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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import tempfile
import numpy.testing.utils as nptu
from six.moves import zip
from io import open
import os
import json
from monty.json import MontyDecode... | setten/pymatgen | pymatgen/util/testing.py | Python | mit | 6,017 | [
"pymatgen"
] | aac48cf2df4ae0e9f98f3147cf0f1aea9d01ebc1d947e625adb514fd2eccd9b3 |
import numpy
import os, inspect
from orbkit import read
from orbkit.core import rho_compute
from orbkit.test.tools import equal
from orbkit import grid
from orbkit import options
options.quiet = True
tests_home = os.path.dirname(inspect.getfile(inspect.currentframe()))
folder = os.path.join(tests_home, '... | orbkit/orbkit | orbkit/test/grid_based/rho_compute.py | Python | lgpl-3.0 | 1,400 | [
"Molpro"
] | 42e7f57573a8c6cadea695bdfb4015146cb17951911c566246f1d714d2fc7728 |
# Copyright 2017 Priscilla Boyd. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law ... | priscillaboyd/SPaT_Prediction | src/analysis/Plotter.py | Python | apache-2.0 | 3,691 | [
"Amber"
] | b57a92b2cfa044743722b4f49269ae15a72192b09c957e820cf1955d688b3947 |
"""
spaceshooter.py
Author: Hagin
Credit: myself, Morgan, Mr. Dennison
Assignment:
Write and submit a program that implements the spacewar game:
https://github.com/HHS-IntroProgramming/Spacewar
"""
from ggame import App, RectangleAsset, ImageAsset, SoundAsset, Sprite, Sound, LineStyle, Color, Frame
import math
import ... | HaginCodes/Space-Shooter | spaceshooter.py | Python | mit | 10,585 | [
"BLAST"
] | 252c2203041f16d13a0ad46cbc8bc5faba7b8bc9b86a7e4a523d673848af72ce |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/MooseDocs/test/extensions/test_pysyntax.py | Python | lgpl-2.1 | 8,466 | [
"MOOSE"
] | 7704a2e3947dbb75501bb46e3c04f18af7c199dc7167a7e1992bf553329e73d3 |
'''
Python script to crunch sprite assets in Unity by a constant value (for reducing filesize with big images
This automatically applies to .meta files, so nothing changes in game, and it works on Multiple sprite assets as well.
PIL (Python Image Library) needs to be installed to use this.
@author: Brian Intile
'''
... | NitorInc/NitoriWare | Assets/Microgames/KnifeDodge/Sprites/ResizeSprite.py | Python | mit | 3,918 | [
"Brian"
] | 89df2968f39aa0592252364ba3d2bacd033f39ede09ab1094edbb942ba2f3e6e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free So... | atlashealth/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 8,348 | [
"Firefly"
] | 0233cb91ac4c2d78ffb4dc1504658b93e51b1ac298383f4af36fdee0ff740489 |
# coding=utf-8
# Copyright 2022 The Tensor2Tensor Authors.
#
# 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... | tensorflow/tensor2tensor | tensor2tensor/models/research/rl.py | Python | apache-2.0 | 29,682 | [
"Gaussian"
] | 95d031cbe72ede90e09bb4c8ce9a980413b66efe7b69ff465f3c635a76d57451 |
# beam_search.py - progressive widening beam search
#
# Copyright 2016 NetworkX developers.
#
# This file is part of NetworkX.
#
# NetworkX is distributed under a BSD license; see LICENSE.txt for more
# information.
"""Beam search with dynamic beam width.
The progressive widening beam search repeatedly executes a beam... | JamesClough/networkx | examples/algorithms/beam_search.py | Python | bsd-3-clause | 3,912 | [
"VisIt"
] | 0663c6c531e97f4a5c1e0f42bdd501d1a44612b5c36c378a45f603b114cc527b |
import sys
import pytest
import numpy as np
from phono3py.sscha.sscha import (
DispCorrMatrix, DispCorrMatrixMesh,
SupercellPhonon, ThirdOrderFC)
from phonopy.phonon.qpoints import QpointsPhonon
from phonopy.phonon.random_displacements import RandomDisplacements
try:
ModuleNotFoundError
except NameError:
... | atztogo/phono3py | test/sscha/test_sscha.py | Python | bsd-3-clause | 4,373 | [
"phonopy"
] | 1886fe5e38c17437d7dde0764488083d5d2a5d9a2fddb4e108d1c50d3779f9c9 |
"""
Functions for manipulating, inspecting, or otherwise working with data types
and data structures.
"""
import copy
import datetime
import fnmatch
import functools
import logging
import re
from collections.abc import Mapping, MutableMapping, Sequence
import salt.utils.dictupdate
import salt.utils.stringutils
impor... | saltstack/salt | salt/utils/data.py | Python | apache-2.0 | 52,366 | [
"VisIt"
] | f9710eccd672622a0ba43e56993c754d50f23e2991e170004fcf62f0fbf0e4e3 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | authman/Python201609 | Jessie Smith/assignments/Flask Olympics/olympics8/server.py | Python | mit | 1,465 | [
"CASINO"
] | cb332b193d6cd4ed3a6d6ebd50e695c9a8ecb523a26140c3c892b615ed9955e5 |
from chempy.util.testing import requires
from ..integrated import pseudo_irrev, pseudo_rev, binary_irrev, binary_rev
try:
import sympy
except ImportError:
sympy = None
else:
one = sympy.S(1)
t, kf, kb, prod, major, minor = sympy.symbols(
"t kf kb prod major minor", negative=False, nonnegative... | bjodah/aqchem | chempy/kinetics/tests/test_integrated.py | Python | bsd-2-clause | 1,549 | [
"ChemPy"
] | 45340eb9303a90db811f9211b635cacc18072f3755c25e06522f32b66c355bfe |
from paraview.simple import *
from paraview import smtesting
import vtk
import vtk.vtkRenderingVolume
import os
paraview.simple._DisableFirstRenderCameraReset()
