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#############################################################################
## Pipeline is now on github: https://github.com/pminguez/geneticaPipeline ##
#############################################################################
import sys
from glob import glob
from subprocess import call
import argparse
import ... | pminguez/geneticaPipeline | pipeline_v5.py | Python | gpl-3.0 | 19,771 | [
"BWA"
] | 9249829fbc9cc87dff283002f64b4e44dc4a1ec5019c047de998f6cc1bae98cf |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | Forage/Gramps | gramps/gui/plug/_windows.py | Python | gpl-2.0 | 43,144 | [
"Brian"
] | dc1b4dd77bf262eaa6ec9f5e941896a6e47bc72d03beecc0c8250071c5483a3a |
#!/usr/bin/python
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 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 vers... | tuffy/python-audio-tools | test/test_streams.py | Python | gpl-2.0 | 18,602 | [
"Brian"
] | 9d6b1c593643ff28a5a909b30eeecb33aae638739e6475ebe20bab31f650aa5e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | t0mk/ansible | lib/ansible/modules/network/lenovo/cnos_conditional_command.py | Python | gpl-3.0 | 7,146 | [
"VisIt"
] | f18eb6146b05bc321a156b4c968f6838f2e065cc4c79c41208f0811a0f8d63bd |
#!/usr/bin/python
#
# (C) 2013, Markus Wildi
#
#
#
# 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, or (at your option)
# any later version.
#
# This program is dis... | xyficu/rts2 | scripts/rts2saf/rts2saf/config.py | Python | gpl-2.0 | 21,088 | [
"VisIt"
] | 407a09501934f4ee7d333666b21ec4124b810c5c1edb73412890f79f71195f65 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/yambo/package.py | Python | lgpl-2.1 | 6,314 | [
"ABINIT",
"NetCDF",
"Yambo"
] | 76e6cd9ae59a398c8701e9eda3122d65046aa02e86fc81fefd3e20b845f8b562 |
"""
Acceptance tests for Studio related to course reruns.
"""
from __future__ import absolute_import
import random
from bok_choy.promise import EmptyPromise
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.lms.courseware import CoursewarePage
from common.test.ac... | ESOedX/edx-platform | common/test/acceptance/tests/studio/test_studio_rerun.py | Python | agpl-3.0 | 4,426 | [
"VisIt"
] | fca6853708063376d47b1af6cd02fe23a58acf12dc4a8c9d215fe199ba5d475e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy o... | jwallen/ChemPy | chempy/ext/thermo_converter.py | Python | mit | 56,584 | [
"ChemPy"
] | 892369da6611fc3d05ad2715d73a71386557a9e0c9a4a8f34e95ef3dc64c0582 |
# Copyright 2008-2010 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SeqIO support for the "tab" (simple tab separated) file format.
You are expected to ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/SeqIO/TabIO.py | Python | gpl-2.0 | 4,058 | [
"Biopython"
] | 88f92c62e6bc5a3a7f6332742c7fc3b890eb087ee57c16541d23fe0e55a3d3b8 |
# test_ksolve.py ---
# Originally written by Upinder S. Bhalla. It has been
# modified by Dilawar Singh Wed Aug 5 19:21:19 2015 to turn it into a
# test script. NOT TO BE USED for scientific demos or tutorials. The sole
# purpose of this script is to benchmark the Ksolve solver with various methods.
import sys
imp... | BhallaLab/moose | moose-examples/kinetics/test_ksolve.py | Python | gpl-3.0 | 20,058 | [
"MOOSE"
] | f173693c60df6083fdc7e154f5b7621b3957f3f9456571a52448c38458fc1b8c |
#!/usr/bin/python
# (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# most of it copied from AWX's scan_packages module
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': ... | amenonsen/ansible | lib/ansible/modules/packaging/os/package_facts.py | Python | gpl-3.0 | 11,588 | [
"Brian"
] | 28d6f429eb1ec7d853c27258552f25eda1ff3735d2820848680fcfbd858f015e |
from scipy.signal import gaussian
from scipy.signal import tukey
from scipy.signal import hann
import numpy as np
class vz:
def __init__(self, channel, length, phi):
self.phi = phi
def is_vz(self):
return True
class vf:
def __init__(self, channel, length, freq):
self.freq = freq
... | ooovector/qtlab_replacement | pulses.py | Python | gpl-3.0 | 10,208 | [
"Gaussian"
] | c0820abc2efa9e00ec777e8d7e6371f6fcb49a3433d81e1c0c7e54214b11b485 |
#===============================================================================
#
# IO.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2013-2016 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you can redistribu... | ANNarchy/ANNarchy | ANNarchy/core/IO.py | Python | gpl-2.0 | 19,379 | [
"NEURON"
] | b360ea099a19210ebe9372e1711fa41922814ec39ddf7f37008cba9ec8c6d438 |
#! /usr/bin/env python
#All Functions
import cv2
import numpy as np
import matplotlib.pyplot as plt
import math
#Select the Image Filename
#FILENAME = 'chessboard.png'
#FILENAME = 'chessboard.jpg'
#FILENAME = 'chessboard_skew.jpg'
#FILENAME = 'checkerboard2.png'
#FILENAME ='image.jpg'
#FILENAME = "lena1.png"
class ... | CospanDesign/python | image_processor/image_processor.py | Python | mit | 9,649 | [
"Gaussian"
] | ba62169f99c489e0e7c7fd6495da78606635087f5c511e1940c7e71cb511ac3f |
"""
defines the ZoomStyle class
"""
import vtk
#left_button_down=self._zoom_picker,
#left_button_up=self._zoom_picker,
#right_button_down=self._zoom_reset,
class ZoomStyle(vtk.vtkInteractorStyleRubberBandZoom):
"""Custom Rubber Band Zoom"""
def __init__(self, parent=None):
"""creates the ZoomStyle ins... | saullocastro/pyNastran | pyNastran/gui/styles/zoom_style.py | Python | lgpl-3.0 | 3,355 | [
"VTK"
] | 9514d75227f826e0b4d917a6d58f130d09916853b7d264a43664fb65cbd4350a |
#!/usr/bin/env python3
try:
from netCDF4 import Dataset
except:
print("netCDF4 is not installed!")
