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""" test File Plugin
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import mock
import unittest
import tempfile
import os
import shutil
import errno
from DIRAC import S_OK
from DIRAC.Resources.Storage.StorageElement import StorageElementItem
def mock... | yujikato/DIRAC | src/DIRAC/Resources/Storage/test/Test_FilePlugin.py | Python | gpl-3.0 | 17,346 | [
"DIRAC"
] | e7e72caeb72c2deafa4ac9a498a094a5a254ba054413d1352e1d0025dc02a380 |
#!/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
"""
Produce word vectors with deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative samp... | dsquareindia/gensim | gensim/models/word2vec.py | Python | lgpl-2.1 | 71,517 | [
"VisIt"
] | d2a9ced1c3f374672347852643c8247a58e3e972725d9e2823544fdcad630b43 |
""" A fantastic python code to determine the quenched SFH parameters of galaxies using emcee (http://dan.iel.fm/emcee/current/). This file contains all the functions needed to determine the mean SFH parameters of a population.
N.B. The data files .ised_ASCII contain the extracted bc03 models and have a 0 in th... | zooniverse/starpy | posterior.py | Python | apache-2.0 | 25,744 | [
"Galaxy",
"Gaussian"
] | a813a206358e6edd134c67e9d7a8b8e69f6c2a2d7154389e4a08fda2ec57e519 |
from builtins import range
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each ... | arasdar/DL | uri-dl/uri-dl-hw-2/assignment2/cs231n/layers.py | Python | unlicense | 33,855 | [
"NEURON"
] | c7d9aadd4ba358069df0a5404904ab541cbb812fb42576dba7690b9f5ba01f81 |
#!/usr/bin/env python
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import glob
import io
import collections
import pickle
import pandas as pd
import numpy as np
import seaborn ... | MobleyLab/SAMPL6 | physical_properties/logP/analysis_of_extra_molecules/logP_analysis.py | Python | mit | 64,011 | [
"Gaussian"
] | d7ea9fcc6f378c8ebe65a75076b69e63c0337856bd896fa62d3aff7cd2b75038 |
import urllib,urllib2,re,cookielib,os,sys
import xbmc, xbmcgui, xbmcaddon, xbmcplugin,time
from resources.libs import main
#Mash Up - by Mash2k3 2012.
from t0mm0.common.addon import Addon
addon_id = 'plugin.video.movie25'
selfAddon = xbmcaddon.Addon(id=addon_id)
addon = Addon('plugin.video.movie25', sys.argv)
art = ma... | noba3/KoTos | addons/plugin.video.movie25/resources/libs/live/nhl.py | Python | gpl-2.0 | 7,302 | [
"VisIt"
] | cda5f5ce8cb9d65b4c8dfe492edcf7ba183cb363e1184a995de566d5a9bfabac |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2016 Shreyas Kulkarni (shyran@gmail.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 withou... | shreyas/lstree | lstree/__main__.py | Python | mit | 1,994 | [
"VisIt"
] | 28356b8047968b09e55fd6173ef0968875db965684b0bc37e10ff27907bf7bd6 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | samples/lj_liquid_structurefactor.py | Python | gpl-3.0 | 5,782 | [
"ESPResSo"
] | e7cffe4a80bd2e76b61ace5be64598886ed6c666631529fbfe4ef9b1ac4e869e |
# 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 u... | Huyuwei/tvm | python/tvm/relay/expr_functor.py | Python | apache-2.0 | 7,259 | [
"VisIt"
] | 4c9037ccf0ec7b9db560349e1d8f1ac940dd84dbc62a4ed49d581e1dd8723d65 |
import clientPackets
import serverPackets
import glob
import consoleHelper
import bcolors
import exceptions
def handle(userToken, packetData):
# read packet data
packetData = clientPackets.joinMatch(packetData)
# Get match from ID
joinMatch(userToken, packetData["matchID"], packetData["password"])
def joinMatch... | osuripple/ripple | c.ppy.sh/joinMatchEvent.py | Python | mit | 2,267 | [
"MOE"
] | 30e68d02428a500f200604813d6ddc4d6bc88529ca553f708b3b288dee560362 |
# -*- coding: utf-8 -*-
"""
pint.util
~~~~~~~~~
Miscellaneous functions for pint.
:copyright: 2013 by Pint Authors, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
from __future__ import division, unicode_literals, print_function, absolute_import
import re
import o... | jmwright/cadquery-freecad-module | Libs/pint/util.py | Python | lgpl-3.0 | 13,383 | [
"Gaussian"
] | cc4e9dcfafb32483e2d06564ca2ef04bacb44f2008ba6ec202d3057faf848485 |
#!/usr/bin/env python3
# Version 1.1
# Author Alexis Blanchet-Cohen
# Date: 09/06/2014
import argparse
import glob
import os
import os.path
import subprocess
import sys
import util
# Read the command line arguments.
parser = argparse.ArgumentParser(description="Generates Bowtie1 scripts.")
parser.add_argument("-s", ... | blancha/abcngspipelines | alignment/bowtie1.py | Python | gpl-3.0 | 4,021 | [
"Bowtie"
] | 8658ab4f43db7c3ecd6629eaa9bad3b1f31b9319b0fece5dbfdf8bb79b0f721f |
########################################################################
# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015.
