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# Python G-Code simulator
#
# Copyright (C) 2011 Peter Rogers
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This... | parogers/gsim | gsim/gcode.py | Python | gpl-2.0 | 15,836 | [
"VisIt"
] | 400fc794d4192fa35e5a976039e494cd1674c12d62658bb11fe0e577f3863698 |
# -*- coding: utf-8 -*-
import os
import __main__
#from __future__ import print_function, division, unicode_literals
"""
langcodes knows what languages are. It knows the standardized codes that
refer to them, such as `en` for English, `es` for Spanish and `hi` for Hindi.
Often, it knows what these languages are called... | darkman66/langcodes | langcodes/__init__.py | Python | mit | 43,215 | [
"ASE"
] | 8183789a7c6cc1eb9022cb6348d8b3b7c9419d8ef5d63de6e93c67f96d6182f2 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the main LMS Dashboard (aka, Student Dashboard).
"""
import six
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.dashboard im... | stvstnfrd/edx-platform | common/test/acceptance/tests/lms/test_lms_dashboard.py | Python | agpl-3.0 | 5,772 | [
"VisIt"
] | 4676d68ad0efe85dacd48e42bab7873471f3305689b7291586aa9c2103582af0 |
from math import sqrt
import optparse
import numpy as np
from ase.atoms import Atoms, string2symbols
from ase.structure import molecule
from ase.tasks.task import OptimizeTask
from ase.data import covalent_radii, atomic_numbers
from ase.data import ground_state_magnetic_moments
from ase.utils.eos import EquationOfSta... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/tasks/molecule.py | Python | gpl-2.0 | 8,533 | [
"ASE"
] | a63948fb9a10d69429b21b1839dbe9cf04a6cc1cb04a88c964c7e33ea5c08de7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
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 you... | LFPy/LFPy | LFPy/tools.py | Python | gpl-3.0 | 2,065 | [
"Gaussian"
] | 5c69ee11e2d9ce638c5592bd24d4612dcb4309377211703088e00132ae41427b |
'''
* Author: Lukasz Jachym
* Date: 9/14/13
* Time: 2:25 PM
*
* This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
* To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
'''
import requests
API_ENDPOINT = 'http://ws.audi... | b1r3k/recruitment-challanges | data-hacking/src/task2/lastfm_api/client.py | Python | mit | 906 | [
"VisIt"
] | 2918c55984d7585d709418f8f7803cfa9666570e559cac6a759a6b3bafc810aa |
# Natural Language Toolkit: Feature Structures
#
# Copyright (C) 2001-2006 University of Pennsylvania
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>,
# Steven Bird <sb@csse.unimelb.edu.au>
# Rob Speer (original code)
# URL: <http://nltk.sourceforge.net>
# For license information, see LICENSE.TX... | RensaProject/nodebox_linguistics_extended | nodebox_linguistics_extended/parser/nltk_lite/parse/featurestructure.py | Python | gpl-2.0 | 59,853 | [
"VisIt"
] | 68fe4c748941a8d0d9c3e5909e9cacc51ad688229780938d759e56e3cf2ed11b |
# 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... | larroy/mxnet | python/mxnet/symbol/numpy/random.py | Python | apache-2.0 | 34,763 | [
"Gaussian"
] | 5bfcac528313cd6549c14c51b0dc9bb2cb198194787074e8d10a8af2dd4adcc7 |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Dominic Lowe <d.lowe@rl.ac.uk>
#
# Contact email: d.lowe@rl.ac.uk
# ========================... | b-cube/OwsCapable | owscapable/coverage/wcs110.py | Python | bsd-3-clause | 16,494 | [
"NetCDF"
] | 869f05acfbce52486f5eeb2a9a541de6e801bd3372cd809236a8a1ffc416511b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
# Copyright (C) 2012 Michiel D. Nauta
#
# This program is free software; you can redistri... | Forage/Gramps | gramps/plugins/tool/check.py | Python | gpl-2.0 | 103,247 | [
"Brian"
] | ef00ae85045534063874e61614fa0cd3ea785d50cfb198f1530bb94837a409c7 |
"""
Test of multi-VO user metadata handling. Assumes a running Dirac instance with the (master?) FileCatalog
"""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
import unittest
import os
import sys
import os.path
import traceback
from DIRAC.Core.Base.Script... | yujikato/DIRAC | tests/Integration/DataManagementSystem/Test_UserMetadata.py | Python | gpl-3.0 | 6,041 | [
"DIRAC"
] | 71aae660f30f800242cc22bbd29783becdc10d01ecf1edec47a593e81f7a7818 |
import os, sys, time
import numpy as np
try:
# Matplotlib is not a dependency
import matplotlib as mpl
mpl.use('Agg') # force the antigrain backend
except (ImportError, RuntimeError):
mpl = None
from ase import Atoms
from ase.structure import molecule
from ase.parallel import paropen
from ase.units ... | robwarm/gpaw-symm | gpaw/test/ut_tddft.py | Python | gpl-3.0 | 11,126 | [
"ASE",
"GPAW"
] | acb8c5f003e5dfbe630862ec6a2c0322f9f6a96845ea58ad32f6a0ed888f00e2 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import tempfile, os, sys, shutil, subprocess
if sys.version_info[0] >= 3:
from urllib import request
else:
import urllib as request
from zeroinstall import support
from zeroi... | 0install/0template | retrieval.py | Python | lgpl-2.1 | 4,876 | [
"VisIt"
] | 2c56b494fc87e4e641dd061333551818ff9e546eed15ece9d00f981e9663abe9 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
from __future__ import division, print_function
import numpy as np
from astropy.io import fits as pyfits
from astropy.modeling import models
from astropy.modeling import fitting
from matplotlib import pyplot as plt
from scipy import interpolate
from scipy import signal
... | b1quint/samfp | samfp/old/spec_plot.py | Python | bsd-3-clause | 4,521 | [
"Gaussian"
] | 4ce91c4795be07b95ef1f2c966d9a7369215eed27bb1c18f72e6e8dbd763090d |
# Author: Prabhu Ramachandran
# Copyright (c) 2004, Enthought, Inc.
# License: BSD Style.
# Modified for VisTrails by the VisTrails team.
"""This module parses the VTK methods, obtains the argument and return
type information, and organizes them.