sys.exit(1)
import numpy as np
import pylab as plt
from optparse import OptionParser
parser = OptionParser()
parser.usage = "usage: %prog [options] FILE"
parser.description = "A script to compare PISM flow... | pism/pism | examples/storglaciaren/plot_flowline_results.py | Python | gpl-3.0 | 3,571 | [
"NetCDF"
] | 4f71875098f9ebd8922180e2898218812697cd101c4c92faa7787f6b92f9aa75 |
# Django Imports
from django import template
from django.utils.safestring import mark_safe
'''
Name and description for trade resources.
'''
register = template.Library()
def resourcemine(resource):
if resource == 1:
name = 'Salmonite Factory'
description = 'Abbasid Salmonite is a vat-grown synth... | heidi666/WorldsAtWar | wawmembers/templatetags/resourcemine.py | Python | mit | 2,702 | [
"CRYSTAL",
"Galaxy"
] | 9b3c158f8da902570e97e6f2b51f0bf82d75e356f3bd84e0b0cea4a67a2358b6 |
# rfc1751.py : Converts between 128-bit strings and a human-readable
# sequence of words, as defined in RFC1751: "A Convention for
# Human-Readable 128-bit Keys", by Daniel L. McDonald.
#
# Part of the Python Cryptography Toolkit
#
# Written by Andrew M. Kuchling and others
#
# =========================================... | nparley/mylatitude | lib/Crypto/Util/RFC1751.py | Python | mit | 21,208 | [
"Elk",
"MOE"
] | a66f628a5027a2194d395170a30c5709b916294485b6271bcf1425cdd0460ef9 |
#!/usr/bin/env python
'''
Master load script that is driven by a dictionary of campaigns and the
commands that load them. This dictionary also drives the campaigns
served by a deployment of stoqs via the stoqs/campaigns.py file.
Mike McCann
MBARI 5 September 2015
'''
import os
import sys
app_dir = os.path.abspath(o... | danellecline/stoqs | stoqs/loaders/load.py | Python | gpl-3.0 | 33,203 | [
"NetCDF",
"VisIt"
] | 06362d5a4a03ad06ae295a248a0fdd0d60be0a1e1c9469d53a6b877d96827a7a |
#!/usr/bin/env python3
import sys
import subprocess as sb
import numpy as np
import argparse
from utilities import filesFromList, writeLog
from plotTools import userLabels, extractFromCSV, addToPlot
import matplotlib.pyplot as plt
'''
Description:
Author: Mikko Auvinen
mikko.auvinen@helsinki.fi
Univ... | mjsauvinen/P4UL | pyAnalyze/approachAnalysis.py | Python | mit | 8,460 | [
"ParaView"
] | 15bfcb17829ba3b07320cb77f5553c2dd10611567021b4ac19569f19551926c8 |
#!/usr/bin/env python
from setuptools import setup, find_packages
setup(name='django-less-styleguide',
version='0.0.1',
url='https://github.com/a-musing-moose/django-less-styleguide',
author="Jonathan Moss",
author_email="jonathan.moss@tangentone.com.au",
description="A Style Guide Genera... | a-musing-moose/django-less-styleguide | setup.py | Python | bsd-3-clause | 924 | [
"MOOSE"
] | 26ae686d26fec89ac887ee61f1bc9f9cdc16d17d45bcae69ffd23381c43eea0d |
#* 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 mooseu... | harterj/moose | python/peacock/utils/qtutils.py | Python | lgpl-2.1 | 1,073 | [
"MOOSE"
] | 64723a672de1ec6a5a55e0ee8e3c0b8259774c7ab1b1b0652469732793ead795 |
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import nipype.interfaces.fsl as fsl
import nipype.interfaces.c3 as c3
def create_nonlinear_register(name='nonlinear_register'):
"""
Performs non-linear registration of an input image to a template using FSL (FLIRT/FNIRT).
Parame... | danlurie/C-PAC | CPAC/registration/registration.py | Python | bsd-3-clause | 41,865 | [
"Gaussian"
] | 65473d04482c56b855d1ea28aef5e0b7e1f86767e8abd2b3b8929a2d8256370b |
"""
==================================================
Image Processing and Analysis (:mod:`mango.image`)
==================================================
.. currentmodule:: mango.image
This module contains various functions for 3D image
processing and analysis.
