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# for rgenetics - lped to fbat
# recode to numeric fbat version
# much slower so best to always
# use numeric alleles internally
import sys,os,time
prog = os.path.split(sys.argv[0])[-1]
myversion = 'Oct 10 2009'
galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/lped_to_fped_converter.py | Python | gpl-3.0 | 3,564 | [
"Galaxy"
] | b5615cbfe98821bcd5404b7e39803ec07158aad6f40fbb60e66c237b4d5bb8e7 |
from __future__ import division
import numpy as np
import scipy.sparse as sp
from sklearn.metrics import euclidean_distances
from sklearn.random_projection import johnson_lindenstrauss_min_dim
from sklearn.random_projection import gaussian_random_matrix
from sklearn.random_projection import sparse_random_matrix
from... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/tests/test_random_projection.py | Python | gpl-2.0 | 14,035 | [
"Gaussian"
] | e914be00fec6da3e31cf605ecaa0f38e474a2ee35a1b78c244f8bf0600318661 |
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 14 01:34:41 2014
@author: deokwoo
"""
from __future__ import division # To forace float point division
import numpy as np
from numpy.linalg import norm
from scipy.interpolate import interp1d
from shared_constants import *
from data_tools import *
from scipy.stats import s... | TinyOS-Camp/DDEA-DEV | Archive/[14_10_10] DDEA sample code/data_preprocess.py | Python | gpl-2.0 | 43,193 | [
"Gaussian"
] | beda84e5a15b81b2cdf6cc9743d1862a3d67510d8e9bf082563b1e547a1d70aa |
"""
3D Starfield Simulation
Developed by Leonel Machava <leonelmachava@gmail.com>
http://codeNtronix.com
http://twitter.com/codentronix
"""
import pygame, math, sys
from random import randrange
from operator import itemgetter
from BitmapFont.BitmapFont import BitmapFont
from BitmapFont.BitmapFont import Bitma... | coon42/FlyFi | pygame_spielereien/pifi_menu.py | Python | gpl-3.0 | 6,868 | [
"VisIt"
] | 9fd5656f8f91ce6321c234ada508a9959e51dcbbcfbe382dffd6d758b87b5c0b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008,2010 Gary Burton
# Copyright (C) 2008 Craig J. Anderson
# Copyright (C) 2009 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Adam Stein <adam@csh.rit.edu>
# Cop... | Forage/Gramps | gramps/gui/plug/_guioptions.py | Python | gpl-2.0 | 73,366 | [
"Brian"
] | 88ea72a8c875482f3d51bd5616ed55eb010ea2971d6b1e506cff39ddd06d2d51 |
'''
The settings for OSMC are handled by the OSMC Settings Addon (OSA).
In order to more easily accomodate future changes and enhancements, each OSMC settings bundle (module) is a separate addon.
The module can take the form of an xbmc service, an xbmc script, or an xbmc module, but it must be installed into the u... | srmo/osmc | package/mediacenter-addon-osmc/src/script.module.osmcsetting.pi/resources/osmc/OSMCSetting.py | Python | gpl-2.0 | 11,555 | [
"VisIt"
] | 05551c83ac609dedf315fd5300606385cf1b476362a2f4b45f1fb904449f1102 |
# Harmonic Oscillator
The harmonic oscillator is omnipresent in physics. Although you may think
of this as being related to springs, it, or an equivalent
mathematical representation, appears in just about any problem where a
mode is sitting near its potential energy minimum. At that point,
$\partial_x V(x)=0$, and th... | CompPhysics/MachineLearning | doc/src/LectureNotes/testbook/_build/jupyter_execute/chapter5.py | Python | cc0-1.0 | 51,527 | [
"Gaussian",
"exciting"
] | 833c9195739457c1429a3d224008d4c96cc16cc529b24b95dfda0846feab4e1b |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical s... | seckcoder/lang-learn | python/sklearn/sklearn/hmm.py | Python | unlicense | 46,219 | [
"Gaussian"
] | 29551e0cb3f92c76da65fe11d5563a443eca4cd797d51886ca3ec757ef6ffd9e |
from parse import Rosetta, parse
def _pytables():
import tables as pytables
tr = Rosetta()
tr.namespace = pytables
expr = open('rosetta/pytables.table').read()
stone = tr.visit(parse(expr))
return dict(a.astuple() for a in stone)
try:
pytables = _pytables()
except IOError:
pytables ... | davidcoallier/blaze | blaze/rosetta/__init__.py | Python | bsd-2-clause | 327 | [
"VisIt"
] | e9f898d1ac68fbcdc1c54a938822461f39ca3687944e8231fc224d10b0ebf2ad |
# -*- coding: utf-8 -*-
#!/usr/bin/python
#
# This is derived from a cadquery script for generating PDIP models in X3D format
#
# from https://bitbucket.org/hyOzd/freecad-macros
# author hyOzd
# This is a
# Dimensions are from Microchips Packaging Specification document:
# DS00000049BY. Body drawing is the same as QFP ... | easyw/kicad-3d-models-in-freecad | cadquery/FCAD_script_generator/Crystal/cq_parameters_Resonator_C38_LF.py | Python | gpl-2.0 | 16,741 | [
"CRYSTAL"
] | 11e2141c0f9dcb230a4325a2a8c4cdfeb858df43854dc7269f7b202e4bce17d2 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/procrouting/response/scf_response.py | Python | lgpl-3.0 | 29,112 | [
"Psi4"
] | ce68e3145f39787ad054b1c1ea51e319011158596054f5703f9a9d1d5beb53ab |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for specific parser behaviors, such as overriden methods."""
