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"""
nanslicer.py
A command-line tool for producing figures with slices through MR images. This is installed
by PIP as ``nanslicer``. Supports overlays, dual-coded overlays and colorbars. Dual-coding is
described here https://www.cell.com/neuron/fulltext/S0896-6273(12)00428-X.
The minimum command-line call is:
``nans... | spinicist/qiview | nanslice/nanslicer.py | Python | mpl-2.0 | 12,382 | [
"NEURON"
] | 38fd312250490c4c5ed168ba2e941a832d49848074fe5f8d447f6180ab395071 |
import itertools
import os
import pprint
import re
from math import isclose
import lmfit
import numpy as np
import pandas as pd
import peakutils as pku
from ImagingReso.resonance import Resonance
import ImagingReso._utilities as reso_util
from cerberus import Validator
import matplotlib.pyplot as plt
x_type_list = ['... | ornlneutronimaging/ResoFit | ResoFit/_utilities.py | Python | bsd-3-clause | 25,822 | [
"Gaussian"
] | 983039911090e1cb53761aa8561e7f2a833d2efd596ca99a0a3b9a068f84bd55 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# https://github.com/shenwei356/bio_scripts
import argparse
import sys
from collections import Counter, defaultdict
import pysam
parser = argparse.ArgumentParser(
description="bam2gff. Extracting the locations of properly mapping paired (single) ends to GFF format.",... | shenwei356/bio_scripts | file_formats/bam2gff.py | Python | mit | 3,401 | [
"pysam"
] | 7ea13683f6c3e095785f8bf660ae255cc38f7cc7f8aa09ffd1ec082520702178 |
#!/usr/bin/env python
# coding: utf-8
"""Test suite for autopep8.
Unit tests go in "UnitTests". System tests go in "SystemTests".
"""
from __future__ import unicode_literals
import os
import re
import sys
if sys.version_info < (2, 7):
import unittest2 as unittest
else:
import unittest
import contextlib
i... | michaelBenin/autopep8 | test/test_autopep8.py | Python | mit | 196,084 | [
"Psi4"
] | a076c001a02bc81f9fb30c3e02242ebbe5f2afd2ec8932b5bb5b410de93520de |
#! python
# encoding: utf-8
# Wellcome Trust Sanger Institute and Imperial College London
# Copyright (C) 2020 Wellcome Trust Sanger Institute and Imperial College London
#
# 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 t... | sanger-pathogens/gubbins | python/scripts/extract_gubbins_clade_statistics.py | Python | gpl-2.0 | 10,002 | [
"Biopython"
] | f3173b70a5f7c18fc4d9c789df6e77d212b6e8a52289250c37f26f969a630ed8 |
#!/usr/bin/env python
# Copyright (C) 2011 by Brian Rowe
# 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, including
# without limitation the rights to use, copy, modify,... | briprowe/RateSongs | banshee.py | Python | gpl-2.0 | 2,047 | [
"Brian"
] | 4eb6af4e07e2d8d80c5e0db2fd2a9607e161a0de1b90047438cb7d0abba6e03e |
# -*- coding: utf-8 -*-
# <Bunch - BDD test tool for Lettuce scenarios>
# Copyright (c) 2012 Grid Dynamics Consulting Services, Inc, All Rights Reserved
# http://www.griddynamics.com
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as ... | griddynamics/bunch | tests/unit/test_dependencies.py | Python | gpl-3.0 | 7,242 | [
"ADF"
] | 752bb51e1ad969cb9c687accff3304bc3a484237236a4997067859bc64fadfde |
# $HeadURL$
"""
DIRAC Wrapper to execute python and system commands with a wrapper, that might
set a timeout.
3 FUNCTIONS are provided:
- shellCall( iTimeOut, cmdSeq, callbackFunction = None, env = None ):
it uses subprocess.Popen class with "shell = True".
If cmdSeq is a string, it specifies the... | vmendez/DIRAC | Core/Utilities/Subprocess.py | Python | gpl-3.0 | 20,895 | [
"DIRAC"
] | 3dc7d32e7ba15378c1a10eb2f882686e2028d032d20f0ce301587c5766f65eb7 |
#!/usr/bin/env python
import os
from bioblend import galaxy
admin_email = os.environ.get('GALAXY_DEFAULT_ADMIN_USER', 'admin@galaxy.org')
admin_pass = os.environ.get('GALAXY_DEFAULT_ADMIN_PASSWORD', 'admin')
url = "http://localhost:8080"
gi = galaxy.GalaxyInstance(url=url, email=admin_email, password=admin_pass)
wf =... | gregvonkuster/docker-galaxy-ChIP-exo | import_workflows.py | Python | mit | 481 | [
"Galaxy"
] | cc12fceb3dc877bdd6891c4d28830e938cfd2d5db221b315fb70e82795a4a5cf |
#!/usr/bin/env python
#
# heatmap.py - Generates heat map images and animations from geographic data
# Copyright 2010 Seth Golub
# http://www.sethoscope.net/heatmap/
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by t... | HoTSStuff/replaylib | replaylib/heatmap.py | Python | apache-2.0 | 44,628 | [
"Gaussian"
] | cb3a3b0e80adc20520c287e60ba4215128850d9b7ced9a53b5923ce6e2ead74d |
import argparse
import os
from os import path
import subprocess
import sys
import socket
import time
import warnings
from math import floor
import gc # garbage collector
import smtplib
import numpy as np
from scipy import signal, linalg
from matplotlib import pyplot as plt
import GPy
import classes as cls
import util... | mdepasca/miniature-adventure | miniature_adventure.py | Python | unlicense | 51,544 | [
"Gaussian"
] | c0bdafe016e1b7acbde4a6db4b89c15246ec8d3f7d4a725c594eccda31668c3c |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | samples/lj-demo.py | Python | gpl-3.0 | 20,993 | [
"ESPResSo",
"Mayavi"
] | d06baa5ae2d1710779c7301da7a931f194cb8871fb4d31cdcced955e5447853a |
from __future__ import absolute_import
import numpy as np
import matplotlib.pyplot as plt
def implot(plt, x, y, Z, ax=None, colorbar=True, **kwargs):
"""
Image plot of general data (like imshow but with non-pixel axes).
