py | Python | mit | 8,300 | [
"VisIt"
] | 74f2b87163f42619d6eb1f6775c25199da9ed61e762a84ac3e107c813cb9fb4c |
from ..utils import *
##
# Minions
# Dalaran Aspirant
class AT_006:
inspire = Buff(SELF, "AT_006e")
AT_006e = buff(spellpower=1)
# Spellslinger
class AT_007:
play = Give(ALL_PLAYERS, RandomSpell())
# Coldarra Drake
class AT_008:
update = Refresh(FRIENDLY_HERO_POWER, {GameTag.HEROPOWER_ADDITIONAL_ACTIVATIONS:... | smallnamespace/fireplace | fireplace/cards/tgt/mage.py | Python | agpl-3.0 | 762 | [
"BLAST"
] | 2cf1613b6e3d89e99113281da8d6b0aefbcf62add4f8d8b30dd352f0a3ff9c83 |
"""Some test functions for bivariate interpolation.
Most of these have been yoinked from ACM TOMS 792.
http://netlib.org/toms/792
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from matplotlib.externals import six
from matplotlib.externals.six.moves i... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/matplotlib/delaunay/testfuncs.py | Python | mit | 21,215 | [
"Gaussian"
] | 47a9c92cd2d67a970eeca6c953f477f72a6349d6eb4eef95c2c0c9f801615577 |
# -*- coding: utf-8 -*-
#
# INDRA documentation build configuration file, created by
# sphinx-quickstart on Tue Jun 23 16:42:17 2015.
#
# 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... | pvtodorov/indra | doc/conf.py | Python | bsd-2-clause | 10,872 | [
"Pybel"
] | 986f3c6fa1aa6540efc5d8192135c321f26910c830a12ab100f0537fdb5aadb8 |
"""
======================================
Sparse inverse covariance estimation
======================================
Using the GraphLasso estimator to learn a covariance and sparse precision
from a small number of samples.
To estimate a probabilistic model (e.g. a Gaussian model), estimating the
precision matrix, t... | thilbern/scikit-learn | examples/covariance/plot_sparse_cov.py | Python | bsd-3-clause | 5,078 | [
"Gaussian"
] | 9281d9897a4020a86fd21c27a692b5eb9407e483b468995c3f4032a2ed708d47 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=1) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=1) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list of fil... | xymz/meron | mimetypes.py | Python | mit | 21,050 | [
"NetCDF"
] | 5494f375a4ce02e57ccf170bfea36f0ea01a0f48a9854a71fed3503a806f2335 |
#ImportModules
import ShareYourSystem as SYS
import operator
#Definition of a brian structure
MyNetworker=SYS.NetworkerClass(
).array(
["Networkers","Connecters"],
[
['A','B'],['1','2']
],
[SYS.NetworkerClass,SYS.ConnecterClass],
).update(
[
(
'<Networkers>ANetworker/Dis_<Connecters>',
[
... | Ledoux/ShareYourSystem | Pythonlogy/draft/Teamers_Networker/01_ExampleDoc.py | Python | mit | 925 | [
"Brian"
] | 8b111191312c51471aedadd0ae96c2488c5bd0fa246b1b81e490e5ad193ccf62 |
from ase.test import NotAvailable
from ase.calculators.gaussian import Gaussian
if Gaussian().get_command() is None:
raise NotAvailable('Gaussian required')
from ase.tasks.main import run
atoms, task = run('gaussian molecule O2 O')
atoms, task = run('gaussian molecule O2 O -s')
ae = 2 * task.data['O']['energy']... | conwayje/ase-python | ase/test/gaussian/gaussian_cmdline.py | Python | gpl-2.0 | 388 | [
"ASE",
"Gaussian"
] | 16a0ce63f4e75cd3b8d797a9e09e835cf94f3bf8ecf2f3c8e26b8b6f6a3564de |
#!/usr/bin/env python
"""
DataCollectingParser subclasses ctypesparser.CtypesParser and builds Description
objects from the CtypesType objects and other information from CtypesParser.
After parsing is complete, a DescriptionCollection object can be retrieved by
calling DataCollectingParser.data().
