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# shamelessly copied from pliExpertInfo (Vali, Mirakels, Littlesat)
from enigma import iServiceInformation, iPlayableService
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHumanReadable
from Tools.Ge... | Ophiuchus1312/enigma2-master | lib/python/Components/Converter/PliExtraInfo.py | Python | gpl-2.0 | 24,850 | [
"Galaxy"
] | b4872a49aa70b9c891a0880fa9a6f72d44d7683f3df2fd97e69b364ba5aeac64 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | dezinezync/TiColorArt | build.py | Python | mit | 6,789 | [
"VisIt"
] | 5933f08361eeaeb8fd5b706ebdbef082fb9c983e6c2589606b750c66cc0a6615 |
# -*- coding: utf-8 -*-
"""Shortest paths and path lengths using A* ("A star") algorithm.
"""
# Copyright (C) 2004-2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from heapq import heappush, heappop
fr... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/networkx/algorithms/shortest_paths/astar.py | Python | agpl-3.0 | 4,913 | [
"VisIt"
] | bbf94c497ea1a56966048c182ffe1a839239b2a78114ce13c177818db6dbf7e5 |
#__BEGIN_LICENSE__
# Copyright (c) 2015, United States Government, as represented by the
# Administrator of the National Aeronautics and Space Administration.
# All rights reserved.
#
# The xGDS platform is licensed under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance ... | xgds/xgds_core | xgds_core/register.py | Python | apache-2.0 | 6,851 | [
"VisIt"
] | 41a28cac43c8ecf0f52321aad80c9b37d720c031e447a5335a01927a685131b5 |
#============================================================================
#
# Copyright (c) Kitware Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses... | KitwareMedical/VesselView | Modules/Scripted/InteractiveSegmentTubes/InteractiveSegmentTubes.py | Python | apache-2.0 | 2,133 | [
"VTK"
] | 7561747797e5420b222a182d601b55f517d7019c099c9a8dbe074d91bf343cb9 |
#!/usr/bin/env python
# Copyright 2007, Michael J. Harms
# This program is distributed under General Public License v. 3. See the file
# COPYING for a copy of the license.
__description__ = "Adds polar hydrogens to a pdb file for a UHBD calculation."
__author__ = "Michael J. Harms"
__date__ = "070727"
import time, ... | harmslab/pdbtools | pdbtools/addH.py | Python | gpl-3.0 | 10,679 | [
"CHARMM"
] | e38da8417ad2778dd6bc798aa8aae9206cb7ac1f076d8ae0813605ab76fdbe5b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 18 21:40:28 2014
@author: Vespa
"""
import urllib2
import time
import sys
from zerocommon import *
def FindAnimate(dblist,inputname):
"""
find animate match input from the database
"""
idx = sorted(dblist)
bestid = []
for id... | Vespa314/zerodm-download | Zerodm_PY/zerodm.py | Python | mit | 6,658 | [
"VisIt"
] | a583bfaccaa8d1945e81f66b616a1b2f4434e4cdb1644684b879d0fbce9636cf |
#!/usr/bin/env python3
from netcdfTools import *
import sys
import argparse
import numpy as np
'''
Description:
'''
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = #
def checkVariables(vnames, vDict):
# Check that variables are found
for vi in vnames:
if( vi not in vDict.keys() ):
sys.exit('... | mjsauvinen/P4UL | pyNetCDF/binaryOperateNetCdf.py | Python | mit | 7,087 | [
"NetCDF"
] | 859f4d40c7bed2b1476912ff9ae953d1ec580e5ff345f7be0bde522375290306 |
# Copyright (c) 2014, Alan Saul
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import unittest
import GPy
from GPy.models import GradientChecker
import functools
import inspect
from GPy.likelihoods import link_functions
from functools import partial
fixed_seed = 7
#np.seterr(divide='rai... | dhhjx880713/GPy | GPy/testing/likelihood_tests.py | Python | bsd-3-clause | 35,530 | [
"Gaussian"
] | 98d4aad98432734a1edc0fd0e7db386764f44815284ce5906874e076df5037b7 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/ncl/package.py | Python | lgpl-2.1 | 10,763 | [
"NetCDF"
] | e805d152b62b7b2a11f9ea8ba1e38ec245c378b52b08e628ed65ba44c5b49cca |
#! /usr/bin/env python
# Copyright (C) 2016 Li Yao <yaoli95@outlook.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... | RNAEDITINGPLUS/main | node/splicingOntology.py | Python | apache-2.0 | 15,218 | [
"pysam"
] | bbef8cbe23a45f6ae62a9ec33a637e7a7dc9b38fdd4888e921136fcc451b3b8b |
import logging
import textwrap
import os
import tempfile
import shutil
from subprocess import check_call
from subprocess import CalledProcessError
from ghtools.exceptions import GithubError
log = logging.getLogger(__name__)
def migrate(src, dst):
src_repo = src.client.get('/repos/{0}'.format(src.org_repo)).json(... | alphagov/ghtools | ghtools/migrators/wiki.py | Python | mit | 1,535 | [
"VisIt"
] | 6d4877c8b84d31a03cb3a8639f5885dcaefe84d0c3c0f1b4d4d4f56f0518851c |