# It is licenced under the GPL 2.1 or higher.
# There is no warranty of any kind. You are welcome to make copies under
# the provisions of the GPL.
# This programme illustrates buildi... | dilawar/moose-full | moose-examples/tutorials/Rdesigneur/chansFromProtoScript.py | Python | gpl-2.0 | 16,290 | [
"MOOSE",
"NEURON"
] | 5827e70e4fe746b269e4232d7aed7891ecdc50676860f2b808714e61450eb1a9 |
'''
Created on Jul 15, 2011
@author: sean
'''
from __future__ import print_function
import _ast
from meta.asttools import Visitor
from string import Formatter
import sys
from meta.utils import py3op, py2op
from contextlib import contextmanager
if sys.version_info.major < 3:
from StringIO import StringIO
else:
... | gutomaia/Meta | meta/asttools/visitors/pysourcegen.py | Python | bsd-3-clause | 24,273 | [
"VisIt"
] | 94bdb62b051bd60f7cb4fb83d81773ac5cd06354868e5b72935189a330a0d451 |
##############################################################################
# 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... | TheTimmy/spack | var/spack/repos/builtin/packages/visit/package.py | Python | lgpl-2.1 | 2,643 | [
"VTK",
"VisIt"
] | 9f4fce70e9353e2ebdc6d17aaedb2f389124865c1e79964c2c5d4e1149e52afa |
import numpy as np
import sys
import time
from ase.units import Bohr
from ase.lattice import bulk
from gpaw import GPAW, FermiDirac
from gpaw.atom.basis import BasisMaker
from gpaw.response.df0 import DF
from gpaw.mpi import serial_comm, rank, size
from gpaw.utilities import devnull
if rank != 0:
sys.stdout = devn... | robwarm/gpaw-symm | gpaw/test/diamond_eps.py | Python | gpl-3.0 | 1,942 | [
"ASE",
"GPAW"
] | c2ff0051981974b2b922fcaee7b746f88d7c514b08a8f6a7ad8473c123d874cf |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | xyproto/turbine | djl/libs/SOAPpy/NS.py | Python | gpl-3.0 | 3,526 | [
"Brian"
] | a98543d852b35bb0216b27dc3b7cd19adf230837867a2fd2f4ec21244c3c9bbf |
# 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 | src/python/espressomd/lbboundaries.py | Python | gpl-3.0 | 2,672 | [
"ESPResSo"
] | aaab859b0673577b5d60ca5f7e83d2037eb9c0b87ae5f8f9f4d14a83cfa13084 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | beernarrd/gramps | gramps/plugins/tool/mergecitations.py | Python | gpl-2.0 | 10,132 | [
"Brian"
] | e116c92ae7f83d36b6d75d75e38060850f523065202e444099498834ff2e539e |
#!/usr/bin/env python
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | jaddison/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 6,150 | [
"Galaxy"
] | 856f88639da827dc65108a83d4c010973921f26d3665bc0fbaa5e4fef39f5c35 |
import sys
if len(sys.argv) != 3:
print "command is 'python <python driver code> <script name> <number of time steps>'"
sys.exit(1)
import paraview
import paraview.vtk as vtk
import paraview.simple as pvsimple
import math
# initialize and read input parameters
paraview.options.batch = True
paraview.options.sym... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Applications/ParaView/Testing/XML/CatalystWaveletDriver.py | Python | gpl-3.0 | 2,670 | [
"ParaView",
"VTK"
] | 69c7cf51fd6c180dee4564aa707367b60ca59b60bd244fb5b0ea50e0496898fb |
#Game.py
#Defines games played in a casino
#Created by: Andrew Davis
#Created on: 1/16/2016
#Open source (MIT license)
#import statements
from Chip import *
from Player import Player
from random import randint
#Game superclass definition
class Game(object):
#constructor
def __init__(self, name, payout, payou... | techgineer/casino-sim | src/Game.py | Python | mit | 10,284 | [
"CASINO"
] | f95b7ae6808937eaa67f28cdbf544ba09a5c538bd974528b40b01525e83273ca |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Separate sequences of a fasta file by MID into different files
__authors__ = "Eric Normandeau"
__program_name__ = "fasta_separate_tags"
__version_info__ = ('0', '0', '1')
__version__ = '.'.join(__version_info__)
__copyright__ = "Copyright (c) 2011 Eric Normandeau"
__lic... | enormandeau/Scripts | fasta_separate_tags.py | Python | gpl-3.0 | 3,616 | [
"Biopython"