"""
import ctypespa... | pombredanne/ctypesgen | ctypesgencore/parser/datacollectingparser.py | Python | bsd-3-clause | 12,623 | [
"VisIt"
] | 8118793ee68d4a80aa280de0c18ad31b23668ef481f563d839008897bd0c34a1 |
r"""wamp is a module that provide classes that extend any
WAMP related class for the purpose of vtkWeb.
"""
import inspect, types, string, random, logging, six, json, re, base64, time
from threading import Timer
from twisted.web import resource
from twisted.python import log
from twisted.internet... | keithroe/vtkoptix | Web/Python/vtk/web/wamp.py | Python | bsd-3-clause | 15,475 | [
"VTK"
] | c5cfbc1c73d4ac60a2b3bf5df92700a263da2cbc1a7f74c50d8a158d20bbb85d |
"""
Boring json which is just a basic
dump of the resource into json format.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from ripozo.adapters import AdapterBase
import json
_CONTENT_TYPE = 'application/json'
... | chenokay/ripozo | ripozo/adapters/basic_json.py | Python | gpl-2.0 | 2,295 | [
"exciting"
] | 7f208346cd9932eecf27a66c9d32f2e66e67943dbabd19bd65d7a09cee2c8915 |
# Copyright (c) 2006-2013 Regents of the University of Minnesota.
# For licensing terms, see the file LICENSE.
# Request object; contains Apache request object and other handy stuff.
try:
from mod_python import apache
import mod_python.util
except ImportError:
pass # script is being run locally
import hashli... | lbouma/Cyclopath | pyserver/gwis/request.py | Python | apache-2.0 | 44,702 | [
"BLAST",
"Galaxy"
] | 782b12439ad2da29dde19a252dfc7e9569953a1bb583c44cfe2804fa65cb8818 |
# -*- coding: utf-8 -*-
#
# one-neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
... | gewaltig/cython-neuron | pynest/examples/one-neuron.py | Python | gpl-2.0 | 1,060 | [
"NEURON"
] | 491a6006998a1ef5909bddf8d647a6d36793205298932301a16859ff0c0242a8 |
#* 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.... | harterj/moose | python/peacock/Input/CheckInputWidget.py | Python | lgpl-2.1 | 2,774 | [
"MOOSE"
] | 774c2092cd6960190dee626813e51b75ba0fb4d69f9bd4ccf2d4b559742cb50e |
''' Create rst documentaiton of the examples directory.
This uses screenshots in the screenshots_dir
(currently doc/sources/images/examples) along with source code and files
in the examples/ directory to create rst files in the generation_dir
(doc/sources/examples) gallery.rst, index.rst, and gen__*.rst
'''
import ... | arlowhite/kivy | doc/gallery.py | Python | mit | 11,144 | [
"exciting"
] | 969b0f25590ed44e86bb20f4e2084501ab286bd24692fb6f59e20c588d685db7 |
# Copyright (C) 2020 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/file_IO.py | Python | bsd-3-clause | 61,312 | [
"VASP",
"phonopy"
] | 34d4b748307f31a578ccaac27480d99d24d5cd03fb1bc22113d5480e86b681ae |
# -*- coding: utf-8 -*-
import os
import time
import shutil
from datetime import datetime
import bisect
import tempfile
import itertools
from math import sqrt
import numpy as np
import pandas as pd
import netCDF4
import pytz
from pyaxiom.netcdf import EnhancedDataset, EnhancedMFDataset
from rtree import index
from wm... | brianmckenna/sci-wms | wms/models/datasets/rgrid.py | Python | gpl-3.0 | 20,561 | [
"NetCDF"
] | a4ba2cfa30dc5ad2c5e3c3754b722b882f91babd2db65f2a4c4f68c5aa05b40e |
# -*- coding: utf-8 -*-
# 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 ve... | FedoraScientific/salome-hexablock | doc/test_doc/cutHexa/cut_hexa.py | Python | lgpl-2.1 | 1,457 | [
"VTK"
] | 6cfadd3f82eaef23f339f710285f685ae825f63ac209d6313d6d286fae4b3350 |
##############################################################################
#
# Author: Alejandro Molina-Sanchez
# Run real-time simulations with yambo
#
# Warning: Real-time simulations requires several data folders for running
# properly. Before using this scripts compulsively is recommended
# to understand the d... | henriquemiranda/yambopy | tutorial/si/kbe-spectra.py | Python | bsd-3-clause | 1,775 | [
"Yambo"
] | 5b3130992bcb8d1348bad4e4e2be3537162206a7fb15591e09bf41fca0c707a6 |
#!/usr/bin/env python
"""
Ben Payne
ben.is.located@gmail.com
Yoga graph
This is a library of functions used by the main YogaGraph program
This file contains no graph data
This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.