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Getting Things GNOME! - a personal organizer for the GNOME desktop
# Copyright (c) 2008-2013 - Lionel Dricot & Bertrand Rousseau
#
# This program is free software: you can redistribute it and/or modify it under
# t... | shtrom/gtg | GTG/core/firstrun_tasks.py | Python | gpl-3.0 | 17,480 | [
"VisIt"
] | 603bb1bee344695b11505c04a03d3c4c7fb00ee40e8850d48e1ced404ca2df07 |
#
# calculation of natural product-likeness as described in:
#
# Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries
# Peter Ertl, Silvio Roggo, and Ansgar Schuffenhauer
# Journal of Chemical Information and Modeling, 48, 68-74 (2008)
# http://pubs.acs.org/doi/abs/10.1021/ci70028... | adalke/rdkit | Contrib/NP_Score/npscorer.py | Python | bsd-3-clause | 3,652 | [
"RDKit"
] | f6e386473050ef3ad10b61c4e53870c062adda91d54a1f90d8d7d126f600b774 |
#
# 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... | witgo/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 91,643 | [
"Gaussian"
] | 69303e8f30c2dac9fdadf3dfb5b181e30afc964b7895ba1a17d7b559b3b04fb8 |
########################################################################
# $HeadURL $
# File: CleanReqDBAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/17 08:31:26
########################################################################
""" :mod: CleanReqDBAgent
=====================
.. modul... | avedaee/DIRAC | RequestManagementSystem/Agent/CleanReqDBAgent.py | Python | gpl-3.0 | 5,377 | [
"DIRAC"
] | add03a273d244928703cd3ade0aa1801277e015e508522712cc2ba3a67ccd889 |
import cv2 as cv
import numpy as np
import matplotlib.pyplot as plt
import scipy.interpolate as si
import scipy.ndimage as scim
import scipy.ndimage.interpolation as sii
import os
import os.path as osp
import cPickle as cp
#import Image
from PIL import Image
from poisson_reconstruct import blit_images
def sample_w... | ankush-me/SynthText | colorize3_poisson.py | Python | apache-2.0 | 17,259 | [
"Gaussian"
] | d90680078439cf60f5973f29985fe37c17315cb53c080b0b6f82ab8b519b089d |
#!/usr/bin/env python
"""dirac-docs-build-commands.py
Build scripts documentation from the scripts docstrings. The scripts are not
very uniform
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import sys
from diracdoctools.cmd.commandReference impor... | yujikato/DIRAC | docs/diracdoctools/scripts/dirac-docs-build-commands.py | Python | gpl-3.0 | 411 | [
"DIRAC"
] | cdf69cedf9364ee797e4cdee6fbbda870a52101a9aaa8ae7a647775abaa45490 |
#
# ColorHandPose3DNetwork - Network for estimating 3D Hand Pose from a single RGB Image
# Copyright (C) 2017 Christian Zimmermann
#
# 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, eithe... | dedoogong/asrada | HandPose_Detector/general.py | Python | apache-2.0 | 29,504 | [
"NEURON"
] | e612f6bd603a69b98a16797853b043a4b6c42a7d6788b0a028df2594d7ba7688 |
import vtk
import requests
# to support alternative baseURL
import os
import os.path
def add_arguments(parser):
parser.add_argument("--table", help="URI to serialized vtkTable", dest="tableURI")
parser.add_argument("--tree", help="URI to serialized vtkTree", dest="treeURI")
parser.add_argument("--width", ... | lukejharmon/tangelohub | app/vtk_tree_heatmap.py | Python | apache-2.0 | 4,270 | [
"VTK"
] | 0f640bee79489ba8af31239b4c1368fd592674a25e8e35be08612dde638f97bb |
#
# Copyright (c) 2013, 2017, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 2 only, as
# published by the Free Softwar... | jjfumero/fastr | mx.fastr/mx_fastr.py | Python | gpl-2.0 | 23,438 | [
"VisIt"
] | 2b84b16bada7d9f433cb8d3430595d087acad1a4118eca1321866b5579383327 |
#!/usr/bin/env python
#
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from builtins import zip
from builtins import map
from builtins import range
from builtins import object
from past.utils import old_div
import os
import sys
from . import extras
import n... | boada/planckClusters | MOSAICpipe/legacy/CLUSTERpipe/maxBCG.py | Python | mit | 90,599 | [
"Galaxy"
] | ff10319df78aab075d844d90feeb9e3e0b9809a66d48af5e553a8b29023cd4e8 |
# 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 roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Variable_Stiffness_Variable_Velocity/HMM/with 0.5s/hmm_crossvalidation_force_motion_10_states_scaled_wrt_all_data.py | Python | mit | 39,683 | [
"Mayavi"
] | 6c712da08280b9eb0544d3ca60fac9bfa8f1d102e3ac83da618e6fed5d8b78b8 |
""" A set of utilities used in the WMS services
Requires the Nordugrid ARC plugins. In particular : nordugrid-arc-python
"""
from tempfile import mkdtemp
import shutil
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getQueue
from DIRAC.ConfigurationS... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Service/WMSUtilities.py | Python | gpl-3.0 | 3,998 | [
"DIRAC"
