text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
# Author: Braden Czapla (2019)
# Last modified: 2019-04-30
# Original data: Tsuda et al. 2018, https://doi.org/10.1364/OE.26.006899
from __future__ import absolute_import, division, print_function
import numpy as np
from scipy.special import wofz
import matplotlib.pyplot as plt
###############... | polyanskiy/refractiveindex.info-scripts | scripts/Tsuda 2018 - PMMA (BB model).py | Python | gpl-3.0 | 4,973 | [
"Gaussian"
] | c7f078c1cff38cf03abcadac5e9be2735c2d3a2aa6639d5b81bc51a9038acc5e |
# MARTINIZE
# A simple, versatile tool for coarse-graining molecular systems
# Copyright (C) 2017 Tsjerk A. Wassenaar and contributors
#
# 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 v... | Tsjerk/Martinize | martinize/cli.py | Python | gpl-2.0 | 10,450 | [
"PyMOL"
] | 3161e494d10fd12e99c3070e15e0399871069235254dd931187002173c17d58c |
import argparse
from coalib.misc import Constants
from coalib.collecting.Collectors import get_all_bears_names
class CustomFormatter(argparse.RawDescriptionHelpFormatter):
"""
A Custom Formatter that will keep the metavars in the usage but remove them
in the more detailed arguments section.
"""
... | arjunsinghy96/coala | coalib/parsing/DefaultArgParser.py | Python | agpl-3.0 | 9,113 | [
"VisIt"
] | 3fb9e8a79c72d80367ca8023a281e06da6d29eab338bdb9b43f07fcf4307aa3a |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | kvar/ansible | lib/ansible/modules/network/avi/avi_alertemailconfig.py | Python | gpl-3.0 | 3,896 | [
"VisIt"
] | ce713bf1a97466b7a55ad2c1f0213fb3ebc53949f93d314a57044274d35c3ecb |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/presentations/lib/mediaitem.py | Python | gpl-2.0 | 15,484 | [
"Brian"
] | 18fb475319efd494cc4c66b0db7f825f03947408c90fa3f82584aad2614835d1 |
#@PydevCodeAnalysisIgnore
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... | rossumai/keras-multi-gpu | keras_tf_multigpu/examples/avolkov1/cifar/tf_examples/cifar10.py | Python | mit | 14,682 | [
"Gaussian"
] | ab5bdb835f102a99fac32288b8768cec538714729daff799e49a0a0b1ffc373a |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkPNMReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkP... | chrisidefix/devide | modules/vtk_basic/vtkPNMReader.py | Python | bsd-3-clause | 464 | [
"VTK"
] | da190df26bf07a8814557c72f612483da2e694467456e329e7048cc1c879b04b |
import numpy
import scipy # use numpy if scipy unavailable
import scipy.linalg # use numpy if scipy unavailable
## Copyright (c) 2004-2007, Andrew D. Straw. All rights reserved.
## Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions ... | DLlearn/PCV | pcv_book/ransac.py | Python | bsd-2-clause | 8,704 | [
"Gaussian"
] | 730996c37437ce9e29d235c3b412354f9af9f68529ca3f00c832590296f96b1e |
"""
The B{0install list-feeds} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _
from zeroinstall.cmd import UsageError
from zeroinstall.injector import model
syntax = "URI... | timdiels/0install | zeroinstall/cmd/list_feeds.py | Python | lgpl-2.1 | 620 | [
"VisIt"
] | d463ab1b3ff3f1fa208a3d76619c343ddf4d1041a4392c21e09fb14dd5e1d329 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/yambo/package.py | Python | lgpl-2.1 | 6,257 | [
"ABINIT",
"NetCDF",
"Yambo"
] | 1a9982aec69efb64e9baadbec49fd9e435fa2283a251d9eaa2540b973c3e1c4d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''plotting/analysis routines on output of example_parallel_network.py
Copyright (C) 2018 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 ... | LFPy/LFPy | examples/bioRxiv281717/example_parallel_network_plotting.py | Python | gpl-3.0 | 25,689 | [
"NEURON"
] | 519f92cd7f84d93882bfa11c7c711892cacbfb7a001c5126d374b1764ab72dbb |
# $Id$
#
# Copyright (C) 2004-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
class ExcludedVolume(object):
def __in... | soerendip42/rdkit | rdkit/Chem/Pharm3D/ExcludedVolume.py | Python | bsd-3-clause | 1,002 | [
"RDKit"
] | 3d73a9ab558ffc364502087010b68a16fa804e38b6ef7cf04faae5fe87ae52c0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | lothian/psi4 | psi4/driver/qcdb/align.py | Python | lgpl-3.0 | 6,553 | [
"Psi4"
] | 0adceeb44195e828c1855bd1670b757959f5aaee7a64195bc6d358822576b38d |
import collections
from importlib import import_module
from enhatts import FieldPreparationErrors, DeleteField
from tinkerpy import anonymous_class
from inspect import isclass
FieldDefinition = collections.namedtuple('FieldDefinition',
'field_class attributes')
def _mapping_repr(header, mapping,
getter=... | IvIePhisto/EnhAtts | enhatts/_fields.py | Python | mit | 11,686 | [
"VisIt"
] | 722cd7d863b9660a837285632df1171b5b4fdfe8a04e498ebf470f8a69a8130f |
# 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... | junghans/espressopp | src/interaction/Harmonic.py | Python | gpl-3.0 | 6,574 | [
"ESPResSo"
] | f2163565888e96b8fa7a3a63a6806c44f8d940124b8c3cef222b355a95b5a036 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import numpy as np
from ..sile import add_sile, sile_fh_open, sile_raise_write, SileError
from .sile import SileSiesta
... | zerothi/sisl | sisl/io/siesta/xv.py | Python | mpl-2.0 | 5,323 | [
"SIESTA"
] | 3d032f3913b3e9661219d9d85159bf96d3707e2b4f474ae5b91c9904e7da662b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Wrapper for netCDF readers."""