"""
import re
import vtksnl
import class_tree
import co... | VisTrails/vistrails-contrib-legacy | vtksnl/vtk_parser.py | Python | bsd-3-clause | 19,321 | [
"VTK"
] | 831575ab4128bd0035016705034e3af88a4f58bbe764341c3b0e17212bbf79cb |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import diaper
import fauxfactory
import hashlib
import iso8601
import random
import re
import command
import yaml
from contextlib import closing
from django.core.cache import cache
from django.core.exceptions import ObjectDoesNotExist
from django.core.mail... | rananda/cfme_tests | sprout/appliances/tasks.py | Python | gpl-2.0 | 83,707 | [
"VisIt"
] | cf37b065adc7c8433d3552b875ae0f9155330f85c502031adb825f84df6aaac3 |
#!/usr/bin/python
"""
!!!!!!!
NOTICE: 1/06/2012:
!!!!!!! Python control scripts have been moved from the main imsim branch
to /sims/control/python. For working with later revisions of ImSim,
please work with the separate python control branch.
Also note: use the newer .cfg files and not ... | lsst-sims/sims_phosim_pythoncontrol | generateVisits.py | Python | gpl-3.0 | 4,364 | [
"VisIt"
] | 86ac058834359d7e6b2900c74c7edd01b8ba24a48003c66c7f8530dd65b01c02 |
# -*- coding: utf-8 -*-
import os
import ast
import subprocess
import tempfile
import inflection
from ast2json import ast2json
from codetoname.features.language import language_to_extension
def extract_feature(path):
code_tree = _parse_code(path)
if not code_tree:
code_tree = _parse_code(path, py2top... | zironycho/source-code-to-name | codetoname/features/python.py | Python | apache-2.0 | 2,049 | [
"VisIt"
] | 26ffd38f59688320536fe95cf08a52fd6365f611e2d80c8635ede01a70b677c4 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/contours/inline_clip.py | Python | lgpl-2.1 | 1,529 | [
"MOOSE",
"VTK"
] | 3bbd159f1f58984f3b64683e8d71a7a00b76fe5e2bf1d5e72fe660c472578ad3 |
# -*- coding: utf-8 -*-
""" Sahana Eden Common Alerting Protocol (CAP) Model
@copyright: 2009-2015 (c) Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to dea... | tudorian/eden | modules/s3db/cap.py | Python | mit | 78,639 | [
"VisIt"
] | ff2cdb1c7036415c29bef7200d425af8581103a64637d3dd5d4bb0e14bb3a685 |
#!/usr/bin/env python
#
# Contributors:
# Zhendong Li <zhendongli2008@gmail.com>
# Qiming Sun <osirpt.sun@gmail.com>
#
from functools import reduce
import numpy
import scipy.linalg
from pyscf import gto, scf, mcscf
from pyscf import tools
mol = gto.Mole()
mol.verbose = 4
mol.output = 'hs.out'
mol.atom = '... | gkc1000/pyscf | examples/dmrg/32-dmrg_casscf_nevpt2_for_FeS.py | Python | apache-2.0 | 16,013 | [
"Jmol",
"PySCF"
] | f48559ef77603603789b23c14d72c10027079a83735a5a7eb9d489fe2e9e7024 |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2016 OpenStack Foundation
#
# 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... | openstack/swift | test/unit/proxy/test_server.py | Python | apache-2.0 | 523,774 | [
"MOOSE"
] | cf6a3e95bfad684203541437ff0dce888f9eec26dfeb4dd7b5be3d0e8f0a6573 |
# Copyright 2017 The TensorFlow Authors. 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 applica... | petewarden/tensorflow | tensorflow/python/kernel_tests/signal/spectral_ops_test.py | Python | apache-2.0 | 15,959 | [
"Gaussian"
] | f86720c253bfbfd046a44bd0af0f8d0809f0cf9ba4be765f125ed07df24b327a |
import os
import core
class EPW:
def __init__(self, epwFileAddress=None):
"""
Import epw data from a local epw file.
epwFileAddress: Local file address to an epw file
"""
if not epwFileAddress:
return
self.fileAddress = self.checkEpwFileAddress(epwFile... | antonszilasi/honeybeex | honeybeex/honeybee/ladybug/epw.py | Python | gpl-3.0 | 35,271 | [
"EPW"
] | 969eb06c009d40927141a1e6ae2964916e38c8d7f527d8fd1c48d97b8ee35003 |
__author__ = 'LT'
import numpy as np
import numpy.linalg as la
# implements lists of kernels
class Kernel(object):
@staticmethod
def gaussian(gamma):
return lambda x, y: \
np.exp(- gamma * (la.norm(x-y) ** 2)) | feuerchop/increOCSVM | kernel.py | Python | gpl-2.0 | 239 | [
"Gaussian"
] | e95dce51f924200e560394a9c7d6e0943c9f18643bc941fb6c29d115a7dc12c2 |
#!/usr/bin/env python
#==============================================================================
#
# CVS Snapshot Generation Script
# Copyright (C) 2000-2005 by Eric Sunshine <sunshine@sunshineco.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the G... | garinh/cs | bin/snapshot-cel.py | Python | lgpl-2.1 | 17,725 | [
"BLAST",
"CRYSTAL"
] | 7dbe7c8dd15164bfdee6c9ad4f75d55aa48fc6331ac91d40f6c33e3d5e8d79c3 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import warnings
from abc import abstractmethod
from math import acos, cos, exp, floor, inf, log, pi, sin, sqrt
from numbers import Number
import numpy as np
import astropy.constants as const
import astropy.units as u
from astropy.utils.compat.optional_d... | mhvk/astropy | astropy/cosmology/flrw.py | Python | bsd-3-clause | 114,859 | [
"Galaxy"
] | 0ebf7f8ca26dcfa41b71a761490b7f6fb6d1c4eb4138e97873d85478e93eb0f4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Utool is released under the Apache License Version 2.0
