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# taken from http://www.piware.de/2011/01/creating-an-https-server-in-python/
# generate server.xml with the following command:
# openssl req -new -x509 -keyout server.pem -out server.pem -days 365 -nodes
# run as follows:
# python simple-https-server.py
# then in your browser, visit:
# https://localhost:4443
... | dpriedel/CollectEDGARData_Test | https_server/simple-https-server.py | Python | gpl-3.0 | 736 | [
"VisIt"
] | e806fcf0945c15d2496ef2d6ba0647f4dd8bc5101c3f8397d343909a257bf2df |
# 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 the G... | kkreis/espressopp | src/analysis/OrderParameter.py | Python | gpl-3.0 | 2,516 | [
"ESPResSo"
] | 21e76fc94da5fefe7a6395461128217ec7cf1b1af3d05f065524d9fa197f2ea4 |
"""
This module defines input sets for CP2K and is a work in progress. The structure/philosophy
of this module is based on the Vasp input sets in Pymatgen. These sets are meant to contain
tested parameters that will result in successful, reproducible, consistent calculations without
need for intervention 99% of the tim... | gmatteo/pymatgen | pymatgen/io/cp2k/sets.py | Python | mit | 48,957 | [
"CP2K",
"Gaussian",
"VASP",
"pymatgen"
] | e17344c993f5df00aa3a278c075ccd8d05f7c5e48936e354d898f8151e7d4c75 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Fstrack(MakefilePackage):
"""Package with tools to analyze symmetry components of elastic ... | iulian787/spack | var/spack/repos/builtin/packages/fstrack/package.py | Python | lgpl-2.1 | 1,871 | [
"NetCDF"
] | 284c163ba8528dcb159e253708b94e56a783bd9508301865c7e2e9782652247e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import math
import os
import json
import collections
import itertools
from abc import ABCMeta, abstractmethod
import random
import warnings
from fnmatch import fnmatch
import re
import functools
from math imp... | dongsenfo/pymatgen | pymatgen/core/structure.py | Python | mit | 141,785 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"NetCDF",
"VASP",
"exciting",
"pymatgen"
] | 5a3c3ffa11863e69ad0c0fc63a708d174aeff414630f101997f03a1b075ac9f5 |
'''
Copyright (C) 2016 Travis DeWolf
Implemented from 'Control-limited differential dynamic programming'
by Yuval Tassa, Nicolas Mansard, and Emo Todorov (2014).
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... | studywolf/control | studywolf_control/controllers/ilqr.py | Python | gpl-3.0 | 17,013 | [
"Gaussian"
] | 258eec645db94c2f4ec7d64f6f3c38dbc30aa321f6ec931b9283747f38df74de |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Module for data simulation, to test algorithms utilized in diagnostics.
Tong Zhang <zhangt@frib.msu.edu>
2017-03-27 11:22:25 AM EDT
"""
from __future__ import division
from __future__ import print_function
from phantasy.library.physics import Point
import numpy as n... | archman/phantasy | phantasy/library/physics/particles.py | Python | bsd-3-clause | 7,093 | [
"Gaussian"
] | ac784a6b0e444cae85bc8dd0f0aa5307b25684efd3dfe642cb913a794170d5a1 |
#!/usr/bin/python
'''
Modified by Bill Bushey <wbushey@acm.org> and Brian Young <byoung061@gmail.com> on August 10th, 2009
'''
import htmllib
import formatter
import string
import sys,urllib
import time
class HtmlTokenParser(htmllib.HTMLParser):
# return a dictionary mapping anchor texts to lists
# of associated ... | aidanf/BTE | BodyTextExtractor.py | Python | gpl-2.0 | 6,102 | [
"Brian"
] | ce849bfdbe36d92378c485d3d3928adabbe5fbf74d3abc7ff54fcbbd8c2269b2 |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as... | CopyChat/Plotting | GCM_changes/climatechange.rsds.py | Python | gpl-3.0 | 6,743 | [
"NetCDF"
] | ab2ae92a47e16510a0b5a36219a80ea917655922b4ec0adb0b58e027d91026e1 |
#
# Copyright (C) 2003-2008 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.
#
""" contains factory class for... | bp-kelley/rdkit | rdkit/Chem/Pharm2D/SigFactory.py | Python | bsd-3-clause | 11,121 | [
"RDKit"
] | 9f508c5266a35f5387e94f3b1b822edc7098a9ba51009103c1b5c45e0283048e |
import os
from .. import utils
from ..qt import *
from .items import *
from ..globals import settings, app_launchers, file_handlers, current_tools
from pyqtconfig import ConfigManager
try:
import xml.etree.cElementTree as et
except ImportError:
import xml.etree.ElementTree as et
EDITOR_MODE_NORMAL = 0
EDITOR... | pathomx/pathomx | pathomx/editor/editor.py | Python | gpl-3.0 | 8,611 | [
"ASE"