Convolution-like Filters
========================
... | pymango/pymango | misc/python/mango/image/__init__.py | Python | bsd-2-clause | 4,612 | [
"Gaussian"
] | 59935aa95df25610a59cf650a6057fff108ebcfdafe010e3280a3e377959fb08 |
# Copyright (c) 2016 Universidade Federal Fluminense (UFF)
# This file is part of PyPosAST.
# Please, consult the license terms in the LICENSE file.
"""PyPosAST Module"""
from __future__ import (absolute_import, division)
import ast
from .visitor import LineProvenanceVisitor as Visitor, extract_code
from .cross_versio... | JoaoFelipe/pyposast | pyposast/__init__.py | Python | mit | 1,704 | [
"VisIt"
] | d524399e343ecbb4bd66f515f6ccb0a779b268d23a82aeadb9e798f3b39920fa |
# Copyright 2008, 2009, 2016 Free Software Foundation, Inc.
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-2.0-or-later
#
import sys
import textwrap
from distutils.spawn import find_executable
from gi.repository import Gtk, GLib
from . import Utils, Actions, Constants
from ..core import Messages... | trabucayre/gnuradio | grc/gui/Dialogs.py | Python | gpl-3.0 | 15,455 | [
"VisIt"
] | 58ccccf0ec0a425e5d49a93abcf1d1f907d09689ae470398000a757a009d1045 |
# 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 ... | lidakanari/NeuroM | neurom/tests/test_viewer.py | Python | bsd-3-clause | 4,652 | [
"NEURON"
] | 0690af4b1873ec6b409e178ec7f44f0c5d28749eaa22d68223f5f4bcb2ca867d |
#
# @file TestAncestor.py
# @brief SBML ancestor objects unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestAncestor.py | Python | gpl-3.0 | 39,155 | [
"VisIt"
] | 1992b9ea3155a609142f2b094d25e0ddb5109eb837e83e485a8b29149142652f |
__RCSID__ = "$Id$"
import socket
import select
import time
import os
from DIRAC.Core.DISET.private.Transports.BaseTransport import BaseTransport
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
class PlainTransport( BaseTransport ):
def initAsClien... | Andrew-McNab-UK/DIRAC | Core/DISET/private/Transports/PlainTransport.py | Python | gpl-3.0 | 4,188 | [
"DIRAC"
] | 6bf35c866b844f854645d54e00ce99ad86bb0569247017845c1877f6e1d8c533 |
"""
#python -c "import cyth, doctest; print(doctest.testmod(cyth.cyth_parser))"
"""
from __future__ import absolute_import, division, print_function
import six
from six.moves import zip, map, filter
from itertools import chain
import utool
import sys
from cyth import cyth_helpers
import ast
#import codegen # NOQA
impo... | aweinstock314/cyth | cyth/cyth_parser.py | Python | apache-2.0 | 36,709 | [
"VisIt"
] | 4da2d6596d8e61222cd62a14ab77c12ffd0cae6ffb99d5ad23c780453ce7bae4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
'''
Created on Jun 27, 2012
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | aykol/pymatgen | pymatgen/entries/tests/test_exp_entries.py | Python | mit | 1,235 | [
"pymatgen"
] | 632d2c14f95eb7449844152ee39d8934cad3524442879b621c44bbbfddb32927 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software Fo... | andrebellafronte/stoq | stoqlib/gui/dialogs/sellablepricedialog.py | Python | gpl-2.0 | 7,152 | [
"VisIt"
] | d3ef3c72fe202b411b070da1ad829b73c655529709829da1fd926c835d645a3b |
#!/usr/bin/env python
# coding: UTF-8
import sys
import os.path
from optparse import OptionParser
# check if the pymol module is installed
try :
import pymol
except :
sys.exit( "error : This script needs 'pymol' module. Please install PyMOL before running." )
def name_check( string, name ):
if os.path.ex... | nishn/pymol-script | pym.py | Python | mit | 1,563 | [
"PyMOL"
] | bfe3f5a512815a751dffde20b95c46e448e4045cc9c3315454f9c13e39498cb1 |
"""
@author: Martin Kuemmel
@organization: LMU / USM
@license: Gnu Public Licence
@contact: mkuemmel@usm.lmu.de
@version: $Revision: $
@date: $Date: $
@changeDate: $LastChangedDate: $
Initialize the test library.
"""
import os.path
import shutil
import unittest
# check tips version
import tips
if float(tips.... | nfourmanoit/TIPS | test/test_tips/testverify/testVerifyWave.py | Python | gpl-3.0 | 19,263 | [
"Gaussian"
] | b7f054e2dc24787c3dc6c02e536d8683ff2034eb5b838379c0584ec887f2af66 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/util/tests/test_decorator.py | Python | bsd-3-clause | 9,683 | [
"scikit-bio"
] | 3ad9d71176fda96bc19616569a9d2b62b7d04cbf728439099cf8b18fde607486 |
# proxy module
from __future__ import absolute_import
from mayavi.preferences.api import *
| enthought/etsproxy | enthought/mayavi/preferences/api.py | Python | bsd-3-clause | 91 | [
"Mayavi"
] | c9a5ad06bace1b13ff12b89d319c8881a63ed9233c6df88f055400fa7745ff54 |
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not... | apache/incubator-airflow | tests/plugins/test_plugin.py | Python | apache-2.0 | 4,156 | [
"Galaxy"
] | f3ce582a7a2f3f05604bf23844b4c288ff687c6fef5f0941597deb63849a7e43 |
# coding: utf8
"""
Tests for the HTTP response section of the ASGI spec
"""
from __future__ import unicode_literals
from unittest import TestCase
from asgiref.inmemory import ChannelLayer
from hypothesis import given
from twisted.test import proto_helpers
from daphne.http_protocol import HTTPFactory
from . import fa... | maikhoepfel/daphne | daphne/tests/test_http_response.py | Python | bsd-3-clause | 4,907 | [
"exciting"
] | 6a7822581dce53c840c13bc5d809346a311aee21fd308dc1e1f4652d3e8db5eb |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | tiagocardosos/stoq | stoqlib/lib/parameters.py | Python | gpl-2.0 | 48,323 | [
"VisIt"
] | 1fbfaf64b100097102fef06ac5715ff2da6ec46cdba84a5723bfe63da50fa04a |
#!/usr/bin/env python
#
# texttable - module for creating simple ASCII tables
# Copyright (C) 2003-2011 Gerome Fournier <jef(at)foutaise.org>
#
# 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 Foundat... | jabbalaci/jabbapylib | jabbapylib/lib/texttable.py | Python | gpl-3.0 | 18,494 | [
"Brian"
] | ea5cd136d78283eed18abc52f5d37f88d6a8b1d3b67429db64e21d458e37d5c5 |
# Copyright (C) 2012-2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | govarguz/espressopp | src/integrator/FreeEnergyCompensation.py | Python | gpl-3.0 | 4,641 | [
"ESPResSo"
