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#!/usr/bin/env python
# encoding:utf8
"""
DragonPy - Dragon 32 emulator in Python
=======================================
http://www.6809.org.uk/dragon/hardware.shtml#sam
$ffc0-ffdf SAM (Synchronous Address Multiplexer) register bits - use
even address to clear, odd address t... | JuhaniImberg/DragonPy | dragonpy/Dragon32/MC6883_SAM.py | Python | gpl-3.0 | 8,433 | [
"FEFF"
] | ad7dbeb439d52f692b6aa4a9c7615ede9aa26727dac4023292e71658a87322ad |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRen... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Sources/Testing/Python/coneResolution.py | Python | bsd-3-clause | 2,016 | [
"VTK"
] | 422fa859e27202fbbac2367fda538cda2164812e10af45a5357acb19569c525f |
# Copyright 2009-2014 Eucalyptus Systems, Inc.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; version 3 of the License.
#
# This program is distributed in the hope that it will be useful,
# b... | eucalyptus/eucalyptus-database-server | eucalib/__init__.py | Python | bsd-2-clause | 993 | [
"VisIt"
] | 8954a12711c889813ff7bdc8f4afaf4971ecf2f943033606b252f746bc79d6e6 |
# -*- coding: utf-8 -*-
"""
Authors: Tim Hessels
UNESCO-IHE 2017
Contact: t.hessels@unesco-ihe.org
Repository: https://github.com/wateraccounting/wa
Module: Function/Three
"""
# import general python modules
import os
import gdal
import pandas as pd
import numpy as np
import netCDF4
def Calculate(WA_HOME_fold... | wateraccounting/wa | Generator/Sheet3/main.py | Python | apache-2.0 | 11,082 | [
"NetCDF"
] | a429fc4cf5a8a21850d2c69bb38145959949a9e731beec646d07b3381a4b5081 |
# (c) 2017, Brian Coca <bcoca@ansible.com>
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed in th... | veger/ansible | lib/ansible/cli/inventory.py | Python | gpl-3.0 | 16,843 | [
"Brian"
] | e480599ee7aca284ed913d2e1d24aada70b4b437ef3d2d3ae1255db99090adff |
from gpaw.utilities import unpack
import numpy as np
from gpaw.mpi import world, rank
from gpaw.utilities.blas import gemm
from gpaw.utilities.timing import Timer
from gpaw.utilities.lapack import inverse_general
from gpaw.transport.tools import get_matrix_index, collect_lead_mat, dot
import copy
import _gpaw
class Ba... | robwarm/gpaw-symm | gpaw/transport/sparse_matrix.py | Python | gpl-3.0 | 37,221 | [
"GPAW"
] | 3ec80967612626eb259e611734476bb2e6b0f55a448dd7ec44812489d8f68ad1 |
import os
import re
import subprocess as sp
from shutil import copyfile
from time import sleep
import pytest
import genomepy.utils
from genomepy.plugins import activate, deactivate, get_active_plugins, init_plugins
from genomepy.plugins.blacklist import BlacklistPlugin
from genomepy.plugins.bowtie2 import Bowtie2Plug... | simonvh/genomepy | tests/test_16_plugins.py | Python | mit | 7,449 | [
"BWA"
] | 9d3bab1026175f232be85cc5668783f0cd0882f0f420aa2db770cdd3dab03ac9 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-logging-ingo
# Author : Stuart Paterson
########################################################################
"""
Retrieve history of transitions for a DIRAC job
"""
__RCSID__ = "$I... | Sbalbp/DIRAC | Interfaces/scripts/dirac-wms-job-logging-info.py | Python | gpl-3.0 | 1,187 | [
"DIRAC"
] | 0edf266aca3fd00726baeb62a972b3ab24dd206eb50bfe21dcd55ba57a2dd9c7 |
"""
Utilities for scripts
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import functools
import os
import shlex
import subprocess
import sys
import time
import humanize
import requests
import yaml
import pysam
import requests.package... | ohsu-computational-biology/server | scripts/utils.py | Python | apache-2.0 | 9,341 | [
"pysam"
] | 75c7eb136cad1782806567ef26f99ae668f748b16928fd581fd4b06ecb84178d |
"""
End-to-end test for cohorted courseware. This uses both Studio and LMS.
"""
import json
from nose.plugins.attrib import attr
from studio.base_studio_test import ContainerBase
from ..pages.studio.settings_group_configurations import GroupConfigurationsPage
from ..pages.studio.auto_auth import AutoAuthPage as Stud... | solashirai/edx-platform | common/test/acceptance/tests/test_cohorted_courseware.py | Python | agpl-3.0 | 9,833 | [
"VisIt"
] | a75b1eb84799bcbb266fc21926b6fd609fba7ab5e217277bf4d90b879c3d3e4f |
# Licensed under GPL version 3 - see LICENSE.rst
'''Add additional scattering to processed photons.
Classes in this file add additional scattering in a statistical sense.
