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"""
Test Python-side generation of cube files
"""
import psi4
from .utils import compare_cubes
def test_pyside_cubegen():
mol = psi4.geometry("""
O 0 0 0
H 0 0 1.795239827225189
H 1.693194615993441 0 -0.599043184453037
symmetry c1
units au
""")
psi4.core.be_qui... | jgonthier/psi4 | tests/pytests/test_pyside_cubegen.py | Python | lgpl-3.0 | 1,124 | [
"Psi4"
] | 254e3fc485e61dcd509d2014cfb491d3be9f53cadbd4d88f8e6579da93192753 |
""" Cache for the Plotting service plots
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os.path
import time
import threading
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.DictCache import DictCache
from D... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/Service/PlotCache.py | Python | gpl-3.0 | 2,364 | [
"DIRAC"
] | 726c5898ec3d4bc5a93e973675b2bc891811e69376da4c00697d9f08502b2a1b |
#
# This file is part of the Pi Entertainment System (PES).
#
# PES provides an interactive GUI for games console emulators
# and is designed to work on the Raspberry Pi.
#
# Copyright (C) 2014-2021 Neil Munday (neil@mundayweb.com)
#
# PES is free software: you can redistribute it and/or modify
# it u... | neilmunday/pes | lib/pes/app.py | Python | gpl-3.0 | 133,635 | [
"VisIt"
] | 0fcf13df50efea56e4dc3634d83f55e3588ae04c59bc60f4ffe9a374ff942d16 |
import os
import multiprocessing
import asyncore
import datetime
class Status(object):
"""process status enum"""
REDY, RUNN, RSTT, STNG, KLNG, STPD, EXTD = \
'READY', 'RUNNING', 'RESTARTING', \
'STOPPING', 'KILLING', 'STOPPED', 'EXITED'
class Process(asyncore.file_dispatcher):
"""main p... | eseom/glide | glide/process.py | Python | mit | 5,210 | [
"BLAST"
] | 5fb6b39466fb867692b4b8dc4c61371e9ec0bad9ba8bad7d59e216aae53b5fd9 |
""" core implementation of testing process: init, session, runtest loop. """
import py
import pytest, _pytest
import os, sys, imp
tracebackcutdir = py.path.local(_pytest.__file__).dirpath()
# exitcodes for the command line
EXIT_OK = 0
EXIT_TESTSFAILED = 1
EXIT_INTERRUPTED = 2
EXIT_INTERNALERROR = 3
EXIT_USAGEERROR = ... | npinto/pytest | _pytest/main.py | Python | mit | 20,958 | [
"VisIt"
] | 26d3491699307820aed2b98ff52474ffa1e45bc12053dea28339fa0df3dfefec |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alxgu/ansible | lib/ansible/modules/network/avi/avi_networkprofile.py | Python | gpl-3.0 | 3,909 | [
"VisIt"
] | cacdbc67eebbc9d93eb00d7c071455c1307a9c781a2997f798acbdfdc3556fae |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ve... | vidartf/hyperspy | hyperspy/tests/model/test_model_as_dictionary.py | Python | gpl-3.0 | 9,162 | [
"Gaussian"
] | 635485d9265a09a0e6aa40291dfc5fe7629b5a90ec6078c0a77b90966c1b542c |
# pybuilder_header_plugin
# Copyright 2015 Michael Gruber
#
# 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 ... | arcivanov/pybuilder_header_plugin | build.py | Python | apache-2.0 | 2,364 | [
"VisIt"
] | f921e9c95b2effbebbb5c1d7d8c879d1d2bc434f3922daad910bd90a5acbade0 |
#!/usr/bin/env python3
"""
Creates graph of three modeled hydrology-related time series from a single file.
"""
# example from grid-sequencing example:
# $ ./hydro-tsshow.py foo.png ts_routing-decoupled.nc
from numpy import *
import pylab as plt
import sys
try:
import netCDF4 as netCDF
except:
print("netCD... | pism/pism | examples/std-greenland/hydro/hydro-tsshow.py | Python | gpl-3.0 | 1,611 | [
"NetCDF"
] | 2524143cc3cf8e6ec14b98aaefe5f045a7e5771748cf30356c337b0c643842c2 |
# -*- coding: utf-8 -*-
"""A plugin that extracts browser history from events."""
import collections
import re
from urllib import parse as urlparse
from plaso.analysis import interface
from plaso.analysis import logger
from plaso.analysis import manager
class BrowserSearchPlugin(interface.AnalysisPlugin):
"""Ana... | Onager/plaso | plaso/analysis/browser_search.py | Python | apache-2.0 | 10,159 | [
"VisIt"
] | 6c960f517db43d1ae4112d0fc676d602f87ca20a3799d0e3023d9763c8e8be50 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/diversity/tests/test_driver.py | Python | bsd-3-clause | 29,199 | [
"scikit-bio"
] | f8d4d9258bb40a7f0f44ab156f0ef0771c572d3c213dc032e8343eb7ac46f0e3 |
# -*- coding: utf-8 -*-
#
# GromacsWrapper documentation build configuration file, created by
# sphinx-quickstart on Tue Jun 23 19:38:56 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't ... | jandom/GromacsWrapper | doc/sphinx/source/conf.py | Python | gpl-3.0 | 6,620 | [
"Gromacs"
] | 0e9941eb9367063f6ae488c9bd5fd965920ec102594fb3cbe96e507725ddff94 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | tatiana/invesalius | invesalius/reader/dicom_reader.py | Python | gpl-2.0 | 6,119 | [
"VTK"
] | 5716333302593cd26540a4dd2f2da0c9809e65ee2267ed39128cd8bbb7bce369 |
# Copyright 2009-2014 Eucalyptus Systems, Inc.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; version 3 of the License.