] | 16d089a02cbb5b8c03fab9e74af0bcdb9f7b259f58252399085bbf981004dceb |
#!/usr/bin/python
#
# Written by Gavin Heverly-Coulson
# Email: gavin <at> quantumgeranium.com
#
# Takes an input cell and uses it to build a potential energy surface following
# the system sheared along the a and b lattice vectors.
# Creates the Quantum ESPRESSO input files for each point on the PES.
#
#
# This wor... | ghevcoul/MaterialsPES | pes_builder.py | Python | bsd-2-clause | 13,150 | [
"CRYSTAL",
"ESPResSo",
"Quantum ESPRESSO"
] | 36c072017fa6205d934af4e0e3bb232edd5db205c7b7308eeacdbeef5e7e849c |
'''
Hom family of models based on: [Drukker2013]_
Following: [Anselin2011]_
'''
__author__ = "Luc Anselin luc.anselin@asu.edu, Daniel Arribas-Bel darribas@asu.edu"
from scipy import sparse as SP
import numpy as np
from numpy import linalg as la
from . import ols as OLS
from pysal.lib.weights.spatial_lag import lag_... | lixun910/pysal | pysal/model/spreg/error_sp_hom.py | Python | bsd-3-clause | 58,029 | [
"COLUMBUS"
] | 959063a34a0a768178c39600fc3b3c4736016bbca279c61f9a27a93431b406c0 |
# Time-stamp: <2015-03-05 13:48:25 Tao Liu>
"""Description: Filter duplicate reads depending on sequencing depth.
Copyright (c) 2011 Tao Liu <taoliu@jimmy.harvard.edu>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included
with the distr... | ENCODE-DCC/chip-seq-pipeline | dnanexus/shell/resources/usr/local/lib/python2.7/dist-packages/MACS2/refinepeak_cmd.py | Python | mit | 6,879 | [
"pysam"
] | 326dc75e53c44868d8e2e7f6611da23eb3d9b2c4499a63d54c8b27083b55cf59 |
# Copyright (c) 2012, CyberPoint International, LLC
# 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 copyright
# notice, this lis... | Anaphory/libpgm | libpgm/nodedata.py | Python | bsd-3-clause | 8,840 | [
"Gaussian"
] | bc05442e78cabdb40ea87cac6fb6d858aa574ead78f7634e4f4df406f926df49 |
""" UserProfileDB class is a front-end to the User Profile Database
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import types
import os
import sys
import hashlib
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.Core.Utilities import Time
from DIRAC.ConfigurationSystem.Client.Helpers impo... | petricm/DIRAC | FrameworkSystem/DB/UserProfileDB.py | Python | gpl-3.0 | 27,595 | [
"DIRAC"
] | 508f9fc1e5fc160915231664f43d969072a429ecb84ac37dc5be6a42a2cf1635 |
# Module:
# Submodules:
# Created:
# Copyright (C) <date> <fullname>
#
# This module is part of the <project name> project and is released under
# the MIT License: http://opensource.org/licenses/MIT
"""
"""
# ============================================================================
# Imports
# =====================... | arielmakestuff/selweb | selweb/core.py | Python | mit | 11,856 | [
"VisIt"
] | 5b47417e644bad2551cc2aa0785db2bb06b87084190ca738a6f5cc1c04d76a8b |
import scipy.stats
import numpy
from numpy import logical_and
def binned_transform(u):
v = numpy.copy(u)
v[:len(v)/2] = 20*v[:len(v)/2] - 10
v[len(v)/2:] = 10**(v[len(v)/2:]*10 - 5)
return v
class BinnedModel(object):
"""
Each bin in the x variable has a distribution (Gaussian or other).
The bin borders have t... | JohannesBuchner/syscorr | syscorr/binned.py | Python | agpl-3.0 | 3,309 | [
"Gaussian"
] | aedc59141c2baa423fe4db62f943e70aec755075f6b9d62d7a174428ef4c4ac4 |
#!/usr/bin/env python
# vim: set fileencoding=utf-8
import os
import argparse
from gff3 import genes, get_gff3_id, get_rbs_from, feature_test_true, feature_lambda, feature_test_type
from cpt_gffParser import gffParse, gffWrite
from Bio import SeqIO
from jinja2 import Environment, FileSystemLoader
import logging
from ma... | TAMU-CPT/galaxy-tools | tools/phage/phage_annotation_table.py | Python | gpl-3.0 | 19,472 | [
"Galaxy"
] | 640b1033db0226962234f43478b02a23b671398f7fc79e99adfdf6d6939c5c9a |
"""
RequestOperation to create a tarball from a list of LFNs.
