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__RCSID__ = "$Id$"
import os
import time
import GSI
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.DISET.private.Transports.BaseTransport import BaseTransport
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.DISET.pr... | Andrew-McNab-UK/DIRAC | Core/DISET/private/Transports/SSLTransport.py | Python | gpl-3.0 | 9,664 | [
"DIRAC"
] | 4dc37ce9d6afaad2f10e40b655e4fe04477cdb1722bae13dbebc6aeb7c0b9049 |
#
# 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/xmlutils.py | Python | apache-2.0 | 5,547 | [
"VisIt"
] | 75b655fa14196949430b01bc9a8b0b44526e3d3478646b6080e62a5a582d3e21 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kevin-coder/tensorflow-fork | tensorflow/contrib/timeseries/python/timeseries/state_space_models/state_space_model.py | Python | apache-2.0 | 57,400 | [
"Gaussian"
] | 76c619cfe8634f64d9e83e6b09d59bafcc4f5fe0ecb25d7ea196acd431674b5f |
# -*- coding: utf-8 -*-
# Copyright (c) 2015 Australian Government, Department of the Environment
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without... | lpinner/metageta | metageta/formats/netcdf.py | Python | mit | 5,361 | [
"NetCDF"
] | cfab67a55482df2fb384ec0ac976c2c09a2e44335dd6eb94c2dee7df8afdf466 |
#!/usr/bin/env python
# Generative Adversarial Networks (GAN) example in PyTorch.
# See related blog post at https://medium.com/@devnag/generative-adversarial-networks-gans-in-50-lines-of-code-pytorch-e81b79659e3f#.sch4xgsa9
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import t... | xiaoxiaoyao/MyApp | PythonApplication1/deeplearning/examples/gan_pytorch.py | Python | unlicense | 5,486 | [
"Gaussian"
] | 9b145505c4e386921d33fefe0fd10b2961aebb5b4376ef6c1a91219baa99457a |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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... | flavioamieiro/pypln.web | pypln/web/core/urls.py | Python | gpl-3.0 | 2,075 | [
"NAMD"
] | 0127d2bbea042b13aca9357eba6b0ffc81671b1b1e07a4b256856101483ae202 |
"""Defines a Collection filter which is a collection of mayavi
filters/components bundled into one.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Bool, List
from traitsui.a... | dmsurti/mayavi | mayavi/filters/collection.py | Python | bsd-3-clause | 6,763 | [
"Mayavi"
] | 19d13aab9b2c7a8d5cc214346b742ce84143c9503784f9acae236dec0d70e9b6 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | hmc_swindles/targets/neals_funnel.py | Python | apache-2.0 | 3,974 | [
"Gaussian"
] | 58ee2c4bb400d86962ae80ac8db5a5c8549d9c2f3848a718b109b96e7dd103fc |
"""Tornado handlers for the notebooks web service.
Authors:
* 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 COPYING, dis... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/html/services/notebooks/handlers.py | Python | apache-2.0 | 5,267 | [
"Brian"
] | d650840390bb3d53e2f86a2ee1b37a34a063dc97ca45f198e71b355bda4f83a4 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to
# make it easier to submit large numbers of jobs on supercomputers. It
# provides a python interface to physical input, ... | pylada/pylada-light | tests/ipython/conftest.py | Python | gpl-3.0 | 2,390 | [
"CRYSTAL",
"VASP"
] | de333bb656027859cd3f5ea772d56dd0b4ea33b5748eae12dc4d4d7975e6e4fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Deep learning via word2vec's "hierarchical softmax skip-gram and CBOW models" [1]_.
The training algorithm was originally ported from... | lewer/gensim | gensim/models/word2vec.py | Python | gpl-3.0 | 34,926 | [
"VisIt"
] | 75fd815b1c8986a6bd3856f5c17e549affab8db389131b6ef97901f88be18092 |
"""
In order to avoid double counting of bases in overlapping paired end reads,
this script accept mapped reads in SAM format, use the position to determine
overlap, and set the lower base-quality of pair overlap to 0.
It is assumed that the reads are name-sorted as when they come from the
aligner.
Usage:
bwa mem... | PeteHaitch/bwa-parclip | bam-merge-pairs.py | Python | mit | 1,281 | [
"BWA"