import os.path
import warnings
import numpy as np
from collections import OrderedDict
from monty.dev import requires
from monty.collections import AttrDict
from monty.functool... | gVallverdu/pymatgen | pymatgen/io/abinit/netcdf.py | Python | mit | 17,629 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | f00d40900c97b58fef33af2f7ccedc9711468e4bd3e26538a38b03c82f7e3bac |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-add-shifter
# Author : Federico Stagni
########################################################################
""" Adds or modify a shifter, in the operations section of the CS
"""
__RCSID__ = "$Id$"
... | coberger/DIRAC | ConfigurationSystem/scripts/dirac-admin-add-shifter.py | Python | gpl-3.0 | 1,627 | [
"DIRAC"
] | f5469967ad81ff48137bce753f2e85e434b0db3899c5f7d983143569e605ffde |
# -*- coding: utf-8 -*-
__author__ = 'akiokio'
from django.core.management.base import NoArgsCommand
from salesReport.models import item as product, brands
from salesReport.pymagento import Magento
from salesReport.views import getBrand, getVMD30ForDatabaseItem
import datetime
def RepresentsInt(s):
try:
i... | akiokio/centralfitestoque | src/salesReport/management/commands/update_product_brand.py | Python | bsd-2-clause | 1,654 | [
"VMD"
] | c73bb0ff6c08e5bb57e8be05800a81b47ddaf63299241e3fb5edd4dcfd95a169 |
"""
Data-driven tests for reads
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import collections
import os
import ga4gh.server.backend as backend
import ga4gh.server.datamodel as datamodel
import ga4gh.server.datamodel.datasets as datasets
import ga4... | saupchurch/server | tests/datadriven/test_reads.py | Python | apache-2.0 | 19,167 | [
"pysam"
] | 6882017c827d773720dd58d603764fdb11c711b6f58cb4d3d84cad68aa11c62c |
##############################################################################
# Copyright (c) 2013-2017, 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... | lgarren/spack | var/spack/repos/builtin/packages/r-aims/package.py | Python | lgpl-2.1 | 1,979 | [
"Bioconductor"
] | 2b562400b9f318a6c23aabd5f7922d1fa9083f86a23695ee93b83dd368f9aa01 |
from time import time
import numpy as np
from petsc4py import PETSc
from src import stokes_flow as sf
from src.objComposite import *
# from src.stokes_flow import obj_dic
# from src.ref_solution import *
# from src.geo import *
__all__ = ['save_singleEcoli_vtk', 'save_singleEcoli_U_vtk', 'save_singleEcoli_U_4part_vtk... | pcmagic/stokes_flow | src/myvtk.py | Python | mit | 10,423 | [
"VTK"
] | ec3874c74464c31e150dfd251488694427e4c3f954d906b24c04d927adfcc954 |
########################################################################
# $HeadURL $
# File: AdlerTestCase.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2011/02/11 09:08:19
########################################################################
""" :mod: AdlerTestCase
=======================
.. ... | Sbalbp/DIRAC | Core/Utilities/test/AdlerTestCase.py | Python | gpl-3.0 | 3,483 | [
"DIRAC"
] | 5c60a5536ad27e2465d8373935e719304e721bbc401da11b23dcafe42c3866f3 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.2
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_vrfcontext.py | Python | gpl-3.0 | 5,176 | [
"VisIt"
] | 2e0e1a959fb2fb7c85680dab191eac5e41a4b916ed27bd3f4e449ab36e5ee937 |
# -*- coding: utf-8 -*-
# Copyright (c) 2014-2018 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014-2015 Brett Cannon <brett@python.org>
# Copyright (c) 2015 Simu Toni <simutoni@gmail.com>
# Copyright (c) 2015 Pavel Roskin <proski@gnu.org>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelmc.ro>
# Copyri... | ekwoodrich/python-dvrip | env/lib/python3.5/site-packages/pylint/checkers/python3.py | Python | mit | 51,928 | [
"VisIt"
] | 3692e4c58a7f54f4df17436361b80ebd11b76ae61f5058cc092cf927fcb6d659 |
"""
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | ojengwa/sympy | sympy/utilities/runtests.py | Python | bsd-3-clause | 77,702 | [
"VisIt"
] | 2275f137bdd6cb746b73c5d0a32d72bd1a361b27a938da1a1bc10e29c8555f61 |
# Python 2.7
# Requires splinter and phantomjs
from splinter import Browser
import os, zipfile
from safesetup import SafeSetup
browser = Browser('phantomjs')
#browser = Browser() # Debugging - runs in Firefox
class SafeSync:
url = ''
username = ''
password = ''
def __init__(self):
self.get_c... | BenElgar/SafeSync | safesync.py | Python | gpl-2.0 | 2,358 | [
"VisIt"
] | 8cad0d98229c8b12d34919bbe955b2ec82e9771f35017d3d48580fab7f999819 |
import numpy as np
def correlated_timeseries_example(N=10000, tau=5.0, seed=None):
"""Generate synthetic timeseries data with known correlation time.
