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|---|---|---|---|---|---|---|---|
"""
This module contains helper methods for accessing operational attributes or parameters of DMS objects
"""
from DIRAC.ConfigurationSystem.Client.Helpers.Path import cfgPath
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
# from Core.Uti... | petricm/DIRAC | DataManagementSystem/Utilities/DMSHelpers.py | Python | gpl-3.0 | 16,378 | [
"DIRAC"
] | 0c6c164c16404768ca9c6b45d692ce768a85bc406ffe6d0731de72da390470a7 |
from __future__ import (absolute_import, division, print_function)
import unittest
from StretchedExpFTTestHelper import isregistered, do_fit
class PrimStretchedExpFTTest(unittest.TestCase):
def testRegistered(self):
self.assertTrue(*isregistered('PrimStretchedExpFT'))
def testGaussian(self):
... | dymkowsk/mantid | Framework/PythonInterface/test/python/plugins/functions/PrimStretchedExpFTTest.py | Python | gpl-3.0 | 1,648 | [
"Gaussian"
] | 2aa93a9d96d577da45b53ccf47c914cdd8e6bad7f4dfc8a7ee57b41a1df392ff |
import os
import sys
import unittest
sys.path.insert(0, os.getcwd())
from csg.core import CSG
from csg.geom import Vector
class TestCSG(unittest.TestCase):
def setUp(self):
print('setup')
def tearDown(self):
print('tear')
def test_sphere(self):
a = CSG.sphere(center=[0.,... | timknip/pycsg | test/test_refine.py | Python | mit | 758 | [
"VTK"
] | a8d7556b1e599054b2882a3c2190a2c4bd012707f2b7a5a59d2ab50514846846 |
# encoding: utf-8
from __future__ import unicode_literals
import mimetypes
import os
import re
from tempfile import NamedTemporaryFile
import requests
from twitter import TwitterError
TLDS = [
"ac", "ad", "ae", "af", "ag", "ai", "al", "am", "an", "ao", "aq", "ar",
"as", "at", "au", "aw", "ax", "az", "ba", "... | jakeshi/python-twitter | twitter/twitter_utils.py | Python | apache-2.0 | 14,730 | [
"CASINO",
"MOE"
] | d1a21fef918bb12a5081b56884e463d85eb8da4d8f9e5780b044fe58d88f3407 |
#!/usr/bin/env python
# Copyright 2020 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/xchem/rmsd_filter.py | Python | apache-2.0 | 6,234 | [
"RDKit"
] | 5615cdb9b442ddfcd390c8359ec33735420385003bc2ba80445c091aa4d49df7 |
#!/usr/bin/env python
#
# Copyright (C) 2014, 2015
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.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 withou... | f0rki/cb-multios | disabled-challenges/CAT/poller/for-release/machine.py | Python | mit | 16,097 | [
"Brian"
] | 8dfb14b6011a70e0c7926cc9946ef4eb6bebf65c34bd3b60c6354ba81dad17c3 |
import numpy as np
from astropy.table import Table
from astropy.io import fits
import matplotlib.pyplot as plt
import matplotlib
import pickle
from TheCannon_2 import dataset,apogee
from TheCannon_2 import model
pkl_file = open('wl.pkl', 'rb')
wl = pickle.load(pkl_file)
pkl_file.close()
# load path
pkl_file = op... | peraktong/Cannon-Experiment | 0217_plot_all_in_paper.py | Python | mit | 58,626 | [
"VisIt"
] | 491c9389e84a6796f71f8fe704c225aca6975259bb25e1cdfffe99a2c9771c2f |
"""
Functions to visualize an Experiment.
"""
__authors__ = "James Bergstra"
__license__ = "3-clause BSD License"
__contact__ = "github.com/hyperopt/hyperopt"
import math
import sys
# -- don't import this here because it locks in the backend
# and we want the unittests to be able to set the backend
##impor... | w1kke/hyperopt | hyperopt/plotting.py | Python | bsd-3-clause | 19,883 | [
"Gaussian"
] | 7452f28616836f4c795cc5bd23f2c42d24f42c5d9278564211dd44117949c7c1 |
#
# Author: Henrique Pereira Coutada Miranda
# Tests for yambopy
# Si
#
import matplotlib
matplotlib.use('Agg')
import unittest
import sys
import os
import argparse
import subprocess
import filecmp
from yambopy import *
from qepy import *
class TestPW_Si(unittest.TestCase):
""" This class creates the input files f... | alexmoratalla/yambo-py | tests/test_si.py | Python | bsd-3-clause | 11,321 | [
"Yambo"
] | 4995e880a9550b3869f1dbbf7864caea26b2acccb5abf430f89a8815a8b9496a |
from __future__ import print_function
from __future__ import absolute_import
from .DataTestTemplate import _DataTest
from owmeta.neuron import Neuron
from owmeta.cell import Cell
from owmeta.connection import Connection
from owmeta_core.context import Context
class NeuronTest(_DataTest):
ctx_classes = (Neuron, ... | openworm/PyOpenWorm | tests/NeuronTest.py | Python | mit | 4,670 | [
"NEURON"
] | e0bdc0c31e75b2bf2b53b562b5ff251d719a7462ecaddfc4d11ecc07b2c7cfab |
#!/usr/bin/env python
################################################################################
# DATE: 2021/March/10
#
# MODULE: add_group_rank.py
#
# VERSION: 2.0
#
# AUTHOR: Zihao Liu (zihaoliu@ufl.edu)
#
# DESCRIPTION: Rank analysis
#
######################################################################... | secimTools/SECIMTools | src/scripts/add_group_rank.py | Python | mit | 2,864 | [
"Galaxy"
] | 998ac21ab733e27ff71d6b3117db5c4aa36b1cb7705a391fca81d54198b6aaab |
#
# 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... | iemejia/incubator-beam | sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner.py | Python | apache-2.0 | 41,958 | [
"VisIt"
] | bdf74802a891ca5d43077fbabfa21c56fde0e19ed2ec62e257e43d596311e657 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines the abstract base classes for battery-related classes.