Download a list of files to local storage, then tars it and uploads it to a StorageElement
This operation requires the following arguments:
* ArchiveLFN: The LFN of the tarball
* SourceSE: Where the files to be archived are downloaded from
* TarballSE:... | fstagni/DIRAC | DataManagementSystem/Agent/RequestOperations/ArchiveFiles.py | Python | gpl-3.0 | 9,341 | [
"DIRAC"
] | ea02c3cef27164b1246c1f568608c9837214c2e6a8c846e875c58b72e77fde2c |
# -*- coding: utf-8 -*-
# Copyright 2019 The GraphicsFuzz Project 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | google/graphicsfuzz | gfauto/gfauto/download_cts_gf_tests.py | Python | apache-2.0 | 5,898 | [
"Amber"
] | 497d6d620bf72c27e5ec98967c4e57410f689b1f39148159acd25c92b7d68d86 |
"""
ComponentMonitoring type used to monitor DIRAC components.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.MonitoringSystem.Client.Types.BaseType import BaseType
__RCSID__ = "$Id$"
class ComponentMonitoring(BaseType):
"""
.. class::... | yujikato/DIRAC | src/DIRAC/MonitoringSystem/Client/Types/ComponentMonitoring.py | Python | gpl-3.0 | 1,284 | [
"DIRAC"
] | 8380193ffb06d1101086d3f862945ccca84c50b61fe30336ba7a4a5e065c944d |
import abc
import numbers
import warnings
import h5py
import numpy as np
from . import bg_estimate
#: default hdf5 compression keyword arguments
COMPRESSION = {"compression": "gzip",
"compression_opts": 9,
}
#: valid background data identifiers
VALID_BG_KEYS = ["data",
... | RI-imaging/qpimage | qpimage/image_data.py | Python | mit | 12,445 | [
"Gaussian"
] | eb5e219c577139d7e56420c20e688d30ab37fae65c3edcb5ccd6e8367e439937 |
##############################################################################
# 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-yarn/package.py | Python | lgpl-2.1 | 2,616 | [
"Bioconductor"
] | da87c28c551a254dcdae358956b5fccc0b994b001a606f9f272bcbed93c7a860 |
#!/usr/bin/env python
"""
initial.py
ROMS initial conditions utilities
Written by Brian Powell on 01/15/14
Copyright (c)2017 University of Hawaii under the BSD-License.
"""
import seapy
import numpy as np
import netCDF4
def from_roms(roms_file, ini_file, record=0, time=None, grid=None):
"""
Given ... | dalepartridge/seapy | roms/initial.py | Python | mit | 2,042 | [
"Brian",
"NetCDF"
] | 58442d6e64224b3ce21823261c1eb83b14acb198c3c9c49debdbf6e8e7fbdbcf |
import argparse
import os
import subprocess
from pylab import *
mtlr_train = 'mtlr_train';
mtlr_test = 'mtlr_test';
model_temp = './model.tmp';
train_data = None;
test_data = None;
intervals_file = None;
intervals_number = 0;
cv_dirs = [];
def findc(k, start, end, loss):
"""
Simple way to find the best C1 value, us... | dluces/cmput466-project | findc/findc.py | Python | mit | 5,973 | [
"FoldX"
] | 737b9186b8f5fae86c3854700bb434f5341415e6e563f590c41a0492f5288338 |
"""
====================================================
How to convert 3D electrode positions to a 2D image.
====================================================
Sometimes we want to convert a 3D representation of electrodes into a 2D
image. For example, if we are using electrocorticography it is common to
create sca... | jaeilepp/mne-python | examples/visualization/plot_3d_to_2d.py | Python | bsd-3-clause | 4,488 | [
"Mayavi"
] | c7a96b53232b2e4465fd381756eeebdb3fc9748e7f21b772a4d3d8253a312f35 |
# $HeadURL$
"""
DIRAC - Distributed Infrastructure with Remote Agent Control
The LHCb distributed data production and analysis system.
DIRAC is a software framework for distributed computing which
allows to integrate various computing resources in a single
system. At the same time it integrates all kin... | vmendez/DIRAC | __init__.py | Python | gpl-3.0 | 5,953 | [
"DIRAC"
] | 0d0e2bf9035615d14978bc4cecafdc2034a76def84a0a2aa5c168f0a83b9d7eb |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | alisonken1/openlp-projector-2.0 | openlp/projectors/__init__.py | Python | gpl-2.0 | 3,515 | [
"Brian"
] | 8b15b42f48b070e4244b710a93ead4cb9f4daef41c4de9bb1f49438c6932a3e2 |
# massfunctions.py: A collection of functions which convert between mass and
# cumulative number density
# Note: all masses and number densities assumed to be logarithmic
# Several functions require the mpmath package.
# Sarah Wellons 6/2016+
import numpy as np
import torrey_cmf
import scipy.interpol... | sawellons/NDpredict | massfunctions.py | Python | gpl-3.0 | 16,288 | [
"Galaxy"
] | 8cbeb12a9cc7622243892a382c9875e7bc9037ba38356b28d12dd2a95631602b |
# Copyright (c) 2006, 2008-2010, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2016 Ashley Whetter <ashley@awhetter.co.uk>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https:/... | arju88nair/projectCulminate | venv/lib/python3.5/site-packages/pylint/pyreverse/diadefslib.py | Python | apache-2.0 | 8,093 | [
"VisIt"