# need a baseline?
saveImage = False
# check for driver support first
rw = vtk.vtkRenderWindow()
rw.SetSize(1,1)
rw.Render()
ptm = vtk.vtkProjectedTetrahedr... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Applications/ParaView/Testing/Python/StructuredGridVolumeRendering.py | Python | gpl-3.0 | 1,007 | [
"ParaView",
"VTK"
] | 13cd691c0b14c442d2aec4a81e18b539aaf83b2f16455d1ca689d2bf27b6609e |
# -*-python-*-
#
# Copyright (C) 2006-2013 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | marcellodesales/svnedge-console | svn-server/lib/viewvc/vcauth/svnauthz/__init__.py | Python | agpl-3.0 | 9,798 | [
"VisIt"
] | 517c3e55b38c3c0b248ec537d5ce33d709e4169a9b7c3eb7ebd471fa70c6d683 |
"""
tests for potential.py
"""
import mdtraj
import numpy as np
from numpy.testing import (assert_almost_equal, assert_array_almost_equal,
assert_allclose, assert_array_equal)
from odin import potential
from odin import exptdata
from odin.testing import ref_file... | tjlane/odin | test/test_potential.py | Python | gpl-2.0 | 2,436 | [
"MDTraj"
] | c3d9569156a9953c82b17a58549d8a2517e657abfa88f3c0059b5ebdadc29331 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2018, F5 Networks Inc.
# GNU General Public License v3.0 (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = r'''
---
module: bigip_asm_policy_server... | F5Networks/f5-ansible-modules | ansible_collections/f5networks/f5_modules/plugins/modules/bigip_asm_policy_server_technology.py | Python | mit | 13,115 | [
"ASE",
"Galaxy"
] | 2d10c2a0d5d6173595d53abeec6eff05518c562f5e85aed8845e3db400863ac5 |
tests = [("python", "UnitTestPackage.py", {}), ]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| greglandrum/rdkit | rdkit/ML/ModelPackage/test_list.py | Python | bsd-3-clause | 221 | [
"RDKit"
] | 24cb664559c9a37aac3e0b10392eba97c4c59d40f5e9269174cec2decd322ea8 |
import numpy as np
from numpy import exp, sin, cos, pi, radians, degrees
from sasmodels.weights import Dispersion as BaseDispersion
class Dispersion(BaseDispersion):
r"""
Cyclic gaussian dispersion on orientation.
.. math:
w(\theta) = e^{-\frac{\sin^2 \theta}{2 \sigma^2}}
This provides a cl... | SasView/sasmodels | example/weights/cyclic_gaussian.py | Python | bsd-3-clause | 1,408 | [
"Gaussian"
] | c77486297aeea9aa1ade35766b4af5ef63e4fd25209a8a83943b68bfffc3eca8 |
# Script to run a second derivative gaussian kernel on a grid
# Author : Isabel Restrepo
# 6-14-2009
import bvpl_batch
import time
#time.sleep(30);
bvpl_batch.register_processes();
bvpl_batch.register_datatypes();
class dbvalue:
def __init__(self, index, type):
self.id = index # unsigned integ... | mirestrepo/voxels-at-lems | bvpl/appearance_tests.py | Python | bsd-2-clause | 2,085 | [
"Gaussian"
] | 0ac59fea4b54cf6cb3d8309595be3a92ebf4b953c35245ca4c940b39191adb63 |
"""
Sheet classes.
A Sheet is a two-dimensional arrangement of processing units,
typically modeling a neural region or a subset of cells in a neural
region. Any new Sheet classes added to this directory will
automatically become available for any model.
"""
# Imported here so that all Sheets will be in the same pack... | ioam/topographica | topo/sheet/__init__.py | Python | bsd-3-clause | 15,889 | [
"NEURON"
] | b53bfd8c6517504a0cf6f10f260dd073b0197b39983dc761b580bf1417727489 |
# (C) British Crown Copyright 2010 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | zak-k/iris | lib/iris/tests/test_cf.py | Python | gpl-3.0 | 14,796 | [
"NetCDF"
] | 118bf84f3d3f40669f82bb1e01bc70ef1e0d06568fa466e8af99a665fe0e027b |
"""
.. _sfm-track:
==================================================
Tracking with the Sparse Fascicle Model
==================================================
Tracking requires a per-voxel model. Here, the model is the Sparse Fascicle
Model, described in [Rokem2014]_. This model reconstructs the diffusion signal
as... | mdesco/dipy | doc/examples/sfm_tracking.py | Python | bsd-3-clause | 4,934 | [
"Brian"
] | 476560b424ccdd7f2226efec8ac60ae2370e38dc15afdff686776e758c25ee17 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/core/__init__.py | Python | bsd-2-clause | 2,453 | [
"Mayavi"
] | c98f3284afd9d997e6e5d5e8abcd78f657246a5e6d33422f2fa7e8185317689d |
from io import StringIO
from collections import defaultdict
from numpy.testing import (
assert_equal, assert_array_equal,)
import pytest
import MDAnalysis
from MDAnalysis.analysis.hydrogenbonds.wbridge_analysis import (
WaterBridgeAnalysis, )
class TestWaterBridgeAnalysis(object):
@staticmethod
@pyt... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_wbridge.py | Python | gpl-2.0 | 34,326 | [
"MDAnalysis"
] | 6d8fc4bc6de530d0ef4f085b1a13170f93d6312ab92604a7496701abbc4b93da |
#!/usr/bin/env python3
"""
refguide_check.py [OPTIONS] [-- ARGS]
- Check for a NumPy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
- Check docstring examples
- Check example blocks in RST files
Example of usage::
$ python refguide_check.py optimize... | numpy/numpy | tools/refguide_check.py | Python | bsd-3-clause | 38,678 | [
"Gaussian"
] | 44a3245bf13a349eac4658635058338196a78afb7ada35ddc2bf584dcf34c9e5 |
########################################################################
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/19 12:16:39
########################################################################
""" :mod: TypedListTests
=======================
.. module: TypedListTests
:synopsis: tes... | arrabito/DIRAC | Core/Utilities/test/Test_TypedList.py | Python | gpl-3.0 | 2,911 | [
"DIRAC"
] | fd85d76a949433226caa94671c28d9c8a662af4d3c7701dfe00601579cc055bb |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import pymatgen
from pymatgen.analysis.cost.cost import CostDBCSV, CostAnalyzer, CostDBElements
module_dir = os.path.join(os.path.dirname(pymatgen.__file__), '..', 'test_files')
clas... | dongsenfo/pymatgen | pymatgen/analysis/cost/tests/test_cost.py | Python | mit | 1,560 | [
"pymatgen"
] | fa3751b8c1b79ff820ba300b8feab1ddee4c5369230218725344b245ad703cba |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
trueCoverage_rematch.py - Estimate the true bacterial chromosome
coverage and detects contamination with different strain or species.
Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
Last modified: February 27, 2018
This program is free software: ... | B-UMMI/INNUca | modules/trueCoverage_rematch.py | Python | gpl-3.0 | 22,715 | [
"Bowtie"
] | 022e45ab2dacede497f9c54173ce74cc8b6ddaf2af1ad580b2464c515abcf656 |
##########################################################################
# this script was generated by openmm-builder. to customize it further,
# you can save the file to disk and edit it with your favorite editor.
##########################################################################
from __future__ import pri... | LCLS/Protein-Folding-Sims | hp24stab/amber03/CUDA/amber03_implicit_noconstraints.py | Python | mit | 1,698 | [
"OpenMM"
] | e200bc6039ea05f1650a16182b09a631e3cd66091bb8d4a2604fa5c3c6fc3e2a |
import numpy as np
from six import string_types, integer_types
from .util import is_missing
from .descriptor import Descriptor
class Result(object):
r"""Result type."""
__slots__ = ("mol", "_values", "_descriptors", "_name_to_value")
def __init__(self, mol, r, d):
self.mol = mol
self._v... | mordred-descriptor/mordred | mordred/_base/result.py | Python | bsd-3-clause | 4,323 | [
"RDKit"
] | e62d7598cc90628f77a763755a9909315f790d063490d9f94a8c7e13870cfdbd |
from __future__ import print_function
import os
import shutil
import itertools
import tempfile
import subprocess
from distutils.spawn import find_executable
import numpy as np
import mdtraj as md
from mdtraj.testing import get_fn, eq, skipif
HAVE_DSSP = find_executable('mkdssp')
DSSP_MSG = "This test requires mkdss... | ctk3b/mdtraj | mdtraj/geometry/tests/test_dssp.py | Python | lgpl-2.1 | 3,549 | [
"MDTraj"
] | 762b68f01ecc2e68fff67aef97cd962e7e030109eb3d0344b5c3c118fba6fef5 |
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2004/2005 James Casbon.
# Copyright 2005 by Regents of the University of California. All rights reserved
# (Major rewrite for conformance to corebio. Gavin Crooks)
#
# This c... | NarlikarLab/DIVERSITY | weblogoMod/corebio/db/astral.py | Python | gpl-3.0 | 12,519 | [
"Biopython"
] | 03e60a9d39d36bed6848d81538892afd396b763db1f2e862873a58cc081366c2 |
"""
Author: Thomas G. Close (tclose@oist.jp)
Copyright: 2012-2014 Thomas G. Close.
License: This file is part of the "NineLine" package, which is released under
the MIT Licence, see LICENSE for details.
"""
from __future__ import absolute_import
try:
from mpi4py import MPI # @UnresolvedImport @Unu... | tclose/PyPe9 | pype9/simulate/neuron/network/cell_wrapper.py | Python | mit | 2,278 | [
"NEURON"
] | 352530795f5972f3df5e62bd6d98f8c138d39af43fe0c02bc286f2d0093306d7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
The phasediagram package implements the analysis tools to perform phase
stability analyses, including the constructing of phase diagrams, determination
of decomposition products, etc. The package is designe... | migueldiascosta/pymatgen | pymatgen/phasediagram/__init__.py | Python | mit | 410 | [
"pymatgen"
] | 60d5b017278ed59c2f604e875e9e957349031fd12b81586ae022cc43a21da222 |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/spglib/package.py | Python | lgpl-2.1 | 1,724 | [
"CRYSTAL"
] | 541421509f89b1964589c7fd7957c878b7594a39eab7e5e0dd791a2f7c10ab94 |
# Copyright 2020 Makani Technologies 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... | google/makani | avionics/network/network_util.py | Python | apache-2.0 | 27,972 | [
"VisIt"
] | ed8f079b7545d6aa3a4748b4dab1eca0f6377d55620fee1e06cf705c52dba493 |
# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for the Earth and Planetary Sciences