Parameters
----------
N : int, optional
length (in number of samples) of timeseries to generate
tau : float, optional
correlation t... | kyleabeauchamp/pymbar | pymbar/testsystems/timeseries.py | Python | lgpl-2.1 | 2,409 | [
"Gaussian"
] | 84304d4f7b5240164751afcea1fe16f4beb60541950c084599afae631cf19384 |
import DIRAC
from DIRAC import gLogger
from DIRAC.Core.Base.Script import parseCommandLine
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.FrameworkSystem.Client.LoggerClient import LoggerClient
parseCommandLine()
LClient = LoggerClient()
retval = LClient.getSites()
if not retval['OK']: print retval['Mess... | sposs/DIRAC | FrameworkSystem/test/testLoggerClient.py | Python | gpl-3.0 | 2,273 | [
"DIRAC"
] | c3fd4f8730f077134592abad689ede5fcd30291e76ce129b761c4388178fd981 |
import unittest
from .cgen import *
class TestModule(unittest.TestCase):
def setUp(self):
self.gen = CodeGenerator()
self.fix = FixGenerator()
def testEmptyModule(self):
p = Module()
p = self.fix.visit(p)
self.assertEqual(self.gen.generate(p), '')
def testEmpty... | myint/pyfuzz | pygen/tests.py | Python | bsd-3-clause | 7,572 | [
"VisIt"
] | db43d437549f3a606c2bce2ee0734412baa8afb4099c6eaf8e093d5e705bf640 |
#!/usr/bin/env python3
"""
extract reads from a bam file and a list
write a fasta file
useful benchmark:
https://timoast.github.io/blog/2015-10-12-extractreads/
"""
import pysam
def extract_reads(options):
with open(options.names, "r") as f:
n = f.readlines()
bamfile = pysam.AlignmentFile(optio... | naumenko-sa/bioscripts | crispr/extract_reads.py | Python | mit | 1,381 | [
"pysam"
] | c48e21b94c02c9c081fa5f9df9400a7902f572e5195a128a42237038badddf06 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform analyses of
the local environments (e.g., finding near neighbors)
of single sites in molecules and structures.
"""
import json
import math
import os
import warnings
... | davidwaroquiers/pymatgen | pymatgen/analysis/local_env.py | Python | mit | 169,341 | [
"Gaussian",
"Jmol",
"VASP",
"pymatgen"
] | 025cb9b39f00b7943ac3870d6cb947bcedc154af4cdc81ab91d4d72246f2b601 |
# vi: ts=8 sts=4 sw=4 et
#
# check.py: form checking
#
# This file is part of Draco2. Draco2 is free software and is made available
# under the MIT license. Consult the file "LICENSE" that is distributed
# together with this file for the exact licensing terms.
#
# Draco2 is copyright (c) 1999-2007 by the Draco2 authors... | geertj/draco2 | draco2/form/check.py | Python | mit | 2,382 | [
"VisIt"
] | 6a01bed99254c135f556f1497be4c90021e207cbb8310ad97b47712818e171d6 |
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Create the data ############################################################
import numpy as np
x, y, z = np.ogrid[- .5:.5:200j, - .5:.5:200j, - .5:.5:200j]
r = np.sqrt(x ** 2 + y ** 2 + z ** 2)
... | s0vereign/Ahti | utils/pyvis/spherical.py | Python | gpl-3.0 | 1,885 | [
"Mayavi"
] | f5cb2261ae9ab45e35c9d9166aecd11638af11abe72cf28e49c492d64d8f706f |
#### PATTERN | DE | INFLECT ########################################################################
# -*- coding: utf-8 -*-
# Copyright (c) 2012 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
######################################################... | clips/pattern | pattern/text/de/inflect.py | Python | bsd-3-clause | 29,028 | [
"ASE"
] | 5974a8a6881715581dc47711f7230a387cedaa8fdc283416393405c55af9753f |
# -*- coding: utf-8 -*-
from sympy.matrices import Matrix
from sympy.core import Add, diff, Symbol
from sympy.simplify import simplify
from tensor_analysis.arraypy import Arraypy, TensorArray, matrix2arraypy, \
matrix2tensor, list2arraypy, list2tensor
from tensor_analysis.tensor_methods import is_symmetric
from te... | AunShiLord/Tensor-analysis | tensor_analysis/riemannian_geometry.py | Python | mit | 61,932 | [
"Gaussian"
] | cf83c2c2cf495d37eddb0825996187a0680733761d25807a0d4faa347e0d96f6 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/basislist.py | Python | lgpl-3.0 | 8,266 | [
"Psi4"
] | 6eb11f2ade7244cb454f96f0a25c96e50039a102f8ad654bd551a86dfa7166d8 |
import random
import string
import pickle
import cherrypy
import numpy as np
import pandas as pd
from scipy.sparse import csr_matrix
from scipy import sparse
import re
import os
from jinja2 import Environment, FileSystemLoader
path = os.path.abspath(os.path.dirname(__file__))
config = {
'global' : {
'tools.proxy... | wkerzendorf/deepthought_web | deepthought_web.py | Python | bsd-3-clause | 4,003 | [
"Galaxy"
] | 60481182a6bbae3a7ac94b1bbd125f5397747b95e70d3430d88ba5662bb520ce |
## Generating simulated data for variations in the object parameters:
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#imp... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/simulation_results/comparision_with_kNN_PCA/Combined/object_training/gen_data_object_training.py | Python | mit | 17,336 | [
"Mayavi"
] | f42df2c53a5e451554062c08da09557e1ec404f37612859bb51c26545551bab6 |
# -*- coding: utf-8 -*-
import base64
import datetime
import json
import time
import mock
from nose.tools import eq_, ok_
from nose.plugins.attrib import attr
from pyquery import PyQuery as pq
from urlparse import urlparse
from django.conf import settings
from django.contrib.sites.models import Site