] | 0705159fa84001ba0a2f297ce24a93a31d1fb1e15f60824e664eaffc6b09432a |
# $Id$
#
# Copyright (C) 2002-2006 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.
#
""" tools for interacti... | soerendip42/rdkit | rdkit/utils/chemdraw.py | Python | bsd-3-clause | 11,651 | [
"RDKit"
] | 9ac7d50016a6e5df916a97032f119ac8254034f2979deaf0e75cb487ee625b96 |
# Copyright (c) 2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
MetPy Declarative Syntax Tutorial
=================================
The declarative syntax that is a part of the MetPy packaged is designed to aid in simple
data exploration and... | metpy/MetPy | v1.0/_downloads/900d76c7356d09e4ca20b90f94a0732e/declarative_tutorial.py | Python | bsd-3-clause | 21,538 | [
"NetCDF"
] | 3fddd2078c2df8bc1307170cbf63b973385f760d05b26b0591341cf4ad2b53bb |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_OC_biofuel_emissions_n96e_360d.py | Python | gpl-3.0 | 17,344 | [
"NetCDF"
] | f4106cd9eddd0e9010da3afe6ef24dd1e0d2d4d1544899f99af213cc884c5cd2 |
#* 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 TestHa... | nuclear-wizard/moose | python/TestHarness/tests/test_Allocations.py | Python | lgpl-2.1 | 5,026 | [
"MOOSE"
] | b3194b17ac9661136ce9c33dddb85d04bfa520d86d5d9187c2deb75df1144fa2 |
# 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... | mlperf/training_results_v0.6 | Fujitsu/benchmarks/resnet/implementations/mxnet/JobScripts/image_classification/train_imagenet.py | Python | apache-2.0 | 6,645 | [
"Gaussian"
] | 15977d15bc032899265e5db8610473bd63ce9bcb1eab8dec4805039c4fd28e09 |
#!/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-examples.py | Python | gpl-3.0 | 6,595 | [
"ABINIT"
] | d2ae6a95584bcb459365f802b7500740adbaa5610513d749e350b7db24768f13 |
import time
from datetime import datetime
from abc import ABCMeta
from .api_entity import APIEntity
class Application(APIEntity):
"""
Firefly application entity.
"""
__metaclass__ = ABCMeta
_export = [
'id', 'eui', 'name', 'description', 'sink', 'created', 'updated'
]
api = None
... | digimondo/python-fireflyapi | fireflyapi/application.py | Python | mit | 1,136 | [
"Firefly"
] | 5090282da3f99a65ab6036c0f833680c233c6a30467856cd4da91c90bdfff8c5 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/interaction/CoulombKSpaceP3M.py | Python | gpl-3.0 | 5,244 | [
"ESPResSo"
] | 95255160bf6d87ed02bea684c7b6d08fee9fff23573ebb0fa4943ff59b45f8f8 |
from aces.materials import Material
from .atomic import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt
from ase.dft.kpoints import ibz_points
class structure(Material):
def set_parameters(self):
pass
def setup(self):
pass
def lmp_structure(self):
col=self.unitcell(self.laty,self.latx) ... | vanceeasleaf/aces | aces/materials/Tgraphene.py | Python | gpl-2.0 | 793 | [
"ASE"
] | db40b5c520c35406484a99276c4e947fcfd5b4b761b355963a94cdf6cb0a9b82 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | jrossyra/adaptivemd | adaptivemd/reducer.py | Python | lgpl-2.1 | 12,009 | [
"MDTraj"
] | 6fd47c007a530ccd90ddeee06ea0ff396ab21c0e0c4661ee3aed1adeaf68689c |
from __future__ import absolute_import
import logging
try:
from urllib2 import urlopen
except ImportError:
from urllib.request import urlopen
try:
from urllib2 import Request
except ImportError:
from urllib.request import Request
try:
from galaxy import eggs
eggs.require("poster")
except Impor... | ssorgatem/pulsar | pulsar/client/transport/poster.py | Python | apache-2.0 | 1,308 | [
"Galaxy"
] | 491dc7284787bb989c0504ac12559b1e9745c949492b79de1c2e3651591a738b |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; you can redistribute it an... | d7415/merlin | Arthur/views/lookup.py | Python | gpl-2.0 | 3,608 | [
"Galaxy"
] | 12b9cc35619d5b7929e4d839a83c2f2bfcc18f58f07262036cfe5a27834124fc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# vim: ai ts=4 sts=4 et sw=4 nu
from __future__ import (unicode_literals, absolute_import,
division, print_function)
import logging
import traceback
import datetime
import reversion
from django.utils.translation import ugettext as _
from snisi_cor... | yeleman/snisi | snisi_trachoma/integrity.py | Python | mit | 25,172 | [
"VisIt"
] | 17f2495095f76c81eccb403d72f16c7e45e44daf02e17ddf24fb94f0588566f8 |
MATH = [
'https://en.wikipedia.org/wiki/Analysis_of_algorithms',
'https://en.wikipedia.org/wiki/Linear_programming',
'https://en.wikipedia.org/wiki/Mathematics',
'https://en.wikipedia.org/wiki/Algorithm',
'https://en.wikipedia.org/wiki/Scalar_multiplication',
'https://en.wikipedia.org/wiki/Maxim... | scivey/relevanced | testing/func_test_lib/urls.py | Python | mit | 47,144 | [
"Gaussian"
] | 54c21210c50e356879325a4ba9e3d215a069fb71124187557597ffe4dbab26d7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Stephane Charette
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the ter... | pmghalvorsen/gramps_branch | gramps/plugins/tool/removeunused.py | Python | gpl-2.0 | 18,587 | [
"Brian"
] | 6f6c56b2a546a959dcccc10b6f8a5532b03f68e618bc593a2208652a003ca115 |
import pdb
import numpy as np
import math
import time
import chainer
import chainer.functions as F
import chainer.links as L
from chainer import cuda
from util import gaussian_kl_divergence
from util import gaussian_logp
from util import gaussian_logp0
from util import bernoulli_logp
class VAE(chainer.Chain):
d... | ashwindcruz/dgm | householder_celebA/model.py | Python | mit | 5,777 | [
"Gaussian"
] | f1e76e964518d8b84afff92e92c79f5ac61f516c9703e275dcd32499fb7a9f37 |
"""
Test the Von-Mises-Fisher mixture model
Author : Bertrand Thirion, 2010
"""
from __future__ import absolute_import
import numpy as np
from ..von_mises_fisher_mixture import (VonMisesMixture,
sphere_density,
select_vmm,
... | alexis-roche/nipy | nipy/algorithms/clustering/tests/test_vmm.py | Python | bsd-3-clause | 2,288 | [
"VMD"
] | 28960f74f58fabede4412dd296946db5d76690f2de59df4e88f96a448ba8ae66 |
"""
==============================================
Plot randomly generated classification dataset
==============================================
This example plots several randomly generated classification datasets.