] | 882ee5a7da55621bdd89c0a39de0797125c6ad2af015969b91b34fcbc2a9ad65 |
#!/usr/bin/env python
# polarizer.py - add Drude oscillators to LAMMPS data file.
# Agilio Padua <agilio.padua@univ-bpclermont.fr>
# Alain Dequidt <alain.dequidt@univ-bpclermont.fr>
# version 2017/02/08
import sys
import argparse
import random
from copy import deepcopy
usage = """Add Drude oscillators to LAMMPS data ... | akohlmey/lammps | tools/drude/polarizer.py | Python | gpl-2.0 | 28,457 | [
"LAMMPS"
] | 833fdddbdea3acc8bb3c2e7dbedf295669d37e5fe6e1b437c8b75daff502438e |
import pandas as pd
from sklearn.ensemble import RandomForestRegressor
from sklearn.ensemble import BaggingRegressor
from sklearn.ensemble import ExtraTreesRegressor
from sklearn.ensemble import AdaBoostRegressor
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.ensemble import RandomTreesEmbedding
fr... | rupakc/Kaggle-Compendium | Walmart Recruiting - Sales in Stormy Weather/storm-baseline.py | Python | mit | 5,165 | [
"Gaussian"
] | 9a9bcc53021db63f18545ce7184e6351ad8ef0143480741bdd3985babf3978ee |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Tool for... | nuclear-wizard/moose | python/mooseutils/eval_path.py | Python | lgpl-2.1 | 805 | [
"MOOSE"
] | bce311a5fd87bdddde1bc0fa1347e4b04a0e7e4f97d6db4ee23b894ff7532129 |
#!/usr/bin/python
"""
This re-aligner script is part of the CLAM pipeline.
It takes bam file as input, and outputs a weighed bam file for multi-mapped reads.
Tested under python 2.7.3
"""
__author__ = 'Zijun Zhang'
__version__ = '1.0.0'
__email__ = 'zj.z@ucla.edu'
from optparse import OptionParser
... | Xinglab/CLAM | deprecated/CLAM.lite_aligner.py | Python | gpl-3.0 | 23,890 | [
"pysam"
] | 0df89cef6b0866ead802db078d3d97bb364880809cad4025e68597839f2f3f30 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# Copyright (c) 2009-2015 Richard Jones, Claudio Canepa
# All rights reserved.
#
# Redistribution and use in source and binary forms, with o... | vyscond/cocos | cocos/particle_systems.py | Python | bsd-3-clause | 10,473 | [
"Galaxy"
] | 4f3f1f3df4b23c9a328c8a0b3acdf5724d5363722a5fc6394bd9a9faf253bef5 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Largest CI coefficients
'''
from pyscf import gto, scf, mcscf, fci
mol = gto.Mole()
mol.build(
verbose = 0,
atom = 'N, 0., 0., 0. ; N, 0., 0., 1.4',
basis = 'cc-pvdz',
symmetry = True,
)
m = scf.RHF(mol)
m.kernel()
ncas = 6
n... | gkc1000/pyscf | examples/fci/11-large_ci.py | Python | apache-2.0 | 984 | [
"PySCF"
] | 6d124bc5dc39892642be08b17ed05356a468e23f8af6a7e9e996aac2dbfa2a05 |
# 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 | jax_dft/jax_dft/utils_test.py | Python | apache-2.0 | 14,150 | [
"Gaussian"
] | 28cb9dfc973ca3119e68e10eb4235496266c58206f345dc7173a22d05fb1ebc1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# 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
__metaclass__ = type
DOCUMENTATION = '''
module: systemd
autho... | azaghal/ansible | lib/ansible/modules/systemd.py | Python | gpl-3.0 | 22,178 | [
"Brian"
] | bcd05735d94684afc48f54a40a584fe00a3397ee9bbcf44c06574f4ad1fe9750 |
import numpy as np
class Function(object):
def __init__(self, usage, name, evaluators):
self.usage = usage
self.name = name
self._evaluator = evaluators
def __call__(self, *args, d=0):
# The optional d parameter is being used to denote power of derivative
return self._... | Shoeboxam/Neural_Network | MFP_Simple/Function.py | Python | mit | 4,531 | [
"Gaussian"
] | 7a063cf7ebd934e3012f041355376555c5f29bb42ff35d0848d794857e98cd6a |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
from pyro.contrib.gp.parameterized import Parameterized
def _zero_mean_function(x):
return 0
class GPModel(Parameterized):
r"""
Base class for Gaussian Process models.
The core of a Gaussian Process is a covari... | uber/pyro | pyro/contrib/gp/models/model.py | Python | apache-2.0 | 8,928 | [
"Gaussian"
] | c4d1c46195863e0bfe1b6e3f0bd8e3d382b34ba672e1d1cf26effe4878412fcc |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/orca_gui_find.py | Python | gpl-3.0 | 8,375 | [
"ORCA"
] | f4bc9b3c21aa439dd7c4ff9762a8d5bcf321853b07dc8624d7dcd19318ee7014 |
# Online haptic_map 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 roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
import os
#import hrl_lib.mayavi2_util as mu
i... | tapomayukh/projects_in_python | rapid_categorization/haptic_map/online_haptic_map_taxel_based_quantitative.py | Python | mit | 17,734 | [
"Gaussian",
"Mayavi"
] | fe4b071e5dce696a33edb5993a24e551d5d2cb713099175d154a73e26b4e5983 |
#!/usr/bin/env python3
import sys
import numpy as np
import argparse
import matplotlib.pyplot as plt
from plotTools import addToPlot
from spectraTools import spectraAnalysis
from netcdfTools import read3dDataFromNetCDF
from analysisTools import sensibleIds, groundOffset, calc_ts_entropy_profile
from utilities import fi... | mjsauvinen/P4UL | pyNetCDF/dataAnalysisNetCdf.py | Python | mit | 8,428 | [
"NetCDF"
] | c6c2b96d1145a7a8fa197407d266557d53dc05e13858612be365641ccb5a4122 |
#! /usr/bin/env python
"""
StochPyTools
============
Written by T.R. Maarleveld, Amsterdam, The Netherlands
E-mail: tmd200@users.sourceforge.net
Last Change: June 08, 2015
"""
import re,sys,copy
from stochpy import model_dir as stochpy_model_dir
from ..modules.PyscesMiniModel import PySCeS_Connector
try:
import... | SystemsBioinformatics/stochpy | stochpy/implementations/StochPyTools.py | Python | gpl-3.0 | 17,061 | [
"PySCeS"
] | 765c373f94fdf00791b12d180133cdcf4f5562431c7e8adc4f66bd145a60b720 |
#!/usr/bin/env python
'''
Force the FCI solver of CASSCF solving particular spin state.