from django.core... | varunkamra/kuma | kuma/wiki/tests/test_views.py | Python | mpl-2.0 | 167,376 | [
"VisIt"
] | 1803705fbc538d294001f92ec5d84b84731b8dafebe7a166c123cabfc124ad8d |
# 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... | sunqm/pyscf | pyscf/pbc/df/test/test_rsdf_scf.py | Python | apache-2.0 | 2,579 | [
"PySCF"
] | 84bc229cb5386a32849cdb757a34a370420621f94f557a57611e4c24c37e5792 |
''' <h1>Library for combined x-ray and neutrons simulations.</h1>
<p>The neutron simulations is capable of handling non-magnetic,
magnetic non-spin flip as well as neutron spin-flip reflectivity. </p>
<h2>Classes</h2>
<h3>Layer</h3>
<code> Layer(b = 0.0, d = 0.0, f = 0.0+0.0J, dens = 1.0, magn_ang = 0.0, magn = 0.0, s... | haozhangphd/genx-py3 | genx/models/spec_nx.py | Python | gpl-3.0 | 28,153 | [
"Gaussian"
] | db5654cc455f7403f8b9e94373f303a06c81636249c90536bb7f5179ee1c23d9 |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | VisTrails/VisTrails | vistrails/packages/vtk/vtkhandler.py | Python | bsd-3-clause | 8,298 | [
"VTK"
] | c6c917bd3f5b3e1c2093922705607b517bb85896f72e46c8c2fc5e0e1d469b15 |
"""
chapter6.py
==========
Models from Chapter 6 of [G&L 2012].
- Model REG = Regional Model (Country divided into North and South regions.)
[G&L 2012] "Monetary Economics: An Integrated Approach to credit, Money, Income, Production
and Wealth; Second Edition", by Wynne Godley and Marc Lavoie, Palgrave Macmillan, 20... | brianr747/SFC_models | sfc_models/gl_book/chapter6.py | Python | apache-2.0 | 21,855 | [
"Brian"
] | f16daa04b222f08e4f5f4123390626035920b06db71e876b66dde7a7b200a577 |
#
# Copyright 2016 The BigDL 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 law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/ray/process.py | Python | apache-2.0 | 3,914 | [
"ORCA"
] | bb0f185d4b31a93c0ecdca08e977f5be2020a3d153bc308a9ee8f2ccba6675c3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
from os.path import join, dirname
from io import open
setup(
name='pandas-charm',
version='0.3.0',
description=(
'A small Python library for getting character matrices '
'(alignments) into and out of... | jmenglund/pandas-charm | setup.py | Python | mit | 1,371 | [
"Biopython"
] | 1d547aad339f8206030c243a4cfab247f7ad542f748f0fc60b3d2f70c66324b4 |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import unicode_literals
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from bok_choy.promise import EmptyPromise
from ...fixtures.course import XBlockFixtureDesc
from ..helpers import create_user_par... | xingyepei/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 19,688 | [
"VisIt"
] | c3aa5696fb9975f637924decc73f941ac811474e022b30584b1a6969288a7431 |
import sys
import os
import random
import numpy as np
from numpy import arange, sin, pi
from .constants import AVOGADRO, E_CHARGE
def isclose(a, b, rel_tol=1e-09, abs_tol=0.0):
return abs(a-b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol)
def getMeanData(data):
sums = {}
n_twin = 0
first_data = data... | CNS-OIST/STEPS_Example | publication_models/API_2/Chen_FNeuroinf__2017/purkinje_model/extra/data_presets.py | Python | gpl-2.0 | 3,135 | [
"Avogadro"
] | 6f18dad425bb28b91d7ae322b0e019265673e811938663172db7552cbf889ab2 |
"""
Proteomics Datatypes
"""
import binascii
import logging
import re
from galaxy.datatypes import data
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.data import Text
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.xml import GenericXml
from galaxy.util import nice_size
log = lo... | icaoberg/cellorganizer-galaxy-tools | datatypes/proteomics.py | Python | gpl-3.0 | 13,937 | [
"Galaxy",
"OpenMS"
] | 037c7f3466ac6d2eb609237294e5a690dc6fa5c448fcb145c1bcc70bb3cec3f4 |
# Copyright (C) 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 versio... | espressomd/espresso | testsuite/scripts/benchmarks/test_ferrofluid.py | Python | gpl-3.0 | 1,335 | [
"ESPResSo"
] | 2c1925a96746866c564f3f14695a37befced6983b8cf65d08d94d3914efaabdb |
#!/usr/bin/env python
import functools
from typing import Union
import metpy.calc
import numpy as np
import numpy.ma
import scipy.signal as spsignal
import seawater
import xarray as xr
from metpy.units import units
from pint import UnitRegistry
_ureg = UnitRegistry()
# All functions in this file (that do not start ... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | data/calculated_parser/functions.py | Python | gpl-3.0 | 26,417 | [
"NetCDF"
] | d47cf5ef74c525e3c4054cfcaa7752bb75468de18c6ce68f21a7cc952b048d02 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2014 Bitergia
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | MetricsGrimoire/Octopus | tests/test_backend.py | Python | gpl-3.0 | 2,139 | [
"Octopus"
] | 9f87cf926e55a541f2b3a94b29b4e0fc86e37eb758694ce04af20e145afbe33d |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Multiple_Contact_Classification/New_classify_2_objects_2_categories_1200ms_scaled.py | Python | mit | 10,144 | [
"Mayavi"
] | 6403fd46f8f88cdfe7ae2780296bbc6c7a157448bb3d22b052870486a0b97fc0 |
# Copyright 2017 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | tensorflow/transform | tensorflow_transform/beam/common.py | Python | apache-2.0 | 7,881 | [
"VisIt"