To view a copy of this license, visit http://cr... | bhpayne/yoga_graph | src/yoga_lib.py | Python | gpl-2.0 | 6,541 | [
"VisIt"
] | f41374f26b11c3b564e86d9d267975ab68b8d9b5056eff79dc6d4dcb87ae6dc3 |
#!/usr/bin/env python
"""
refguide_check.py [OPTIONS] [-- ARGS]
Check for a Scipy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
Example of usage::
$ python refguide_check.py optimize
Note that this is a helper script to be able to check if things ar... | WarrenWeckesser/scipy | tools/refguide_check.py | Python | bsd-3-clause | 31,826 | [
"Gaussian"
] | e53e8e5c49bf4ba9387108ec8124622d25f4e8ea526f20a49c38659775422445 |
#########################################################
#
# DO NOT EDIT THIS FILE. IT IS GENERATED AUTOMATICALLY. #
# PLEASE LOOK INTO THE README FOR MORE INFORMATION. #
#
#########################################################
# coding: utf-8
# # Image Loading and Preprocessing
#
# In this tutorial we're g... | Yangqing/caffe2 | caffe2/python/tutorials/py_gen/Image_Pre-Processing_Pipeline.py | Python | apache-2.0 | 25,119 | [
"TINKER"
] | b305fdee59e7dab521f731cc394640a65801c12ebf712caf55bcee3cbd8fb579 |
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of cha... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/qm/gaussian.py | Python | mit | 21,266 | [
"Gaussian",
"MOPAC",
"cclib"
] | ab4676492c0dab364e08c2de31a8f61b1107189cb952483d821cde06e9f9c79f |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.2
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | bearstech/ansible | lib/ansible/modules/network/avi/avi_gslbgeodbprofile.py | Python | gpl-3.0 | 4,055 | [
"VisIt"
] | a9e17eb46a0f6ca981c9ef9e68bc3feb5bef06c382cd5e3880a50b95365017ac |
#!/usr/bin/env python
"""
This is a script to converge the geometry of a system
"""
from __future__ import division
__author__ = "Stephen Dacek"
__version__ = "0.1"
__maintainer__ = "Stephen Dacek"
__email__ = "sdacek@mit.edu"
__status__ = "Beta"
__date__ = "11/3/13"
import logging
from custodian.custodian import ... | specter119/custodian | custodian/cli/converge_geometry.py | Python | mit | 3,807 | [
"VASP",
"pymatgen"