The classes in this module do not trace the photon to a specific location, they
just add the scatter at the point of the last interaction. For exa... | hamogu/marxs | marxs/optics/scatter.py | Python | gpl-3.0 | 6,078 | [
"Gaussian"
] | e43f423d7cd55bcf8f521c54aee1359f1ce6d88fb37fd32e54cc77050bbc53d6 |
import sys
from pyneuroml import pynml
####################################################################
# Choose a LEMS/NeuroML2 file and run it with jNeuroML
example_lems_file = 'LEMS_NML2_Ex5_DetCell.xml'
results1 = pynml.run_lems_with_jneuroml(example_lems_file, nogui=True, load_saved_data=True)
######... | rgerkin/pyNeuroML | examples/run_jneuroml_plot_matplotlib.py | Python | lgpl-3.0 | 1,213 | [
"NEURON"
] | db4fdcd3ee3f47fde75849cabe1cd23d4114256a92e8368818bc1d3b0e9f9eac |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
from django.contrib import ad... | rstreif/rvi_backend | web/dblog/admin.py | Python | mpl-2.0 | 1,207 | [
"Jaguar"
] | 651bc0eac24c74a2211244ef94cea30705d50b77181e1cbf90aef75056cc5235 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | eadgarchen/tensorflow | tensorflow/contrib/layers/python/layers/feature_column_test.py | Python | apache-2.0 | 49,241 | [
"MOOSE",
"Octopus"
] | 863b1bb40ccb1c0f9b1694b210c38150a27dc6d659f1651a7075db42c6630497 |
#!/usr/bin/env python
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#Process the database for essential pathways
#Essential Pathways v1.0.2
#Author:realasking
#Email:realasking@gmail.com,tomwangsim@163.com
#Aug-23,2017,in USTB
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... | realasking/essential-pathway | epw/epprocess.py | Python | lgpl-3.0 | 7,919 | [
"EPW"
] | 8b67bfb3867bde0463ed13da0aa6be4427b8af4aa4d2e1d637528f056d387265 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test single point logfiles in cclib."""
import os
import unittest
import numpy
from common import get_... | Schamnad/cclib | test/data/testSP.py | Python | bsd-3-clause | 14,485 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 08554816f5a4ea8a08173f8f0ba766278b7b69f394292c2577c6192af7588837 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/reporting/xunitwriter.py | Python | mit | 3,433 | [
"VisIt"
] | 491f81a3372bbd8261449de0927dd299c2ecf9d69677b64e2e59f807feef415b |
#!/usr/bin/python
'''
TODO:
write all the atoms of the solvent molecule to the index file.
'''
import math
import sys
import os
import numpy
import MDAnalysis
from itertools import izip
from MDPackage import Index
from MDPackage import Simple_atom
from MDPackage import usage
import MDPackage
import time as Time
im... | zhuhong/pRDF | pRDF_test.py | Python | gpl-2.0 | 11,895 | [
"MDAnalysis"
] | c4e8fb9ca4a2c111710ec77c3f2fcbe365adec4f39e70f0d0d117f41a7f1b73f |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-dialogflow-cx | tests/unit/gapic/dialogflowcx_v3/test_webhooks.py | Python | apache-2.0 | 93,229 | [
"Octopus"
] | e6504d5773acea97f2c65a9f569efd4bda7c05fc3c5e0bf798198c9375895c75 |
# coding: utf-8
from __future__ import unicode_literals
"""
Module containing class to create an ion
"""
__author__ = "Sai Jayaraman"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.0"
__maintainer__ = "Sai Jayaraman"
__email__ = "sjayaram@mit.edu"
__status__ = "Production"
__date__ = "Dec 1... | Dioptas/pymatgen | pymatgen/core/ion.py | Python | mit | 7,247 | [
"pymatgen"
] | 73354b072970c87612de6ee6cf2dc69b2ee9fd643734db6906801ffe29821638 |
"""
Copyright (c) 2011-2015 Nathan Boley, Marcus Stoiber
This file is part of GRIT.
GRIT 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.
G... | nboley/grit | simulator/reads_simulator.py | Python | gpl-3.0 | 21,253 | [
"pysam"
] | 71bdac6736b4bab6af3fbc25adfc62e4ba6519b73817f81c11c439f437a88df9 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | brianmay/karaage | karaage/plugins/kgapplications/management/commands/application_cleanup.py | Python | gpl-3.0 | 2,645 | [
"Brian"
] | b0fc3a4ce6b9dd1efd1ea19b486b6b3ea0f4c906e6ff206363afb7d3152ba966 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
hist.py |github|
----------------
Histograms of the occultation events as a function of mean longitude, duration,
and impact parameter for each of the seven TRAPPIST-1 planets, as well as a
marginalized histogram of the total number of potentially detectable
planet-... | rodluger/planetplanet | scripts/hist.py | Python | gpl-3.0 | 27,529 | [
"Gaussian"
] | 03519b7d6d060582b4998747c47857e9d5a7e8392b587afc307ae6d9a1e5fe03 |
"""
Align V and J starting from an adaptive CSV file
"""
import collections
import contextlib
import csv
import functools
import itertools
import logging
import operator
import tempfile
import pysam
from .. import imgt, util
from . import align_fastq
log = logging.getLogger('vdjalign')
TAG_COUNT = 'XC'
TAG_CDR3_LEN... | cmccoy/ighutil | python/vdjalign/subcommands/adaptive_tsv.py | Python | gpl-3.0 | 3,850 | [
"pysam"
] | 200a9c6ab4c2bb9d7f7cc473436ae8fbc49ba1c8dcc2bcad6b3ba87bf098111c |
# -*- coding: utf-8 -*-
#
# test_stdp_triplet_synapse.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of t... | nest/nest-simulator | testsuite/pytests/test_stdp_triplet_synapse.py | Python | gpl-2.0 | 12,739 | [
"NEURON"
] | 746c818ba3f3e685f60673bfd209254e8b4b8215bdc9302014b8c621d7773572 |
"""
MultiRenderWidget
:Authors:
Berend Klein Haneveld
"""
from vtk import vtkOpenGLGPUMultiVolumeRayCastMapper
from vtk import vtkRenderer
from vtk import vtkInteractorStyleTrackballCamera
from vtk import vtkImagePlaneWidget
from vtk import vtkVolume
from vtk import vtkImageData
from vtk import vtkColorTransferFunct... | berendkleinhaneveld/Registrationshop | ui/widgets/MultiRenderWidget.py | Python | mit | 12,737 | [
"VTK"
] | aa88733036368474152fa995b916ca01a0c4f9de59b9b91fe8abe4b937b409ce |
# -*- coding: utf-8 -*-
import os
import moojoos as mj
import numpy as np
from pylab import *
from PIL import Image
from scipy.ndimage import filters
# target files for comparison
files = [ 'rena_sharp.jpg', 'rena_gaussian_2.jpg' ]