] | 3880e2a1abd10480a5704a080c5a88a16c39d4622a60ddad315df13c088d3966 |
##############################################################################
#
# Copyright (c) 2003 Zope Foundation and Contributors.
# All Rights Reserved.
#
# This software is subject to the provisions of the Zope Public License,
# Version 2.1 (ZPL). A copy of the ZPL should accompany this distribution.
# THIS SOF... | Oslandia/vizitown_plugin | zope/interface/advice.py | Python | gpl-2.0 | 7,546 | [
"VisIt"
] | 315338747c970ede68c71ce46d114e5a50d57f9ff0fd00e7b667a6d39218f78b |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import os
import cmath
import math
import sys
import numpy as np
import glob
import subprocess
import re
from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
i... | enguy/FAST-iCLIP | bin/oldscripts/fastclip_icountData.py | Python | gpl-2.0 | 65,861 | [
"Bowtie"
] | 16df97c299334f384c83bf1642afd372c2974ce4c6264f5aafd34c4710515d86 |
# License: BSD 3 clause
import pickle
import itertools
import numpy as np
import pytest
from sklearn.neighbors import DistanceMetric
from sklearn.neighbors._ball_tree import (
BallTree, kernel_norm, DTYPE, ITYPE,
NeighborsHeap as NeighborsHeapBT,
simultaneous_sort as simultaneous_sort_bt,
nodeheap_so... | glemaitre/scikit-learn | sklearn/neighbors/tests/test_neighbors_tree.py | Python | bsd-3-clause | 9,427 | [
"Gaussian"
] | 392f83db9d88ff0b7a0f58aefb4417108892ffae335a62095bb5f9dd872cbff0 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
import ast
import gyp.common
import gyp.simple_copy
import multiprocessing
import optparse
import os.path
import re
import s... | turbulenz/gyp | pylib/gyp/input.py | Python | bsd-3-clause | 116,420 | [
"VisIt"
] | c6d3ab54b0a655ff8db2e9037604ea00442d5d548d5b36c023d7da47701692d7 |
#=========================================================================
# ast_tranformer_test.py
#=========================================================================
from __future__ import print_function
from ast_transformer import *
from ..ast_helpers import get_method_ast, print_simple_ast, print_ast
#-... | Glyfina-Fernando/pymtl | pymtl/tools/deprecated/ast_transformer_test.py | Python | bsd-3-clause | 6,898 | [
"VisIt"
] | 816a9a0505e076ecbb12c5881cfed866d2a2c6d9683750dabca75e70f4f91fe5 |
import numpy as np
import numpy.linalg as LA
import math as m
def gaussianKernel(x1, x2, sigma):
"""returns a gaussian kernel between x1 and x2
and returns the value in sim
"""
# RBF Kernel
return m.exp(-(LA.norm(x1.ravel() - x2.ravel())**2)/(2*sigma**2))
| robotenique/mlAlgorithms | supervised/SVMclassifier/gaussianKernel.py | Python | unlicense | 278 | [
"Gaussian"
] | 0cc0f2f5dfa551ffd8a6fea1d6066846238ae8746180d24e32c736f4ca99b97a |
# -*- coding: utf-8 -*-
"""Builds the relational database on all graphs with subgraph annotations"""
import logging
import time
from typing import Optional
import pybel
from .algorithm import get_drug_scores
from .models import Score
logger = logging.getLogger(__name__)
NEUROMMSIG_DEFAULT_URL = 'https://arty.scai.... | pybel/pybel-tools | src/pybel_tools/analysis/epicom/build.py | Python | mit | 2,122 | [
"Pybel"
] | 40bfdcec31f556c31deee6dfe6b03950c00975ba8185115b794c7bf1d7b5f743 |
#! /usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------... | Jorge-C/bipy | skbio/maths/stats/distance/base.py | Python | bsd-3-clause | 7,477 | [
"scikit-bio"
] | 63b34fbf87b3e5b24f1df2ad9e276be99e7b219b432dff758c1a09e65c0f4674 |
"""
======================================
Probability calibration of classifiers
======================================
When performing classification you often want to predict not only
the class label, but also the associated probability. This probability
gives you some kind of confidence on the prediction. However,... | NelisVerhoef/scikit-learn | examples/calibration/plot_calibration.py | Python | bsd-3-clause | 4,795 | [
"Gaussian"
] | 65b86889448378704d623814da242516e01c893c83c99c2262fed0f56b3ac69d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# PROGRAM : checkMissing
# AUTHOR : codeunsolved@gmail.com
# CREATED : November 28 2016
# VERSION : v0.0.1
# UPDATE : [v0.0.1] December 13 2016
# 1. Check Pos extend to 2414 point and seperate to a file(check_pos_v0.2);
# 2. add filter - Alt frequency < 0.5%;
# 3... | codeunsolved/NGS-Dashboard | py/checkMissing.py | Python | mit | 13,549 | [
"pysam"
] | 9cdf2c6ffe7ed6ee791932d7e486ba428bd183837c6c0c1077490580d44310a4 |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subresultants,
resu... | maniteja123/sympy | sympy/polys/tests/test_polytools.py | Python | bsd-3-clause | 106,358 | [
"Gaussian"
] | 0dac82814c8b37630c89724bbe43c707e7e3623b3599eab9ebb326a439fd02d0 |
__author__ = 'mnowotka'
from django.db import models
from chembl_core_db.db.models.abstractModel import ChemblAppAbstractModel
#-----------------------------------------------------------------------------------------------------------------------
class InchiErrors(ChemblAppAbstractModel):
#api_exclude = []
... | thesgc/chembiohub_ws | chembl_business_model/models/meta.py | Python | gpl-3.0 | 3,671 | [
"Open Babel",
"RDKit"
] | 79436bce9a8eb9c96113b8e3d48677f1b538c354177a223f0bdee92fe4254c61 |
"""
Wrapper for launching an index & strategy on images
"""
__license__ = """
This file is part of RAPD
Copyright (C) 2016-2018 Cornell University
All rights reserved.
RAPD 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 Sof... | RAPD/RAPD | src/plugins/index/commandline.py | Python | agpl-3.0 | 22,235 | [
"CRYSTAL"
] | 8892bf84fde85acb3393acf0cf7c5c5491df0238f03ab153e236184c7ca070fc |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | SNoiraud/gramps | gramps/plugins/webreport/introduction.py | Python | gpl-2.0 | 4,021 | [
"Brian"
] | 5e110950016b04709376d8294bb40e4cc62c87394d4c11d03000f5b113ccdd9d |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/mp/test/test_gmp2.py | Python | apache-2.0 | 7,895 | [
"PySCF"
] | 30b33d7a771cfece58063fca9b4ac4b86842983502b4f7df9ec1138079994302 |
#!/usr/bin/env python
# Run most of AmberTools serial tests
''' Require: AMBERHOME
You need to call amber.setup_test_folders first (only do once)
amber.setup_test_folders
Then run test (anywhere)
amber.run_tests
Adjust the test by updating env TEST_TASK (please lookt at the code)
'''
from time import tim... | Amber-MD/ambertools-conda-build | conda_tools/amber_run_tests.py | Python | mit | 15,723 | [
"Amber",
"NetCDF"
] | 652d1080e79eb495210d0fc69603f8f516ba756309786f21fc0aa7faad6c0fd1 |
"""Base classes and utilities for readers and writers.