'''
from pyscf import scf
from pyscf import gto
from pyscf import mcscf
mol = gto.M(
atom = '''
8 0 0 0
8 0 0 1.1''',
basis = 'ccpvdz',
symmetry = True,
spin = 2,
)
mf = scf.RHF(mol)
mf.kernel()... | gkc1000/pyscf | examples/mcscf/18-spatial_spin_symmetry.py | Python | apache-2.0 | 1,718 | [
"PySCF"
] | 41a0cf729dc465ed25ee118e0f266c8387fadc03d6546920562cd6391c4b4a1c |
#!/usr/bin/python
import itk
from sys import argv
from optparse import OptionParser, OptionGroup
class unsharpMaskImageFilter():
def __init__(self, InputImage, sigmaArray, ammount):
"""
Simple workflow implementing unsharp masking.
"""
im = itk.image(InputImage)
InType = i... | pmajka/poSSum | possum/dev_possum_unsharp_mask.py | Python | mit | 6,096 | [
"Gaussian"
] | aa059905cbc277bbd15a3ff2509eff4211ef24da87fe1001af789a351d8dd579 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
Implementation for `pmg query` CLI.
"""
import json
import re
from monty.serialization import dumpfn
from tabulate import tabulate
from pymatgen.ext.matproj import MPRester
def do_query(args):
"""
... | gmatteo/pymatgen | pymatgen/cli/pmg_query.py | Python | mit | 2,070 | [
"pymatgen"
] | 27fb44d989f9188e29a625f22bb87f479db5a1c5cb7388150d583d1823ca694c |
"""Distutils file for metagenomix."""
from setuptools import setup, find_packages
requires = ['BioPython']
setup(
name = 'metagenomix',
description = 'Metagenomic analysis pipeline',
url = 'github/pgnd-meta',
author = 'Ana Bulovic',
author_email = 'bulovic.ana@gmail.com',
license = 'MIT',
... | abulovic/pgnd-meta | setup.py | Python | mit | 1,033 | [
"Biopython"
] | ea99d08514312285a70a5e24cce2ee4168e4a6d25c127bb7acc937f915a8f270 |
#!/usr/bin/env python
from datetime import datetime, timedelta
from collections import OrderedDict
import calendar
import sys
from ecmwfapi import ECMWFDataServer
import time
from dateutil.relativedelta import *
start_time = time.time()
server = ECMWFDataServer()
def retrieve_interim(strtDate,endDate,latNorth,latSout... | joelfiddes/toposubv2 | workdir/eraRetrieveSURFACE.py | Python | gpl-3.0 | 4,560 | [
"NetCDF"
] | 6432cedaa22526d6c1adaf0607c3b4c7340fadb2f54213289f20229ef7fd5738 |
# Authors: Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
"""
Test the infomax algorithm.
Parts of this code are taken from scikit-learn
"""
import numpy as np
from numpy.testing import assert_almost_equal
from scipy import stats
from scipy import linalg
from mne.preprocessing.infomax_ imp... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/mne/preprocessing/tests/test_infomax.py | Python | bsd-3-clause | 5,400 | [
"Gaussian"
] | 0fdec7cb4af7ee78853827daaa578ad793bdd3a6ca4d0f93b3db85c772926ee8 |
###########################################################################
#
# 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_run_dag.py | Python | apache-2.0 | 4,285 | [
"VisIt"
] | b0305933cd000753dd323bc3a5388549c7eeffcfa02ac8dbec25d3d14dfe7125 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/fst/_neuronfunc.py | Python | bsd-3-clause | 8,297 | [
"NEURON"
] | 8f60532af439ff5cc532ea2acf9f7212399f408142bfb84c1bc61d95c925780f |
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, thi... | wolfram2012/nimo | perception/ros_track_ssd/scripts/pyvision/other/normalize.py | Python | gpl-3.0 | 6,490 | [
"Gaussian"
] | a66e76fc26b6d6ac3b6ff1ccb54d6ca6ba9a3ecbb6a120a8b3bebfd0f660794b |
# Orca
#
# Copyright 2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This libr... | h4ck3rm1k3/orca-sonar | src/orca/generator.py | Python | lgpl-2.1 | 46,495 | [
"ORCA"
] | a1e0426a1af61357f2158e596c66bcdf98e6e672a5ba728909079884dba9f9c0 |
# Copyright 2013 OpenStack Foundation
# 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 requ... | openstack/glance | glance/api/v2/image_members.py | Python | apache-2.0 | 19,582 | [
"Brian"
] | 186bc85070462fbabe53841ed2827a6bbec22bf1c56010c22fd470be52b50a1d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | jacobparra/redditclone | config/urls.py | Python | bsd-3-clause | 1,276 | [
"VisIt"
] | 3b2a7bb9f02c701cabc3c989499bfabd097ee460bcfea416d683148a2cba9f72 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Interfaces to assorted Freesurfer utility programs.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpat... | mick-d/nipype | nipype/interfaces/freesurfer/utils.py | Python | bsd-3-clause | 138,762 | [
"Gaussian",
"VTK"
] | fe52e21dc6385238c3ecb97a7427ba06dd8d01d417a4ae8d5a6252805c9766e9 |