# targetting rena's lips?
r = 260
cd = os.path.dirname(os.path.abspat... | buruzaemon/moojoos | src/blur_estimate.py | Python | bsd-2-clause | 4,805 | [
"Gaussian"
] | 524e74206aaddc27a2db04d663c15cf44f2fac46f39fb2ed4de47d8c328e43a9 |
"""
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... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/util/none_like.py | Python | gpl-3.0 | 1,064 | [
"Galaxy"
] | 22c715c634511eeb1d5594fba86139cd7c03e2d49c5a68369c734fbeafe81636 |
import time
import sys
import os
import numpy
import math
from past.utils import old_div
try:
import cosmology
import extras
import astrometry
import aux
except ImportError:
sys.path.append(f'{os.environ["HOME"]}/Projects/'
'planckClusters/MOSAICpipe/pipe_utils')
import cosmo... | boada/planckClusters | CLUSTERpipe/plugins/_galaxies.py | Python | mit | 15,299 | [
"Galaxy"
] | 52e64fa7b21d2fb03128c14c66677ea49cb7f6c9946ef1791bbb24be72c203c0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | kalahbrown/HueBigSQL | apps/useradmin/src/useradmin/tests.py | Python | apache-2.0 | 37,759 | [
"MOE"
] | 098a3a33e0b588466db6067aa00d821dbf7ebafbae36cf25006abf6070e464d9 |
../../../../../../../share/pyshared/orca/scripts/apps/Thunderbird/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Thunderbird/script.py | Python | gpl-3.0 | 75 | [
"ORCA"
] | 3922391b837543ef6fc33fc9942bd76254c2f9bebd3315fcafcbe03dfb0ee81f |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008 Daniel Moisset, Ricardo Quesada, Rayentray Tappa, Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the follow... | adamwiggins/cocos2d | cocos/scenes/transitions.py | Python | bsd-3-clause | 21,816 | [
"VisIt"
] | 3b455ab1a70c6c0d77df79af6aa9f80873fb1acd9b708ac51da0599521d04b2e |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RS4vectors(RPackage):
"""Foundation of vector-like and list-like containers in Bioconducto... | LLNL/spack | var/spack/repos/builtin/packages/r-s4vectors/package.py | Python | lgpl-2.1 | 1,947 | [
"Bioconductor"
] | 49e8cc72e7f3ae978e97a23b77b9a96bbf4e207bee2236b38d5ba7a60cb26a13 |
from __future__ import print_function
import json
import os
import re
import sys
import xml.etree.ElementTree as etree
from Cython.Compiler.Main import compile_single, CompilationOptions
from Cython.Compiler.TreeFragment import parse_from_strings
from Cython.Compiler.Visitor import TreeVisitor
from Cython.Compiler i... | pupil-labs/PyAV | docs/includes.py | Python | bsd-3-clause | 11,341 | [
"VisIt"
] | b3a269c13ad75da94acd0693677bff4bdf5182ec7d25583c89dd7201f75717f4 |
""" :mod: TransformationCleaningAgent
=================================
.. module: TransformationCleaningAgent
:synopsis: clean up of finalised transformations
"""
__RCSID__ = "$Id$"
# # imports
import re
import ast
import os.path
from datetime import datetime, timedelta
# # from DIRAC
from DIRAC impor... | Andrew-McNab-UK/DIRAC | TransformationSystem/Agent/TransformationCleaningAgent.py | Python | gpl-3.0 | 25,929 | [
"DIRAC"
] | 4b544d2e648d83a6749096e112bde584d23cc02fcdc63eb8c906d578da6cf744 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | src/cclib/method/nuclear.py | Python | lgpl-2.1 | 1,630 | [
"cclib"
] | a86c86f86385d4f8db0105a7a98d9467c11d20a3ef42f04c7d697556595bba35 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | leezu/mxnet | python/mxnet/contrib/onnx/onnx2mx/_op_translations.py | Python | apache-2.0 | 37,203 | [
"Gaussian"
] | 653df359680aef6e22e9505410c6ebde50f260ac1ce64da20e96a5ae684261fb |
# -*- coding: utf-8 -*-
#
# kmos documentation build configuration file, created by
# sphinx-quickstart on Fri Aug 19 14:58:17 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All co... | mieand/kmos | doc/source/conf.py | Python | gpl-3.0 | 7,963 | [
"ASE"
] | a59c97463152f23066388189dce8d066781c0c81088fc8094c9bf00d01b12f31 |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Alchemical factory for free energy calculations that operates directly on OpenMM swig S... | choderalab/brokenyank | src/yank/alchemy-tests.py | Python | lgpl-3.0 | 11,648 | [
"OpenMM"
] | 678855a2441c15ff2b4ee6bbc786d193ca11f9de8206330d1513850e701cff86 |
# proxy module
from __future__ import absolute_import
from mayavi.sources.poly_data_reader import *
| enthought/etsproxy | enthought/mayavi/sources/poly_data_reader.py | Python | bsd-3-clause | 100 | [
"Mayavi"
] | 8e1192105594fce0574f6204b1b3ff5ab95f988c38bc159983111192eeaf02da |
# TODO: to be removed in a future release, ATLAS pipeline was purely developmental
# import os.path as op
# import pytest
# import ssbio.io
# import shutil
# import pandas as pd
# from ssbio.pipeline.atlas2 import ATLAS2
#
#
# @pytest.fixture(scope='class')
# def reference_gempro(test_files_gempro):
# gp = ssbio.io... | SBRG/ssbio | ssbio/test/test_pipeline_atlas.py | Python | mit | 6,592 | [
"Biopython"
] | 45eb43ec2dc131d99f556f791c3c1224ab415c7410b7844430028897190f3f1a |
../../../../../../../../share/pyshared/orca/scripts/apps/yelp/yelp_v3/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/yelp/yelp_v3/script.py | Python | gpl-3.0 | 79 | [
"ORCA"
] | 9a4ff0724360e8da9705c4930fe6f238003d2dc951ce31406a69c6f9702ea497 |
# encoding: utf-8
"""A simple configuration system."""