#
# This program is distributed in the hope that it will be useful,
# b... | eucalyptus/eucalyptus-database-server | eucadb/config.py | Python | bsd-2-clause | 3,228 | [
"VisIt"
] | fb7f2d9ccd077e28db50dcf69d5ff79bc4fdc3a01e2de6b9b93e637a1f649588 |
# Copyright 2016 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... | maciekcc/tensorflow | tensorflow/python/ops/distributions/distribution.py | Python | apache-2.0 | 38,421 | [
"Gaussian"
] | 52b1f6e56430215d9be30f1664ecdec5c09c9fe81be83c55c62b8ced99dba09c |
######################################################################
# SolvationToolkit: A toolkit for setting up molecular simulations of mixtures
# Copyright 2011-2016 UC Irvine and the Authors
#
# Authors: David Mobley and Gaetano Calabro
# With thanks to Kyle Beauchamp, whose liquid_tools.py provided an initial b... | nividic/SolvationToolkit | solvationtoolkit/solvated_mixtures.py | Python | lgpl-2.1 | 30,218 | [
"Amber",
"Gromacs",
"MDTraj",
"OpenMM"
] | bc549487400c97e7bef19f03847e477c644705c4768f2efb9394850cd16966c3 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Cblas(Package):
"""The BLAS (Basic Linear Algebra Subprograms) are routines that
pr... | LLNL/spack | var/spack/repos/builtin/packages/cblas/package.py | Python | lgpl-2.1 | 1,360 | [
"BLAST"
] | 641dec226b8f6fc2037a703984c23575c829513f14966aeb339fe184330afce9 |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
"""Validator classes are used for ComplexInputs, to... | tomkralidis/pywps | pywps/validator/complexvalidator.py | Python | mit | 10,267 | [
"NetCDF"
] | 11f96e3c046eb673c161ee704a92cd97d56eda26cdee691df274931ff9004921 |
"""
This module defines export functions for decision trees.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Dawe <noel@dawe.me>
# Satrajit Gosh <satrajit.ghosh@gmail.com>
# Licence: BSD 3 ... | depet/scikit-learn | sklearn/tree/export.py | Python | bsd-3-clause | 4,623 | [
"Brian"
] | f329a8affbafbe85fdb707bb457c6e3291130c713d337740ade6ebb953ba1325 |
import warnings
class GenomeRanges(object):
"""
Split and manage a GenBank range string as converted by BioPython.
@param rangeStr: A C{str} indicating the (0-based) genome nucleotide
offsets covered by a protein. This can have the following example
forms:
[9462:10137](+)
... | terrycojones/dark-matter | dark/genbank.py | Python | mit | 9,316 | [
"Biopython"
] | cb93622f6eb03b014da707155b8d312088aa6a0ff6491139b284382c798e219f |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import warnings
from scipy.special import comb
from scipy.misc.doccer import inherit_docstring_from
from scipy import special
from scipy import optim... | jsilter/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 106,977 | [
"Gaussian"
] | 7fba641b6a570b962849d69726bc977972117b02faf7c8cc0e2ad6963cfa47d7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#
# www.genesilico.pl
#
#creates ranked 3D models of macromoleular complexes
#based on experimental restraints and a whole complex shape.
__author__ = "Joanna M. Kasprzak"
__copyright__ = "Copyright 2010, The PyRy3D Project"
__credits__ = ["Janusz Bujnicki"]
__licen... | mdobrychlop/pyry3d_chimera_extension | PyRy3D_input_generator.py | Python | gpl-3.0 | 14,149 | [
"Biopython"
] | 7315283642a90f9f259dc884b9a2506db65c960100f0ac662459c101215e18a5 |
"""
Test of ordinalInference
w are generated from N(0,1)
"""
from ordinalInference import *
VERBOSE = False
def testModel(d, n, sigma, true_w, B, useSigma, selfComparisons=False):
global VERBOSE
training_y = np.zeros(n).astype(float)
training_ab = np.zeros((n,2)).astype(int)
num_data_errors = 0.0
... | jkbradley/peergrade | cardinalVSordinal/ordinalInference_test.py | Python | apache-2.0 | 2,809 | [
"Gaussian"
] | 8a63d6552d177ba2a904bd7f48d7195f228e68cc19ffed770bd884ade8534153 |
#
# Copyright (C) 2000-2008 greg Landrum
#
""" Training algorithms for feed-forward neural nets
Unless noted otherwise, algorithms and notation are taken from:
"Artificial Neural Networks: Theory and Applications",
Dan W. Patterson, Prentice Hall, 1996
"""
import numpy
class Trainer(object):
""" "virt... | ptosco/rdkit | rdkit/ML/Neural/Trainers.py | Python | bsd-3-clause | 7,994 | [
"RDKit"
] | 0704b9617a658f0e6aa6e507cd21218a17f4c8765cd46d2804dba0cf3b23400a |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_machine_types.py | Python | apache-2.0 | 67,348 | [
"Octopus"