] | aa62e56548667c06816212787bea1f2b955dded562c806b35934c0ae9d4c0395 |
# SPDX-License-Identifier: Apache-2.0
#
# Copyright (C) 2015, ARM Limited and contributors.
#
# 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
#
# ... | ARM-software/lisa | lisa/analysis/functions.py | Python | apache-2.0 | 32,153 | [
"VisIt"
] | 7a8f9739112af853f91c0dca8a8dee8061596c93a22eca3d0e6c6d9113eb22e7 |
# Copyright 2017 The Meson development team
# 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 ... | mesonbuild/meson | mesonbuild/dependencies/__init__.py | Python | apache-2.0 | 9,768 | [
"NetCDF"
] | a055966b60b9afc880e38dd55794b4cedd5638d3b6ca76ca0bef2c2adba556bb |
################################################################################
#
# Author: Bastian Knippschild (B.Knippschild@gmx.de)
# Date: October 2014
#
# Copyright (C) 2014 Bastian Knippschild
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General P... | knippsch/LueschersZetaFunction | zeta.py | Python | gpl-3.0 | 13,244 | [
"Gaussian"
] | ac5dd52704357692bbc8d3502315285a515e2f811d1a95cdd14bc702e4e90439 |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2005 CCLRC Daresbury Laboratory
#
# 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 ... | alexei-matveev/ccp1gui | interfaces/mmtools.py | Python | gpl-2.0 | 5,076 | [
"CHARMM"
] | 1105b185f7a36df53629d276138ac95f055e8b7ffba86e646a39a8be16aebcd0 |
# ===========================================================================
# Copyright 2013 University of Limerick
#
# This file is part of DREAM.
#
# DREAM 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 Founda... | jerome-nexedi/dream | dream/simulation/Queue.py | Python | gpl-3.0 | 17,117 | [
"VisIt"
] | 9666f205ff14edf11649c069e0fd6dd24354f553bb9fce6946dd7f256d864102 |
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2004/2005 James Casbon. 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.
#
# Changes made by ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SCOP/__init__.py | Python | gpl-2.0 | 32,657 | [
"Biopython"
] | b9f9a872f69e582ee74154eb320ea91403c825a8223ea2863b920e5bce70cec0 |
#Brian Windle
import yaml
import json
yaml_file = 'myyaml.yml'
json_file = 'myjson.json'
file = open('/home/bwindle/device', 'r')
device = list(file.read().split())
with open('/home/bwindle/detail', 'r') as document:
detail = {}
for line in document:
x = line.split(",")
a=x[0]
b=x[1... | bkwin66/pyclass | week1/ex6.py | Python | apache-2.0 | 552 | [
"Brian"
] | 02f2f1cceacaab5ee87b3411cdb572c663d6ecbcd2494c8de99fa12733501816 |
# coding=utf8
# 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.
"""Collection of subprocess wrapper functions.
In theory you shouldn't need anything else in subprocess, or this module failed.
"""
import... | chinmaygarde/depot_tools | subprocess2.py | Python | bsd-3-clause | 15,980 | [
"VisIt"
] | a18d4d522e5989a361ab8b3470aeaa4e9f197ffaa259aca6343f4c95b116bb1b |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from textwrap import dedent
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.courseware import ... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 9,654 | [
"VisIt"
] | 1d95edd6207490bf81ef4f7f8d83c5dc2e66e11c0ef4a5135162056d76770f3e |
from nose.tools import assert_equal, assert_not_equal #@UnresolvedImport
import copy
from whoosh import fields, query
from whoosh.compat import u
from whoosh.filedb.filestore import RamStorage
from whoosh.qparser import QueryParser
from whoosh.query import (And, AndMaybe, ConstantScoreQuery, Every, DateRange,
... | mzdaniel/oh-mainline | vendor/packages/whoosh/tests/test_queries.py | Python | agpl-3.0 | 12,920 | [
"VisIt"
] | e807451012edf90a378189270cada306ecf609300df6dd0fd807c9a7b317a074 |
#!/usr/bin/env python
#! -*- coding: utf-8 -*-
###
# Copyright (c) Rice University 2012-13
# This software is subject to
# the provisions of the GNU Affero General
# Public License version 3 (AGPLv3).
# See LICENCE.txt for details.
###
"""
This is to test the user service once it is up and running on http.
We *sh... | jbarmash/rhaptos2.user | rhaptos2/user/test_client.py | Python | agpl-3.0 | 1,721 | [
"Brian"
] | 9d67d017c008bd798c02a7f495c33bbfffb91cb74969f6556e9ba80a74053bed |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the courseware unit bookmarks.