# Copyright (c) IPython Development Team.
# Distributed under the terms of the Modified BSD License.
import argparse
import copy
import logging
import os
import re
import sys
import json
from ast import literal_eval
from ipython_genutils.path import filefind
fro... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/traitlets/config/loader.py | Python | gpl-3.0 | 28,943 | [
"Brian"
] | e87bbc8e0760616e574ea336b4d21920f0b4f8efba4c866aa4341a7573919c7f |
import dmenu_extended
import sys
import datetime
import os
import subprocess
import json
import pexpect
import keyring
path_config = dmenu_extended.path_prefs + '/jrnl.txt'
class extension(dmenu_extended.dmenu):
# Set the name to appear in the menu
title = 'Jrnl'
# Determines whether to attach the submenu in... | markjones112358/dmenu-extended-plugins | plugin_jrnl.py | Python | mit | 15,055 | [
"VisIt"
] | e5b5024647e2fd36e0af2a20afe56865b9f2e7b288de3db4248681255c5ef999 |
# -*- coding: utf-8 -*-
def url(url_str=''):
"""
Decorator for specifying the URL the test should visit, relative to the test
class's `base_url`.
"""
def decorator(method):
method.__url = url_str
return method
return decorator
def waitfor(css_selector, text=None, classes=None)... | hammerlab/seltest | seltest/helpers.py | Python | apache-2.0 | 2,817 | [
"VisIt"
] | 4ea9f2348d82baeade49b47a29af1e2ba55b8155069bdadbcba590b26eaac9b6 |
# coding=utf-8
# Copyright 2016 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 app... | pombredanne/grumpy | grumpy-tools-src/grumpy_tools/compiler/imputil_test.py | Python | apache-2.0 | 13,627 | [
"VisIt"
] | 438cd0e3a9a5e15de220a661852e58e81fde0da5030e318ac6d62a20c4fc2a73 |
import argparse
import graph as gg
from itertools import chain
from parse_pv import parse_file
import subprocess
import os
def main(file_name, trimmed='trimmed.out'):
"""
This script greps the unit cell parameters, pressure and volume
parsing a cp2k output
"""
# trimmed files
cmd = 'grep -A16 ... | ccaratelli/insertion_deletion | get_structural_param.py | Python | gpl-3.0 | 1,872 | [
"CP2K"
] | 22a42ff3cb04a385e84846c2f8d802239955db9c6fbdf7b68e77869dcc6302a5 |
# -----------------------------------------------------------------------------
# User configuration
# -----------------------------------------------------------------------------
dataset_destination_path = '/Users/seb/Desktop/vtk_volume_v2'
# -------------------------------------------------------------------------... | Kitware/arctic-viewer | scripts/examples/vtk/samples/syntax-evolution-volume_v2.py | Python | bsd-3-clause | 4,349 | [
"VTK"
] | 936e4fd5ea3857947c1d8d9c798835ea280aab6eb8f7d4eb426486f55f9423ea |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | Bismarrck/pymatgen | pymatgen/io/vaspio_set.py | Python | mit | 611 | [
"VASP",
"pymatgen"
] | cf9d74b5b8d2be064b70c0d4a180151ba3fe24f1cbb473871f4377c1d6a956f1 |
from threading import Thread
import json, requests, os, urllib, time
# Open config.json to get token (used for downloading replays of banned players) - Only for Community Managers
with open("config.json", "r") as f:
config = json.load(f)
# Gets JSON from a given beatnap
def getJSON(url):
try:
data = r... | Swan/Riplay | riplay.py | Python | mit | 6,821 | [
"MOE"
] | 152940d5746903bd011aaeed9570ff1c09bdc60a9e0e9dd2cb6d4872ec59d1e4 |
import numpy as np
from numpy import atleast_2d as vec
from scipy.stats import multivariate_normal
def gaussian_mix(query):