Regardless of the kind of electrode, conversion or insertion, there are many
common definitions and properties, e.g., average voltage, capacity, etc. which
can be defined in... | Dioptas/pymatgen | pymatgen/apps/battery/battery_abc.py | Python | mit | 12,188 | [
"pymatgen"
] | 668839731720b389d99b79978caac346360853f724ec470a6b1e50bff5197516 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2018 David Arroyo Menéndez
# Author: David Arroyo Menéndez <davidam@gnu.org>
# Maintainer: David Arroyo Menéndez <davidam@gnu.org>
# This file is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | davidam/python-examples | matplotlib/stackplot_demo.py | Python | gpl-3.0 | 2,255 | [
"Gaussian"
] | 5210542175ae4d0bb472065fe12c5b609d1ccd8d521573b70e93e009f248c07f |
# Copyright (c) Corporation for National Research Initiatives
import operator
import org
from BaseEvaluator import BaseEvaluator
class FlowControlException(Exception):
pass
class DoBreak(FlowControlException):
pass
class DoContinue(FlowControlException):
pass
class DoReturn(FlowControlException):
... | mcarlson/openlaszlo | 3rd-party/tools/jythonc/PythonInterpreter.py | Python | epl-1.0 | 5,387 | [
"VisIt"
] | b135291e71fbe22447f5bb672b2dfce3911c02c292bca3363fb7f8605daeaf05 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/lb_interpolation.py | Python | gpl-3.0 | 4,976 | [
"ESPResSo"
] | 2c99767ada72da478dd317f743ef7f46d87bf1eebfdde823d656a882e95211e5 |
"""
Tests to make sure that the sites that we scrape haven't changed their
data formats.
"""
import unittest
from datetime import date
from time import sleep
from puzzletools.enumerations_web import *
from puzzletools.enumerations_web import _us_states
from puzzletools.subway import *
def canonicalize(item):
if i... | dgulotta/puzzle-tools | puzzletools/tests_web.py | Python | mit | 5,782 | [
"CRYSTAL"
] | fbe11abe5a8e4f79b00245682faa7794694da417167758b37b887052f2633428 |
import json
import socket
import numpy as np
import pytest
from pysisyphus.calculators.XTB import XTB
@pytest.mark.skip
def test_socketcalc():
host = "localhost"
port = 8080
calc = XTB(pal=2)
funcs = {
"energy": calc.get_energy,
"forces": calc.get_forces,
"hessian": calc.get... | eljost/pysisyphus | tests/test_socketcalc/test_socketcalc_client.py | Python | gpl-3.0 | 1,274 | [
"xTB"
] | bafe0f3e1364366dae3b440a6c5c71b1c85a3ffe0916e700f26bb9cd8d3e0555 |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
QtCore.QString = str
except ImportError:
raise ImportError("Cannot load either PyQt or PySide... | danielru/moose | gui/vtk/ExodusResultRenderWidget.py | Python | lgpl-2.1 | 50,602 | [
"VTK"
] | c96af7d31ca877ba2bff022df0ae8cef731942464667d34dd656a3b784670bac |
#!/usr/bin/env python3
"""
This script is a python version of TimingAccuracy. We use some numpy functions
to simplify the creation of random coefficients.
"""
import time
import numpy as np
from pyshtools import expand
from pyshtools import spectralanalysis
# ==== MAIN FUNCTION ====
def main():
TimingAccuracyDH(... | SHTOOLS/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyDH.py | Python | bsd-3-clause | 2,525 | [
"Gaussian"
] | 11ec7e0e4f5d482b176bb4b898fb7d352df8b711aee4ba69019bda77cb5e7144 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/preprocessing/data.py | Python | mit | 94,481 | [
"Gaussian"
] | 178013fe7f4fbaefe9d6182f728e4dc0d83ef6a0c5e0f2302cc834ab2b058614 |
import h5py
import sys
import numpy as np
"""
sl files use an lz4 compression filter for which a plugin needs to be installed
Mac:
sudo port install hdf5-lz4-plugin
Ubuntu: (http://gisaxs.com/index.php/HDF5)
sudo add-apt-repository ppa:eugenwintersberger/pni
sudo apt-get update
sudo apt-get install hdf5-plugin-lz4
... | alexandrovteam/pyImagingMSpec | pyImagingMSpec/convert/sl.py | Python | apache-2.0 | 8,348 | [
"VisIt"
] | e862e8e24cc273d371d9ebc16905ec4600649187ed058f8a4ef9411bb85f860d |
import numpy as np
import scipy as scipy
import lxmls.classifiers.linear_classifier as lc
import sys
from lxmls.distributions.gaussian import *
class MultinomialNaiveBayes(lc.LinearClassifier):
def __init__(self,xtype="gaussian"):
lc.LinearClassifier.__init__(self)
self.trained = False
se... | SimonSuster/lxmls-toolkit | lxmls/classifiers/multinomial_naive_bayes.py | Python | mit | 2,722 | [
"Gaussian"
] | 9036d4e496369c0b31ce97c6d8f31a4988b80d2c4ca3e697e7a41812184a9dcc |
from setuptools import setup
def readme():
with open('README.md') as f:
return f.read()
setup(name='kmbio',
version='0.01.04',
description='Cheap Personal bio-library',
author='Keith Murray',
author_email='kmurrayis@gmail.com',
license='MIT',
packages=['kmbio'],
i... | CrakeNotSnowman/BioLibrary | setup.py | Python | mit | 489 | [
"Biopython"
] | 817eca1f9964196efff1f2f9bd58a8c9d42b657cfb57955ebe9e8d6ccd5cb38b |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/automl/search/__init__.py | Python | apache-2.0 | 921 | [
