text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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from behave import *
from time import time, sleep
from selenium.common.exceptions import NoSuchElementException, WebDriverException
from selenium.webdriver import ActionChains
try:
from mist.io.tests.settings import LOCAL
except ImportError:
LOCAL = True
pass
@when(u'I visit mist.io')
def visit(context):... | johnnyWalnut/mist.io | src/mist/io/tests/gui/features/steps/general.py | Python | agpl-3.0 | 6,245 | [
"VisIt"
] | dd163a2e8ec29cad89020284206218f978ebeae2aadf0ac5370ac20b731803c2 |
#!/bin/env python
"""
Module openmm.unit.quantity
Physical quantities with units, intended to produce similar functionality
to Boost.Units package in C++ (but with a runtime cost).
Uses similar API as Scientific.Physics.PhysicalQuantities
but different internals to satisfy our local requirements.
In particular, there ... | mdtraj/mdtraj | mdtraj/utils/unit/quantity.py | Python | lgpl-2.1 | 32,230 | [
"OpenMM"
] | 8708ac30d4205bfda4c6cde5959ae6421766e752958bf29e0628959f29ed9f9e |
__author__ = "Brian O'Neill"
__version__ = '0.3.0'
from log_calls import log_calls
import doctest
##############################################################################
# doctests
##############################################################################
#================================================... | Twangist/log_calls | tests/test_log_calls__class_deco.py | Python | mit | 41,448 | [
"Brian"
] | 188bbeae63a1c91556d3634c6eb32a66670fea3ae583a3496c2e9d821ddcd7ff |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# relevant imports
import sys
import time
import espressopp
import mpi4py.MPI as MPI
import Tetracryst # Preparation of tetrahedral crystal and constuctions of bonds in tetrahedral liquid
from espressopp import Real3D, Int3D
from espressopp.tools import decomp
from espre... | capoe/espressopp.soap | examples/hadress/hadressFEC/hadressDensityFEC.py | Python | gpl-3.0 | 8,464 | [
"CRYSTAL"
] | f47ae5e1c4d7d99cfdf60f82f80295b0df00710424facfbf8f7c21464797fd44 |
'''A reporter class to prepare reports and network accounting plots.
Supports:
* packet loss rate (standard and magnified),
* one-way delay, jitter, jitter over one-way delay
'''
__RCSID__ = "$Id$"
import numpy as np
from DIRAC import S_OK
from DIRAC.AccountingSystem.Client.Types.Network import Network
from DIRAC... | fstagni/DIRAC | AccountingSystem/private/Plotters/NetworkPlotter.py | Python | gpl-3.0 | 9,034 | [
"DIRAC"
] | 5adc790be8e31e76e9bcfbab0e349e938a96bd22040d8bfc39ce944a4b8aff5f |
#!/usr/bin/env python3
from olctools.accessoryFunctions.accessoryFunctions import MetadataObject
from genemethods.geneseekr.geneseekr import GeneSeekr
from genemethods.geneseekr.blast import BLAST
import multiprocessing
from glob import glob
from time import time
import os
test_path = os.path.abspath(os.path.dirname(_... | OLC-Bioinformatics/GeneSeekr | tests/test_tblastn.py | Python | mit | 7,418 | [
"BLAST"
] | 0c47d3851a24ebc7e16001501363435e6307d1486c008ebf25c1b7860d0e30ef |
#
# @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
#... | susilehtola/psi4 | psi4/driver/qcdb/molecule.py | Python | lgpl-3.0 | 86,255 | [
"CFOUR",
"Molpro",
"ORCA",
"Psi4",
"Q-Chem"
] | c285a59139e558a64b6d09d7f7f7485246a27681cd872a04ec736656b5453664 |
"""
FileCatalogClientBase is a base class for the clients of file catalog-like
services built within the DIRAC framework.
The class contains variables defining lists of implemented catalog methods
READ_METHODS
WRITE_METHODS
NO_LFN_METHODS
ADMIN_METHODS
Those lists must be complemented ... | DIRACGrid/DIRAC | src/DIRAC/Resources/Catalog/FileCatalogClientBase.py | Python | gpl-3.0 | 4,119 | [
"DIRAC"
] | dd7fc8991b5e44fa1f21c12ad5e840b427749559a9efb5d76acef43203659fbf |
import os
from PyQt4 import QtGui, QtCore
class Start(QtGui.QLabel):
def __init__(self, useData, parent):
QtGui.QLabel.__init__(self)
self.pcode = parent
self.useData = useData
mainLayout = QtGui.QHBoxLayout()
mainLayout.setMargin(0)
self.setScaledContents(True)... | ntoll/Pcode | Extensions/Start.py | Python | gpl-3.0 | 5,925 | [
"VisIt"
] | ffc139b1f19d3bea97ddfd1cc56511040bafaf591e59d539002ad60a7c4e20fa |
# Custom GPAW setup for Mahti (Bull Sequana XH2000)
import os
parallel_python_interpreter = True
# compiler and linker
compiler = os.environ['CC']
mpicompiler = 'mpicc'
mpilinker = 'mpicc'
extra_compile_args = ['-std=c99', '-O3', '-fopenmp', '-fopenmp-simd',
'-march=native', '-mtune=native', '-ma... | mlouhivu/build-recipes | gpaw/setup/siteconfig-mahti-mt.py | Python | mit | 871 | [
"GPAW"
] | 95d34a19b2b199fccd4cc076dbcbb40665b1036ed58066c54c350c45a436bd23 |
# Author: Alex Wolf (http://falexwolf.de)
"""Simulate Data
Simulate stochastic dynamic systems to model gene expression dynamics and
cause-effect data.
TODO
----
Beta Version. The code will be reorganized soon.