Parameters
----------
plt : plot object
Plot object, typically `matp... | ZeitgeberH/nengo | nengo/utils/matplotlib.py | Python | gpl-3.0 | 2,968 | [
"NEURON"
] | 5ec0ee23fde1c05f9d904b6b687a920a0e8c9d07c896efca9c0c81aae90a1f07 |
# DicomAligner.py by Francois Malan - 2011-06-23
# Revised as version 2.0 on 2011-07-07
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
from module_kits.misc_kit import misc_utils
import wx
import os
import vtk
import itk
import math
import numpy
class DICOMAligner(
NoConfigModule... | chrisidefix/devide | modules/filters/DICOMAligner.py | Python | bsd-3-clause | 7,460 | [
"VTK"
] | 2d2577945ed2d4a7e4ecb984b3954ab5085fff4a915fd999f0d222c2197c2a7c |
#!/usr/bin/env python
"""renum_pdb_to_aln.py - renumber a pdb file based on the alignment.
author: A. Zyla under supervision of mmagnus
.. warning:: works only for single chain! and requires Biopython (tested with v1.68)
"""
import logging
import argparse
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
fro... | mmagnus/rna-pdb-tools | rna_tools/tools/renum_pdb_to_aln/renum_pdb_to_aln.py | Python | gpl-3.0 | 3,954 | [
"Biopython"
] | 508bc4f1780db6315fc03c43889f0f978d6688a4360e1ce0d74d84a633e0cfc6 |
#!/usr/bin/env python
import itertools
import os
import logging
import shutil
import subprocess
import sys
import tempfile
import pandas
import requests
from Bio import SeqIO
from cref.app import BaseApp
logger = logging.getLogger('CReF')
class TerminalApp(BaseApp):
"""
App to be run on the terminal
"... | mchelem/cref2 | cref/evaluation/benchmark.py | Python | mit | 6,209 | [
"BLAST",
"PyMOL"
] | bd02752518225d1dfec1b55126fc8edba1159833d05c882c1e8ee61c6f7224b6 |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/ragf2.py | Python | apache-2.0 | 35,794 | [
"PySCF"
] | 6da33d7141098472eb091220d324bcf9cb63d5b225418c496e888af9012ef170 |
import matplotlib
matplotlib.use('Agg')
from msmbuilder.dataset import dataset
from msmbuilder import msm, featurizer, utils, decomposition
import numpy as np
import mdtraj as md
import matplotlib.pyplot as plt
from glob import glob
import os
# Source directory for MEK simulations
source_directory = '/cbio/jclab/pr... | choderalab/MSMs | shanson/mek-10488/msmbuilder-finding4/msmbuilder-finding4-chi1/msmbuilder-finding4-mek.py | Python | gpl-2.0 | 2,180 | [
"MDTraj"
] | 8f7f65e985a5a158eef7f5ad0b5783f8e7a738c0c5c3e0d5f05931ef7186aecd |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
class Synchronizer(object):
"""Class encapsulating a lock
allowing it to be used as a synchronizing
decorator making the call thread-safe"""
def __init__(self, lockName="",... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/ThreadSafe.py | Python | gpl-3.0 | 1,256 | [
"DIRAC"
] | 4f246e7474a34db55118007c787163d8e8d25b63fc3abd1f6f7cedf3f0124f6e |
import numpy as np
import lasagne
import lasagne.layers as L
import lasagne.nonlinearities as NL
import theano
import theano.tensor as TT
from rllab.misc.ext import compile_function
from rllab.core.lasagne_layers import ParamLayer
from rllab.core.lasagne_powered import LasagnePowered
from rllab.core.network import Conv... | brain-research/mirage-rl-qprop | rllab/regressors/gaussian_conv_regressor.py | Python | mit | 11,624 | [
"Gaussian"
] | 376336a9171827d37768123d3aece6df310bd6a1e2d3782c24bdf74767ad7683 |
"""
ETB Parser based on parsimonious.
The grammar is defined in the docstring, essentially EBNF, but
uses ``/`` (first match) instead of ``|``. ``+``, ``*``, ``?`` have usual meaning
regex's start with ``~``.
The grammar.parse function generates parsimonious Nodes, which are
then translated to ETB terms using the vi... | SRI-CSL/ETB | etb/parser.py | Python | gpl-3.0 | 13,054 | [
"VisIt"
] | 3c1bd40c7f867e2bc0b205e466b88789752c3406afe7fd17750bc30c2d874ae9 |
#!/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
##---------------------------------------------------------------------------##
##
## Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
## Copyright (C) 2003 Mt. Hood Playing Card Co.
## Copyright (C) 2005-2009 Skomoroh
##
## This program is free ... | TrevorLowing/PyGames | pysollib/games/klondike.py | Python | gpl-2.0 | 52,598 | [
"CASINO"
] | cbae46a210a1f95301bbffdbf82b2dc287b3d0d9bd00045e5bac2ead1934de08 |
# 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 RBiobase(RPackage):
"""Biobase: Base functions for Bioconductor
Functions that are... | LLNL/spack | var/spack/repos/builtin/packages/r-biobase/package.py | Python | lgpl-2.1 | 1,151 | [
"Bioconductor"
] | ce53428b682555d2bc28c88c3468e9b0efab5c52d7afc1b4105da4013bc968d8 |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://www... | stuart-knock/tvb-library | tvb/simulator/models/oscillator.py | Python | gpl-2.0 | 20,193 | [
"NEURON"
] | 8d9c8e926da7ae08a5c3213e93f0a7c72f24d96f995aaac3e7b3c1071cf692c2 |
""" StaticExpressions gathers constant expression that involve types. """
from pythran.passmanager import NodeAnalysis
class HasStaticExpression(NodeAnalysis):
def __init__(self):
self.result = False
super(HasStaticExpression, self).__init__()
def visit_Attribute(self, node):
self.g... | pombredanne/pythran | pythran/analyses/static_expressions.py | Python | bsd-3-clause | 2,105 | [
"VisIt"
] | bf327b10766f5542b95526370dbfa3998c8175298f6e2223f40a56b15b4962d5 |
#!/usr/bin/env python
"""Pygme: Python Gaussian ModElling - a python implementation of the Multi-Gaussian Expansion Method.