import unittest
class NormalisesymTest(unitt... | langner/cclib | test/parser/testspecificparsers.py | Python | bsd-3-clause | 3,256 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"MOLCAS",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Psi4",
"TURBOMOLE",
"cclib"
] | 5caec82fd244af482156a879363ffcbbbf3c26dc6a926f6caf9f49cc75d06c06 |
import glob, os, sys
sys.path.append(os.getcwd() + '/lib/')
sys.path.append(os.getcwd() + '/cloudtracker/')
# Multiprocessing modules
import multiprocessing as mp
from multiprocessing import Pool
PROC = 16
import model_param as mc
from conversion import convert
import cloudtracker.main
# Default working directory fo... | lorenghoh/ent_analysis | run_analysis.py | Python | mit | 3,709 | [
"NetCDF"
] | 83d45baed1bd76755f843457cd89b5131a2c11bbe07e78904c38b54e96eff910 |
__author__ = 'algol'
import sqlite3
from datetime import datetime
from configparser import ConfigParser
class Singleton(object):
instance = None
inited = False
def __new__(cls, *a, **kwa):
if cls.instance is None:
cls.instance = object.__new__(cls)
return cls.instance
... | migihajami/memin | memin/core.py | Python | bsd-3-clause | 15,539 | [
"VisIt"
] | d94ccca2dae0f23c1dcebcce2ac3fb08395d2ba4ce50eb19abba624f9bed1781 |
########################################################################
# $HeadURL$
# File : ComputingElementFactory.py
# Author : Stuart Paterson
########################################################################
""" The Computing Element Factory has one method that instantiates a given Computing Element
... | avedaee/DIRAC | Resources/Computing/ComputingElementFactory.py | Python | gpl-3.0 | 2,631 | [
"DIRAC"
] | 7de1e3feeadc53eee5456cb929e6bdf72ad16410c5c349360091a56a2d6ce744 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/interaction/LennardJonesEnergyCapped.py | Python | gpl-3.0 | 14,335 | [
"ESPResSo"
] | 302ce51dda8867c843279f8aea5c1e7b13ae5555c59aebcf0c54fe77ace10c53 |
"""bluesky.dispersers.hysplit.hysplit
The code in this module was copied from BlueSky Framework, and modified
significantly. It was originally written by Sonoma Technology, Inc.
v0.2.0 introduced a number of chnanges migrated from BSF's hysplit v8.
Heres are the notes coped from BSF:
'''
Version 8 - mod... | pnwairfire/bluesky | bluesky/dispersers/hysplit/hysplit.py | Python | gpl-3.0 | 48,822 | [
"Gaussian",
"NetCDF"
] | 8445c3d7e14b040edc92ae1b93adf6d6278f85068ee84b479a816a6dd58743d0 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your optio... | kasioumis/invenio | invenio/modules/deposit/models.py | Python | gpl-2.0 | 47,359 | [
"VisIt"
] | abc61528e22424f9b61a01984ffe99debd9571547e72e5ba0a5267d1324c94e2 |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/dcm_to_storage_dag.py | Python | apache-2.0 | 4,669 | [
"VisIt"
] | 64b936af397dbaaaf35f82425f7d21bc72f094901c57771797672535a1cc2fc9 |
#!/usr/bin/env python
""" update local cfg
"""
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__.split( '\n' )[1],
'Usage:',
' %s [option|cfgFile] ... DB ...' % Script.scriptName,
... | Andrew-McNab-UK/DIRAC | tests/Jenkins/dirac-cfg-update-services.py | Python | gpl-3.0 | 1,938 | [
"DIRAC"
] | 1e661b6cac62ecbd030dbcfe34533d29f4b6edd959402a1dae8801a4c16aa507 |
# Copyright (c) 2021, Alliance for Open Media. All rights reserved
#
# This source code is subject to the terms of the BSD 2 Clause License and
# the Alliance for Open Media Patent License 1.0. If the BSD 2 Clause License
# was not distributed with this source code in the LICENSE file, you can
# obtain it at www.aomedi... | AlienCowEatCake/ImageViewer | src/ThirdParty/aom/aom-v3.2.0/tools/auto_refactor/auto_refactor.py | Python | gpl-3.0 | 29,568 | [
"VisIt"
] | fbc943e39d45e8bdc890c7608785b0dddb9d9819f5f0187e9f3f094b44276c6e |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | KernelAnalysisPlatform/KlareDbg | tracers/qemu/decaf/scripts/qapi-types.py | Python | gpl-3.0 | 6,007 | [
"VisIt"
] | 8d58db2dc784e9056750bf8e1ec7687d3c17d29c968b0b89d1c49458f09626a5 |
from __future__ import division, print_function, absolute_import
import sys
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info
import numpy as np
config = Configuration('siesta',parent_package,top_pat... | zerothi/siesta-es | sids/siesta/setup.py | Python | gpl-3.0 | 741 | [
"SIESTA"
] | ea5e87a51bbe655735f78d4c313a54b1a606854ca99039359567e3e1ffee822b |
from math import e
from StringIO import StringIO
from urllib import urlopen
from subprocess import Popen
from tempfile import mkstemp
from urlparse import urlparse
from os.path import splitext
from os import write, close, unlink
try:
import PIL
except ImportError:
import Image
from ImageDraw import ImageDr... | stamen/fieldpapers | decoder/imagemath.py | Python | gpl-2.0 | 7,355 | [
"Gaussian"
] | ef513e5475118a1f7c525d59fc0966b33beaf61a50085f5c56b8569217a6b8c2 |
#!/usr/bin/python
# -------------------------------------------------------------------
# Import statements
# -------------------------------------------------------------------
import math
import os
import re
import sys
from decimal import *
from operator import *
import marvin.db.models.SampleModelClasses as sample... | sdss/marvin | python/marvin/db/models/DataModelClasses.py | Python | bsd-3-clause | 30,632 | [
"Galaxy"
] | 54ffaa2ec35245176f45131e007abf3d2b7e53768081dfec1848651f8102b561 |
# Copyright 2020 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/python/experimental/sequential/ensemble_kalman_filter.py | Python | apache-2.0 | 11,621 | [
"Gaussian"
] | c23275853fa765897651eba62ef213a11b14a9bcd69b454e4f34fc7b043743e5 |
''' Some standard routines for PySCF IO and queue interaction.'''