] | b1dd81bcfe781e1e4a2caf391fff3d4e0773a7c4fcd255fad306a982d34cb9a2 |
#!/usr/bin/env python
#
# Wrapper script for invoking the jar.
#
# This script is written for use with the Conda package manager and is ported
# from a bash script that does the same thing, adapting the style in
# the peptide-shaker wrapper
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-sha... | ThomasWollmann/bioconda-recipes | recipes/cromwell/cromwell.py | Python | mit | 2,298 | [
"Bioconda"
] | 9f11e14a9c79ba170939e74cf5d0927a0609bcb62f285c7ddd919397dd5c240e |
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Author: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort
# License: BSD 3 clause
import war... | florian-f/sklearn | sklearn/decomposition/fastica_.py | Python | bsd-3-clause | 14,739 | [
"Gaussian"
] | 7c8bf18ca788e26c2eaf9fed9485bdf872d24cd7f5a48adce3e21c4212e29c23 |
import unittest
import numpy
from pyface.ui.qt4.util.modal_dialog_tester import ModalDialogTester
from traits.etsconfig.api import ETSConfig
from mayavi import mlab
from simphony_mayavi.show import show
from simphony.cuds.lattice import make_cubic_lattice
from simphony.cuds.mesh import Mesh, Point
from simphony.cuds... | simphony/simphony-mayavi | simphony_mayavi/tests/test_show.py | Python | bsd-2-clause | 3,093 | [
"Mayavi"
] | b2af45e85a557990064c170411d75f961c32b99ca5c35e71f615ba9d5db56be9 |
from __future__ import annotations
import logging
from math import pi
from scitbx import sparse
from scitbx.array_family import flex
from dials_refinement_helpers_ext import CalculateCellGradients
logger = logging.getLogger(__name__)
DEG2RAD = pi / 180.0
RAD2DEG = 180.0 / pi
class DerivedParameterTie:
"""Cal... | dials/dials | algorithms/refinement/restraints/restraints.py | Python | bsd-3-clause | 17,973 | [
"CRYSTAL"
] | ad1eacd544e6339a11da9450bd48c7d6bba4cc7dfc6690393d3cf566809c3359 |
import re
import types
import imp
import pkgutil
import collections
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import List, DIRACSingleton
from DIRAC.ConfigurationSystem.Client.Helpers import CSGlobals
class ObjectLoader( object ):
__metaclass__ = DIRACSingleton.DIRACSingleton
def __init_... | avedaee/DIRAC | Core/Utilities/ObjectLoader.py | Python | gpl-3.0 | 6,137 | [
"DIRAC"
] | f8c49d359641c756317428f8c8d18ff9d5f902b34d9dfb8b2ef5a4667219fe37 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Trekload is licensed under the Revised BSD License:
#
# Copyright (c) 2013, Arvid Rudling
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# *... | arru/trekload | trekload.py | Python | bsd-3-clause | 18,631 | [
"Amber"
] | a048dda055501ed3d8d529514ff6a05fa2e6065a219ae96d02ca9ebb288858ff |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
from __future__ import print_function
import numpy as np
from scipy.cluster import vq
from scipy.spatial import cKDTree
from pytim_dbscan import dbscan_inner
def determine_samples(threshold_... | balazsfabian/pytim | pytim/utilities_dbscan.py | Python | gpl-3.0 | 3,974 | [
"MDAnalysis"
] | 649e60e09c7ff6b788d6686a22b86685140323cbd1b34401a31a813f22da4805 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2009 Stephane Charette
# Copyright (C) 2008 Brian Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the... | sam-m888/gramps | gramps/plugins/tool/notrelated.py | Python | gpl-2.0 | 20,402 | [
"Brian"
] | 27161d7c6d27a8fe21c5bb6c94808457b6d6abafb6a860a0e48a92d10aea9229 |
# -*. coding: utf-8 -*-
# Copyright (c) 2008-2012, Noel O'Boyle; 2012, Adrià Cereto-Massagué
# All rights reserved.
#
# This file is part of Cinfony.
# The contents are covered by the terms of the GPL v2 license
# which is included in the file LICENSE_GPLv2.txt.
"""
pybel - A Cinfony module for accessing Open Babel
G... | stevenvdb/openbabel | scripts/python/pybel.py | Python | gpl-2.0 | 33,493 | [
"Open Babel",
"Pybel"
] | 81b39a49528dbbeacd1ad6fbe5f0549e18feff7a27431d8a9239db43db5b1b47 |
# -*- coding: utf-8 -*-
#
# vulture - Find dead code.
#
# Copyright (C) 2012 Jendrik Seipp (jendrikseipp@web.de)
#
# 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 Licens... | Neon22/python-flavin | wake.py | Python | gpl-2.0 | 12,499 | [
"VisIt"
] | 07013272181068533c7bc48c9ee20cbf190638ce4b22cdd12e37baa338db3fb0 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Teon Brooks <teon.brooks@gmail.com>
# Daniel McCloy <dan.mccloy@gmail.com>
#
#... | Teekuningas/mne-python | mne/channels/channels.py | Python | bsd-3-clause | 66,479 | [
"Mayavi"
] | 241d5f76705c3e88b9b463d1a9c39acddeb44aa0411a88c01ef6d0bc2d0a710c |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkMFIXReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkMFIXReader.py | Python | bsd-3-clause | 468 | [
"VTK"
] | 5754f251550747634045208d5d339ea2eaa09c916f9b8ee2f03a048fdd06b59b |
#
# 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 us... | fharenheit/template-spark-app | src/main/python/ml/generalized_linear_regression_example.py | Python | apache-2.0 | 2,506 | [
"Gaussian"
] | 9a2f4b4205a6797f30345bfa55669ffa6ec6af07fd8c143c4316b6dd6dba9622 |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the foll... | beiko-lab/gengis | bin/Lib/site-packages/scipy/ndimage/filters.py | Python | gpl-3.0 | 39,925 | [
"Gaussian"
] | 4c2f7292da7788db07bc5d8f893c48e98dc468d800e4a2b1a4db71e2ba1e096f |
from datetime import datetime, timedelta
import re
from wye.base.constants import WorkshopStatus
from .. import factories as f
def test_workshop_flow(base_url, browser, outbox):
user = f.create_user()
user.set_password('123123')
user.save()
url = base_url + '/workshop/'
browser.visit(url)
bro... | DESHRAJ/wye | tests/functional/test_workshops_flow.py | Python | mit | 2,827 | [
"VisIt"