] | bf92876944566374c5abed7c95fd905bd618e1f8df3defb7ce3e33afee2405e9 |
#!/usr/bin/env python
# This example demonstrates the use of streamlines generated from seeds,
# combined with a tube filter to create several streamtubes.
import vtk
from vtk.util.misc import vtkGetDataRoot
from vtk.util.colors import *
VTK_DATA_ROOT = vtkGetDataRoot()
# We read a data file the is a CFD a... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/VisualizationAlgorithms/Python/officeTubes.py | Python | bsd-3-clause | 12,926 | [
"VTK"
] | 890e7b1c3c0234e2e54b04fad1e6d8ffcb0530343d41554f04fbc69face4d541 |
# $Id$
#
# Copyright (C) 2007-2009 Greg Landrum
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
try:
import sqlalchemy
except ImportError:
from... | rvianello/rdkit | rdkit/Chem/MolDb/Loader.py | Python | bsd-3-clause | 408 | [
"RDKit"
] | 1f2526622ef6fd016d7d3cf9e0ad42451e52f4becf5e8f81de9bf09cb1005cd1 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/ajax/satellites.py | Python | gpl-2.0 | 5,541 | [
"VisIt"
] | e484785630b3e29b516503660d38c29a364cc6095470a1e7646abddc3b41d07e |
import os
import sys
import csv
from itertools import count
def parse(basename, ordinal, outfd):
outcsv = csv.writer(outfd)
for i in count(0):
fname = "{}_{:08d}.vtk".format(basename, i)
try:
infd = open(fname, "r")
except IOError:
break
print "Timeste... | bsmedberg/smedberg-pointsbytime | parser.py | Python | apache-2.0 | 1,925 | [
"VTK"
] | 54e6456c1d85b7ab069f67f45bf525fdd174821a48d912b3e3a097c56f1c382c |
# $HeadURL$
__RCSID__ = "$Id$"
import os
import os.path
try:
import hashlib as md5
except ImportError:
import md5
import time
import threading
from DIRAC import S_OK, S_ERROR, gLogger, rootPath
from DIRAC.Core.Utilities.ThreadSafe import Synchronizer
from DIRAC.Core.Utilities import Time
gSynchro = Synchronizer(... | Sbalbp/DIRAC | Core/Utilities/FileCache.py | Python | gpl-3.0 | 3,614 | [
"DIRAC"
] | 511e4c41a54b118690aa6741f8e91d92866d25c66c2bc1bc7dff74a4dfeafa34 |
#!/usr/bin/env python3
"""
script for scaffolding contigs based on paired read coverage
"""
import os
import sys
import networkx as nx
from operator import itemgetter
import ctbRA.re_assemble_errors as curate
from ctbBio.search import search as search
from ctbBio.fasta import iterate_fasta as parse_fasta
from ctbBio... | christophertbrown/fix_assembly_errors | ctbRA/scaffolder.py | Python | gpl-2.0 | 13,711 | [
"BLAST"
] | 10f54552830387dd74e72af976c7b2a93ef09a72181fcad88dafd76faf4ffda4 |
import re
from ez_setup import use_setuptools
from setuptools import setup
MIN_SETUPTOOLS_VERSION = "0.7"
use_setuptools(version=MIN_SETUPTOOLS_VERSION)
# Following the recommendations of PEP 396 we parse the version number
# out of the module.
def parseVersion(moduleFile):
"""
Parses the version string from... | shajoezhu/server | setup.py | Python | apache-2.0 | 2,177 | [
"pysam"
] | 4ebbe357789d5d4f61560a9f8d591b13a74293eb25edbde4cbe8ebed5198f612 |
# Copyright (C) 2010-2018 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... | mkuron/espresso | testsuite/python/observable_cylindricalLB.py | Python | gpl-3.0 | 9,280 | [
"ESPResSo"
] | ef09311b41db63ff603b87e9a42664718ff6bcaee1b3452047f14380d5a5089b |
#!/usr/bin/env python
import unittest
from fastparser import*
from bike.parsing.load import*
from bike.parsing.fastparserast import*
from bike.testutils import *
class TestFastParser(BRMTestCase):
def test_doesntGetClassDeclsInMLStrings(self):
src = trimLines('''
"""
class foo bah
"... | srusskih/SublimeBicycleRepair | bike/parsing/test_fastparser.py | Python | mit | 4,300 | [
"VisIt"
] | 6374b32b1eba62c3bd6871253293b0df9a2aaec0ccfb3c7118a36a439d06a649 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Test the io/__init__.py module.
"""
# import iris tests first so that some things can be initialised before importing any... | pp-mo/iris | lib/iris/tests/test_io_init.py | Python | lgpl-3.0 | 5,188 | [
"NetCDF"
] | 39fc5ea840c3ef0d0af53e595a2636c622c2a76bfdd860ff5459fdd7b009d70d |
# -*- coding: utf-8 -*-
"""
This module contains a custom streamlining class derived from the MayaVi2
streamlining class, modified to accept an array of seed points for visulaisation
using mayavi.
.. warning::
The documentation for this class cannot be built on Read The Docs, it is possible to build it locally.
Y... | Cadair/solarbextrapolation | solarbextrapolation/mayavi_seed_streamlines.py | Python | mit | 4,759 | [
"Mayavi"
] | 6ce5874e7508f752abe8d2779c7d07495fa792e0182bba66b92968bcfbabff3c |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RRots(RPackage):
"""Reproducibility-Optimized Test Statistic.