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,... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/nbformat/v2/rwbase.py | Python | bsd-2-clause | 5,997 | [
"Brian"
] | 8c7ea29844c412fc81d079846a30df700845dd1e1e120d484bd23e8dbe8c7df8 |
# -*- coding: utf-8 -*-
''' The object representing one crystal as it evolves during the simulation. '''
import numpy as np
class Crystal:
'''Class representing one growth chamber/surface/crystal.'''
def __init__(self, m, n, initial_grid = 0, mode="step", hist_int=10, \
border_policy="loop... | roesel/growth | crystal.py | Python | cc0-1.0 | 5,661 | [
"CRYSTAL"
] | 33e18500e47e5febb093a9e4b75961f7e16d53d51799e2efba411f9fcafecf0e |
"""Contains code for an SmatrMatrix Shield connected to a Teensy"""
# smartmatrix.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Thanks to Eli Curtz for finding and figuring the pieces to make this happen!
# Released under the MIT License. (See license info at the end of this file.)
# Document... | spierepf/mpf | mpf/platform/smartmatrix.py | Python | mit | 3,933 | [
"Brian"
] | 512042a112c39126e8ad90af8c85c946d6f653993d62c0194b119ef33b81fdf3 |
# Copyright (c) 2012, Cloudscaling
# 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 applicable... | jeffrey4l/nova | nova/hacking/checks.py | Python | apache-2.0 | 22,100 | [
"VisIt"
] | d14438bf8d23fff3f7cb1b6822f2eeccff9a1deb26900fe6e42c6df103341715 |
# -*- coding: utf-8 -*-
r"""
.. _dicedBentAnalyzers:
Comparison of 2D-bent Bragg crystal analyzers
---------------------------------------------
Files in ``\examples\withRaycing\07_AnalyzerBent2D``
This study compares simply bent (Johann) and ground-bent (Johansson) analyzers
in diced and non-diced versions. This t... | kklmn/xrt | examples/withRaycing/07_AnalyzerBent2D/01BD_SourceZCrystalThetaAlpha.py | Python | mit | 29,711 | [
"CRYSTAL"
] | be8f824c9957278d8ef85942573603c2992144be40c17bae71b16b48c54030ef |
#!/bin/env python
import sys
import os
from pycparser import parse_file, c_generator, c_ast
sys.path.extend(['.', '..'])
class StructVisitor(c_ast.NodeVisitor):
def visit_Struct(self, node):
try:
if not 'cef_base_t' in node.decls[0].type.type.names:
return
except Attr... | schachmat/smurf | implement_interface.py | Python | isc | 6,348 | [
"VisIt"
] | 512498dbb4353eab81a25c622d54daa2223b920f5628c3a16bdd9730aac0e1ac |
"""
.. _ex-electrode-pos-2d:
====================================================
How to convert 3D electrode positions to a 2D image.
====================================================
Sometimes we want to convert a 3D representation of electrodes into a 2D
image. For example, if we are using electrocorticography ... | pravsripad/mne-python | examples/visualization/3d_to_2d.py | Python | bsd-3-clause | 4,815 | [
"Mayavi"
] | 152e0bf5aa3877492d8dac6e36ab201c2222f3a4eb4dffa7743386522da1852e |
"""
docstring needed
:copyright: Copyright 2010-2017 by the NineML Python team, see AUTHORS.
:license: BSD-3, see LICENSE for details.
"""
from __future__ import division
from future.utils import itervalues
from collections import defaultdict
from nineml.exceptions import NineMLUsageError
from nineml.utils import asse... | INCF/lib9ML | nineml/abstraction/dynamics/visitors/validators/general.py | Python | bsd-3-clause | 8,451 | [
"VisIt"
] | 40eaf04f7240a3c9b1b9d89f37d4eed1ec226900e4540e75503fae41a6c79c17 |
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout
from dcdreporter import DCDReporter
import numpy as np
def OPLS_LJ(system):
forces = {system.getForce(index).__class__.__name__: system.getForce(
index) for index in range(system.getNumForces())}
n... | leelasd/LigParGenTools | PLIQ_OPENMM.py | Python | mit | 3,116 | [
"OpenMM"
] | 5f2d763120e326ebef3865701d2735f18e31563c28742e38d2454fe8b54654be |
'''
(c) 2011-2012 Thomas Holder, MPI for Developmental Biology
'''
from __future__ import print_function
__author__ = 'Thomas Holder'
__version__ = '1.1'
__license__ = 'BSD-2-Clause'
from pymol import cmd, CmdException
def save_pdb_without_ter(filename, selection, **kwargs):
'''
DESCRIPTION
Save PDB file witho... | weitzner/Dotfiles | pymol_scripts/tmalign.py | Python | mit | 6,746 | [
"PyMOL"
] | 0775eb945aae4a27fc9a8e0a6af1e0a591ec46457c0936e3118f20dd2f66bf43 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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 Li... | Karaage-Cluster/python-tldap | tests/a_unit/test_database.py | Python | gpl-3.0 | 23,969 | [
"Brian"
] | 7d9d2083a08cd0d147fd5d9a96480f60f7aeabbd70bf948187ca0f4cd673ba42 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_conv_yzx2xyz.py | Python | apache-2.0 | 4,688 | [
"PySCF"
] | 42fa64c65f59f7b573ee8fd7b5ffa943cd927169c4297cfc8be9bfd08f9988ad |
import falcon
import json
from sqlalchemy import and_, text, desc, func
from sqlalchemy.orm import load_only
from sqlalchemy.exc import SQLAlchemyError
from db import session
import model
import util
class Thread(object):
def on_put(self, req, resp, id):
try:
user_id = req.context['user'].id... | fi-ksi/web-backend | endpoint/thread.py | Python | mit | 9,427 | [
"VisIt"
] | bc0677a89ea2c91edebdd56a5bf160cce6b9d95294e217d50a09e20d8772a9b9 |
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 7 21:55:12 2014
@author: lucio tolentino
Script for calculating the movement of stars under different amount of dark
matter.
