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#!/usr/bin/env python
"""
Kyle McChesney
Ruffus pipeline for simple bowtie alignment
"""
from ruffus import *
from bowtie_extras import BowtieExtras
import ruffus.cmdline as cmdline
import subprocess
import logging
import os
import pprint
import re
import time
# EMAIL
import smtplib
from email.MIMEMultipart import M... | mbiokyle29/pipelines | bowtie/bowtie_pipeline.py | Python | mit | 8,900 | [
"Bowtie"
] | a44d23c8c41d2db4d1e2e371aeb0dc0d6755fe19da787a737de48aa167ea9ba1 |
"""
Projection and related classes.
$Id$
"""
__version__='$Revision$'
import numpy
from numpy import array,asarray,ones,sometrue, logical_and, logical_or
import param
from param.parameterized import overridable_property
from topo.misc.keyedlist import KeyedList # CEBALERT: not in base
from sheet import Sheet
from ... | jesuscript/topo-mpi | topo/base/projection.py | Python | bsd-3-clause | 25,003 | [
"NEURON"
] | 60c7dab1f77b07ca3a699e1d85ebb97bc5df190d3b201b5085f7f0257ea457b4 |
# -*- coding: utf-8 -*-
"""
Catch-up TV & More
Copyright (C) 2016 SylvainCecchetto
This file is part of Catch-up TV & More.
Catch-up TV & More 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 Foundat... | SylvainCecchetto/plugin.video.catchuptvandmore | plugin.video.catchuptvandmore/resources/lib/skeletons/it_live.py | Python | gpl-2.0 | 5,980 | [
"GULP"
] | f7e51700008e85078c21e502b4893b0a98c10db26e547c7ed91e5312a9d55469 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Xeralux/tensorflow | tensorflow/contrib/py2tf/converters/builtin_functions.py | Python | apache-2.0 | 2,589 | [
"VisIt"
] | 51e24fda25f803363d77222d5ef69ea4b82a5aee4638d84691885ae8abf226e8 |
# -*- coding: utf-8 -*-
import numpy as np
from numpy.testing import assert_almost_equal, assert_equal
from probfit import (
AddPdf,
AddPdfNorm,
BlindFunc,
Convolve,
Extended,
Normalized,
describe,
rename,
)
from probfit._libstat import integrate1d
from probfit.decorator import extended... | iminuit/probfit | tests/test_functor.py | Python | mit | 6,928 | [
"Gaussian"
] | ce35c5ae14e3e6b99478f71274f56cd08c4ad377cb771cbb7686a5e1144bdb57 |
from Sire.MM import *
from Sire.IO import *
from Sire.Mol import *
from Sire.Units import *
from Sire.Qt import *
from nose.tools import assert_almost_equal
(waters,space) = Amber().readCrdTop("../io/waterbox.crd", "../io/waterbox.top")
coul_cutoff = 25 * angstrom
lj_cutoff = 10 * angstrom
cljwaters = []
for i in... | chryswoods/SireTests | unittests/SireMM/test_cljboxes.py | Python | gpl-2.0 | 2,561 | [
"Amber"
] | a4e69f173001c8bbf8d65be44385c260083d16088a016be396c0649c70cf96b8 |
"""A VTK file reader object.
"""
# Author: Martin Weier
# Copyright (c) 2006, California Institute of Technology
# License: GPL Style
# Standard library imports
import re
from os.path import split, join, isfile
from glob import glob
from os.path import basename
# Enthought library imports
from enthought.traits impor... | geodynamics/citcoms | visual/Mayavi2/citcoms_display/plugins/VTKFileReader.py | Python | gpl-2.0 | 10,740 | [
"Mayavi",
"VTK"
] | 504dd05b6d9c72814a96a6219736359bd2ff5131417dcdd909ccc6228c166b4e |
# 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 'NeuronConceptMap'
db.create_table('neuroelectro_neuronconceptmap', (
... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0019_auto__add_neuronconceptmap.py | Python | gpl-2.0 | 14,047 | [
"NEURON"
] | e0866ea24a5396356870003421a86c98d0a831bc06e0b6b888b7be7ec2446f79 |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | pburdet/hyperspy | hyperspy/io.py | Python | gpl-3.0 | 16,826 | [
"NetCDF"
] | 978be072daacb2e107a655572fa3575e284c805a294d41390357a50d5df72511 |
"""
Provides functions for simulation of GCMS data
"""
#############################################################################
# #
# PyMS software for processing of metabolomic mass-spectrometry data #
# Copyright (C) 2005-20... | dgarnier/pyms | Simulator/Function.py | Python | gpl-2.0 | 8,000 | [
"Gaussian"
] | fcbf72902e855dfd48caf6d43dc79e5464bff41ad0b5fe41db065ed1953b5d62 |
""" This is the Proxy storage element client """
import os
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Storage.Utilities import checkArgumentFormat
from DIRAC.Resources.Storage.StorageBase import StorageBase
from DIRAC.ConfigurationSystem.Client import ... | andresailer/DIRAC | Resources/Storage/ProxyStorage.py | Python | gpl-3.0 | 7,695 | [
"DIRAC"
] | 1e786d83a37d6757934638d66f7ad07442fdc066ac71c50909d69bdef9ffa5a0 |
# -*- coding: utf-8 -*-
"""
A real simple app for using webapp2 with auth and session.
It just covers the basics. Creating a user, login, logout
and a decorator for protecting certain handlers.