"""
import json
from unittest import skip
import requests
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common import BASE_URL
fr... | lduarte1991/edx-platform | common/test/acceptance/tests/lms/test_bookmarks.py | Python | agpl-3.0 | 23,481 | [
"VisIt"
] | 161ad193e37905df6d261954a0eeed20b087c398581fd903091659a2f1fa2155 |
import numpy as np
from scipy.stats import norm as ndist
from ...tests.instance import gaussian_instance
from ..screening import marginal_screening
from ..lasso import lasso
def test_marginal(n=500,
p=50,
s=5,
sigma=3,
rho=0.4,
... | selective-inference/selective-inference | selectinf/randomized/tests/test_marginal_screening.py | Python | bsd-3-clause | 7,138 | [
"Gaussian"
] | 9ac981222361a708faaaa45d329f7d99175b7e6fff7af60bc0f1f105ce3dde57 |
#Copyright ReportLab Europe Ltd. 2000-2004
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/pdfbase/cidfonts.py
#$Header $
__version__=''' $Id: cidfonts.py,v 1.1 2006/05/26 19:19:46 thomas Exp $ '''
__doc__="""CID (Asian multi-byte) font ... | tschalch/pyTray | src/lib/reportlab/pdfbase/cidfonts.py | Python | bsd-3-clause | 15,413 | [
"Brian"
] | d8c1bf5ad4d7a98bb62bbd3b7520163f6792e421389ab454d2646fd5029c23f1 |
#! /usr/bin/env python3
# findlinksto
#
# find symbolic links to a path matching a regular expression
import os
import sys
import re
import getopt
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], '')
if len(args) < 2:
raise getopt.GetoptError('not enough arguments', None)
... | andreparrish/python-for-android | python3-alpha/python3-src/Tools/scripts/findlinksto.py | Python | apache-2.0 | 1,072 | [
"VisIt"
] | 80adee14b913f652e3640dbe1680b3c1483775eac8d264d28eefa297abf89cc5 |
#!/usr/bin/python
#
# convert a blastn outfmt=6 file to BED6 format.
import sys
import datetime
if len(sys.argv)!=2:
print "blast2bed.py <blast-file>"
sys.exit(0)
filename = sys.argv[1]
f = open(filename, 'rU')
for line in f:
chunks = line.split('\t')
name = chunks[0]
chromosome = chunks[1]... | carnegie-dpb/biotools | blast2bed.py | Python | gpl-2.0 | 661 | [
"BLAST"
] | 354c5a7aa8b8ab77274bed75692d2177cbc3b943e493b9289b99691b7acf298c |
import logging
from cl.donate.paypal import process_paypal_payment
from cl.donate.forms import DonationForm, UserForm, ProfileForm
from cl.donate.stripe_helpers import process_stripe_payment
from cl.users.utils import create_stub_account
from django.conf import settings
from django.contrib.auth.models import User
from... | brianwc/courtlistener | cl/donate/views.py | Python | agpl-3.0 | 9,731 | [
"Brian"
] | 025a83be90da53bd20a5c95d8b4c0fc0bf9947ccb87b7a55111912a881aaacb4 |
""" Python version of getting started tutorial.
Please see https://github.com/snoplusuk/echidna/wiki/GettingStarted or the
jupyter notebook form of this tutorial for further details.
This script:
* Creates :class:`echidna.core.spectra.Spectra` instance
* Fills `Spectra`
* Plots `Spectra`
* Applies cuts and smears... | arushanova/echidna | echidna/scripts/tutorials/getting_started.py | Python | mit | 15,553 | [
"Gaussian"
] | 2d3d84b42ae1a109eb0414f7576c07254bb67cf735bef3f21edc079eceeada3e |
import h5py
import numpy as np
from scipy.optimize import curve_fit
from upho.analysis.functions import FittingFunctionFactory
from upho.irreps.irreps import extract_degeneracy_from_ir_label
__author__ = 'Yuji Ikeda'
class SFFitter:
def __init__(self, filename='sf.hdf5', name='gaussian'):
self._name = na... | yuzie007/upho | upho/phonon/sf_fitter.py | Python | mit | 5,575 | [
"Gaussian"
] | 171ced1e08e71c7f423ccbf9c2c84719d85b3290ded3da5fca7b7a88b25af625 |
#!/usr/bin/env python
"""Run signal-to-reference alignments
"""
from __future__ import print_function
import pandas as pd
from signalAlignLib import *
from alignmentAnalysisLib import CallMethylation, get_first_sequence
from variantCallingLib import scan_for_proposals
from multiprocessing import Process, Queue, curren... | ArtRand/signalAlign | scripts/bonnyDoon.py | Python | mit | 11,702 | [
"BWA"
] | 53f4ffcfa6112d276041fba3e168b31d33c921291a1c5b368658482112fc86c2 |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
ReconstructLine
QGIS tool to reconstruct linear features from points
The main idea of the processing is to construct Hamiltonian path.