# no warenty liability blah blah blah blah legal blah
# just use the software, don't be a jerk.
from __future__ import absolute_import, division, print_function
from setuptools import setup
import sys
from os.path imp... | Erotemic/utool | setup.py | Python | apache-2.0 | 7,352 | [
"VisIt"
] | 60c01f51ee1a0d6abe0e895abfe12ec198ca9be429184bb6fa5b3baf600b20cf |
__author__ = 'bptripp'
import numpy as np
import matplotlib.pyplot as plt
import cPickle
from quaternion import angle_between_quaterions
# def interpolate(point, angle, points, angles, values, sigma_p=.01, sigma_a=(4*np.pi/180)):
# """
# Gaussian kernel smoothing.
# """
# # q = to_quaternion(get_rotat... | bptripp/grasp-convnet | py/interpolate.py | Python | mit | 5,452 | [
"Gaussian"
] | f98d5d3d3626964fd694b0d0f90a53342f8a68ee741d19fafea5c5223d0aa0d5 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/songs/lib/importer.py | Python | gpl-2.0 | 16,355 | [
"Brian"
] | f111a24d6d95db7d030beb3b7f8ce4f478ece6190b53f79db2036816e727f9db |
#!/usr/bin/env python
''' script for filtering insertions vs. the human reference GRCh37/hg19 '''
''' may be useful as a template for extension to other species '''
import pysam
import sys
import os
import logging
import argparse
import align
import numpy as np
import subprocess
from uuid import uuid4
ver... | adamewing/tebreak | scripts/misc/annotate_chimera.py | Python | mit | 7,354 | [
"pysam"
] | 72de04e9649720a645f17af7bfa27d3c56ecdf2322b78d20dcdd65aebfdb9be1 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import platform
import sys
import os
from spack import *
import llnl.util.tty as tty
class Namd(MakefilePackage, CudaPac... | iulian787/spack | var/spack/repos/builtin/packages/namd/package.py | Python | lgpl-2.1 | 9,781 | [
"NAMD"
] | 367bc372b610b42ae68e28ec91d95c8490a2a20c25f82733294a058d862ba89d |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/geom/tests/test_geom.py | Python | bsd-3-clause | 3,373 | [
"NEURON"
] | 6181fc521976149f3dd4239d968275d09a592daf79f3d09a6246bdae9053e68f |
# (C) British Crown Copyright 2010 - 2013, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | kwilliams-mo/iris | lib/iris/tests/test_trajectory.py | Python | gpl-3.0 | 8,439 | [
"NetCDF"
] | 5eaad81ae71a0eea10914286c9e54ca74ec7a1e165b693df68694a251bfda7d9 |
# $Id$
# Hop --- a framework to analyze solvation dynamics from MD simulations
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | Becksteinlab/hop | hop/siteanalysis.py | Python | gpl-3.0 | 58,836 | [
"MDAnalysis"
] | 4e346c5d5dd899db7967ee8be01d88b364d7730959eef0c2fe7c1428e031deea |
import logging
import re
import cgi
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.exceptions import ImproperlyConfigured
from django.shortcuts import redirect
from django.utils.translation import ugettext as _
from wiki.core.exceptions import NoRootURL
from wiki.models... | XiaodunServerGroup/xiaodun-platform | lms/djangoapps/course_wiki/views.py | Python | agpl-3.0 | 4,341 | [
"VisIt"
] | e4ad36ebabb36a99f5baa364ad66a3b265254f3bab5537f2a75c6dfe368fc296 |
#!/usr/bin/env python
"""Module cma implements the CMA-ES, Covariance Matrix Adaptation Evolution
Strategy, a stochastic optimizer for robust non-linear non-convex
derivative-free function minimization for Python versions 2.6, 2.7, 3.x
(for Python 2.5 class SolutionDict would need to be re-implemented, because ... | raphaelvalentin/qtlayout | syntax/optimize/cma/cma-0.92.04/cma.py | Python | gpl-2.0 | 308,029 | [
"exciting"
] | 67ca281541617c8735119d621f1e9b3cce6efb7f69f2c0f89e948b3d07a823e9 |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library i... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/soffice/script_utilities.py | Python | gpl-3.0 | 16,643 | [
"ORCA"
] | 7d1140c0eeb7a421dc2e2a4b1f77eddd810bb109932946b0d3dd2e111b62e01b |
# $HeadURL$
""" SystemAdministrator service is a tool to control and monitor the DIRAC services and agents
"""
__RCSID__ = "$Id$"
import datetime
import socket
from types import ListType, StringTypes, BooleanType
import os, re, commands, getpass, importlib
from datetime import timedelta
from DIRAC import S_OK, S_ERR... | vmendez/DIRAC | FrameworkSystem/Service/SystemAdministratorHandler.py | Python | gpl-3.0 | 23,269 | [
"DIRAC"
] | ad77e7be3ffdf15681a73a49f2432740b49bb7df973f89533e02c3415edee72f |
import os
from flask import Flask, render_template, request, redirect, url_for
from flask_pymongo import PyMongo
from flask_googlemaps import GoogleMaps
from flask_googlemaps import Map
from flask_login import LoginManager, login_required, login_user, logout_user, current_user
app = Flask(__name__, static_folder="stati... | YaxinCheng/WebResume | 1.0/app.py | Python | apache-2.0 | 6,618 | [
"VisIt"
] | ef24aa5f5b6a3fac3940a88a0fa28f14bc7641b6f5abb86ec8340ab8795accca |
"""Support for Abinit input variables."""
