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import re
from .torque import Torque
__all__ = ('SlurmTorque',)
class SlurmTorque(Torque):
""" A CLI job executor for Slurm's Torque compatibility mode. This differs
from real torque CLI in that -x command line is not available so job status
needs to be parsed from qstat table instead of XML.
"""
... | ssorgatem/pulsar | pulsar/managers/util/cli/job/slurm_torque.py | Python | apache-2.0 | 905 | [
"Galaxy"
] | 6d02c5a4b80c644c5b7cbdd882879e919a39d6484f3b501d4857124d881c38e4 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/scf/stability.py | Python | apache-2.0 | 19,152 | [
"PySCF"
] | 8abd85aa78721287001e5bbf1dbe844f359f87948f17c991fd0e9f09d450cf96 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | francisco-dlp/hyperspy | hyperspy/components1d.py | Python | gpl-3.0 | 3,552 | [
"Gaussian"
] | 58ad9cfbc21e36cc72cad2cfe2bae764e67e687a5865a5d8c69c855ec40a726e |
# asciixmas
# December 1989 Larry Bartz Indianapolis, IN
#
# $Id$
#
# I'm dreaming of an ascii character-based monochrome Christmas,
# Just like the ones I used to know!
# Via a full duplex communications channel,
# At 9600 bits per second,
# Even though it's kinda slow.
#
# I'm dreaming of an asc... | teeple/pns_server | work/install/Python-2.7.4/Demo/curses/xmas.py | Python | gpl-2.0 | 25,446 | [
"Amber"
] | b12576cf11d4b3c462884198a09cd45828431f7fc8061906c69acda6748b16a5 |
from six import assertRaisesRegex
from unittest import TestCase
from tempfile import mkstemp
from os import close, unlink, write
from contextlib import contextmanager
from pysam import CHARD_CLIP, CMATCH
from dark.reads import Read, ReadFilter
from dark.sam import (
PaddedSAM, SAMFilter, UnequalReferenceLengthErr... | terrycojones/dark-matter | test/test_sam.py | Python | mit | 45,018 | [
"pysam"
] | 5b68ab0d24d25142d4d8997eec32e48bd42ad1ed194eb176a67bb39ba4bfc6e3 |
# Copyright 2019 DeepMind Technologies Limited and Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applic... | deepmind/deepmind-research | cs_gan/gan.py | Python | apache-2.0 | 6,384 | [
"Gaussian"
] | 25a3c621cabfc064457b585c105e7be51def91c5422b60cd3f4c74784088d355 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | wkeeling/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 4,814 | [
"VisIt"
] | 6397c3eef0a90da12135bf9fb54e3d804283d4dfda12438a2002cbca6788a874 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/qcdb/basislistother.py | Python | lgpl-3.0 | 32,066 | [
"ORCA",
"Psi4"
] | 77929127012ab222a7499557bbdb52c85cb14c95060cf6facc0744ac198bc5d8 |
from __future__ import print_function, division
from os.path import join
import tempfile
import shutil
from io import BytesIO
try:
from subprocess import STDOUT, CalledProcessError
from sympy.core.compatibility import check_output
except ImportError:
pass
from sympy.utilities.exceptions import SymPyDepre... | hrashk/sympy | sympy/printing/preview.py | Python | bsd-3-clause | 11,827 | [
"VisIt"
] | 56c63caefdb6b8c0cf7f2c7107b9ff8345717068d170c03f37339d94754f8d3e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | alejob/mdanalysis | package/MDAnalysis/topology/GMSParser.py | Python | gpl-2.0 | 3,946 | [
"GAMESS",
"MDAnalysis"
] | 2610f9166f9dde3a5eb6432f706caff3d886c7894b49c9850df672273da15423 |
# -------------------------------------------------------------------------
# Name: Waterdemand module
# Purpose:
#
# Author: PB
#
# Created: 15/07/2016
# Copyright: (c) PB 2016
# -------------------------------------------------------------------------
import numpy as np
from cwatm.management_module... | CWatM/CWatM | cwatm/hydrological_modules/water_demand/water_demand.py | Python | gpl-3.0 | 52,255 | [
"NetCDF"
] | 69cda85a640966890de11b70cfdce53fb60babf50e0769f70fe00f9beac77441 |
from setuptools import setup
setup(name='gmshtoparticles',
version='0.1',
description='Transforms a .msh file generated with Gmsh into a particles centered inside each triangle or quad element. Outputs a .csv file description and .vtk/.vtu visualization set of files',
url='https://github.com/IaPCS/g... | IaPCS/gmsh-to-nodes | setup.py | Python | gpl-3.0 | 526 | [
"VTK"
] | 77800d466430e5b7d577d2280d744c00b92aa83961cfa22b115c89a84ef73a43 |
# -*- coding: utf-8 -*-
"""
SpykeDemo.py creates a Layer of neurons and a connection matrix and steps
it through several iterations with an injected current.
