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#!/usr/bin/env python
"""Tests different Genetic Algorithm crossover classes.
"""
# standard library
import unittest
# biopython
from Bio.Seq import MutableSeq
from Bio.Alphabet import SingleLetterAlphabet
# local stuff
from Bio.GA.Organism import Organism
from Bio.GA.Crossover.General import SafeFitnessCrossover
fro... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_GACrossover.py | Python | gpl-2.0 | 18,105 | [
"Biopython"
] | 026f1a6f9efbebd008d6886cbad728b6729dfeba30810a07b425b4923a780884 |
"""
Test Kkit capabilities of PyMOOSE
"""
from __future__ import print_function
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ ... | rahulgayatri23/moose-core | tests/python/test_kkit.py | Python | gpl-3.0 | 2,059 | [
"MOOSE"
] | fd2d007de3fd7001cff798f2277a690807cdf4b0bed0308693961e03a9b0c6b6 |
"""
A Gaussian Process Classifier interface for the active learning module
Author(s): Wei Chen (wchen459@umd.edu)
"""
import logging
LOGGER = logging.getLogger(__name__)
import numpy as np
from gpc import GPClassifier
from sklearn.gaussian_process import GaussianProcessRegressor
from libact.base.interfaces import Co... | IDEALLab/domain_expansion_jmd_2017 | al_models.py | Python | mit | 3,099 | [
"Gaussian"
] | 86ccd7e26ace6c795ee97bbfa083970cb9e8c352bbf19f6f8aa1eaf4be86c381 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2012 Nick Hall
# Copyright (C) 2012 Brian G. Matherly
# Copyright (C) 2012-2014 Paul Franklin
#
# 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
# t... | SNoiraud/gramps | gramps/plugins/textreport/tableofcontents.py | Python | gpl-2.0 | 4,908 | [
"Brian"
] | 65915962bef5945512fad45b8c24d676efe4477ea7df565b1f0a566903e85f32 |
#!/ysr/bin/env python
from __future__ import division
import numpy as np
import numpy.random as npr
import theano
import theano.tensor as T
from theano import tensor
#-----------------------------------------------------------------------------
def my_batched_dot(A, B):
"""
Batched version of dot-product.... | capybaralet/Sequential-Generation | BlocksAttention.py | Python | mit | 15,978 | [
"Gaussian"
] | 3310982b7d5e089d496aa232d07dd78dbfffdd20b00e6e8882f2810fe5403fcc |
#################################################################################
## $HeadURL $
#################################################################################
#__RCSID__ = "$Id: $"
#
#'''
# Set the fixture needed to run this test.
#'''
#from DIRAC.ResourceStatusSystem.Service.test.Test_ResourceStat... | Sbalbp/DIRAC | ResourceStatusSystem/Service/test/Test_ResourceStatusHandler/Test_Description.py | Python | gpl-3.0 | 842 | [
"DIRAC"
] | 7e51b6da016822c8942c286d3f35d89be925b7843b0cd0f6098286109a494a72 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/py-pymol/package.py | Python | lgpl-2.1 | 2,120 | [
"PyMOL"
] | 08fbd801889afbef9aa1efccf7efdc44cd1270b02eba9e382aeef7a3187e8145 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-affycoretools/package.py | Python | lgpl-2.1 | 2,578 | [
"Bioconductor"
] | 7400f9ceb3553b895db8ba9bfc01dad9d47f3fe133cc26f3202c43a9a9050f6b |
"""
complete Pade analysis workflow
from E-V fitted data to
the precision data, plots and
histograms
GOAL: to be the one script that is used by
the database web app to be activated in part
on sensibly crossfiltered data
and also on the a complete new set of data
in an object oriented way.
"""
# must be executed within
... | joshgabriel/dft-crossfilter | benchmark-view/precisions.py | Python | mit | 25,240 | [
"VASP"
] | f6d7acfcd8bc965e5130e75f849e9f1b379aa0e3cdd5d262f340954346e38ff0 |
"""Rewrite assertion AST to produce nice error messages"""
import ast
import _ast
import errno
import itertools
import imp
import marshal
import os
import re
import struct
import sys
import types
from fnmatch import fnmatch
import py
from _pytest.assertion import util
# pytest caches rewritten pycs in __pycache__.
... | razvanc-r/godot-python | tests/bindings/lib/_pytest/assertion/rewrite.py | Python | mit | 36,368 | [
"VisIt"
] | 4c8a09c2ef4584c3c0ed746f86b5be54600342872ccc54a8850acef249ff53f8 |
# Lint as: python2, python3
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... | karllessard/tensorflow | tensorflow/tools/common/public_api.py | Python | apache-2.0 | 4,960 | [
"VisIt"
] | ae499b44ad7e7d28635c13f7dd917c540db5d54fa601c032ac34e70cdfc56efc |
import pytest
import MDAnalysis as mda
import numpy as np
from pmda.density import DensityAnalysis
from MDAnalysis.analysis import density as serial_density
from numpy.testing import assert_almost_equal
from MDAnalysisTests.datafiles import GRO_MEMPROT, XTC_MEMPROT
from MDAnalysisTests.datafiles import PSF_TRICLINIC, D... | MDAnalysis/pmda | pmda/test/test_density.py | Python | gpl-2.0 | 2,749 | [
"MDAnalysis"
] | e524390ccf4950fd4526765cbb2652620ee580ca22c6d300551013b4c76b0c7e |
import time
import numpy as np
from gpaw.utilities.blas import gemmdot, dotu, gemv
def getrand(shape, dtype):
if type(shape) is int:
shape = (shape,)
nelements = np.prod(shape)
if dtype == float:
return np.random.normal(size=nelements).reshape(shape)
elif dtype == complex:
retu... | robwarm/gpaw-symm | gpaw/test/gemv.py | Python | gpl-3.0 | 4,852 | [
"GPAW"
] | ca9c6a34709e176fb2ec9b6d672c2f1284613ad75cb7b357fb14f0a363268d0d |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import time
import threading
from DIRAC import gLogger, S_ERROR
from DIRAC.Core.Utilities.ThreadScheduler import gThreadScheduler
class TransportPool(object):
def __init__(self, logger=False):
if logge... | yujikato/DIRAC | src/DIRAC/Core/DISET/private/TransportPool.py | Python | gpl-3.0 | 4,309 | [
"DIRAC"
] | 5431a5ea5470214917734b791a924ced4acaecaf9a7320f525320fdb3b41ca03 |
#!/usr/bin/env python
try:
import netCDF4 as netCDF
except:
print "netCDF4 is not installed!"