import collections
import string
import numpy as np
__all__ = [
"InputVariable",
]
_SPECIAL_DATASET_INDICES = (":", "+", "?")
_DATASET_INDICES = "".join(list(string.digits) + list(_SPECIAL_DATASET_INDICES))
_INTERNAL_DATASET_INDICES = ("__s", "__i", "__a")
_SPECIAL_CO... | materialsproject/pymatgen | pymatgen/io/abinit/variable.py | Python | mit | 6,652 | [
"ABINIT"
] | 270d3f5873b43638b04248c9fffbb6fd162e4a427b38e661cdbf8d14bcb98c17 |
# setuptools installation of Hop
# Copyright (c) 2007-2013 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
from __future__ import print_function
from setuptools import setup, find_packages
import versioneer
import sys
if sys.... | Becksteinlab/hop | setup.py | Python | gpl-3.0 | 2,255 | [
"MDAnalysis"
] | fe250c05f107353371a73905efe0db6837e8ac5d0d3206e015ad6cf52dab6d49 |
import sys, os
sys.path.insert(1, os.path.join("..",".."))
import h2o
from tests import pyunit_utils
def weights_and_distributions():
htable = h2o.upload_file(pyunit_utils.locate("smalldata/gbm_test/moppe.csv"))
htable["premiekl"] = htable["premiekl"].asfactor()
htable["moptva"] = htable["moptva"].asfactor()
... | pchmieli/h2o-3 | h2o-py/tests/testdir_algos/deeplearning/pyunit_weights_and_distributions_deeplearning.py | Python | apache-2.0 | 1,285 | [
"Gaussian"
] | 6a3a81dad5207b6800d157d4358e4015457c5d222b3ea47e5a11ffb15feca2c3 |
import datetime
import functools
from numbers import Number
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Hashable,
Iterable,
List,
Mapping,
Optional,
Sequence,
Tuple,
TypeVar,
Union,
cast,
)
import numpy as np
import pandas as pd
from ..plot.plot imp... | xray/xray | xarray/core/dataarray.py | Python | apache-2.0 | 148,815 | [
"NetCDF"
] | 888a4b780466988bab6a6926c7e66e4c807c45d2af070397c6bba51e4853680d |
# 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/ParticleGroup.py | Python | gpl-3.0 | 1,885 | [
"ESPResSo"
] | ce3f970ec2364aec6de7fbd6255d8312ea3a265b96fb7624b770aa00492681a1 |
"""
.. automodule::
:members:
Trajectories Class
==================
.. autoclass:: Trajectories
:members:
"""
try:
from mayavi import mlab
from tvtk.tools import visual
except:
print('mayavi not installed')
import numpy as np
import scipy as sp
import pdb
import matplotlib.pyplot as plt
import py... | dialounke/pylayers | pylayers/mobility/trajectory.py | Python | mit | 23,362 | [
"Mayavi"
] | 54e13fe641a11d46401cea71790cd892211c5f746a01bb44d49701b02cb86756 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# crystals.py
# Copyright (C) 2018 xent
# Project is distributed under the terms of the GNU General Public License v3.0
import numpy
import exporter
import primitives
class CrystalSMD(exporter.Footprint):
def __init__(self, spec, descriptor):
super().__init... | stxent/kmodgen | footprints/crystals.py | Python | gpl-3.0 | 4,449 | [
"CRYSTAL"
] | a78f2f911bf731457affe6ec51d057c00df74869ad0bf7a4722489c73bb2dad6 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import os
import sys
import sphinx_rtd_theme
# import pkg_resources
# -*- coding: utf-8 -*-
#
# Pyro documentation build configuration file, created by
# sphinx-quickstart on Thu Jun 15 17:16:14 2017.
#
# This file is execfile()... | uber/pyro | docs/source/conf.py | Python | apache-2.0 | 6,902 | [
"Biopython"
] | 0e45a1a54c9054324171f286830e5de350c5e215d60a66ba4179498520b84822 |
## twofish.py - pure Python implementation of the Twofish algorithm.
## Bjorn Edstrom <be@bjrn.se> 13 december 2007.
##
## Copyrights
## ==========
##
## This code is a derived from an implementation by Dr Brian Gladman
## (gladman@seven77.demon.co.uk) which is subject to the following license.
## This Python implement... | pschmitt/pykeepass | pykeepass/kdbx_parsing/pytwofish.py | Python | gpl-3.0 | 15,444 | [
"Brian"
] | 166be34c7cbda5b36069a3226a5197fa64dd389f0c7bb2294c19d13251e16d4c |
import numpy as np
import tensorflow as tf
from yadlt.models.boltzmann import rbm
from yadlt.utils import datasets, utilities
# #################### #
# Flags definition #
# #################### #
flags = tf.app.flags
FLAGS = flags.FLAGS
# Global configuration
flags.DEFINE_boolean('encode_train', False, 'Whether... | blackecho/Deep-Learning-TensorFlow | cmd_line/boltzmann/run_rbm.py | Python | mit | 4,657 | [
"Gaussian"
] | 6f3df3393e68154a2271f36a6e2a4447b440d74b6b3768bec44084396a5abd7c |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-lfn-replicas
# Author : Stuart Paterson
########################################################################
"""
Obtain replica information from file catalogue client.