] | 2c7302afb59b1f1d5eadf8f833386e30c20827e59e3cdcdff550b81abe5d23b7 |
#!/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
##---------------------------------------------------------------------------##
##
## Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
## Copyright (C) 2003 Mt. Hood Playing Card Co.
## Copyright (C) 2005-2009 Skomoroh
##
## This program is free ... | TrevorLowing/PyGames | pysollib/help.py | Python | gpl-2.0 | 5,147 | [
"VisIt"
] | 268a30983212bcc45966f97dccac9048d4e9c6460b442a82c0adfb347d44b0ae |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | arunkgupta/gramps | gramps/gen/plug/menu/_enumeratedlist.py | Python | gpl-2.0 | 3,749 | [
"Brian"
] | 5797dd6bbee1a011a6a4aa3722418f804ee4aa587e52207bd4e66630e789b185 |
"""
Displays Agg images in the browser, with interactivity
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
# The WebAgg backend is divided into two modules:
#
# - `backend_webagg_core.py` contains code necessary to embed a WebAgg
# plot inside of a web... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/backends/backend_webagg.py | Python | bsd-2-clause | 12,190 | [
"VisIt"
] | 7f775a3cde595ee69e35d67bec6074d4724a2b2b569c82790aaf054ec79c6183 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'Blast'
db.create_table('bugle_blast', (
('id', self.gf('django.db.models.field... | devfort/bugle | bugle_project/bugle/migrations/0001_initial.py | Python | bsd-2-clause | 8,132 | [
"BLAST"
] | 1c031d387ab40195b6e96ab67afa16c5d8040cc0238bda627e0317401f04c55c |
#!/usr/bin/env python3
########################################################################
# Solves problem 24 from projectEuler.net.
# Finds the 1000000th lexicographic permutation of the 10 digits.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribute it and/o... | sanSS/programming-contests | project-euler/problem024.py | Python | gpl-3.0 | 1,503 | [
"VisIt"
] | 9cc2881ca3f0c0c27eeca3614d5ccdf6e687d3ff869e9d0e8b35b471c90dbeb4 |
from . import moose
| python-security/pyt | examples/import_test_project/package_with_folder_and_alias/nested_folder_with_init/__init__.py | Python | gpl-2.0 | 20 | [
"MOOSE"
] | 401e787b78170e9dfb42f0a71cc82e92760d6c370075a46ea8b4f13bba2a828c |
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
""" unit testing code for molecular descriptor calculators
"""
import os.path
import pickle
import unittest
from io import BytesIO, StringIO
import numpy
from rdkit import Chem, RDConfig
from rdkit.ML.Descriptors import Descriptors, MoleculeDesc... | bp-kelley/rdkit | rdkit/ML/Descriptors/UnitTestMolDescriptors.py | Python | bsd-3-clause | 3,435 | [
"RDKit"
] | dd8bfb0eff553b729e9afc08fa6034218bf2cf5e4a0de6eb0aa0e65e57873e1e |
#########################################################################################
# Condor.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" Condor.py is a DIRAC independent class representing Condor batch system.