Calculates the Repro... | iulian787/spack | var/spack/repos/builtin/packages/r-rots/package.py | Python | lgpl-2.1 | 1,045 | [
"Bioconductor"
] | 65d8686d58f09509fba698785528c920a9706cdc01129c336338ee3b87132a37 |
# -*- coding: utf-8 -*-
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the ... | pescobar/easybuild-easyblocks | easybuild/easyblocks/l/lammps.py | Python | gpl-2.0 | 16,981 | [
"LAMMPS"
] | c6d89207e42ccd5c4e2195c738c01190ec9801e38d6d798b094234f001eea421 |
#!/usr/bin/python
# -*- encoding: utf-8; py-indent-offset: 4 -*-
# +------------------------------------------------------------------+
# | ____ _ _ __ __ _ __ |
# | / ___| |__ ___ ___| | __ | \/ | |/ / |
# | | | | '_ \ / _ \/ __| |/ /... | oposs/check_mk_mirror | web/htdocs/userdb.py | Python | gpl-2.0 | 38,867 | [
"VisIt"
] | ccb114cb5382b3aafef99a1db8a38d63ccb04eb275db41a699c33ec01d8906b8 |
# $HeadURL$
__RCSID__ = "$Id$"
import os
import types
import time
import GSI
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.DISET.private.Transports.BaseTransport import BaseTransport
from DIRAC.FrameworkSystem.Client.Logger import gLogger... | calancha/DIRAC | Core/DISET/private/Transports/SSLTransport.py | Python | gpl-3.0 | 9,393 | [
"DIRAC"
] | 6d3d3b1b8a8853522a3646b09d0d63eb9aa6f4a0b13ff47f39606049f15b5c2a |
__author__ = 'Jonas Eberle <jonas.eberle@eberle-mail.de>'
import subprocess
import os
import osr
import ogr
import numpy as np
from osgeo import gdal, gdalconst, gdalnumeric, gdal_array
import shutil
from pyEOM import log
LOGGER = log.LOGGER
def TestMODISHDFProcessor():
geom = 'POLYGON((7.807615733070551 26.259... | jonas-eberle/pyEOM | pyEOM/processing.py | Python | mit | 15,654 | [
"NetCDF"
] | e994e11eff38332d7162eb680f557dd994eb6f88ddd835030075135f9355fb7a |
import os.path as op
import pytest
from ssbio.pipeline.gempro import GEMPRO
from ssbio.core.genepro import GenePro
from ssbio.databases.kegg import KEGGProp
from ssbio.databases.uniprot import UniProtProp
from ssbio.databases.pdb import PDBProp
from cobra.core import Model, DictList
import cobra.manipulation
@pytest.... | SBRG/ssbio | ssbio/test/test_pipeline_gempro.py | Python | mit | 10,016 | [
"Biopython"
] | 78fe11af21a0de11feffec05e3375e701de70d4a6558d6a7071687f6439326b4 |
"""
okeanidanalysis.lib
===================
Generally useful methods that span across submodules.
"""
import numpy as np
import scipy as sp
import scipy.interpolate
import matplotlib as mpl
import matplotlib.patches
golden_ratio = 1.61803398875
def injectlocals(l, skip=['self','args','kwargs'], **kwargs):
"""... | bluesquall/okeanidanalysis | okeanidanalysis/lib.py | Python | mit | 5,322 | [
"NetCDF"
] | 9faeebd3106a270d6917968f65289bf3ab9642caa2b24547ffaf8da88fccad05 |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self, scene_map):
self.scene_map = scene_map
def play(self):
curr... | AisakaTiger/Learn-Python-The-Hard-Way | ex43.py | Python | mit | 8,783 | [
"BLAST"
] | 9df4abc6bd6d02262a1f52031590add9c532e37153264d66f14e5cdfc6c0e9b2 |
# $HeadURL$
"""
Extremely simple utility class to send mails
"""
__RCSID__ = "$Id$"
import socket
from smtplib import SMTP
from email.mime.text import MIMEText
from getpass import getuser
from DIRAC import gLogger, S_OK, S_ERROR
class Mail( object ):
def __init__( self ):
self._subject = ''
self._messa... | vmendez/DIRAC | Core/Utilities/Mail.py | Python | gpl-3.0 | 1,461 | [
"DIRAC"
] | 9fc63eac3f05a099b6ff1f57fda10f795d264b8c2eaf6157f363ec8bbbe6e74c |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RImpute(RPackage):
"""impute: Imputation for microarray data
Imputation for microa... | LLNL/spack | var/spack/repos/builtin/packages/r-impute/package.py | Python | lgpl-2.1 | 968 | [
"Bioconductor"
] | 891d1c28324612bb4b500b9cfd5948c394534139a2966d3c7eda0920c4653fd8 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/esutil/Grid.py | Python | gpl-3.0 | 1,420 | [
"ESPResSo"
] | e3917553add8daf8b1e82f200d3af717bbbbfcb454f0da8543185116567352e2 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | samzhang111/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 38,647 | [
"Brian"
] | 1a4662889ebe38a312932060026e98ee737f8fb94475030b6efc406fa44492e6 |
# -*- coding: utf-8 -*-
"""Geocoding Module
Use GDAL to make output products resampled to geographic projection with
constant lat/lon spacing.
Authors: Brian Hawkins, Michael Denbina
Copyright 2016 California Institute of Technology. All rights reserved.
United States Government Sponsorship... | mdenbina/kapok | kapok/geo.py | Python | gpl-3.0 | 14,657 | [
"Brian",
"Gaussian"
] | 6eb9d78cdcd575df8cb81554dd5c04203a6d91768d33c298296b712d5ba645e8 |
# -*- coding: utf-8 -*-
# Copyright 2013-2014 Victor Amin, http://vamin.net/
"""MESS.DB mopac method
This module contains the mopac method class and load function.
"""
from __future__ import print_function
from __future__ import unicode_literals
import codecs
import json
import os
import subprocess
import sys
impor... | vamin/MESS.DB | mess/methods/mopac.py | Python | agpl-3.0 | 15,237 | [
"MOPAC"
] | 8a311ee7770b7c1770170d0eae4ffa7beed20032e416afb7d2c1b26614d177b4 |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/pmv_dev/APBSCommands.py is part of ePMV.