Routes are setup in routes.py and added in main.py
"""
# standard library imports
import logging
import jso... | Bezoar/surrender-rides | bp_includes/handlers.py | Python | mit | 64,168 | [
"VisIt"
] | 5920a2b9978c023192f9ff0aefb2f6aac3a8a4a1f7a64200fa0781306fc23459 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/moosesqa/SQADocumentReport.py | Python | lgpl-2.1 | 1,575 | [
"MOOSE"
] | 95ff0fe0ab761453430991fc347d7f001ed68b0a6981ab8fbb052dfb6f01d5ef |
##############################################################################
# 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-yarn/package.py | Python | lgpl-2.1 | 2,615 | [
"Bioconductor"
] | becd15cac5d462fe24d226255477bef4d3a9c79f944e278c24c5b7d549af7dc8 |
"""Soundex algorithm
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/11 19:11:21 $"
__copyright__ ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/soundex/stage3/soundex3d.py | Python | mit | 1,646 | [
"VisIt"
] | 44e263c66d6f76bdddf6e8f7f501893b780b9c04d6f1ae9d7626848d16a2a86f |
"""
===================================================
Simple sentiment analysis for the english language
===================================================
one-class-binary-classifier (1 : good / 0 : bad)
Sentiment analysis based on Support Vector Machine (SVM) by scikit-learn with data provided by Michigan State... | libeanim/simple-sentiment-analysis | simple_sentiment_analysis.py | Python | gpl-2.0 | 2,460 | [
"VisIt"
] | 55e934f39f7f224ee7e4efbcfbf1111c63185e3751c749b75aadecc7cd7d7894 |
from . import logger
from . import HTTP_VERBS, PAYLOAD_ENCODING
import sys
import logging
try:
import ujson as json
except ImportError:
import json
import requests
from .api_exception import APIException, EntityNotFoundError, EntityAlreadyCreatedError
from .device import Device
from .device_class import DeviceC... | digimondo/python-fireflyapi | fireflyapi/api.py | Python | mit | 8,008 | [
"Firefly"
] | f6a5d92bd2d514c21e0b800a3a53a0b973887a91a2393e2fd7d056c26011635d |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/__init__.py | Python | apache-2.0 | 13,160 | [
"VisIt"
] | f61d14be67baaa817a8865b3068493cfa11d74770abcfdbaed4def40a805ce91 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This code is designed soley for the purposes of demonstrating the tools
# for timeshifting.
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUT... | sparkslabs/kamaelia_ | Sketches/MPS/BugReports/FixTests/Kamaelia/Examples/DVB_Systems/Macro.py | Python | apache-2.0 | 9,073 | [
"CRYSTAL"
] | 9fcfae05678342e419dcbb218a2b8cb744cb64742e50fafa06724286871eb709 |
#!/usr/bin/env python
import os,glob,string,sys
from numpy.distutils.core import setup, Extension
from numpy.distutils import fcompiler
from distutils.dep_util import newer
## -------- set these
KM = 28
JM = 1
IM = 1
NC_INC = '/usr/include'
NC_LIB = '/usr/lib'
##----------------------
if '--lite' in sys.argv:
sy... | JoyMonteiro/CliMT | setup.py | Python | bsd-3-clause | 10,526 | [
"NetCDF"
] | 19d6f8322d532480ce4c2c153997efac65597bccef98cd78ffd77cb092734d56 |
#------------------------------------------------------------------------
# Copyright (c) 1998 by Total Control Software
# All Rights Reserved
#------------------------------------------------------------------------
#
# Module Name: fcgi.py
#
# Description: Handles communication... | drewcsillag/skunkweb | pylibs/fcgi.py | Python | gpl-2.0 | 12,177 | [
"TINKER"
] | 56e550681529093936c0ed49df5ad84544841e2435365a868a93493cef03c092 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import time
import warnings
from . import basex
from . import hansenlaw
from . import dasch
from . impor... | huletlab/PyAbel | abel/transform.py | Python | mit | 16,835 | [
"Gaussian"
] | cfab5fd73f6c1ca5d8ca94f8b0225c1f0ce42cf31027e1bad175a57f31a0fc2d |
import os
import sys
import unittest
sys.path.insert(0, os.getcwd())
from csg.core import CSG
from csg.geom import Vector
class TestCSG(unittest.TestCase):
def setUp(self):
print('setup')
def tearDown(self):
print('tear')
def test_cs(self):
print('ss')
def test_toPo... | timknip/pycsg | test/test_csg.py | Python | mit | 4,120 | [
"VTK"
] | 849535045c94efd443f4e92637d01ab83136f70dbdec17082e3cd90fcf7d3f7e |
import math
import util
class NeuralNetwork:
def __init__(self):
self.neurons = []
self.synapses = []
def make_copy(self):
""" Create and return a deep-copy of this NeuralNetwork """
copy = NeuralNetwork()
for neuron in self.neurons:
copy.add_neuron(neuron.make_copy())
for synapse in self.synapses:
... | pkorth/intraspecies-cooperation | nnet.py | Python | mit | 4,229 | [
"NEURON"
] | 5f5043db7e8c930b8ece8d93cb408679a0290019d6cf08bb231a46699d4695b6 |
# Copyright 2020 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/distributions/generalized_normal.py | Python | apache-2.0 | 11,566 | [
"Gaussian"
] | 0845cdf76366e494e338897aeea39381b3f2646c0804834d7277c6e9c0e15c0d |
"""Gulp installer class."""
import subprocess
from grow.sdk.installers import base_installer
class GulpInstaller(base_installer.BaseInstaller):
"""Gulp installer."""