sys.exit(1)
from matplotlib import pyplot as pp
from matplotlib import colors as mc
from optparse import OptionParser
from siple.reporting import endpause
import numpy as np
usage = """Usage: %prog [options]
Ex... | talbrecht/pism_pik07 | examples/inverse/tauc_compare.py | Python | gpl-3.0 | 2,423 | [
"NetCDF"
] | 59eb82aef29cf7d30b89508c4cb4f32b1c6e65769fabe6c16df9e6cfc498956d |
#!/usr/bin/env python
import glob
import os
try:
from setuptools import setup
have_setuptools = True
except ImportError:
from distutils.core import setup
have_setuptools = False
kwargs = {'name': 'openmc',
'version': '0.6.2',
'packages': ['openmc'],
'scripts': glob.glob('... | lilulu/openmc | setup.py | Python | mit | 1,283 | [
"VTK"
] | 066ec1b1951c60a30d2ff61d0b9c8e3e052ded64d9ab06ee79f8c1a1825e1f1c |
"""Undocumented Module"""
__all__ = ['indent',
'StackTrace', 'traceFunctionCall', 'traceParentCall', 'printThisCall',
'doc', 'adjust', 'difference', 'intersection', 'union',
'sameElements', 'makeList', 'makeTuple', 'list2dict', 'invertDict',
'invertDictLossless', 'uniqueElements', 'disjoint', 'contains',
'replace', '... | jjkoletar/panda3d | direct/src/showbase/PythonUtil.py | Python | bsd-3-clause | 94,350 | [
"Gaussian"
] | 3bb5e73a01b18779dd8db0ca9e35c7e788cc23e21d25bf43229cbe96021ede7b |
# coding: utf-8
# # Logistic Regression with a Neural Network mindset
#
# Welcome to your first (required) programming assignment! You will build a logistic regression classifier to recognize cats. This assignment will step you through how to do this with a Neural Network mindset, and so will also hone your intuiti... | jinzishuai/learn2deeplearn | deeplearning.ai/C1.NN_DL/week2/Logistic+Regression+with+a+Neural+Network+mindset+v4.py | Python | gpl-3.0 | 29,517 | [
"NEURON"
] | d448785bf0e623aaf13a2934e4e8bded6b1cb547de9af81488548cac20e5f74b |
import numpy as np
from scipy import ndimage as ndi
from scipy import stats
from ..util import img_as_float, pad
from ..feature import peak_local_max
from ..feature.util import _prepare_grayscale_input_2D
from ..feature.corner_cy import _corner_fast
from ._hessian_det_appx import _hessian_matrix_det
from ..transform i... | Hiyorimi/scikit-image | skimage/feature/corner.py | Python | bsd-3-clause | 27,202 | [
"Gaussian"
] | bb4b7b24ba06e9c89ac437de63613460a91d9f8f7b8c2b1b59163da478df533b |
#!/usr/bin/python
"""
author: R. Essick (ressick@mit.edu)
date: 20 July 2012
this module written to help automate the process of estimating pdfs and cdfs from a set of observations.
we implement several simple algorithms, all based on the concept of kernal estimation. They are:
k-th nearest neighbor volume estima... | reedessick/bayesburst | triangulation/pdf_estimation.py | Python | gpl-2.0 | 21,038 | [
"Gaussian"
] | 2329703a0a7951a47c25aa90b116b0810ba404f65790aade8ed570d081e6a258 |
"""
==========================
Gaussian HMM of stock data
==========================
This script shows how to use Gaussian HMM.
It uses stock price data, which can be obtained from yahoo finance.
For more information on how to get stock prices with matplotlib, please refer
to date_demo1.py of matplotlib.
"""
from __f... | jmargeta/scikit-learn | examples/plot_hmm_stock_analysis.py | Python | bsd-3-clause | 2,783 | [
"Gaussian"
] | a47464b57d7bdf210a4d7a06e2c804fcee61fe39e488cca8a8dc3a51f73ffd3c |
"""
A simple vtkTkRenderWidget for tkinter.