"""
import sys
import os
import numpy as np
import numpy.random as random
import matplotlib
matplotlib.use('Agg')
from matplotlib import rcPar... | HacktheUniverse/transparent-matter | star_simulator2.py | Python | mit | 7,048 | [
"Galaxy"
] | 914074b1e666db3e2d256a102dfe074759f6ed811ae870c1a4ff46388266480a |
#!/usr/bin/env python
from math import sqrt
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack, Help
class DFT(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_title(_('DFT'))
vbox = gtk.VBox()
combo = gtk.combo_box_new_text()
... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/gui/dft.py | Python | gpl-2.0 | 1,473 | [
"ASE"
] | b7f8e077b72af13e10283f58a9becb6f3a954f69d9d51c7d6b92708ee70acabf |
# -*- coding: utf-8 -*-
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleads/google-ads-python | google/ads/googleads/v10/resources/types/custom_audience.py | Python | apache-2.0 | 5,424 | [
"VisIt"
] | 456ff87f278386555631e0be6085dd1b56e7e7bfc482b236d2134d9eb8e19c69 |
"""
Chi2 primer
-----------
A simple chi-square test statistic which tests how close an observation is
to an expectated value (a model) is::
Chi2 = (Obs - Exp)**2 / Exp
The Chi2 statistic (fit value) used by MATCH is a bit more complicated and
is based on Poisson probability, but the idea is the same. The "null
h... | jesaerys/match-wrapper | match_wrapper/dev/runcalcsfh_fits.py | Python | mit | 9,472 | [
"Gaussian"
] | db8417a6866aa03c532272774bb7c090dab73177faa929aa5edbe2e83e944afe |
# Copyright 2013 craigslist
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | idxos/python-clblob | clblob/server.py | Python | apache-2.0 | 6,010 | [
"VisIt"
] | 3ffd525280be391d52bc0d71e68a35d9f37dae55be0e2cd04b66c97f3b790821 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | jswanljung/iris | lib/iris/cube.py | Python | lgpl-3.0 | 158,383 | [
"NetCDF"
] | 9aff23e50e3bbd1c3aa81dc547c400831e31cf21ec6f78d93acfeb351b8d822b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Authors: TurBoss
# Models: TurBoss
# Main
#import pdb
import sys
import os
import time
import json
from pprint import pprint
from math import pi, sin, cos
from direct.showbase.ShowBase import ShowBase
from direct.task import Task
from direct.actor.Actor import Acto... | TurBoss/HostilGalaxy | main.py | Python | gpl-3.0 | 4,432 | [
"Galaxy"
] | adfc022c8f8c50bd972b2d544d31fc507eed328298187bdc1998f20a7d7e613a |
# $HeadURL$
__RCSID__ = "$Id$"
import os, stat, tempfile, shutil
from DIRAC import S_OK, S_ERROR, gConfig, rootPath, gLogger
import DIRAC.Core.Security.Locations as Locations
import DIRAC.Core.Security.File as File
from DIRAC.Core.Security.BaseSecurity import BaseSecurity
from DIRAC.Core.Security.X509Chain import X509... | rajanandakumar/DIRAC | Core/Security/VOMS.py | Python | gpl-3.0 | 9,992 | [
"DIRAC"
] | 52ccfc102f3f0bbf11f186feaa3f19cf0f8bba52509a0883f3708dcb2840148a |
""" A command model that can be easily transformed into jobs.