# Copyright 2004-2015 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, m... | joxer/Baka-No-Voltron | tmp/android.dist/private/renpy/display/motion.py | Python | gpl-2.0 | 46,158 | [
"VisIt"
] | f70d43ce59af44ac8057de77d5cab4d9d73c39ae8783ed071e8bd17c53a7d74c |
"""
Student Views
"""
import traceback
import datetime
import logging
import uuid
import json
import warnings
import re
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib... | MakeHer/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 108,939 | [
"VisIt"
] | aaa202329aab57ca8a075a5fe97a02a4c118aa78ead396e9b3efbf254d06e733 |
"""Kernel K-means"""
# Author: Mathieu Blondel <mathieu@mblondel.org>
# License: BSD 3 clause
import numpy as np
from sklearn.base import BaseEstimator, ClusterMixin
from sklearn.metrics.pairwise import pairwise_kernels
from sklearn.utils import check_random_state
class KernelKMeans(BaseEstimator, ClusterMixin):
... | yao-matrix/mLearning | ml-workshop/src/kernel_kmeans.py | Python | apache-2.0 | 4,055 | [
"Brian"
] | 2e58b40d7d904fec8757ae17ce3b59132d9cae5334dfdaca8cd7eb4911a21d77 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | francisco-dlp/hyperspy | hyperspy/tests/signal/test_remove_background.py | Python | gpl-3.0 | 6,366 | [
"Gaussian"
] | 48da13e32a0603201afa9ac552ed7e51f1e619bf5ff7885a92a2315c512777d9 |
import pytest
from io import BytesIO
from thefuck.types import Command
from thefuck.rules.gulp_not_task import match, get_new_command
def output(task):
return '''[00:41:11] Using gulpfile gulpfile.js
[00:41:11] Task '{}' is not in your gulpfile
[00:41:11] Please check the documentation for proper gulpfile formatt... | SimenB/thefuck | tests/rules/test_gulp_not_task.py | Python | mit | 875 | [
"GULP"
] | 7dcc944f7840d803ab6da8736c3ee56551e03c5fe6b6600cc2a86d35a6baea8b |
import os
import pysam
import unittest
import collections
import copy
import array
from TestUtils import checkFieldEqual
SAMTOOLS = "samtools"
WORKDIR = "pysam_test_work"
DATADIR = "pysam_data"
class ReadTest(unittest.TestCase):
def buildRead(self):
'''build an example read.'''
a = pysam.Alig... | bioinformed/pysam | tests/AlignedSegment_test.py | Python | mit | 26,632 | [
"pysam"
] | cfc9736e24cc11d157dbbf5acbba413959dc4913a915b457fd056d88f9463881 |
# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
Implementation for `pmg query` CLI.
"""
import json
import re
from monty.serialization import dumpfn
from tabulate import tabulate
from pymatgen.ext.matproj import MPRester
def do_query(args):
"""
Perform query to... | materialsproject/pymatgen | pymatgen/cli/pmg_query.py | Python | mit | 2,031 | [
"pymatgen"
] | 873563a6cc22207e00118e685113fa50dd3a0eb58f5200978af3e77232e804a4 |
""" Testing the API and a bit more.
It will submit a number of test jobs locally (via runLocal), using the python unittest to assess the results.
Can be automatized.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-acce... | yujikato/DIRAC | tests/Workflow/Integration/Test_UserJobs.py | Python | gpl-3.0 | 9,610 | [
"DIRAC"
] | 09e20f36df2734003aa50572993a5070860d33e0d0c7165e586ddef0c47523d8 |
## @package shesha.init.rtc_init
## @brief Initialization of a Rtc object
## @author COMPASS Team <https://github.com/ANR-COMPASS>
## @version 5.2.1
## @date 2022/01/24
## @copyright GNU Lesser General Public License
#
# This file is part of COMPASS <https://anr-compass.github.io/compass/>
#
# Copyrig... | ANR-COMPASS/shesha | shesha/init/rtc_init.py | Python | gpl-3.0 | 27,942 | [
"Gaussian"
] | 34617da23210c4e0c12964ec19645fed5ae0ebb5539261547d5d04ecd4d5e2ca |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/__init__.py | Python | gpl-2.0 | 1,317 | [
"VisIt"
] | 6b08c533955082cae8fa7eef4bb5dc2f4f0449eb69d89179b8d2f20acae3c92d |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import mock
import time
import unittest
import logging
import functools
from nose.tools import * # noqa: F403
import pytest
from framework.auth.core import Auth
from website import settings
import website.sea... | mfraezz/osf.io | osf_tests/test_elastic_search.py | Python | apache-2.0 | 62,142 | [
"Brian"
] | c0993646c7fa74d40354c066b4355558695bd98d77fd9b40f2b23ffc4d65dd74 |
from ase import *
from ase.dft.bee import BEEF_Ensemble
from gpaw import GPAW
from gpaw.test import equal
import numpy as np
xc = 'BEEF-vdW'
d = 0.75
tol1 = 1.e-10
tol2 = 1.e-2
tol3 = 1.e-1
# H2 molecule
h2 = Atoms('H2',[[0.,0.,0.],[0.,0.,d]])
h2.center(vacuum=2.)