For easy visualization, all datasets have 2 features, plotted on the x and y
axis. The color of each po... | lesteve/scikit-learn | examples/datasets/plot_random_dataset.py | Python | bsd-3-clause | 2,550 | [
"Gaussian"
] | 936ce1a46d9876492448d367f81a1184dbece9d06dc383b70d21cac44cb894c3 |
"""
State Space Analysis using the Kalman Filter
References
-----------
Durbin., J and Koopman, S.J. `Time Series Analysis by State Space Methods`.
Oxford, 2001.
Hamilton, J.D. `Time Series Analysis`. Princeton, 1994.
Harvey, A.C. `Forecasting, Structural Time Series Models and the Kalman Filter`.
Cambrid... | yarikoptic/pystatsmodels | statsmodels/tsa/kalmanf/kalmanfilter.py | Python | bsd-3-clause | 30,496 | [
"Gaussian"
] | ea64fd8de6e3fdbbf02bd790643c5e354f84debf46791c967a056299197b43ab |
# -*- coding: utf-8 -*-
"""Page and page Component classes
The keteparaha Page and Component classes represent web pages and components
of web pages.
Pages are identified by the URL of the browser, and components by the CSS
selector that is used to retrieve them.
If you perform an action that causes the browser to v... | tomdottom/keteparaha | keteparaha/page.py | Python | mit | 18,789 | [
"VisIt"
] | 41431ba98d0eca0bff0f5b2bfd24a3c53c0ecd76a5c5e55622fb530504ac9679 |
# coding: utf-8
from __future__ import unicode_literals
import unittest
from pymatgen.optimization.linear_assignment import LinearAssignment
import numpy as np
class LinearAssignmentTest(unittest.TestCase):
def test(self):
w0 = np.array([[19, 95, 9, 43, 62, 90, 10, 77, 71, 27],
... | yanikou19/pymatgen | pymatgen/optimization/tests/test_linear_assignment.py | Python | mit | 6,889 | [
"pymatgen"
] | cd4cf865bff2d8996e61041d05c2e8801f74665bd34c3c48e1d7f1dcd8d4e87a |
# Orca
#
# Copyright (C) 2015 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at yo... | pvagner/orca | src/orca/scripts/apps/evolution/speech_generator.py | Python | lgpl-2.1 | 5,188 | [
"ORCA"
] | dcd69fff8d45edd807e367031d520310d6332fb1c72f190e98fbd0b4658d3f5b |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
# Disable the "wildcard import" warning so we can bring in all methods from
# course helpers and ui helpers
# pylint: disable=wildcard-import
# Disable the "Unused import %s from wildcard import" warning
# pylint: disable=unused-wildcard-impor... | eestay/edx-platform | common/djangoapps/terrain/steps.py | Python | agpl-3.0 | 7,478 | [
"VisIt"
] | 8fbcf23b006a2914a5ca4007258503ee0ccb20f1a314e9c394e4563b41c5536c |
"""
This module finds diffusion paths through a structure based on a given
potential field.
If you use PathFinder algorithm for your research, please consider citing the
following work::
Ziqin Rong, Daniil Kitchaev, Pieremanuele Canepa, Wenxuan Huang, Gerbrand
Ceder, The Journal of Chemical Physics 145 (7), 0... | gmatteo/pymatgen | pymatgen/analysis/path_finder.py | Python | mit | 19,178 | [
"Gaussian",
"VASP",
"pymatgen"
] | 7843812635cd561d046956b2264b351e5b119f4b9b1aebf4098b1c3038a3bc9f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source
##
## 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 Foundation; either version 2
## of the License, or... | tiagocardosos/stoq | stoqlib/lib/osutils.py | Python | gpl-2.0 | 5,881 | [
"VisIt"
] | e1e0a55dfe7bc265dbd7dc75706fcf461f452f7124dfc7326788e1bc2e63bde1 |
import requests
import h2o
import h2o_test_utils
from h2o_test_utils import ModelSpec
from h2o_test_utils import GridSpec
def build_and_test(a_node, pp, datasets, algos, algo_additional_default_params):
####################################################################################################
# Bui... | h2oai/h2o-dev | py/rest_tests/test_models.py | Python | apache-2.0 | 16,970 | [
"Gaussian"
] | 05d4e460f3fcb4dc7cdc51a6d455a0318caa7a75e97eaba6f91fc8b9e4c850c3 |
#
# unit tests for edgegrid. runs tests from testdata.json
#
# Original author: Jonathan Landis <jlandis@akamai.com>
#
# For more information visit https://developer.akamai.com
# Copyright 2014 Akamai Technologies, Inc. All Rights Reserved
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may ... | akamai-open/AkamaiOPEN-edgegrid-python | akamai/edgegrid/test/test_edgegrid.py | Python | apache-2.0 | 9,332 | [
"VisIt"
] | c60881ee8909215949fd97b3e56dbb5df5d9a5cdfbe9259387be0f2bdb0278d8 |
"""Visual effects"""
import pygame
try:
_arraytype = pygame.surfarray.get_arraytype()
if _arraytype == 'numeric':
from Numeric import UInt8 as uint8, minimum, array, Float32 as float32, Int32 as int32
elif _arraytype == 'numpy':
from numpy import uint8, minimum, array, float32, int32
Nu... | smmosquera/serge | blocks/visualeffects.py | Python | lgpl-3.0 | 7,901 | [
"Gaussian"
] | e5e7f5b8861b53c2d37f612e97b116664f0776c0e4b0854cdcf7bbc745a3129f |
#!/usr/bin/env python2
'''
This script collects PDBs corresponding to certain TCIDs (of any level) and assigns TMSs based on STRIDE and PDBTM (and a pinch of geometry)
'''
from __future__ import print_function, division
import xml.etree.ElementTree as ET
import os, re, subprocess, sys