"""
import itertools
import shutil
import sys
from pathlib import Path
from types import MappingProxyType
... | theislab/scanpy | scanpy/tools/_sim.py | Python | bsd-3-clause | 46,864 | [
"Gaussian"
] | 497a93d6c0f3712ff18c250aebe1f208c086c87b874f179e530ee062e4de6ecf |
#!/usr/bin/python
"""
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* isingrand: postprocessing of isingrand data
* Copyright (c) 2013 Analabha Roy (daneel@utexas.edu)
*
* This is free software: you can redistribute it and/or modify it under the
* terms of version 3 of the GNU L... | hariseldon99/archives | isingrand/scripts/disorder_average.py | Python | gpl-2.0 | 4,032 | [
"Gaussian"
] | 6a57757e01001713aa3d3616cdcaf1037e5ce46bbed118ad59a2d4a3787c578d |
import simtk.openmm.app as app
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import testsystems
testsystem = testsystems.DHFRExplicit()
system, topology, positions = testsystem.system, testsystem.topology, testsystem.positions
platform = mm.Platform.getPlatformByName('CUDA')
properties = {'C... | kyleabeauchamp/HMCNotes | code/old/test_clocktime.py | Python | gpl-2.0 | 996 | [
"OpenMM"
] | 7e31e88a875fb3667b4db5ed624a860b0060fd04005647588a7f950efa235363 |
# -*- coding: utf-8 -*-
#
# hh_phaseplane.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, ... | apeyser/nest-simulator | pynest/examples/hh_phaseplane.py | Python | gpl-2.0 | 4,973 | [
"NEURON"
] | 38e6a392d8af35905c26a01f4d9f88f01105b3e7daa7fdc5b160f6211c7a47ef |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Sof... | andrebellafronte/stoq | plugins/bikeshop/tests/test_bikeshopui.py | Python | gpl-2.0 | 2,076 | [
"VisIt"
] | 6788d7d2a9a857fed12cd2c13c139926d4dd4014c6aa7416fc0bf1e06c040165 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Sof... | tiagocardosos/stoq | stoqlib/reporting/test/test_transferreceipt.py | Python | gpl-2.0 | 2,590 | [
"VisIt"
] | 98a2810ccd62c7c4479cf32d0fa4ff3c438107fba0160d197fecf5d60317eae4 |
from sympy import Rational, pi, sqrt, sympify, S
from sympy.physics.units.quantities import Quantity
from sympy.physics.units.dimensions import (
acceleration, action, amount_of_substance, capacitance, charge,
conductance, current, energy, force, frequency, information, impedance, inductance,
length, lumino... | wxgeo/geophar | wxgeometrie/sympy/physics/units/definitions.py | Python | gpl-2.0 | 19,777 | [
"Avogadro",
"Gaussian"
] | 4598c9f7ba24a04064d586752028ec6c985424af6197e9839dfdc50447dcc58a |
# (c) 2017, Brian Coca
#
# 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 dist... | tszym/ansible | lib/ansible/plugins/cache/yaml.py | Python | gpl-3.0 | 1,664 | [
"Brian"
] | 1697cce34edbe8c6f3f9e50df83b350bc3c74341ba25e0e11ad07b8e9e98f016 |
""" JobPolicy encapsulates authorization rules for different groups
with respect to job related operations
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security import Properties
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getUsernameForDN, getGroupsForUser, \
getPr... | petricm/DIRAC | WorkloadManagementSystem/Service/JobPolicy.py | Python | gpl-3.0 | 7,146 | [
"DIRAC"
] | 6946a7d40ebdac2818a1a5607317f00d00f6624c8756c50b6611edc12f45e202 |
# Tilde project: plotting interfaces
# for flot.js browser-side plotting library
# Author: Evgeny Blokhin
import math
from numpy import dot, array, linalg, arange
from tilde.berlinium.cubicspline import NaturalCubicSpline
from tilde.berlinium.dos import TotalDos, PartialDos
from ase.data.colors import jmol_colors
... | ansobolev/tilde | tilde/berlinium/plotter.py | Python | mit | 7,069 | [
"ASE",
"CRYSTAL",
"VASP",
"exciting"
] | 3964cc9b36084e93a402c52cd4d4f83f07bbbcdeef3817e6018c1f1f180a6c64 |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# 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 Software without restriction, inc... | rspivak/slimit | src/slimit/visitors/nodevisitor.py | Python | mit | 2,877 | [
"VisIt"
] | e49a534b5a272d03fbcb9b2a82493c993356367a30c5e8e67481e4ac058e0aa6 |
import numpy as np
import tensorflow as tf
import classification.svm.svm
import preprocessing.data_set
import preprocessing.ttree
import ROOT
# Generates two 2D normal distributions in two TTrees.
signal = ROOT.TNtuple("ntuple", "ntuple", "x:y:signal")
background = ROOT.TNtuple("ntuple", "ntuple", "x:y:signal")
for i... | AidanGG/tensorflow_tmva | examples/svm_test.py | Python | gpl-2.0 | 2,202 | [
"Gaussian"
] | bce9d604bc29e7ee1c9d272c4233a2857a1a37a702056a35bab1e60d6721e518 |
# 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... | chemelnucfin/tensorflow | tensorflow/python/autograph/pyct/transformer.py | Python | apache-2.0 | 16,880 | [
"VisIt"
] | 5b31513abd696ddf1f149f10365773616a26b58a80d1cdd61156f57eb233d401 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import unittest
import os
import warnings
import numpy as np
from pymatgen.io.cif import CifParser, CifWriter, CifBlock
from pymatgen.io.vasp... | matk86/pymatgen | pymatgen/io/tests/test_cif.py | Python | mit | 40,036 | [
"VASP",
"pymatgen"
] | 34864aa797366a805455b68ba217dd5f09595e78c25ebeab3c6cadafdf27f9c6 |
# Copyright 2004 by Thomas Hamelryck.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
KD tree data structure for searching N-dimensional vectors.