Created by David Gobbi, April 1999
May ??, 1999 - Modifications peformed by Heather Drury,
to rewrite _pan to match method in TkInteractor.tcl
May 11, 1999 - Major rewrite by David Gobbi to make the
interactor bindings identical to ... | hlzz/dotfiles | graphics/VTK-7.0.0/Wrapping/Python/vtk/tk/vtkTkRenderWidget.py | Python | bsd-3-clause | 16,664 | [
"VTK"
] | 79eb482c785c19682149a7d2e6b39079bb6d68817548598c0038e60a3fc4b460 |
# Copyright 2017 Battelle Energy Alliance, 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 agreed t... | joshua-cogliati-inl/raven | framework/SupervisedLearning/ScikitLearn/NaiveBayes/BernoulliNBClassifier.py | Python | apache-2.0 | 5,970 | [
"Gaussian"
] | 0b66714a5641b1001bce0ffedfdd97be563200bcbf6e68cecb234dcb83621b1d |
# Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of ... | kkreis/espressopp | src/analysis/ConfigurationsExt.py | Python | gpl-3.0 | 3,337 | [
"ESPResSo"
] | a44a3743862ec73ecdcdf607a3ae988bee08acb6b18404c3d4fa7b3e4a6a125a |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | PeterLauris/aifh | vol1/python-examples/examples/example_random.py | Python | apache-2.0 | 1,639 | [
"VisIt"
] | 55180644abbaca82bee3bf1a12a0a257ae8ac5e3f97c80cd107996a5063f4558 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | rmfitzpatrick/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 112,385 | [
"VisIt"
] | 0aa2023e5639ffc8d6140b15420cff97ed9b00a03e7394aac0bd0178c50cc904 |
#!/usr/bin/env python
"""Make sequence context specific bigbed per sample"""
import argparse
import os
import gzip
import xml.etree.cElementTree as ET
def parse_args():
"""Parse command line arguments"""
parser = argparse.ArgumentParser(description='Concatenate reference for display in jbrowse')
parser.a... | thomasvangurp/epiGBS | jbrowse/make_annotation_gff3.py | Python | mit | 6,390 | [
"BLAST"
] | 623acdbe8ae582d5a2003dbdddd75f09b8ad1c92ecdbe5e701eeea0bc1c8648c |
""" Priority corrector for the group and in-group shares
"""
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.ObjectLoader import ObjectLoader
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.WorkloadManagementSystem.private.correctors.BaseCorrector import BaseCorr... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/private/SharesCorrector.py | Python | gpl-3.0 | 4,976 | [
"DIRAC"
] | 3dc4f0ae0736a1f16a4df1dca111f3cd2f4b46676dac802af8f0e9cc2ddf1c4b |
# -*- coding: utf-8 -*-
# Copyright 2011 Takeshi KOMIYA
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | aboyett/blockdiag | src/blockdiag/imagedraw/svg.py | Python | apache-2.0 | 9,500 | [
"Gaussian"
] | 3ad121bf3713cf055e6f7207f969e40acfbb749d2697e1d82ac17e2eac6e7861 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/mobile/index.py | Python | gpl-2.0 | 5,581 | [
"VisIt"
] | cb5e6d9ad93c066f7ebf2b2320f3b05d8793f934b458eb3c8801cb20adc16724 |
"""
UI-level acceptance tests for OpenAssessment accessibility.
"""
import os
import unittest
from tests import OpenAssessmentTest, StaffAreaPage, FullWorkflowMixin, MultipleOpenAssessmentMixin
class OpenAssessmentA11yTest(OpenAssessmentTest):
"""
UI-level acceptance tests for Open Assessment accessibility.
... | nttks/edx-ora2 | test/acceptance/accessibility.py | Python | agpl-3.0 | 11,405 | [
"VisIt"
] | c63d1d0f8ca9cb3369c94b5c361ed34f27c8f6f06fafcb8846c83ea7f51b6ccb |
# Brian Cottingham
# spiffytech@gmail.com
# Originally created on 2009-05-07
# Plays Russian Roulette
#This file is part of Spiffybot.
#
#Spiffybot 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... | spiffytech/spiffybot | modules/roulette/roulette.py | Python | gpl-3.0 | 2,672 | [
"Brian"
] | b3c2ada405f4f906b36990da0ea0a23dab5e5a58bb09da483fa71086a9c9215e |
import numpy as np
from scipy.stats import norm, cauchy
from pytes import Analysis, Constants
def pulse(pha=1.0, tr=2e-6, tf=100e-6, points=1024, t=2e-3, duty=0.5, talign=0.0):
"""
Generate Dummy Pulse
Parameters (and their default values):
pha: pulse height (Default: 1.0)
tr: r... | robios/PyTES | pytes/Simulation.py | Python | mit | 7,202 | [
"Gaussian"
] | a420c71bb4403e7d5002f03c2ed69f6295c1b726f4ff9e4d8171efdc8eb7a776 |
from org.python.parser import Visitor
from org.python.parser.PythonGrammarTreeConstants import *
import string, org
class FreezeVisitor(Visitor):
def __init__(self, events, props, packages=None, classes=None, proxies=None,
classname=None):
if packages is None:
self.packages = {}
else:
self.pac... | DarioGT/OMS-PluginXML | org.modelsphere.sms/lib/jython-2.2.1/Tools/freeze/FreezeVisitor.py | Python | gpl-3.0 | 5,951 | [
"VisIt"
] | d23e76bafcaf0cd596ae60a6aadfdff417c11709568a4f485d255fdc2bed5b8d |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have purchased from
# Numenta, Inc. a separate commercial license for this software code, the
# following terms and conditions apply:
#
# This pro... | Petr-Kovalev/nupic-win32 | py/nupic/research/FDRCSpatial2.py | Python | gpl-3.0 | 109,678 | [
"Gaussian",
"VisIt"
] | 86f3d858001f9a8222d3fe5fc89812a9fca8e4adec6e365aa11a7136e2128b26 |
#from paraview.simple import Disconnect, ReverseConnect
from fabric.api import (env, run, cd, get, hide, settings,
remote_tunnel, show, shell_env)
from fabric.tasks import execute
from multiprocessing import Process, Value
import traceback
import sys
import multiprocessing as mp
# from multipr... | zenotech/ParaViewConnect | pvconnect/connect.py | Python | bsd-3-clause | 11,506 | [
"ParaView"
] | e6240ab93a69fbeaf409aee1b8812a75d26957ab8cd43632c2a3154a7e7bc57e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Matt Keenan (matt.keenan@gmail.com)
# Copyright (C) 2013-2014 Paul Fr... | beernarrd/gramps | gramps/plugins/textreport/descendreport.py | Python | gpl-2.0 | 21,578 | [
"Brian"
] | 35474beb3404624a63bdd10e1a3da93851fcb0735d8dff661c835de9202c8037 |
#!/usr/bin/env python
#
# view_stl.py - A simple vtk based stl file viewer
#
# Author: William Dickson 12/21/04
#
# --------------------------------------------------------------
import vtk
import sys
import optparse
import pickle
# Default parameters
background = (0.1, 0.2, 0.4)
window_sz = (600,600)
# Set up optio... | acrobotic/py2scad | examples/view_stl.py | Python | apache-2.0 | 2,780 | [
"VTK"
] | 75ae191761becfc2f2c24c503cc6ac64fc4e90a615367b6bcaa6c2bde03ff8c5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
r""" A JSON data encoder and decoder.