To do it we use 1-d Self Organising Map. It allows:
order data points
co... | nextgis/ReconstructLine | src/connector.py | Python | gpl-2.0 | 8,060 | [
"Gaussian"
] | 3e57e8a68a9182010cb974c990dc6ac9b66a391716e7e41c226178ea7cb4af32 |
""" The mind is a service the distributes "task" to executors
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pprint
import six
from DIRAC import gLogger
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR, isReturnStructure
from DIRAC.Co... | yujikato/DIRAC | src/DIRAC/Core/Base/ExecutorMindHandler.py | Python | gpl-3.0 | 11,068 | [
"DIRAC"
] | d0c682ad1aac9f2a0cc5d9fbcb3776f16cb760cef735418cd74041f57be738b3 |
# 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... | szha/mxnet | python/mxnet/ndarray/numpy_extension/_op.py | Python | apache-2.0 | 61,890 | [
"Gaussian"
] | 712b35362408b41f1b832756802093d255c8020e5e5e15914e9607afbccea202 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.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, or
# (at your option) an... | ganeshnalawade/ansible | lib/ansible/playbook/conditional.py | Python | gpl-3.0 | 10,815 | [
"VisIt"
] | b50e5bfd512b577dc0f84f781bb1d51e5894f2d3c04b5dc53699c5487d30afe2 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2009-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | src/cclib/parser/ccopen.py | Python | lgpl-2.1 | 3,930 | [
"ADF",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 276f21c7ea5deff793edc9b545a83ed1ab0e86b568f33fbd2a3d4e18e6956efc |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2020, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | mrcslws/nupic.research | src/nupic/research/frameworks/vernon/mixins/noise_robustness_test.py | Python | agpl-3.0 | 5,346 | [
"Gaussian"
] | 8543e7d2935788b7093691e5ea8d720a7109feaecf9a5eb387c415db51e2d51d |
# Copyright 2017 Google Inc.
#
# 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 wri... | google/tangent | tests/test_transformers.py | Python | apache-2.0 | 2,880 | [
"VisIt"
] | aff7cd6ac5edfbc8a9fe2b926f81b1ed4e57c6b9302271f5a7374e7c23cc4d07 |
"""
Acceptance tests for the certificate web view feature.
"""
from ..helpers import UniqueCourseTest, EventsTestMixin
from nose.plugins.attrib import attr
from ...fixtures.course import CourseFixture
from ...fixtures.certificates import CertificateConfigFixture
from ...pages.lms.auto_auth import AutoAuthPage
from ...p... | kamalx/edx-platform | common/test/acceptance/tests/lms/test_certificate_web_view.py | Python | agpl-3.0 | 3,336 | [
"VisIt"
] | dc3d6a405197104c5d6d937bc5b2e62c118218bd72b07c79e1bc1b796c7811f0 |
# -*- coding: utf-8-*-
import re
import facebook
WORDS = ["FACEBOOK", "NOTIFICATION"]
def handle(text, mic, profile):
"""
Responds to user-input, typically speech text, with a summary of
the user's Facebook notifications, including a count and details
related to each individual notificat... | benhoff/plugins | listenerplugins/Notifications.py | Python | gpl-3.0 | 1,744 | [
"VisIt"
] | ae9ac9aca773144533435c25422eb8b82fcf285f9a16e46f4f96765f08549ab7 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/io/_exception.py | Python | bsd-3-clause | 2,595 | [
"scikit-bio"
] | 68dfc3958a70b5d38d4f91f57e82bb24e6e8aa9a3f9ca52101ee92847c348fd0 |
# 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 | testsuite/python/random_pairs.py | Python | gpl-3.0 | 3,581 | [
"ESPResSo"
] | 0536b1e286306b172f1e14f5eacdb276f92a25e887b4a00117dfacb5291a7874 |