import os, json, shutil, ccq_sub_py
from pyscf.gto import Mole
from pyscf.pbc.gto import Cell
from pyscf.pbc.lib.chkfile import save_cell
from pyscf.lib.chkfile import load_mol, save_mol
from h5py import File
from pyscf.pbc.tools.pyscf_ase import ase_ato... | bbusemeyer/mython | busempyer/runpyutils.py | Python | gpl-2.0 | 3,822 | [
"ASE",
"PySCF"
] | 98144cbe566ea34c9cb0658945a6022a03870abef65c4184a16567cb539fe451 |
# encoding: utf-8
"""
System command aliases.
Authors:
* Fernando Perez
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License.
#
# The full license is in the file... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/core/alias.py | Python | bsd-3-clause | 8,950 | [
"Brian"
] | 3bcca9636dee57c705ad81c347382561c93210f11d9fbb4c38a3e826eab8f4bc |
#!/usr/bin/env python
# $Id: FJExample.py 545 2012-01-18 06:10:03Z cvermilion $
#----------------------------------------------------------------------
# Copyright (c) 2010-12, Pierre-Antoine Delsart, Kurtis Geerlings, Joey Huston,
# Brian Martin, and Christopher Vermilion
#
#---------------------------... | mickypaganini/SSI2016-jet-clustering | spartyjet-4.0.2_mac/examples_py/FJExample.py | Python | mit | 4,761 | [
"Brian"
] | b5e576fabb5bdf9761fc5b2aefa8dfcdabf0943685f6fadef50e519e3f67df32 |
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License Version
# 1.1 (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.mozilla.org/MPL/
#
# Softwa... | centrumholdings/buildbot | buildbot/schedulers/manager.py | Python | gpl-2.0 | 4,863 | [
"Brian"
] | ef244466cd62347cdc15cf93d709e9173997b5c24aa57d14d629e43f49b639cf |
""" Munch is a subclass of dict with attribute-style access.
>>> b = Munch()
>>> b.hello = 'world'
>>> b.hello
'world'
>>> b['hello'] += "!"
>>> b.hello
'world!'
>>> b.foo = Munch(lol=True)
>>> b.foo.lol
True
>>> b.foo is b['foo']
True
It is safe to import * from th... | Infinidat/munch | munch/__init__.py | Python | mit | 22,610 | [
"Brian"
] | 77747daa9bb70d6c11accb0bf7f8acbe6a7bf960faeb188d7d500cf0ad94bf75 |
# (C) British Crown Copyright 2013 - 2016, 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... | SusanJL/iris | lib/iris/fileformats/pp_rules.py | Python | gpl-3.0 | 40,034 | [
"NetCDF"
] | 8411e5bd196222358e2038f48ad9a726f05ade0d9a44099774f5267bbbec5274 |
from builtins import zip
import math
import sympy
from itertools import chain
from .base import BaseVisitor, BaseDualVisitor, DualWithContextMixin
from nineml.exceptions import (NineMLDualVisitException,
NineMLDualVisitValueException,
NineMLDualVisitTypeExce... | INCF/lib9ML | nineml/visitors/equality.py | Python | bsd-3-clause | 12,226 | [
"VisIt"
] | cd4bf0f75f043707a88522baec5a8674f85e5d81be0a5532586cb994c53264d1 |
""" This is a test of the chain
ProductionClient -> ProductionManagerHandler -> ProductionDB
It supposes that the ProductionDB, TransformationDB and the FileCatalogDB to be present
It supposes the ProductionManager, TransformationManager and that DataManagement/FileCatalog services running
"""
from DIRAC.... | petricm/DIRAC | tests/Integration/ProductionSystem/Test_Client_TS_Prod.py | Python | gpl-3.0 | 10,151 | [
"DIRAC"
] | 2299967525261722566e7fd75410633030d5d0b22e40bd283715f629e61dd1b3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Wrapper classes for Cif input and output from Structures.
"""
import math
import re
import os
import textwrap
import warnings
from collections import OrderedDict, deque
from io import StringIO
import numpy... | gVallverdu/pymatgen | pymatgen/io/cif.py | Python | mit | 59,382 | [
"Avogadro",
"CRYSTAL",
"pymatgen"
] | 5d9bd7b76369af70cbe94421dfc493d948dc697b740b0bd08294ee23c959ebf7 |
#!/usr/bin/env python
############################################################
from vtk import *
############################################################
# Create sources
line1 = vtkLineSource()
line1.SetPoint1( 1, 0, 0 )
line1.SetPoint2( -1, 0, 0 )
line1.SetResolution( 32 )
points = vtkPoints()
points.Insert... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Graphics/Python/SegmentAndBrokenLineSources.py | Python | gpl-3.0 | 1,389 | [
"VTK"
] | 3d34c1ffcc884f93c773f6b90d3f6483747b35d4bb885d464c7a632d33ebd66d |
# -*- coding: utf-8 -*-
#
# one-neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
... | INM-6/nest-git-migration | pynest/examples/one-neuron.py | Python | gpl-2.0 | 3,633 | [
"NEURON"
] | 8d35118f3b9997c12040f436280c732c769c681ac5e84760ca673e4af4726a4a |
# sql/compiler.py
# Copyright (C) 2005-2017 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.c... | amisrs/one-eighty | venv2/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py | Python | mit | 107,732 | [
"VisIt"
] | d789ef142e0ffe6e6df2f404e816f5ab947662b30457e6013dda60978c48fa18 |
#!/usr/bin/python
"""Test of line nav after loading a same-page link."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
sequence.append(utils.StartRecordingAction())
sequence.append(KeyComboAction("Down"))
sequence.appen... | chrys87/orca-beep | test/keystrokes/firefox/line_nav_follow_same_page_link_3.py | Python | lgpl-2.1 | 721 | [
"ORCA"