The KD tree data stru... | bryback/quickseq | genescript/Bio/KDTree/KDTree.py | Python | mit | 8,117 | [
"Biopython"
] | 74bb157d7490745e5b7fff441ce0b3b5040bca2729ffe8fe964e4feaf12c3183 |
"""
Test functions for GEE
External comparisons are to R and Stata. The statmodels GEE
implementation should generally agree with the R GEE implementation
for the independence and exchangeable correlation structures. For
other correlation structures, the details of the correlation
estimation differ among implementat... | yl565/statsmodels | statsmodels/genmod/tests/test_gee.py | Python | bsd-3-clause | 58,559 | [
"Gaussian"
] | b98c8a349ccf1fc7dadfb4d6e5300d3fda84a459f95de2c1f0ba8c67bd3745a8 |
def uniform_random(sample_size) :
pass
def gaussian(sample_size) :
pass
pdf_types = { 'uniform random': uniform_random,
'gaussian': gaussian
}
def create_pdf(sample_size=None, pdf_type=None) :
return pdf_types[pdf_type](sample_size)
| cavestruz/L500analysis | utils/averaging/probability_distributions.py | Python | mit | 282 | [
"Gaussian"
] | 5202824f555ac9202ae49099b108c9022bb4204140f968897e9b80a5308eaca0 |
""" """
# Standard library modules.
import unittest
import logging
import xml.etree.ElementTree as etree
# Third party modules.
# Local modules.
from pyhmsa.spec.condition.detector import \
(DetectorCamera, DetectorSpectrometer, DetectorSpectrometerCL,
DetectorSpectrometerWDS, DetectorSpectrometerXEDS,
... | pyhmsa/pyhmsa | pyhmsa/fileformat/xmlhandler/condition/test_detector.py | Python | mit | 17,274 | [
"CRYSTAL"
] | cecfc806bbb48188909a0c9a3f673913794038debe41dd921e32761f43aa64a3 |
# Jython Database Specification API 2.0
#
# $Id: runner.py 6647 2009-08-10 17:23:22Z fwierzbicki $
#
# Copyright (c) 2001 brian zimmer <bzimmer@ziclix.com>
"""
To run the tests, simply invoke this script from the commandline:
jython runner.py <xml config file> [vendor, ...]
If no vendors are given, then all vendor... | zephyrplugins/zephyr | zephyr.plugin.jython/jython2.5.2rc3/Lib/test/zxjdbc/runner.py | Python | epl-1.0 | 6,056 | [
"Brian"
] | db549dd2f1e16e54f3685d91fbe6fdbf83382b87de6326f44a05b5ab86bdc9fa |
#!/usr/bin/env python
'''
Online example from :
http://www.vtk.org/Wiki/VTK/Examples/Python/Graphs/EdgeWeights
Going to heavly comment out the steps to understand how to edit
this into what we need to make other graphs
'''
import vtk # Manditory on all python VTK
import random
g = vtk.vtkMutableUndirecte... | espinm2/interactive-vtk | pysrc/DisconnectedGraph.py | Python | mit | 1,355 | [
"VTK"
] | b03a5f6876e45500b79896ebd16c737e086bfde7b63eaa4ab204b18e56af9ad8 |
#
# @file TestSBMLConstructorException.py
# @brief SBMLConstructorException unit tests
# @author Akiya Jouraku
#
#<!---------------------------------------------------------------------------
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version ... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestSBMLConstructorException.py | Python | bsd-3-clause | 37,247 | [
"VisIt"
] | e916cb79e70c9d0173eb84a91ea9d7b00eb0c26ae4084a53f3810c16e7971c1d |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 OpenStack Foundation
# 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.apach... | ntt-sic/nova | nova/tests/api/openstack/test_xmlutil.py | Python | apache-2.0 | 30,954 | [
"VisIt"
] | 70bf2e82df3bfe01e6bde1c636a39f57afa0cacd2dfd852faf2a578e7b130480 |
#!/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/e2-openwbif | plugin/controllers/views/ajax/bqe.py | Python | gpl-2.0 | 13,021 | [
"VisIt"
] | 191db5464ccccb6e5724f2c21288d39394d62e9196a88bf8de611c341a24727e |
#!/usr/bin/python
import struct
from sys import argv, exit
def ensure(condition, message, exitCode=-1):
if not condition:
print(message if exitCode != -1 else 'ERROR: %s' % message)
exit(exitCode)
def warn_if(condition, message, args=None):
if condition:
print('WARNING: %s' % (message ... | rschiang/swatch.py | swatch.py | Python | mit | 2,709 | [
"ASE"
] | 387b290c6978a430266a3199420ded4f98f899f8e1a41a76fcf6c21536e8304f |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | Chuban/moose | python/MooseDocs/commands/presentation.py | Python | lgpl-2.1 | 6,184 | [
"MOOSE"
] | 18ffe7b469d2f9bf2a6c1a2beb5e292a7cdfc67d2cddb3a7fa789c9e25bdf62d |
import os
import ase
tests = [
'N2Cu_relax.py',
'Cu_bulk.py',
'CO_Au111.py',
'H2.py',
'C5H12.py',
'nanoparticle.py', # SLOW
# 'C2_Cu100.py', # Extremely slow
]
for test in tests:
filename = ase.__path__[0] + '/optimize/test/' + test
exec(compile(open(filename).read(), filename, 'exe... | suttond/MODOI | ase/optimize/test/test.py | Python | lgpl-3.0 | 330 | [
"ASE"
] | 78e8bec5eceb647e90b3791c939a3146c13f037f52a48835383e24564326baf5 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: asadm2
"""
###DESCRIPTION
#This script runs an MC to get an estimate of number of GCs we could
#potentially detect as well as an estimate of the halo mass given total mass
#of GC system. Histograms of 1000 realizations are plotted at the end.