Condor objects are... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/Condor.py | Python | gpl-3.0 | 8,507 | [
"DIRAC"
] | 058934ee7b5285b9f7fcd0164411de4dbd14d9f8183807af6d2c4dc6d42530d0 |
# -*- coding: UTF-8 -*-
# 引入必要的库
from imutils.perspective import four_point_transform
from imutils import contours
import numpy as np
import argparse
import imutils
import cv2
import squares
# 构建命令行参数解析并分析参数
# 对应使用方式 python test_grader.py --image images/test_01.png
ap = argparse.ArgumentParser()
ap.add_argument("-i", ... | EdgarNg1024/PaperHelper | main.py | Python | apache-2.0 | 3,834 | [
"Gaussian"
] | 9fbfd5b160359df8135b3bf9e59cbf255d77a6ab18aa90693326999f8f547654 |
import os
from os.path import join as path_join
import sys
import unittest
import shutil
import tempfile
import numpy.testing
from numpy.testing import assert_array_equal
import numpy as np
import galore
import galore.formats
from galore.cli.galore import simple_dos_from_files
import galore.plot
from contextlib impo... | SMTG-UCL/galore | test/test.py | Python | gpl-3.0 | 10,385 | [
"Gaussian",
"pymatgen"
] | 1dd4bcbcc478aed60d2f7ea399620c98e0251f536bef6bf8577658d789e6beeb |
#
#
# This example shows the diffraction by a Si 111 crystal calculated in a variety of modes (see main):
#
# - make_plots( calculate_standard_interface() )
# using the standard interface via definition of a photon grid (DiffractionSetupSweeps) and
# the DiffractionResult object
#
# - calculate_with_co... | edocappelli/crystalpy | crystalpy/examples/Si111.py | Python | mit | 15,040 | [
"CRYSTAL"
] | 7035b4446a58978832c948f9e07c698a0dd86d403fa932c5a034364e86fde9f8 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# sut
from DIRAC.DataManagementSystem.Service.StorageElementHandler import getDiskSpace, getFreeDiskSpace, getTotalDiskSpace
def test_getDiskSpace():
res = getDiskSpace("/")
assert res["OK"]
res ... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Service/test/Test_Service.py | Python | gpl-3.0 | 414 | [
"DIRAC"
] | 58dfcae599032c065a691a8af7aab12c47b8a5fbddcf1e0d73aa51c7bde8eb12 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | Chuban/moose | python/MooseDocs/__init__.py | Python | lgpl-2.1 | 5,924 | [
"MOOSE"
] | 6a82458f0fc196b643a8714c393e613e65515118003cd9ac5f8fd3b0221c7d76 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a simple algorithm for extracting nearest neighbor
exchange parameters by mapping low energy magnetic orderings to a Heisenberg
model.
"""
import copy
import logging
import sys
from ast import liter... | materialsproject/pymatgen | pymatgen/analysis/magnetism/heisenberg.py | Python | mit | 37,336 | [
"pymatgen"
] | 29d25b612a777ae5f716725d9c90b4e3eb184da9c6d21e38b3c3545862fa3d12 |
##
# Copyright 2009-2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | omula/easybuild-easyblocks | easybuild/easyblocks/a/aladin.py | Python | gpl-2.0 | 14,519 | [
"NetCDF"
] | 2701e7d0e4247aec96c00f5c4ba094b2ad8565ac2dec1b4691f4116134a46489 |
#!/bin/python
def run_viterbi_test():
"""A simple tester for Viterbi algorithm.
This function generates a bunch of random emission and transition scores,
and computes the best sequence by performing a brute force search over all
possible sequences and scoring them. It then runs Viterbi code t... | sameersingh/uci-statnlp | hw3/viterbi_test.py | Python | apache-2.0 | 2,941 | [
"Gaussian"
] | 9d81906df274a0dff946f751f5b8fe035ab635b2812d61b96247c5022aa30247 |
#!/usr/bin/env python
from __future__ import print_function
import math
import logging
import argparse
import numpy as np
from PIL import Image
import geoip2.database
from PIL import ImageColor
from itertools import imap
from colorsys import hsv_to_rgb
from collections import defaultdict
__version__ = '0.0.3'
cla... | cxhernandez/fah-map | scripts/fahmap.py | Python | mit | 23,681 | [
"Gaussian"
] | 059383add32e2101570683c59fdb0a29359a54213093ccccbf99eeedac358348 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0058_remove_visit_involvement_other'),
]
operations = [
migrations.AddField(
model_name='involvementtyp... | koebbe/homeworks | visit/migrations/0059_auto_20150815_0354.py | Python | mit | 748 | [
"VisIt"
] | dd10c372e1e68b4daab9f6b86c536f1f7d7e4b99fdb54c2de3e2b115248d9aec |
# -*- coding:utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2012, 2013 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (... | MSusik/invenio | invenio/modules/indexer/testsuite/test_indexer_engine_tokenizer.py | Python | gpl-2.0 | 18,602 | [
"Brian",
"Galaxy"
] | 40ad3e3259af338da14801791fba4317c219f3236e3b1d3b38797040af79fcfd |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | hpcuantwerpen/easybuild-easyblocks | easybuild/easyblocks/o/openfoam.py | Python | gpl-2.0 | 27,029 | [
"ParaView"
] | 5f367d01c990be7be910c6a9f0a4826a42f38f1b813e090fb441cc2f910d8a34 |
#!/usr/bin/env python
# Copyright (C) 2014 Swift Navigation Inc.
# Contact: Colin Beighley <colin@swift-nav.com>
#
# This source is subject to the license found in the file 'LICENSE' which must
# be be distributed together with this source. All other rights reserved.
#
# THIS CODE AND INFORMATION IS PROVIDED "AS... | denniszollo/piksi_tools | piksi_tools/console/update_view.py | Python | lgpl-3.0 | 22,317 | [
"VisIt"
] | d7027d87daac293e3ccda7f706e75bad62ada9356989a8a9fe8224d81cb74cfc |
#### PATTERN | NL | INFLECT ##############################################
# -*- coding: utf-8 -*-
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
##########################################################################
# Reg... | shubhangiKishore/pattern | pattern/text/nl/inflect.py | Python | bsd-3-clause | 16,372 | [
"MOE"
] | 3c32a395d7bb370fa0d24269ea1d53a29ca532e60853eb2e96f9bfc61827f4d9 |
# -*- coding: utf-8 -*-
"""The status view."""