This Python module implements the JSON (http://json.org/) data
encoding format; a subset of ECMAScript (aka JavaScript) for encoding
primitive data types (numbers, strings, booleans, lists, and
associative arrays) in a language-n... | Dave667/service | plugin.video.kinobaza.tv/resources/lib/demjson.py | Python | gpl-2.0 | 87,948 | [
"CDK"
] | dc90dbda68fd55b1e2d0b7995b1839fa63b3d63f9ab6ef74a3e87c29e16e57d2 |
#
# Copyright (C) 2013,2014 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... | sehrhardt/espresso | samples/python/load_properties.py | Python | gpl-3.0 | 4,238 | [
"ESPResSo"
] | e3e6085ad34085d9ce02268a0c977b7e1eacc5a97746386b14b3607ee4318fee |
import unittest
import numpy as np
import nest
import nix
# TODO find nicer injection way
import nix4nest
from nix4nest.nix.signal import Signal
from nix4nest.nix.node import Node
class TestSignal(unittest.TestCase):
def setUp(self):
self.file = nix.File.open("/tmp/unittest.h5", nix.FileMode.Overwrite)... | asobolev/nix4nest | nix4nest/test/test_signal.py | Python | lgpl-3.0 | 2,505 | [
"NEURON"
] | ceb87c90255cbe3a6c053aa49926cfb6081723782a5c5eef0ef61e6ea5c91ede |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004 Martin Hawlisch
# Copyright (C) 2004-2006, 2008 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/o... | Forage/Gramps | gramps/plugins/export/exportgeneweb.py | Python | gpl-2.0 | 19,720 | [
"Brian"
] | 59f2cefbf8ac77cdfcc4748d8cad7b932308644b45efade26ff5f92f4e613044 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# this script tests vtkImageReslice with different slab modes
# Image pipeline
reader = vtk.vtkImageReader()
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/ReslicePermuteSlab.py | Python | gpl-3.0 | 3,561 | [
"VTK"
] | 0dbd793180f39d0600152eae84f17854f236aaed7412a9e80c948293c4a97212 |
"""
test_BuiltinFunctions.py
This file is part of ANNarchy.
Copyright (C) 2016-2020 Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
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 F... | vitay/ANNarchy | tests/Unittests/test_BuiltinFunctions.py | Python | gpl-2.0 | 3,738 | [
"NEURON"
] | 632d2b58dbceb608bc17a4dc93158ae03ee0cb34940c0e964c027bd308523407 |
from ase.lattice.spacegroup import crystal
a = 4.05
al = crystal('Al', [(0,0,0)], spacegroup=225, cellpar=[a, a, a, 90, 90, 90])
| grhawk/ASE | tools/doc/tutorials/spacegroup/spacegroup-al.py | Python | gpl-2.0 | 130 | [
"ASE",
"CRYSTAL"
] | e17eec23aa2e656fa8bf03a6ebbb66f1ebbf86da45b303be9477173c7caf3f0e |
from property import *
# Neuron common parameters
iaf_neuronparams = {'E_L': -70.,
'V_th': -50.,
'V_reset': -67.,
'C_m': 2.,
't_ref': 2.,
'V_m': -60.,
'tau_syn_ex': 1.,
'tau_syn_i... | research-team/NEUCOGAR | NEST/cube/noradrenaline/scripts/parameters.py | Python | gpl-2.0 | 2,793 | [
"NEURON"
] | 93cdd98d9f730b5d72bf0e0d90d0086fd9d98a59f98db9d75b95b9ed3346042a |
import json
import pytest
import demistomock as demisto
def load_json_file(path):
with open(path, 'r') as _json_file:
return json.load(_json_file)
@pytest.mark.parametrize(argnames="threatconnect_score, dbot_score",
argvalues=[(500, 3),
(450,... | demisto/content | Packs/FeedThreatConnect/Integrations/FeedThreatConnect/FeedThreatConnect_test.py | Python | mit | 1,361 | [
"Amber"
] | b86ed5909e5fa2e429711e39d5a2dd12ba6f4e58e2abda9593e53cf42275055b |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from bok_choy.page_object import XSS_INJECTION
from datetime import datetime
from pytz import timezone, utc
from common.test.accep... | longmen21/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 19,507 | [
"VisIt"
] | 969c4ef611aeea2194f176f0755a81d3027537be68ba0390dd1a50910bf9e040 |
from DIRAC import S_OK, S_ERROR
from DIRAC.AccountingSystem.private.Plotters.BaseReporter import BaseReporter
from DIRAC.AccountingSystem.Client.Types.PilotSubmission import PilotSubmission
__RCSID__ = "$Id$"
class PilotSubmissionPlotter(BaseReporter):
'''
Plotter for the Pilot Submission Accounting
'''
_t... | andresailer/DIRAC | AccountingSystem/private/Plotters/PilotSubmissionPlotter.py | Python | gpl-3.0 | 5,337 | [
"DIRAC"
] | 088e75fca43e8305868a9c7838d8d174650314a0d8217cba39033c8cb8298648 |
"""
Server Density
www.serverdensity.com
----
Server monitoring agent for Linux, FreeBSD and Mac OS X
Licensed under Simplified BSD License (see LICENSE)
"""
# SO references
# http://stackoverflow.com/questions/446209/possible-values-from-sys-platform/446210#446210
# http://stackoverflow.com/quest... | canerdogan/sd-agent | checks.py | Python | bsd-3-clause | 121,543 | [
"VisIt"
] | 874ed61de346eb4380495e982f33477b134f5dc76f7f75c095e297c2939d0cf1 |
##############################################################################
# Medical Image Registration ToolKit (MIRTK)
#
# Copyright 2016 Imperial College London
# Copyright 2016 Andreas Schuh
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | MIRTK/Deformable | lib/python/mirtk/deformable/neonatal_cortex.py | Python | apache-2.0 | 94,057 | [
"VTK"
] | 17a669509ccc2bd98022c3b9f30540ed9f453b78620447d74aa6b386b47265d7 |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