ePMV 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
... | corredD/ePMV | pmv_dev/APBSCommands.py | Python | gpl-3.0 | 239,066 | [
"Amber",
"CHARMM",
"VisIt"
] | 5731eaad36101ca3362ad8bcb9b07acee57ffa9fdf570e068a8ca8979bf6175a |
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 15 14:48:48 2016
@author: ivaltchanov
"""
# coding: utf-8
# In[1]:
import matplotlib.pyplot as plt
import numpy as np
import math
from astropy.io import fits
import zipfile
import tarfile
from astropy.modeling import models, fitting
from astropy.stats import median_ab... | ivvv/spireFts | POCT-py35-test.py | Python | mit | 15,645 | [
"Gaussian"
] | 5b4954740d603cb86cb16e029072ecdf23b9d8067cceb95e0daad7207bbaed7a |
import sys
if sys.version_info < (3, 2):
print('This antlr3 module requires Python 3.2 or later. You can '
'download Python 3 from\nhttps://python.org/, '
'or visit http://www.antlr.org/ for the Python target.')
sys.exit(1)
# bootstrapping setuptools
import ez_setup
ez_setup.use_setuptools... | ekcs/congress | thirdparty/antlr3-antlr-3.5/runtime/Python3/setup.py | Python | apache-2.0 | 8,719 | [
"VisIt"
] | 24bec9a8f4a4e8ccb571892a7465db0d84fdb96bc5369a54a30e7399b22686cb |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
"""
Tests specific functionality of the grid plot.
Different inputs are tested (siesta .RHO and sisl Hamiltonian).
""... | zerothi/sisl | sisl/viz/plots/tests/test_grid.py | Python | mpl-2.0 | 9,819 | [
"SIESTA",
"VASP"
] | 955328d53415cfc1406f2faecd74a19e853354c58b8c48fa8cc050baff515475 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/custom/lib/db.py | Python | gpl-2.0 | 3,501 | [
"Brian"
] | 13672b3bd39ffa81d08a8021858f73201282b1105ce0476b3109d431be9fea6f |
import datetime
import gzip
from itertools import count
import os
curdir = os.path.join(os.getcwd(), os.path.dirname(__file__))
import sys
import threading
import time
import urllib
import cherrypy
from cherrypy._cpcompat import next, ntob, quote, xrange
from cherrypy.lib import httputil
gif_bytes = ntob(
'GIF89a... | xpavlus/parabaramba | venv/lib/python2.7/site-packages/cherrypy/test/test_caching.py | Python | gpl-3.0 | 12,892 | [
"VisIt"
] | 77888bfb3782cace8e2c3477553863541fe32fd55ee5bb9e978ab491021656c8 |
#!/usr/bin/python
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
from optparse import make_option
from os import makedirs, path, listdir, remove
import os, sys, re, errno, ... | Koonkie/MetaPathways_Python_Koonkie.3.0 | libs/python_modules/grid/blast_using_grid.py | Python | mit | 19,645 | [
"BLAST"
] | 313c61747682e52bcb93861c62a7742de8765560566bce6facdd7bb57329b6e4 |
"""
viscount.api
provides the framework for the REST api
"""
from functools import wraps
from flask import jsonify
from flask.ext.security.decorators import login_required, roles_required
from ..core import ViscountException, ViscountFormException
from .datatables import DataTablesException, handle_DataTablesExcept... | dacb/viscount | viscount/api/__init__.py | Python | bsd-2-clause | 1,855 | [
"Cytoscape"
] | 2c85668f279194f971eb3388e37956054b3e32d3fc49786f17f36d5596529ac7 |
# Copyright (c) 2013, 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
# ... | bp-kelley/rdkit | Contrib/mmpa/rfrag.py | Python | bsd-3-clause | 8,087 | [
"RDKit"
] | 51cc3f38e32aaf275ceb88ad4ccccf3cca83544edbffc32e5627f525cf82e60d |
# -*- coding: utf-8 -*-
#
# brunel_alpha_evolution_strategies.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 versio... | terhorstd/nest-simulator | pynest/examples/brunel_alpha_evolution_strategies.py | Python | gpl-2.0 | 21,035 | [
"Gaussian",
"NEURON"
] | 8b8e69281a0b20f260f7192307a62f90feebf45f2250d12aff2f0f5181ffd396 |
from sys import argv
from os import mkdir, path
import time
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import FormatStrFormatter
from matplotlib.font_manager import FontProperties
# Timing Decorator
def timeFunction(f):
def wrap(*args):
time1 = time.time()
ret = f(*ar... | CompPhysics/MachineLearning | doc/Programs/Sampling/analysis.py | Python | cc0-1.0 | 7,905 | [
"Gaussian"
] | be2d367a43206a9e9e45dd299f20c6cd67885307e2ec7f9357a9bb5b030cc6be |
# demo.py ---
#
# Filename: demo.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri Feb 5 23:19:44 2010 (+0530)
# Version:
# Last-Updated: Sat Feb 6 00:05:48 2010 (+0530)
# By: Subhasis Ray
# Update #: 41
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
#... | BhallaLab/moose-thalamocortical | pymoose/gui/demo/demo.py | Python | lgpl-2.1 | 2,597 | [
"MOOSE"
] | 0309c7b7e17ffe404019821cd20c83ef857b156483b28f27fbe35e8ac3448d99 |
#!/usr/bin/env python
import numpy as np
from statsmodels.sandbox.pca import Pca
x=np.random.randn(1000)
y=x*2.3+5+np.random.randn(1000)
z=x*3.1+2.1*y+np.random.randn(1000)/2
#create the Pca object - requires a p x N array as the input
p=Pca((x,y,z))
print('energies:',p.getEnergies())
print('vecs:',p.getEigenvectors... | hlin117/statsmodels | statsmodels/sandbox/examples/example_pca.py | Python | bsd-3-clause | 517 | [