from __future__ import unicode_literals
import ctypes
import sys
import time
try:
import win32api
import win32console
except ImportError:
win32console = None
from dfvfs.lib import definitions as dfvfs_definitions
import plaso
from plaso.cli import tools
from pl... | rgayon/plaso | plaso/cli/status_view.py | Python | apache-2.0 | 18,822 | [
"NAMD"
] | ff8283f53978afaee1818f937c75c8babc0a640268f3f3bba9ce927a0d39242c |
from math import exp, pi, sin, sqrt, cos, acos
import numpy as np
from ase.data import atomic_numbers
# Table (1) of
# D. WAASMAIER AND A. KIRFEL, Acta Cryst. (1995). A51, 416-431
waasmaier = {
# a1 b1 a2 b2 a3 b3 a4 b4 a5 b5 c
'... | grhawk/ASE | tools/ase/xrdebye.py | Python | gpl-2.0 | 3,657 | [
"ASE"
] | 4e671a1f15d34c7337d933ce77073856d37d50fbae5e138fc718a9c276426a84 |
# -*- coding: utf-8 -*-
'''
This module provides an access to HITRAN data.
Data is downloaded and cached.
This module serves as a simple database manager frontend.
API is aimed to be RESTful, which means that interaction
between local API and remote data-server will be held
via sending RESTful queries (API->remote)... | michaelaye/hapi | hapi/hapi.py | Python | bsd-3-clause | 541,258 | [
"Gaussian"
] | f0b42587786374a604316b674bffcd3b166fc8602c639616e25a203350642910 |
###
# Copyright 2008-2011 Diamond Light Source Ltd.
# This file is part of Diffcalc.
#
# Diffcalc 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 late... | DiamondLightSource/diffcalc | test/diffcalc/hkl/willmot/test_calcwill.py | Python | gpl-3.0 | 13,345 | [
"CRYSTAL"
] | 9e05d99a0b1fe007ca391e996fb0edc7cdd90c086ddc9980931aaaee492166d8 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/metadata/_testing.py | Python | bsd-3-clause | 36,975 | [
"scikit-bio"
] | 0689eb1e55a4ec4a01f2f45499a7fa002a070ea9ae1d89019d9b55c78e939094 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006, 2008 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 Lesser General Public License as published by
## the Free Soft... | andrebellafronte/stoq | stoqlib/gui/dialogs/devices.py | Python | gpl-2.0 | 2,339 | [
"VisIt"
] | c8caa8d2b1683759053cc357289fa44491bc8eddb7b3b14937f0397ef12ce1e5 |
""" DIRAC Basic MySQL Class
It provides access to the basic MySQL methods in a multithread-safe mode
keeping used connections in a python Queue for further reuse.
These are the coded methods:
__init__( host, user, passwd, name, [maxConnsInQueue=10] )
Initializes the Queue and tries to connect to... | rajanandakumar/DIRAC | Core/Utilities/MySQL.py | Python | gpl-3.0 | 58,684 | [
"DIRAC"
] | b422f9440046e902880e19be9bfd31d951e7cd19ba343792aab9ab03a187a69e |
#
# Copyright (C) 2017-2019 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... | KaiSzuttor/espresso | testsuite/python/time_series.py | Python | gpl-3.0 | 1,973 | [
"ESPResSo"
] | 57309b4934e20c491e003af82d00a76c004a70aeea20734733cbaa125eebe76f |
"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
from clawpack.pyclaw import io
#------------------------------
def setrun(claw_pkg='classic'... | clawpack/adjoint | examples/acoustics_1d_heterogeneous/forward/setrun.py | Python | bsd-2-clause | 7,368 | [
"Gaussian",
"NetCDF"
] | f44bef74b6c6eef9996b6617be5093de81045cc8107f25eec3362b795b63db62 |
#!/usr/bin/python
import os
import sys
import Bio
import vcf
import pandas as pd
from mrbait import sequence_tools as s
from mrbait import misc_utils as utils
from Bio import AlignIO
"""Functions for parsing and manipulating sequence alignment files
Functions by Zach Zbinden and Tyler Chafin"""
#Write FASTA from pan... | tkchafin/mrbait | mrbait/aln_file_tools.py | Python | gpl-3.0 | 11,249 | [
"Biopython"
] | 1a71b86a69dd6485a2c064ce2cf8ceb85bb8d1f680a12b9ca392ce3c34af1f22 |
import cv2
import numpy as np
from matplotlib import pyplot as plt
img = cv2.imread('/home/pi/Desktop/image.jpg',0)
img = cv2.medianBlur(img,5)
ret,th1 = cv2.threshold(img,127,255,cv2.THRESH_BINARY)
th2 = cv2.adaptiveThreshold(img,255,cv2.ADAPTIVE_THRESH_MEAN_C,\
cv2.THRESH_BINARY,11,2)
... | agdal1125/sicp2 | document-scanner/please.py | Python | mit | 743 | [
"Gaussian"
] | b44870f5544a040f26978d6f25c6fac04d59c05d022d0f22ce13573e723f0416 |
__version__="v3.2 beta1"
welcome_block="""
# Multi-Echo ICA, Version %s
#
# Kundu, P., Brenowitz, N.D., Voon, V., Worbe, Y., Vertes, P.E., Inati, S.J., Saad, Z.S.,
# Bandettini, P.A. & Bullmore, E.T. Integrated strategy for improving functional
# connectivity mapping using multiecho fMRI. PNAS (2013).
#
# Kundu, P., ... | ME-ICA/me-ica | meica.libs/select_model_fft20d.py | Python | lgpl-2.1 | 25,477 | [
"Gaussian"
] | a473b69124309b773660c2daefe990f276e5c9d8b5d91d9a7e72e5cd59eec80f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2008 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | andrebellafronte/stoq | stoqlib/importers/productimporter.py | Python | gpl-2.0 | 4,371 | [
"VisIt"
] | 41400bc5928067163b3bdbd3d61e3422285bd20dfcb617462e20976d7e4d6de1 |
"""
:Authors: - Iason
"""
from collections import defaultdict
import numpy as np
def inside(forest, topsort, omega=lambda edge: edge.log_prob):
"""
Inside recursion.