"ORCA"
] | 9c578b1eadd527e809f068e5a26fc1832374f5b044a88140d1f0729f658b9a37 |
from rpython.rtyper.lltypesystem.lltype import (Struct, Array, FixedSizeArray,
FuncType, typeOf, GcStruct, GcArray, RttiStruct, ContainerType, parentlink,
Void, OpaqueType, Float, RuntimeTypeInfo, getRuntimeTypeInfo, Char,
_subarray)
from rpython.rtyper.lltypesystem import llmemory, llgroup
from rpython.tra... | oblique-labs/pyVM | rpython/translator/c/node.py | Python | mit | 37,249 | [
"VisIt"
] | 42dfd3e14b58e92f8b9397284dbd22e1cccad715ac10be8f95870c6926f23183 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_getpass,
compat_HTTPError,
compat_http... | msingh172/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 55,808 | [
"VisIt"
] | 15838e15d9cfa9c507e7c96e44652baefd189fc6cd7fab89f580cc0e344dd32d |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from collections import OrderedDict
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import setti... | knehez/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 66,170 | [
"VisIt"
] | 427b58afd4e0481e3d258f6a74a4eaa24d71b51eeceed556ad8f4f0ad17006cc |
import sys, time, threading, os
from DIRAC import gLogger
from DIRAC import S_OK, S_ERROR, gConfig, gLogger, gMonitor, rootPath
from DIRAC.ConfigurationSystem.Client import PathFinder
from DIRAC.FrameworkSystem.Client.MonitoringClient import MonitoringClient
from DIRAC.Core.Utilities.Shifter import setupShifterProxyInE... | Sbalbp/DIRAC | Core/Base/ExecutorModule.py | Python | gpl-3.0 | 7,148 | [
"DIRAC"
] | fe8807d41ee508f35cfffe62d082bca5cb938a5efde43589583d0d45b55b8d2b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/share/psi4/databases/HSG.py | Python | gpl-2.0 | 46,440 | [
"Psi4"
] | 91bb2a3447cb096bab87757314166986d219a12373db4d4b15603db983d57f97 |
# 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 re
import abc
import six
from abc import ABCMeta, abstractproperty, abstractmethod
"""
Error handlers for errors originating from the S... | xhqu1981/pymatgen | pymatgen/io/abinit/scheduler_error_parsers.py | Python | mit | 14,014 | [
"pymatgen"
] | 42d0f11079a25997346761885d95042e591a27b68daad326a8daf7716953e412 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c) 2011-2020, Gianluca Fiore
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as publishe... | Donearm/CryptandDrop | CryptandDrop.py | Python | lgpl-3.0 | 12,034 | [
"VisIt"
] | 6e7681ff9bc4d575a52b4aed9250cdb5c2c855c0c271d54eb64c465713016a35 |
# -*- coding: utf-8 -*-
"""
equip.visitors.blocks
~~~~~~~~~~~~~~~~~~~~~
Callback the visit basic blocks in the program.
:copyright: (c) 2014 by Romain Gaucher (@rgaucher)
:license: Apache 2, see LICENSE for more details.
"""
class BlockVisitor(object):
"""
A basic block visitor. It first receives the... | neuroo/equip | equip/visitors/blocks.py | Python | apache-2.0 | 798 | [
"VisIt"
] | 2ab16158041a8080d0617922db95c7991f9fd53cc3fe5049ab6d028a8af104b7 |
import numpy as np
import xarray as xr
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import pf_dynamic_cart as pfc
import pf_dynamic_sph as pfs
import Grid
from scipy import interpolate
from timeit import default_timer as timer
if __name__ == "__main__":
# ---- INITIALIZE G... | kseetharam/genPolaron | amp_reconstruct_plot.py | Python | mit | 19,401 | [
"Gaussian"
] | f1f3b498b946b5058417125f7d7a41677e9b53dfc5ee69a20025230a47f96d43 |
#!/usr/bin/env python
#
# $File: simuGen.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute it... | BoPeng/simuPOP | docs/simuGen.py | Python | gpl-2.0 | 1,716 | [
"VisIt"
] | d3ad573dcfadd88c67b63b89d62dde45cd85468f411e0bfeb85919b16a22845d |
#
# Copyright (C) 2004-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import doctest
import gzip
... | greglandrum/rdkit | rdkit/Chem/Pharm3D/UnitTestEmbed.py | Python | bsd-3-clause | 9,483 | [
"RDKit"
] | 7e8f1f290661edc0c4fc082c91b51988fdfdd961fdccab9102c86cc3b3440e39 |
#
# This file is part of CasADi.
#
# CasADi -- A symbolic framework for dynamic optimization.
# Copyright (C) 2010-2014 Joel Andersson, Joris Gillis, Moritz Diehl,
# K.U. Leuven. All rights reserved.
# Copyright (C) 2011-2014 Greg Horn
#
# CasADi is free software; you can... | ghorn/debian-casadi | docs/tutorials/python/make_tutorials.py | Python | lgpl-3.0 | 2,555 | [
"VisIt"
] | fc03238b2dbc8965d1546da7497b58392c8971a42442a4376fc1b0a48db93cb2 |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
"""
Input sets for VASP GW calculations
Single vasp GW work: Creates input and jobscripts from the input sets for a specific job
"""
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ = "0.9"
__maintainer__ = "Michiel v... | Dioptas/pymatgen | pymatgen/io/vaspio/GWvaspinputsets.py | Python | mit | 26,515 | [
"VASP",
"Wannier90",
"pymatgen"
] | fed106818d6820fdb8f61e88de54f883ecf52362be953e0b052af1f3cd9ff7cf |
"""
A simple VTK widget for wxPython.