"Mayavi"
] | a84c8c6b9eb947822a335164db9f16dd24a8c9d39f67fb9ceaf000a3438eb0cb |
"""
====================================================================
K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
====================================================================
Provides routines for k-means clustering, generating code books
from k-means models, and quantizing vectors ... | Universal-Model-Converter/UMC3.0a | data/Python/x86/Lib/site-packages/scipy/cluster/vq.py | Python | mit | 25,565 | [
"Gaussian"
] | cf369f824de50363759e0a79ba8693dcc431cf6eb70d05d0b076cf1a03dfcd9c |
"""
Tests: src/python/structure.py
"""
import mdtraj
import numpy as np
from numpy.testing import (assert_almost_equal, assert_array_almost_equal,
assert_allclose, assert_array_equal)
from scipy import ndimage
from thor import structure
from thor import math2
fr... | tjlane/thor | test/test_structure.py | Python | gpl-2.0 | 2,365 | [
"MDTraj"
] | 194b179722b0e635336d3216dd13af9ee85df580fa920dda156c12d73978e0dd |
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
star... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t34_rlvps01.py | Python | mit | 7,663 | [
"NEURON"
] | 8898de875ae2168087be5e0103b62628c3cc3bf0f9e00d9a970a08be624d0667 |
from setuptools import setup
import sys
if not sys.version_info[0] == 3:
sys.exit("Sorry, only Python 3 is supported")
files = ["data/*"]
setup(name='sam2gfa',
version='1.0',
description='SAM to GFA Converter ',
author='Hamza Khan',
author_email='hamza.khan@alumni.ubc.ca',
packages=... | hamzakhanvit/sam2gfa | setup.py | Python | mit | 566 | [
"Biopython"
] | ec0731f618231fdc5e8c2d5166c5d114f4ca3d5377500868f6bee072c4600e06 |
#!/usr/bin/env python
"""
Tracking of rotating point.
Rotation speed is constant.
Both state and measurements vectors are 1D (a point angle),
Measurement is the real point angle + gaussian noise.
The real and the estimated points are connected with yellow line segment,
the real and the measured points... | makelove/OpenCV-Python-Tutorial | 官方samples/kalman.py | Python | mit | 3,318 | [
"Gaussian"
] | 6e2cf77ce8f701952b66a6c29c2aaac527d1e7b3f9433c74b595e031887550ad |
#!/usr/bin/python
#
# \file 1_export.py
# \brief Export ig
# \date 2010-05-24 13:42GMT
# \author Jan Boon (Kaetemi)
# Python port of game data build pipeline.
# Export ig
#
# NeL - MMORPG Framework <http://dev.ryzom.com/projects/nel/>
# Copyright (C) 2010 Winch Gate Property Limited
#
# This program is free software... | osgcc/ryzom | nel/tools/build_gamedata/processes/ig/1_export.py | Python | agpl-3.0 | 4,775 | [
"MOE"
] | 56e40d28b195a0c995f6823761fe67d739916c22d9ff864d86883b6b2ed4184f |
import requests
import pytest
from lxml.html import fromstring
class TestRouting:
''' Handles the routing tests and assertion
as well as the global pass/fail state
the methods with test_ in their names will be run automatically.
'''
def root(self):
'''Hack to get the root url init... | tchalvak/fractalish | tests/test_routing.py | Python | mit | 2,868 | [
"TINKER"
] | bbbbd344149d6fa92936d6b06c49f9408733b0e068ec5b70357c2a67d846fcb8 |
from typing import Optional, Callable, cast
import numpy as np
import scipy.stats
import ert
class Distribution:
def __init__(
self,
*,
size: Optional[int],
index: Optional[ert.data.RecordIndex],
rvs: Callable[[int], np.ndarray], # type: ignore
ppf: Callable[[np.... | joakim-hove/ert | ert3/stats/_stats.py | Python | gpl-3.0 | 3,959 | [
"Gaussian"
] | 0ac18170d41bd7e7d003ec664551845dd89949600c83ea78a3f6edc8e880dda2 |
import superimport
import numpy as np
import math
from cycler import cycler
from sklearn.preprocessing import MinMaxScaler
from matplotlib import pyplot as plt
from scipy.stats import multivariate_normal
from scipy.special import digamma
import pyprobml_utils as pml
np.random.seed(0)
# Using Colorblind friendly colo... | probml/pyprobml | scripts/polyfitRidgeBayes.py | Python | mit | 6,899 | [
"Gaussian"
] | 3738be805e326c398ba31e8a6d5ae8031a3a9f4e20f3f04ad501642e352bf0c5 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import (
UniqueCourseTest,
EventsTestMixin,
... | doganov/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 46,766 | [
"VisIt"
] | 942096c397e3fec3f7d1756e1269b5c89ccec29b454ea9a0c51005231cae9c47 |
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 15 12:25:40 2016
@author: Luciano Masullo, Federico Barabas
"""
import os
import time
import math
import numpy as np
from scipy import ndimage as ndi
import tifffile as tiff
from PIL import Image
import pyqtgraph as pg
from pyqtgraph.Qt import QtGui, QtCore
import matp... | fedebarabas/ringfinder | ringfinder/ringFinder.py | Python | gpl-3.0 | 29,403 | [
"NEURON"
] | 2aeaa7f087294f470a2dbcb7a26a5960d72766d8c888098e0decbf58b55db915 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
from django.contrib.auth.models import User
user, created = User.objects.get_or_create(username='kumbu')
... | praekelt/txtalert | txtalert/core/migrations/0003_auto__del_field_pleasecallme_group__add_field_pleasecallme_user__del_f.py | Python | gpl-3.0 | 15,015 | [