:param forest: an acyclic hypergraph.
:param topsort: a partial ordering of the nodes in the forest.
:param omega: a function that ... | wilkeraziz/pcfg-sampling | inference.py | Python | apache-2.0 | 1,152 | [
"VisIt"
] | b2be1a92d24e21a25517f42006043d6cb34299095c2dc8934139f8e12934bf8e |
"""
Objects with No values
"""
from galaxy.datatypes.metadata import MetadataCollection
from galaxy.datatypes.registry import Registry
class RecursiveNone:
def __str__( self ):
return "None"
def __repr__( self ):
return str( self )
def __getattr__( self, name ):
value = RecursiveNon... | volpino/Yeps-EURAC | lib/galaxy/util/none_like.py | Python | mit | 952 | [
"Galaxy"
] | 8524ab96f43277eeb3bbc19e01951e4896990035ab39a6b19bc1f08128661706 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create pipeline
#
# create sphere to color
sphere = vtk.vtkSphereSource()
sphere.SetThetaResolution(20)
sphere.SetPhiResolution(40)
def colorCells (__vtk__temp0=0,__vtk_... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Core/Testing/Python/ScalarBar.py | Python | bsd-3-clause | 2,359 | [
"VTK"
] | e99b3f9860cd5bd179f47bb1dd8a0a23b3b4ad338f3319cade8edd7f88b8193b |
# Copyright 2019,2020,2021 Sony Corporation.
# Copyright 2021 Sony Group Corporation.
#
# 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
#
# Un... | sony/nnabla | python/src/nnabla/experimental/parametric_function_class/module.py | Python | apache-2.0 | 4,013 | [
"VisIt"
] | 253a691228f72be20f922a74ffbdad929d19b2d203494a0626eb9be99dd4ce2f |
import sys
import os.path
import logging
import asyncio
from ._requires import click
from .http import HTTPError
log = logging.getLogger(__name__)
class _VolumeBinds:
def visit(self, obj):
return obj.accept(self)
def visit_RO(self, _):
return 'ro'
def visit_RW(self, _):
retu... | vmagamedov/pi | pi/run.py | Python | bsd-3-clause | 5,105 | [
"VisIt"
] | 796daef18b7cfc97ef17973d63d62dd2b6ff48879895a9cffe526ef545edd034 |
import os
import subprocess
import sys
import pandas as pd
from minedatabase import utils
from minedatabase.databases import MINE
from rdkit.Chem import AllChem
def load_cdmine_rxns(mine_db, excel_file, pic_dir=""):
abrv = {"hn": "[*]"}
if pic_dir and not os.path.exists(pic_dir):
os.mkdir(pic_dir)
... | JamesJeffryes/MINE-Database | Scripts/add_rxns_from_excel.py | Python | mit | 2,201 | [
"RDKit"
] | 9cb9ef63c4e2ab432f600ae9647ac048c3bd77f60f427bdc629cef1cbc4099e5 |
import os
import pickle
import pylab as pl
from operator import itemgetter
import netcdf
import numpy as np
import sys
from operator import mul
from ncdftools import nccopydimension
from Scientific.IO import NetCDF
from array import array
import struct
def nctypecode(dtype):
# purose: netcdf-typecode from array... | hendrikwout/pynacolada | trash/pynacolada-2013-11-1.py | Python | gpl-3.0 | 37,771 | [
"NetCDF"
] | cd38e04b5ede47eec45455e074591fd2182d67b3bca1bc8225b5bbbdf30bb97e |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Christian Schwantes
# Contributors: Robert McGibbon
#
# MDTraj... | leeping/mdtraj | tests/test_contact.py | Python | lgpl-2.1 | 4,069 | [
"MDTraj"
] | 4bd9a7d944318e047219fc72cf3abd1b0d0a48e11fce861f5438e587d0b4bf5b |
# $Id$
#
# Copyright (C) 2004-2006 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | bp-kelley/rdkit | rdkit/ML/UnitTestAnalyzeComposite.py | Python | bsd-3-clause | 1,647 | [
"RDKit"
] | 13bf3ec6814f97ad812a3d45a75418f6fcbbc895f21c56aba0b6c490446de662 |
# Copyright 2018 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... | ghchinoy/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2.py | Python | apache-2.0 | 98,859 | [
"Gaussian",
"VisIt"
] | ee046f88496e5f8053d673ce88ed2bae48fc830b3f938e38f264d57abf2e8766 |
# -*- coding: utf-8 -*-
"""
pygments.lexers._vim_builtins
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This file is autogenerated by scripts/get_vimkw.py
:copyright: Copyright 2006-2019 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
# Split up in multiple functions so it's import... | wakatime/wakatime | wakatime/packages/py27/pygments/lexers/_vim_builtins.py | Python | bsd-3-clause | 57,090 | [
"BLAST"
] | 225fe98eb3f43d652330b0913ce64fa0b81dff78dabafbfd486b413a4ce65360 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.