Fit MGE models, and Generate initial conditions for N body simulations
See Monnet et al. 1992 and Emsellem et al. 1994 for more details
"""
## Distribution for the PyMGE packag... | emsellem/pygme | setup.py | Python | bsd-3-clause | 1,232 | [
"Gaussian"
] | 597d065efe3b216afb27c0f70f18ddbbc0cea0aecd49d7bd6e931f031271db02 |
import numpy
import pylab
import moose
import time
'''
This example implements a reaction-diffusion like system which is
bistable and propagates losslessly. It is based on the NEURON example
rxdrun.py, but incorporates more compartments and runs for a longer time.
The system is implemented as a hybrid of a reaction a... | dilawar/moose-full | moose-examples/snippets/rxdReacDiffusion.py | Python | gpl-2.0 | 2,345 | [
"MOOSE",
"NEURON"
] | ccfaff21192fffed053a6e29af2bac9d91ebd686c2722dd52a69aec916764700 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | Framework/PythonInterface/test/python/mantid/api/FunctionFactoryTest.py | Python | gpl-3.0 | 3,273 | [
"Gaussian"
] | 1f283ddb65d86e939fc4c7770d662185cdb2b9a46a0bff327e4c6959ae463c41 |
"""Test operator support in VTK-Python
The following operators are supported:
- The << operator becomes python str() and print()
- The < <= == != > >= operators become richcompare
- The [int] operator become the sequence protocol
The following operators are not yet supported:
- The () operator
- The [] opera... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/Core/Testing/Python/TestOperators.py | Python | bsd-3-clause | 1,492 | [
"VTK"
] | 8b6f37d8a72997e5129c7b72991e117d60f26030218b443151bde6c6f089bacf |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Douglas S. Blank
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
# Copyright (C) 2013 Vassilii Khachaturov
#
# Th... | sam-m888/gramps | gramps/plugins/export/exportcsv.py | Python | gpl-2.0 | 23,769 | [
"Brian"
] | 332c965224b216bf41bdef70b927a4cc66db97594df57b2d1b4ae8bccc906060 |
#! /usr/bin/env python
# Quex is free software; you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 2.1 of the License, or (at your option)
# any later version.
#
# This software is distribute... | dkopecek/amplify | third-party/quex-0.65.2/quex/DEFINITIONS.py | Python | gpl-2.0 | 3,233 | [
"VisIt"
] | c7e53107b4057f1504d0be3d905e8207cbd657ae414acc5fa8bc6889b7644915 |
#!/usr/bin/python
import os, sys
from argparse import ArgumentParser
from pylab import*
current_path = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.abspath(os.path.join(current_path,"../../../tools")))
import sumatra_tracking.io_manager as smt
import analysis.colormaps as cmaps
from analysis.t... | miladh/lgn-simulator | apps/stimuliAnalysis/analysis/patch_stim.py | Python | gpl-3.0 | 2,631 | [
"Gaussian"
] | b031befe302151b4cdc1448e0da3c1617b69b6ec76d4cdd088711fa945fa0ef5 |
#!/usr/bin/env python
"""
Show distribution after a change of variables with y = x^(1/2), where the pdf for x is Gaussian
"""
import matplotlib.pyplot as pl
from scipy.stats import norm
import numpy as np
# normal distribution
mu = 5. # the mean, mu
sigma = 1 # standard deviations, sigma
x = np.linspace(0, 10, 1000... | mattpitkin/GraWIToNStatisticsLectures | figures/scripts/change_of_variables_1d.py | Python | mit | 870 | [
"Gaussian"
] | b11835e5533e08545e9fe25fc1fdb426c57bf488549d58f697a9417f385ba2c5 |
import os
from setuptools import setup
from setuptools import find_packages
version = '0.1'
shortdesc = "Klarna Payment for bda.plone.shop"
setup(
name='bda.plone.klarnapayment',
version=version,
description=shortdesc,
classifiers=[
'Environment :: Web Environment',
'License :: OSI Ap... | espenmn/bda.plone.klarnapayment | setup.py | Python | bsd-3-clause | 1,088 | [
"MOE"
] | 42f0f544f5aafe2f39ebcbae6e0a78b08a1aaa5ff98edac95aaf58a5b4d6f2cf |
#!/usr/bin/env python3
#-*- coding: utf-8 -*-
# Copyright 2017, National University of Ireland and The James Hutton Insitute
# Author: Nicholas Waters
#
# This code is part of the riboSeed package, and is governed by its licence.
# Please see the LICENSE file that should have been included as part of
# this package.
i... | nickp60/riboSeed | riboSeed/riboTry.py | Python | mit | 6,211 | [
"BWA"
] | be5a3c0f2dd56d8e852534a82138791282cd6b62a428949389121bbbfd5e288b |
"""Functions to process .aaf (Alignment Analysis Format) files """
import tempfile
from collections import namedtuple
from multiprocessing import Process, Queue
import pysam
import cytoolz
import cytoolz.curried as cyt
import logging
logger = logging.getLogger(__name__)
AafRead = namedtuple('AAF', ['chrom', 'pos', ... | sbg/Mitty | mitty/analysis/aaftoolz.py | Python | apache-2.0 | 4,292 | [
"pysam"
] | 4d6d4d7e252eff39342c15596bb33ccafe056e2a1863eee3d642eb3b16be9378 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/python/p4util/optproc.py | Python | gpl-2.0 | 4,666 | [
"Psi4"
] | 68e9acd7a7278b9678132a09fa0b485e2102ae9ecaf9511b9ad7ebd2754fc1fe |
#!/usr/bin/env python
'''
The LIF network is based on:
Ostojic, S. (2014).