... | madscatt/zazzie | src_2.7/sassie/test_sassie/simulate/complex_monte_carlo/test_complex_monte_carlo.py | Python | gpl-3.0 | 107,412 | [
"CHARMM"
] | abe43c9e853476df200940e9a8a52e39ace389258c9ee315a610766618126742 |
from .core import UnitedStates
from ..core import MON
from ..registry_tools import iso_register
@iso_register('US-AL')
class Alabama(UnitedStates):
"Alabama"
include_confederation_day = True
martin_luther_king_label = "Robert E. Lee/Martin Luther King Birthday"
presidents_day_label = "George Washingto... | novapost/workalendar | workalendar/usa/alabama.py | Python | mit | 1,153 | [
"COLUMBUS"
] | 54d0bac4d622b60d4dfa94d34caff95463cbe260aa48ca94bfc4ef6b29136689 |
from __future__ import annotations
import logging
from libtbx.phil import parse
from dials.array_family import flex
from dials.model.experiment.profile import ProfileModelExt
logger = logging.getLogger(__name__)
phil_scope = parse(
"""
gaussian_rs
{
scan_varying = False
.type = bool
.h... | dials/dials | algorithms/profile_model/gaussian_rs/model.py | Python | bsd-3-clause | 20,657 | [
"CRYSTAL"
] | f013f887211d3017c52418fac7e51a715acf265567755608f187a3a98ded03fd |
import h5py
import functools
import re
import numpy as np
from . import lclsDet
from .toolsLog import log
from .toolsConf import config
from .toolsVarious import iterfy,DropObject,CodeBlock,filterList
from . import lclsSpecialDet
memory = config.joblibcache
@memory.cache
def visitH5(h5file):
subFolders = []
h5da... | marcocamma/x3py | lclsH5.py | Python | gpl-3.0 | 4,365 | [
"VisIt"
] | 8051334ef03388630f247eb37cabfbf0b8fe7928f06bb2b302121a205fad7f9c |
from spectacles.common import DEFAULT_WAIT_TIME, get_absolute_url as u
import time, glob, yaml, random
class YAMLDriver:
def __init__(self, testcase, browser):
self.testcase = testcase
self.b = browser
def run_many(self, glob_pattern):
paths = glob.glob(glob_pattern)
for path... | CariZa/django-spectacles | spectacles/yamldriver.py | Python | mit | 6,747 | [
"VisIt"
] | 4f48371b0ccab497ebed5edad41d00000d8dedee97eb89c81c33afd72eb10c64 |
"""
The equilibrium module defines routines for interacting with
calculated phase equilibria.
"""
import warnings
from collections import OrderedDict
from collections.abc import Mapping
from datetime import datetime
import pycalphad.variables as v
from pycalphad.core.utils import unpack_components, unpack_condition, un... | tkphd/pycalphad | pycalphad/core/equilibrium.py | Python | mit | 15,941 | [
"pycalphad"
] | 6e49ee32ddea0509d97a70855923925e0be445c00a0ee51996b6bcd7702e5c83 |
# Copyright 2017 Battelle Energy Alliance, 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 agreed t... | idaholab/raven | framework/Models/Model.py | Python | apache-2.0 | 24,501 | [
"NetCDF"
] | f372da78a1f630eddb6c9517c9ba56828c1b9680e76a2e97e53a68034319ed4d |
"""
Unit tests for masquerade.
"""
import json
import pickle
from mock import patch
from nose.plugins.attrib import attr
from datetime import datetime
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.utils.timezone import UTC
from capa.tests.response_xml_factory import OptionR... | prarthitm/edxplatform | lms/djangoapps/courseware/tests/test_masquerade.py | Python | agpl-3.0 | 18,424 | [
"VisIt"
] | a37f01dac4e0e40a48e7bc79405db859f44074b9fd028ba3817c3ab5cf77d88c |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import combinations
from itertools import product
import numpy ... | Titan-C/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 42,990 | [
"Brian"
] | 05341a521be695a8c82402d445ab693515f44c9b38d314e6f62e425b0d77acf3 |
#!/usr/bin/env python
parameter_list = [[1000,2,8],[1000,4,8]]
from numpy import *
#from pylab import *
def run_clustering(data, k):
from modshogun import KMeans
from modshogun import Math_init_random
from modshogun import EuclideanDistance
from modshogun import RealFeatures
fea = RealFeatures(data)
distance =... | sanuj/shogun | examples/undocumented/python_modular/evaluation_clustering_simple.py | Python | gpl-3.0 | 2,586 | [
"Gaussian"
] | ea1666809e4df92c321d9e079c04fe8d46a1d24ab5dfada314297f8cd5fddd73 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The freesurfer module provides basic functions for interfacing with
freesurfer tools.
Change directory to provide relative paths for doctests
>>> import os
>>> filepa... | mick-d/nipype | nipype/interfaces/freesurfer/model.py | Python | bsd-3-clause | 65,780 | [
"Gaussian"
] | 3591e21623598ac2bf78bea64623e7f8661479c8d1a544159bfb5d331f8b065a |
# Lint as: python3
# Copyright 2020 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | tensorflow/lingvo | lingvo/core/conformer_layer_test.py | Python | apache-2.0 | 28,180 | [
"MOE"
] | 7ac4a528418eb51bf44b1c6afdf21793d19a8a19a8c529338818d150ec0bd35d |
# Copyright (C) 2014
# Pierre de Buyl
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute... | junghans/espressopp | src/interaction/MirrorLennardJones.py | Python | gpl-3.0 | 4,717 | [
"ESPResSo"
] | 3111fbcb50e47b11c4b44179b848cf5c85c6dbcfa2a60e1ba9d5f7cc4c43a00c |
# encoding: utf-8
"""
System command aliases.