Created on Sun Oct 04 23:26:52 2015
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License a... | DrSpyke/Spyke | SpykeDemo.py | Python | gpl-2.0 | 1,335 | [
"NEURON"
] | a384d2be2b8c432250d31404fe8e78fe03908d84ff19a0d68b4e287e7671b018 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Setup.py for pymatgen."""
import sys
import platform
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext as _build_ext
class build_ext(_build_ext):
... | gVallverdu/pymatgen | setup.py | Python | mit | 9,220 | [
"ABINIT",
"ASE",
"CRYSTAL",
"FEFF",
"Gaussian",
"LAMMPS",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | ad9e7528aed142aff31ba13d14b530f3e99396b8ec8c3911e5b0d6555b7667db |
#! /usr/bin/env python
import math, sys, os , platform
from collections import Iterable
from optparse import OptionParser
import pybel2
import openbabel as op
import numpy as np
# http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml
Molecule=pybel2.Molecule
Atom=pybel2.Atom
Bond=pybel2.Bond
def pqrbug(filename... | platinhom/CADDHom | python/molecule/OBabel/pybel_feature.py | Python | gpl-2.0 | 18,144 | [
"Pybel"
] | b9d12280a21c0807d7f77f8c6f65ca15a88de554e8f283a41e3aef2c5a924551 |
# $HeadURL$
""" Cache for the Plotting service plots
"""
__RCSID__ = "$Id$"
import os
import os.path
import time
import threading
from DIRAC import S_OK, S_ERROR, gLogger, rootPath
from DIRAC.Core.Utilities.DictCache import DictCache
from DIRAC.Core.Utilities import Time
from DIRAC.Core.Utilities.Graphs import grap... | calancha/DIRAC | FrameworkSystem/Service/PlotCache.py | Python | gpl-3.0 | 2,388 | [
"DIRAC"
] | 400e1f876497612ad5d398315f762fa27418bd6588ec1f85d479572f8f189d73 |
""" PilotCommand
The PilotCommand class is a command class to know about present pilots
efficiency.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.Re... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Command/PilotCommand.py | Python | gpl-3.0 | 5,800 | [
"DIRAC"
] | 154042b7cb2afb7c0af35d93793286e4cda6e62cdae391646334d3451eaab8b2 |
"""
The controllers module provides different controller classes,
applicable to different simulations.
A controller object's job is to control simulations-
At a high level a controller objects accepts a list of
parameters and chromosomes and (usually) returns
corresponding simulation data.