Find wxPython info at http://wxPython.org
Created by David Gobbi, December 2001
Based on vtkTkRenderWindget.py
Updated to new wx namespace and some cleaning by Andrea Gavana,
December 2006
"""
"""
Please see the example at the end of this file.
-------------------------------... | collects/VTK | Wrapping/Python/vtk/wx/wxVTKRenderWindow.py | Python | bsd-3-clause | 23,312 | [
"VTK"
] | 3fddd7620f866892e1b422f5d861fe56d000b59ba2628c04553af34177456a84 |
#!/usr/local/bin/python3
# ---------------------------------------------------------------------------------------------------------------------
#
# Bioinformatics Research Group
# http://biorg.cis.fiu.edu/
# ... | camilo-v/Neural-Networks | single-layer-networks/perceptron/perceptron.py | Python | gpl-3.0 | 4,529 | [
"NEURON"
] | 98fc02c7984acd6596b5f90a2ad3ab51ae19fab4fa95db9a335e440600eb2e2f |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/diversity/alpha/_lladser.py | Python | bsd-3-clause | 17,245 | [
"scikit-bio"
] | 982033c2ec1562d6d55cd44fe31c768ecc585d84fbd2816c314835ba9eeab5f4 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'PatientInformation'
db.create_table(u'patient_patientinformation', (
(u'id', sel... | aazhbd/medical_info01 | patient/migrations/0001_initial.py | Python | bsd-3-clause | 55,374 | [
"VisIt"
] | 89b5bc51c49dfd0e813bbe50aba9d85e00bc6143c36c17e1eaab85783c6d4653 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 3: Deep Learning and Neural Networks
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2015 by Jeff Heaton
Licensed under the Apache License, V... | trenton3983/Artificial_Intelligence_for_Humans | vol3/vol3-python-examples/examples/example_deep_belief.py | Python | apache-2.0 | 2,936 | [
"VisIt"
] | 9e028db4c3bffc8da943c2b7d60d61a2a4b8de7b2700c68641768c797a4dd222 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 ... | sam-m888/gprime | gprime/plug/menu/_string.py | Python | gpl-2.0 | 1,754 | [
"Brian"
] | 76c8ec737bff7a24775f5bf954e62e16ad1301c13efb83c72122e1a11c2dfdd7 |
#
# Copyright 2015 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful, but WITHOUT ANY WARRANTY expressed... | vojtechtrefny/anaconda | tests/dracut_tests/parse-kickstart_test.py | Python | gpl-2.0 | 13,829 | [
"Brian"
] | 51d4dbf579b7c3c2d9db8c16054ae89b23345437600c8be387b23bf430f905e3 |
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 4.05
d = a / 2**0.5
bulk = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (0.5, 0.5, 0.5))], pbc=True)
bulk.set_cell((d, d, a), scale_atoms=True)
h = 0.25
calc = GPAW(h=h,
nbands=2*8,
kpts=(2, 2, 2),
... | robwarm/gpaw-symm | gpaw/test/davidson.py | Python | gpl-3.0 | 955 | [
"ASE",
"GPAW"
] | 665b53de689d78a4d30ac6a2df2aa8d31d567a0b926f41b95ee6daf78da429ef |
""" :mod: GFAL2_SRM2Storage
=================
.. module: python
:synopsis: SRM2 module based on the GFAL2_StorageBase class.
"""
from types import StringType, ListType
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
fro... | miloszz/DIRAC | Resources/Storage/GFAL2_SRM2Storage.py | Python | gpl-3.0 | 6,711 | [
"DIRAC"
] | 8b5d2b7db865719c697fe6de2989681b4e6a25c006ee294589fab9f902ad0b6d |
from uaperrors import StepError
import sys
import os
from logging import getLogger
from abstract_step import AbstractStep
logger = getLogger('uap_logger')
class Bowtie2GenerateIndex(AbstractStep):
'''
bowtie2-build builds a Bowtie index from a set of DNA sequences.