import matplotl... | MehnaazAsad/ECO_Globular_Clusters | src/visualization/MC.py | Python | mit | 8,449 | [
"Galaxy",
"Gaussian"
] | d77b4fa801e974327f90aad13d163fe193def6f28052008bd9500db80a87ff73 |
#
# Copyright (C) 2016 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Descriptors derived from a molecule's 3D structure
"""
f... | bp-kelley/rdkit | rdkit/Chem/Descriptors3D.py | Python | bsd-3-clause | 5,877 | [
"RDKit"
] | 4f829caca5d2d318ebed2669afc84702f9c222ddf313571487032bfb51d10d5c |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# 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... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_actiongroupconfig.py | Python | bsd-3-clause | 5,299 | [
"VisIt"
] | 603c00eb0dd69ee1bb6a9512deeb766d70035ce5e3880bfbd8e77fabec1edfbc |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | src/python/espressomd/accumulators.py | Python | gpl-3.0 | 11,580 | [
"ESPResSo",
"exciting"
] | 1f5d26965e5a18c3a281706736fd092a73466b97d18a97bdd5e65d4fac59dfd2 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008-2009 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
# Co... | sam-m888/gprime | gprime/plugins/export/exportgedcom.py | Python | gpl-2.0 | 57,288 | [
"Brian"
] | c109f97f61cec726c39476b7657b7c6af9ebe6d7bd2ba061445d7710479609da |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from compiler.ast import Const
from compiler.ast import Dict
from compiler.ast import Discard
from compiler.ast import List
from compiler.ast import Module
from co... | tkelman/utf8rewind | tools/gyp/pylib/gyp/input.py | Python | mit | 116,141 | [
"VisIt"
] | e6effadb3e0042d58c35e4417070f62c5ca0038166de20bdba9a4d72bf9a6b52 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains some math utils that are used in the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materi... | matk86/pymatgen | pymatgen/analysis/chemenv/utils/math_utils.py | Python | mit | 9,533 | [
"pymatgen"
] | c342492acc5d4cfd557ee7355d97e4d4ccbe2cd58a3483fc2c1e15fdde2aa371 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
import pickle
import timeit
from pymatgen.util.testing import PymatgenTest
from pymatgen.electronic_structure.core import Magmom
from pymatgen.core.periodic_table import Element, Specie
fro... | gVallverdu/pymatgen | pymatgen/core/tests/test_sites.py | Python | mit | 12,095 | [
"pymatgen"
] | 27942125f9d3a9d072e55e9433837c2fa36c35d317ebef88a6a7d2d7d8f94651 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParallel import R... | jhbradley/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 44,070 | [
"MOOSE",
"VTK"
] | 80339a08789fc098dd88877dd0722b17225d5fcc9a771ea5ecb491d4553eaef5 |
import os
import time
import requests
from django.conf import settings
from django.core.urlresolvers import reverse, NoReverseMatch
import pytest
from splinter.driver.webdriver import chrome
class WebDriver(chrome.WebDriver):
django_live_server_url = ''
def _resolve_url(self, url, *args, **kwargs):
... | tomchuk/meetup | tests/functional/fixtures.py | Python | mit | 2,849 | [
"VisIt"
] | af6e834396d797cf4a40d82fec39daed10a87032fd416a313000053345cff15b |
#!/usr/bin/python
"""Test to verify bug #363802 is still fixed.
When navigating in Calc from cell to cell, Orca should not say "cell".
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
######################################################################
# 1. Start oocalc. There is a b... | h4ck3rm1k3/orca-sonar | test/keystrokes/oocalc/bug_363802.py | Python | lgpl-2.1 | 5,603 | [
"ORCA"
] | 86a33178cd035d3139b7cce063c37eabda60df90ee19fe3806c0e5ef3959cbc4 |
# Copyright 2008-2011 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code for dealing with sequence alignments.
One of the most important things in this mo... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Align/__init__.py | Python | gpl-2.0 | 27,452 | [
"Biopython"
] | c5901f5f18b046cb937c4e17491e2826e1d578eee409f763256f63fc12baa8a4 |
# -*- coding: utf-8 -*-
"""
Working with 3D point clouds with Python: GeoPython 2017, Basel - Switzerland
@author: Joao Paulo Pereira
University of Freiburg
Chair of Remote Sensing and Landscape Information Systems - FeLis
------------------------------... | pereirapysensing/GeoPython_2017_3D | Auxiliary3DFunctions.py | Python | mit | 24,243 | [
"Mayavi"
] | 427a36135cac86ebe9145fc6f844911ecdbc1268c46217d878cd1e25feffca21 |
#!/usr/bin/python
"""
Library to access the RAM database
Uses WALK_OUT's WALKER class
"""
import os
import sys
from subprocess import call
HAS_IMG = True
#constants
curr_path = os.path.abspath(os.curdir)
print "importing vcf_walk"
sys.path.insert(0, '.')