# Copyright (C) 2012 - 2015 by the BurnMan team, released under the GNU
# GPL v2 or later.
"""
example_user_input_material
---------------------------
Shows user how to input a mineral of his/her choice w... | CaymanUnterborn/burnman | examples/example_user_input_material.py | Python | gpl-2.0 | 5,259 | [
"Avogadro"
] | dda3a8469e8c8d122d319ccadb71aeb7f01f7064b7dc6eeb86a763a9b450db9c |
########################################################################
# File : AgentModule.py
# Author : Adria Casajus
########################################################################
"""
Base class for all agent modules
"""
from __future__ import absolute_import
from __future__ import division
from __... | yujikato/DIRAC | src/DIRAC/Core/Base/AgentModule.py | Python | gpl-3.0 | 20,512 | [
"DIRAC"
] | 157cb4fa27397f18f3332802b6fdc821f49d7c9702dca417cce7561344b53772 |
from spectrum import *
from numpy.testing import assert_almost_equal
import pytest
def test_class_Window():
w = Window(65, name='hann')
w.enbw
w.mean_square
w.frequencies
w.plot_time_freq()
w.compute_response(NFFT=32)
try:
w = Window(64, name='wrong')
assert False
ex... | cokelaer/spectrum | test/test_window.py | Python | bsd-3-clause | 9,764 | [
"Gaussian"
] | 6c55017c3ba17228953863383416033a038cfc2c3304d1e3b3065ed7df18cdbe |
"""
This class brings together a L{solve.Solver} to choose a set of implmentations, a
L{fetch.Fetcher} to download additional components, and the user's configuration
settings.
@since: 0.53
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall impor... | timdiels/0install | zeroinstall/injector/driver.py | Python | lgpl-2.1 | 7,057 | [
"VisIt"
] | bf40e8156b9dc95f533d8747e42d2bc9f06545b42fc06814cf3f607055be875d |
#!/usr/bin/env python
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Main Madpack installation executable.
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
import sys
import getpass
import re
import os
import glob
import traceback
import subprocess
import datetime
import tempfile
import shutil... | cooper-sloan/incubator-madlib | src/madpack/madpack.py | Python | apache-2.0 | 62,959 | [
"ORCA"
] | 5d8f1d08e4f632aee3624fac4a0f32cc675e8072a770a55666d4965a6a516692 |
import os
def read_babel_set(filename,atom):
#os.system('babel -i cml %s -o mol2 %s.mol2' % (filename,filename))
newfile = '%s.mol2' % filename
run_antechamber(newfile,atom)
def run_antechamber(filename,atom):
#os.system('module load amber')
#os.system('antechamber -i %s -fi mol2 -o %s -fo mol2 -... | sipjca/cmlparser_py | babel.py | Python | apache-2.0 | 842 | [
"Amber"
] | b5f6df2fdc2cf99b28c2c0f6906f968f0fb464ad28f2669afd61edd6aca9b97b |
"""
Provides Accounting functionality to DIRAC
It includes 2 different Services:
* DataStore: where new records are inserted
* ReportGenerator: that produce reports using the inserted records
and the associated Clients:
* DataStoreClient
* ReportsClient
DIRAC Accounting uses a number of predefined Types that must in... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/__init__.py | Python | gpl-3.0 | 649 | [
"DIRAC"
] | 81d279eab842a38958f2102c5cdc92cc04d7bbda32d8934c74c7cb0fd7a62f15 |
#
# Copyright (C) 2009, 2015, 2016, 2017, 2018, 2019, 2020
# Smithsonian Astrophysical Observatory
#
#
# 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 Lic... | anetasie/sherpa | sherpa/stats/__init__.py | Python | gpl-3.0 | 37,702 | [
"Gaussian"
] | f33c1ef5cbb8be1f8270f4c6d644b54d5ef8244118227e4b2b771adfa577cba9 |
# $Id$
#
# Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above... | AlexanderSavelyev/rdkit | Projects/DbCLI/CreateDb.py | Python | bsd-3-clause | 20,730 | [
"RDKit"
] | e28c7b1aeabc2585ba2c228882363431c11cf8ebf0e1eaddb712c34ab15c6f72 |
from __future__ import unicode_literals
import io
import json
import traceback
import hashlib
import os
import subprocess
import sys
from zipimport import zipimporter
from .compat import compat_realpath
from .utils import encode_compat_str
from .version import __version__
def rsa_verify(message, signature, key):
... | mx3L/archivczsk | build/plugin/src/resources/libraries/youtube_dl/update.py | Python | gpl-2.0 | 7,957 | [
"VisIt"
] | 5c978e036d24bccda9fbaadd5a07b23258d2424978d4267ec85094fcbaf61e2a |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
import click
from flask.cli import with_appcontext
from flask import current_app
click.disable_unicode_literals_warning = True
import os
@click.group()
def pfamscan():
"... | ecolell/pfamserver | pfamserver/commands/library/pfamscan.py | Python | agpl-3.0 | 1,820 | [
"MOOSE"
] | 8d446fbb8ba92fe73c27f704053fa057723f9da0b0ad4b926167f4649d84f04d |
# -*- mode: Python; indent-tabs-mode: nil -*- #
import awe
import numpy as np
import sys
import os
#-----Simulation Default Values-----
iterations = 5
nwalkers = 4
nstates = 100
restarts = float('inf')
maxreps = 50
#-----WQ Default Values-----
wq_port = 9123
wq_fast_abort_multiplier = -1.0
#-----Get u... | cooperative-computing-lab/awe | awe-ala.py | Python | gpl-2.0 | 5,432 | [
"Gromacs"
] | b492a3119d9b5fd62d37ada2f54b0fff94cbc53debb621e9fac609c9885bf9c3 |
""" Collection of user jobs for testing purposes
"""
import os
from DIRAC.tests.Utilities.utils import find_all
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Interfaces.API.Dirac import Dirac
# parameters
# Common functions
def getJob( jobClass = None ):
if not jobClass:
jobClass = Job
oJob = jobClass... | Andrew-McNab-UK/DIRAC | tests/Utilities/testJobDefinitions.py | Python | gpl-3.0 | 1,543 | [
"DIRAC"
] | deea7d8d84b56b078f951919daaac8d6330371859f27b706206c27a45818b7b3 |
from ase.constraints import FixAtoms as ASE_FixAtoms
from ase.constraints import Filter as ASE_Filter
import numpy as np
class ConstraintMixin:
"""Mixin class FixAtoms and Filter"""
def prepare_for_asap(self, atoms):
"""Prepare this constraint for optimized Asap dynamics
This... | auag92/n2dm | Asap-3.8.4/Python/asap3/constraints.py | Python | mit | 3,624 | [
"ASE"
] | dd8e9a25b69944c34fc41ab6d3ef457c02ad0ca99361d670e104da5e5da03ed0 |
###UI
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#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 withou... | kdaily/altanalyze | UI.py | Python | apache-2.0 | 382,733 | [
"Cytoscape"
] | dcc010ab148e0e1c01b269c3abbdc34ea17d07dd84c252d1ff02a38ef8574f9d |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2014 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 Soft... | andrebellafronte/stoq | plugins/bikeshop/bikeshopui.py | Python | gpl-2.0 | 1,591 | [
"VisIt"
] | fcd66eeaddf6326724f81546957542ada19c549c279f87dfedfdbee410558532 |
'''
Functions and classes for generating 1D random fields.