] | 70b448b59896b71eefd8bf4650746ca8393b5a2e8fd575b13d1094cacfbcca83 |
#!/usr/bin/python
# This was written for educational purpose only. Use it at your own risk.
# Author will be not responsible for any damage!
# !!! Special greetz for my friend sinner_01 !!!
# !!! Special thanx for d3hydr8 and rsauron who inspired me !!!
#
#############################################################... | knightmare2600/d4rkc0de | exploits/090117.py | Python | gpl-2.0 | 6,260 | [
"VisIt"
] | d982e49874f6ff8dd43e152eb2bca389923d45cf6c7e861479007cb60d9808d6 |
""" Contains a class used for evaluating policies for accessing jobs/WMS/pilots accounting
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security import Properties
from DIRAC.AccountingSystem.private.Policies.FilterExecutor import FilterExecutor
class JobPolicy( object ):
def __init__( se... | fstagni/DIRAC | AccountingSystem/private/Policies/JobPolicy.py | Python | gpl-3.0 | 3,030 | [
"DIRAC"
] | 51a6191c77dbd67caeffc82d1923ec73f78124017a0e1f41d4d0d08adc8429e4 |
########################################################################
# $HeadURL$
# File : AgentReactor.py
# Author : Adria Casajus
########################################################################
"""
DIRAC class to execute Agents
Agents are the active part any any DIRAC system, they execute in a cycl... | Sbalbp/DIRAC | Core/Base/AgentReactor.py | Python | gpl-3.0 | 7,331 | [
"DIRAC"
] | 3e875e46d2a5316e287aa15be9a61e599750ccc6c73f61dbfebcd52bfb38c0c4 |
import logging
import numpy as np
import pytest
from numpy.testing import assert_allclose, assert_array_equal
from ginga.AstroImage import AstroImage
from ginga.util import iqcalc, iqcalc_astropy
from ginga.util.iqcalc import have_scipy # noqa
from ginga.util.iqcalc_astropy import have_photutils # noqa
@pytest.ma... | pllim/ginga | ginga/tests/test_iqcalc.py | Python | bsd-3-clause | 12,829 | [
"Gaussian"
] | 73dea002619e98992d78a50a3f3b53ddc88838de906ae081466c4cf27bfced66 |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | shikhardb/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 34,542 | [
"Gaussian"
] | ac4fd1a44c41b98062481f9f79194d7b1b5a7e4f50a27a9229ddc4e4ab3441d1 |
import os
import struct
import logging
from collections import deque
from dropbox import client, rest, session
from StringIO import StringIO
from util import *
import re
from appkeys import *
#use /dev/random if security matters
class WrongDiskSize(Exception):
def __init__(self,message):
super(WrongDiskSize, self).... | uzyszkodnik/blockcrypt | src/DiskDrivers.py | Python | bsd-3-clause | 6,850 | [
"VisIt"
] | bef6eaff7b222425db031945faf8ee9207df124ccf63a0bac61d84398f70ae59 |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2015 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | AdamWill/anaconda | pyanaconda/pwpolicy.py | Python | gpl-2.0 | 4,777 | [
"Brian"
] | 96f0e629e1866e3afe5c66e7c96d9821a49586943c313dc7fea01bc0632ba017 |
"""
BIANA: Biologic Interactions and Network Analysis
Copyright (C) 2009 Javier Garcia-Garcia, Emre Guney, Baldo Oliva
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 vers... | emreg00/biana | biana/biana_globals.py | Python | gpl-3.0 | 14,395 | [
"BLAST"
] | 3e109d7210010add83336b8883503ee57434c2bce2fa5666c5febf1d898f195e |
import os.path
import paste.fileapp
from pylons.middleware import error_document_template, media_path
from dirac.lib.base import *
class ErrorController(BaseController):
"""Generates error documents as and when they are required.
The ErrorDocuments middleware forwards to ErrorController when error
relat... | DIRACGrid/DIRACWeb | dirac/controllers/error.py | Python | gpl-3.0 | 1,344 | [
"DIRAC"
] | f44a175bdb0b751f5c3dad45bd2a2e72ff777e633c06b8db51acb1ffcdf7d1f5 |
import pandas as pd
import pickle
from rdkit import Chem
from rdkit.Chem import AllChem
import os.path as osp
import mastic.selection as masticsel
import mastic.molecule as masticmol
import mastic.system as masticsys
import mastic.interactions as masticinx
from mastic.interactions.hydrogen_bond import HydrogenBondTy... | salotz/mast | prototypes/interactions_example.py | Python | mit | 3,748 | [
"RDKit"
] | 9b09dc30a16c55f50f3916667f23fb6af7b4c38b1e0aaa5d65a173cc4f8d7213 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | hainm/mdtraj | mdtraj/__init__.py | Python | lgpl-2.1 | 3,268 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF"
] | a2894037e71846b4af6d0237703c82c3fea032f56e2e3fa5624fe67acbd2d059 |
import numpy as np
from cs231n.layers import *
from cs231n.fast_layers import *
from cs231n.layer_utils import *
def two_layer_convnet(X, model, y=None, reg=0.0, dropout=1.0):
"""
Compute the loss and gradient for a simple two-layer ConvNet. The architecture
is conv-relu-pool-affine-softmax, where th... | UltronAI/Deep-Learning | CS231n/reference/cnn_assignments-master/assignment3/cs231n/classifiers/convnet.py | Python | mit | 15,991 | [
"Gaussian",
"NEURON"
] | 5f1da709a74cf49c572d8a8936bca2e82b14c6146e8f06f017176e97d10c01a5 |
#!/usr/bin/env python
"""
Demonstrate basic usage of the numpy package.