KIND = 'gulp'
@property
def should_run(self):
"""Should the installer run?"""
return self.pod.file_exists('/gulpfile.... | grow/pygrow | grow/sdk/installers/gulp_installer.py | Python | mit | 1,001 | [
"GULP"
] | f4d7ab07c80185478d26e08c9f85c1954fed852e495044fdeedc14c87d487e34 |
import argparse
import svm
import svmutil
from core import pssm2feature
from core import valid
PATH = "/home/ubuntu/galaxy-dist/tools/bilab/"
class predictor(object):
# Contain Information of preditor.
def __init__(self,model,reverse = False):
self.model = svmutil.svm_load_model(model)
if reverse:
self.comp... | BILAB/SBRP | predict_pssm.py | Python | mit | 2,098 | [
"Galaxy"
] | e293de431bfa7fdbd54d95b168c55ebdac0a252bc611364a2f5ec4b6dc9e6f34 |
import sys
import argparse
import iCheck
import vcfwriter
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='iEVA: identification and Extraction of Variant Attributes.')
parser.add_argument('-v','--verbose', action="store_true", help="Increase output verbosity. Enable iEVA extraction progress ... | Matteodigg/iEVA | iEVA/iEVA.py | Python | mit | 11,796 | [
"pysam"
] | 06234cc24b3e66779ef6712905a12c66d0962fc538a4f8517bc11f82d1d85957 |
# Copyright (c) 2017 Brian Ginsburg, Julie Rutherford-Fields
# This work is available under the "3-clause ('new') BSD License”.
# Please see the file COPYING in this distribution
# for license terms.
from app import app, manager
if __name__ == '__main__':
manager.run()
| thuselem/teergrube | run.py | Python | bsd-3-clause | 278 | [
"Brian"
] | 2e850e30731622098afed0101fd82339563fbc7acc935bdde33b8f2eeb3b70e2 |
"""
* Copyright (c) 2004, Brian Hawkins
* Permission is granted to use this code without restriction as long
* as this copyright notice appears in all source files.
THIS BUILD FILE DOES NOT WORK
"""
bldoutdir = "build"
srcdir = "src"
sourceFiles = make.createFileList(srcdir, ".*\\.java")
classFiles = make... | brianhks/tablesaw | test/java/build.py | Python | apache-2.0 | 2,304 | [
"Brian"
] | 2153c52270e4edc4ef76c0bbf9e4e8474891fdc68485bd75f522e18c3134e4a0 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014, 2015 CERN.
#
# INSPIRE 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... | jalavik/inspire-next | inspire/modules/forms/views.py | Python | gpl-2.0 | 3,060 | [
"VisIt"
] | e6db3d452aeaf006432cfdc835b55d16ec40e73656a16d08ce0688f3eae09fa4 |
""" JobRunningMatchedRatioPolicy
Policy that calculates the efficiency following the formula::
( running ) / ( running + matched + received + checking )
if the denominator is smaller than 10, it does not take any decision.
"""
from __future__ import absolute_import
from __future__ import division
from __fut... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/JobRunningMatchedRatioPolicy.py | Python | gpl-3.0 | 2,206 | [
"DIRAC"
] | 48303200ac949f2cf68ba63eb597d27aa0d4862b884f45571f85431f0b3f8a5f |
# 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/FixedTripleAngleList.py | Python | gpl-3.0 | 3,818 | [
"ESPResSo"
] | aeed895737807ad2bb5722614b7c59dcc3dc6bf4de24e4a8cf653cae0d9198c8 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | nuclear-wizard/moose | python/peacock/base/ViewerCornerWidget.py | Python | lgpl-2.1 | 2,030 | [
"MOOSE"
] | bdd6ae2e9ae9fbe37bda4d789ea5c1fdede8950eb55db3e4dac30bd07b362c9e |
import logging
import iris
from cis.data_io import gridded_data as gridded_data
from cis.data_io.products import AProduct
class NetCDF_Gridded(AProduct):
def get_file_signature(self):
# We don't know of any 'standard' netCDF CF model data yet...
return [r'.*\.nc']
@staticmethod
def load_m... | cedadev/cis | cis/data_io/products/gridded_NetCDF.py | Python | lgpl-3.0 | 9,097 | [
"NetCDF"
] | db18362edbf3090cbab9f77725abf1568c166499c4697d1a2b41258553467008 |
import pytest, py
import tox
import os
import sys
from py.builtin import print_
from fnmatch import fnmatch
import time
from tox._config import parseconfig
from tox._venv import VirtualEnv
from tox._cmdline import Action
from tox.result import ResultLog
def pytest_configure():
if 'TOXENV' in os.environ:
de... | marcoantoniooliveira/labweb | oscar/lib/python2.7/site-packages/tox/_pytestplugin.py | Python | bsd-3-clause | 9,665 | [
"VisIt"
] | 280d0fa598289e8a8c648e39bada9e1ae3490bdec83d3936b6c562bdebe58e53 |
from __future__ import division
from scipy.signal import convolve2d, correlate2d
import numpy as np
import numpy.random as random
import sys
def _random_weights(shape):
size = np.prod(shape)
#random.seed(42) # use only for debugging
return random.uniform(-np.sqrt(1/size), np.sqrt(1/size), shape)
class La... | chinmayhegde/retinopathy-detection | retinopathy/cnn/layers.py | Python | mit | 11,295 | [
"NEURON"
] | 8202f9f9c1bb3a5133838e9ec631ac0d723811a2d78ab2a7c7f77d73cb944db4 |
# Copyright (C) 2015 Philipp Baumgaertel
# All rights reserved.
#
# This software may be modified and distributed under the terms
# of the BSD license. See the LICENSE.txt file for details.
import numpy as np
from skgpuppy.Covariance import tracedot
cython = False
try:
from scipy import weave
weaving = True
except... | snphbaum/scikit-gpuppy | skgpuppy/UncertaintyPropagation.py | Python | bsd-3-clause | 16,390 | [
"Gaussian"
] | 6578f17a73646df2275ea0ad610326beb46b3b8dc78af71c807c5f45898332c0 |
#
# Copyright 2017 Google Inc.
#
# 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 writin... | google/joint_vae | joint_vae/utils.py | Python | apache-2.0 | 24,097 | [
"Gaussian"
] | 071489415baa60140753ab60a6b31161e415959d02c9a33676eedda69725be39 |
__author__ = 'jeddy'
import sys, os, re, argparse, time
"""generateBatchSubmitParams
This script is used to generate a batch submit file for Globus Genomics Galaxy,
with all parameters specified for the selected Workflow for each library
(sample).