bowtie2-build outputs a set of 6 files ... | kmpf/uap | include/steps/bowtie2_generate_index.py | Python | gpl-3.0 | 13,469 | [
"Bowtie"
] | fd03cb505da35cb1d3f6ead27de4d9dfdb1e73d68545d498f0b2bd39e4442f90 |
#* 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
import funct... | nuclear-wizard/moose | python/peacock/utils/InputTesting.py | Python | lgpl-2.1 | 12,482 | [
"MOOSE"
] | 8421da3546c56c9685e5e24ea3737fc7d897b99524790b6810629ead17a4616b |
__author__ = "Brian O'Neill"
__version__ = '0.3.0'
'''
Four tests changed because of a Python bug fixed in 3.5:
http://bugs.python.org/issue23775
Fix pprint of OrderedDict
Pre-3.5, pprint printed the repr of OrderedDict if it fit on one line,
and printed the repr of dict if the output would be wrapped... | Twangist/log_calls | tests/test_log_calls_more.py | Python | mit | 28,627 | [
"Brian"
] | c421c44596c05744178f3d8cd5ef9953017ad2fb22180964386fdc3b47cc2434 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | hgl888/chromium-crosswalk-efl | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 16,386 | [
"Galaxy"
] | 27ced583e2682ac4bc9e21d250b2dc7d75c6f8eed6440cb1a226d8c48df8cfc8 |
import pytest
from devito import Grid, Dimension, Eq, Function, TimeFunction, Operator # noqa
from devito.ir import Expression, Iteration, FindNodes
class TestCodeGenSkewing(object):
'''
Test code generation with blocking+skewing, tests adapted from test_operator.py
'''
@pytest.mark.parametrize('exp... | opesci/devito | tests/test_skewing.py | Python | mit | 6,973 | [
"VisIt"
] | 53e901067cc5a09dfc11123aecfa8e466ea2d588eb9d619de4c5b0ddee8ee1e9 |
# -*- coding: utf-8 -*-
#
# pymetro documentation build configuration file, created by
# sphinx-quickstart on Sun Jul 26 19:08:49 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All... | unbracketed/pymetro | docs/conf.py | Python | bsd-2-clause | 6,287 | [
"Brian"
] | 2ba6da997c6ebd62e1df7e045d52edd31cb4fd01661b52811fec583ac1581c96 |
""" X509Chain is a class for managing X509 chains with their Pkeys
Link to the RFC 3820: https://tools.ietf.org/html/rfc3820
In particular, limited proxy: https://tools.ietf.org/html/rfc3820#section-3.8
There are also details available about Per-User Sub-Proxies (PUSP)
here: https://wiki.egi.eu/wiki/Usage_of_the_per_... | fstagni/DIRAC | Core/Security/m2crypto/X509Chain.py | Python | gpl-3.0 | 34,574 | [
"DIRAC"
] | 7712cd3e3e9d7a67cd77d1db4d8edcaae06cf4ff5e2d50036c15a3a965c6e33c |
## \file
## \ingroup tutorial_roofit
## \notebook
## Basic functionality: numerical 1st, and 3rd order derivatives w.r.t. observables and parameters
##
## ```
## pdf = gauss(x,m,s)
## ```
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Set up model
# ... | root-mirror/root | tutorials/roofit/rf111_derivatives.py | Python | lgpl-2.1 | 2,476 | [
"Gaussian"
] | dba144a551baa6d5f8bf6ce97920e5b55b8085946940a10490237e365197694b |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | testsuite/python/lb_density.py | Python | gpl-3.0 | 2,417 | [
"ESPResSo"
] | e68fb91a81df2b261170d4b8aa492b0bcc2f7932923b0055e319e5f3c771870a |
#!/usr/bin/env python
# This simple example shows how to do basic rendering and pipeline
# creation.
import pychemia
if pychemia.HAS_VTK:
import vtk
# The colors module defines various useful colors.
from vtk.util.colors import tomato
# This creates a polygonal cylinder model with eight circumferen... | MaterialsDiscovery/PyChemia | tests/test_code_vasp_02.py | Python | mit | 2,010 | [
"VTK"
] | 4c488d61facea8cf1c24a507ce5434180c562f32973fb20c176df55f397e128c |
# 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 | dedal/smith_waterman.py | Python | apache-2.0 | 28,920 | [
"Gaussian"
] | 72422530211ceae233073825f0c86243e07f276aede095ae95b1e6ef787768d0 |
"""
Add-on to make the MonitoringClient works with an IOLoop from a Tornado Server
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import tornado.ioloop
from DIRAC import gLogger
class MonitoringFlusherTornado(object):
"""
T... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/Client/MonitoringClientIOLoop.py | Python | gpl-3.0 | 969 | [
"DIRAC"
] | 60e05e56a1116d9bf1c3aa71eb8b7b93faac127cb6dbca7be04d4effcaf02876 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from pymatgen.analysis.elasticity.tensors import SquareTensor
from collections import namedtuple
from pymatgen.core.units import FloatWithUnit
from pymatgen.c... | gpetretto/pymatgen | pymatgen/analysis/nmr.py | Python | mit | 8,292 | [
"pymatgen"
] | 013eb94f81a919ba6897221885a5a6a380aae6b3e9d111b1e73c7a5652990b1c |
#!/usr/bin/env python
#coding=utf-8
# from __future__ import with_statement # This isn't required in Python 2.6
"""
Modulo core de FIRtro
"""
#----------------------------------------------------------------------
# v2.0a (2016-oct)
#
# - (a) Se reincorpora la funcionalidad clock :-|
#
# - Se etiquetan los printado... | rripio/FIRtro | bin/server_process.py | Python | gpl-3.0 | 44,520 | [
"DIRAC"
] | 05edf011566cd6b2a5514808d5955b71fb659fdddd1fab76aa04b71a327fead5 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-datacatalog | scripts/fixup_datacatalog_v1_keywords.py | Python | apache-2.0 | 8,604 | [
"VisIt"
] | 2650874124f758d20c29bf331c892836b1ef95eee4a1f1c9b16de7fb4c339750 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# Copyright 2009 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import sys
# Add path to Bio
sys.pa... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/ExPASy/Enzyme.py | Python | gpl-2.0 | 4,551 | [
"Biopython"
] | 26e0f40fd567608f85b81f358a9e42865b245eb41f8fe91e5c10af653515d2c3 |
'''Defines the Cavity class for theia.'''
# Provides:
# class Cavity
from units import *
from component import OpticalComponent
class Cavity(OpticalComponent):
'''
Cavity class.