from vcf_walk import walker
from vcf_walk impo... | sauloal/introgressionbrowser | vcfmerger/vcf_walk_ram.py | Python | mit | 23,142 | [
"Bioconductor"
] | 2da71396889ec71d925bf5e3f5cb7120a352935af10dd738584461175e2b6a0f |
# Copyright (c) 2010 OpenStack, 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 agreed to in wr... | VictorLowther/swift | test/unit/common/middleware/test_staticweb.py | Python | apache-2.0 | 31,153 | [
"VisIt"
] | 828c02fac0c3c1e5b63bbed41ddc6cc80386e7c531c12a6dac1cf876d345c088 |
from ast import literal_eval
from operator import attrgetter
import re
from typing import Callable, Iterable, List, Match, NamedTuple, Optional, Tuple, Union
from .errors import MarkupError
from .style import Style
from .text import Span, Text
from .emoji import EmojiVariant
from ._emoji_replace import _emoji_replace
... | willmcgugan/rich | rich/markup.py | Python | mit | 8,033 | [
"VisIt"
] | 5f3ae7f82197a128f0edbb8d86416c2c2cb1b4e52e12553e22c7945ef34f3529 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
=========================================================
Logit function
=========================================================
Show in the plot is how the logistic regression would, in this
synthetic dataset, classify values as either 0 or 1,
i.e. class one or two, u... | loli/sklearn-ensembletrees | examples/linear_model/plot_logistic.py | Python | bsd-3-clause | 1,426 | [
"Gaussian"
] | 20e0b09c4501c17519170ed9acb76f234d9ec8785fcbf865508d0bb039c5400c |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from nose.plugins.attrib import attr
from textwrap import dedent
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.accept... | chrisndodge/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 23,865 | [
"VisIt"
] | cf355bd7fc65c7d8891d42385f89599eaab52fe61a7f6c1b1402f1621c785319 |
from django import template
from django.core.urlresolvers import reverse
from django.conf import settings
from pylmth.dom import *
from profiles.models import (DataDomain, Time, GeoRecord, GeoLevel,
Value, DataPoint, Indicator, IndicatorPart)
from profiles.utils import format_number as u... | 216software/Profiles | communityprofiles/profiles/templatetags/profiles_tags.py | Python | mit | 28,234 | [
"MOE"
] | cb7b527d5fb7ec52dc67a8d21d3b53dd73fbad6db954d63eeb78a61a561e0d29 |
"""Read and write notebooks in JSON format.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distribute... | liberorbis/libernext | env/lib/python2.7/site-packages/IPython/nbformat/v3/nbjson.py | Python | gpl-2.0 | 2,189 | [
"Brian"
] | dfac13b7104def3950a35e530ee55e9dd2b6f833f51addb71da3aef598129113 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | Bismarrck/pymatgen | pymatgen/io/feff/tests/__init__.py | Python | mit | 472 | [
"pymatgen"
] | 2c238b48cb9859c485e2647d5d3aac69dfbe8bdefc5814f7c2bc023822cc1570 |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/pmv_dev/strutsCommands.py is part of ePMV.
ePMV 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
... | corredD/ePMV | pmv_dev/strutsCommands.py | Python | gpl-3.0 | 37,794 | [
"PyMOL"
] | 5667049e68e85c838bfff7015d5973c3ce06e3894282cef88918aa84a3b63c77 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Some plottin' functions used by the example scripts
Copyright (C) 2017 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 Fo... | espenhgn/LFPy | examples/example_suppl.py | Python | gpl-3.0 | 8,078 | [
"NEURON"
] | bdb31d02876dbd4c569dab04022a2da32e0904f54d1c661c22a1dc6876ff13aa |
from __future__ import print_function
import time
from math import pi
import requests
from requests.exceptions import ConnectionError
import pandas as pd
from bokeh.objects import (Plot, ColumnDataSource, DataRange1d, FactorRange,
LinearAxis, CategoricalAxis, Grid, Glyph, Legend, SingleIntervalTicker, HoverTool... | sahat/bokeh | examples/glyphs/population_server.py | Python | bsd-3-clause | 5,339 | [
"VisIt"
] | 110381abaa509c96ee1c7f239859f71a7744251bfbe3de01828b764c61743780 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | tmerrick1/spack | var/spack/repos/builtin/packages/adios/package.py | Python | lgpl-2.1 | 7,472 | [
"NetCDF"
] | 5ddd4b72d2583116bd6a4199d5f9cfdf895a6460fb5836b97becfdbe20d19663 |
import pytest
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.drivers import run_perf, print_perf_results
from pysisyphus.helpers import geom_loader
from pysisyphus.testing import using
@using("pyscf")
@pytest.mark.parametrize(
"pals, mems, pal_range, mem_range, repeat",
[
(None, 500, ... | eljost/pysisyphus | tests/test_perf/test_perf.py | Python | gpl-3.0 | 1,306 | [
"PySCF"
] | 44b378afb4251a1d42cc6e4edd224349e12bb2adbf13d3486b82c30976149bda |
#Brian Stamm
#CSC 110 - Dr. West
#10.21.14
#Homework 4 - Drawing
#This program is NOT interactive, and it draws the same picture every time. Running this program, you must
#have the Gui tool (Gui3.py) to run this properly, and it must be saved in the same file as this.