import numpy as np
import yaml
im... | khendarg/ubi | Deuterocol1.py | Python | bsd-3-clause | 17,513 | [
"BLAST",
"Biopython"
] | adc53c5d5f962a38ce233e55c5ecbc86a1b93fcad5ffea336bf45527583fafe7 |
import os
import re
import sys
import glob
import gzip
import json
import time
import errno
import shutil
import urllib
import logging
import tarfile
import urllib2
import requests
import feedparser # For LOVD atom data
import subprocess # For transvar
from distutils.spawn import find_executable # https://docs.pyt... | kantale/MutationInfo | MutationInfo/__init__.py | Python | mit | 108,229 | [
"Biopython",
"VisIt"
] | 6ccca32fafb4716c03b6d5443997177a04fbc3643d59d8cf6e58b21be4f0eeda |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
# make yield compatible with Python 2.2
from __future__ import generators
from Numeric im... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/ResidueDepth.py | Python | apache-2.0 | 4,506 | [
"Biopython"
] | d1322fa0245130db57c70b9458e8e8ffb904998be4ddfd134671175383e61698 |
"""
Utility functions for cloud endpoints.
"""
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
import sys
import os
import six
from DIRAC import S_OK, S_ERROR
from email.mime.text import MIMEText
from email.mime.multipart import MIMEMultipart
STATE_MAP = ... | ic-hep/DIRAC | src/DIRAC/Resources/Cloud/Utilities.py | Python | gpl-3.0 | 10,367 | [
"DIRAC"
] | 77acfe06fa73b4027f68003f5d35a69744ec8a6c4f6867727992fec539186f09 |
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | zhaofang0627/cuda-convnet-for-hashing | layer.py | Python | apache-2.0 | 85,482 | [
"Gaussian",
"NEURON"
] | 8ca5d8110434d7b350a00212ba131cce7d560288855d75328bc7564739a61068 |
import sys
import blib
import pymc
import numpy as np
import simtk.openmm.app as app
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
ff = blib.ff
def set_parms(f, sigma, epsilon, q=0.0):
print("\nsigma=%f, epsilon=%f" % (sigma, epsilon))
for k in range(f.getNumParticles()):
f.set... | kyleabeauchamp/DBayes | dbayes/test_pymc3.py | Python | gpl-2.0 | 3,035 | [
"MDTraj",
"OpenMM"
] | acf1ec45280151bb50ebecaebee100e250b8a45b7c330c44f638b91f4c526f10 |
import numpy as np
import cv2
from matplotlib import pyplot as plt
import heapq
img = cv2.imread('color.jpg')
#edges = cv2.Canny(img,100,200)
#plt.subplot(121),plt.imshow(edges,cmap = 'gray')
#plt.title('Edge Image'), plt.xticks([]), plt.yticks([])
#imgray = img
imgray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
plt.subp... | SimplyPaper/SimplyPaper.github.io | Python Files/find_contours.py | Python | apache-2.0 | 1,644 | [
"Gaussian"
] | abc7b03296e55cd0437dcefd710f5ee68e94d3c577d475f5f5f85228edc3722c |
#!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Provide cache classes to handle creation of OpenMM Context objects.
"""
# ====================================... | choderalab/openmmtools | openmmtools/cache.py | Python | mit | 32,415 | [
"OpenMM"
] | 5288b1e184b0d99bfb146fc3ab544a12c384d4f35a86998ea93397c5593f9c18 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jun 16 04:29:13 2020
@author: mathieumoog
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Jun 14 05:54:11 2020
@author: mathieumoog
"""
import cpmd
import filexyz
import numpy as np
import matplotlib.pyplot as plt
from msmbuild... | CondensedOtters/PHYSIX_Utils | Projects/Moog_2016-2019/CO2/CO2_NN/hmm_bonds.py | Python | gpl-3.0 | 5,753 | [
"CPMD"
] | 92513d00fe7d2fb03b752df41d5307b09920fc81f34b25ed2c2d9338d1ef85ed |
"""Unit test for kgp.py
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.2 $"
__date__ = "$Date: 2004/05/05 21:57:19 $"
__copyright... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/kgptest.py | Python | mit | 1,303 | [
"VisIt"
] | 86b6750eb53fc3befe337d5db138b38401842d9e4b8eb4b644341dc22cd351d3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# relevant imports
import sys
import time
import espresso
import mpi4py.MPI as MPI
import Tetracryst # Preparation of tetrahedral crystal and constuctions of bonds in tetrahedral liquid
from espresso import Real3D, Int3D
from espresso.tools import decomp
from espresso.to... | BackupTheBerlios/espressopp | examples/hadress/hadressPlain/hadress.py | Python | gpl-3.0 | 7,398 | [
"CRYSTAL",
"ESPResSo"
] | f92246b24977039c7e02a302efc532b3eb53426fbb0a51ef1dbd2f69a7ab62c9 |
from datetime import datetime
from django.core.management.base import BaseCommand
from schools.models import School, BoundaryType
from stories.models import (
Question, Questiongroup, QuestionType,
QuestiongroupQuestions, Source, UserType)
class Command(BaseCommand):
args = ""
help = """Populate DB w... | klpdotorg/dubdubdub | apps/stories/management/commands/archived_commands/populateanganwadiv1.py | Python | mit | 4,188 | [
"VisIt"
] | 72c30654bc62848e5a9431ad942697d03951915071d7f9cb615cdfe2e74b70bb |
"""
Univariate Kernel Density Estimators
References
----------
Racine, Jeff. (2008) "Nonparametric Econometrics: A Primer," Foundation and
Trends in Econometrics: Vol 3: No 1, pp1-88.