"""
from numpy import *
# create an array a of length n, with zeroes and
# double precision float type:
n = 4
a = zeros(n)
print 'zeros(n):', type(a), type(a[0]), a
a = zeros(n) # becomes array of integers (!)
print 'zeros(n)', type(a), a
p = q =... | sniemi/SamPy | sandbox/src1/TCSE3-3rd-examples/src/py/intro/NumPy_basics.py | Python | bsd-2-clause | 12,819 | [
"Gaussian"
] | abda0e4fae4284aa8c7176bc2a44b0d240423b8a78e2c48818db938857d84326 |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | CraigHarris/gpdb | src/test/tinc/tincrepo/mpp/gpdb/tests/storage/uao/uao_udf/test_uao_udf.py | Python | apache-2.0 | 1,688 | [
"ORCA"
] | 34f154a75382ad382c3d8a6e38903807a2693e4c28206afcb816af3169f40b7b |
from os import system
# Exciting stuff!
def linux():
apt("build-essential")
apt("git-core")
apt("ruby")
apt("ruby1.8-dev")
apt("irb")
apt("sqlite3")
apt("libxslt-dev")
apt("libxslt-ruby")
apt("rubygems")
both()
def mac():
mac_check_install_homebrew()
both()
def both():... | geeksoflondon/grid4rails | doc/setup.py | Python | agpl-3.0 | 1,623 | [
"exciting"
] | acdb3c610eee04641a34983be43d9ade51ef6c23489473cf011458bfbc65af38 |
# -*- coding: utf-8 -*-
#
# io3d documentation build configuration file, created by
# sphinx-quickstart on Mon Nov 27 12:01:57 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | mjirik/io3d | docs/conf.py | Python | mit | 7,122 | [
"VTK"
] | 69cc1ea1ef0eb9dbab78fcf8b0488af53f66500fe09c82a0c16c74309ace200a |
#! /usr/bin/env python
"""
This script aims to list informations on a given Galaxy instance.
"""
########### Import ###########
import os
import argparse
import sys
from bioblend import galaxy
########### Constant(s) ###########
MOTIF = "toolshed"
########### Function(s) ###########
def list_toolsheds_fro... | khillion/galaxyxml-analysis | galaxyxml_analysis/get_galaxy_info.py | Python | mit | 3,410 | [
"Galaxy"
] | 04a6149556dce3dfc84e1fe024016c0a99ada69d82ca2ee05d4866eb425a108f |
#!/usr/bin/env python
"""Search for inlined CPP macros in ABINIT src files"""
__author__ = "M. Giantomassi"
import os
import re
import sys
# Files that will be checked.
re_srcfile = re.compile("\.([Ff]|[Ff]90|finc)$")
def is_srcfile(dirpath, fname):
return re_srcfile.search(fname)
# List of macros that should n... | SamKChang/abinit-7.10.5_multipole | special/scripts/check_inlined_macros.py | Python | gpl-3.0 | 2,974 | [
"ABINIT"
] | 0a27e29ac767ebe251abbaa9a23f1294e5d8c40b7dc8b56f00ead122e7e48b63 |
# Copyright (C) 2012-2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 GNU General... | espressopp/espressopp | src/analysis/LBOutputScreen.py | Python | gpl-3.0 | 2,481 | [
"ESPResSo"
] | 5f9835d6f2ccb6ffafe949dc6ee416c66f7d32459d72181d106a853674e6253e |
# -*- coding: utf-8 -*-
import datetime
import hashlib
import json
import os
import stat
import tarfile
from copy import deepcopy
from tempfile import mkdtemp
from django.conf import settings
from django.core import mail
from django.core.files.storage import default_storage as storage
from django.core.management impor... | mstriemer/zamboni | mkt/webapps/tests/test_tasks.py | Python | bsd-3-clause | 32,207 | [
"exciting"
] | 6dfa112b17444bc1fb4dd53fa82eaa6b65af8cab8a41177c042a105fca05e28e |
#!/usr/bin/env python
import gtk
import gobject
from ase.gui.languages import translate as _
from ase.gui.widgets import pack
class Movie(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_position(gtk.WIN_POS_NONE)
self.connect('destroy', self.close)
#self.c... | freephys/python_ase | ase/gui/movie.py | Python | gpl-3.0 | 3,528 | [
"ASE"