The functions **randn1d** and **multirandn1d** are similar to the
**numpy.random.randn** and **np.random.multivariate_normal** functions.
If a large number of random fields are required (e.g. for RFT validations)
it may be more efficient to use the **Generator... | 0todd0000/spm1d | spm1d/rft1d/random.py | Python | gpl-3.0 | 8,036 | [
"Gaussian"
] | b5d4fc840a5f7c8e57de180a38ec6480dff034e2620bf2e43f7f69f618e9541f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# SQRL Server (Python) documentation build configuration file, created by
# sphinx-quickstart on Wed Jun 28 05:29:34 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present... | Perlkonig/sqrlserver-python | docs/conf.py | Python | mit | 9,574 | [
"Dalton"
] | 82340f4c21121fc046b3329d8ec63fea3e38a0900776e89e853114dedd501da7 |
"""This module contains the "Viz" objects
These objects represent the backend of all the visualizations that
Superset can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import copy
import hashlib
import l... | lina9527/easybi | viz.py | Python | mit | 54,580 | [
"VisIt"
] | 2cdcb39f79ec70e41e65226893558f5faf5b55184ce9f267ee06de658b3f75c1 |
from datetime import datetime
from dateutil.relativedelta import relativedelta
from django.test import TestCase, tag
from ..visit import WindowPeriod
from ..visit import Visit, VisitCodeError, VisitDateError
class TestVisit(TestCase):
def test_repr(self):
visit = Visit(code='1000',
... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/tests/test_visit.py | Python | gpl-2.0 | 4,371 | [
"VisIt"
] | 39473f6c9bedfa193043a31cb28c4b7514502d8a846c81d19d1eda1f4e54e9fb |
from django.test import SimpleTestCase
from corehq.apps.app_manager.tests.app_factory import AppFactory
from corehq.apps.app_manager.tests.util import TestXmlMixin, patch_get_xform_resource_overrides
from corehq.util.test_utils import flag_enabled
@patch_get_xform_resource_overrides()
class GridMenuSuiteTests(Simple... | dimagi/commcare-hq | corehq/apps/app_manager/tests/test_grid_menus.py | Python | bsd-3-clause | 8,419 | [
"VisIt"
] | d66a0979bb1ff0302b79860cf1c7e6bc2f9632ffac337d229d75df3183032b0e |
#!/opt/local/bin/python
"""
Calculate the total energy as a function of lattice constant,
by altering the lattice constant in in.pw file.
And if possible, calculate equilibrium lattice size and
bulk modulus, too.
Assume using Quantum ESPRESSO (QE).
PREPARE mode creates directories and in.pw files to be computed by QE.... | ryokbys/nap | nappy/espresso/etot_vs_size.py | Python | mit | 8,878 | [
"ASE",
"Quantum ESPRESSO",
"VASP"
] | 535d1309b3c16d109803fd809687d594b6ea824ad220ed689a910652cf0bf183 |
import ast
import configparser
import os
import botocore.session
import botocore.exceptions
from platform import system
from types import MethodType
def get_prepared_config(
profile,
region,
ssl_verification,
adfs_ca_bundle,
adfs_host,
output_format,
provider_id... | venth/aws-adfs | aws_adfs/prepare.py | Python | mit | 9,150 | [
"ADF"
] | ae09b620d7ed7fe21b2171acf5305dcf13f898a59b9e5046d3827c5bb8b84e7a |
# Copyright (C) 2008-2009 Mark A. Matienzo
#
# This file is part of worldcat, the Python WorldCat API module.
#
# worldcat 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
# ... | anarchivist/worldcat | worldcat/request/search.py | Python | gpl-3.0 | 8,497 | [
"ASE"
] | a6a338c2f76bc20c8e56c1c3194fec9faf2df50daf490c3585220c24b6807030 |
"""
molvs.cli
~~~~~~~~~
This module contains a command line interface for standardization.
:copyright: Copyright 2016 by Matt Swain.
:license: MIT, see LICENSE file for more details.