from __future__ import print_function, absolute_import
from pymatgen.core.structure import Molecule
from monty.json import MSONable
import re
import os
from monty.itertools import chunks
from monty.io import reverse_readline
__author__ = 'Xin Chen, chenxin13@mails.tsinghua.edu.cn'
def is_numeric(s):
"""
Re... | matk86/pymatgen | pymatgen/io/adf.py | Python | mit | 31,523 | [
"ADF",
"Gaussian",
"NWChem",
"pymatgen"
] | 81cd0be3eab6bfd6a9ff3fd09ae3015dd9e861000aeb9c02c66ec378c38ca273 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/sequence/_genetic_code.py | Python | bsd-3-clause | 19,481 | [
"scikit-bio"
] | f2e54d3a9b023ef89877c7f219cf927ac83140eea3a6edf256958292d4604952 |
# sql/visitors.py
# Copyright (C) 2005-2015 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 express... | odubno/microblog | venv/lib/python2.7/site-packages/sqlalchemy/sql/visitors.py | Python | bsd-3-clause | 9,943 | [
"VisIt"
] | ec2375d309f6ae03eda2a622bd833b9486d2246210034ca2577c2cd4687edbbf |
"""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... | Cuuuurzel/KiPyCalc | sympy/polys/tests/test_polytools.py | Python | mit | 105,808 | [
"Gaussian"
] | 89f75ce42d56474844e7d340bc6a8a9aa6380559d4b150244459f1ad09de048f |
# Data sources
database(
#overrides RMG thermo calculation of RMG with these values.
#libraries found at http://rmg.mit.edu/database/thermo/libraries/
#if species exist in multiple libraries, the earlier libraries overwrite the
#previous values
thermoLibraries = ['KlippensteinH2O2','primaryThermoLibrary','DFT_... | pierrelb/RMG-Py | examples/rmg/commented/input.py | Python | mit | 9,925 | [
"Gaussian",
"MOPAC"
] | dc9d7de958b15c500f648301bb3d0b798d4f68f4cfbd01edc6e146374d885045 |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | mhmdfy/autopsy | pythonExamples/Aug2015DataSourceTutorial/FindContactsDb.py | Python | apache-2.0 | 9,361 | [
"Brian"
] | 5d5b87a74ea749741118a9dd586f0e9efd87c7b6c2740b8627efb1649be62743 |
# 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... | BackupTheBerlios/espressopp | src/integrator/LBInitPopWave.py | Python | gpl-3.0 | 2,164 | [
"ESPResSo"
] | 965c9985c9266516ebfa93bffc89611e71d5d2a140f90b40c549db8f4729c79d |
from __future__ import absolute_import
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, warning=object... | fabianrost84/cython | Cython/Compiler/ParseTreeTransforms.py | Python | apache-2.0 | 122,793 | [
"VisIt"
] | 64dc568c732fbbe6c329711aa399df8b83b797fea968a7d6cbeb9b941a820bf6 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-service
# Author : Adria Casajus
########################################################################
__RCSID__ = "$Id$"
import sys
import DIRAC
from DIRAC.ConfigurationSystem.Client.LocalCon... | vmendez/DIRAC | Core/scripts/dirac-service.py | Python | gpl-3.0 | 1,614 | [
"DIRAC"
] | 04a115589565e4f89a916392b109796df0691781fa3cad34b72d1bca590d1821 |
"""pure-Python sugar wrappers for core 0MQ objects."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYIN... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/sugar/__init__.py | Python | lgpl-3.0 | 1,187 | [
"Brian"
] | 148ca83686df6f3223524a70a2d73000e76521605cbdcc937781052b96619f15 |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c960/Generate960Centreline.py | Python | gpl-2.0 | 975 | [
"VTK"
] | 74b5b9ccf24a8a197080e87bda0cf7c9cbf46f9f63cd85cb10532fa3ce7eb6f3 |
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