author: Brian Schrader
since: 2015-12-21
"""
from .tokens import Input, Output, FileToken, PathToken, alias_pattern
class Command(object):
def __init__(self, alias, parts=[]):
self.alias = alias
self.parts = parts
if len(self... | TorkamaniLab/metapipe | metapipe/models/command.py | Python | mit | 2,935 | [
"Brian"
] | 51ffb05c6212f52f36454ef6bbc27483a5ed12b7e9bc5bab63036679c17356cc |
# sql/compiler.py
# Copyright (C) 2005-2012 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`~sql... | landier/imdb-crawler | crawler/libs/sqlalchemy/sql/compiler.py | Python | gpl-3.0 | 79,281 | [
"VisIt"
] | 15d7f623c08bf58fcb92e5ab3a0cb9d2780ec683d0391ee380883895e764aa8e |
# This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Implements support for high-level access to ... | ryfeus/lambda-packs | Tensorflow_Pandas_Numpy/source3.6/h5py/_hl/group.py | Python | mit | 19,193 | [
"VisIt"
] | f4cc9964f3c7066c2bd3fd8d76160718677f352d7a856acc20573ce25f8b6f4b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
from __future__ import print_function
import numpy as np
import MDAnalysis
def _writepdb(interface,
filename='layers.pdb',
centered='no',
group='all... | Marcello-Sega/pytim | pytim/writepdb.py | Python | gpl-3.0 | 4,701 | [
"MDAnalysis"
] | fedf5488935158ab38d36e154018db7e71bfe4a5748e6517c19d74bd5c642d16 |
# -*- 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):
# Adding field 'SurveyQuestionResponse.display_on_dashboard'
db.add_colum... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0008_auto__add_field_surveyquestionresponse_display_on_dashboard.py | Python | bsd-2-clause | 11,815 | [
"VisIt"
] | dd224fcb5a8a546ea5e143588051ffc63f7ba9b870bc02e2bba521cc8c8e1ac1 |
#!/usr/bin/env python
'''Generate models for affinity predictions'''
# initialization: gaussian, positive_unitball, uniform, xavier, msra, radial
# kernel size: 3, 5
modelstart = '''layer {
name: "data"
type: "MolGridData"
top: "data"
top: "label"
top: "affinity"
include {
phase: TEST
}
molgrid_d... | gnina/scripts | affinity_search/makemodels4.5.py | Python | bsd-3-clause | 4,729 | [
"Gaussian"
] | 6ce847cf7f19a11fca2a6a9dd60f15280f0d731d27e583ed9e719182ed192cbd |
import matplotlib
matplotlib.use('Agg')
from astropy.io import fits as pyfits
import numpy as np
from numpy import median,sqrt,array,exp
import scipy
from scipy import signal,special,optimize,interpolate,integrate
import scipy.special as sp
import copy
import glob
import os
import matplotlib.pyplot as plt
import sys
i... | rabrahm/ceres | utils/GLOBALutils/GLOBALutils.py | Python | mit | 113,727 | [
"Gaussian"
] | c7db63153d2438337f56d2073926d92a64849dcbe4a1c6eac750605877439188 |
import simtk.openmm.app as app
import pdbfixer
mutation_string = "GLY-112-ALA"
fixer = pdbfixer.PDBFixer(pdbid='2LCB')
fixer.applyMutations([mutation_string])
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.removeHete... | kyleabeauchamp/fah-projects | old/fix_pdbs.py | Python | gpl-2.0 | 1,924 | [
"OpenMM"
] | 337c496b798703fb8ec47b1bc6ee65dd1ccaf268dc832157532f4c290175c5fa |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_rating_area.py | Python | apache-2.0 | 9,989 | [
"VisIt"
] | 959587c795a0ac7c50882c8b68a9cfc265c3e9a9d4d06b2d891602bc91f80f30 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.structure import Structure
from pymatgen.core.units import Ha_to_eV... | migueldiascosta/pymatgen | pymatgen/io/abinit/tests/test_abiobjects.py | Python | mit | 4,559 | [
"ABINIT",
"pymatgen"
] | 0b1acd371ec4adfea911cb42dc3586b5186021126602d5301c753487d94251fd |
#!/usr/bin/python
"""
Copyright 2016 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/feeds.py | Python | gpl-3.0 | 2,766 | [
"Galaxy"
] | de7bb9ba5a7c282648a7ddc54d6dcff9c065716f0a5935896a376ecb7a7e021f |
from __future__ import division
import numpy as np
from utils import msqrt, check_type, round_array, float_dtypes, integer_dtypes, bool_dtypes, safe_len, find_generations, logp_of_set, symmetrize
from numpy import ones, zeros, log, shape, cov, ndarray, inner, reshape, sqrt, any, array, all, abs, exp, where, isscalar, ... | matthew-brett/pymc | pymc/StepMethods.py | Python | mit | 48,232 | [
"Gaussian"
] | 81012bb78849c24a7cce2b1d4a11c69f86604f900164e111a62df9d38eb9622e |
#!/usr/bin/env python
# Copyright 2017 Informatics Matters Ltd.
#
# 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... | InformaticsMatters/pipelines | src/python/pipelines/docking/plip.py | Python | apache-2.0 | 5,148 | [
"RDKit"
] | 4eff4ba6b67f0b6ba931c31b10a956e89717429eeef0bbffdceac47ced652841 |
#!/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_postprocessor/test_check_postprocessor.py | Python | lgpl-2.1 | 1,489 | [
"MOOSE"
] | af7b4f27aeee15d8aa3e7a058e816c50650a5bded3b5a64062051577ad6f6ea9 |
# Copyright 2017 Chr. Hansen A/S and The Novo Nordisk Foundation Center for Biosustainability, DTU.
# 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.... | biosustain/marsi | marsi/chemistry/molecule.py | Python | apache-2.0 | 3,838 | [
"RDKit"
] | 62d87c8d2ace33aa3a89d8e37cfc1bde58300fdf9d2979be7493cc44b3488b69 |
from behave import *
import operator
from django.db.models import Q
use_step_matcher("parse")
@given('Exists song at group "{group_name}" by "{username}"')
def step_impl(context, group_name, username):
from django.contrib.auth.models import User
user = User.objects.get(username=username)
from musicseaapp.... | julio77nz/MusicSea | musicsea/features/steps/register_song.py | Python | gpl-3.0 | 3,022 | [
"VisIt"
] | 3062d1586b34d55d39115f32933526c308fe5f35b2c266f0884c18d288f77f3e |
##############################################################################
#
# Copyright (C) 2018 Compassion CH (http://www.compassion.ch)
# @author: Emanuel Cino <ecino@compassion.ch>
#
# The licence is in the file __manifest__.py
#
#########################################################################... | CompassionCH/compassion-switzerland | website_event_compassion/models/event_registration.py | Python | agpl-3.0 | 33,149 | [
"VisIt"
] | c2f3dad503c8f0d132c8f3ad3725efffcca8d7ba97de031e6e0f86f0d275a563 |
#!/usr/bin/env python
__author__ = 'waroquiers'
import unittest2 as unittest
from pymatgen.analysis.chemenv.utils.func_utils import CSMFiniteRatioFunction
from pymatgen.analysis.chemenv.utils.func_utils import CSMInfiniteRatioFunction
from pymatgen.analysis.chemenv.utils.func_utils import DeltaCSMRatioFunction
impor... | aykol/pymatgen | pymatgen/analysis/chemenv/utils/tests/test_func_utils.py | Python | mit | 6,466 | [
"pymatgen"
] | 009ea7d614ea029551d58f8e6627b4a8f61d2723ec79f5a7b0cbf3b9b0899e94 |
"""
BoltzTraP2 is a python software interpolating band structures and
computing materials properties from dft band structure using Boltzmann
semi-classical transport theory.