http://dx.doi.org/10.1561/0800000009
https://en.wikipedia.org/wiki/Kernel_%28statistics%29
Silverman, B.W. Density Estimatio... | jseabold/statsmodels | statsmodels/nonparametric/kde.py | Python | bsd-3-clause | 19,093 | [
"Gaussian"
] | c75b92909f497984a72e8870a0886d8af16dcfb01d20b27d1070c6a0da01868b |
# -*- coding: utf-8 -*-
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2019 Dave Hocker
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Fou... | dhocker/athomepowerlineserver | commands/DeviceAllUnitsOff.py | Python | gpl-3.0 | 1,464 | [
"xTB"
] | d8fd030ec028fcb16b77ca5601e80e339585218dde35bae9b6458b7ddc31584c |
# Copyright (c) 2008-2010, 2013 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014 Google, Inc.
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015-2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelmc.ro>
# Copyright (c) 2016 Dere... | PyCQA/pylint | tests/pyreverse/test_diadefs.py | Python | gpl-2.0 | 8,602 | [
"VisIt"
] | 38ed937fc354c3d59ec50f4214162b84bffed03a2f43ec54a7a40a627fcbe355 |
"""
===================
pacbio
===================
Tools for processing PacBio sequencing data.
"""
import os
import gzip
import re
import io
import math
import subprocess
import collections
import tempfile
import numbers
import regex
import numpy
import pandas
import pysam
import Bio.SeqFeature
# import dms_tools... | jbloomlab/dms_tools2 | dms_tools2/pacbio.py | Python | gpl-3.0 | 63,182 | [
"Biopython",
"pysam"
] | ee76889395550b4d207b07425dd417446d044bfe86241d83103449c3fb60ddea |
"""Receives Android tablet input data transmitted via UDP
by the GfxTablet Android app and pushes it to WebSocket client.
GfxTablet: https://github.com/rfc2822/GfxTablet
"""
import logging
import socket
from tornado.websocket import WebSocketHandler
from tornado.ioloop import IOLoop
_logger = logging.getLogger(__nam... | jzitelli/yawvrb | GfxTablet/GfxTablet.py | Python | mit | 2,216 | [
"Galaxy"
] | 6e69cea41fbc6db4f46ebcbad0e87de0bf307eb5307833cfbd0647a095a15e52 |
import math
from typing import Optional, List, Tuple, Sequence, Union, cast, TypeVar
from typing import Iterator, overload
import numpy
import itertools
from .. import registry
from ..types import Xp, Shape, DTypes, DTypesInt, DTypesFloat, List2d, ArrayXd
from ..types import Array3d, Floats1d, Floats2d, Floats3d, Flo... | explosion/thinc | thinc/backends/ops.py | Python | mit | 50,092 | [
"Gaussian"
] | b5209f3ccb4db923d1f0cd8aeb80f7069651bc74ec8269beef3be9088343ed4d |
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:... | InformaticsMatters/pipelines | src/python/setup.py | Python | apache-2.0 | 3,975 | [
"RDKit"
] | f8cd1e646286ca2e70164e5a9411bf449097e780cbf916ee4cbaa96904c994ff |
""" This tests only need the PilotAgentsDB, and connects directly to it
Suggestion: for local testing, run this with::
python -m pytest -c ../pytest.ini -vv tests/Integration/WorkloadManagementSystem/Test_PilotAgentsDB.py
"""
from __future__ import absolute_import
from __future__ import division
from __fu... | yujikato/DIRAC | tests/Integration/WorkloadManagementSystem/Test_PilotAgentsDB.py | Python | gpl-3.0 | 6,050 | [
"DIRAC"
] | ff59ba3228616071bb2fc7d53b194e553d724c1b0e28e8284b1df04c694a1abd |
'''
SASMOL: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
... | StevenCHowell/zazmol | src/python/test_sasmol/test_file_io/test_intg_file_io_Files_read_pdb.py | Python | gpl-3.0 | 12,561 | [
"CHARMM"
] | 75f223299e5c65a8ccc53ee7310c8a20234f715c17a657bd8d35999293473374 |
import sys
tests=[
("testExecs/testReaction.exe","",{}),
("python","test_list.py",{'dir':'Wrap'}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| soerendip42/rdkit | Code/GraphMol/ChemReactions/test_list.py | Python | bsd-3-clause | 279 | [
"RDKit"
] | 5b3320062925cfa3dd1de5e651e86a5ef252aede248e747501621e761bd02707 |
from __future__ import print_function
import copy
import warnings
import graphviz
import matplotlib.pyplot as plt
import numpy as np
def plot_stats(statistics, ylog=False, view=False, filename='avg_fitness.svg'):
""" Plots the population's average and best fitness. """
if plt is None:
warnings.warn(... | CodeReclaimers/neat-python | examples/single-pole-balancing/visualize.py | Python | bsd-3-clause | 5,821 | [
"NEURON"
] | 267eadd16e586d9d4db1d047b56799d40a5dce7bfd85a7f94417dd6769353fb8 |
from django.db import models
class Team(models.Model):
class Meta:
db_table = 'teams'
name = models.CharField(db_column='fullname', max_length=50)
class Player(models.Model):
class Meta:
db_table = 'players'
first_name = models.CharField(db_column='gname', max_len... | michzimny/teamy-quick-lineup | ql/orm/models.py | Python | mit | 2,396 | [
"VisIt"
] | de5e421717f51637e5d8cd9c2dd3412b8e1dcf2a8840411187118517446007e3 |
import theano
import theano.tensor as T
from helper import activations