Example:
$ dirac-dms-lfn-... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_lfn_replicas.py | Python | gpl-3.0 | 1,587 | [
"DIRAC"
] | 5f91dd336ba8845797fb8bebe0bb3678a129103b3b1f44d98c1cef9e5d0b9460 |
#!/usr/bin/python
"""Test of sayAll."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(utils.StartRecordingAction())
sequence.append(KeyComboAction("KP_Add"))
sequence.append(utils.AssertPresentationAction(
"1. KP_Add to do a SayAll",
["SPEECH OUTPUT: 'FAQ'",
"S... | pvagner/orca | test/keystrokes/firefox/say_all_empty_anchor.py | Python | lgpl-2.1 | 1,470 | [
"ORCA"
] | 441517d4887737aa529acef92ff2e1fcb3abd7f508e415bedb8f2a4b7d5dbc4c |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 2012, 2013 CERN.
##
## Invenio 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 (at yo... | labordoc/labordoc-next | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 103,043 | [
"ADF"
] | 00719aea5a39b2520c783aa0a2b7f6c85be19b3765a3883ea7de55e12f5eda00 |
#!/usr/bin/python
# usage: python upload.py --file test/test.mp4 --noauth_local_webserver
import http.client
import httplib2
import os
import random
import sys
import time
from apiclient.discovery import build
from apiclient.errors import HttpError
from apiclient.http import MediaFileUpload
from oauth2client.client ... | kidsfm/cms | youtube/upload.py | Python | gpl-3.0 | 6,858 | [
"VisIt"
] | 296ca683c8fa9e1c4ad4de4972c4fc079566a2937b0d7768e3d92c181d4b4175 |
# ----------------------------------------------------------------------------
# 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/tests/test_workflow.py | Python | bsd-3-clause | 13,199 | [
"scikit-bio"
] | 9ec5f3dbc8db1947ac6e6ba427b66754d5122e3a619cff9a80aa5a1cc7ab1a82 |
# pylint: disable=missing-docstring
# pylint: disable=no-member
# pylint: disable=redefined-outer-name
import os
from logging import getLogger
from django.conf import settings
from lettuce import step, world
from selenium.webdriver.common.keys import Keys
from openedx.core.lib.tests.tools import assert_in # pylint:... | philanthropy-u/edx-platform | cms/djangoapps/contentstore/features/common.py | Python | agpl-3.0 | 12,791 | [
"VisIt"
] | fe3a525e9a1e20aeeccf25b8da6648f7d82bfc82c249c64c817a6ae145cc26e6 |
try: paraview.simple
except: from paraview.simple import *
def RequestDataDescription(datadescription):
"Callback to populate the request for current timestep"
if datadescription.GetForceOutput() == True:
for i in range(datadescription.GetNumberOfInputDescriptions()):
datadescription.GetIn... | openmichigan/PSNM | NavierStokes/Programs/NavierStokes3dFortranMPIParaView/node-based/pipeline.py | Python | bsd-2-clause | 23,765 | [
"ParaView"
] | b6f7cf72fd027980d414d817ac3bdf5fee8739ebf145e7f4df12f9810055d308 |
#!/usr/bin/env python
"""Automatically install required tools and data to run bcbio-nextgen pipelines.
This automates the steps required for installation and setup to make it easier to get started with
bcbio-nextgen. The defaults provide data files for human variant calling.
Requires: git, wget, bgzip2, Python 3 or 2... | chapmanb/bcbio-nextgen | scripts/bcbio_nextgen_install.py | Python | mit | 13,409 | [
"BWA",
"Bioconda",
"Bowtie",
"Galaxy"
] | 37709c321b7fa0e66671b5d96683ce6da439adf43992ea199e2fe75dc524dd3e |
import argparse
import imp
import os
import re
from functools import wraps
from operator import methodcaller
import orca
from flask import (
Flask, abort, jsonify, request, render_template, redirect, url_for)
from pygments import highlight
from pygments.lexers import PythonLexer
from pygments.formatters import Htm... | jiffyclub/orca | orca/server/server.py | Python | bsd-3-clause | 13,114 | [
"ORCA"
] | 05cc14ba4d707060bef4d40dba84c6e42df0ed77991bf759eb0d192f1244ea9c |
#!/usr/bin/env python
import argparse
import pysam
import numpy as np
import pandas as pd
import sys
# use matplotlib without x-server
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
"""
Simulator reads have 'fwd' and 'rev' appended to their pair names
"""
simu_parser = lambda r: (r.qname[:-3]... | koadman/proxigenomics | simulation/hic_simulator/src/contact_map.py | Python | gpl-2.0 | 12,249 | [
"pysam"
] | bca203fa56677a679a4607f023ad38c0576ecdbb2238fb4b852068bc8b95ae01 |
#!/usr/bin/env python
#######################################################################################
### ###
### Copyright (C) 2017 Pawel Krawczyk (p.krawczyk@ibb.waw.pl) ###
### ... | smaegol/LINE_1_RACE_seq_analysis | analyze_race_seq.py | Python | gpl-3.0 | 66,937 | [
"Bowtie"
] | 004f8676f465f9b4af1e8c3acb765c5b92bb1785f16beaa94854b715f381dc58 |
# Portions Copyright (c) Facebook, Inc. and its affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# match.py - filename matching
#
# Copyright 2008, 2009 Matt Mackall <mpm@selenic.com> and others
#
# This software may be used and distribute... | facebookexperimental/eden | eden/hg-server/edenscm/mercurial/match.py | Python | gpl-2.0 | 53,143 | [
"VisIt"
] | 0e9b4ed0e3b193efb0f0c4d26649dbbae1559b15537828f4310d36f768f52ce5 |
import fileinput
from Game import Game
from Team import Team
from datetime import date
class HReferenceParser:
mode = 1
csvPath = ""
teams = {
'Anaheim Ducks' : 'ANA',
'Boston Bruins' : 'BOS',
'Buffalo Sabres' : 'BUF',
'Calgary Flames' : 'CGY',
'Carolina Hurricanes' : 'CAR',... | cabusto/nhlchampionshipbelt | app/HReferenceParser.py | Python | mit | 2,561 | [
"COLUMBUS"
] | c42706ddb0e82a712062a4fc558a9b02cd44075709bc3a44a82fc2ba4db37f90 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2017, Cisco and/or its affiliates.