Authors:
* Fernando Perez
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License.
#
# The full license is in the file... | Vvucinic/Wander | venv_2_7/lib/python2.7/site-packages/IPython/core/alias.py | Python | artistic-2.0 | 9,931 | [
"Brian"
] | 92ceff723e9f36b02faf8c739b8164d7df274243aa030b8b3c5aed3cf4996cc0 |
##
# Copyright 2009-2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | omula/easybuild-easyblocks | easybuild/easyblocks/c/cp2k.py | Python | gpl-2.0 | 30,581 | [
"CP2K"
] | b6de6bfdfbe4a9fc7108c21427f213f4224eded21ae99c4d8a1ece7c3ec18447 |
"""
Helper functions for fast generation of Hamiltonians.
"""
import os
import numpy as np
def get_random_hV(nao):
"""Generate random Hamiltonian of size n.
"""
from pyscf import ao2mo
h = np.random.rand(nao,nao)
h += h.T
nao2 = nao*(nao+1)//2
nao4 = nao2*(nao2+1)//2
V = ao2mo.restor... | hongzhouye/frankenstein | tools/lat_utils.py | Python | bsd-3-clause | 3,173 | [
"PySCF"
] | 4dcdb003b915f446464b5972a83ca627549105036a7637355eb3c627c98376dc |
#!/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/hessian/test/test_thermo.py | Python | apache-2.0 | 3,379 | [
"PySCF"
] | ef620cc4fcaae4bd413468321fecf3d4768b95d064e49ce21365757272e9f4a8 |
# SPDX-FileCopyrightText: 2014-2020 Martin Roelfs
#
# SPDX-License-Identifier: MIT
# -*- coding: utf-8 -*-
from symfit import variables, Parameter, exp, Fit, Model
from symfit.distributions import Gaussian
from symfit.contrib.interactive_guess import InteractiveGuess
import numpy as np
x, y, z = variables('x, y, z'... | tBuLi/symfit | symfit/contrib/interactive_guess/examples/simple_3D_example.py | Python | gpl-2.0 | 935 | [
"Gaussian"
] | 2eb64a880234a57ccebdad82da0578616ed7408a498bfd34ecc66fb8836291f0 |
# Copyright 2017 Battelle Energy Alliance, 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 agreed t... | joshua-cogliati-inl/raven | framework/SupervisedLearning/ScikitLearn/GaussianProcess/GaussianProcessClassifier.py | Python | apache-2.0 | 18,726 | [
"Gaussian"
] | 7f64a82c090ca0c6e12ff00d8f85ec0d35314ac2bbb319915709bb86d1026003 |
#!/usr/bin/env python
import csv
import json
from sets import Set
from dateutil.parser import *
from django.contrib.gis.gdal import DataSource
from etc.gdocs import GoogleDoc
def write_aggregates():
"""
Prepares an aggregates file for each county.
Only counties with at least one visit will be aggregated... | nprapps/visits | data.py | Python | mit | 8,053 | [
"VisIt"
] | 445158418e181abccb1682a496746b98cd3d02e33f21ab74df9ec6847403ef46 |
import os,unittest
from lammps import PyLammps
try:
import numpy
NUMPY_INSTALLED = True
except ImportError:
NUMPY_INSTALLED = False
@unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available")
class PythonPyLammps(unittest.TestCase):
def setUp(self):
machine = None
if 'LAMMPS_MACHIN... | akohlmey/lammps | unittest/python/python-pylammps.py | Python | gpl-2.0 | 5,470 | [
"LAMMPS"
] | f7eff405586e767b5dab75d672717c7909cdcd924cdc48384bb54a1e5ef9c43a |
import pytest
from pathlib import Path
from loprop.dalton import MolFragDalton as molfrag
class TestException:
def test_raise_exception_if_symmetry(self):
self.thisdir = Path(__file__).parent
self.tmpdir = self.thisdir / "h2o_sym" / "tmp"
with pytest.raises(AssertionError):
mol... | vahtras/loprop | tests/test_exceptions.py | Python | gpl-3.0 | 338 | [
"Dalton"
] | 1a15666f0f377964856b63565ecf364669350a921cce164676eb5af4f69f1e44 |
##Copyright 2008-2013 Jelle Feringa (jelleferinga@gmail.com)
##
##This file is part of pythonOCC.
##
##pythonOCC 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... | tpaviot/pythonocc-utils | OCCUtils/face.py | Python | lgpl-3.0 | 12,073 | [
"Gaussian"
] | 2a893f4e326ff9e802d310951ea8f2b5ddc1d5b6d3735dad5929e13c1ea7c9b4 |
#!/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.
"""\
Wrapper script around Rietveld's upload.py that simplifies working with groups
of files.