] | dbc3798152168792a1b00f82dd466a7915b9ec7459fadf2f69b412f368451603 |
#
# Copyright 2009 Eigenlabs Ltd. http://www.eigenlabs.com
#
# This file is part of EigenD.
#
# EigenD 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) an... | barnone/EigenD | pi/policy.py | Python | gpl-3.0 | 24,392 | [
"VisIt"
] | a2d9f082da9646622e66950e36fee9d5533ea1c60a22b3d6b132e75baf54ea12 |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | wschaeferB/autopsy | pythonExamples/Aug2015DataSourceTutorial/FindContactsDb.py | Python | apache-2.0 | 9,193 | [
"Brian"
] | 98a93215f856a75ad39317039edd83fd9e005c4cec069dd20b812acef477f585 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: André Felipe Dias <andref.dias@pronus.eng.br>
from __future__ import unicode_literals
import re
import shutil
from os import makedirs
from os.path import join, dirname, basename, isfile, exists, curdir, split, splitext, abspath
from docutils import nodes
from ... | wdv4758h/rst2html5slides | src/rst2html5slides.py | Python | mit | 22,222 | [
"VisIt"
] | 6d7be278ff33b014e0ef3a734cf4adc1d32baf99ec578feff3d2f14e21ad47dc |
import os
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
import numpy as np
from lmfit import Parameters
from lmfit.models import GaussianModel, LinearModel
from astropy.constants import c
from fitelp.label_tools import line_label
import fitelp.constants as constants
constants.init()
def v... | daniel-muthukrishna/GiantStarFormingRegions | fitelp/fit_line_profiles.py | Python | mit | 16,449 | [
"Gaussian"
] | 2c59b08874ad0440c1a6c1cbc3f805fc573fb1aeac86cc0e36247be2bc9a603d |
from . import get_calibration_dict, gaussian_array, cos_gaussian_array, \
sin_gaussian_array
from . import Waveform, Element, Sequence
import numpy as np
def make_readout_seq_points(channels=[4]):
"""
Square pulse duting readout time with one marker at start
"""
readout_sequence = Sequence(name='p... | QCoDeS/Qcodes-contrib | qdev_transmon_helpers/sequencing/legacy.py | Python | mit | 61,861 | [
"Gaussian"
] | d8e97d67590b29efd5f195c730e2c86cb6b64ccda8444f743d002d385dbac537 |
# 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... | HaebinShin/tensorflow | tensorflow/contrib/distributions/python/ops/normal.py | Python | apache-2.0 | 12,593 | [
"Gaussian"
] | d0c0c04f01a85302539a0ebb61e06fe5e0a1a60d978342397a681265705bcc39 |
# This file is part of wger Workout Manager.
#
# wger Workout Manager is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wger W... | DeveloperMal/wger | wger/core/tests/test_temporary_users.py | Python | agpl-3.0 | 6,675 | [
"VisIt"
] | 78c7d09c33ea7fd05214b6499defb530c8139335eec4cd48e5504c2354eff522 |
#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""
Bio.Wise contains modules for running and processing the output of
some of the models in the Wise2 package by Ewan Birney av... | zjuchenyuan/BioWeb | Lib/Bio/Wise/psw.py | Python | mit | 3,715 | [
"Biopython"
] | f6c3532585a9ddb62195d0267651b0acd2a1ba0940db608b7a48b8b6b171c915 |
# ===========================================================================
# eXe
# Copyright 2004-2005, University of Auckland
# Copyright 2004-2008 eXe Project, http://eXeLearning.org/
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | mclois/iteexe | exe/export/websiteexport.py | Python | gpl-2.0 | 22,456 | [
"VisIt"
] | 3abec6232cf1a5cb234d5c351bdf8b7b7f95abf9b02071eb013432994f84163d |
# setuptools installation of GromacsWrapper
# Copyright (c) 2008-2011 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
#
# See the files INSTALL and README for details or visit
# https://github.com/Becksteinlab/GromacsWrapper
from __future__ import with_statement
... | Becksteinlab/GromacsWrapper | setup.py | Python | gpl-3.0 | 2,912 | [
"Gromacs",
"VisIt"
] | eabbe59a2ff88e4a92f787ae03d53029ca64c516bf3e86ad251afcca59a654e1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Scour
#
# Copyright 2010 Jeff Schiller
# Copyright 2010 Louis Simard
#
# This file is part of Scour, http://www.codedread.com/scour/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Lice... | flosse/scour | scour/scour.py | Python | apache-2.0 | 122,876 | [
"VisIt"
] | 4b93ae2367a856fc703354dc80cfe0e8dcfe85c2275d25f447d7fe8eb3418a51 |
#!/usr/bin/env python3
"""This module implements an interface for reading LOFAR TBB data.
This module is strongly based on pyCRtools module tbb.py by Pim Schellart, Tobias Winchen, and others.
However, it has been completely re-written for use with LOFAR-LIM
Author: Brian Hare
Definitions:
LOFAR is split into a nu... | Bhare8972/LOFAR-LIM | LIM_scripts/IO/raw_tbb_IO.py | Python | mit | 47,210 | [
"Brian"
] | 5395df6cc969d2bfc0df5410cd9848aa8dcc7984ab66623b21b80997e1cf1cc3 |
'''
Compiler classes for Cheetah:
ModuleCompiler aka 'Compiler'
ClassCompiler
MethodCompiler
If you are trying to grok this code start with ModuleCompiler.__init__,
ModuleCompiler.compile, and ModuleCompiler.__getattr__.