] | 3e790d8b1fad883d1e3d175d00d4de319931c77eba499b36177c064ffc69f29c |
##############################################################################
#
# Copyright (c) 2003 Zope Corporation and Contributors.
# All Rights Reserved.
#
# This software is subject to the provisions of the Zope Public License,
# Version 2.1 (ZPL). A copy of the ZPL should accompany this distribution.
# THIS SO... | anakinsolo/backend | Lib/site-packages/venusian-1.0-py2.7.egg/venusian/advice.py | Python | mit | 2,846 | [
"VisIt"
] | ca9508fa62104239fbd44c3bb96ca672fcfa0ae12c1f679f6c129b911e549d3b |
#!/usr/bin/env python
import pyemma
import numpy as np
import mdtraj
import time
import os
# Source directory
source_directory = '/cbio/jclab/projects/fah/fah-data/munged3/no-solvent/11401' # Src ensembler
################################################################################
# Load reference topology
####... | jchodera/MSMs | jchodera/src-11401/pyemma/cluster.py | Python | gpl-2.0 | 3,309 | [
"MDTraj"
] | 7f4a331da9b3e69e0e81f05c84f65a37be7eb746b84c3e7fa9620ee6693f4588 |
#
# co_co_function_have_rhs.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your ... | kperun/nestml | pynestml/cocos/co_co_function_have_rhs.py | Python | gpl-2.0 | 2,035 | [
"NEURON"
] | 70d50c2074d66dc086eeaa61169a6220dae5cabbe2202fd5de87b4d80fbf4a70 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011-2013 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 General Public License as published by
## the Fre... | tiagocardosos/stoq | stoq/gui/financial.py | Python | gpl-2.0 | 32,037 | [
"VisIt"
] | 99efd0d362ab859d4bfe59477b695a53177df3411402c977add603c752eb5e6f |
# Copyright (c) 2012, GlaxoSmithKline Research & Development Ltd.
# 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
# ... | rdkit/rdkit-orig | Contrib/mmpa/rfrag.py | Python | bsd-3-clause | 9,430 | [
"RDKit"
] | 1931c5b018f3f9094d7bf142fb22010203d246cc73744f7907956ef43d8fa261 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import hrl_lib.mayavi2_util as mu
impor... | tapomayukh/projects_in_python | sandbox_tapo/src/AI/Code for Project-3/HMM Code/hmm_crossvalidation_force_1_states.py | Python | mit | 14,803 | [
"Gaussian",
"Mayavi"
] | e23d446b03917258c309293b2fa12ba52e4055b331388775845387e0130729ae |
#----------------------------------------------------------------------
# This file was generated by encode_bitmaps.py
#
from wx.lib.embeddedimage import PyEmbeddedImage
AutoRefresh = PyEmbeddedImage(
"iVBORw0KGgoAAAANSUhEUgAAABYAAAAWCAYAAADEtGw7AAAABmJLR0QA/wD/AP+gvaeTAAAA"
"CXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTU... | garrettcap/Bulletproof-Backup | wx/tools/XRCed/images.py | Python | gpl-2.0 | 83,540 | [
"VMD"
] | 0e1eb1fe093b0f3f5d37c6d27a868dcb7b5e4188658e791180ab7cb44d5710e7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Hybrid LFP scheme example script, applying the methodology with the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (3): 785-806.
doi: ... | espenhgn/hybridLFPy | examples/example_microcircuit.py | Python | gpl-3.0 | 23,377 | [
"NEURON"
] | 1b155f9448edd35868f24dfd687b6c46012dd9f3b9d75fea52a20c577188ea25 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from django.contrib import messages
from... | analyseuc3m/ANALYSE-v1 | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 20,778 | [
"VisIt"
] | 6b9d05fb31ed3f67fc5e4d3d16810f0ff9e94a3a4258180533d098e91616010b |
# utilities for data file managements for the tests
"""\
gromacs.tests.datafiles
=======================
In the test code, access a data file "fixtures.dat" in the ``data`` directory with::
from gromacs.tests.datafiles import datafile
test_something():
filepath = datafile("fixtures.dat")
contents = ope... | Becksteinlab/GromacsWrapper | tests/datafiles.py | Python | gpl-3.0 | 585 | [
"Gromacs"
] | 8e5540da87b3b4e47173c0b8e09a0b87b533ee6a2075d93f3426c0a171a1eb26 |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import unicode_literals
import six
from owmeta_core.dataobject import DatatypeProperty, ObjectProperty
from .biology import BiologyType
from .cell import Cell
__all__ = ['Connection']
class SynapseType:
Chemical = 'sen... | openworm/PyOpenWorm | owmeta/connection.py | Python | mit | 3,024 | [
"NEURON"
] | 617f762343813c6939198e0244c80ab753671585ab9ce9cca55b560177b4018e |
#! /usr/bin/env python
import sys
from matplotlib.pyplot import *
from numpy import *
def Usage():
print '='*80
print 'Usage: ./%s [photo_file] [kernel_size]' % sys.argv[0]
print 'Eg: ./%s myphoto.png 3' % sys.argv[0]
print '='*80
def fspecial(func_name,kernel_size=3,sigma=1):
if func_name=='gaussian':
m=n=(ke... | Urinx/SomeCodes | Python/GaussianFilter/gaussian_filter.py | Python | gpl-2.0 | 1,746 | [
"Gaussian"
] | 5c7d15ae4af7c8a2df2e747cb965172ac2c7ee84b53e72408c4310786204bb9b |
"""
neurotools.analysis
===================
A collection of analysis functions that may be used by
neurotools.signals or other packages.