*Adapted for purposes of integration of MolVS into RDKit
"""
import argparse
import logging
import sys
from rdkit import Chem
from r... | bp-kelley/rdkit | Contrib/MolVS/molvs_cli.py | Python | bsd-3-clause | 3,536 | [
"RDKit"
] | 04e2210436e49ac9d08ad3beefa967b0470e66d340e5be9c0737c83a23184dc3 |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import webnotes
import webnotes.utils
from webnotes.utils import cstr, flt, getdate
from webnotes.model.bean import getlist
from webnotes.model.code... | saurabh6790/tru_app_back | selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 16,170 | [
"VisIt"
] | f319a73c0a92212eeb18d514d4ce31b3621111b6e36329da891a9ac62b201207 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
import sys
@process
def source(chan_out):
for i in range(10):
chan_out("Hello... | runefriborg/pycsp | examples/TerminationRaceRetire.py | Python | mit | 550 | [
"Brian"
] | 7446af6971c8759e490160ea8f9b8bcc78c2ddbe8e43ddeead849fc7dd2ed9c9 |
import factory
# http://factoryboy.readthedocs.org/en/latest/index.html
from tao.models import Job, TaoUser, Simulation, GalaxyModel, DataSet, DataSetProperty, StellarModel, Snapshot, BandPassFilter, DustModel, GlobalParameter, WorkflowCommand, SurveyPreset
class UserFactory(factory.Factory):
FACTORY_FOR = TaoUse... | IntersectAustralia/asvo-tao | web/tao/tests/support/factories.py | Python | gpl-3.0 | 5,101 | [
"Galaxy"
] | b48a9827dca1e801ce7be35d6950421d5412562ac37b5209f64b2e526bab7c59 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | goozbach/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,428 | [
"Brian",
"Galaxy"
] | 7c7b36827fdafbbd40de5cb2e737162e2205af53b91885edbd266806af09054e |
# -*-python-*-
#
# Copyright (C) 1999-2006 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | foresthz/fusion5.1 | www/scm/viewvc/lib/vclib/ccvs/rcsparse/__init__.py | Python | gpl-2.0 | 704 | [
"VisIt"
] | 6cb25f7eb24c0d7c59abfaf03a50736bf4c326c235ca2410d824036f4e3f500f |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/MDIntegrator.py | Python | gpl-3.0 | 2,807 | [
"ESPResSo"
] | bc147dfd00114c39981df4b644a33b8aa05f3049825eca9b98556a3ba982fad9 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Writes compressed data from a wiggle file by chromosome.
usage: %prog score_file < wiggle_data
"""
from __future__ import division
import sys
import psyco_full
import bx.wiggle
from bx.binned_array import BinnedArray
from fpconst import isNaN
from bx.cookbook import doc_... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/wiggle_to_chr_binned_array.py | Python | bsd-3-clause | 947 | [
"Galaxy"
] | 09487ad05331386f7b49f10ab740d0baef23d5d9b97b8b1586305cc3253b15e2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Defines classes and methods used for recurrent neuronal networks.
Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fr... | LFPy/LFPy | LFPy/network.py | Python | gpl-3.0 | 69,051 | [
"NEURON"
] | e8907f13bebfa657e927bc6eac7b2255c2ee26a340b7d7dcc81692f3f743ada1 |
from __future__ import absolute_import
from __future__ import print_function
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.adsorption import *
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen import Structure, Lattice, Molecule
test_dir = os.path.join(os... | czhengsci/pymatgen | pymatgen/analysis/tests/test_adsorption.py | Python | mit | 8,128 | [
"pymatgen"
] | 38848a00c08dfb01c547b0174d0ef8a2fff8096c8b7827ce166f9aa15931bfcd |
'''
digitallockin.py, Digital Lockin amplifier using NI PXI devices
Copyright: Zeust the Unoobian <2noob2banoob@gmail.com>, 2014
This file is part of DigitalLockin.
DigitalLockin is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the ... | zeusttu/DigitalLockin | digitallockin.py | Python | gpl-3.0 | 27,071 | [
"Gaussian"
] | 41e923b27a7c3726e0360b88ac65dd071285927d896abe7f624a55f08deaa5eb |
from numpy import linspace, zeros, array, meshgrid, abs, empty, arange, \
int32, unravel_index, dtype
from multiprocessing import Pool
from ..solvers import solver_dict, get_solver_name
# attempt to import plotting libraries
try:
from matplotlib import pyplot
from mpl_toolkits.mplot3d import axes3d
except... | JuBra/cobrapy | cobra/flux_analysis/phenotype_phase_plane.py | Python | lgpl-2.1 | 12,249 | [
"Mayavi"
] | 87f9ac34f5395c3c6e5b9cd1da002a0cffd762d164a6915415bbe4af54c5df4d |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | sileht/ansible | lib/ansible/runner/action_plugins/assemble.py | Python | gpl-3.0 | 4,345 | [
"Brian"
] | 55dbee2d4b60a371f36fb5b16b8fa1dbc7c76be74fbb84d939f6c81723e439cb |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/common/test_box.py | Python | lgpl-2.1 | 833 | [
"MOOSE"
] | 57239e5f8c052b6418380b861056e03e51a64b26e1d8b469e1455d802f1beecd |
"""Ordinary Least Squares regression classes."""
__author__ = "Luc Anselin luc.anselin@asu.edu, David C. Folch david.folch@asu.edu"
import numpy as np
import copy as COPY
import numpy.linalg as la
import user_output as USER
import summary_output as SUMMARY
import robust as ROBUST
from utils import spdot, sphstack, Reg... | pastephens/pysal | pysal/spreg/ols.py | Python | bsd-3-clause | 19,613 | [
"COLUMBUS"
] | 417e7903b281ad559905083b4110d42b6e1ee181d5b0be0cbd7d96484272dff5 |
"""
Gaussian mixture model vs. hidden Markov model with Gaussian mixture emissions vs.
hidden Markov model.