Inputs:
-u / --unalignedDir : directory with unaligned FASTQs fro... | jaeddy/bripipetools | scripts/_deprecated/generate_batch_submit_params.py | Python | mit | 11,059 | [
"Galaxy"
] | 745977174d1e4dee2c4ba0eff38803b11d2a829b945a76c8a05a3e4c94c8a5bc |
import cv2
import numpy as np
import math
from math import sin,cos,radians
img_filename = '' #Name of the image over which to perform line detection
img = cv2.imread(img_filename)
img_smooth = cv2.GaussianBlur(img,(7,7),3) #Gaussian filter to make image smooth
img_edges = cv2.Canny(img_smooth[:,:,2],50,150)... | ashimb9/hough_transform | hough_lines.py | Python | gpl-3.0 | 3,903 | [
"Gaussian"
] | ee5879af6bf3f23f1932f43a14edb3b2949a1e0d334a3c8bc71157f6b467a7e9 |
##############################################################################
# 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/r-rsamtools/package.py | Python | lgpl-2.1 | 2,420 | [
"Bioconductor"
] | 87c974ddaa0b2294b1c2505324bc6c8b16bda1c4f533ed8359402c53b4184e23 |
from wikitables import import_tables
import json, os
vessels = import_tables("List_of_Star_Trek_Starfleet_starships_ordered_by_class")
classes = ["Akira class ",
"Ambassador class ",
"Andromeda class ",
"Antares class ",
"Apollo class ",
"Archer class ",
... | MaximeGir/StarTrekCorpora | resources/extractors/wikipedia_vessels_extractor.py | Python | mit | 2,953 | [
"Galaxy"
] | a3edf80714254fc65356ff2439a8ac1c77d6a91f47d894ea55bb4789f51c4406 |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#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 2... | R-a-dio/python-audio-tools | test/test_utils.py | Python | gpl-2.0 | 208,326 | [
"Brian"
] | 27a79ff24d65a799417a7bde87f5bc96b12b41757c9a2315b64d439110f895eb |
#!/usr/bin/env python
# Copyright (C) 2007 CAMP
# Please see the accompanying LICENSE file for further information.
from distutils.core import setup, Command
from distutils.command.build_py import build_py as _build_py
from glob import glob
from os.path import join
import os
import sys
import shutil
long_descript... | PHOTOX/fuase | ase/setup.py | Python | gpl-2.0 | 4,970 | [
"ASE"
] | c122ad6d8c61e9d420ef03b4e00721b928a2da2ba97ea467776e5e24ccd4f6c8 |
from .common import Benchmark
import numpy as np
class LaplaceInplace(Benchmark):
params = ['inplace', 'normal']
param_names = ['update']
def setup(self, update):
N = 150
Niter = 1000
dx = 0.1
dy = 0.1
dx2 = (dx * dx)
dy2 = (dy * dy)
def num_updat... | WarrenWeckesser/numpy | benchmarks/benchmarks/bench_app.py | Python | bsd-3-clause | 2,649 | [
"NEURON"
] | 49858e7bb71b14dbbb8be150810d61598736604448c18ae00d4fafe5efb0a99f |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
# $Id$
#
# Copyright (C) 2007 by Greg Landrum
# All rights reserved
#
from __future__ import print_function
from rdkit import Geometry
from rdkit.Chem.Subshape import SubshapeObjects
import math
import numpy
#------------------------------------------... | soerendip42/rdkit | rdkit/Chem/Subshape/BuilderUtils.py | Python | bsd-3-clause | 11,219 | [
"RDKit"
] | e586ae2a4d7ef4f5fc9d7e7fb49643e988693e4d96f3a015e9ec08a5b2389437 |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-rhtslib/package.py | Python | lgpl-2.1 | 1,973 | [
"Bioconductor"
] | ff5a88b06cc94a780fdded34981f0c136382b05c317fa62a7f4d2889bf37fd09 |
from datetime import datetime
import logging
log = logging.getLogger(__name__)
import numpy
from box import BoundingBox, Vector
from mclevelbase import exhaust
import materials
from entity import Entity, TileEntity
from copy import deepcopy
def convertBlocks(destLevel, sourceLevel, blocks, blockData):
return ma... | skinny121/MCEdit-TallWorlds | pymclevel/block_copy.py | Python | isc | 7,251 | [
"VisIt"
] | 565a5d9bd2eaf87ea67862b67c478107c6ff3285db3c74e3887b4d277a74d375 |
# coding: utf8
{
' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages using SMS & Email to various groups and individuals before, during and after a disaster.': ' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages usin... | flavour/porto | languages/ur.py | Python | mit | 347,246 | [
"VisIt"
] | 44c4f89560e01eab7b09b991080cbcae85b8c1b6e5cbf0fd5891f466e869fb37 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# cat - [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 the G... | heromod/migrid | mig/cgi-bin/cat.py | Python | gpl-2.0 | 1,094 | [
"Brian"
] | c1319feba6510b8e98dbc09f92c3248c808e1ac1898ea954197c78c0d549a535 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinitio.utils import *
class RpnTest(PymatgenTest):
def test_mongodb_like... | sonium0/pymatgen | pymatgen/io/abinitio/tests/test_utils.py | Python | mit | 2,264 | [
"pymatgen"
] | 9404a6963983a293a0510ef833fd2a0c71d3cd810b0d9f14ddd25a9a338ceb93 |
"""
View for Courseware Index
"""
# pylint: disable=attribute-defined-outside-init
import logging
import urllib
from django.conf import settings
from django.contrib.auth.views import redirect_to_login
from django.db import transaction
from django.http import Http404
from django.template.context_processors import cs... | EDUlib/edx-platform | lms/djangoapps/courseware/views/index.py | Python | agpl-3.0 | 26,121 | [
"VisIt"
] | b1f0473d49fa65fa34efd3e3aaf9504773cb20c36c639bc71166d7cd4b531b97 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | pkom/gestionies | config/urls.py | Python | bsd-3-clause | 1,279 | [
"VisIt"
] | 5761944ca6718dd87101b81f0f04ff4aecf41e4971d586b21169aa415f8dba88 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This Script test the euclidean to polar by coverting 2D vectors