Two types of asynchronous activity in networks of
excitatory and inhibitory spiking neurons.
Nat Neurosci 17, 594-600.
Key parameter to change is synaptic coupling J (mV).
Tested with Brian 1.4.1
'''
from brian import *
from pylab import *... | adityagilra/from-papers | Ostojic2014_ExcInhNet.py | Python | lgpl-3.0 | 7,101 | [
"Brian",
"Gaussian",
"NEURON"
] | 9e8939f74ffc5e61f5f9e80c8fe2a0c9091ea45d66e482febf751d69ca66bc54 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Stefan Siegel
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Genera... | arunkgupta/gramps | gramps/plugins/rel/rel_de.py | Python | gpl-2.0 | 11,411 | [
"Brian"
] | b5ad36d4c5c59489e4aae9684f43ee97a7666cbba123634874f79412562d16d8 |
##############################################################################
# Minimal working example
# Parameter inference in Gaussian IID model
# using correlated psuedo-marginal Metropolis-Hastings
#
# (c) Johan Dahlin 2016 ( johan.dahlin (at) liu.se )
#############################################################... | compops/pmmh-correlated2015 | scripts-mwe/mwe-gaussian-iid-1parameter.py | Python | gpl-3.0 | 4,164 | [
"Gaussian"
] | c389d2325a433f25bba169d59d2896407d8550092d01b60286bad7ea35e88f91 |
#!/usr/bin/env python
from operator import itemgetter
import numpy
import re
try: import psyco; pysco.full()
except: pass
def dag_array(dagf):
recs = [] #collections.defaultdict(list)
fh = open(dagf, 'r')
qname_len = 0
sname_len = 0
qchr_len = 0
schr_len = 0
for line in fh:
if li... | asherkhb/coge | scripts/synmap/dag_tools.py | Python | bsd-2-clause | 5,069 | [
"BLAST"
] | 14744f65f4b2a45ae26db9b381f94e661973a074a9dfccdc6c1bdffd5735509d |
"""
.. currentmodule:: pylayers.antprop.coverage
.. autosummary::
:members:
"""
from pylayers.util.project import *
#from pylayers.measures.mesuwb import *
from pylayers.simul.radionode import *
import pylayers.util.pyutil as pyu
from pylayers.util.utilnet import str2bool
from pylayers.gis.layout import Layout
imp... | dialounke/pylayers | pylayers/antprop/coverage.py | Python | mit | 35,555 | [
"Mayavi"
] | 366d359db4d3b2d5c0105f9679703d674e9ef5b69eec329c1dc8724c796cb13d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Douglas S. Blank
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | SNoiraud/gramps | gramps/plugins/quickview/samesurnames.py | Python | gpl-2.0 | 7,150 | [
"Brian"
] | f7113b450d85cfbf9f55f752bfe6513c35ee7c497bc490d8c23b346ab14ca746 |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
#import slicer.modules.ChestImagingPlatform
#
# LungRegistration
#
class LungRegistration:
def __init__(self, parent):
parent.title = "LungRegistration" # TODO make this more human readable by adding spaces
parent.categories = ["Chest Imagin... | acil-bwh/SlicerCIP | Scripted/attic/LungRegistration/LungRegistration.py | Python | bsd-3-clause | 18,130 | [
"VTK"
] | 4b40259fab9fca21918534b4c719ede5e4de1fc84646de39d1f954fbbd232fb7 |
#!/usr/bin/python
# rmbh11
# v0.72
# corects and builds on release version - v0.5
######################################
# USAGE: prepFragsLAMW.py database-prefix file.fasta > logfile
# Originally written by Ryan Hoffmann from Wolynes group
# Modified by Shubham Tripathi 10/21/2016
#################################... | luwei0917/awsemmd_script | MultCha_prepFrags_index_HO.py | Python | mit | 18,545 | [
"BLAST"
] | 5ff35b45880c9eda90101dbad8f2382eb44029358b209e967a01243f008048d5 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay 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 t... | gyang/nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 69,034 | [
"FEFF"
] | 4497194566e089a254e569fe6b9f1dd2eb2841c2546c46fb929b0757fda9de75 |
import numpy
import sys
from mayavi import mlab
import time
import pylab
from numba import jit
@jit
def absolute_speed(vx,vy,vz,multiplier=100, kb=1.38065):
return numpy.sqrt(((vx*vx) + (vy*vy) + (vz*vz)))*multiplier;
@jit
def absolute_temp(vx,vy,vz,m,multiplier=100, kb=1.38065):
return multiplier*m*((vx*vx) + (... | detorto/mdvis | src/mmdlab/utils.py | Python | mit | 2,042 | [
"Mayavi"
] | 55da2b89446e22bd8e1711eb20d5c52a297d21a62ccffcf96c3efbba375a6fd6 |
#!/usr/bin/env python
'''
CREATED:2013-02-12 16:33:40 by Brian McFee <brm2132@columbia.edu>
Beat tracking with HPSS filtering
Usage: ./hpss_beats.py [-h] input_audio.mp3 output_beats.csv
'''
from __future__ import print_function
import argparse
import numpy as np
import sys
import librosa
# Some magic number defaul... | Cortexelus/librosa | examples/hpss_beats.py | Python | isc | 2,556 | [
"Brian"
] | 487760e0ce3ad400633ff419089ed28bbe57d6aa099bbe8abe21da20b60772ad |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import urllib.parse
import http.client as httplib
import ftplib
from zeroinstall import SafeException
def get_http_size(url, ttl = 3, method = None):
address = urllib.parse.urlparse(url)
if url.lower().startswi... | 0install/0repo | repo/urltest.py | Python | lgpl-2.1 | 2,418 | [
"VisIt"
] | 0c58df7cbf5f3da24d7d31a1a5a7a507787216f514f1236bb8d2300949689eb5 |