cell = h2.get_cell()
calc = GPAW(xc=xc)
h2.set_calcul... | robwarm/gpaw-symm | gpaw/test/beefvdw.py | Python | gpl-3.0 | 901 | [
"ASE",
"GPAW"
] | 85d584095e5a05cc0e2ff602f636e19151dfcf00e3225cb3eafa1977b8020b1c |
import cairo
import pango
import gtk
from core.world import TheWorld
from ontology.thing import Thing
from widgets.primitives import Primitives
class NodeTree(Thing):
def __init__(self, root_node):
Thing.__init__(self)
self.root_node = root_node
self.x_offset = 0.0
self.y_offset = 0.... | antoinevg/survival | widgets/asteditor/nodetree.py | Python | gpl-2.0 | 4,118 | [
"BLAST"
] | 933b125acf6f3a03b35f209d74ab18d2896f38274dd27d2a1811f459e082aea9 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Carlos Hernande... | marscher/mdtraj | MDTraj/formats/pdb/pdbfile.py | Python | lgpl-2.1 | 26,143 | [
"MDTraj",
"OpenMM"
] | dd8f702494b3c67fecaab8297b4e76e9ca2e4e0c6856c794f6a2607f07c766de |
from stencil_kernel import *
import sys
import numpy
import math
width = 50
height = 50
image_in = open('mallard_tiny.raw', 'rb')
stdev_d = 1
stdev_s = 70
radius = 1
class Kernel(object):
def kernel(self, in_img, filter_d, filter_s, out_img):
for x in out_img.interior_points():
for y in in_img.ne... | shoaibkamil/asp | tools/debugger/bilateral_filter.2.py | Python | bsd-3-clause | 1,694 | [
"Gaussian"
] | 424eafc92fcb224709a5dbba0542d8b4d1d0e0e03d57dda3af63c90341a3e312 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
import sys
import gzip
import pysam
import BioClasses
import cPickle
def main( gtf_fn, genes_fn ):
# genes
genes = dict()
with open( gtf_fn ) as f:
c = 0
for row in f:
if c > 10000:
break
l = row.strip( "\n" ).split( "\t" )
record = BioClasses.GT... | polarise/Code | identify_overlapping_UTR_genes.py | Python | gpl-2.0 | 1,644 | [
"pysam"
] | 1c9ad206e5105d89454cd5334a7ffbc737248b615a840335c4d7034f521f5710 |
#!/usr/bin/env python
#
# A basic functional test of the total impact API
#
import mechanize
import urllib2
import urllib
import json
import time
import sys
import pickle
import urlparse
from pprint import pprint
from optparse import OptionParser
REQUEST_IDS = [
("crossref", ('doi', '10.1371/journal.... | total-impact/total-impact-core | extras/functional_tests/alt_functional_test.py | Python | mit | 7,133 | [
"CDK"
] | dcd40ebce7dd9107f41661d2a4d53099d2d2c88334f49820b72856d9a9e7e2bc |
from __future__ import absolute_import
import unittest
import numpy as np
<<<<<<< HEAD
=======
import warnings
>>>>>>> a41cc069c865a5d0f35d0731f92c547467395b1b
from pymatgen.analysis.elasticity.stress import Stress
from pymatgen.analysis.elasticity.strain import Deformation
from pymatgen.util.testing import Pymatgen... | Bismarrck/pymatgen | pymatgen/analysis/elasticity/tests/test_stress.py | Python | mit | 3,021 | [
"pymatgen"
] | 9dac3cf80cbbcccfebe99f0281158896821be46f9ac0012567f707ed866a76c4 |
# 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.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | ropik/chromium | PRESUBMIT.py | Python | bsd-3-clause | 13,604 | [
"VisIt"
] | b7bba8a608e9064da2cc7cb86c772e2c121a09c6c441d2975ee39b11a831b574 |
#!/usr/bin/env python
"""
Copyright (c) 2006-2016 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import cookielib
import glob
import inspect
import logging
import httplib
import os
import random
import re
import socket
import string
import sys
import tempfile
import threa... | glaudsonml/kurgan-ai | tools/sqlmap/lib/core/option.py | Python | apache-2.0 | 91,797 | [
"VisIt"
] | 4b6db88dd85f9a9d425bd3cc93e3ac549119d42f04b9260b03ee41f60a4d457a |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
'''
Miscellaneous algorithms for 2D contours and 3D triangularized meshes handling
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.... | wanderine/nipype | nipype/algorithms/mesh.py | Python | bsd-3-clause | 10,921 | [
"VTK"
] | 45e8fc0a7da6898974667ae50f8ed1c24f19374c8f17afa904ffcd968a979f00 |
# spector.py
# ALS 2017/06/01
import sys
import numpy as np
import astropy.table as at
import matplotlib.pyplot as plt
import astropy.units as u
from astropy.io import fits
import astropy.constants as const
import modelBC03
import os
from ..obsobj import Operator
from .. import filters
from . import getconti
from . ... | aileisun/bubbleimg | bubbleimg/spector/spector.py | Python | mit | 26,316 | [
"Gaussian"
] | c19b16089d00a1b605b6d870a8f6a4570b1480656425cd3c9f6e7dd318570788 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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... | mlperf/training_results_v0.5 | v0.5.0/google/research_v3.32/gnmt-tpuv3-32/code/gnmt/model/t2t/tensor2tensor/layers/common_layers.py | Python | apache-2.0 | 132,971 | [
"Gaussian"
] | 68ff514ffcdb5d969400bc78b612ad25e991031b5bd80f0eab7b68663f32e37e |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | nickvandewiele/RMG-Py | rmgpy/reaction.py | Python | mit | 54,551 | [
"RDKit"
] | 0dcd544a5bb22e875f4eea76096de463caace9dfd3739cf3f6c9f3b1b879fc80 |
"""
Copyright (c) 2013-2014 Benedicte Ofstad
Distributed under the GNU Lesser General Public License v3.0.