"VisIt"
] | e2de7f7bb3025aee2b6b70634b816a4ff9718146c0bbcd3cf308082c6ae29cbf |
#!/usr/bin/env python
'''
Copyright (C) 2015 The Regents of the University of California.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any late... | Alexhuszagh/Lan-Huang-Scripts | python/gmm_to_imp.py | Python | gpl-3.0 | 7,388 | [
"Gaussian"
] | a216394a94a8763fb1d429979f04cbc5d34d1d0a4e5f074751935b9ffe9b6375 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/LangevinThermostat.py | Python | gpl-3.0 | 1,956 | [
"ESPResSo"
] | 5a74f3c5ff18d60ea0a09122a602edef33435342d83c25bc93f8aa25cfcfba00 |
from django.conf import settings
from django.core.mail import send_mail
emails = {
'donation_thanks': {
'subject': 'Thanks for your donation to Free Law Project!',
'body': ('Hello %s,\n\nThanks for your donation of $%0.2f to Free '
'Law Project. We are currently using donations lik... | voutilad/courtlistener | cl/donate/utils.py | Python | agpl-3.0 | 1,288 | [
"Brian"
] | 3a6ad8b795988696cbf3674fba18551f89c17bf8788b9193e46848dd878de6c4 |
import unittest
import os
import warnings
import numpy as np
import json
import random
from scipy.misc import central_diff_weights
from copy import deepcopy
from pymatgen.analysis.elasticity.elastic import ElasticTensor,\
ElasticTensorExpansion, NthOrderElasticTensor, ComplianceTensor,\
find_eq_stress, gener... | dongsenfo/pymatgen | pymatgen/analysis/elasticity/tests/test_elastic.py | Python | mit | 22,568 | [
"pymatgen"
] | a4747f118058fcba340f53de12c800807b506196b127a5cd161ab7676e54badd |
# Copyright 2001 by Gavin E. Crooks. 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.
"""Unit test for Residues"""
import unittest
from Bio.SCOP.Residues import *
class Residu... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SCOP_Residues.py | Python | gpl-2.0 | 2,402 | [
"Biopython"
] | 118a3cc41bc444d6e0aa83966cb342635db4f30f5cea6395ec42e0874bb13cca |
#!/usr/bin/env python
def error(msg,code=9):
print 'Error: ' + msg
exit(code)
# Imports
try: import argparse
except: error('This version of python is not new enough. python 2.7 or newer is required.')
try: from netCDF4 import Dataset
except: error('Unable to import netCDF4 module. Check your PYTHONPATH.\n'
... | StevePny/NOAA-GFDL-MOM6-examples | tools/python/025gridGeneration/addDimension.py | Python | gpl-3.0 | 1,233 | [
"NetCDF"
] | 295cbc918c0c01dbd60a21a72ff58730dff79503add05d5db19dd5732489dd00 |
# 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.
""" Visitor Object for traversing AST """
#
# IDLVisitor
#
# The IDLVisitor class will traverse an AST truncating portions of the tree
# when 'VisitFilt... | blackenough/mediaAdapter | ppapitest/sdk/ppapi/generators/idl_visitor.py | Python | gpl-3.0 | 1,498 | [
"VisIt"
] | 87d68ff83ece95962e14d362f703562d8f781256741fd7048ad4d2a6bfba9823 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""I/O function wrappers for phylogenetic tree formats.
This API follows the same seman... | asherkhb/coge | bin/last_wrapper/Bio/Phylo/_io.py | Python | bsd-2-clause | 3,157 | [
"Biopython"
] | 17768b91382f568e4d60c9359da77cde89081f22cf17791f293b619d7bffeaaf |
# -*- coding: utf-8 -*-
"""
Li-aung "Lewis" Yip
minecraft@penwatch.net
Json port "leagris" Léa Gris
lea.gris@noiraude.net
"""
import json
import os
import urllib
import unshortenit
from file_handling import fetch_url
from mod_file import Mod_File
from mod_pack import Mod_Pack
import re
URL_BASE = "http://download.no... | LiaungYip/Cat-Herder | atlauncher_import.py | Python | mit | 8,074 | [
"ADF"
] | db9a7001f15b2197b13ebb1f3e3f6c97bcea82edf72f3facf57f5071fd3aacfb |
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
import os
import shutil
import unittest
class ArvOptions:
debug = os.getenv("ARV_DEBUG", False)
debug_symbols = False
hidden_symbols = True
strip = True
warnings = True
# Currently just assume we have gc... | cslarsen/arv | setup.py | Python | gpl-3.0 | 4,942 | [
"Biopython"
] | 407db5af9549bb1b9f5932e4d074c385f8e1dac1952e0a8aa4acdbc77d2650f7 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Routines to get corrected p-values estimates, based on the observations.
It implements 3 approaches:
- Benjamini-Hochberg FDR: http://en.wikipedia.org/wiki/False_discovery_rate
- a class that fits a G... | ellisdg/3DUnetCNN | unet3d/utils/nipy/empirical_pvalue.py | Python | mit | 19,189 | [
"Gaussian"
] | 9714fd3482f333116fc4fe2d6002c331145d50afd9681f3d8b92f89397acd653 |
from __future__ import print_function
from __future__ import absolute_import
import itertools
import tensorflow as tf
import numpy as np
TINY = 1e-8
floatX = np.float32
class Distribution(object):
@property
def dist_flat_dim(self):
"""
:rtype: int
"""
raise NotImplementedErro... | fducau/infoVAE | misc/distributions.py | Python | gpl-3.0 | 14,122 | [
"Gaussian"
] | 4ef4964441522cb53576eee51bf1e84d4e8b625d2fbc9b3296aab0bfb6c3c114 |
#!/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.