# from a gradient into polar, which is converted into HSV, and then to RGB.
# Image pipeline
gauss = vtk.vtkImageGaus... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestEuclideanToPolar.py | Python | gpl-3.0 | 917 | [
"VTK"
] | 80952bc0226bfb0f5dd2f5b82bcb5221805dd036e9d80fad852b9f449e937bba |
#from pysqlite2 import dbapi2 as sqlite
import sqlite3 as sqlite
import re
import math
def getwords(doc):
splitter=re.compile('\\W*')
#print doc
# Split the words by non-alpha characters
words=[s.lower() for s in splitter.split(doc)
if len(s)>2 and len(s)<20]
# Return the unique set... | 0111001101111010/cs595-f13 | assignment10/q1/docclass.py | Python | mit | 6,057 | [
"CASINO"
] | 0b23dab77c00821247bfc1c676e04a4d0161a509806379dea14093c8cb6a4239 |
import copy
import functools
from nxtools import logging, log_traceback
from firefly.api import api
from firefly.common import pixlib
from firefly.core.common import config
from firefly.core.enum import ObjectStatus
from firefly.dialogs.send_to import show_send_to_dialog
from firefly.dialogs.batch_ops import show_bat... | immstudios/firefly | firefly/modules/browser.py | Python | gpl-3.0 | 21,829 | [
"Firefly"
] | 238a290dd6079a18e19d819e2546fe7fc203487bd30d56948ec29f85efcf8a33 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | nuclear-wizard/moose | python/peacock/base/Plugin.py | Python | lgpl-2.1 | 4,879 | [
"MOOSE"
] | cbb02fbc58660d6d874c37e6e2b5ddbe24bd8a1506dd304e983277b6d547435f |
#!/usr/bin/python
import pymol
import pymol
from pymol import stored
from pymol import pymol, CmdException
cmd=pymol.cmd
import export_to_gl as glmol
def out_atoms(modelName):
#print modelName
| S-John-S/MAT | hbb_script_gl.py | Python | mit | 197 | [
"PyMOL"
] | 2b2fb23e2f049b296d829fb2352e284f8811bf24c8c237aa72e1998711703caa |
"""
Authors: Thomas J. Sargent, John Stachurski
Filename: lss.py
Computes quantities related to the Gaussian linear state space model
x_{t+1} = A x_t + C w_{t+1}
y_t = G x_t
The shocks {w_t} are iid and N(0, I)
"""
from textwrap import dedent
import numpy as np
from numpy.random import multivariate_no... | chenxulong/quanteco | quantecon/lss.py | Python | bsd-3-clause | 8,432 | [
"Gaussian"
] | 8f99601c4623c01cf59980f3a46da25924e33508cebf60bf7f00c4e697855be8 |
"""PyDockDNA scoring function parameters"""
default_hydrogen_extension = '.H'
default_amber_extension = '.amber'
# Energetic terms
scoring_vdw_weight = 1.0
vdw_input_file = 'vdw.in'
default_max_electrostatics_cutoff = 1
default_min_electrostatics_cutoff = -1
default_vdw_cutoff = 1.0
# AMBER
amber_elec_constant = 18.2... | brianjimenez/lightdock | lightdock/scoring/dna/energy/parameters.py | Python | gpl-3.0 | 324 | [
"Amber"
] | 2ac0f7057611875f20cc8820e6b819384a48b465b2b5db732f893a6b8f3ebd73 |
# 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... | hfp/tensorflow-xsmm | tensorflow/contrib/tpu/python/tpu/tensor_tracer.py | Python | apache-2.0 | 39,565 | [
"VisIt"
] | c3c757014de5974a8d6be628bf1ff407967f0067225f552f49496572e88d4fdc |
import glob
import h5py
import mahotas as mh
import matplotlib.pyplot as plt
import numpy as np
import partition_comparison
import os
from scipy import ndimage as nd
import skimage.measure
import tifffile as tif
class Cremi(object):
@staticmethod
def read_section(path, z, verbose=True):
'''
'''
imag... | VCG/gp | gp/cremi.py | Python | mit | 1,951 | [
"VisIt"