.. currentmodule:: neurotools.analysis
Classes
-------
.. autosummary::
TuningCurve
Functions
---------
.. autosummary::
:nosignatures:
ccf
crosscorrelate
make_ke... | tbekolay/neurotools | neurotools/analysis.py | Python | gpl-2.0 | 17,953 | [
"Gaussian",
"NEURON"
] | 6f5e38bc491e153e0cd17dbac08a68e7902d8381edeea83cc640098e0f6048e5 |
# GNU Solfege - free ear training software
# Copyright (C) 2000, 2001, 2002, 2003, 2004, 2006, 2007, 2008 Tom Cato Amundsen
#
# 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... | gabrielelanaro/solfege | solfege/soundcard/__init__.py | Python | gpl-3.0 | 11,078 | [
"CRYSTAL"
] | 4356f3bc13804a2bc89294ae09638ce6215f5e6e4057fb0689f2ef99fd77ef95 |
#
# -*- coding: utf-8 -*-
#
# Copyright (C) 2008-2011 Red Hat, Inc.
# This file is part of python-fedora
#
# python-fedora 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 Li... | vivekanand1101/python-fedora | fedora/wsgi/csrf.py | Python | gpl-2.0 | 13,006 | [
"VisIt"
] | 52f5602a9b25664e242771e4ea9df850fceca9c26e9a1095dc760d94be63d6f0 |
"""Utility modules for the VTK-Python wrappers."""
__all__ = ['colors', 'misc', 'vtkConstants', 'vtkImageExportToArray',
'vtkImageImportFromArray', 'vtkMethodParser', 'vtkVariant',
'numpy_support']
| collects/VTK | Wrapping/Python/vtk/util/__init__.py | Python | bsd-3-clause | 221 | [
"VTK"
] | 4b616e8a755f7c82ec43b2127b1bf359f9310cb06e609657ee4b49a0b256d0d3 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import hashlib
import io
import os
import tarfile
import tempfile
import threading
from io import StringIO
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.FrameworkSystem.Client.Logger ... | ic-hep/DIRAC | src/DIRAC/Core/DISET/private/FileHelper.py | Python | gpl-3.0 | 14,574 | [
"DIRAC"
] | e88a6d222de609f1a9507078f5ef5a9ff5ca8246022c6bec38c1f62162b317b0 |
###############################################################################
# Copyright 2016 - Climate Research Division
# Environment and Climate Change Canada
#
# This file is part of the "EC-CAS diags" package.
#
# "EC-CAS diags" is free software: you can redistribute it and/or modify
# it under... | neishm/EC-CAS-diags | eccas_diags/interfaces/geoschem_tailong_nc.py | Python | lgpl-3.0 | 7,502 | [
"NetCDF"
] | 7fe5b0d64533dd70905262fc3c8eca5c7f93127097e8dd9523c3c3e6950d8f7d |
#
# 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/autots/deprecated/feature/test_time_sequence_feature.py | Python | apache-2.0 | 26,161 | [
"ORCA"
] | 26253dc5ed241b5aebae08ef3224389556131bf69d9f427d3d0a2ddc2b12ee3d |
# Written by David McDougall, 2017
"""
BUILD COMMAND
./setup.py build_ext --inplace
"""
import numpy as np
import scipy.ndimage
import random
import copy
from genetics import Parameters
from encoders import *
from classifiers import *
from sdr import SDR, SynapseManager, Dendrite
class SpatialPoolerParameters(Parame... | ctrl-z-9000-times/HTM_experiments | htm.py | Python | mit | 41,441 | [
"Gaussian",
"NEURON"
] | 5f0a9472655939c73eae29d13ab4c7969d6b98254b3a64200e3a84d03c965b47 |
import collections
import scipy
import numpy as np
import pandas as pd
import warnings
from .plot_utils import ranged_colorbar, make_x_y_ranges, is_cmap_diverging
# matplotlib is technically optional, but required for plotting
try:
import matplotlib
import matplotlib.pyplot as plt
except ImportError:
HAS_M... | dwhswenson/contact_map | contact_map/contact_count.py | Python | lgpl-2.1 | 14,734 | [
"MDTraj"
] | 20411736f0656ac2ee1b3cfcf2ebd8e96f70df3408bcd8ceac64160868e74b84 |
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
import cv2
from moviepy.editor import VideoFileClip
from IPython.display import HTML
import math
import sys
def grayscale(img):
"""Applies the Grayscale transform
This will return an image with only one color channel
but N... | akshaybabloo/Car-ND | Project_1/test2.py | Python | mit | 10,295 | [
"Gaussian"
] | d51a208638308cc31746f530386b67959b279d74e3255d954500866f99faca85 |
import netCDF4 as netcdf
import numpy as np