"""Makes sure that all files contain proper licensing information."""
import optparse
import os.path
import subprocess
import sys... | codenote/chromium-test | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 15,687 | [
"Galaxy"
] | 0acdc323c87446f635c05fccb06a21fa93e7a7d8d668ed24a3d0b36df0c94b3c |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2010, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.Splunk | ZenPacks/community/Splunk/interfaces.py | Python | gpl-2.0 | 1,447 | [
"VisIt"
] | ad0b29dc6a64c6cf9684c43b00b7b6dfa94d8618b3edb3b4ada02b91faa0bbe0 |
# -*- coding: utf-8 -*-
""" Sahana Eden Common Alerting Protocol (CAP) Model
@copyright: 2009-2015 (c) Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to dea... | ahaym/eden | modules/s3db/cap.py | Python | mit | 99,732 | [
"VisIt"
] | 1772eb66d0bf0517417b2385a89d1091771237846bd97157d3ae59e981a87c9c |
#
# @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/libcubeprop/__init__.py | Python | lgpl-3.0 | 937 | [
"Psi4"
] | c4463698e426e982c1a19b334316ac2a16102ffa194708e5c758cf7fb247c450 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Routines to compute quadrature points and weights.
:copyright:
Martin van Driel (Martin@vanDriel.de), 2015
:license:
GNU Lesser General Public License, Version 3
(http://www.gnu.org/copyleft/lgpl.html)
"""
import numpy as np
import sympy as sp
def gauss_q... | SalvusHub/salvus | src/py/pysalvus/code_generation/quadrature_points_weights.py | Python | mit | 3,791 | [
"Gaussian"
] | 9ba6a7dfe0e2c786c72aeb6a212cdb667bb90fb419428b1636ca64db57bbe053 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-dialogflow-cx | tests/unit/gapic/dialogflowcx_v3/test_flows.py | Python | apache-2.0 | 127,294 | [
"Octopus"
] | 8904904eb632f05dc49a0d9b246c3995e7ca5375876bcf41c92e82c33afa347a |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | wcmckee/brobeurdotcom | conf.py | Python | mit | 37,216 | [
"VisIt"
] | 4e11985e8b543b640dc5c7984390c9ef2ae9705f0ad7e3603fcca88212482bf4 |
import datetime
import functools
import copy
import time
from django.conf import settings as django_settings
from django.core import management
from django.core import serializers
import django.core.mail
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.test.client import Client
... | samhoo/askbot-realworld | askbot/tests/email_alert_tests.py | Python | gpl-3.0 | 38,178 | [
"VisIt"
] | a8e13922bfc48017962374255db244971d683eb3d8e4159516ed62812a460f27 |
# Copyright: 2005 Gentoo Foundation
# Author(s): Brian Harring (ferringb@gentoo.org)
# License: GPL2
try:
anydbm_module = __import__("anydbm")
except ImportError:
# python 3.x
import dbm as anydbm_module
try:
import cPickle as pickle
except ImportError:
import pickle
from portage import _unicode_encode
from porta... | Neuvoo/legacy-portage | pym/portage/cache/anydbm.py | Python | gpl-2.0 | 2,308 | [
"Brian"
] | 09c14e875c724ae02aff931362f49e5f641151f5b89e5451b06dbb3c11865d95 |
#!/usr/bin/python
"""Test of presentation of links that contain images."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
# Work around some new quirk in Gecko that causes this test to fail if
# run via the test harness rather than manually.
sequence.append(KeyComboAction("<Control>r"))
se... | pvagner/orca | test/keystrokes/firefox/line_nav_images_in_links.py | Python | lgpl-2.1 | 19,464 | [
"ORCA"
] | 40937058194183863f77d847c82f79ed08bd26ce55f3af9b49c6c29005fe3eab |
"""
Membership functions for Fuzzy Sets
"""
import numpy as np
import math
from pyFTS import *
def trimf(x, parameters):
"""
Triangular fuzzy membership function
:param x: data point
:param parameters: a list with 3 real values
:return: the membership value of x given the parameters
"""
... | petroniocandido/pyFTS | pyFTS/common/Membership.py | Python | gpl-3.0 | 2,249 | [
"Gaussian"
] | 90da4d71a233bf2f7c986217d73a848109d7d95a89e6d7bdb31032be25cced13 |
import os
import sys
from os.path import abspath, dirname, join
from site import addsitedir
VIRTUALENV_BASE = "/Users/brian/virtualenvs/pinax-dev"
if not VIRTUALENV_BASE:
raise Exception("VIRTUALENV_BASE is not set correctly.")
activate_this = join(VIRTUALENV_BASE, "bin/activate_this.py")
execfile(activate_this... | ericholscher/pinax | pinax/projects/code_project/deploy/modpython.py | Python | mit | 1,181 | [
"Brian"
] | c0175670f121746482f5c125a5026b41505b706f51d1e40b0fc2a4859e08d21b |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | tatiana/invesalius | invesalius/project.py | Python | gpl-2.0 | 11,457 | [
"VTK"
] | 422e9bc293adb0999c1955668afa71f137e6d9c5ab351da88a64c40a5bfd5fd7 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_namdbin.py | Python | gpl-2.0 | 2,866 | [
"MDAnalysis",
"NAMD"
] | 5bab3a40e1076e378c912c608a11f03bc41abc6dbe5e0d96b2377eb9f309a253 |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for the
IDL version is:
... | tomevans/utils | mpfit.OLD.py | Python | gpl-2.0 | 78,409 | [
"Gaussian"
] | 9bf60d373a494b0f4977a61a44cd4d9d9ca413c0b09f2870e818dfdfeab6825d |
# -*- coding: utf-8 -*-
"""
Test MOOSE installation with moose-examples.