"""
import json
import optparse
impo... | cybertk/depot_tools | gcl.py | Python | bsd-3-clause | 50,970 | [
"VisIt"
] | 9df7dbdcad4d5fde4919a0d6c1b759ac211efaf60e44c4cbbc84fbc8012c89f4 |
#!/usr/bin/env python
import matplotlib.pyplot as plt
import numpy as np
#
# The two phase radial injection problem has a similarity solution (r^2/t)
#
# Read MOOSE simulation data for constant time (tdata) and constant
# radial distance (rdata)
tdata = np.genfromtxt('../../tests/dirackernels/theis3_line_0016.csv', d... | paulthulstrup/moose | modules/porous_flow/doc/tests/radialinjection.py | Python | lgpl-2.1 | 1,434 | [
"MOOSE"
] | 93812109aafdd203dbcd83aff1fb3674af5445b230819c9a12595f63c7659374 |
"""Collection of functions to train the hierarchical model."""
from __future__ import print_function
import numpy as np
import models
import batch_utils
import data_transforms
import McNeuron
from keras.optimizers import RMSprop
import matplotlib.pyplot as plt
def clip_weights(model, weight_constraint):
"""
... | RoozbehFarhoodi/McNeuron | train.py | Python | mit | 12,617 | [
"NEURON"
] | 06a0ed21b4aef79cf789a8220f70e9b6f2dce90f421d9ca83ab5cae2d78d5947 |
""" ComponentMonitoring class is a front-end to the Component monitoring Database
"""
__RCSID__ = "$Id$"
import random
import types
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Utilities import Time, List, Network
class ComponentMonitoringDB( DB ):
def __init__( self... | Sbalbp/DIRAC | FrameworkSystem/DB/ComponentMonitoringDB.py | Python | gpl-3.0 | 21,247 | [
"DIRAC"
] | f22b73a986ff8c13c69efa2521d5355d52857876ff7a4faed91d3fad38814e71 |
import sys
from ase.build import molecule, fcc111, add_adsorbate
from ase.optimize import QuasiNewton
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.vibrations import Vibrations
sys.path.append("../..")
from __init__ import AnharmonicModes
slab = fcc111('Au', size=(2, 2, 2), vacuu... | keldLundgaard/ase-anharmonics | examples/translate_on_surface/translate_H_on_Au__EMT.py | Python | lgpl-2.1 | 1,027 | [
"ASE"
] | 0712aef0862d71da71e4326f447454988a6f769f6c08ceb2cc7dc20ad4be1eb3 |
"""
===========================
Formaldehyde cm-line fitter
===========================
This is a formaldehyde 1_11-1_10 / 2_12-2_11 fitter. It includes hyperfine
components of the formaldehyde lines and has both LTE and RADEX LVG based
models
Module API
^^^^^^^^^^
"""
from __future__ import print_function
import nu... | e-koch/pyspeckit | pyspeckit/spectrum/models/formaldehyde.py | Python | mit | 23,649 | [
"Gaussian"
] | de9237de0250ad7fc7b72b37d0263421c671485686c63ccb24455a81a07fb193 |
import os
import gc
import sys
import time
import signal
import traceback
import numpy as np
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters
from gpaw.utilities import devnull, compiled_with_sl
from gpaw import setup_paths
from gpaw import mpi
import gpaw
def equal(x, y, to... | ajylee/gpaw-rtxs | gpaw/test/__init__.py | Python | gpl-3.0 | 13,829 | [
"GPAW"
] | bb663f090968a46cbf993913796a6e16e49847fe4c94ddf3541228c17393b269 |
from data.data_generation import generate_gaussian
from manifold_alignment.ssma import ManifoldAlignment
import numpy as np
from utils.classification_list import lda_pred, accuracy_stats
import matplotlib.pyplot as plt
# my test function to see if it works. Should be in the 80s range of
# accuracy
def test_ma_gaussia... | jejjohnson/manifold_learning | src/python/ssma_demo.py | Python | mit | 2,339 | [
"Gaussian"
] | 1a70f1db990ee6105a8bd55ad8498c905760c505cfcd2b0c2da6f66526e7168c |
# (C) British Crown Copyright 2010 - 2015, 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... | mo-g/iris | lib/iris/__init__.py | Python | gpl-3.0 | 13,779 | [
"NetCDF"
] | 5ac0324d2a3f33b3b4159f20700dc9fb82282813c57c15f1142bbeacff1b80d1 |
import sys
try:
import numpy
except ImportError:
print("Numpy (http://numpy.scipy.org) not found.")
print("This test requires numpy!")
sys.exit(0)
import vtk
import vtk.numpy_interface.dataset_adapter as dsa
import vtk.numpy_interface.algorithms as algs
w = vtk.vtkRTAnalyticSource()
bp = vtk.vtkBrow... | gram526/VTK | Common/Core/Testing/Python/TestNumpyInterface.py | Python | bsd-3-clause | 6,293 | [
"VTK"
] | 47c53beebd2551fe01eb7cb3d36035cb94b136f156a9c3ef022f52ad633690f3 |
import numpy as np
from ase import Atoms
from ase.data import atomic_numbers, reference_states
def Icosahedron(symbol, noshells, latticeconstant=None):
"""
Returns a cluster with the icosahedra symmetry.
Parameters
----------
symbol: The chemical symbol (or atomic number) of the element.
nos... | slabanja/ase | ase/cluster/icosahedron.py | Python | gpl-2.0 | 4,324 | [
"ASE"
] | b2ccc9c6c7b30da25379a30769f0db3c2490191d53e73d2686adebd24b26d95e |
#!/usr/bin/python3
import json
import os
import sys
import tarfile
from argparse import ArgumentParser
from copy import deepcopy
from functools import partial
from itertools import chain
from subprocess import call
###############################################################################
RPATH = "/u... | gthar/nucleServ | nucleosome_dynamics.py | Python | unlicense | 28,297 | [
"Gaussian"
] | 4d3a0225920d5df2fda41ba78fc7abe6e4c1a74d8fc79a9590f4273e15d2b110 |
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 The SCons Foundation
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitati... | bleepbloop/Pivy | scons/scons-local-1.2.0.d20090919/SCons/Taskmaster.py | Python | isc | 39,536 | [
"VisIt"
] | be03e2e80eba5fcbe44740308ed6c5dbaf9d1b30bc2af29de121ba985b013700 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/formattingtagform.py | Python | gpl-2.0 | 9,916 | [
"Brian"
] | 3acee59c026d21e1a2c48cbf4124e12d618f7ef0337e73596961e9badf89ab01 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import itertools
import json
import os
import unittest
import numpy as np
from monty.json import MontyDecoder
from pymatgen.core.periodic_table import Element
from pymatgen.core.lattice import Lattice
from pymatgen.core.str... | vorwerkc/pymatgen | pymatgen/analysis/tests/test_structure_matcher.py | Python | mit | 47,973 | [
"VASP",
"pymatgen"
] | 57f53437523db7d63878f9d065e2cb94003cd0553d17ae56afe605ef64cb715e |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/thememanager.py | Python | gpl-2.0 | 40,072 | [
"Brian"
] | 100ca7ff8b56f0c85b73b8f34d81abf5417fa803253e36cd8e2280c3350eb919 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This script wraps calling a SeqWare workflow, in this case, the BWA workflow.