f = netcdf.Dataset('data/md-solvent-langevin.nc', 'r')
dis = f.variables['distance']
chunksize = 50000
data = []
maxstep = dis.shape[0]
i = range(0, maxstep + chunksize, chunksize)
for k in xrange(len(i)-1):
print i[k], i[k+1]
data.append(dis[i[k]:i[k+1]])
d = np... | nrego/westpa | lib/examples/wca-dimer_openmm/bruteforce/extract_distance.py | Python | gpl-3.0 | 388 | [
"NetCDF"
] | ae0767187e9141e7b018ee6fab75b053fb246f62e77947fe538b372b198a3ed9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import proteindf_bridge as bridge
from .taskobject import TaskObject
from .process import Process
import logging
logger = logging.getLogger(__name__)
class QcProtonate(TaskObject):
''' execute protonate
>>> tmp_pdb = bridge.Pdb('./data/sample/1AKG.p... | ProteinDF/QCLObot | qclobot/qcprotonate.py | Python | gpl-3.0 | 4,364 | [
"Amber"
] | 9fbbbd027e7583cd991a7b4254b3a50cf4f93e2014d6fb319ffec1e4d2c0308f |
#!/usr/bin/env python
from __future__ import division
from myplot.xsection import XSection
from myplot.xsection import VectorXSection
from myplot.axes3d import Axes3D
from psgi.parameterized import state_parser
from matplotlib.widgets import Slider
from traits.api import HasTraits, Range, Instance, on_trait_change, Arr... | treverhines/PSGI | psgi/plot_state.py | Python | mit | 4,860 | [
"Mayavi"
] | c34cc13438e811efd3bb30928c55cd3f352fbc0845b9ab67fb3fda906d12c204 |
from __future__ import print_function
import os
import pytest
from os.path import join
import unittest
import subprocess
@pytest.mark.js
class TestBokehJS(unittest.TestCase):
def test_bokehjs(self):
os.chdir('bokehjs')
proc = subprocess.Popen([join('node_modules', '.bin', 'gulp'), "test"],
... | saifrahmed/bokeh | tests/test_bokehjs.py | Python | bsd-3-clause | 582 | [
"GULP"
] | 8e5d25aa1b033590126bb5deed2c7958e5780bc6a4fadcfad682b6069325b243 |
#!/usr/bin/python
#
# Copyright 2010 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | mashery/io-wraps | google-apis-client-generator/src/googleapis/codegen/api.py | Python | mit | 30,151 | [
"VisIt"
] | 7766f8d5dafca12b80fa5fda3cca220b7dbb35311aedd9eca1c7d17f523a4ec0 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Unit tests for misc.GritNode'''
from __future__ import print_function
import contextlib
import os
import sys
import tempfile
i... | endlessm/chromium-browser | tools/grit/grit/node/misc_unittest.py | Python | bsd-3-clause | 22,766 | [
"xTB"
] | c9e9f4fb798a7ad09d2fee240709e2785deb0d410e798cec2cf9ce12c1e2bc83 |
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import mdtraj.reporters
cutoff = 0.95 * u.nanometers
output_frequency = 25000
n_steps = 500000000
temperature = 298.
pressure = 1.0 * u.atmospheres
platform_name = "CUDA"
pdb_filename = "./1d3z_equil.pdb"
dcd_filename = "./1d3z.dcd"
l... | choderalab/open-forcefield-group | nmr/code/simulate_ubiquitin.py | Python | gpl-2.0 | 1,442 | [
"MDTraj",
"OpenMM"
] | be049a729fd327bdf96f8f418ad563298c18c1579b15d1697fb3551fb391f321 |
# Copyright (C) 2010-2019 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 v... | psci2195/espresso-ffans | testsuite/python/oif_volume_conservation.py | Python | gpl-3.0 | 2,797 | [
"ESPResSo",
"VTK"
] | 4c6a5d00aecd5372d1fcc7cc7b98d7874d5812a6104c4a05020c87f0f8825823 |
"""
A VTK RenderWindowInteractor widget for wxPython.
Find wxPython info at http://wxPython.org
Created by Prabhu Ramachandran, April 2002
Based on wxVTKRenderWindow.py
Fixes and updates by Charl P. Botha 2003-2008
Updated to new wx namespace and some cleaning up by Andrea Gavana,
December 2006
"""
... | hlzz/dotfiles | graphics/VTK-7.0.0/Wrapping/Python/vtk/wx/wxVTKRenderWindowInteractor.py | Python | bsd-3-clause | 25,228 | [
"VTK"
] | 1a915e4094e5ec8a11a79f9613b90c1b6f6b2f413ab7a116c5a82896c08ac7f4 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | evolve/core/constants.py | Python | agpl-3.0 | 6,458 | [
"Gaussian"
] | 6882717a180d4c184065e3f701a7a2950dcc8e0b3b87f0f65e2d9bf00aba1fe3 |
"""Tool for sorting imports alphabetically, and automatically separated into sections."""