"""
from __future__ import print_function, division
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2016, Dilawar Singh"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = ... | upibhalla/moose-core | python/moose/moose_test.py | Python | gpl-3.0 | 5,954 | [
"MOOSE"
] | 964b553fbb5704d710b5308061e5262ba0261b1fec260da6c1c4187a96e1d30a |
'''
Created on 16/03/2010
@author: jose
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of project.
# franklin 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... | JoseBlanca/franklin | test/backbone/blast_runner_test.py | Python | agpl-3.0 | 6,161 | [
"BLAST"
] | 7c2c45793c3129cb2658d09480728c7c4b67f4f289356562c9299467310e1f3e |
"""
`commonutils` contains some helpful functions and classes
which are often used (by other modules)
"""
from __future__ import print_function, division, absolute_import
import math
from multiprocessing.pool import ThreadPool
import numbers
import numpy
import pandas
from numpy.random.mtrand import RandomState
from ... | anaderi/hep_ml | hep_ml/commonutils.py | Python | apache-2.0 | 14,546 | [
"Gaussian"
] | a719294bcf0f15a76fe7c6590e85c79345681068b33e1a482641c795e9495408 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'SurveyQuestionResponse.response'
db.alter_column(u'sur... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0007_auto__chg_field_surveyquestionresponse_response.py | Python | bsd-2-clause | 11,650 | [
"VisIt"
] | e8c6b4b9c06605123b7fe235e0980b2f69dcc7a1f01c8991f1629c6a3b5a3d5e |
# Load dependencies
import ovito.vis
# Load the native code modules.
import Particles
import ParticlesImporter
import ParticlesExporter
import CrystalAnalysis
# Inject selected classes into parent module.
ovito.vis.DislocationDisplay = CrystalAnalysis.DislocationDisplay
ovito.vis.PartitionMeshDisplay = CrystalAnalysi... | srinath-chakravarthy/ovito | src/plugins/crystalanalysis/resources/python/ovito/vis/crystalanalysis/__init__.py | Python | gpl-3.0 | 430 | [
"OVITO"
] | f64a5e71712b88b307f5e82e89fdca136f332338be763ac292f94229a5fa7ea9 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'experiment'
tab.settings['Output file name'] = 'mayerhofer.exp'
#
# Handle the special case of the first scenario
#
self.notebook.switchScenario(0,scenarioType="Single crystal")
#
#
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'experiment'
... | JohnKendrick/PDielec | Examples/Experiment/Mayerhofer/script.py | Python | mit | 4,622 | [
"CRYSTAL"
] | af5bea0bee9383a65878a4c017f169939449b7e0e289b0cf5cb487735957e41c |
# -*- coding: utf-8 -*-
{
'!langcode!': 'nl',
'!langname!': 'Nederlands',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN',
'%(nrows)s rec... | urrego093/proyecto_mv | applications/datos/languages/nl.py | Python | gpl-3.0 | 20,902 | [
"Elk"
] | d62b162929c2f72de495965dc9a5362b67afd78facd378ef62482220e719a9ee |
# Copyright 2001 by Tarjei Mikkelsen. 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.
"""
This module provides code to work with data from the KEGG database.
References:
Kaneh... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/KEGG/__init__.py | Python | apache-2.0 | 2,731 | [
"Biopython"
] | 7243784ef396e4087350c53bf06fb99ac99a5425be9aca57b972311584063129 |
# -*- coding: utf-8 -*-
# Copyright (C) Duncan Macleod (2014-2020)
#
# This file is part of GWpy.
#
# GWpy 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)... | gwpy/gwpy | gwpy/timeseries/timeseries.py | Python | gpl-3.0 | 86,221 | [
"Gaussian"
] | c21dfa59f1ed1583cfa904416182d96b35e730cf3edaf4cae088945b26111a84 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
# Create a graph
g = vtk.vtkMutableUndirectedGraph()
# Add 4 vertices to the graph
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
v4 = g.AddVertex()
# Add 3 edges to the graph
g.AddEd... | lorensen/VTKExamples | src/Python/Graphs/GraphToPolyData.py | Python | apache-2.0 | 1,633 | [
"VTK"
] | 4a4ecff39f3f43b4a77467bf552957efb974d86f74822419a242298364cf6bb1 |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
def grid_wineGBM():
wine = h2o.import_file(path=pyunit_utils.locate("smalldata/gbm_test/wine.data"))
#wine.summary()
x_cols = range(2,14) + [0]
from h2o.estimators.gbm import H2OGradientBoostingEstimator
... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_NOFEATURE_grid_wineGBM.py | Python | apache-2.0 | 896 | [
"Gaussian"
] | e933bffb76d4a5dce3fc97a422634378b5eed8a07f5180e175bac9c82a5881c9 |
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