This module provides a pymatgen interface to BoltzTraP2.
Some of the code is written following the examples provided in BoltzTraP2
BoltzTraP2 has... | mbkumar/pymatgen | pymatgen/electronic_structure/boltztrap2.py | Python | mit | 48,176 | [
"ASE",
"BoltzTrap",
"VASP",
"pymatgen"
] | 705afe412841c22b26f96293123e9d1ac2f0a71b8f902f2072169017a613d4f2 |
########################################################################
# File : JobCleaningAgent.py
# Author : A.T.
########################################################################
""" The Job Cleaning Agent controls removing jobs from the WMS in the end of their life cycle.
This agent will take care... | andresailer/DIRAC | WorkloadManagementSystem/Agent/JobCleaningAgent.py | Python | gpl-3.0 | 10,023 | [
"DIRAC"
] | 054bafa18b658d2aacb7bde623f290f520785e9e7d4ed694a161cf11b78d2cb6 |
#-------------------------------------------------------------------------------
# Name: opan_utils_vector
# Purpose: Test objects for opan.utils.vector
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 19 Apr 2016
# Copyright: (c) Brian Skinn 2016
# License: The MIT Li... | bskinn/opan | opan/test/opan_utils_vector.py | Python | mit | 30,864 | [
"Brian"
] | c82fd0c234792c9d3ae5c0f66a69a76a24064c8ede4a1f87980d97355726d08e |
__all__ = ['fsvd']
import numpy as np
def fsvd(A, k, i, usePowerMethod=False):
#function [U,S,V] = fsvd(A, k, i, usePowerMethod)
# FSVD Fast Singular Value Decomposition
#
# [U,S,V] = FSVD(A,k,i,usePowerMethod) computes the truncated singular
# value decomposition of the input matrix A upto rank k using i level... | aasensio/pyAndres | fsvd.py | Python | mit | 2,897 | [
"Gaussian"
] | db691e6b9bbfe42c4ab7b992a627fef2efe9a3c61aa3ab86ac921fc600551968 |
from django.test import LiveServerTestCase
from selenium import webdriver
class NewVisitorTest(LiveServerTestCase):
def setUp(self):
self.browser = webdriver.Firefox()
self.browser.implicitly_wait(2)
def tearDown(self):
self.browser.quit()
def test_sees_an_empty_page_message(se... | mkoistinen/aldryn-newsblog | aldryn_newsblog/tests/browser/test_aldryn_newsblog.py | Python | bsd-3-clause | 843 | [
"VisIt"
] | 6a80f02d18a8dc358814e11d1b8af7265cd545f93d284b49688b2e0e648f4a20 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import os
import re
import json
import warnings
from io import open
from enum import Enum
from pymatgen.core.units import Mass, Length, unitiz... | xhqu1981/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 37,542 | [
"CRYSTAL",
"pymatgen"
] | e37dd4e2b467aed05e3955bca9f67c97369eba6bad3219e3f64cfa397b539fde |
#!/usr/bin/env python
import math,cmath
import collections
from numpy.linalg import norm
class hamiltonian(object):
"""
n_wann:
"""
def __init__(n_wann,n_R):
n_wann=0
n_R=0
degeneracy=dict()
HmnR=dict()
def ham_parser(filename='wannier90_hr.dat',cutoff=None):
"""
... | mailhexu/pyDFTutils | pyDFTutils/wannier90/read_ham.py | Python | lgpl-3.0 | 1,669 | [
"Wannier90"
] | 4f7ea83ff18743791a9899214343d0cad7b3803f4ed38ff66ebf4649ade1942f |
#
# Copyright (C) 2017-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | testsuite/python/force_cap.py | Python | gpl-3.0 | 2,014 | [
"ESPResSo"
] | 82efcc6d29df25c0ddd569647b15643b9b125ef3629f3e3ea8e42561d802432b |
# 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... | rsepassi/tensor2tensor | tensor2tensor/layers/common_layers.py | Python | apache-2.0 | 90,204 | [
"Gaussian"
] | 95ddd2693e94b4896e0a36ce08a8668e7037dbed51b47f4f463ef75ca633d827 |
import pytest
import os
from fontTools.ttLib import TTFont
from fontbakery.checkrunner import (DEBUG, INFO, WARN, ERROR,
SKIP, PASS, FAIL, ENDCHECK)
from fontbakery.codetesting import (assert_results_contain,
assert_PASS,
... | graphicore/fontbakery | tests/profiles/googlefonts_test.py | Python | apache-2.0 | 145,498 | [
"Galaxy"
] | 144f8990b99625796107ac0398a5f15ee77d6217425e08bf925ab2db8916b359 |
#!/usr/bin/env python
# coding: utf-8
import os
from pymatgen.io.vasp import Potcar
def proc_dir(dirname, procfilefunction):
for f in os.listdir(dirname):
if os.path.isdir(os.path.join(dirname, f)):
proc_dir(os.path.join(dirname, f), procfilefunction)
else:
procfilefuncti... | tschaume/pymatgen | pymatgen/cli/pmg_potcar.py | Python | mit | 1,152 | [
"VASP",
"pymatgen"
] | 4aa6769f649e690d78f4c5a3d0b5e3f7f96d9a7ac6ed1c2a11093a508b4e531b |
# -*- coding: utf-8 -*-
#
# hl_api_spatial_distributions.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 o... | SepehrMN/nest-simulator | pynest/nest/spatial_distributions/hl_api_spatial_distributions.py | Python | gpl-2.0 | 3,650 | [
"Gaussian"
] | f759ed632a629ee4d6f5b9b14e7835bf5e64afb5110b4ae9fda3e53c3fb5ce26 |
from gpyconf import Configuration
from gpyconf.fields import IntegerField, BooleanField, MultiOptionField
from gpyconf.fields import ColorField, FontField
from gpyconf.backends.python import PythonModuleBackend
themes = ((theme, theme.title()) for theme in (
'amber', 'c64', 'darkgreen', 'locontrast', 'banker', 'cu... | jonashaag/gpyconf | examples/pyroom.remake.py | Python | lgpl-2.1 | 1,496 | [
"Amber"
] | 2630828b38e563a334e3f67f3804ad14c87a3dd04baf32acacaad5d2ee76c986 |
import numpy as np
from falass import dataformat
import matplotlib.pyplot as plt
import MDAnalysis as mda
class Files:
"""File parsing.