from helper import misc,updates
from scipy.stats import gaussian_kde
from matplotlib import pyplot as plt
from matplotlib.pyplot import *
'''
from foxhound import activations
from foxhound import updates
'''
from helper import inits
from helper.th... | iamharshit/ML_works | GAN learns Gaussion Function/gan_learn_gaussian.py | Python | mit | 4,239 | [
"Gaussian"
] | e7f50bb2ad6e0623844c5192ec30c5440779fee2bc3161a5c7119aa98f87f55b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
"""
This example shows how to use pytim classes on trajectories
loaded with MDTraj (http://mdtraj.org/)
(see also the openmm interoperability)
"""
import mdtraj
import pytim
from... | Marcello-Sega/pytim | pytim/examples/example_mdtraj.py | Python | gpl-3.0 | 507 | [
"MDTraj",
"OpenMM"
] | 41d364b1197aaacbfbace7363cf492f47b1fa4cf708c886be25ac31a33e690fa |
from collections import OrderedDict
from edc_visit_schedule.classes import (
VisitScheduleConfiguration, site_visit_schedules, MembershipFormTuple, ScheduleTuple)
from ..models import AntenatalVisitMembership, MaternalVisit
from .entries import (maternal_antenatal1_entries,
maternal_antenat... | botswana-harvard/tshilo-dikotla | td_maternal/visit_schedule/antenatal_visits_v3.py | Python | gpl-2.0 | 2,040 | [
"VisIt"
] | 16d2e0664b88bec930261c51f0cf1b77ca5ccfc6dfedaa298f3577cf947e7de2 |
#!/usr/bin/env python2
# Copyright (C) 2016
# Max Planck Institute for Polymer Research
#
# 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 ver... | acfogarty/espressopp | examples/adress/hadress_water/water.py | Python | gpl-3.0 | 10,346 | [
"ESPResSo",
"Gromacs"
] | 98b2d06e0ded28bd0d1bc892e59ac97594fbced579ca748b4838e90ed0ccc8fe |
########################################################################
# File : ExecutorReactor.py
# Author : Adria Casajus
########################################################################
"""
DIRAC class to execute Executors
Executors are an active part of DIRAC.
All DIRAC executors must inherit fr... | ic-hep/DIRAC | src/DIRAC/Core/Base/ExecutorReactor.py | Python | gpl-3.0 | 9,476 | [
"DIRAC"
] | 0b668a39a378107780c468e433e6605169a56c31035de452736573844c09c0da |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/movielistrss.py | Python | gpl-2.0 | 8,420 | [
"VisIt"
] | a4c951e701cd430c3b0b16efd2b59ca1d1677f14f52b72cb265a4506f2fe31ae |
# $Id$
#
# Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# 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 abov... | rdkit/rdkit-orig | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | Python | bsd-3-clause | 16,101 | [
"RDKit"
] | 8fe0f7e47f7cc9d4d24dbeb401bfd017184fcbedd36f48b068b4427562ba29f2 |
"""Galaxy Reports root package -- this is a namespace package."""
__import__( "pkg_resources" ).declare_namespace( __name__ ) | volpino/Yeps-EURAC | lib/galaxy/webapps/__init__.py | Python | mit | 126 | [
"Galaxy"
] | 004b4f55fc989ada6e4d8253c4b30ad52c22f0a955b9c7debcc36508494dd131 |
# (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... | webdev1001/ansible | lib/ansible/utils/__init__.py | Python | gpl-3.0 | 60,245 | [
"Galaxy",
"VisIt"
] | eda554cd31658f6a3f759c8615ee80f67537c76fd8d484eb0943091ff7a6ccbb |
#!/usr/bin/env python
#####
## readProbe.py
## Read in PetaVision probe output
## Display time-course plots and histograms of values
## Should work with any standard probe. Currently tested with LIF, OjaSTDPConn, LCALIF probes.
##
##Dylan Paiton and Sheng Lundquist
#####
import sys
import matplotlib
from readPro... | dpaiton/OpenPV | pv-core/python/probe_analysis/readProbe.py | Python | epl-1.0 | 11,571 | [
"NEURON"
] | 5371d8134e639065899831db7ddb3b2ba5821ca5129f2cb4c732ad2e478e66fa |
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | deepmind/alphafold | alphafold/relax/relax.py | Python | apache-2.0 | 3,343 | [
"Amber"
] | 9c0b963e0919f98d6254e3477bae7f873331e26d22ed3653c3d8abe33e9e6e42 |
# coding=utf-8
# main codes, call functions at stokes_flow.py
# Zhang Ji, 20170518
import sys
import petsc4py
petsc4py.init(sys.argv)
import numpy as np
from src import stokes_flow as sf
from src.stokes_flow import problem_dic, obj_dic
from petsc4py import PETSc
from src.geo import *
from time import time
import pic... | pcmagic/stokes_flow | try_code/try_sample.py | Python | mit | 8,533 | [
"VTK"
] | 8068707b16f638eb7fbeb9f86d836ea82d6c536613c5f40a5b0745f4ee9b5b31 |
<<<<<<< HEAD
<<<<<<< HEAD
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+-... | ArcherSys/ArcherSys | Lib/concurrent/futures/process.py | Python | mit | 52,862 | [
"Brian"
] | ce1d5987f70cb25db801023dbecbfc07af4aa428801a3d05e1520a1b324e93be |
#!/usr/bin/python3
"""This is a small command line utility to grab pictures from a web
site/gui to view them locally. Which links to follow and what to
download can be configured using regular expressions.