For full terms see the file LICENSE.md.
"""
import unittest
import abavib as av
import read_input as ri
import numpy as np
import pydoc
molecule = "fluoromethane"
input_name = "input_" + molecule + "/"
output_f... | Benedicte/vibrational_motion | chiral_tester.py | Python | lgpl-3.0 | 11,124 | [
"Dalton"
] | f034c35d5d8664a68385ac055796dcdc38372f025f6bf739da109a57e77f453f |
#! /usr/bin/python
from setuptools import setup
from setuptools import find_packages
setup(name='project-euler',
version='0.1',
description='Code to solve project euler problems',
author='Brian Kinney',
author_email='briankanokinney@gmail.com',
url='https://github.com/briankinney/project... | briankinney/project-euler | setup.py | Python | mit | 395 | [
"Brian"
] | 0d91820995e4183dde38d6713895fecd22011d3579a1569ff6e6668fe2860881 |
#!/usr/bin/python2.7
# 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 requi... | Duikmeester/google-api-dotnet-client | ClientGenerator/src/googleapis/codegen/api.py | Python | apache-2.0 | 36,022 | [
"VisIt"
] | b181fcd38b1eedac829ab954aaba604c8e568ba154c6aa34034c70bd18acf3ac |
#!/usr/bin/env python
from __future__ import print_function
from Bio import SeqIO
from Bio.Seq import Seq
from collections import OrderedDict
import sys
import argparse
# TODO:
# - create some logic to 'group' mutations that will be applied to the same sequence, to
# make all switches at once
# - This will also... | jrjhealey/bioinfo-tools | Mutate.py | Python | gpl-3.0 | 5,669 | [
"Biopython"
] | 917d11bcb5182c790ce585111cb01c29bd9a2c58bc94311022726e2608fcf615 |
# 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... | kkreis/espressopp | src/interaction/AngularUniquePotential.py | Python | gpl-3.0 | 2,594 | [
"ESPResSo"
] | 55b8ed140ba6d64cdaceafda881f3d47aacc8e6029222905843fc740b51bca32 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/peacock_app/check_result/test_check_result.py | Python | lgpl-2.1 | 2,327 | [
"MOOSE"
] | 317bcc6995e24973a5db9adae9ffb53b3c10d0bc3b7b395d4b2649484674e6b0 |
# Copyright (c) 2009 Leif Johnson <leif@leifjohnson.net>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify,... | mxlian/neuror | dataProcessing/kohonen.py | Python | gpl-2.0 | 27,576 | [
"Gaussian",
"NEURON"
] | dac46cc1fe12aa3bb646b85d78dafccdc21836e550d97c16d3e2cb7d42fea918 |
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain
# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z
obj = [
CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.... | weitzner/Dotfiles | pymol_scripts/axes_cyl.py | Python | mit | 853 | [
"PyMOL"
] | a887831096b4e17eb5e693b1ebd7c8a886f94059f644e93715b1f8292f73fdda |
import argparse
import csv
from decimal import Decimal
import distutils.spawn
import glob
import json
import logging
import os
import shutil
from subprocess import call
import sys
import tempfile
import numpy
import pandas
import pydicom
from radiomics import featureextractor
scriptlogger = logging.getLogger('radiom... | Radiomics/pyradiomics | labs/pyradiomics-dcm/pyradiomics-dcm.py | Python | bsd-3-clause | 21,948 | [
"Gaussian"
] | e59853ee62ddfc2b8284d5c604808a4fc9679532961e7688f57fe012bfb6880e |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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... | susilehtola/psi4 | doc/sphinxman/document_driver.py | Python | lgpl-3.0 | 4,542 | [
"Psi4"
] | b4ab8f708050eeb56de6de8325e34d71d3796489a2ec7c4afb18e70c7b7b14bb |
# 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 os import symlink
from spack import *
class LtrRetriever(Package):
"""LTR_retriever is a highly accurate and s... | LLNL/spack | var/spack/repos/builtin/packages/ltr-retriever/package.py | Python | lgpl-2.1 | 1,604 | [
"BLAST"
] | aafb38bb65942ec216a8a3ba083ead0a6e7b47b733b72a31817ca40bc50c3e4c |
# 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 use ... | Verizon/libcloud | libcloud/compute/providers.py | Python | apache-2.0 | 8,385 | [
"VisIt"
] | a6b40290b8d7da2c187d8f578675faad1e7f601e4ef0b0620ab50735ad328677 |
#
# Copyright (c) 2017 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/extractcode/sevenzip.py | Python | apache-2.0 | 12,308 | [
"VisIt"
] | 68e3beb6edd4d432eed30a47a3359e5eec77c20659d7d2270f11b935679038af |
from ase.structure import molecule
from ase.constraints import FixAtoms
N = 2
atoms = molecule('CO2')
atoms.set_cell((15.,15.,15.))