] | ee3bb5e260a89ffbc348fd2345ec1dd3754db25889affd77fa4ad24c56b62f1f |
# -*- coding: utf-8 -*-
#
# AiiDA VASP Plugin documentation build configuration file, created by
# sphinx-quickstart on Wed Feb 17 11:53:17 2016.
#
# 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 f... | abelcarreras/aiida_extensions | plugins/jobs/vasp/docs/source/conf.py | Python | mit | 9,316 | [
"VASP"
] | 6682d401ac0ba5eb7bf7a884d8b648660e110550c6493835f5d7accf9a95cd52 |
#!/usr/bin/env python
import argparse
import logging
import subprocess
import sys
import os
import re
# Set logging
logging.basicConfig(filename="smrtsv.log", level=logging.DEBUG)
# Set cluster parameters
CLUSTER_SETTINGS = ' -V -cwd -e ./log -o ./log {cluster.params} -w n -S /bin/bash'
CLUSTER_FLAG = ("--drmaa", CLU... | EichlerLab/pacbio_variant_caller | bin/smrtsv.py | Python | mit | 26,810 | [
"BWA"
] | e10ecbf8b40e7ac98c6dfa38270b73ad3859edbab3a4ff0c3253835eab9696ec |
#!/usr/bin/env python
mi=16;mj=mi;mk=mi # Dimension of the coarsest grid
Lx=3e17;Ly=Lx;Lz=Lx # Length of the Domain
Critical_value=-119 # Density Criterion
Max_level=4 # Max hierachical level
import numpy as np
import array
from math import *
from tables import *
from tables.nodes import filenode
wri... | itahsieh/sparx-alpha | preprocessor/script/nested3D_ZEUS.py | Python | gpl-3.0 | 21,387 | [
"VTK"
] | bfbff6ded0f0df0c6e20e61d6de0e056ee7719dd46662822f4c25ec3376cc8ac |
# Copyright 2016 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... | xuleiboy1234/autoTitle | tensorflow/tensorflow/contrib/factorization/python/ops/gmm_ops.py | Python | mit | 22,026 | [
"Gaussian"
] | 738cd22d3a37ae3bd1997cb52dc0797e94892f548de962a785dd2bfcd7e0db14 |
#!/usr/bin/env python
#
# Copyright 2013 Tristan Bereau and Christian Kramer
#
# 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... | MMunibas/FittingWizard | scripts/calc_LRA.py | Python | bsd-3-clause | 23,340 | [
"Gaussian",
"RDKit"
] | 02a0582d4d35aa233b358da7b367fd22d54c21c43cfa8d3b30b12ad8ee783061 |
#!/usr/bin/env python
# =========================================================================
#
# Copyright NumFOCUS
#
# 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:/... | blowekamp/SimpleITK | Examples/Python/ImageCreateAndSet.py | Python | apache-2.0 | 1,323 | [
"Gaussian"
] | 7102a13b3cb064b7ff7fed93d04b9f083c7a131d20c56ad0fa168315661300c7 |
#!/usr/bin/env python2.7
import h5py, os, sys, argparse
import cStringIO as StringIO
from Bio import SeqIO
from fast5tools.f5class import *
from fast5tools.barcodeclass import *
from fast5tools.f5ops import *
from fast5tools.barcodeops import *
from fast5tools.helperops import *
from glob import glob
###############... | JohnUrban/fast5tools | bin/fast5_sw_bardecoder.py | Python | mit | 20,901 | [
"BWA"
] | 2d615b04c547e7d83f72cdecc16c6cc779211f58c0f805526c3d5e1c094f2504 |
# -*- coding: utf-8 -*-
'''
Some of the utils used by salt
'''
# Import python libs
from __future__ import absolute_import, division, print_function
import contextlib
import copy
import collections
import datetime
import distutils.version # pylint: disable=import-error,no-name-in-module
import errno
import fnmatch
im... | stephane-martin/salt-debian-packaging | salt-2016.3.2/salt/utils/__init__.py | Python | apache-2.0 | 93,870 | [
"VisIt"
] | dba6828bd1056d4bdb2c8d0eb3ccef766f449451d73bab0c49b0f387f39ce324 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Licence: BSD 3 clause
from collections import Hashable
import numpy as np
from sklearn.base import clone
from sklearn.externals.funcsigs import signature
from sklearn.gaussian_process.kernels \
import ... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/gaussian_process/tests/test_kernels.py | Python | mit | 11,615 | [
"Gaussian"
] | 6cbe372ddbcb0cb334ca29bcd142571d8888e69ef1caa6bcda06f17e893d1405 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Stephane Charette
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009-2010 Gary Burton
# Contribution 2009 by Bob Ham <rah@bash.sh>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This... | Forage/Gramps | gramps/plugins/graph/gvfamilylines.py | Python | gpl-2.0 | 43,919 | [
"Brian"
] | fd9ae781a495bd6fbae20b9c26101e89f39c013f294c90f5f4836fa8ed408465 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
from SceneObject import SceneObject
class Axes(SceneObject):
'''
A template for drawing axes.
Shouldn't really be in a class of it's own, but it's cleaner here and like this we can move it easily.
Ref: http://vtk.org/gitweb?p=VTK.git;a=blob;f... | GearsAD/semisorted_arnerve | sandbox/bot_vis_platform_post3b/scene/Axes.py | Python | mit | 1,801 | [
"VTK"
] | b52e980e822cec5eb7cdb46f57e267c7882556f19370d43d28675d52d3bd86e1 |
#
# A file that opens the neuroConstruct project LarkumEtAl2009 and run multiple simulations stimulating ech terminal apical branch with varying number of synapses.
#
# Author: Matteo Farinella
from sys import *
from java.io import File
from java.lang import System
from java.util import ArrayList
from uc... | pgleeson/TestArea | models/LarkumEtAl2009/pythonScripts/PAP_multibranches.py | Python | gpl-2.0 | 13,934 | [
"NEURON"
] | d5e31a5ff4edf928cdc955f92c7e4c05287b8987dcfd9b20d73deb5b29c03773 |
#!/usr/bin/env python
"""
Read a maf and output intervals for specified list of species.