.. module:: pic-grab
.. moduleauthor:: Sebastian Schmittner <sebastian@schmittner.pw>
Copyright 2017 Sebastian... | Echsecutor/pic-grab | main.py | Python | gpl-3.0 | 8,444 | [
"VisIt"
] | 1dc8b156faa3d05ca6f547dce3e15e5c92dc4e2f68bd4ee1a15d2a0f40931393 |
#!/usr/bin/env python
import sys
sys.path.append( '.' )
from optparse import OptionParser
from sfepy.base.base import *
from sfepy.fem import gen_block_mesh
usage = """%prog [options]
Block mesh generator.
"""
help = {
'filename' :
'output file name [default: %default]',
'dims' :
'dimensions of the b... | olivierverdier/sfepy | script/blockgen.py | Python | bsd-3-clause | 1,856 | [
"VTK"
] | 13890a82d3cab0a231f750aebe572d9e73235f3fc41a07f4fa1fce04c935460c |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from .fake_webapp import EXAMPLE_APP
from splinter.request_handler.status_code import HttpResponseError
class StatusCodeTest(object):
... | lrowe/splinter | tests/status_code.py | Python | bsd-3-clause | 867 | [
"VisIt"
] | 9ab776a244b7953329f07e12610bdbbd424c8167e4a12dd5bab982ec89c92366 |
#!/usr/bin/env python3
"""Perform quality trimming with the same algorithm as
bwa_trim_read() in bwaseqio.c, BWA. For Solexa quliaty,
the scores are converted to Phred quality for trimming.
Formula to convert Solexa quality to Phred quality is:
Phred = 10 * log_10(1 + 10 ** (Solexa / 10.0))
Formulas t... | jnktsj/DNApi | utils/qual_trim.py | Python | mit | 3,943 | [
"BWA"
] | 7c40250043f0cf8dbdc977b12894c5cfcabc3fe38bc35d84279e965b496f88b0 |
"""
Includes various submodular functions used throughout the submodular examples.
Note that all functions are of the form F(X, A, args), where args is a
dictionary containing additional arguments needed by a particular function.
==============
Copyright Info
==============
This program is free software: you can redi... | bdol/bdol-ml | submodularity/utils/submodular_functions.py | Python | lgpl-3.0 | 2,354 | [
"Brian"
] | eb11e26b03cc3645cdfbfdcdf0d6fdce05d52f46d0dee99d3685f8f1c1e84ada |
# LOFAR IMAGING PIPELINE
#
# BBS Source Catalogue List
# Bart Scheers, 2011
# L.H.A.Scheers@u... | jjdmol/LOFAR | CEP/GSM/bremen/src/gsmutils.py | Python | gpl-3.0 | 14,187 | [
"Gaussian"
] | a9b8feca9d1b6baa82f36e099d21f1a6b2a5e3524b77566933c63ac26795c054 |
#! python
__author__ = 'forgacs.daniel@gmail.com'
__version__ = '0.1'
# Houdini 13
# WORK IN PROGRESS
import time
import hou
def _message(txt):
print( '-----> {0}'.format( txt))
def pyro_setup(objroot = False):
try:
selection = hou.selectedNodes()[0]
except:
print('SELECTION ERRRRROR')
if objroot:
r... | danielforgacs/houdini-tools | archive/setupPyro.py | Python | mit | 4,241 | [
"BLAST"
] | 6292e0a4aa71b97d49ade0555e8233a578ba7b1cbc7af7a687906f75184008fb |
#!/usr/bin/env python
#
# $File: backTrajectory.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistri... | BoPeng/simuPOP | docs/backTrajectory.py | Python | gpl-2.0 | 2,557 | [
"VisIt"
] | 9909ae4d4740d3b3640030a135a572f9761c5154d60be01158138c9948ed8930 |
'''
This Script will generate geometries around the conical intersection, linear
and circle.
It needs a geometry file (xyz) and two vectors (that can be read by np.loadtxt)
'''
import numpy as np
import glob
from collections import namedtuple
from argparse import (ArgumentParser,RawTextHelpFormatter)
from quantumprop... | acuzzio/GridQuantumPropagator | Scripts/generateGeomsAroundConical.py | Python | gpl-3.0 | 9,811 | [
"MOLCAS"
] | ac2317d8e4c8217feb17fe6b3b2b09cb6039052854c00ede6f033b7d8c007051 |
# -*- coding: utf-8 -*-
#
# DiracDocs documentation build configuration file, created by
# sphinx-quickstart on Sun Apr 25 17:34:37 2010.
#
# 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.
#
# A... | petricm/DIRAC | docs/source/conf.py | Python | gpl-3.0 | 10,979 | [
"DIRAC"
] | a586341af2bff42a8fa63efb8f95e1c694aa902696afc9071ac28f62ed2b54d9 |
#!/usr/bin/env python
#
# Copyright 2007 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 o... | elsigh/browserscope | third_party/appengine_tools/sdk_update_checker.py | Python | apache-2.0 | 14,468 | [
"VisIt"
] | 37e13b34a37c3b9d7f79e36f43a71f227a68a353e4b3f404b4fa21290987fa35 |
from .agents import *
import utils as u
class AgentXTypeTwoClass(Agent):
def __init__(self, x=2, y=2):
Agent.__init__(self)