from Gui import * # - as mentioned, Gu... | bkstamm67/python | pastHW/guiDrawing.py | Python | mit | 4,176 | [
"Brian"
] | ef68600cb6e077721b4e3fc9dc5ff4689752d032ed7596c44df1cb83d932aa0a |
#!/usr/bin/env python
#import tkinter as Tk
#from tkinter import ttk
import matplotlib
import numpy as np
import numpy.ma as ma
import sys
sys.path.append('../')
import new_cmaps
from new_cnorms import PowerNormWithNeg, PowerNormFunc
import matplotlib.colors as mcolors
import matplotlib.gridspec as gridspec
import mat... | pcrumley/Iseult | src/mag_panel.py | Python | gpl-3.0 | 28,580 | [
"Gaussian"
] | a2ba8a49b8e03fbb6211f0abf438ce3852e58dc06a0d9947a9f14f735988320b |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import numpy as np
from astropy.units import Quantity
import astropy.units as u
from .meta import NDUncertaintyGaussian
__all__ = ['VarianceUn... | MSeifert04/nddata | nddata/nddata/nduncertainty_var.py | Python | bsd-3-clause | 16,019 | [
"Gaussian"
] | 50de8a590ed439c7a72387d74eedbe78d715b0116248d52bd54d14fd844b2cfa |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""\
Distances in a grid
jill-jenn vie et christoph durr - 2014-2018
--------------------------------------------
"""
from collections import deque
# snip{
def dist_grid(grid, source, target=None):
"""Distances in a grid by BFS
:param grid: matrix with 4-neighb... | jilljenn/tryalgo | tryalgo/dist_grid.py | Python | mit | 1,347 | [
"VisIt"
] | 93cae54b0e20d0716fb0f07b3b183aa6f45d6b070b17912ada7d90a802155bd3 |
"""
Gaussian Distribution with Gaussian Errors
------------------------------------------
Figure 5.25
The posterior pdf for mu and sigma for a Gaussian distribution with
heteroscedastic errors. This is the same data set as used in figure 5.7, but
here each measurement error is assumed unknown, treated as a model param... | kcavagnolo/astroML | book_figures/chapter5/fig_gaussgauss_mcmc.py | Python | bsd-2-clause | 4,455 | [
"Gaussian"
] | 952a9d36d52e51ca4a109b6a75bececce4fdc7e13c74a7bc128897d45c7a3778 |
import os
import logging
import math
import numpy
try:
from rdkit import Chem
from rdkit.Chem import AllChem
except ImportError:
logging.debug("To use QM calculations you must correctly install rdkit.")
import rmgpy.quantity
from rmgpy.thermo import ThermoData
import rmgpy.statmech
import rmgpy.therm... | nyee/RMG-Py | rmgpy/qm/molecule.py | Python | mit | 19,401 | [
"MOPAC",
"RDKit",
"cclib"
] | d49b30e1ec68521787e7e6c577d176336be495d4f830ea85c388fa4f3d5be7df |
import scrapelib
import datetime
import os
import re
from collections import defaultdict
from functools import wraps
from pupa.scrape import Scraper, Bill, VoteEvent
from pupa.utils.generic import convert_pdf
import lxml.html
import urllib
# Workaround to prevent chunking error (thanks @showerst)
#
# @see https://st... | openstates/openstates | openstates/sc/bills.py | Python | gpl-3.0 | 18,036 | [
"VisIt"
] | e36a500ebdf1f360e4a10756b2407cdc1d6a305119ac4a3f2faf31ad8dec0a0e |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
pyLATTICE is...
"""
from __future__ import division #necessary for python2
from __future__ import unicode_literals
# define authorship information
__authors__ = ['Evan Groopman', 'Thomas Bernatowicz']
__author__ = ','.join(__authors__)
__credits__... | eegroopm/pyLATTICE | gui/pyLATTICE.py | Python | gpl-2.0 | 74,321 | [
"CRYSTAL"
] | 106dae858d0bcdf16c68ad8cd5aaea6d02ecb964bb368b7338e0e75feebdb866 |
#!/usr/bin/env python
#
# Copyright (C) 2009-2011 University of Edinburgh
#
# This file is part of IMUSim.
#
# IMUSim 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 y... | martinling/imusim | setup.py | Python | gpl-3.0 | 2,744 | [
"Mayavi"
] | afadd5e789f010571c0b06c86f5ed5d48315e90632132677e8709f1fab1d448f |
""" Classes for remixing audio files.
(c) 2017 - Dave Rensin - dave@rensin.com
This module contains classes for remixing audio files. It started
as an attempt to re-create the amazing Infinite Jukebox (http://www.infinitejuke.com)
created by Paul Lamere of Echo Nest.
The InfiniteJukebox class can do it's processing i... | drensin/Remixatron | Web UI/Remixatron.py | Python | apache-2.0 | 40,638 | [
"Brian"
] | f1db90a84e344bb7e17ef9605386acd5f7123fa2616384fd0e46beff64f5820b |
'''
Author: Bruno Santeramo <bruno.santeramo@ba.infn.it>
Last Update: 26 dec 2013
Tested Versions:
DIRAC v6r9p33
'''
'''
submit a job
set the job name
'''
import DIRAC
from DIRAC.Core.Base import Script
Script.parseCommandLine()
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.Interfaces.API.Job import ... | SuperDIRAC/TESTDIRAC | sample-script/api/naming.py | Python | gpl-3.0 | 616 | [
"DIRAC"
] | 10d804908dec79b13ce141607e84fa89412c4b12830337e720dc8bba95001458 |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from __future__ import unicode_literals
from xml.etree.ElementTree import ElementTree
from pymatgen.io.cif import CifParser
from pymatgen.core.periodic_table import Element
import os
from io import StringIO
im... | bbusemeyer/mainline | utils/autogen/cif2crystal.py | Python | gpl-2.0 | 15,709 | [
"Brian",
"CRYSTAL",
"pymatgen"
] | 67540ec7ac848361465b788c2b277a1323e76b8a3327155360101fbfb8b4d45a |
from itertools import product
import cgen
from devito.ir.iet import (Expression, List, Prodder, FindNodes, FindSymbols,
Transformer, make_efunc, compose_nodes, filter_iterations,
retrieve_iteration_tree)
from devito.passes.iet.engine import iet_pass
from devito.to... | opesci/devito | devito/passes/iet/misc.py | Python | mit | 5,805 | [
"VisIt"
] | da11db730f62b348e0928a859d1826698a061966790e5113eabd72d1877590e2 |
# Script Name : getbox.py
# Author : Jianqiu Wang
# Created : 05 Dec 2015
# Last Modified : 17 Dec 2015
# Version : 1.0
# Description : get indexes of box for simulation. Input: datafile of lammps, output: a list contains 3 lengths and 3 tilt values for each time.