# Assign multivariate gaussians to be present in the space.
gaussians = [multivariate_normal(mean = [0.9, 0.1], cov = [[.05, 0], [0, .05]])]
gaussians.append(multivariate_normal(mean... | RuiShu/Neural-Net-Bayesian-Optimization | learning_objective/gaussian_mix.py | Python | mit | 907 | [
"Gaussian"
] | d271d019c87341757988d261d04a18daeace82e82535daf9eaadb4dc4220f028 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
from monty.json import MontyDecoder, MontyEncoder
from pymatgen.apps.battery.insertion_battery import (
InsertionElectrode,
InsertionVoltagePair,
)
from pymatgen.entries.compute... | materialsproject/pymatgen | pymatgen/apps/battery/tests/test_insertion_battery.py | Python | mit | 7,049 | [
"pymatgen"
] | a173e37bab2ecad8b4a56af1514a18eaa673ad9a1245404d4cbc489f70003f28 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck ... | WangWenjun559/Weiss | summary/sumy/sklearn/metrics/pairwise.py | Python | apache-2.0 | 42,672 | [
"Gaussian"
] | a7c986089684e78e1785fbd500e312521ddcaf62f9cf0deb99dca32df7f88825 |
# 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 | examples/local_orb/ulocal.py | Python | apache-2.0 | 4,775 | [
"PySCF"
] | c46221c36c2436c15a9a96b36da210f8c9ce53bac8aa5049c71c29826d4252c9 |
# Copyright 2008-2011 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools.
You are ... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/AlignIO/FastaIO.py | Python | gpl-2.0 | 23,277 | [
"Biopython"
] | ada36c7a9e6814b36da1b2ff1a2aa89aee90423de742bd242e3d202665e62ee6 |
# -*- coding=utf-8 -*-
"""
All entry points for API are defined here.
Attributes:
mod (Blueprint): Flask Blueprint object used to separate api from
website code.
"""
from flask import Blueprint, request, send_from_directory
from flask_restful import Api, Resource
import os
fr... | Pseudonick47/sherlock | backend/api/data.py | Python | gpl-3.0 | 37,646 | [
"VisIt"
] | 6322772d45662b437821e175086b836b355ded89247d1faaf990b50ce689cab0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 19 07:43:49 2019
@author: arijit
"""
import numpy as np
import os,zipfile
from PIL import Image
from scipy.optimize import curve_fit
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator
import scipy.constants as cn
import ... | ColdMatter/EDMSuite | MoleculeMOTScripts/analysis2.py | Python | mit | 41,931 | [
"Gaussian"
] | 81d018bb5a779007e098906a51f30f0db31aee3cad39f7219135192e5da2801d |
import sys
import subprocess
import os
DNA_COMP = None
def comp(seq_str):
"""complements the provided DNA sequence and returns it"""
global DNA_COMP
if DNA_COMP is None:
DNA_COMP = str.maketrans("ATCGMRWSYKNatcgmrwsykn",
"TAGCKYWSRMNtagckywsrmn")
return seq_s... | gmcvicker/WASP | mapping/util.py | Python | apache-2.0 | 4,288 | [
"pysam"
] | d75919ebbd50c8d8ff43191b5c418eab7af9fbec5452dbbd242ff3fdc2d224b3 |
"""Dirac Jobs Table."""
import logging
from copy import deepcopy
from collections import Counter, defaultdict
from sqlalchemy import Column, Integer, Enum, ForeignKey
from sqlalchemy.orm import relationship
from lzproduction.rpc.DiracRPCClient import dirac_api_client
from ..utils import db_session
from ..statuses imp... | alexanderrichards/LZProduction | lzproduction/sql/tables/DiracJobs.py | Python | mit | 5,198 | [
"DIRAC"
] | 84a49c762050bf90b45874d549b76898a1354d5fccd626826558d583ee731555 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this pa... | LyonsLab/coge | bin/last_wrapper/Bio/Phylo/NewickIO.py | Python | bsd-2-clause | 10,986 | [
"Biopython"
] | da68b1e82dbc5f83d2eea225e44bf952980cd49f6a0a02e247ad43e875b713f5 |
"""
A module defining various plotting functions that generally act on a :class:`~dffit.DFFit` instance.
The primary function for general use is :func:`~mfplot`, which is a wrapper around :func:`~dfplot`, and shows a fitted
mass function optionally with uncertainty region, and binned data, along with a histogram of da... | steven-murray/pydftools | pydftools/plotting.py | Python | mit | 20,237 | [
"Gaussian"
] | 8c7401382c9f1382b70f29fcf96a67efa4ba28ca798475b33c6ad3fd97b94893 |
# Manual stimulus used to find the receptive field position and size.
#
# Copyright (C) 2010-2012 Huang Xin
#
# See LICENSE.TXT that came with this file.
from Experiments.Experiment import ExperimentConfig,ManbarExp,MangratingExp
ExperimentConfig(data_base_dir='data',new_cell=False)
# When a neuron is isolated in P... | chrox/RealTimeElectrophy | Experimenter/man_stimulus_current_cell.py | Python | bsd-2-clause | 718 | [
"NEURON"
] | f894d4a24bcd753f965abd50cada1dacfc43cb737dfd893d46d51a350dd2bcc5 |
"""High level summaries of samples and programs with MultiQC.
https://github.com/ewels/MultiQC
"""
import collections
import glob
import io
import json
import mimetypes
import os
import pandas as pd
import shutil
import numpy as np
from collections import OrderedDict
import pybedtools
import six
import toolz as tz
im... | lbeltrame/bcbio-nextgen | bcbio/qc/multiqc.py | Python | mit | 26,918 | [
"HTSeq"
] | e5b1aa1aae46942039d1a1f7fa3904a663b5e8253830777f21b52e7a7b0fa39a |
"""
This class is used to define the plot using the plot attributes.