# coding=utf-8
# Copyright 2022 The TensorFlow Datasets 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 appl... | tensorflow/datasets | tensorflow_datasets/graphs/ogbg_molpcba/ogbg_molpcba.py | Python | apache-2.0 | 9,433 | [
"RDKit"
] | d5d3bcc9c4c0554b0bef291db17d17871368914158f0f2ec0ee0967fb0cfc376 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright (c) 2019 Jeremie DECOCK (http://www.jdhp.org)
# 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, including witho... | jeremiedecock/pyai | ailib/tsa/data/toymodels.py | Python | mit | 3,601 | [
"Gaussian"
] | 4d2ed6f8dce815fbc04c7447784c6acc53c71d3390872873f9fffda36debdf46 |
import scrapelib
import datetime
import os
import re
from collections import defaultdict
from functools import wraps
from openstates.scrape import Scraper, Bill, VoteEvent
from openstates.utils import convert_pdf
import lxml.html
import urllib
# Workaround to prevent chunking error (thanks @showerst)
#
# @see https:... | sunlightlabs/openstates | scrapers/sc/bills.py | Python | gpl-3.0 | 18,396 | [
"VisIt"
] | 2b9e988ad37686b3f0a65c5b61bd6000429225d4708090080cc3fa7fe2985cdf |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_lbf.py | Python | gpl-3.0 | 1,525 | [
"ESPResSo"
] | 5cebe56bcd870cb868567e0121765f1eb64373f2a109073dd1ddf12747cbba5d |
# $Id$
#
# Copyright (c) 2009, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above... | adalke/rdkit | rdkit/Chem/BRICS.py | Python | bsd-3-clause | 30,959 | [
"RDKit"
] | 85b0c5f8516faba796f86dee871a33ef4b9f0fdfa305e3f3584d0b1e7c3ea042 |
"""
Graphical model (GM)-based optimization algorithm using Theano
"""
__authors__ = "James Bergstra"
__license__ = "3-clause BSD License"
__contact__ = "github.com/jaberg/hyperopt"
import logging
import time
import numpy as np
from scipy.special import erf
import pyll
from pyll import scope
from pyll.stochastic imp... | CVML/hyperopt | hyperopt/tpe.py | Python | bsd-3-clause | 30,055 | [
"Gaussian"
] | 2741c446bb87c12fc664b3c01455bf1cd4533012602cdc5743a6415dffa0d53f |
from __future__ import print_function
import os
import pprint
import re
try:
from urllib import urlretrieve
except ImportError:
pass
try:
from urllib.request import urlretrieve
except ImportError:
pass
import zipfile
import shutil
import datetime
import numpy as np
from ase.units import Bohr
from ase... | suttond/MODOI | ase/data/gmtkn30.py | Python | lgpl-3.0 | 12,170 | [
"ASE"
] | a10ab5f785f29ef4416a42d1e6a11e54a7df5d166944378bedd11bd95b6cf14b |
## Copyright (C) 2010- Alexey Petrov
## Copyright (C) 2009-2010 Pebble Bed Modular Reactor (Pty) Limited (PBMR)
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the Lic... | asimurzin/hybridFlu | hybridFlu/vtkPlotter.py | Python | gpl-3.0 | 4,107 | [
"VTK"
] | 7e6a453ceaba2501d38190b73606d6f10402fa3a6caae830d176250554215bce |
# Copyright 1999 by Jeffrey Chang. 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.
# Patched by Brad Chapman.
# Chris Wroe added modifications for work in myGrid
"""
This modul... | bryback/quickseq | genescript/Bio/Blast/NCBIWWW.py | Python | mit | 10,089 | [
"BLAST",
"Biopython"
] | 04f52da34b717d2de21fc187555d89f548a552f82a0dc5e6e96ec21bac48559a |
"""Most things relating to article definitions reside here"""
import os
import re
import yawt.default_templates
from yawt.article import make_article
from yawt.utils import call_plugins, call_plugins_arg, save_file, \
joinfile, ensure_path, base_and_ext, ReprMixin
class YawtSiteManager(object):
"""The defaul... | drivet/yawt | yawt/site_manager.py | Python | mit | 6,502 | [
"VisIt"
] | 23e71d0d57e2adf52911bf213a280857f106ef108bf36ca885e4466bc8309b32 |
import argparse
from itertools import count
import numpy as np
import h5py
from traits.api import HasTraits, Range, Instance, Bool, Int, on_trait_change
from traitsui.api import View, Item, HGroup, RangeEditor
from tvtk.api import tvtk
from tvtk.pyface.scene_editor import SceneEditor
from tvtk.common import configure_i... | tneumann/splocs | view_splocs.py | Python | mit | 3,302 | [
"Mayavi"
] | aa40883ea90a18e59b1ef4618492dd7208f9770f0f5668ff12f8f6fb31b22ef3 |
#!/usr/bin/env python
""" Archive a transformation
"""
from __future__ import print_function
import sys
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
if len( sys.argv ) < 2:
print('Usage: dirac-transformation-archive transID [transID] [transID]')
sys.exit()
else:
transIDs = [int( arg )... | fstagni/DIRAC | TransformationSystem/scripts/dirac-transformation-archive.py | Python | gpl-3.0 | 905 | [
"DIRAC"
] | 5344dfcff9c446d9f8da5c639448553ac7fd923bcb77f58c4deef5163c46fa8e |
#!/usr/bin/python
###########################################################################################
# Filename:
# Device.py
###########################################################################################
# Project Authors:
# Juhapekka Piiroinen
# Brian Wu
#
# Changes:
# June 14, 20... | antonvino/inmoov-basic | hexapod_scripts_base/maestro_test_limits.py | Python | mit | 14,902 | [
"Brian"