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from ansible.module_utils.basic import env_fallback
from ansible.module_utils.urls import open_url
from ansible.module_utils._text import to_text
im... | alxgu/ansible | lib/ansible/module_utils/network/nso/nso.py | Python | gpl-3.0 | 30,015 | [
"VisIt"
] | cc66603d130e5587b1881913dc4ebf6abf11279b8ef3c2485c5e116e28d9d801 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | evolve/core/mutators.py | Python | agpl-3.0 | 45,090 | [
"Gaussian"
] | 6698990207a2cf8c5f2527a51831d830ebc0fa58f9163ee5cd0bc1da58e0b59f |
import multiprocessing as mp
import random
def obscene_overcalculation(x):
blast = [random.randint(0, 1E6) for element in range(x)]
blorst = sum(blast[0::2]) - sum(blast[1::2])
return blorst
if __name__ == '__main__':
pool = mp.Pool(processes=4)
results = pool.map(obscene_overcalculation, range(... | whitehaven/Cryophor-cryOS | experimental/multiprocessing_experiment.py | Python | gpl-3.0 | 382 | [
"BLAST"
] | edd8743ba339fde1652f44918e4da04ff097c22c07ca5382cca437b0f27a8ef7 |
# Copyright 2015 The TensorFlow Authors. 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 applica... | ryfeus/lambda-packs | Tensorflow_Pandas_Numpy/source3.6/tensorflow/python/ops/gradients_impl.py | Python | mit | 38,970 | [
"VisIt"
] | ad8dc29bec8e2436abcc54046cf3cf15a4d624a86ba0132ed4074b04c7e4ef19 |
# Copyright (c) 2006-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2013-2015 Google, Inc.
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Michal Nowikowski <godfryd@gmail.com>
# Copyright (c) 2015 Mike Frysinger <vapier@gentoo.org>
# Copyright (c) 2015 Mihai ... | rogalski/pylint | pylint/checkers/format.py | Python | gpl-2.0 | 43,749 | [
"VisIt"
] | 964c8f98d082c8af90117c293e83f1c0c1002061f495b508e88c4b668669bc54 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# ... | dictoon/blenderseed | translators/__init__.py | Python | mit | 1,369 | [
"VisIt"
] | a592b1d91a5f425d4681cbfc3a1c3fea65e1c87c6efc8bc65d8e90124e36d03f |
# -*- coding: utf-8 -*-
""" Sahana Eden Population Outreach Models
@copyright: 2015-2016 (c) Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the S... | flavour/ifrc_qa | modules/s3db/po.py | Python | mit | 39,079 | [
"VisIt"
] | 30c6b0f317641cad38835d1660a40fbc946fb46c87e232eef2f71d5954f35149 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Entries are containers for calculated information, which is used in
many analyses. This module contains entry related tools and implements
the base Entry class, which is the basic entity that can be used to... | davidwaroquiers/pymatgen | pymatgen/entries/__init__.py | Python | mit | 6,060 | [
"pymatgen"
] | 1b6e78829d1a7844ef490ebad9132ce91a00cf22eeb1fe748bf1341b55c7ef2c |
# Orca
#
# Copyright 2007-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | h4ck3rm1k3/orca-sonar | src/orca/app_gui_prefs.py | Python | lgpl-2.1 | 11,458 | [
"ORCA"
] | 13a25b28c86de60740075e09ceadba6273f7bdf17506ccda16e02380c1214c2e |
# -*- coding: utf-8 -*-
import unittest
import os
from os import getenv
from os.path import expanduser
import logging # https://docs.python.org/2/library/logging.html#logging-levels
import glob
import sys
sys.path.append( os.getcwd() )
sys.path.insert( 1, 'lib' ) #Pickup libs, rdflib etc., from shipped lib directory
... | unor/schemaorg | tests/test_graphs.py | Python | apache-2.0 | 19,165 | [
"ASE"
] | b66c17c79616c645327982b1d6ab78ef99f67eaec508445f3e9305ee3430082f |
# -*- coding: utf-8 -*-
"""
ambari_jinja2.compiler
~~~~~~~~~~~~~~~
Compiles nodes into python code.
:copyright: (c) 2010 by the Jinja Team.
:license: BSD, see LICENSE for more details.