'''
import sys
import os
import os.path
from os.path import getmtime, exi... | jacklee0810/QMarkdowner | Cheetah/Compiler.py | Python | mit | 80,447 | [
"VisIt"
] | d3f6ceb9621a62d733b1477dfbdcec4be1dcbd5efd48ac1217a754cf09fe1959 |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/packagedcode/nevra.py | Python | apache-2.0 | 3,033 | [
"VisIt"
] | 16998c178acd9739f88df272123736c9ac8c30e9394e666ae0c220042f85411d |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'abinit'
tab.settings['Output file name'] = 'BaTiO3.out'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 5
tab.settings['Mass definition'] ... | JohnKendrick/PDielec | Examples/SizeEffects/BaTiO3/script.py | Python | mit | 2,397 | [
"ABINIT"
] | 932ee8cfc15ea2d325ba7102100174304913939986dab31bfd3cc7a0aec9ef21 |
""" Author: Ning Guo <ceguo@connect.ust.hk>
run `mv retainingSmooth.yade.gz 0.yade.gz`
to generate initial RVE packing
"""
from esys.escript import *
from esys.finley import Rectangle
from esys.weipa import saveVTK
from esys.escript.pdetools import Projector
from msFEM2D import MultiScale
from saveGauss import ... | anna-effeindzourou/trunk | examples/FEMxDEM/retainingSmooth.py | Python | gpl-2.0 | 3,320 | [
"VTK"
] | e0cf2fe02f09df9b3cc99f411f5af2c391c7788623d7abab3733c8bcee88604a |
#!/usr/bin/env python3
from runtime import EspNone, EspList, EspString, EspDict
import re
from multimethod import multimethod
def join(sep, v):
return sep.join(str(x) for x in v if x is not None)
COLOR = True
if COLOR:
num = '\033[38;5;202m%s\033[0m'
color = {
str: '\033[38;5;247;4m%r\033[0m',
EspString: '\03... | ConsciousCode/espresso | src/ast.py | Python | bsd-2-clause | 16,300 | [
"ESPResSo",
"VisIt"
] | f4e2af1dbaa906de2d93775995e388b46c826e21359a7d0f80ca3b399e9d1ae3 |
from __future__ import print_function
import json
import os
import os.path
import re
import sys
import warnings
from collections import defaultdict
from distutils.command.build_scripts import build_scripts as BuildScripts
from distutils.command.sdist import sdist as SDist
try:
from setuptools import setup, find... | KohlsTechnology/ansible | setup.py | Python | gpl-3.0 | 10,363 | [
"Galaxy"
] | 26025e60aa123d4eaa2c0fe43fd884f889e54e1654d46bdf1a4fce132a30e66f |
#
# Konstrukteur - Static Site Generator
# Copyright 2013-2014 Sebastian Fastner
# Copyright 2014 Sebastian Werner
#
"""
**Konstrukteur - Static Site Generator**
Konstrukteur is a website generator that uses a template and content files
to create static website output.
"""
__version__ = "0.1.15"
__author__ = "Sebast... | fastner/konstrukteur | konstrukteur/__init__.py | Python | mit | 850 | [
"VisIt"
] | 95e050a51ea35de7da7b620de00a32c03d13211a59e4db14b5be79148578db04 |
<<<<<<< HEAD
<<<<<<< HEAD
"""
A number of functions that enhance IDLE on Mac OSX.
"""
import sys
import tkinter
from os import path
import warnings
def runningAsOSXApp():
warnings.warn("runningAsOSXApp() is deprecated, use isAquaTk()",
DeprecationWarning, stacklevel=2)
return isAquaTk()... | ArcherSys/ArcherSys | Lib/idlelib/macosxSupport.py | Python | mit | 25,772 | [
"VisIt"
] | 9768f0fa6d61fddd147d4c5a64fd121ed428199bc8de63fd04d2aa4f6f2d8d63 |
# -----------------------------------------------------------------------------------------------------
# CONDOR
# Simulator for diffractive single-particle imaging experiments with X-ray lasers
# http://xfel.icm.uu.se/condor/
# -------------------------------------------------------------------------------------------... | FXIhub/condor | condor/utils/material.py | Python | bsd-2-clause | 23,942 | [
"Dalton"
] | 550d07c04637f8ea86ddb7650420bb491416acce506c6ec08a7ad0ecbb1d2d76 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/test/bigdl/chronos/simulator/test_doppelganger_simulator.py | Python | apache-2.0 | 6,273 | [
"ORCA"
] | bb35381ede393335d7005fb5920be1d6a998d5e8172c7e6584c0674e681e5683 |
from __future__ import division, print_function
from __future__ import absolute_import
from __future__ import unicode_literals
from os import path
import io
import string
from pysces import model, PyscesModel
from ._paths import get_model_name
__all__ = ['psc_to_str',
'mod_to_str',
'strip_fix... | PySCeS/PyscesToolbox | psctb/modeltools/_pscmanipulate.py | Python | bsd-3-clause | 4,111 | [
"ORCA",
"PySCeS"
] | 2b3c033b2e5c3a4856cd35a4a2a31d1f02e8e493e8b6746438c72fd6897ebaf4 |
from mayavi import mlab
import sys
sys.path.append("..")
import data_tools as dt
import plotting as plot
import linear_algebra as la
import numpy as np
def plot_coords_interactive(coords, res, color=(1,0,0), radius=None, out_path=None):
if radius is None:
radius = calculateRadius(coords, res)
xs = coords[:,0]
ys ... | seqcode/miniMDS | scripts/fig9.py | Python | mit | 1,962 | [
"Mayavi"