"""
from DIRAC import S_OK, gLogger
from DIRAC.MonitoringSystem.Client.Types.ComponentMonitoring import ComponentMonitoring
from DIRAC.MonitoringSystem.private.Plotters.BasePlotter import BasePlotter
__RCSID__ = "$Id$"
class ComponentMonitoringPl... | andresailer/DIRAC | MonitoringSystem/private/Plotters/ComponentMonitoringPlotter.py | Python | gpl-3.0 | 5,913 | [
"DIRAC"
] | d1ddfe1ee2f0a3d7e4f9b12a20cd123bfadf9b00c471b3fd14f91758bc0a7ff6 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2017 Petra Gospodnetic, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a c... | est77/appleseed | sandbox/tests/test scenes/many light sampling/generators/grid_point_lights.py | Python | mit | 10,508 | [
"VisIt"
] | 3b16bb5b2540aea902714ae3c9d61b785d1aa49883d7328efbee5307d70393c3 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create four cursors configured differently
cursor = vtk.vtkCursor2D()
cursor.SetModelBounds(15, 45, 15, 45, 0, 0)
cursor.SetFocalPoint(30, 30, 0)
cursor.AllOff()
cursor.AxesOn()
cu... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/General/Testing/Python/cursor2D.py | Python | gpl-3.0 | 2,161 | [
"VTK"
] | 82bd1e3f668f96bc024828911f224869666695cfb17f22acff27b365c6e8bc10 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
''' Header reading / writing functions for nifti1 image format
Author: Matthew Brett
'''
import numpy as np
import numpy.linalg as npl
from nipype.externals.pynifti.volumeutils import Recoder, make_dt_co... | satra/NiPypeold | nipype/externals/pynifti/nifti1.py | Python | bsd-3-clause | 53,052 | [
"Gaussian"
] | 73ebef063bc96bc4c1fac9c1979cb8a8762e22961929d9bbe73830d3a2597c42 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | snippets/helloMoose.py | Python | gpl-2.0 | 1,500 | [
"MOOSE"
] | 951216ac76366a615ac22e913b5b99eb8df6b804e065dcb77f5a1207d861fc86 |
# fMBT, free Model Based Testing tool
# Copyright (c) 2012, Intel Corporation.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms and conditions of the GNU Lesser General Public License,
# version 2.1, as published by the Free Software Foundation.
#
# This program is distribut... | madhavpai2000/fMBT | utils/eyenfinger.py | Python | lgpl-2.1 | 68,009 | [
"Gaussian"
] | 5e9337bc90eb30b2d0a0a2685b46687c4a3d0187ee5906dd016c5bfa5448de37 |
#!/usr/bin/env python
# Copyright (c) 2012, Vasilis Pappas <vpappas@cs.columbia.edu>
# This file is part of Orp http://nsl.cs.columbia.edu/projects/orp
import pydasm
import pickle
import inp
import util
class SimpleGadget(object):
def __init__(self, start, end, overlap, red, ins_num, func_ea):
self.star... | kevinkoo001/ropf | gadget.py | Python | bsd-3-clause | 12,832 | [
"VisIt"
] | 0518a7bf2cf5cfcfe751a76f03724d9d247408e215cc07129bc8ad0ad3cd7c98 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/io/utils.py | Python | bsd-3-clause | 7,484 | [
"NEURON"
] | b7c620f41948ed7a9bb99ee0b707cfd5bab97be521955878c50d5b3f5f41e6a5 |
"""
Tools for the instructor dashboard
"""
import dateutil
import json
from django.conf import settings
from django.contrib.auth.models import User
from django.http import HttpResponseBadRequest
from django.utils.timezone import utc
from django.utils.translation import ugettext as _
from courseware.models import Stud... | edcast-inc/edx-platform-edcast | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 8,692 | [
"VisIt"
] | de6e14f12c406162da0f8f6341a7fd40ca7e937f26d7a83fd0e50d3f30ad5ca3 |
import unittest
from nn.models.neurons.neuron import SigmoidNeuron
class NeuronsTests(unittest.TestCase):
__sigmoid_neuron = None
def setUp(self):
self.__sigmoid_neuron = SigmoidNeuron()
def tearDown(self):
pass
def test_should_compute_sigmoid(self):
input_value = 5
... | ADozois/ML_Challenge | tests/nn/models/neurons/neurons_tests.py | Python | mit | 496 | [
"NEURON"
] | 57174e68e2be904ed5c075d547f73e6c50959e550c59ae24300d23d8782916fb |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/lib/powersongimport.py | Python | gpl-2.0 | 9,259 | [
"Brian"
] | f0f818054169b52a512d1e66579485e1184945e20dee0f8f632cf35db69a46c0 |
from copy import deepcopy
import logging
import os
import time
import nibabel as nib
from nibabel.streamlines import detect_format
from nibabel.streamlines.tractogram import Tractogram
import numpy as np
from dipy.io.stateful_tractogram import Origin, Space, StatefulTractogram
from dipy.io.vtk import save_vtk_streaml... | FrancoisRheaultUS/dipy | dipy/io/streamline.py | Python | bsd-3-clause | 9,234 | [
"VTK"