"""
import sdsModels as sdsm
exp = sdsm.Experiment(pathToData='../data/complete_april_2014_ratings-latest.csv')
exp2 = sdsm.Experiment(pathToData='../data/complete_april_2014_ratings-latest.csv')
gmmhmm = sdsm... | phihes/sds-models | examples/all_models_different_features__plain.py | Python | mit | 1,051 | [
"Gaussian"
] | 538735de047779d2cbc145e5125a59805731f7b6285a4ab53c7ce87b3b1cfed9 |
# changelog bisection for mercurial
#
# Copyright 2007 Matt Mackall
# Copyright 2005, 2006 Benoit Boissinot <benoit.boissinot@ens-lyon.org>
#
# Inspired by git bisect, extension skeleton taken from mq.py.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 ... | iaddict/mercurial.rb | vendor/mercurial/mercurial/hbisect.py | Python | mit | 9,226 | [
"VisIt"
] | 82d9a1cdbfe930cd84b89b75c1c811bf9709fa8ad803688cf5019a79a67279d7 |
from django.test import TestCase
from django.core import mail
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User
from model_mommy import mommy
from .models import Location
class DetailTest(TestCase):
def setUp(self):
user = User.objects.create_user('test', 'no@no.no... | nasa/39A | spaceapps/locations/tests.py | Python | apache-2.0 | 9,651 | [
"VisIt"
] | 020efcb62d43a687f605dbed282484e27cf4f2a92cd7799a084535068735a619 |
from ase.lattice.surface import fcc100, add_adsorbate
from gpaw import GPAW
from gpaw.poisson import PoissonSolver
from gpaw.dipole_correction import DipoleCorrection
slab = fcc100('Al', (2, 2, 2), a=4.05, vacuum=7.5)
add_adsorbate(slab, 'Na', 4.0)
slab.center(axis=2)
slab.calc = GPAW(txt='zero.txt',
... | robwarm/gpaw-symm | doc/tutorials/dipole_correction/dipole.py | Python | gpl-3.0 | 777 | [
"ASE",
"GPAW"
] | 728fbf431b1cb91ed371ba23dd912a012752e8412554bf46d40246ed33b31e0f |
"""Copyleft 2010 Forrest Sheng Bao http://fsbao.net
PyEEG, a Python module to extract EEG features, v 0.02_r2
Project homepage: http://pyeeg.org
**Data structure**
PyEEG only uses standard Python and numpy data structures,
so you need to import numpy before using it.
For numpy, please visit http://numpy.scipy.org
... | fergalbyrne/nupic.kaggle-eeg | tools/pyeeg.py | Python | gpl-3.0 | 22,998 | [
"VisIt"
] | a90365b66d25d616adae31f318bf04119218b4b5dba944eb91773790ad10725b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import logging as log
from synergetics.config import config as cfg
from synergetics.neurons.neurons import Neuron
class LIF(Neuron):
def __init__(self, position, excitatory=True,
update_rule= Default_update(),
discover_ru... | synergetics/neuron | src/neurons/LIF/LIF.py | Python | mit | 488 | [
"NEURON"
] | c1a3d3749bde63f978ea36b3ff3c103f9ca6facfac838cb7ce1dc610565749dc |
"""
idnest
"""
__author__ = "Brian Balsamo"
__email__ = "balsamo@uchicago.edu"
__version__ = "0.0.1"
from uuid import uuid4
from abc import ABCMeta, abstractmethod
import logging
from flask import Blueprint, jsonify, abort, Response
from flask_restful import Resource, Api, reqparse
import redis
from pymongo import ... | uchicago-library/idnest | idnest/blueprint/__init__.py | Python | gpl-3.0 | 17,401 | [
"Brian"
] | ee64f4e864887143e30ff4ec618823216fdfaa59d49f78e2badea8770ea9812b |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.9 on 2018-01-18 17:09
from __future__ import unicode_literals
import advisornotes.models
import autoslug.fields
import django.core.files.storage
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dep... | sfu-fas/coursys | advisornotes/migrations/0006_on_delete.py | Python | gpl-3.0 | 8,094 | [
"VisIt"
] | fad20dc48f8d817b4a24e9b1f5e10cf7dbcda9ad8e9047b8c03e1c0b2a4165aa |
#!/home/scollis/anaconda/bin/python
from __future__ import print_function
import netCDF4
#import time
def grab_hrrr_slice(outname, reftime_index, time1_index):
""" Grab select variables and reftime/time1 slice from HRRR file. """
ncep_hrrr = netCDF4.Dataset('http://thredds-jumbo.unidata.ucar.edu/thredds/dodsC... | scollis/SULI-2015 | code/get_hrrr.py | Python | bsd-2-clause | 2,256 | [
"NetCDF"
] | e6b80e9bcc67d11670b71e0bcac19f8f5e429f079c0b4634f53046c116215222 |
from bs4 import BeautifulSoup
import requests
from operator import itemgetter
class TopMembers:
def __init__(self, username, password):
self.username = username
self.password = password
self.members = []
#Start session
self.session = requests.Session()
def __popupula... | rbonick/care-tags_scripts | care_tags_topposts/topmembers.py | Python | mit | 4,751 | [
"VisIt"
] | 58ccdbf5d79ff7903e688f54d517e194b5b0d22d3a344cbe25a4c90d57ae2aa2 |
from ase.atoms import Atom, Atoms
from ase.calculators.singlepoint import SinglePointDFTCalculator
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
def index_startswith(lines, string):
for i, line in enumerate(lines):
if line.startswith(s... | slabanja/ase | ase/io/gpawtext.py | Python | gpl-2.0 | 3,757 | [
"ASE",
"GPAW"
] | d7df74c9b8c8c2c3b2d7628d0d9084f315f69df1fbb4f11dd0ccd082fd5d4b68 |
#!/usr/bin/python
#
# Copyright (c) 2012 The Native Client Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
"""
Checks (rule) patterns associated with rows in tables, and adds an
additional column to each row (in each table) which cap... | wilsonianb/nacl_contracts | src/trusted/validator_arm/dgen_add_patterns.py | Python | bsd-3-clause | 10,951 | [
"VisIt"
] | 4b705b7111d254ce9bfce323b81be7d48167f43c51a7a90752d7ef76bd61eae4 |
__all__ = [
'CombineTables',
'ReshapeTable',
'ExtractArray',
'SplitTableOnArray',
'AppendTableToCellData',
]
__displayname__ = 'Table Operations'
import numpy as np
import vtk
from vtk.numpy_interface import dataset_adapter as dsa
import pyvista as pv
from .. import _helpers, interface
from ..ba... | banesullivan/ParaViewGeophysics | PVGeo/filters/tables.py | Python | bsd-3-clause | 15,362 | [
"ParaView",
"VTK"
] | dba7903a7ca9da3207b669327448361341c39f8ce6bf3b78cf408154026d26a2 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gdmlogin/__init__.py | Python | gpl-3.0 | 845 | [
"ORCA"