] | 9901972d3e45dca87f5333da22a7e543df6dda2e0622da764a8aa7e55d667da5 |
# Copyright 2017,2018,2019,2020,2021 Sony Corporation.
# Copyright 2021 Sony Group Corporation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-... | sony/nnabla | python/test/test_graph.py | Python | apache-2.0 | 49,780 | [
"VisIt"
] | f3fae2489f1bc99897e9d03815b1026a88aa48019dd7257d3cf4d3c906e61944 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# sandbox_list_users - [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... | heromod/migrid | mig/server/sandbox_list_users.py | Python | gpl-2.0 | 1,664 | [
"Brian"
] | 9329b8df9066b8ec9619931e65d81446e90d8c8e29bf39bc39b44f4513af6b3b |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | asnorkin/sentiment_analysis | site/lib/python2.7/site-packages/scipy/special/add_newdocs.py | Python | mit | 158,460 | [
"Gaussian"
] | 044702d7778929d8bca2e7570b93ae2fabef0288606375daa5759f5f5eadd7a6 |
# (C) British Crown Copyright 2013 - 2018, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | dkillick/iris | lib/iris/fileformats/pp_load_rules.py | Python | lgpl-3.0 | 41,025 | [
"NetCDF"
] | 72619d7844426adc44f4ef3868a9dd0f513a4a6e3be230d106208e01d2283bf8 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/win/win_GetSystemTmpPath.py | Python | gpl-3.0 | 1,416 | [
"ORCA"
] | d5185712f6428daeedfb517cd89b28edfb161e58f6f099f947b518addabd3716 |
import math
from itertools import izip_longest
class NeuronConnection(object):
def __init__(self, parent, child, weight=0.4):
self.parent = parent
self.child = child
self.weight = weight
class Neuron(object):
def __init__(self, input=None, output=None, is_bias=False):
self... | dev-coop/neural-net-hacking-examples | python/Part 4/neural_network_with_connections.py | Python | mit | 4,949 | [
"NEURON"
] | 339fa77391b6a83dad0cc7a2ed77fd35ef99c168034d02f6e63d6161150301c2 |
# -*- coding: utf-8 -*-
#
# pyps documentation build configuration file, created by
# sphinx-quickstart on Wed May 07 14:26:13 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.... | mearns/pyps | sphinx/source/conf.py | Python | agpl-3.0 | 10,470 | [
"Brian"
] | 536116985b929a2bf4fa5ed64d55d899248f8c7dc9dfe54eeca5285f1a3e5388 |
from distutils.core import setup, Extension
from distutils.sysconfig import get_python_inc, get_python_lib
from kapteyn import __version__ as version
from glob import glob
import sys, os
try:
import numpy
except:
print '''
-- Error.
The Kapteyn Package requires NumPy, which seems to be unavailable here.
Please c... | cdeil/kapteyn-mirror | setup.py | Python | bsd-3-clause | 5,946 | [
"Gaussian"
] | 08beb6ff480c440f7699f7a360933f943ed958ee474f187763fb5ec2c5f2e7c6 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007,2012,2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 ... | ghutchis/cclib | test/data/testTDun.py | Python | lgpl-2.1 | 2,030 | [
"cclib"
] | 6238d9b393cbb779c2c6c1220798ab3eb942fdd3151e6913a6093e16fb365afc |
from repESP import resp_helpers, charges, graphs
from repESP.field_comparison import rms_and_rep, difference
from repESP.esp_fit_calc import FitCalc, IOpCalcSet
import shutil
import os
import copy
import pickle
import numpy as np
import matplotlib.pyplot as plt
# The purpose of the script is investigating the change ... | jszopi/repESP | scripts/old/fit_points_iop.py | Python | gpl-3.0 | 5,502 | [
"Gaussian"
] | f7a988eef3951a07751f82f3d7fa40f1538fbadaec3622d342cd66cdf9fb3506 |
#* 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
"""Develope... | harterj/moose | python/MooseDocs/commands/syntax.py | Python | lgpl-2.1 | 1,734 | [
"MOOSE"
] | 81b237763c9e0f1de41cfcd6253fedae017f9898728d44f7bc2fbffa8c5a2efb |
import subprocess
import os
import json
from scipy.optimize import linprog
import sys
import pickle
import math
import numpy
from collections import namedtuple
from docplex.mp.model import Model
from docplex.util.environment import get_environment
#This program computes bidding strategy with the IBM Decision Optimizat... | kosticlab/aether | lp/ilp.py | Python | mit | 13,665 | [
"VisIt"
] | 90917a0f333d144605f4a94f4735b4fe1c66ce09621f5c5b994bee231cbcae68 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
from OVarCall.utilOVar.exceptionUtil import InvalidBamFileManagement,InvalidMutationType,InsufficientBamReadFilter
import pysam
import math
import distutils.util
import logging
import contextlib
import re
import copy
class BamDAO:
def __init__(self, bamPath... | takumorizo/OVarCall | lib/OVarCall/utilOVar/bamDAO.py | Python | gpl-3.0 | 34,172 | [
"pysam"
] | 6c7265315d06f1411cd29b2be2fcbb019b354d32d8bb3512631274edfc689947 |
__all__ = [
'get_selected_array_name',
'get_selected_array_field',
'copy_arrays_to_point_data',
'get_numpy_array',
'get_vtk_array',
'add_array',
'get_selected_array',
'search_for_array',
'get_all_array_names',
]
import vtk
from vtk.numpy_interface import dataset_adapter as dsa
from... | banesullivan/ParaViewGeophysics | PVGeo/_helpers/arrays.py | Python | bsd-3-clause | 9,733 | [
"VTK"
] | fa12563c67dae7a214458dd97bfd5d14584cf0ba72357d596f76829b3d20886b |
#!/usr/bin/python3
#
# File: lsf_status.py
#
# Author: George Papadimitriou
# e-mail: georgpap@isi.edu
# Author: Brian Bockelman
# e-mail: bbockelm@cse.unl.edu
#
#
# Copyright (c) University of Nebraska-Lincoln. 2012
# Copyright (c) University of Wisconsin-Madison. 2012
#
# Licensed under the Apache ... | htcondor/htcondor | src/blahp/src/scripts/lsf_status.py | Python | apache-2.0 | 21,206 | [
"Brian"
] | 9a99061639c1c975c971d8d5d65a40a0aa5af6d3858577c63bdc79ba971ce542 |
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