d... | Jianqiu-Wang/Molecular-Simulation | getbox.py | Python | gpl-2.0 | 935 | [
"LAMMPS"
] | eb6f8d3c4b69feca12b77f851d4840cb16e37790db4b827ac4ac6891ae6a87dc |
# 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... | sem-geologist/hyperspy | hyperspy/tests/signal/test_1D_tools.py | Python | gpl-3.0 | 13,552 | [
"Gaussian"
] | 8204c28e7f7e52ad07c50b8cc71f19f659997afe2fb7661fafacb3a81206cfbb |
''' Module: filter
Classes contained: Filter
Created by S.T. Castle on 2015-01-16
Create filters for image convolutions.
'''
import string
import math
class Filter:
'''A box, tent, or gaussian filter.'''
# Constructor.
# params: filter_type: string with value BOX, TENT, or GAUSSIAN.
# ... | castlest/shell-detection | manual-filters/filters-py/filter.py | Python | bsd-3-clause | 2,801 | [
"Gaussian"
] | a75edf4aacda8f1fa03e715ca8cde6def63da08d505f1f9cc50cc4dc69b84a61 |
#
# @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 ... | kratman/psi4public | psi4/driver/aliases.py | Python | gpl-2.0 | 7,631 | [
"Psi4"
] | 72558dd4fc8f4c66be7ab9af146617a19d4aee4de9b3f99a61175ce3a1ccb93c |
# coding=utf-8
from ._commandbase import RadianceCommand
from ..datatype import RadiancePath
import os
class Epw2wea(RadianceCommand):
"""epw2wea transforms an EnergyPlus weather data (.epw) file into
the DAYSIM weather file format, for use with the RADIANCE gendaymtx
program.
Attributes:
ep... | ladybug-analysis-tools/honeybee | honeybee_plus/radiance/command/epw2wea.py | Python | gpl-3.0 | 2,274 | [
"EPW"
] | 280f5f05f8e3126bf4964c25dd7c12f4e6857acb2f1f6d155d4b696262d68b64 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/backends.py | Python | gpl-3.0 | 1,409 | [
"Brian"
] | e882f96cdba904970995532f9d137516c118b45eef9722eeab184ef6762aa7d6 |
from copy import deepcopy
import logging
from math import floor
import os
from os.path import join as pjoin
import warnings
from warnings import warn
import numpy as np
import nibabel as nib
from mayavi import mlab
from mayavi.tools.mlab_scene_model import MlabSceneModel
from mayavi.core import lut_manager
from maya... | mwaskom/PySurfer | surfer/viz.py | Python | bsd-3-clause | 145,308 | [
"Mayavi",
"VTK"
] | 8905a501e319f42c26a23b20f8bfe71fb556a7274adb971e06713015f11e9fed |
#!/usr/bin/env python
""" load mWGS Raw Seq Set into OSDF using info from data file """
import os
import re
from cutlass.HostWgsRawSeqSet import HostWgsRawSeqSet
import settings
from cutlass_utils import \
load_data, get_parent_node_id, list_tags, format_query, \
write_csv_headers, values_to_node_dic... | TheJacksonLaboratory/osdf_submit | nodes/host_WgsRawSeqSet.py | Python | gpl-3.0 | 5,239 | [
"VisIt"
] | 7524cc25627ba7cba08480a7fb86a3819d848771ada36948ccbf22ea6c0dbbe8 |
# $Id$
# stuff used during debugging/testing
def load_my_sims():
"""Dict of CombinedGraph instances as input for HeatmapAnalysis.
Hard coded loader for testing.
"""
ligand = {0:'apo',1:'plm'} # state --> ligand
hopgraphs = {}
# hard coded list for testing, use expressive keys
# Single ho... | Becksteinlab/hop | hop/tests/analysis_test.py | Python | gpl-3.0 | 1,567 | [
"LAMMPS"
] | c2df777ee2f6e4d5f3d84d89ba028641cc75342bc7565808c3eb5d7f98c8ed9c |
"""
Copyright 2015 Brian Quach
Licensed under MIT (https://github.com/brianquach/udacity-nano-fullstack-tournament/blob/master/LICENSE) # noqa
"""
import random
import psycopg2
from contextlib import contextmanager
@contextmanager
def get_cursor():
"""Returns a context manager that will handle our database conne... | brianquach/udacity-nano-fullstack-tournament | tournament/tournament.py | Python | mit | 9,909 | [
"Brian"
] | 1c87df9391a01e79a2b5a39d1359012efa48d6e2c9b2bf3490ba512d2065d36a |
#!/usr/bin/env python2
# vtasks, a terminal google tasks client, MIT license
# this file deals with the Google tasks API - creidt to the following blog post:
# http://parezcoydigo.wordpress.com/2011/05/16/google-tasks-terminal-geek-tool/
# which is what this code was initially based on
import string
import time
impor... | IanFinlayson/vtasks | gtasks.py | Python | mit | 5,366 | [
"VisIt"
] | aac5f6e1485bdf18917adf4f02080c47d249d3878d5e4e17f897e6ca92be3eaa |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# Introduction: Integrating all results
# Created by galaxy on 2017/3/9 0009 16:48
import os
from collections import defaultdict
def integrate_enc(output_dir):
enc_dir = os.path.join(output_dir, 'ENC_GC3s')
integrate_dir = os.path.join(output_dir, 'integrate_result')... | cvn001/codonPY | src/integrate_results.py | Python | mit | 1,112 | [
"Galaxy"
] | 1f7b49098b4ce08af8d06fbd0ab5e6f1d70e4c03a31feaea536326ec2d033e15 |
# -*- coding: utf-8 -*-
# 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... | francisco-dlp/hyperspy | hyperspy/_components/gaussian.py | Python | gpl-3.0 | 6,180 | [
"Gaussian"
] | de9f7febebcf3b8187e82a31327238fd8c62bc8e34fdb214318c2590bc4ef4e7 |
../../../../../../../share/pyshared/orca/scripts/apps/pidgin/script_utilities.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/pidgin/script_utilities.py | Python | gpl-3.0 | 80 | [
"ORCA"
] | eebf9347de7c28a213fcdafcb3fdb1431600231814824cf12bf003c6f807cdd5 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/cc/__init__.py | Python | apache-2.0 | 4,726 | [
"PySCF"
] | 0d084f0618bad7d44fa4cd6b221b61bd0a381dd92903236f561104f49fd5408b |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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. Y... | ntt-sic/nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 116,884 | [
"FEFF"
] | 4c7d642ad537f243d955d8d3a50e491c56689fd7a592119c825a4bbfa2cc1b01 |
#! /usr/bin/env python
"""
This program plots the average electronic energy during a NAMD simulatons
averaged over several initial conditions.