] | e17ed95edd78f68dfdbf26b494d002c96d3f22ce34a5b2bf622b45f2e27271ce |
#!/usr/bin/env python
#
# Copyright 2007 Google Inc.
#
# 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 o... | GdZ/scriptfile | software/googleAppEngine/google/appengine/tools/appcfg.py | Python | mit | 142,906 | [
"VisIt"
] | 28072a09f0071743dc504505d60e51f95616c5a83540be662ec736e88516451f |
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from DIRAC import gConfig, S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import Time
import json
class PublicStateManagerHandler( WebHandler ):
AUTH_PROPS = "authenticated"
@asyncGen
def web_getTreeMenuItems( self ):
applications =... | chaen/WebAppDIRAC | WebApp/handler/PublicStateManagerHandler.py | Python | gpl-3.0 | 425 | [
"DIRAC"
] | 9b58b4eae90746a96da0fa3b710c136274cd1aef236ed8074c7854dc30028dc6 |
# 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 ... | BlueBrain/NeuroM | tests/features/test_morphology.py | Python | bsd-3-clause | 20,903 | [
"NEURON"
] | bdd5d3a121230b1433dc581f596303abfd24a2d383f114a3e9f64003df968243 |
import pprint
from moogli.visualization.pipeline import Clock
from moogli.visualization.pipeline import Pipeline
from moogli.extensions.swc import SwcNetwork
from moogli.extensions.table import TableContinuousDataProducer
from moogli.visualization.pipeline import SimulationDataMediator
from moogli.visualization import ... | dilawar/moogli | examples/test.py | Python | gpl-2.0 | 1,992 | [
"NEURON"
] | d985c98d6cdb46d588345a4eaf13d423056533c4368f83dd7353523fc6e9f929 |
# $HeadURL$
""" RequestDBMySQL is the MySQL plug in for the request DB
:deprecated:
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Base.DB import DB
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities.List import intListToString, stringListToString
from DIRAC.RequestManagementSystem.Client.Reque... | avedaee/DIRAC | RequestManagementSystem/DB/RequestDBMySQL.py | Python | gpl-3.0 | 47,328 | [
"DIRAC"
] | 0b7645ec5f40a65fa57243553ec7e7789d1542fec05a7c83d6fe4a8aec9b54be |
# -*- coding: utf8 -*-
# # #
# Downscale PCMDI AR5 data to a pre-processed climatology
# extent, resolution, reference system
#
# Author: Michael Lindgren (malindgren@alaska.edu)
# # #
import rasterio, os
import numpy as np
import pandas as pd
import geopandas as gpd
from downscale import utils
class Baseline( object... | ua-snap/downscale | downscale/dataset.py | Python | mit | 6,957 | [
"NetCDF"
] | 52bec459ef73ddad9730b439323527ca03408385a8fb7fd3c1bf01617b38e16d |
# 2017 DeepCrystal Technologies - Patrick Hop
#
# Message Passing Neural Network SELU [MPNN-S] for Chemical Multigraphs
#
# MIT License - have fun!!
# ===========================================================
import math
import deepchem as dc
from rdkit import Chem, DataStructs
from rdkit.Chem import AllChem
impor... | deepchem/deepchem | contrib/mpnn/mpnn.py | Python | mit | 5,567 | [
"RDKit"
] | cca29f33eb42575f67c4ec782d0b772ddd62d9f05b43c66ffcabb74259f0cb0d |
from six.moves import range
class NodeVisitor(object):
def visit(self, node):
# This is ugly as hell, but we don't have multimethods and
# they aren't trivial to fake without access to the class
# object from the class body
func = getattr(self, "visit_%s" % (node.__class__.__name__)... | Acidburn0zzz/servo | tests/wpt/web-platform-tests/tools/wptrunner/wptrunner/wptmanifest/node.py | Python | mpl-2.0 | 4,763 | [
"VisIt"
] | ea71fd38697c30bab3dbadb13d41362eff9ae31fc08beca0588231f7902e97ac |
"""A GTK dialog which displays a list of Zero Install applications in the menu."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
from zeroinstall.support.tasks import get_loop
import os, sys
import gtk, pango
import subprocess
if sys.ver... | linuxmidhun/0install | zeroinstall/gtkui/applistbox.py | Python | lgpl-2.1 | 12,309 | [
"VisIt"
] | 04d2ed09b4ba957f4a868888c78396cfb5cede49fa941910c8baaf45eee2b0eb |
import datetime
import json
import os
import re
from collections import OrderedDict
import csv
import matplotlib
import matplotlib.pyplot as plt
import numpy
import urllib3
from scipy import stats
from sqlalchemy.orm import sessionmaker
from django.conf import settings as djangoSettings
from django.contrib.auth.decor... | tom-heimbrodt/oeplatform | modelview/views.py | Python | agpl-3.0 | 23,905 | [
"Gaussian"
] | 5d39bf04139014fb1abf880574c1643389d9b552003a3d36ffcb3e0fa79a1a5b |
# -*- 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_v3beta1/test_test_cases.py | Python | apache-2.0 | 153,549 | [
"Octopus"
] | f3bde0d70e7e93ce39e00a4b50912a938818665c216ab80d0c79649479478b93 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
from scipy.io import netcdf
import scipy.interpolate as intrp
import os
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap
from matplotlib.patches import Polygon
class ExtractEnvFor:
"""
Class with methods to extract the e... | SEGGroup/PhytoSFDM | phytosfdm/EnvForcing/envforcing.py | Python | gpl-2.0 | 14,667 | [
"NetCDF"
] | 3d1b02f6fa2cbdb04807fd6d7a3d28badaf0109c754e7725e6e59d515b3cdde4 |
# 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/Single_Contact_Classification/Final/results/2-categories/test10_cross_validate_categories_mov_fixed_1200ms.py | Python | mit | 4,331 | [
"Mayavi"
] | c526ef1bf4101854d4ac640f25cb0def9fc139cc58011cdcc433ac08b3673251 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Base types for nodes in a GRIT resource tree.