] | a3544d697635f9dec6f5b874aa0eb27813987a007b40fb6c5fdd00614d957ba5 |
#!/usr/bin/env python
# Mesa 3-D graphics library
# Version: 4.1
#
# Copyright (C) 1999-2001 Brian Paul All Rights Reserved.
#
# 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 ... | CPFDSoftware-Tony/gmv | utils/Mesa/Mesa-7.8.2/src/mesa/glapi/gen/mesadef.py | Python | gpl-3.0 | 7,099 | [
"Brian"
] | 9c5cf024656a583741d04f7eff7583e3810c7a4e6ddc4cc0019f2128c257ecac |
# Lint as: python3
# Copyright 2020 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 ... | tensorflow/lingvo | lingvo/core/batch_major_attention_test.py | Python | apache-2.0 | 195,451 | [
"Gaussian"
] | 81708869351170c260a5452665a8c3df31a270b6923c681401a8f746f6cc3b46 |
#!/usr/bin/env python
"""A build script which (thus far) works on Ubuntu 14."""
# TODO(powdercloud): Make a gulp file or similar for this. For now
# it's simply split off from the main build.py in the parent
# directory, but this is not an idiomatic use to build a Javascript or
# Polymer project, and unlike for the pa... | honeybadgerdontcare/amphtml | validator/js/webui/build.py | Python | apache-2.0 | 4,986 | [
"GULP"
] | dda4b815f7eeb060b00ccd54e7d3a17b84904816a0262d0f1a4c3cabc2b07187 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tombstone/models | research/object_detection/core/preprocessor.py | Python | apache-2.0 | 192,656 | [
"Gaussian"
] | 72ee6610f299158ec79c72d3dde8ebb5a1062ce9523f0b999d178f2608be5b08 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_poolgroupdeploymentpolicy.py | Python | bsd-3-clause | 5,648 | [
"VisIt"
] | d8ebf4582e7edfd107b7ac6db62606b331bb4664b05811d48fe63188cd9a4bb4 |
#!/usr/local/bin/env python
"""
Test various utility functions.
"""
#=============================================================================================
# GLOBAL IMPORTS
#=============================================================================================
import textwrap
import openmoltools as o... | andrrizzi/yank | Yank/tests/test_utils.py | Python | mit | 15,068 | [
"MDTraj"
] | bbe7aafc214e37a2aee04b879e6a90de76c3d31e6fd15f008b66d55ca70b2f6b |
# external modules
import numpy as num
# ANUGA modules
import anuga.utilities.log as log
from anuga.config import netcdf_mode_r, netcdf_mode_w, netcdf_mode_a, \
netcdf_float
from generic_asc2dem import generic_asc2dem
def generic_dem2pts(name_in, name_out=None... | mperignon/anuga-sedtransport | file_conversion/generic_dem2pts.py | Python | gpl-2.0 | 6,790 | [
"NetCDF"
] | 29ea80cec1253c0cb34ea5b8629bcd0bf8cf1be195177ec09b41dba89a664eea |
#* 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
import os
i... | nuclear-wizard/moose | python/mooseutils/MooseDataFrame.py | Python | lgpl-2.1 | 3,786 | [
"MOOSE"
] | 22c5942f8d013018182989b67d0bf4c01f910ba1a76b73728b44ee92f158dab0 |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed ... | Kleptobismol/scikit-bio | skbio/sequence/_exception.py | Python | bsd-3-clause | 932 | [
"scikit-bio"
] | 1aef83b4796288b4b4cb54c6ee3c13f2af17166ef581fd8ce48903be8a343bc9 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.LearningObjects.PostgresqlMonitor | setup.py | Python | gpl-2.0 | 3,322 | [
"VisIt"
] | 5ac0853f6145493f5a6b0de88797ba1d6999d192680730237d526ff1a329b9f4 |
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
#
""" ID3 Decision Trees
contains an implementation of the ID3 decision tree algorithm
as described in Tom Mitchell's book "Machine Learning"
It relies upon the _Tree.TreeNode_ data structure (or something
with the same API) defined local... | rdkit/rdkit-orig | rdkit/ML/DecTree/ID3.py | Python | bsd-3-clause | 6,741 | [
"RDKit"
] | bffcbad8efedb142865ebed9ff79036e64dbfd30c1bb8fadba0719f0f66261eb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Basis Pursuit DeNoising with Joint Sparsity
===========================================
This example demonstra... | bwohlberg/sporco | examples/scripts/sc/bpdnjnt_opt.py | Python | bsd-3-clause | 4,338 | [
"Gaussian"
] | a1043d796d1b665fa67f81ea9ea384d8f9c852cf191537e9c740fad163d8907b |
"""
parser.http.movieParser module (imdb package).
This module provides the classes (and the instances), used to parse the
IMDb pages on the akas.imdb.com server about a movie.
E.g., for Brian De Palma's "The Untouchables", the referred
pages would be:
combined details: http://akas.imdb.com/title/tt0094226/combi... | MosheBerman/brisket-mashup | source/libraries/IMDbPY-4.9/imdb/parser/http/movieParser.py | Python | mit | 78,655 | [
"Brian"
] | a84860574cfeb8f37e5c274b6c60fb1a7c40706d76b4de782c6a977510023b5e |
#/* FILE INFORMATION
#** Based mostly on the traub91proto.g by Dave Beeman
#** Main difference is addition of Glu and NMDA channels
#** The 1991 Traub set of voltage and concentration dependent channels
#** Implemented as tabchannels by : Dave Beeman
#** R.D.Traub, R. K. S. Wong, R. Miles, and H. Michelson
#** ... | BhallaLab/moose-examples | tutorials/Rdesigneur/chans/proto22.py | Python | gpl-2.0 | 23,141 | [
"MOOSE"
] | 84cf1562771542e6fe95c0b877c2e2ccecf05ca92d4c53e78bbde6b0b440b766 |
"""Parsers related to tinker file formats from Molden.