This class represents optical cavities, which are distict from mirros and
lenses and declared as such. Essential the in... | bandang0/theia | trash/cavity.py | Python | gpl-3.0 | 775 | [
"Gaussian"
] | 225f448076434daf99088f3ee5b58c08649e3b1dfe11251058130093835a8ac4 |
# ============================================================================
#
# 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/bin/__init__.py | Python | gpl-2.0 | 1,153 | [
"VisIt"
] | da177b3cb5f7b52160dfc8bd29803c4af344c9473543f913674e4faf2ebad674 |
from __future__ import print_function
import numpy as np
from bokeh.browserlib import view
from bokeh.document import Document
from bokeh.glyphs import *
from bokeh.objects import (
Plot, Range1d, LinearAxis, Grid, ColumnDataSource, PanTool, WheelZoomTool
)
from bokeh.session import Session
document = Document()... | jakevdp/bokeh | examples/glyphs/prim_server.py | Python | bsd-3-clause | 1,829 | [
"VisIt"
] | e8197d282bc71ef129a1c7897ac81e4765f613a017adcba40b59948d376d8ef5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
| This file is part of the web2py Web Framework
| Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
| License: LGPLv3 (http://www.gnu.org/licenses/lgpl.html)
The widget is called from web2py
----------------------------------
"""
import datetime
import sys
i... | nonnib/eve-metrics | web2py/gluon/widget.py | Python | mit | 46,136 | [
"VisIt"
] | 0968bd38af81db845d4ad65d9415d96b32053b86b6a22c2743bdbfd989ab1735 |
full_response_before_filtering = [
{
"Event": {
"Attribute": [
{
"Galaxy": [],
"ShadowAttribute": [],
"category": "Payload installation",
"comment": "mock",
"deleted": False,
... | demisto/content | Packs/MISP/Integrations/MISP_V2/test_data/test_constants.py | Python | mit | 19,871 | [
"Galaxy"
] | 5342e30ebef8c5f2dcfb4700327d29f18283da32d865d1180c2b4abf1b243950 |
''' file name : morphology_1.py
Description : This sample shows how to erode and dilate images
This is Python version of this tutorial : http://opencv.itseez.com/doc/tutorials/imgproc/erosion_dilatation/erosion_dilatation.html#morphology-1
Level : Beginner
Benefits : Learn to 1) Erode, 2) Dilate and 3) Use trackbar... | asrob-uc3m/rpc_rpi | src/python/opencv_python_tutorials/Official_Tutorial_Python_Codes/3_imgproc/morphology_1.py | Python | gpl-3.0 | 1,489 | [
"VisIt"
] | 7c6f740bfb496329d7ec28533281916ee5dbbdb6b23a7cd604193d8c5f1b9937 |
import copy
import tempfile
import collections
import numpy as np
from .. import util
def load_pyassimp(file_obj,
file_type=None,
resolver=None,
**kwargs):
"""
Use the pyassimp library to load a mesh from a file object
and type or file name if file_o... | dajusc/trimesh | trimesh/exchange/assimp.py | Python | mit | 7,572 | [
"ASE"
] | c17c7829bf7a5d6ad43c3092206ab1181073d2125513dce22a97ff622f6e438e |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | yang-guangliang/android_guard | androguard/decompiler/dad/writer.py | Python | apache-2.0 | 25,618 | [
"VisIt"
] | 007996c1260a8193de3cd15f51ddc8c69a7e35411c70a7779a5aaae1df197ad8 |
from django import forms
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc.base.form.forms import BaseModelForm
from edc.subject.off_study.forms import BaseOffStudyForm
from ..models import HnsccVisit, HnsccOffStudy
from ..models.choices import OFF_STUDY_REASON
class HnsccVi... | botswana-harvard/bhp065_project | bhp065/apps/hnscc_subject/forms/main.py | Python | gpl-2.0 | 915 | [
"VisIt"
] | f1b1fbd6c17a15e337b00f330de12a46653c8644816f17d07a2437fafc062cee |
#!/usr/bin/python
def directory_crawler(pathname):
import sys
import os
lst_R1_R2= []
i = 0
if pathname[-1] != '/':
pathname += '/'
if os.path.isdir(pathname):
for flds in os.listdir(pathname):
if os.path.isdir(pathname + flds):
run_dir = pathname + flds + '/'
lst_R1_R2 = Parse_Files_To_Reads_... | ibest/APER | scripts/bwa_2.0_crawler.py | Python | apache-2.0 | 3,640 | [
"BWA"
] | ed60ceed1bc7af4e6dd6f365eeddc631341fed2c2d6565e6df371597717fd275 |
import pytest
import os
import numpy as np
from flare.otf import OTF
from flare.gp import GaussianProcess
from flare.struc import Structure
from flare.dft_interface.vasp_util import *
# ------------------------------------------------------
# test otf runs
# ---------------------------------------... | mir-group/flare | tests/test_OTF_vasp.py | Python | mit | 1,580 | [
"CP2K",
"VASP"
] | 7a689b0107c097f4a150d7aa40562a608e223000fda21f2a7a6b7b8ccfa77510 |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from math import pi
from compas.geometry import angle_points
__all__ = [
'trimesh_mean_curvature',
'trimesh_gaussian_curvature'
]
def trimesh_mean_curvature(mesh):
pass
def trimesh_gaussian_c... | compas-dev/compas | src/compas/datastructures/mesh/curvature.py | Python | mit | 1,810 | [
"Gaussian"
] | fc9aa25028e8ce29703d08350445f8c91336a9cf1497c86ed741c3c51986ef8d |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/meanfield/test/test_hamiltonian.py | Python | gpl-3.0 | 5,501 | [
"Gaussian"
] | 5b473797191776730856c55c7aa97dbc0a888eec109b4b501124494be547c580 |
# pylint: disable=no-init,too-few-public-methods
import stresstesting
from mantid.simpleapi import *
from mantid.geometry import CrystalStructure
# The reference data for these tests were created with PredictPeaks in the state at Release 3.5,
# if PredictPeaks changes significantly, both reference data and test may n... | dymkowsk/mantid | Testing/SystemTests/tests/analysis/PredictPeaksTest.py | Python | gpl-3.0 | 4,734 | [
"CRYSTAL"
] | d07191b5cca1b53d40ec2a4879f87b2bdef53062f43b25ed0b57e26aa461ab2d |
"""
A family of high-level user commands acting on the entire simulation.