"""
from cStringIO import StringIO
from itertools import chain
from copy import deepcopy
from ambari_jinja2 impor... | alexryndin/ambari | ambari-common/src/main/python/ambari_jinja2/ambari_jinja2/compiler.py | Python | apache-2.0 | 61,433 | [
"VisIt"
] | a9c1fba607e725c5e2b40aa135c527fdd1bcd8ec632913d045bd91b3fea8c42d |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
aren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(aren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
#
# Create surfaces F(x,y,z) = constant
#
# Sampl... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/ContourQuadric.py | Python | apache-2.0 | 1,714 | [
"VTK"
] | b0690059143e6251c2584418b2b97cacbd18b476f78ee3bf13e8316e66cb6c80 |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems 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.o... | Bam4d/neon | tests/test_model.py | Python | apache-2.0 | 5,883 | [
"Gaussian"
] | 7815e6b40c03cc6a11033a224a62292862a1ed3561ca8e18ea44a017f21ac265 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/driver/qcdb/orca.py | Python | gpl-2.0 | 13,133 | [
"ORCA",
"Psi4"
] | 6d9e905d2aee8768b3d52892eab1920db4d15ccc32f8bede1b1c7ccaf8d428f2 |
#!/usr/bin/env python
# encoding: utf-8
class Table(object):
def config_db(self, pkg):
tbl = pkg.table('nazione', pkey='code', name_long='Nazione', rowcaption='code,name')
tbl.column('code', size='2', group='_', readOnly=True, name_long='!!Code')
tbl.column('name', size=':48', name_long='!!... | poppogbr/genropy | packages/glbl/model/nazione.py | Python | lgpl-2.1 | 17,103 | [
"BWA"
] | 3eb715157e07eb33d798a8fa27a4161494827c2576cf3b1decc50b24fdfec1bb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import datetime as dt
import httplib as http
import logging
import unittest
import httpretty
import markupsafe
import mock
from nose.tools import * # flake8: noqa (PEP8 asserts)
import re
from addons.wiki.utils import to_mongo_key
fr... | aaxelb/osf.io | tests/test_webtests.py | Python | apache-2.0 | 46,618 | [
"VisIt"
] | 2b7b84dd02d1807ec2b36a466fd8ac398f08c9a25252b37316ef92f2a9279b86 |
"""
Test suite for EgadsData class.
Uses NetCDF4 Python library to test know inputs and outputs against the EGADS
NetCDF library (based on NetCDF4).
"""
__author__ = "mfreer, ohenry"
__date__ = "2016-12-6 11:19"
__version__ = "1.1"
import unittest
import egads
import numpy
from numpy.testing import assert_array_equa... | eufarn7sp/egads-eufar | egads/tests/egads_tests.py | Python | bsd-3-clause | 9,020 | [
"NetCDF"
] | bda253caa1e14e97e3099448b0836dd705bff9cf1a5ba447cabeabccf183a06b |
# 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.
"""Parser for PDB files."""
import warnings
import numpy
from Bio.PDB.PDBExceptions i... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/PDBParser.py | Python | gpl-2.0 | 12,166 | [
"Biopython"
] | bfa839c3b8ac50578aa9ed82f33c6d9ebf79361d18e46aec6d25810ec8be60fc |
#!/usr/bin/python
"""
This module contains an OpenSoundControl implementation (in Pure Python), based
(somewhat) on the good old 'SimpleOSC' implementation by Daniel Holth & Clinton
McChesney.
This implementation is intended to still be 'simple' to the user, but much more
complete (with OSCServer & OSCClient classes) ... | benji-york/x32-player | OSC.py | Python | gpl-3.0 | 89,911 | [
"VisIt"
] | 7927841f99db2e59469c00197bb4179bd017b7806817e062f3d7cec43a4ab001 |
"""Input handling and transformation machinery.
The first class in this module, :class:`InputSplitter`, is designed to tell when
input from a line-oriented frontend is complete and should be executed, and when
the user should be prompted for another line of code instead. The name 'input
splitter' is largely for histor... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/core/inputsplitter.py | Python | bsd-3-clause | 23,152 | [
"Brian"
] | 8fc8e9fe896512aea027c7469a2f2c336041218bfd2366e0ad69c4efbcf50d01 |
"""
This sample sets up a polymer and tests the available cell systems.
"""
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013-2018 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 Publ... | hmenke/espresso | samples/cellsystem_test.py | Python | gpl-3.0 | 2,597 | [
"ESPResSo"
] | c932046af467c1f00779eba5d5921a8a60c91c46f9b4c47ce8112c9f8383eb9e |
#!/usr/bin/env python
#
# This file is part of Buildbot. Buildbot 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.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# A... | cmouse/buildbot | master/setup.py | Python | gpl-2.0 | 22,767 | [
"Brian"
] | 62c810c1a2cbedf378786e769383e09fe49a3773810382571e6572e405acf03b |
# pylint: disable=missing-docstring
import json
import platform
import re
import time
from textwrap import dedent
from urllib import quote_plus
# django_url is assigned late in the process of loading lettuce,
# so we import this as a module, and then read django_url from
# it to get the correct value
import lettuce.d... | a-parhom/edx-platform | common/djangoapps/terrain/ui_helpers.py | Python | agpl-3.0 | 21,614 | [
"VisIt"
] | 9d1d5a05934470e769557b65ea856710b884e1b8868f1735984fb01666f77e21 |
# Author: Travis Oliphant 2001
# Author: Nathan Woods 2013 (nquad &c)
from __future__ import division, print_function, absolute_import
import sys
import warnings
from functools import partial
from . import _quadpack
import numpy
from numpy import Inf
__all__ = ['quad', 'dblquad', 'tplquad', 'nquad', 'quad_explain',
... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/scipy/integrate/quadpack.py | Python | agpl-3.0 | 28,448 | [
"Gaussian"
] | 2ae9f2de071c50e939503489624a8741b131680bf2e977a2391f098ffb11a48c |
## \example pmi/atomistic.py
"""This script shows how to simulate an atomic system with MD,
with a secondary structure elastic network to speed things up.