It plots both the SH and SE population based energies.
Example:
plot_average_energy.py -p . -nstates 26 -nconds 6
Note that the number of states is the same as given in the ... | SCM-NV/qmworks-namd | scripts/pyxaid/plot_average_energy.py | Python | mit | 3,318 | [
"NAMD"
] | 31e9520c795bb6e9e03642e191842524a12b1d333c3b2c89f2e51163d82ee3f9 |
from lino.api.shell import *
from lino.utils.instantiator import Instantiator
def objects():
author = Instantiator(
'tables.Author', 'first_name last_name country').build
adams = author("Douglas", "Adams", "UK")
yield adams
camus = author("Albert", "Camus", "FR")
yield camus
huttner = ... | khchine5/book | lino_book/projects/tables/fixtures/demo.py | Python | bsd-2-clause | 702 | [
"Galaxy"
] | 7df308c0cd1419c5de46ae1e077b80103b12a36a9e127c485d06cf5ba5e5c8df |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import glob
import numpy as np
from monty.json import jsanitize
from monty.json import MSONable
scipy_old_piecewisepolynomial = True
try:
from s... | czhengsci/pymatgen | pymatgen/analysis/transition_state.py | Python | mit | 17,253 | [
"VASP",
"pymatgen"
] | 43ebd5f53970005075f7e7b81cfa95d27eef50e5ba56acad3f10e160f6d06693 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2020, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later.... | ATenderholt/cclib | test/regression.py | Python | bsd-3-clause | 147,036 | [
"ADF",
"Dalton",
"Firefly",
"GAMESS",
"Gaussian",
"Jaguar",
"MOLCAS",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Psi4",
"Q-Chem",
"TURBOMOLE",
"cclib"
] | 8b5adf0593ce640e8466fc25e614e79da72d44f69c693bdfc915ca723c5ac5fa |
# -*- coding: utf-8 -*-
# Author: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
from contextlib import contextmanager
import inspect
from textwrap import dedent
import gc
import os
import os.path as op
from pathlib import Path
import shutil
import sys
import warnings
import pytest
import numpy as np... | drammock/mne-python | mne/conftest.py | Python | bsd-3-clause | 29,210 | [
"VTK"
] | 32400369010df2790ee27c7de350a9e277afa1718e15d2eb1f95047c19715112 |
# -*- coding: utf-8 -*-
#
# test_stdp_dopa.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | magnastrazh/NEUCOGAR | nest/dopamine/test_files/test_stdp_dopa_3n.py | Python | gpl-2.0 | 6,677 | [
"NEURON"
] | e4b0b2d12aca0bbf7f4031674c9a96e2083347fdf3fded92f2d506d4dcd165ac |
import numpy as np
class IzNetwork:
"""
Network of Izhikevich neurons.
"""
def __init__(self, _neuronsPerLayer, _Dmax):
"""
Initialise network with given number of neurons
Inputs:
_neuronsPerLayer -- List with the number of neurons in each layer. A list
[N1, N2, ... N... | pmediano/ComputationalNeurodynamics | Fall2015/Exercise_2/IzNetwork.py | Python | gpl-3.0 | 3,501 | [
"NEURON"
] | f222a0106235e6af4933672b4d5106856b75bb3759358f3f2dcc2206c0467434 |
from datetime import datetime
from sqlobject import SQLObject, SQLObjectNotFound, StringCol, DateTimeCol
from sqlobject.sqlbuilder import Update
from gearshift import config
from gearshift.database.so import PackageHub
from gearshift.util import load_class
from gearshift.visit.api import BaseVisitManager, Visit
hub ... | dbrattli/python-gearshift | gearshift/visit/sovisit.py | Python | mit | 3,248 | [
"VisIt"
] | 229c197980d44c4ac95b75ecdb9345553fa9f98a801a24ff92007de193c9cdcc |
import numpy as np
from Numeric import pi, sqrt
from tools import factorial
from tools import Rational as Q
"""
This is a script designed for construction of the real solid spherical
harmonics (RSSH) in cartesian form. These can be written as::
m |m| l |m|
Y = Y = C r P (cos theta) Phi (phi)
... | qsnake/gpaw | c/bmgs/sharmonic.py | Python | gpl-3.0 | 25,747 | [
"GPAW",
"Gaussian"
] | c47a51cd4b0c7849568ee45e766525fea422372863b92a0db218e13166be5fa4 |
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