Definition of the files to be used in the analysis; such as the .pdb file, .lgt file (is one exists), .dat file
(is one exists). Also defined at this time are the resolu... | arm61/falass | falass/readwrite.py | Python | mit | 13,883 | [
"Gaussian",
"MDAnalysis"
] | dad0a1c7cb71611fdf379cd2bb0062cb8dfca95d787feb6850717b91268d3fb1 |
import numpy as np
import numpy.random as ra
from gpaw.setup import create_setup
from gpaw.xc import XC
from gpaw.test import equal, gen
if 1:
for functional in [
'LDA_X', 'LDA_X+LDA_C_PW', 'LDA_X+LDA_C_VWN', 'LDA_X+LDA_C_PZ',
'GGA_X_PBE+GGA_C_PBE', 'GGA_X_PBE_R+GGA_C_PBE',
'GGA_X_B88+GGA_C... | qsnake/gpaw | gpaw/test/lxc_xcatom.py | Python | gpl-3.0 | 2,710 | [
"GPAW"
] | e60b365073b4ab44bf021eecf949c319c14592f4f0c7989c9633d6a5a929a58a |
import enum
import inspect
import pydoc
import unittest
from collections import OrderedDict
from enum import Enum, IntEnum, EnumMeta, unique
from io import StringIO
from pickle import dumps, loads, PicklingError, HIGHEST_PROTOCOL
# for pickle tests
try:
class Stooges(Enum):
LARRY = 1
CURLY = 2
... | PennartLoettring/Poettrix | rootfs/usr/lib/python3.4/test/test_enum.py | Python | gpl-2.0 | 56,811 | [
"MOE"
] | 5aeea681b6237a2a04934cd7598e59a40c531f6d98410819f43137d647afe554 |
"""Factor Analysis.
A latent linear variable model.
FactorAnalysis is similar to probabilistic PCA implemented by PCA.score
While PCA assumes Gaussian noise with the same variance for each
feature, the FactorAnalysis model assumes different variances for
each of them.
This implementation is based on David Barber's B... | Titan-C/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 12,178 | [
"Gaussian"
] | b6e7447b69ec7c33ef9874130fa2d2eee555dbc096bd56eb3fb1299c6b68b29f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/client/tabs/campaign.py
#
# 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
# not... | securestate/king-phisher | king_phisher/client/tabs/campaign.py | Python | bsd-3-clause | 32,510 | [
"VisIt"
] | 97378ae9fa9dbbbdafa9141dbaaaa65f463bc0f0cd646c56cd4eeb93ddd70ba3 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# GeomAlgo documentation build configuration file, created by
# sphinx-quickstart on Thu Aug 18 13:09:05 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# a... | geomalgo/geomalgo-doc | conf.py | Python | gpl-3.0 | 10,246 | [
"Mayavi"
] | d5187299550201b085ce678ffa637c2ab1d757e3ec4c951e68050a15b8295d7f |
"""
DIRAC.WorkloadManagementSystem.Service package
"""
__RCSID__ = "$Id$"
| fstagni/DIRAC | WorkloadManagementSystem/Service/__init__.py | Python | gpl-3.0 | 78 | [
"DIRAC"
] | 696e766ed4fb2c5b2c7f65f1f38f43ff5efd30a5485c64af7a0b3a16ce6c8e38 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | tonyyarusso/ansible-modules-core | cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 27,104 | [
"Dalton"
] | 8f95e371f39dc8d195b39643fbe622f8509322199345d64fa4119569ab436213 |
"""
functions for finding, retrieving data from and updating the Galaxy .loc files
"""
import os
from bcbio.distributed.transaction import file_transaction
from bcbio.utils import file_exists
import tempfile
import shutil
REF_FILES = {"bwa": "bwa_index.loc",
"bowtie": "bowtie_indices.loc",
"s... | SciLifeLab/bcbio-nextgen | bcbio/galaxy/loc.py | Python | mit | 3,104 | [
"BWA",
"Bowtie",
"Galaxy"
] | fb72e3cfbd0792ddfd3d28812b737c468390d129417b5a5b81a44c01625325d9 |
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