'''
from __future__ import print_function
import ast
import os
import struct
import sys
from xml.sax i... | endlessm/chromium-browser | tools/grit/grit/node/base.py | Python | bsd-3-clause | 23,797 | [
"xTB"
] | 5336a3a93034b04693d4436ec73e83ba8a784edd71009c87fe2d7ce40811ad88 |
import os
import tempfile
import unittest
from pyepw.epw import Comments1, EPW
class TestComments1(unittest.TestCase):
def setUp(self):
self.fd, self.path = tempfile.mkstemp()
def tearDown(self):
os.remove(self.path)
def test_create_comments_1(self):
obj = Comments1()
v... | rbuffat/pyepw | tests/test_comments_1.py | Python | apache-2.0 | 585 | [
"EPW"
] | 58014db93f8b16d96af71aab01d4ecfb7025085f33435292f6311b15a8019668 |
#!/usr/bin/python
import argparse
import hashlib
import sys
import os
import subprocess
import signal
import getpass
import urlparse
import simplejson
from termcolor import colored
import ConfigParser
import StringIO
import functools
import time
import random
import string
from configobj import ConfigObj
import tempf... | zstackorg/zstack-utility | zstackctl/zstackctl/ctl.py | Python | apache-2.0 | 465,802 | [
"VisIt"
] | 8f3413a7a98dabcae3bb7bd757b237f6fbe20e51e74cf3e6a2499b6bf980c817 |
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
import sqlite3
import sys
import xml.etree.ElementTree as ET
from classes import *
class CustomTreeWidgetItem(QTreeWidgetItem):
def __init__(self, parent, status, name, dateStart=None, dateEnd=None):
super().__init__(parent)... | zhaladshar/HealthView | gui.py | Python | gpl-3.0 | 14,028 | [
"VisIt"
] | 3d68fe0761ea83a8c71e49613f5d370a5e32ea341e927c149b23417df3bf0b11 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-select-jobs
# Author : Stuart Paterson
########################################################################
"""
Select DIRAC jobs matching the given conditions
"""
import DIRAC
from DIRAC import gLo... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_select_jobs.py | Python | gpl-3.0 | 4,150 | [
"DIRAC"
] | 9fea4eefbff2e3ceaa973668036d3c5e52c68e8270371a90ad376838027abb35 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/model/fixture.py | Python | gpl-2.0 | 7,030 | [
"VisIt"
] | 28a318f1fed4875563d1a16d3093e0e95b8be5de6220fbace59fcf3c56089707 |
# -*- coding: utf-8 -*-
import unittest
from scrapy.http import HtmlResponse
from manoseimas.scrapy.items import Suggestion
from manoseimas.scrapy.spiders.suggestions import SuggestionsSpider
from manoseimas.scrapy.tests.utils import fixture
class TestHelpers(unittest.TestCase):
def test_truncate(self):
... | ManoSeimas/manoseimas.lt | manoseimas/scrapy/tests/test_suggestions.py | Python | agpl-3.0 | 63,392 | [
"Amber"
] | 2d59e88d695aa338c3e77a7fef17b0544920e66967143c7a08801c88abf3ecaf |
"""
Cylindrical mesocrystal on a substrate
"""
import bornagain as ba
from bornagain import deg, angstrom, nm
def get_sample():
"""
Returns a sample with a cylindrically shaped mesocrystal on a substrate.
"""
# defining materials
m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0)
m_substrate... | waltervh/BornAgain | Examples/python/simulation/ex04_ComplexShapes/MesoCrystal.py | Python | gpl-3.0 | 2,066 | [
"CRYSTAL"
] | f76002a1b6dec8ca5becb5d03376180ff903d2fb1b059e11ca41780fa45d27c7 |
"""
Decorates a function for Bowtie.
Reference
---------
https://gist.github.com/carlsmith/800cbe3e11f630ac8aa0
"""
from typing import Callable
import sys
import inspect
from subprocess import call
import click
from bowtie._app import _WEBPACK, App
class WrongNumberOfArguments(TypeError):
"""The "build" funct... | jwkvam/conex | bowtie/_command.py | Python | mit | 3,150 | [
"Bowtie"
] | 001dab62bcc1728b851f579d7559da977d40d7eaaa1944490fb8f6898c62d7dc |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print('Group', name, 'has', count, 'articles, range', first, 'to', last)
Group comp.lang.python has 51 articles, ran... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.0/Lib/nntplib.py | Python | mit | 21,112 | [
"Brian"
] | 303b991cc4f4f251e34129faeba76e9f9dff95af6b7b03061fc5849eab836dfb |
#* This file is part of Zapdos, an open-source
#* application for the simulation of plasmas
#* https://github.com/shannon-lab/zapdos
#*
#* Zapdos is powered by the MOOSE Framework
#* https://www.mooseframework.org
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.htm... | lindsayad/zapdos | problems/Jacobians.py | Python | lgpl-2.1 | 762 | [
"MOOSE"
] | 56cc1afb366f6dcc35b6c3313294c5d2a9c2052e6a25901a3fe8a3d865bc3bd1 |
########################################################################
# $HeadURL $
# File: ReplicateAndRegister.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 18:49:12
########################################################################
""" :mod: ReplicateAndRegister
=========================... | coberger/DIRAC | DataManagementSystem/Agent/RequestOperations/ReplicateAndRegister.py | Python | gpl-3.0 | 19,200 | [
"DIRAC"
] | 6ccd97c1e4d4126996b6cdb7fcf4529b28ded03d65ec9083fb1003af06bb588f |
#!/usr/bin/env python
#
# commands.py
#
# commands for RNA 3D structure prediction.
#
# http://iimcb.genesilico.pl/moderna/
#
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__version__ = "1.7.1"
... | mmagnus/rna-pdb-tools | rna_tools/tools/mini_moderna3/moderna/commands.py | Python | gpl-3.0 | 44,552 | [
"Biopython"
] | 938e21dcb25a43c4768cb8aaf6ba8a4add18ecbb8798481bf288ae4dfde61c4c |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ThreadPoolExecutor."""