Any new commands added to this directory will automatically become
available for any program.
Commands here should be 'bullet-proof' and work 'from scratch'.
That is, they should print warnings if required but should not raise
errors that would... | Tasignotas/topographica_mirror | topo/command/__init__.py | Python | bsd-3-clause | 38,216 | [
"Gaussian"
] | c95e035cc08e44cd3c83b14e8812f691b35c8a95b9502fe768d66bfd40e4bc87 |
import json
import numpy as np
import pytest
import pandas.util._test_decorators as td
from pandas import (
DataFrame,
Index,
Series,
json_normalize,
)
import pandas._testing as tm
from pandas.io.json._normalize import nested_to_record
@pytest.fixture
def deep_nested():
# deeply nested data
... | rs2/pandas | pandas/tests/io/json/test_normalize.py | Python | bsd-3-clause | 29,490 | [
"COLUMBUS"
] | a488004712900e7bea118ef974c13a28bb8da0dbf258912359f7f3cfddce947f |
#
#-*- coding:utf-8 -*-
"""
Gentoo-keys - config.py
Holds configuration keys and values
@copyright: 2012 by Brian Dolbec <dol-sen@gentoo.org>
@license: GNU GNU GPL2, see COPYING for details.
"""
import os
import sys
# py3.2
if sys.hexversion >= 0x30200f0:
import configparser as ConfigParser
els... | dol-sen/gentoo-keys | gkeys/config.py | Python | gpl-2.0 | 4,041 | [
"Brian"
] | 70fbc1ca87139624eba0f7161a5f165969f43e8b266e9808428f87ee070ee83a |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2019 Compassion CH (http://www.compassion.ch)
# Releasing children from poverty in Jesus' name
# @author: Emanuel Cino <ecino@compassion.ch>
#
# The licence is in the file __manifest__.py... | ecino/compassion-switzerland | website_event_compassion/migrations/10.0.1.7.0/post-migration.py | Python | agpl-3.0 | 991 | [
"VisIt"
] | 2114d3d89915f51340d6bcfa585cafac86ca23eb5194ae3bf983480cba765318 |
# Mixture of Factor analyzers for CelebA images
# from
# https://github.com/eitanrich/gans-n-gmms
import superimport
import numpy as np
import torch
from torch.utils.data import DataLoader, RandomSampler, SequentialSampler
import time
import math
import warnings
"""## MFA"""
class MFA(torch.nn.Module):
"""
... | probml/pyprobml | scripts/mfa_celeba_helpers.py | Python | mit | 28,051 | [
"Gaussian"
] | 1ce211e520dd106b5313ae18786f5f8489289790191f82d1feec7efd5b9bf431 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/kraken/Kraken.py | Python | bsd-3-clause | 15,592 | [
"PySCeS"
] | 57a91334e154d95ccf01f6d3a8622d63c3f92d82df3cc34174015886f79b89eb |
"""
Consumption-saving models with aggregate productivity shocks as well as idiosyn-
cratic income shocks. Currently only contains one microeconomic model with a
basic solver. Also includes a subclass of Market called CobbDouglas economy,
used for solving "macroeconomic" models with aggregate shocks.
"""
import numpy... | econ-ark/HARK | HARK/ConsumptionSaving/ConsAggShockModel.py | Python | apache-2.0 | 119,384 | [
"VisIt"
] | 8f7a75b25df8ea650db1026f8777f3f22b651f0499e7ad692024ee269a9ff694 |
##############################################################################
# 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... | wscullin/spack | var/spack/repos/builtin/packages/r-yaqcaffy/package.py | Python | lgpl-2.1 | 1,723 | [
"Bioconductor"
] | 495b34f7d2b767e1ef0ae821c5e6b02691c95ef2db43ff6acff7bf06198570f8 |
# -*- coding: utf-8 -*-
"""
This file demonstrates writing tests using the unittest module. These will pass
when you run "manage.py test".
Replace this with more appropriate tests for your application.