It reads param line options, which are easier to deal with in CWL, then
creates an INI file, and, finally, executes the workflow. This workflow
is setup to run in local file mode so you just ... | ICGC-TCGA-PanCancer/Seqware-BWA-Workflow | scripts/run_seqware_workflow.py | Python | gpl-3.0 | 14,055 | [
"BWA"
] | 1f015819b1b93379a807f746893a5ba348a08a943ed0df2386b581b2a0123453 |
# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016-2017 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
# Mélissa Cardon <melissa.cardon@pasteur.fr>,
#
# Distributed under the terms of the 3-clause BSD license.
# The full... | sequana/sequana | sequana/pacbio.py | Python | bsd-3-clause | 40,879 | [
"BWA",
"pysam"
] | 9463732659cbc1ea52efa45ac83d0c219edfb34ad422041b75a5995e5dc7a653 |
#!/usr/bin/python
from __future__ import print_function
import sys
import json
import time
import socket
import struct
import tempfile
class Connection:
def __init__(self, name = "avogadro"):
# create socket
self.sock = socket.socket(socket.AF_UNIX,
socket.SOCK_STREAM)
# ... | OpenChemistry/avogadroapp | scripts/avogadro-remote.py | Python | bsd-3-clause | 1,504 | [
"Avogadro"
] | 30e9b48d380c585d3d0517e0a0c49507d9574d59831a2f50e237025f8957c397 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import logging
import time
from peewee import JOIN_LEFT_OUTER
from fetch.api import make_request, default_requests_session
from models import Search, SearchResult, WebPageContent, SearchResultContent
logger = logging.getLogger('d... | andrewhead/Package-Qualifiers | fetch/results_content.py | Python | mit | 4,074 | [
"VisIt"
] | 8d5ce2f4fddd0c951ecdf5efc5571b3f903e283c462d57e01c95313cf5a735c1 |
languages = (
(u'aaa', u'', u'', u'', u'I', u'L', u'Ghotuo', u'\r\n'),
(u'aab', u'', u'', u'', u'I', u'L', u'Alumu-Tesu', u'\r\n'),
(u'aac', u'', u'', u'', u'I', u'L', u'Ari', u'\r\n'),
(u'aad', u'', u'', u'', u'I', u'L', u'Amal', u'\r\n'),
(u'aae', u'', u'', u'', u'I', u'L', u'Arb\xebresh\xeb Albanian', u'\r\n'),... | jrwdunham/old-webapp | onlinelinguisticdatabase/lib/languages/iso_639_3.py | Python | gpl-3.0 | 474,141 | [
"ADF",
"ASE",
"BWA",
"Elk",
"MOE",
"MOOSE",
"VMD",
"xTB"
] | ad2ede549ba8f30d704fd27ef63ee0558a28d631ff728075cc4b2efd9cde18e1 |
import os
from setuptools import setup
from setuptools import find_packages
version = '0.1'
shortdesc = "Klarna Invoice for bda.plone.shop"
setup(
name='bda.plone.klarnainvoice',
version=version,
description=shortdesc,
classifiers=[
'Environment :: Web Environment',
'License :: OSI Ap... | espenmn/bda.plone.klarnainvoice | setup.py | Python | bsd-3-clause | 1,083 | [
"MOE"
] | 849ef3f26097ee4bd97433c9256c8b8495c714d269cc451938601bb2e197cdcb |
import sys
import numpy as np
from numpy import mean, cov, dot, linalg, transpose
from McNeuron import Neuron
from McNeuron import Node
from McNeuron import visualize
from __builtin__ import str
from copy import deepcopy
class collection(object):
def __init__(dataset):
self.database = database
sel... | RoozbehFarhoodi/McNeuron | McNeuron/NeuronCollection.py | Python | mit | 1,019 | [
"NEURON"
] | 11b85a982042434acfcf40565ddfa8bece60024a14cf0a77f0d13f4484fb559b |
"""
Metadata for four-body terms listed in alphabetical order
Each functional_form has the following values:
- form: The overall mathematical expression of the term
- parameters: The ordered name of the terms as they will be stored with their expected unit contexts
- units: A dictionary that contains the unit co... | dgasmith/EEX_scratch | eex/metadata/four_body_terms.py | Python | bsd-3-clause | 6,827 | [
"CHARMM",
"Gromacs"
] | 62e9612ed460744f88b5347c21114126227e5e29433d0d817c9926f0894044ed |
# -*- coding: utf-8 -*-
#
# sensitivity_to_perturbation.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of... | sanjayankur31/nest-simulator | pynest/examples/sensitivity_to_perturbation.py | Python | gpl-2.0 | 8,880 | [
"NEURON"
] | 3a3acb38fb94415c9dc87ec8cf93db6441d18113455bb6271fc73d888df24515 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
from pandas import read_csv
import os, os.path
import csv
import matplotlib.pyplot as plt
import re
import dateutil.parser
os.chdir('/home/will/HIVReportGen/')
# <codecell>
def extract_YOB(inp):
try:
return float(inp.split('-')[0])
exc... | JudoWill/ResearchNotebooks | DemoGraphs.py | Python | mit | 15,483 | [
"VisIt"
] | ebb23ede3110bb1b7250d87389f21b39347d63fce60c87af627a9a653a63cf09 |
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