import argparse
import functools
import json
import os
import sys
from io import TextIOWrapper
from pathlib import Path
from typing import Any, Dict, Iterable, Iterator, List, Optional, Sequence, Set
from warnings import warn
fro... | TeamSPoon/logicmoo_workspace | packs_web/butterfly/lib/python3.7/site-packages/isort/main.py | Python | mit | 35,851 | [
"VisIt"
] | 6ad016c8065a1f9370ced22b9804c60a99ca73b1f5134444955dd52fcfd13d14 |
input_name = '../examples/linear_elasticity/linear_elastic.py'
output_name = 'test_linear_elastic.vtk'
from tests_basic import TestInput
class Test( TestInput ):
pass
| RexFuzzle/sfepy | tests/test_input_linear_elastic.py | Python | bsd-3-clause | 172 | [
"VTK"
] | 2dfc47f626a4ed09e216b977950fd72793e2ad623ef0833ae27fd7cef3d0b66a |
#!/bin/env python
""" create rst files for documentation of DIRAC """
import os
import shutil
import socket
import sys
def mkdir(folder):
"""create a folder, ignore if it exists"""
try:
folder = os.path.join(os.getcwd(), folder)
os.mkdir(folder)
except OSError as e:
print "MakeDoc: Exception %s when... | arrabito/DIRAC | docs/Tools/MakeDoc.py | Python | gpl-3.0 | 10,459 | [
"DIRAC"
] | 34149a2dc283a4a2ec84f1bac589e6445c47418ddf15b41208079e37a8a5e371 |
################################################################################
# Peach - Computational Intelligence for Python
# Jose Alexandre Nalon
#
# This file: tutorial/self-organizing-maps.py
# Extended example on self-organizing maps
#############################################################################... | PaulGrimal/peach | tutorial/neural-networks/self-organizing-maps.py | Python | lgpl-2.1 | 2,858 | [
"Gaussian",
"NEURON"
] | f3b54befe61de6c59a12f7295065e8b8cfa8b6eaa1c0da55024d4e5723030722 |
#
# 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 us... | mrchristine/spark-examples-dbc | src/main/python/ml/gaussian_mixture_example.py | Python | apache-2.0 | 1,522 | [
"Gaussian"
] | d2661a7e43ca8904cad4361a58d58366c67dede0368cd9ec97fa2101e73f278d |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'EphysProp.nlex_id'
db.add_column(u'neuroelectro_ephysprop', 'nlex_id',
... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0068_auto__add_field_ephysprop_nlex_id.py | Python | gpl-2.0 | 31,214 | [
"NEURON"
] | 42b21d10c48bab87d0f460a8a02dccb9e0533d56656f15f8ac49638b71eba1e4 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Scaled_Features/best_kNN_PCA/2_categories/test11_cross_validate_categories_mov_fixed_1200ms_scaled_method_ii.py | Python | mit | 5,012 | [
"Mayavi"
] | 6e08c9b493863857a94f3ba35134a60f6a5ed09c7a3f638e975c711bc4e7feba |
## Copyright (c) 2020 The WebM project authors. All Rights Reserved.
##
## Use of this source code is governed by a BSD-style license
## that can be found in the LICENSE file in the root of the source
## tree. An additional intellectual property rights grant can be found
## in the file PATENTS. All contributing p... | youtube/cobalt | third_party/libvpx/tools/3D-Reconstruction/MotionEST/Anandan.py | Python | bsd-3-clause | 6,520 | [
"Gaussian"
] | 1bd75a0b3e78d65046b0060d0601e44eeed90c3cc1af91b16599909702c26de0 |
import pdb
import itertools as it
def scinot(string):
"""Takes a string in MCNP scientific notation (without 'E' character), and returns a string of standard scientific notation."""
"""If there is no '+' or '-' character in string, returns it as it is."""
"""If the argument is not string, returns the argument"""
i... | haupt235/waldo | modules.py | Python | mit | 2,660 | [
"VTK"
] | e5427902e17f0b3a259ae077c12324694e09ccd3e168602b37187520de3b0300 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2017, Brian Coca <bcoca@ansible.com>
# (c) 2017, Adam Miller <admiller@redhat.com>
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__m... | roadmapper/ansible | lib/ansible/modules/system/sysvinit.py | Python | gpl-3.0 | 13,491 | [
"Brian"
] | ad907beda49bec1e69751e5c3321bd8cf457c28e570063f8f7298b1a7db13824 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
from itertools import count
import re, os, cStringIO, time, cgi, urlparse
from xml.dom import minidom as dom
from xml.sax.handler import ErrorHandler, feature_validation
from xml.dom.pulldom import SAX2DOM
from xml.sax import make_parser
from xml... | skycucumber/Messaging-Gateway | webapp/venv/lib/python2.7/site-packages/twisted/lore/tree.py | Python | gpl-2.0 | 40,135 | [
"VisIt"
] | 2c62f97f2d81b8091be481353148ba5802c98a0af16e0648765dd229f28116e6 |
#!/usr/bin/env python
# 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
#
# U... | sunqm/pyscf | pyscf/scf/jk.py | Python | apache-2.0 | 11,425 | [
"PySCF"
] | 3a42b6ed1a3698deb533a9d1cdad2fda53be33413fbbb96c55f35ec0dcfdcc6f |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
#import os
#from unittest import TestCase
#from exatomic import Universe
#from exatomic.gaussian import Output, Input
#from exatomic.gaussian.inputs import _handle_args
#class Test... | exa-analytics/exatomic | exatomic/gaussian/tests/test_inputs.py | Python | apache-2.0 | 1,613 | [
"Gaussian"
] | 606dfb0575f6b143ca50ba5f3bbdf8278ec3a258fa6cdf1e99b1d7292bced958 |
from . import picard, bamUtil, samtools,bwa
import os
opj = os.path.join
class FilterBamByRG_To_FastQ(samtools.FilterBamByRG,picard.REVERTSAM,bamUtil.Bam2FastQ):
name = "Extract ReadGroup from BAM and Convert to FastQ"
inputs = ['bam']
outputs = ['1.fastq.gz','2.fastq.gz','unpaired.fastq.gz']
time_req ... | LPM-HMS/GenomeKey | obsolete/genomekey/tools/pipes.py | Python | mit | 2,573 | [
"BWA"
] | 0f196095218b56a5778b639cddca845a4db5273bb86b7a9973367e08528e6882 |
# -*- coding: utf-8 -*-
# These tests don't work at the moment, due to the security_groups multi select not working
# in selenium (the group is selected then immediately reset)
import fauxfactory
import pytest
from riggerlib import recursive_update
from textwrap import dedent
from cfme import test_requirements
from c... | okolisny/integration_tests | cfme/tests/cloud/test_provisioning.py | Python | gpl-2.0 | 26,691 | [
"VisIt"