from __future__ import with_statement
import atexit
import threading
import weakref
import sys
from serge.blocks.concurrent.futures import _base
try:
import queue
except Imp... | smmosquera/serge | blocks/concurrent/futures/thread.py | Python | lgpl-3.0 | 4,808 | [
"Brian"
] | 3535fd5b3709ca759282cd99a6e01ef24916c22a5fcb3d441636d23d5b59a7c5 |
# $HeadURL$
__RCSID__ = "$Id$"
import types
import os
import threading
import time
from DIRAC import gLogger, gConfig, rootPath, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.Utilities.SiteCEMapping import getCESiteMapping
from ... | Sbalbp/DIRAC | FrameworkSystem/Service/SiteMapHandler.py | Python | gpl-3.0 | 10,363 | [
"DIRAC"
] | 3741e312afd4771e5f4d0a6dcf03d8e53f5891bb4c3e8a574342c326bcc6bc0d |
# -*- coding: utf-8 -*-
DIST_GAUSSIAN = "Gaussian" # Gaussian(mu, Lambda, \*\*kwargs)
DIST_GAUSSIAN_ARD = "GaussianARD" # GaussianARD(mu, alpha[, ndim, shape])
DIST_GAMMA = "Gamma" # Gamma(a, b, **kwargs)
DIST_WISHART = "Wishart" # Wishart(n, V, **kwargs)
DIST_EXPONENTIAL = "Exponential" # Exponential(l, **kwargs... | math-a3k/django-ai | django_ai/bayesian_networks/bayespy_constants.py | Python | lgpl-3.0 | 2,695 | [
"Gaussian"
] | 5f5b688b44c53075b7e7dc255004be16a237acd5f83cce3209efa88f438ff7e2 |
#!/usr/bin/env python2
# * **************************************************************** **
# File: io.py
# Requires: Python 2.7+ (but not Python 3.0+)
# Note: For history, changes and dates for this file, consult git.
# Author: Brian Danilko, Likeable Software (brian@likeablesoftware.com)
# Copyright 2015-2017 Micr... | Bdanilko/EdPy | src/lib/io.py | Python | gpl-2.0 | 12,972 | [
"Brian"
] | 762c7f719632038dc0fbdb42eb2cfa3f711f09acfd150be3ded17acf51283034 |
"""
Filename: gth_solve_jit.py
Author: Daisuke Oyama
Routine to compute the stationary distribution of an irreducible Markov
chain by the Grassmann-Taksar-Heyman (GTH) algorithm.
"""
import numpy as np
from numba import jit
try:
xrange
except: # python3
xrange = range
def gth_solve(A, overwrite=False):
... | oyamad/gth_solve_numba | gth_solve_jit.py | Python | bsd-3-clause | 4,521 | [
"Gaussian"
] | 4588c862e6de0df288e838f0f6c2912d3a8c1171462ab7545231b1cba7dbd0f8 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/transform/scale_2d.py | Python | lgpl-2.1 | 737 | [
"MOOSE"
] | aaa9d8afe5f3703f3e7166b06e44992073e8a083d3c3e1f1184e559f94bd3f5f |
###
# 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/ub/test_ub.py | Python | gpl-3.0 | 31,264 | [
"CRYSTAL"
] | 14927a240b68fcf4ee024e341ebb8d3fe621b862adcb0ff58b5b05324238d950 |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of seq_crumbs.
# seq_crumbs 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, ... | JoseBlanca/seq_crumbs | crumbs/seq/split_mates.py | Python | gpl-3.0 | 4,858 | [
"BLAST"
] | 2515e0ab545ae87cb50658c16003407577b5597f41c6053dd06d7a1e452b4ca9 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree.py
lttree.py is an extension of the generic ttree.py pr... | anshumang/lammps-analytics | tools/moltemplate/src/lttree.py | Python | gpl-2.0 | 35,179 | [
"LAMMPS"
] | ea9ca85c2d112325d847c5cb6b48185ff502e598411a569e148bedc55d7ee62b |
#!/usr/bin/env python2.7
# John Vivian
"""
Batch alignment script using Toil
Runs BWA to produce the SAM followed by BAMSORT to produce the BAM
If the option is specified (s3_dir), the output bam will be placed
in S3. ~/.boto config file and S3AM: https://github.com/BD2KGenomics/s3am
are required for this step.
Dep... | jpfeil/toil-scripts | src/toil_scripts/bwa_alignment/old_alignment_script/batch_align.py | Python | apache-2.0 | 11,512 | [
"BWA"
] | e97fc25284ae775d98032c8ac8df3b8d756e496dbae87e4f2cd7e99e06e5b7c1 |
import math
import re
import numpy as np
from .utilities import unittest
import cantera as ct
from . import utilities
class TestReactor(utilities.CanteraTest):
reactorClass = ct.Reactor
def make_reactors(self, independent=True, n_reactors=2,
T1=300, P1=101325, X1='O2:1.0',
... | Heathckliff/cantera | interfaces/cython/cantera/test/test_reactor.py | Python | bsd-3-clause | 45,223 | [
"Gaussian"
] | 21ea0de46b71bf36be6dbdd08f22088d92795e7ef89cf3a6e83e3a4500fc1383 |
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