] | ab4f3e9db7591a49e86d17fc16b68841e1d131a503fdf56b9e54dd67694521e8 |
# -*- coding: utf8 -*-
#
# Copyright 2011 Kyrre Ness Sjøbæk
# This file is part of AcdOpti.
#
# AcdOpti is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at you... | kyrsjo/AcdOpti | src/acdOpti/AcdOptiSettings.py | Python | gpl-3.0 | 1,972 | [
"ParaView"
] | 574ad7858a80e8364bc9ba63d6b51c52c2fca230076718a2aea271362607751b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# statusexe - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of... | heromod/migrid | mig/cgi-bin/statusexe.py | Python | gpl-2.0 | 1,106 | [
"Brian"
] | 891a94b84a47036f1fd4110342a70a9e8caab256d78f4be57f8d4ebb6ab02887 |
"""
dashi documentations goes here
"""
from . import histfactory as factory
from .fitting import model,gaussian,poly,leastsq #,poissonllh
from .visual import visual
from .storage import histsave,histload
from .objbundle import bundle, emptybundle, bundleize
from . import junkbox
import logging
logging.basicConfig(l... | achim1/dashi | dashi/__init__.py | Python | lgpl-3.0 | 360 | [
"Gaussian"
] | 7db3304ee528633aeef732dec22e32572b74c8fd49267823d749d33057477c5a |
# https://docs.aws.amazon.com/AmazonS3/latest/API/API_Operations.html
# https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/s3.html#S3.Client.list_objects
"""
Configuration of an S3 storage
Like others, but in protocol S3 add:
* SecureConnection: true if https, false otherwise
* Aws_access_key_i... | DIRACGrid/DIRAC | src/DIRAC/Resources/Storage/S3Storage.py | Python | gpl-3.0 | 28,163 | [
"DIRAC"
] | 4f39a4387e7d2ecc4747bfc7040c515211121d24c6085c0b3a95acddaaa0e884 |
##############################################################################
# Copyright (c) 2017, Los Alamos National Security, LLC
# Produced at the Los Alamos National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, ... | mfherbst/spack | var/spack/repos/builtin/packages/parsplice/package.py | Python | lgpl-2.1 | 1,997 | [
"LAMMPS"
] | eefa2b5a4068326d720f7be6c43b83a84b971aa0036ca966853198aa210710f3 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'phonopy'
tab.settings['Output file name'] = 'OUTCAR.born'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 5
tab.settings['Mass definition'... | JohnKendrick/PDielec | Examples/Phonopy/Na2SO42/script.py | Python | mit | 2,605 | [
"phonopy"
] | babd59538ef9f2b8f39629287d67d791dec371e257f8effa91a64f810e76c56b |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ben-albrecht/cclib | cclib/parser/__init__.py | Python | lgpl-2.1 | 1,333 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 199d2d1006f50b189f93b68e066a5c7fbbe25877bd3a57ad3349be638513fe6e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from monty.serialization import loadfn
import warnings
import numpy as np
import multiprocessing
import logging
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, Pourba... | tschaume/pymatgen | pymatgen/analysis/tests/test_pourbaix_diagram.py | Python | mit | 14,093 | [
"pymatgen"
] | 26d42ca632fb1951309888806e9153f5df67009306a9cb390b26c2ef5efc46bc |
# 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 the G... | espressopp/espressopp | src/ParticleAccess.py | Python | gpl-3.0 | 1,506 | [
"ESPResSo"
] | 5f1237e7573460f8e7be5b654096117c98844a343b727268282a075f791a6f5f |
'''
Steps for problem.feature lettuce tests
'''
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
from common import i_am_registered_for_the_course
from problems_setup import PROBLEM_DICT, answer_problem, problem_has_answer, add_problem_to_course
fro... | abo-abo/edx-platform | lms/djangoapps/courseware/features/problems.py | Python | agpl-3.0 | 7,370 | [
"VisIt"
] | a07acadf22a250158e3094c7f13d057e7c012353418cc8e281ce829130bde103 |
from __future__ import print_function
import functools
from copy import copy
import numpy as np
import scipy
from scipy import matrix
import regreg.api as rr
import regreg.affine as ra
from .query import query, optimization_sampler
from .reconstruction import reconstruct_full_from_internal
from .randomization import... | selective-inference/selective-inference | selectinf/randomized/sandbox/group_lasso.py | Python | bsd-3-clause | 33,512 | [
"Gaussian"
] | d0e993bdf2d20e497298241c92c6d9ca3ed2b26ee2f8e625582d5dc3d4300bee |
"""
"""
import warnings
import os
import sys
import posixpath
import fnmatch
import py
# Moved from local.py.
iswin32 = sys.platform == "win32" or (getattr(os, '_name', False) == 'nt')
try:
from os import fspath
except ImportError:
def fspath(path):
"""
Return the string representation of the ... | UK992/servo | tests/wpt/web-platform-tests/tools/third_party/py/py/_path/common.py | Python | mpl-2.0 | 14,626 | [
"VisIt"
] | d1910e325726000244f0c9d7eb892a826f2b10358e74fac1f837d4ef2d92ba99 |
# -*- coding: utf-8 -*-
"""
Copyright (c) 2016 Malte Gotz
This contains mainly the DoseWidget class to display a dose in a QWidget
and acess its methods
ToDo:
save advanced settings?