"""
import sys, os, tempfile
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
input_filename = sys.a... | dbcls/dbcls-galaxy | tools/maf/maf_to_bed.py | Python | mit | 3,486 | [
"Galaxy"
] | 14616c24758748d6b523790f93ab01b74730158e3649fabec64114029489437d |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | treycausey/scikit-learn | sklearn/covariance/robust_covariance.py | Python | bsd-3-clause | 28,528 | [
"Gaussian"
] | e3afca6b9f085401bcac78ae83834240792c1bcf473d39dd4440dcaba983f7ec |
class Node:
left = None
right = None
def __init__(self, data):
self.data = data
def triangleTransverse(root, result):
result.append(root)
visitLeft(root.left, True, result)
visitRight(root.right, True, result)
def visitLeft(root, visit, result):
if root == None:
return
... | yubinbai/python_practice | triangleTransverse.py | Python | apache-2.0 | 1,165 | [
"VisIt"
] | d408efb3a718adf3c35dff2d66d35813f0231276ffc1dbba1c21a42f50322d66 |
# Copyright 2017 Starbot Discord Project
#
# 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... | dhinakg/BitSTAR | plugins/wikia.py | Python | apache-2.0 | 3,152 | [
"VisIt"
] | cd0e315c66cc30952730309c0307c5211edca9109579a9a3fbbce515a5ab6e05 |
#!/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/mediaplayerremove.py | Python | gpl-2.0 | 5,282 | [
"VisIt"
] | b3f1764f424cbd6e4d7affbdc2203b6637a4c14afe74ebe3253621131947a2b1 |
""" NOTA BENE: This agent should NOT be run alone. Instead, it serves as a base class for extensions.
The TaskManagerAgentBase is the base class to submit tasks to external systems,
monitor and update the tasks and file status in the transformation DB.
This agent is extended in WorkflowTaskAgent and Reque... | Sbalbp/DIRAC | TransformationSystem/Agent/TaskManagerAgentBase.py | Python | gpl-3.0 | 25,297 | [
"DIRAC"
] | cbb5a3871b8ef20b3b2151c0aa98e74660626cd1739c1d0e2140b04d7c119510 |
# pylint: disable=no-init
"""These are more integration tests as they will require that the test data is available
and that mantid can be imported
"""
import stresstesting
import platform
import numpy as np
from mantid.api import (WorkspaceGroup, MatrixWorkspace)
from mantid.simpleapi import *
from vesuvio.commands im... | dymkowsk/mantid | Testing/SystemTests/tests/analysis/VesuvioCommandsTest.py | Python | gpl-3.0 | 11,168 | [
"Gaussian"
] | 82d2e3a57939a4b1423b578ed8bb11447b1938f4ecc8b717dc2d89478c512353 |
# -*- coding=utf-8 -*-
from wheel.bdist_wheel import bdist_wheel
from skbuild import setup
import sys
import os
import re
# Read the version from chemfiles/__init__.py without importing chemfiles
__version__ = re.search(
r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]', open("chemfiles/__init__.py").read()
).group(1)
... | Luthaf/Chemharp-python | setup.py | Python | mpl-2.0 | 1,599 | [
"Chemfiles"
] | 2a60e5fd562ab3054f42a87e64668809e5d92de9f928877532358b6a6c022f7a |
#!/usr/bin/env python3
import json
import random
import const
from const import MM, MEV
from particle import Particle
from detector import Detector
from initial import Beam, Profile, Energy
random.seed(91400)
N = 1000
# Define the beam parameters
beam = Beam(
# Initial position is in a centered uniform disc wi... | DanielBrookRoberge/MonteCarloExamples | particle-beam/particle-beam.py | Python | mpl-2.0 | 1,211 | [
"Gaussian"
] | 3c7ae57affd91c9b8d40e1b59f479a82f06721655880f468edcabd08fdfaf557 |
from collections import OrderedDict
import itertools
import logging
from pathlib import Path
import shutil
import subprocess
import tempfile
import numpy as np
import pyparsing as pp
from pysisyphus.config import Config
from pysisyphus.helpers_pure import chunks
CIOVL="""mix_aoovl=ao_ovl
a_mo=mos.1
b_mo=mos.2
ncore... | eljost/pysisyphus | pysisyphus/calculators/WFOWrapper.py | Python | gpl-3.0 | 13,194 | [
"TURBOMOLE"
] | 0976d422dbdb4a310542a90cda7ccac17cefc03154e3ec2a0ae16bbd7a275fdb |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_plans_api.py | Python | apache-2.0 | 10,125 | [
"VisIt"
] | 67ec9fe59b61f9b8ae9ae551afbfdc97fc4348f7bfb54632eedbe4513867d66f |
import os
from distutils.version import LooseVersion
import numpy as np
import pandas as pd
from shapely.geometry import Point, Polygon, LineString, GeometryCollection, box
from fiona.errors import DriverError
import geopandas
from geopandas import GeoDataFrame, GeoSeries, overlay, read_file
from geopandas import _c... | jdmcbr/geopandas | geopandas/tests/test_overlay.py | Python | bsd-3-clause | 23,953 | [
"Bowtie"
] | 5e3d575d19a5433db5eb3fc37c3f91ef98d73f5e878180e8cd08e0ec1c212097 |
#!/home/aubbwc/usr/bin/python3
# ABOUT-----------------------------------------------------------------------
# setting up jobs for Ewald alternative calculations.
# CATIONS =
# Imidazolium based: MMIM, EMIM, BMIM, HMIM, OMIM
# Pyridinum based: MPYR, EPYR, BPYR, HPYR, OPYR
# ANIONS =
# BF4, PF6, Cl, AlC... | thebillywayne/research_utilities | boss/Ewald.equil.py | Python | bsd-3-clause | 6,692 | [
"CHARMM"
] | 2e1fc0ea36cb3e04b7c9ac40ddb298d70468c9c5979a8747c96a87b350aca542 |
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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.... | Multiscale-Genomics/mg-process-fastq | tests/test_tb_filter.py | Python | apache-2.0 | 9,613 | [
"BWA"
] | 0305b3d4858435f6ba2b8116058ab05fbe5b204d76bc6afa50b72e55bcc4ece7 |
# Copyright (C) 2016, Craig Warren
#
# This module is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.
# To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.
#
# Please use the attribution at http://dx.doi.org/10.1016/j.sigpro.2016.04.010
import arg... | gprMax/gprMax | user_libs/antenna_patterns/plot_fields.py | Python | gpl-3.0 | 5,571 | [
"VisIt"
] | 3e387fd1e1eb3a95167543de726591d959bf0ae7c691a4f8e296a662ffe45d57 |
#!/usr/bin/env vpython
# Copyright 2019 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Helper script used to manage locale-related files in Chromium.