"""
from __future__ import print_function
import IMP
import IMP.atom
import IMP.rmf
import IMP.pmi
import IMP.pmi.topology
import IMP.pmi.dof
import IMP.pmi.macros
... | shanot/imp | modules/pmi/examples/atomistic.py | Python | gpl-3.0 | 2,687 | [
"CHARMM"
] | 4df762f1043e00107271acce3dfec3f0cd4b3d6424383a46c60000a32c02d329 |
""" codecs -- Python Codec Registry, API and helpers.
Written by Marc-Andre Lemburg (mal@lemburg.com).
(c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
"""#"
import __builtin__, sys
### Registry and builtin stateless codec functions
try:
from _codecs import *
except ImportError, why:
raise SystemErr... | willworth/thermos | thermos/Lib/codecs.py | Python | mit | 36,098 | [
"FEFF"
] | 462b4ba27bca6b7c1e6718f587ce75f4bf95bfd929e5a961ab4dd25141cf413f |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.moltemplate.org
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
ttree.py is a simple... | quang-ha/lammps | tools/moltemplate/moltemplate/ttree.py | Python | gpl-2.0 | 237,497 | [
"LAMMPS",
"VisIt"
] | 88d2cff51e19c63127f75d6e788da1ea42c1a2c5ef4359eb3117102ea795a532 |
from rdkit import RDConfig
import unittest
from rdkit import Chem
from rdkit.Chem import Draw,AllChem
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test1(self) :
m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
AllChem.Compute2DCoords(m)
d = Draw.MolDraw2DSVG(300,300)
... | AlexanderSavelyev/rdkit | Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py | Python | bsd-3-clause | 925 | [
"RDKit"
] | a46b68267b4e88fe11cda3277dbdb5f61e2852ddea591e620dee5526e5a8ac05 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pprint
import sys
import textwrap
import py
import pytest
from _pytest.main import _in_venv
from _pytest.main import EXIT_NOTESTSCOLLECTED
from _pytest.main import Session
class TestCollector(object)... | txomon/pytest | testing/test_collection.py | Python | mit | 38,814 | [
"VisIt"
] | 92b45799aadf32076c8c33d433967ba18490d3c3ae3a1860b706ffa76e06f77e |
# -*- coding: utf8 -*-
from setuptools import setup
from os import path
this_directory = path.abspath(path.dirname(__file__))
with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
setup(name='tmscoring', version='0.4.post0',
description='Python implementation ... | Dapid/tmscoring | setup.py | Python | bsd-3-clause | 1,167 | [
"Biopython"
] | ce9c2cdbc5a8a004577396530df554d9413db8f61d84dc8066d8ff96267a3e13 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General... | Forage/Gramps | gramps/plugins/tool/extractcity.py | Python | gpl-2.0 | 25,451 | [
"Brian"
] | 425a00e5dd852ef677091f9cf34fe84134cdd1b6d05a9ad97928c0950b57d164 |
# 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.
#Python stuff
from string import atoi, atof, letters
from Numeric import array, Float0
# ... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/MMCIFParser.py | Python | apache-2.0 | 5,760 | [
"Biopython"
] | 13287788ff77b205055927d3d0308d1b86a605dfa4d44856dbe70f2cea807bcd |
#!/usr/bin/env python
#import argparse
#from glob import glob
#Usage: python ../fox_wgs/jointgenotyping_GATK.py
#-s ./samples.txt
#-b /mnt/lfs2/hend6746/wolves/reference/canfam31/canfam31.fa
from os.path import join as jp
from os.path import abspath
import os
import sys
import argparse
parser = argparse.ArgumentPa... | shendri4/wolves_capture_130 | GATK_merge_GVCF_wolves.py | Python | apache-2.0 | 2,352 | [
"BWA"
] | 5e5d3f7c89fe37f6af462b0c5169869b0f3cea1ad9a9ae6dcb8506ac6f4b1fbb |
import numpy as np
import sys
import os
import time
from ase.units import Bohr
from ase.lattice import bulk
from gpaw import GPAW, PW
from gpaw.test import findpeak
from gpaw.eigensolvers.rmm_diis_old import RMM_DIIS
from gpaw.mixer import Mixer
from gpaw.atom.basis import BasisMaker
from gpaw.response.df import Dielec... | robwarm/gpaw-symm | gpaw/test/aluminum_EELS.py | Python | gpl-3.0 | 2,216 | [
"ASE",
"GPAW"
] | e58a4371f60034e430ae11fca485f49c6457aa14fde2aebb77f9e4c8bb67dd5c |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | liumingxing/titanium_module_alipay_ios | iphone/build.py | Python | mit | 8,504 | [
"VisIt"
] | eb2188ad4184d75e3ea6cbc45a5d521838113416292b4b6a28163224743d7d12 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Translate NetCDF files to GeoTiff format
IMPORTANT: GDAL >=1.10.1 compiled with libnetCDF
and GDAL Python bindings
Author: Cayetano Benavent Vinuales 2014
GIS Analyst at
www.geographica.gs
"""
# This program is free software; you can... | GeographicaGS/Medinageoportal | data_tools/netCDF_translate.py | Python | gpl-3.0 | 4,043 | [
"NetCDF"
] | 4cfaaaaa0728c7aeb1f2e6c90ee9d7836fb1c864a7b5d80b639b41d1e58cb450 |
#!/usr/bin/python
# 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) any later version.
#
# Ansible is distributed... | amandolo/ansible-modules-core | cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,335 | [
"Dalton"
] | cb277058b827b1f600a7f236364214b5b14f290fa50d3d81ed029fe8d2d886bf |
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