"""
from django.test import TestCase
import salesReport.models as salesReportModels
import salesReport.views as sale... | akiokio/centralfitestoque | src/salesReport/tests.py | Python | bsd-2-clause | 14,178 | [
"VMD"
] | 5a37257a03fce6194de218236b329257d237e00901a7b311fedd57811e32f68a |
# -*- coding: utf8 -*-
"""
Importing and Exporting
"""
from mathics.core.expression import Expression, from_python
from mathics.builtin.base import Builtin, Predefined, Symbol, String
from pymimesniffer import magic
import mimetypes
mimetypes.add_type('application/vnd.wolfram.mathematica.package', '.m')
# Seems t... | benley/Mathics | mathics/builtin/importexport.py | Python | gpl-3.0 | 27,429 | [
"MOPAC",
"NetCDF"
] | 9817fc414f4db18af48d5cb8412f5622c22eb42bdcabfac4f0651fa784d13504 |
import numpy as np
from ..lsfit import Fitter
from ..lsfit.tools import convert_params
class PlotData(object):
"""Class containing data plotting methods
Methods
-------
plot
plot_line
plot_contour
plot_volume
"""
def plot(self, x=None, y=None, z=None, w=None, show_err=True, to_... | granrothge/neutronpy | neutronpy/data/plot.py | Python | mit | 14,579 | [
"Gaussian"
] | 5cc23c9f5ba61d693e6426ba305bfb2025581dd5e2f5b82a1e2e3b35ee05029e |
###############################################################################
# ilastik: interactive learning and segmentation toolkit
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# mod... | nielsbuwen/ilastik | ilastik/applets/dataSelection/dataSelectionGui.py | Python | gpl-3.0 | 39,285 | [
"VisIt"
] | e4ff392ff88b563f74a903f6603a26eb1d65d6c0fdd4387e97d65b0dab38a88b |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
import warnings
import numpy as... | toastedcornflakes/scikit-learn | sklearn/mixture/gmm.py | Python | bsd-3-clause | 31,651 | [
"Gaussian"
] | d5218f97024dae42d9f24069f6f493424fad18cf0e98f60a661a654f60639e30 |
import decimal
import json
import networkx as nx
import re
from operator import itemgetter
from datetime import datetime, timedelta
from collections import defaultdict
from itertools import chain
from django.core.serializers.json import DjangoJSONEncoder
from django.http import HttpResponse
from django.shortcuts impor... | fzadow/CATMAID | django/applications/catmaid/control/skeleton.py | Python | agpl-3.0 | 56,514 | [
"NEURON"
] | 45b8a280aeda330091d765a202ee00e1db718a5a4726b6a27b31582e91de4cde |
#!/usr/bin/env python3
# coding=utf-8
# ly2video - generate performances video from LilyPond source files
# Copyright (C) 2012 Jiri "FireTight" Szabo
# Copyright (C) 2012 Adam Spiers
# Copyright (C) 2014 Emmanuel Leguy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the... | aspiers/ly2video | ly2video/synchro.py | Python | gpl-3.0 | 8,011 | [
"VisIt"
] | a7b4a562bc0b7b248124e59d470146b0342e70504401e99cc2836f0f7237e1d3 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
import os,sys,traceback
import re,shutil
from pyramid.view import view_config, view_defaults
from pyramid.response import FileResponse
import logging
from pprint import pformat
import textwrap
import datetime
import humanize
from github import Github
from pygments im... | askomics/askomics | askomics/ask_view.py | Python | agpl-3.0 | 77,243 | [
"Galaxy"
] | 226a56054e94f6bdc489181f518d2c740939d42d296169bf1b3d6696c1341f63 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""Utility functions and classes."""
import os
import re
from operator import mul
from math import sqrt, exp
import numpy as np
import _gpaw
from gpaw import debug
from numpy import linalg
elementwise_multiply_add = _gpa... | qsnake/gpaw | gpaw/utilities/__init__.py | Python | gpl-3.0 | 10,071 | [
"GPAW"
] | d99d21248cac5bfbf3c5b60921b53661e0b3268ce02de7952afeb1c2be5ccb18 |
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
... | espressopp/espressopp | src/interaction/TabulatedDihedral.py | Python | gpl-3.0 | 6,636 | [
"ESPResSo"
] | 16f640793e1a01a7c6e1ab14852279ad2e2650288cba85e3c0b8a4e2972b1fad |
"""
This example shows how to use the VTK postprocessing functions.
"""
import os.path as osp
from linear_homogenization import *
from sfepy.postprocess.utils_vtk import get_vtk_from_mesh,\
get_vtk_by_group, get_vtk_surface, get_vtk_edges, write_vtk_to_file,\
tetrahedralize_vtk_mesh
options.update({
'post... | RexFuzzle/sfepy | examples/homogenization/linear_homogenization_postproc.py | Python | bsd-3-clause | 904 | [
"VTK"
] | 298bd67242e9a6fa7fbe4a751481b2cbf3a7b33867cabbb284e5724a0183f57e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.ext.jhu import get_kpoints
from pymatgen.io.vasp.inputs import Incar
from pymatgen.io.vasp.sets import MPRelaxSet
__autho... | gVallverdu/pymatgen | pymatgen/ext/tests/test_jhu.py | Python | mit | 883 | [
"VASP",
"pymatgen"
] | 75748ca1114ffee131bc56ad9346b249305a00138a2ac1d6a4b7b082d5c34aaf |
#-----------------------------------------------------------------
# pycparser: clex.py
#
# CLexer class: lexer for the C language
#
# Copyright (C) 2008, Eli Bendersky
# License: LGPL
#-----------------------------------------------------------------
import re
import sys
import ply.lex
from ply.lex import TOKEN
cl... | Stratos42/EveBot | plugins.disabled/pycparser/pycparser/c_lexer.py | Python | gpl-3.0 | 12,027 | [
"NAMD"
] | 46da7b224023244f7cd29b5376bd0bdd638ddb3a011e5139feaa1c66338872e2 |
'''Add the tax id to a blast output file. This will place the tax id on the end of the line, so the rest of the columns are the same'''
import sys
sys.path.append('/home3/redwards/bioinformatics/Modules')
import taxon
try:
f=sys.argv[1]
type=sys.argv[2]
except:
sys.exit(sys.argv[0] + " <blast output file... | linsalrob/PhageHosts | code/blast2taxid.py | Python | mit | 908 | [
"BLAST"
] | 729a870ce0f5c6f4e95ba7e641bb56540a83ea6b229929fa0212a9065aae85f5 |
import logging
import os
import shutil
import tarfile
import tempfile
import urllib
from galaxy import util
from galaxy import web
from galaxy.datatypes import checkers
from galaxy.web.base.controller import BaseUIController
from tool_shed.dependencies import attribute_handlers
from tool_shed.galaxy_install import de... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/controllers/upload.py | Python | gpl-3.0 | 30,283 | [
"Galaxy"
] | 1e48375a37c59751c0379e708752eb3d0e745c79b9c6149e77a1a1ed10a2862e |
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