This script is used to check, and potentially fix, many locale-rela... | endlessm/chromium-browser | build/locale_tool.py | Python | bsd-3-clause | 51,300 | [
"xTB"
] | 35646385c45a01ee503db530012c4f2c53b7a5870acf1bdfd5456f7c0ba3d26c |
#!/usr/bin/env python
"""
MakePDB
---------
title parm mdtraj
"""
import sys
def makepdb(title,parm,traj):
"""
Make pdb file from first frame of a trajectory
"""
cpptrajdic ={'title':title,'parm':parm,'traj':traj}
cpptrajscript="""parm {parm}
trajin {traj} 0 1 1
center
rms first @CA,C,... | avishek-r-kumar/dfitools | MD_DFI_analysis/makepdb.py | Python | bsd-3-clause | 787 | [
"MDTraj"
] | 7ddbd25e54838822d770833142b5013e6127082e1207b99d771ec6aa9c780c41 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/procrouting/mcscf/__init__.py | Python | lgpl-3.0 | 953 | [
"Psi4"
] | 97f635de6e6cc1a6fe4487c195f342a11f6b83f0d3cf577804961c69f6f7f352 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and, cint
from frappe import _
from frappe.model.utils ... | mbauskar/erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | gpl-3.0 | 26,900 | [
"VisIt"
] | 56e63d59c7e9580fe704c24056291a5ea9802d6594962784321403a7f25c871b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
========================================================================
Gaussian Processes regression: goodness-of-fit on the 'diabetes' dataset
========================================================================
This example consists in fitting a Gaussian Process m... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/gaussian_process/gp_diabetes_dataset.py | Python | bsd-3-clause | 2,021 | [
"Gaussian"
] | 56f467e5f041de3a4caf83fb15f45f6c5003d8a4d96effbab8d5df8eab043996 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides input and output mechanisms
for the xr file format, which is a modified CSSR
file format and, for example, used in GULP.
In particular... | aykol/pymatgen | pymatgen/io/xr.py | Python | mit | 6,270 | [
"GULP",
"pymatgen"
] | ac0668f4564a53654f9002a2f126b92827d0a50031749a811eb271a6e85b05f1 |
########################################################################
# $HeadURL$
# File : AgentModule.py
# Author : Adria Casajus
########################################################################
"""
Base class for all agent modules
"""
__RCSID__ = "$Id$"
import os
import threading
import types
import... | sposs/DIRAC | Core/Base/AgentModule.py | Python | gpl-3.0 | 17,556 | [
"DIRAC"
] | 94c9eb5dab19a1644234154c4bc4e800cb9ff21620b3fd32cda234bb7dd9d82d |
"""
This module calculates corrections for the species listed below, fitted to the experimental and computed
entries given to the CorrectionCalculator constructor.
"""
import os
import warnings
from collections import OrderedDict
from typing import Dict, List, Tuple, Union, Optional
import numpy as np
import plotly.g... | gmatteo/pymatgen | pymatgen/entries/correction_calculator.py | Python | mit | 20,772 | [
"pymatgen"
] | 7afbfb7b4107558f50ac2635ad7d9177904f13b20c15c0d454271e135abd7797 |
from Inference import Inference
from Gaussian import Gaussian | aerialhedgehog/VyPy | trunk/VyPy/regression/gpr/inference/__init__.py | Python | bsd-3-clause | 63 | [
"Gaussian"
] | cd7906a55cde184987b45bf9dd38fd0045c880deb16439ba44b312f703b7c95e |
import matplotlib.pyplot as plt
import numpy as np
import pytest
from pysisyphus.calculators.AnaPot import AnaPot
from pysisyphus.calculators.MullerBrownSympyPot import MullerBrownPot
from pysisyphus.cos.NEB import NEB
from pysisyphus.cos.SimpleZTS import SimpleZTS
from pysisyphus.Geometry import Geometry
from pysisyp... | eljost/pysisyphus | tests/test_cos/test_cos.py | Python | gpl-3.0 | 5,184 | [
"PySCF"
] | 8201d5d06ac110dab3fb3e5aec50f6c3d736863488a980a4611e686d82b138ac |
"""
Acceptance tests for Studio's Setting pages
"""
import re
from .base_studio_test import StudioCourseTest
from ...pages.studio.settings_certificates import CertificatesPage
class CertificatesTest(StudioCourseTest):
"""
Tests for settings/certificates Page.
"""
def setUp(self): # pylint: disable=ar... | vikas1885/test1 | common/test/acceptance/tests/studio/test_studio_settings_certificates.py | Python | agpl-3.0 | 9,745 | [
"VisIt"
] | d600d27d01125328b1a67db5d5efec2037e044962be24702c183175d9fac6094 |
from setuptools import setup
setup(
name='moltemplate',
packages=['moltemplate',
'moltemplate.nbody_alt_symmetry'],
package_dir={'moltemplate': 'moltemplate'}, #.py files are in "moltemplate/"
package_data={'moltemplate': ['force_fields/*.lt']}, #.lt files are in "moltemplate/force_f... | jewettaij/moltemplate | setup.py | Python | mit | 4,930 | [
"ESPResSo",
"LAMMPS"
] | 5decf54ca8bc37ba19ab6e57ed88178f8c72d9b505feadbe58339ee20c54f190 |
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