] | 507e4b1a296f63d2f890f38c955c9f329e5b86fd120e359a3caad9f753450358 |
# ##########################################
# Version 1.0
# Author: Brian Torres-Gil
#
# About this script:
# Triggered when a WildFire syslog indicates a file has been analyzed by WildFire.
# This script retrieves the WildFire data relating to that syslog from the WildFire
# cloud service API.
#
# Script's acti... | PaloAltoNetworks-BD/SplunkforPaloAltoNetworks | SplunkforPaloAltoNetworks/bin/retrieveWildFireReport.py | Python | isc | 5,572 | [
"Brian"
] | c356a97be83082c1a54e3812770b4eefc09c2f5e995578ef547c33dd8efb56c5 |
#! /usr/bin/env python
#
# plot_connections.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License... | QJonny/CyNest | topology/doc/old_doc/plotting_tools/plot_connections.py | Python | gpl-2.0 | 3,753 | [
"Mayavi"
] | 505c4f98b9521fa4fca1aa2258f985c3cfd6493ae3511d75ade8ce3927e9dcf7 |
#!/usr/bin/env python3
#
# Copyright (c) 2022, NVIDIA
#
import sys
if sys.version_info >= (3, 3):
from time import process_time as timer
else:
from timeit import default_timer as timer
import numpy as np
def nttk_sd_t_s1_1(d3,d2,d1,d6,d5,d4,triplesx,t1sub,v2sub):
for h1,h2,h3,p4,p5,p6 in np.ndindex((d1,d... | jeffhammond/nwchem-tce-triples-kernels | new-languages/nttk.py | Python | apache-2.0 | 32,514 | [
"NWChem"
] | 2161f0292a50c01fa73ea2c999fc48caed8aaa3d748948c9cef43d96c11b6509 |
#!/usr/bin/python
# Copyright 2011-2012 Erik Reckase <e.reckase@gmail.com>,
# Steven Robertson <steven@strobe.cc>.
import numpy as np
from copy import deepcopy
from itertools import izip_longest
import spectypes
import specs
from use import Wrapper
from util import get, json_encode, resolve_s... | stevenrobertson/cuburn | cuburn/genome/blend.py | Python | gpl-2.0 | 12,134 | [
"VisIt"
] | 2620a268991e7a85d9e52d3c18828f83b3e9e7ddaecb3c769c1011579ed6fe14 |
# to be imported to access modbus registers as analogue io
# 03.04.2014 neeme
# 04.04.2014 it works, without periodical executuoin and without acces by svc reg
# 06.04.2014 seguential register read for optimized reading, done
# 14.04.2014 mb[mbi] (multiple modbus connections) support. NOT READY!
# 16.04.2014 fix... | dcneeme/droidcontroller | droidcontroller/achannels.py | Python | gpl-3.0 | 28,405 | [
"BLAST"
] | c9380f8b7b03ae6856e8ce6959dd06901d20d3c44634c888f5fff6673603db09 |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | google/python-temescal | temescal/__init__.py | Python | apache-2.0 | 9,284 | [
"BLAST"
] | b3f28f5dc6f38119f6302a06c97fa398323656a95308966907198580bc0fab5d |
""" NormalizeMethodCalls turns built in method calls into function calls. """
from pythran.analyses import Globals
from pythran.passmanager import Transformation
from pythran.syntax import PythranSyntaxError
from pythran.tables import attributes, functions, methods, MODULES
import ast
class NormalizeMethodCalls(Tra... | artas360/pythran | pythran/transformations/normalize_method_calls.py | Python | bsd-3-clause | 6,717 | [
"VisIt"
] | 65df8747c3456b08189110269e61288108b936a624a6cfb8e2124676c56eeaa1 |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
#
# VesselDisplay
#
class VesselDisplay(ScriptedLoadableModule):
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "Vessel Display"
... | KitwareMedical/VesselView | Modules/Scripted/VesselDisplay/VesselDisplay.py | Python | apache-2.0 | 5,072 | [
"VTK"
] | 0e8c65cae1098e6cb76cc32a360d04069365dc646c9a10befbb813a9063526f0 |
# Copyright 2019 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import re
import test_util
import time
from absl import app
from selenium import webdriver
from pywinauto.application import Application
UnsafePageLink = "h... | endlessm/chromium-browser | chrome/test/enterprise/e2e/policy/safe_browsing/safe_browsing_ui_test.py | Python | bsd-3-clause | 2,371 | [
"VisIt"
] | ee82781da096b78e56580a0567a2b880272cd4a88fdc1b11adeecf432e4a515e |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | kashif/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 67,091 | [
"Gaussian"
] | be8a75df89231e2cf719a033304ae5a7e3135dd75bf47248563f9ffa0452e3be |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/gtensor/test/test_uhf.py | Python | apache-2.0 | 7,596 | [
"PySCF"
] | f22cfeecf4ed25bfbd8ec20e84c79a310c2394c3603df8f3aac4c01c14b2b51b |
import numpy as np
import matplotlib
import matplotlib.pylab as plt
import healpy as hp
import string
import yt
import os
import glob
from PIL import Image as PIL_Image
from images2gif import writeGif
from scipy.special import sph_harm,sph_jn
import beatbox
from beatbox.multiverse import Multiverse
# ===============... | LaurencePeanuts/Music | beatbox/universe.py | Python | mit | 41,104 | [
"Gaussian"
] | e6661f064a65cb7e2acb0440e3a3824a2500187e5f366101b049eab523c14ec4 |
import urllib
from galaxy import datatypes, config
def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
data_name = param_dict.get( 'name', 'Biomart query' )
data_type = param_dict.get( 'type', 'text' )
name, data = out_data.items()[0]
data =... | jmchilton/galaxy-central | tools/data_source/biomart_filter.py | Python | mit | 1,427 | [
"Galaxy"
] | a863f5eeef938439d5fe747f50155ca2e36fc9f988d6cd93f502f484dfd29ce4 |
##############################################################################
# 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/tcoffee/package.py | Python | lgpl-2.1 | 2,140 | [
"BLAST"
] | 2fb2b9da990d7daba18ffeed95cf34a7fcce5a46e2ba74e0bcc3f959eedf26c1 |
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