print('indices method')
atomsi = atoms.copy()
atomsi.set_constraint(FixAtoms(indices=[0,]))
atomsi = atomsi.repeat((N,1,1))
atomsiref = atoms.copy().repeat((N,1,1))
atomsiref.set_const... | grhawk/ASE | tools/ase/test/repeat_FixAtoms.py | Python | gpl-2.0 | 1,066 | [
"ASE"
] | c584d3224f68f84cadff54d5b0dc897a6bcaf5835bb538a8ce9730cd9d681e9d |
import glob
import os
import pickle
import sys
import numpy as np
import subprocess as sp
from morphct.definitions import PROJECT_ROOT, SINGLE_RUN_MOB_KMC_FILE
from morphct.code import helper_functions as hf
def main(
AA_morphology_dict,
CG_morphology_dict,
CG_to_AAID_master,
parameter_dict,
chrom... | matty-jones/MorphCT | morphct/code/mobility_KMC.py | Python | gpl-3.0 | 6,372 | [
"ORCA"
] | a65a9caa979ed51fb2ddda1da21cfaec2826ca0afcb4bb858f2a20fbee2c926e |
#!/usr/bin/env python -E
"""
Script to set up a custom genome for bcbio-nextgen
"""
import argparse
from argparse import ArgumentParser
import os
import toolz as tz
from bcbio.utils import safe_makedir, file_exists
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transaction
from ... | SciLifeLab/bcbio-nextgen | scripts/bcbio_setup_genome.py | Python | mit | 9,589 | [
"Galaxy"
] | b52dfc0dea02c1909d57ec122d537a842973df583fec93cd835836375de63b8c |
#!/usr/bin/env python
import numpy as np
import vtk
def main():
named_colors = vtk.vtkNamedColors()
# Make a 32 x 32 grid.
size = 32
# Define z values for the topography.
# Comment out the following line if you want a different random
# distribution each time the script is run.
np.rand... | lorensen/VTKExamples | src/Python/DataManipulation/LineOnMesh.py | Python | apache-2.0 | 5,546 | [
"VTK"
] | 77c42ca20c6752d1a3a13aa5f45049ae05adbfcf165c96cec9262fe317c38611 |
# Copyright 2015 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... | tensorflow/tensorflow | tensorflow/python/ops/nn_impl.py | Python | apache-2.0 | 101,157 | [
"Gaussian"
] | 8d057e51c19fa199de6ce339d7ce9895d5a6e32f2d8b0c8788687994013362f4 |
"""@namespace IMP.pmi.restraints.basic
Some miscellaneous simple restraints.
"""
from __future__ import print_function
import IMP
import IMP.core
import IMP.algebra
import IMP.atom
import IMP.container
import IMP.pmi.tools
import IMP.pmi.restraints
class ExternalBarrier(IMP.pmi.restraints.RestraintBase):
"""Res... | shanot/imp | modules/pmi/pyext/src/restraints/basic.py | Python | gpl-3.0 | 16,155 | [
"Gaussian"
] | 033a96b7687591c7a7dda7a2de5df248637c85ac32b086ed11e8252a7db00a43 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/lib/__init__.py | Python | gpl-2.0 | 14,174 | [
"Brian"
] | d23234ceaf18620c1f269a5c49626c8fd4e4ed94257ea3bfc90dab0c06e71e78 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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 Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_callsearch.py | Python | gpl-2.0 | 3,489 | [
"VisIt"
] | 0f223e66d9e8b5026a917694f634d47f66f85b482407935d1b5d6bd6434785b1 |
#@author Caoimhe Harvey
#Python 2.7
"""
Things left to do:
- Get date to increment by interval
- Add recurisive call
"""
from google_flight import google_flight_api
import datetime
def findBestRoute(array, start):
g = google_flight_api.GoogleFlight('')
temp = {}
end = {}
cheapest = array[0]
for ... | caoimheharvey/Backpacking_Solution | tsp.py | Python | mit | 2,341 | [
"VisIt"
] | 4cfe1a06797af19ada47604d49fe36d1c3d5300bb766e187ffe9e9aac9185c9f |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Mads Jensen <mje.mads@gmail.com>
#
# License: BSD (3-clause)
import contextlib
import copy
import os.path as op
from types import Generator... | Teekuningas/mne-python | mne/source_estimate.py | Python | bsd-3-clause | 119,565 | [
"Mayavi"
] | 2e7552617bca38dd24ca89fa742eace109827df5668f60b65938618f1c7dd208 |
# lintory - keep track of computers and licenses
# Copyright (C) 2008-2009 Brian May
#
# 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 ... | VPAC/lintory | lintory/backends/__init__.py | Python | gpl-3.0 | 721 | [
"Brian"
] | a5d3fddc7e631edd413d6b0dc907a8571503aca03426f6e062f48acc8d89dd9a |
# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CCopasiStaticString.py | Python | artistic-2.0 | 1,477 | [
"COPASI"
] | 80e7aeec44e217ee16bc5bb38888badb92fad0b2f0a23392ba451b58c8c1ea6b |
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