##
# Personalize the identifier of this class.
# Will be used instead of the class name
# in neighbours info
self.name = 'AgentXTyp... | valefranz/AI-Project-VacuumEnvironment | AgentiStudenti2016/AgentXTypeTwo.py | Python | apache-2.0 | 9,111 | [
"VisIt"
] | 5546723548fff155c0f3a7fef1ee9a12047cddb2285453285389f53c3d44191f |
# -*- coding: utf-8 -*-
# Copyright 2016-2017 Jaap Karssenberg <jaap.karssenberg@gmail.com>
import tests
from zim.tokenparser import *
from zim.formats import ParseTreeBuilder
class TestTokenParser(tests.TestCase):
def testRoundtrip(self):
tree = tests.new_parsetree()
#~ print tree
tb = TokenBuilder()
tre... | Osndok/zim-desktop-wiki | tests/tokenparser.py | Python | gpl-2.0 | 1,072 | [
"VisIt"
] | 41056fc020df0495c61807e89a96f8054f44843f0253bb8aafaeb813a5463019 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/grad/ump2.py | Python | apache-2.0 | 13,859 | [
"PySCF"
] | 9a9b813854e77a0bdc5e3a9f3152baf5683df7523d5a965c68b8f6e75416a32f |
#!python
# coding=utf-8
import os
import glob
import shutil
import netCDF4
import logging
import tempfile
import operator
import itertools
import multiprocessing as mp
import pytz
import numpy as np
logger = logging.getLogger("pyncml")
logger.addHandler(logging.NullHandler())
try:
from lxml import etree
except ... | axiom-data-science/pyncml | pyncml/pyncml.py | Python | mit | 9,730 | [
"NetCDF"
] | 5f5118fda8be847a436b2c9bcffc1fb660280d4cb996ff0e9a377e520f141efa |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Development script to get the multiplicity of the separation facets for some model coordination environments
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "2.0"
... | materialsproject/pymatgen | dev_scripts/chemenv/plane_multiplicity.py | Python | mit | 1,422 | [
"pymatgen"
] | 6ecc69c52634a270222611b193bd02096f5f766d3e954c12b933b2b2db69b082 |
from selene.browser import execute_script
from tests.examples.todomvc.pagemodules_approach.pages import tasks
class TestTodoMVC(object):
def teardown(self):
execute_script('localStorage.clear()')
def test_filter_tasks(self):
tasks.visit()
tasks.add('a', 'b', 'c')
tasks.shou... | SergeyPirogov/selene | tests/examples/todomvc/pagemodules_approach/todomvc_test.py | Python | mit | 701 | [
"VisIt"
] | 755bfa541485556cc23dc6fca4d59706e82c7afc66c8b0e05066c832dcde4ddf |
# 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... | lewismc/climate | RCMES/run_RCMES.py | Python | apache-2.0 | 13,922 | [
"NetCDF"
] | e47909ddd8d3245495bfc6b5d5aafa23632cdb6eb5d2fd56c184dde3b7af904e |
import numpy as np
from numpy import sqrt, empty, zeros
import numba as numba
from numba import jit
from . import Image, IO
from skimage.morphology import skeletonize
@jit(nopython=True, nogil=True)
def sobel_filt(im):
H = im.shape[0]
W = im.shape[1]
buf = empty((H,W))
out = empty((H,W))
# Pr... | kitizz/edge3d-paper | src/tools/Canny.py | Python | gpl-3.0 | 6,960 | [
"Gaussian"
] | c41e6d992d81a07e1bd2832422404e4e8ae2796c7ab7ccfbd26eee440123999a |
"""
# Copyright (C) 2007 Nathan Ramella (nar@remix.net)
#
# 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.
#
# T... | xl7dev/WebShell | Udp/LiveHack/__init__.py | Python | gpl-2.0 | 1,298 | [
"VisIt"
] | 5d6acbd69a8b26652b9e8940c4a7f9ff24c3220a93585c204f9c5be8f94e0458 |
"""
Acceptance tests for Content Libraries in Studio
"""
from ddt import ddt, data
from nose.plugins.attrib import attr
from flaky import flaky
from .base_studio_test import StudioLibraryTest
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.utils ... | waheedahmed/edx-platform | common/test/acceptance/tests/studio/test_studio_library.py | Python | agpl-3.0 | 28,096 | [
"VisIt"
] | acedcec1253110d1840c9feb1f1983ef4fb4b8b7058e4e02a07d043bf61554c3 |
""" Meager code path measurement tool.
Ned Batchelder
http://nedbatchelder.com/blog/200803/python_code_complexity_microtool.html
MIT License.
"""
from __future__ import with_statement
import optparse
import sys
from collections import defaultdict
try:
import ast
from ast import iter_child_nodes
exc... | yhoshino11/pytest_example | .tox/flake8/lib/python2.7/site-packages/mccabe.py | Python | mit | 9,536 | [
"VisIt"
] | 268219eb10946412f1709993c2432ed93687390bdadc045d8c585a70053c86cd |
#
# Gramps - a GTK+ based genealogy program
#
# Copyright (C) 2006 Brian Matherly
# Copyright (C) 2008 Stephen George
#
# 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... | rdp/legado | windows/builder/build_GrampsWin32.py | Python | gpl-2.0 | 25,910 | [
"Brian"
] | 64ba3fc187b7d372a4fb29d411c5c577d1834aa9563594534f293b741f0a0f2a |
"""
Migration script to create initial tables.
"""
from sqlalchemy import *
from migrate import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import *
import sys, logging
log = logging.getLogger( __name__ )
log.setL... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py | Python | gpl-3.0 | 7,193 | [
"Galaxy"
] | 42d0375fb430b1ac5176403cd7748243d319b32dceef08b37b0951e901c55522 |
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