ideas:
click and drag for selection of area
or click and drag moves center for new input style, and area selec... | mgotz/EBT_evaluation | ebttools/gui/dosewidget.py | Python | mit | 60,487 | [
"Gaussian"
] | b2e68fafe2851b504ad591dab8542fddbc9a9cdd98f9169227b38ec0ffe67fab |
import numpy as np
from ase import Atoms
from ase.calculators.calculator import kptdensity2monkhorstpack as kd2mp
kd = 25 / (2 * np.pi)
a = 6.0
N = kd2mp(Atoms(cell=(a, a, a), pbc=True), kd)[0]
assert N * a / (2 * np.pi) >= kd, 'Too small k-point density'
| suttond/MODOI | ase/test/calculator/kd2mp.py | Python | lgpl-3.0 | 256 | [
"ASE"
] | 07ba7da3a780466431f185050110d715a00cfaf7290c865b0a2dfa2a2e3c8f64 |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, inc... | slideclick/slimit | src/slimit/visitors/ecmavisitor.py | Python | mit | 12,757 | [
"VisIt"
] | aa8973e27c335f46a42c768d84ec43ea2c2dd837843de7a85c232c7d9eff63b3 |
#
# 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 ... | jenniew/BigDL | pyspark/bigdl/nn/criterion.py | Python | apache-2.0 | 28,129 | [
"Gaussian"
] | bab341a3e4b0f70fc4374a0e5f4ac7bc01ef136b5449cd563e7d9de5bb6b980b |
import os
import sys
import os.path as op
import pysam
from bcbio.utils import file_exists, safe_makedir, chdir, get_perl_exports
from bcbio.provenance import do
from bcbio.distributed.transaction import file_transaction
from bcbio.pipeline import datadict as dd
from bcbio.pipeline import config_utils
def run(data)... | Cyberbio-Lab/bcbio-nextgen | bcbio/srna/mirdeep.py | Python | mit | 4,242 | [
"pysam"
] | 14cc4e468a1ec4163eedd4a8f91bb981843633427fdbfb512870b8e01a7b3d63 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Plotting function helper script
'''
from matplotlib.colors import LogNorm # , SymLogNorm
from mpi4py import MPI
import analysis_params
import plotting_helpers as phlp
import neuron
import LFPy
from hybridLFPy import helpers
import h5py
import glob
from mpl_toolkits.axe... | espenhgn/hybridLFPy | examples/Hagen_et_al_2016_cercor/plot_methods.py | Python | gpl-3.0 | 64,229 | [
"NEURON"
] | 19f7912bb39df56169625e0e4cf105caa8cadcbfa8e8355f3ea29c1a117806e5 |
import numpy
import chainer
from chainer.backends import cuda
from chainer import function_node
from chainer import utils
from chainer.utils import argument
from chainer.utils import type_check
class Gaussian(function_node.FunctionNode):
"""Gaussian sampling function.
.. note::
In forward calculat... | rezoo/chainer | chainer/functions/noise/gaussian.py | Python | mit | 4,523 | [
"Gaussian"
] | 667e6a33a78c0ad3b72108f6a9bd7eed22e76b258555caffac866598f0b54376 |
"""
def getAllRelatedClasses(root,classfqn):
classobj = getTypeOf(root,classfqn)
rootClasses = _getRootClasses(classobj)
#print rootClasses
relatedClasses = [] + rootClasses
for rootClass in rootClasses:
relatedClasses += _getAllSubClasses(rootClass,root)
return relatedClasses
def _g... | srusskih/SublimeBicycleRepair | bike/query/getAllRelatedClasses.py | Python | mit | 1,498 | [
"VisIt"
] | d1c4233dec086e430e9d647735cda888237e93f69a78101547eb688536880162 |
#!/usr/bin/python
#
# Copyright (C) 2014, Jaguar Land Rover
#
# This program is licensed under the terms and conditions of the
# Mozilla Public License, version 2.0. The full text of the
# Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
#
#
# Simple RVI service caller
#
import sys
from rvilib impor... | afan1/rvi_core | python/rvi_call.py | Python | mpl-2.0 | 1,624 | [
"Jaguar"
] | 117ef2b5174f9da775d9843fc16437c9b7558a4de161034343f9d9d27047e1b8 |
# coding=utf-8
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | google-research/ott | ott/tools/gaussian_mixture/scale_tril.py | Python | apache-2.0 | 6,657 | [
"Gaussian"
] | 92421b4cb264f26ba62d0d6fb5fb024c57cd4ce2085d0aaef13d57001a204269 |
#!/usr/bin/env python
"""A kernel that creates a new ASCII file with a given size and name.
"""
__author__ = "The ExTASY project <vivek.balasubramanian@rutgers.edu>"
__copyright__ = "Copyright 2015, http://www.extasy-project.org/"
__license__ = "MIT"
from copy import deepcopy
from radical.ensemblemd.exceptions... | radical-cybertools/ExTASY | examples/grlsd-on-archer/kernel_defs/gromacs.py | Python | mit | 3,445 | [
"Gromacs"
] | 92f7c7136374cd0206ed59d45d921e8cede50a5b0ece98892e10cb15f71d7b2c |
# Copyright (c) 2013 Per Unneberg
#
# 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 writing,... | percyfal/ratatosk | test/test_wrapper.py | Python | apache-2.0 | 32,311 | [
"BWA"
] | f97990ee22442ce8e0370e7666ecf2eb39b50400f5f17b09ce2c2fe6b770060b |
import cv2
import numpy as np
import os
import math
from scipy import ndimage
class vp():
def __init__(self, pos, score, numLines):
self.pos = pos
self.score = score
self.numLines = numLines
self.lines = None
class VP_imgLines():
def __init__(self, imgLines, imgLinesPosMap):
... | takahiromorita/heroku-python-flask5 | source/extract/extract_plane.py | Python | bsd-2-clause | 8,810 | [
"Gaussian"
] | 058fef62eca3b41864300b469480b0fb71edcbe3ceae649d080144457b4a4696 |
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