"""
import re
from .. import Molecule, Atom
class TinkerXyzDataParser(object):
def __init__(self, filename):
self.filename = filename
def get_avail_properties(self):
return ["geometry"]
def get_property(self, prop):
... | chemlab/chemlab | chemlab/io/handlers/tinker.py | Python | gpl-3.0 | 2,950 | [
"TINKER"
] | 680d4ad816762ffdab3291db10f27ec9344f8dfd65fade9aa3bd33ba01739fa5 |
import utilities
from ..automation import CommandSequence
from ..automation import TaskManager
from openwpmtest import OpenWPMTest
expected_lso_content_a = [
1, # visit id
u'localtest.me',
u'FlashCookie.sol',
u'localtest.me/FlashCookie.sol',
u'... | natasasdj/OpenWPM | test/test_storage_vectors.py | Python | gpl-3.0 | 5,128 | [
"VisIt"
] | cb1f7ee7e20d36a61a5293c7b5d4eba4ec21aa91691be842e90b808dadb9dd99 |
#!/usr/bin/env python3
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | espressopp/espressopp | testsuite/verlet_list_buffer/verlet_list_buffer.py | Python | gpl-3.0 | 3,568 | [
"ESPResSo"
] | 9bec2550f5ac7e87e3bd142ae3de76f983f8a51f5c6d6d7ad3be11a4fca9c4af |
"""
Test helper functions.
"""
import os
import requests
from regression.pages.studio.utils import get_course_key
from regression.pages.studio import BASE_URL
from regression.pages import (
BASIC_AUTH_USERNAME, BASIC_AUTH_PASSWORD, LOGIN_EMAIL, LOGIN_PASSWORD
)
from regression.pages.lms import LMS_BASE_URL
from re... | raeeschachar/edx-e2e-mirror | regression/tests/helpers.py | Python | agpl-3.0 | 5,864 | [
"VisIt"
] | 8018ba289d7ca3012affbbf8a82f03693aeebfd042edf59ea48a97cfa3c105b8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import sys
import platform
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext as _build_ext
class build_ext(_build_ext):
def finalize_options(self):... | matk86/pymatgen | setup.py | Python | mit | 8,781 | [
"ABINIT",
"ASE",
"FEFF",
"Gaussian",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | cd2aa4e0433afd9a6a6bac60787475e8d7a32a0fcc43b29b3d27c17f0be6a14a |
import ptt_board_url as ptt
import pandas as pd
import sys
# import psycopg2 as pg
import time
start_time = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
hoturl = 'https://www.ptt.cc/bbs/hotboards.html'
hot_board = ptt.get_js_page(hoturl)
df = ptt.get_hotboard_df(hot_board)
end_time = time.strftime("%Y-%m-%d ... | AmberFu/ptt_crawler | ptt_hotboard_crawler.py | Python | mit | 2,638 | [
"Amber"
] | d543b537e4ed5763c612b5d5e9d00b79c89fec17d34d3344fdca46ed2f969198 |
#!/usr/bin/env python
"""
This file tests vtk.vtkMolecule, and verifies that atoms/bonds are added.
"""
import sys
import vtk
from vtk.test import Testing
class TestMolecule(Testing.vtkTest):
def testCreation(self):
"Testing if molecules can be created/modified."
mol = vtk.vtkMolecule()
... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Common/DataModel/Testing/Python/TestMolecule.py | Python | gpl-3.0 | 839 | [
"VTK"
] | 2b7b20631a37e4169455b5218a64e57cb873ea76a31548c377725342f7b057b4 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | pvagner/orca | src/orca/scripts/apps/soffice/formatting.py | Python | lgpl-2.1 | 3,726 | [
"ORCA"
] | 0cffe2c793785d44a74c20a234330772175af8b6cc09226fd4e9d0919e21ba00 |
"""
Migration script to add the includes_datatypes, has_repository_dependencies, includes_tools, includes_tool_dependencies and includes_workflows
columns to the repository_metadata table.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
# Need our custom... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py | Python | gpl-3.0 | 5,505 | [
"Galaxy"
] | ecf4ec72302c95dfa98fc784524519b75487c4c49ad107969b5c82fb9f245865 |
import math
from chainer.functions.activation import softplus
from chainer.functions.math import exponential
from chainer.functions.math import sum
from chainer import variable
def gaussian_kl_divergence(mean, ln_var):
"""Computes the KL-divergence of Gaussian variables from the standard one.
Given two vari... | cemoody/chainer | chainer/functions/loss/vae.py | Python | mit | 3,838 | [
"Gaussian"
] | 288aaa87273bfc6a45834ead935c74ef6ce08189aa8f5bba6b77f5e72139ff4a |
"""
@name: /home/briank/workspace/PyHouse/Project/src/Modules/House/Lighting/_test/test_outlets.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Dec 7, 2019
@summary:
Passed all 8 tests - DBK - 2019-12-08... | DBrianKimmel/PyHouse | Project/src/Modules/House/Lighting/Outlets/_test/test_outlets.py | Python | mit | 5,980 | [
"Brian"
] | e67c245f8ca16b5c68b06801d4e63a19def041980b89fbe100e3bc54ac0fb70e |
#!/usr/bin/env python
from __future__ import print_function
import wx
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
from matplotlib.backends.backend_wx import NavigationToolbar2Wx
from matplotlib.figure import Figure
try: # Necessary for wx2.8.11.0
from wx.lib.pubsub import setu... | hschovanec-usgs/magpy | magpy/gui/magpy_gui.py | Python | gpl-3.0 | 186,304 | [
"Gaussian"
] | bc2af2b4698b422bb86212446b9793507cf4b407f7b71353e8dcc00d6a5ee688 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_ipamdnsproviderprofile.py | Python | gpl-3.0 | 6,384 | [
"VisIt"
] | 447380d936c535bba5670eb2e5706827e5222eaf392a87618dd1ddf2f233826c |
# -*- coding: utf-8 -*-
# Spearmint
#
# Academic and Non-Commercial Research Use Software License and Terms
# of Use
#
# Spearmint is a software package to perform Bayesian optimization
# according to specific algorithms (the “Software”). The Software is
# designed to automatically run experiments (thus the code name
... | DavidMcDonald1993/ghsom | spearmint/spearmint/sampling/slice_sampler.py | Python | gpl-2.0 | 13,950 | [
"Gaussian"
] | 3ae698a502c3a5611b69d32aef920553c727b8b45c757545d2701f9e7af65934 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | mkuron/espresso | testsuite/scripts/tutorials/test_11-ferrofluid_2.py | Python | gpl-3.0 | 1,473 | [
"ESPResSo"
] | 22a1e1814d5b58be2a920c3e21b46e07a808596e941ca0f39e266c512406ee91 |
#!/usr/bin/env python
import os, sys, io
import m6plot
import m6toolbox
import netCDF4
import numpy
def run():
try: import argparse
except: raise Exception('This version of python is not new enough. python 2.7 or newer is required.')