] | 7c252a75f4e7db2bc99d67fcc96997a21279067d3dce0600833bdb3f21ccdced |
# KSparseVector.py
#
# This python script uses distributed-memory library
# Elemental.
#
# Copyright 2012, Hatef Monajemi (monajemi@stanford.edu)
# http://www.stanford.edu/~monajemi
def KSparseVector(k,N,field='R'):
# Have the root process (rank=0) broadcast its seed
# Have each process set its seed to the broadcaste... | monajemi/TensorPT | Python/DEP/kSparseVector.py | Python | bsd-3-clause | 788 | [
"Gaussian"
] | 34155c7335bab69f4285050f4fc154bc26409aae2d4094d4007d38fafe742400 |
# (c) 2015 - Jaguar Land Rover.
#
# Mozilla Public License 2.0
#
# Library to process updates
import json
import os
import subprocess
import dbus
import swm
#
# Software operation
# Contains a single software operation
# loaded from a manifest file.
#
class SoftwareOperation:
def __init__(self, manifest, op_obj):... | magnusfeuer/genivi_software_management | software_loading_manager/software_operation.py | Python | mpl-2.0 | 7,694 | [
"Jaguar"
] | 63ab654a7a202fa608593f580618ef3aad915cb48045535ada11f35d4e27e3aa |
"""Miscellaneous utilities."""
import numpy as np
import logging
class Normalizer():
"""
An abstract class for normalizing inputs.
"""
def normalize(self, X):
raise NotImplementedError()
def unnormalize(self, X):
raise NotImplementedError()
class BoundedNormalizer(Normalizer):
... | meyersw3476/active_subspaces | active_subspaces/utils/misc.py | Python | mit | 8,530 | [
"Gaussian"
] | 48e603242765287601ce9c883e491ce1aac2736d2edff8c865d54f64e82bb859 |
##########################################################################
#
# Copyright (c) 2015, John Haddon. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of so... | lucienfostier/gaffer | python/GafferImageUI/BlurUI.py | Python | bsd-3-clause | 2,831 | [
"Gaussian"
] | dd00b6b1baa72750a3997454297dea605ed4dd18ccf7932f69d65e7c6fad9bdf |
#!/usr/bin/env phenix.python
"""
xds_plot_integrate.py
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
"""
TODO: plot differences in direct beam and rotation axis
"""
import sys
import re
import collections
from cctbx import sgtbx... | keitaroyam/yam_scripts | xds_plot_integrate.py | Python | bsd-3-clause | 8,422 | [
"CRYSTAL"
] | 85742eedb368bd7fbe8b6e48fa1d89cfade5593a7b752fdb6364f06783c74b2d |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import random
import pytz
import io
import json
import os
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.cor... | mtlchun/edx | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 177,188 | [
"VisIt"
] | 2d50eb94961e1024c3cecd79e21a8525e3c61b7f3f1fbc76a8ada9d4eb7adb4a |
from pymol.cgo import *
from pymol import cmd
from random import random, seed
from chempy import cpv
obj = []
scale = 1.0
# display VMD-like coordinate axes
obj.extend( [ SAUSAGE,
0.0, 0.0, 0.0, # XYZ 1
scale, 0.0, 0.0, # XYZ 2
0.1 * scale, # Radius
... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/cgo_axes.py | Python | gpl-2.0 | 2,380 | [
"ChemPy",
"PyMOL",
"VMD"
] | 73382231a5e122be87d3147453fff5868cb582a0fa271c31ec01798b04010d71 |
# Git version - should use this one for now.
print "Welcome to BOBadventure, please enter your name and hit 'Enter' to see more text. To make a choice, please enter the character infront of the option then hit 'Enter'. You might encounter questions that requires you to check on the internet."
name= raw_input("What is y... | Jawcris/BOBadevnture | word_adventure.py | Python | apache-2.0 | 41,526 | [
"VisIt"
] | bb0276ce0fd1db4b90052295fe6abcd59ab4c49cb834f4b7c65dace5c2817aac |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from datetime import datetime
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.lms.learner_profile import LearnerProfi... | stvstnfrd/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 6,505 | [
"VisIt"
] | fe099151b69416e286ab0f25cf9580b5662e3c1d332c1d07c2eab28f7553f2c0 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
import numpy as np
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.core.composition import Composition
from pymatgen.core.lattice import Lattice
from pymatgen.c... | materialsproject/pymatgen | pymatgen/io/tests/test_cif.py | Python | mit | 42,693 | [
"ABINIT",
"VASP",
"pymatgen"
] | 88e879e171a83a83775c2025a56733f31fd4042062ff31f08aacc86b447e53ba |
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