parser = argparse.ArgumentParser(description='''Script for plotting annual-ave... | nicjhan/MOM6-examples | tools/analysis/SST_bias_WOA05.py | Python | gpl-3.0 | 4,755 | [
"NetCDF"
] | 3f348705c4a9346ce54900911f34a0b8ea8ca9ec4106f5c1304468f1833c4285 |
# a tentative script to upload all existing drstree "versions" into CMIP sqlite database
# each variable, mip, experiment, model, ensemble combination add a new instance in "instance"
# for each instance there should be at least one version in "version" table
# for each version add at least one file in table "files"
... | coecms/ARCCSSive | database_updates/update_db.py | Python | apache-2.0 | 4,854 | [
"NetCDF"
] | a65f34278ec49cca1262cb92f3244e30ad68b709051626c349543c0639dd005f |
# -*- coding: utf-8 -*-
'''
lucterios.contacts package
@author: Laurent GAY
@organization: sd-libre.fr
@contact: info@sd-libre.fr
@copyright: 2015 sd-libre.fr
@license: This file is part of Lucterios.
Lucterios is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public Licens... | Diacamma2/asso | diacamma/member/tests_adherent.py | Python | gpl-3.0 | 254,243 | [
"Dalton"
] | 1a68b29d0584f350e247ff339f72efa1ab2e8fc7e1a5a5806f28834a9e5536e6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#====================================================
# FILE: img2sdat.py
# AUTHORS: xpirt - luxi78 - howellzhu
# DATE: 2016-12-23 16:47:24 CST
#====================================================
import sys, os, errno, tempfile
import common, bloc... | Nevax07/FreedomOS | build/tools/img2sdat/img2sdat.py | Python | apache-2.0 | 2,383 | [
"VisIt"
] | b17e3d93946d833ad28cb1b731acbf5d42967f6122a78b382ef1d7fd7d7284fd |
# -*- coding: utf-8 -*-
import sys
import math
import time
import wx
import shutil
import wx.lib.scrolledpanel
import platform
import webbrowser
from tools import *
class GFIntermediate:
"""Class defining the intermediates in a GeoFold DAG"""
def __init__(self,number=0, center=(0,0), radius=0.,dagfile=''):
... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/dagview.py | Python | gpl-2.0 | 36,575 | [
"PyMOL"
] | 5add170d030ef60ee976658b9435b6ff79fa66baa5f729d235d5daaaf6c7a09a |
# standard modules
import copy
import datetime
import logging
import os
import sys
import traceback
# 3rd party modules
# PFP modules
from scripts import pfp_clim
from scripts import pfp_compliance
from scripts import pfp_cpd_barr
from scripts import pfp_cpd_mchugh
from scripts import pfp_cpd_mcnew
from scripts import ... | OzFlux/PyFluxPro | scripts/pfp_batch.py | Python | gpl-3.0 | 25,051 | [
"NetCDF"
] | 9496b467f4a8aa0a6bf72536d4f4d91d274fe43cc37279446f1f235fbb0e75cd |
# $HeadURL$
__RCSID__ = "$Id$"
import GSI
requiredGSIVersion = "0.3.9"
if GSI.version.__version__ < requiredGSIVersion:
raise Exception( "pyGSI is not the latest version (installed %s required %s)" % ( GSI.version.__version__, requiredGSIVersion ) )
GSI.SSL.set_thread_safe()
nid = GSI.crypto.create_oid( "1.2.42.4... | myco/VMDIRAC | Security/__init__.py | Python | gpl-3.0 | 680 | [
"DIRAC"
] | 98e95cdfe41b82eb3f2081240f4051b2f2ced20e59f42dcf07cdf858f57f0723 |
""" Test_RSS_Policy_AlwaysActivePolicy
"""
import unittest
import DIRAC.ResourceStatusSystem.Policy.CEAvailabilityPolicy as moduleTested
################################################################################
class CEAvailabilityPolicy_TestCase(unittest.TestCase):
def setUp(self):
"""
... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/test/Test_RSS_Policy_CEAvailabilityPolicy.py | Python | gpl-3.0 | 2,480 | [
"DIRAC"
] | 6cfe9a8d531f968d6af34f8abedd53b72b4797ae1eba2f784b545336e63cfb46 |
#!/usr/bin/env python2
###############################################################################
# ------------------------- Description ---------------------------------------
###############################################################################
# The purpose of this script is read the hdf5 GFED4s dat... | stevenjoelbrey/PMFutures | Python/GFED4s_to_nc.py | Python | mit | 16,988 | [
"NetCDF"
] | e8e5f7da2ae1526aeb6a495b2d890cda5c5c360b66aced80e8418cab84f94162 |
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