This is implemented polympo... | vellamike/neurotune | neurotune/controllers.py | Python | bsd-3-clause | 17,830 | [
"NEURON"
] | 2ce68aa3babc85e70e722695cc13b853e45912f5e7fcdff5fef0702c5ff3e570 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=no-member
# pylint: disable=too-many-arguments
import RNA
def run(cmd, sequences, temp, ... | neilswainston/PathwayGenie | parts_genie/vienna_utils.py | Python | mit | 3,317 | [
"VisIt"
] | 93f387907354379e3b3e501da41e6c41f4be0ce5970d3c70155cee68073aa894 |
# -*- coding: utf-8 -*-
"""
Unitary Event (UE) analysis is a statistical method to analyze in a time
resolved manner excess spike correlation between simultaneously recorded
neurons by comparing the empirical spike coincidences (precision of a few ms)
to the expected number based on the firing rates of the neurons
(see... | alperyeg/elephant | elephant/unitary_event_analysis.py | Python | bsd-3-clause | 28,001 | [
"NEURON"
] | 05d30f6eaf7a6268d866dacdba24f472c197a96e3caefc60fb2849e0f48d00a7 |
import numpy as np
from ase import Atoms
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
from gpaw.test import equal
bulk = Atoms('Li', pbc=True)
k = 4
calc = GPAW(mode=PW(200), kpts=(k, k, k), eigensolver='rmm-diis')
bulk.set_calculator(calc)
e = []
niter = []
A = [2.6, 2.65, 2.7, 2.75, 2.8]
for a in A:
... | robwarm/gpaw-symm | gpaw/test/pw/bulk.py | Python | gpl-3.0 | 488 | [
"ASE",
"GPAW"
] | bc3361a389c903f40dcc01dc485614ef74cf0727452bb2753b7f16f403236e9f |
import time, sys
import numpy as np
import matplotlib.pyplot as plt
sys.path.append('../../')
from py2Periodic.physics import twoLayerQG
from numpy import pi
params = {
'f0' : 1.0e-4,
'Lx' : 1.0e6,
'beta' : 1.5e-11,
'defRadius' : 1.5e4,
'H1' : 500.0,
'H2' ... | glwagner/py2Periodic | tests/twoLayerQG/testTwoLayerTopography.py | Python | mit | 1,545 | [
"Gaussian"
] | 7dd55bea08f080aca4f4d7d2b819460d7e559f3ba0689103ef3795721d337a06 |
# $ ipython --gui=wx
# In [1]: %run visualization/plot-2.py
# In [2]: plot("z_dual_1.norms")
from mayavi import mlab
import numpy
import re
def mycolor(x):
"""Returns a color vector (a triple of floats) based on x, where x is
in the range [0, 1].
"""
lut = [
[ 0, 0, 0, 255],
... | FreeON/spammpack | spammsand/visualization/plot-2.py | Python | bsd-3-clause | 24,103 | [
"Mayavi"
] | 0946fc64eb57e449d5dd7ffc64ff8d1e91104d25b14c36c789a9dc1eb3bb179d |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2018 by Tobias Houska
This file is part of Statistical Parameter Optimization Tool for Python(SPOTPY).
:author: Tobias Houska
'''
from . import _algorithm
from .. import analyser
class list_sampler(_algorithm):
"""
This class holds the List sampler, which samples from a... | thouska/spotpy | spotpy/algorithms/list_sampler.py | Python | mit | 3,003 | [
"Gaussian"
] | 65eabddea901838ed9d187a057b93ec11d3fb6fe630b443f957a389020df76e6 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/sequence/tests/test_sequence.py | Python | bsd-3-clause | 56,349 | [
"scikit-bio"
] | 278d9eaf95c56c0c1c0b9b35cc369837e872090170b43bbf5636f735cf77a668 |
#-*- coding: utf8
# Author: David C. Lambert [dcl -at- panix -dot- com]
# Copyright(c) 2013
# License: Simple BSD
"""The :mod:`random_layer` module
implements Random Layer transformers.
Random layers are arrays of hidden unit activations that are
random functions of input activation values (dot products for simple
ac... | ashishbaghudana/mthesis-ashish | resources/tees/Utils/Libraries/PythonELM/random_layer.py | Python | mit | 18,828 | [
"Gaussian"
] | 26318986f16c89ee5ea3c6b356471999c3afbad256050cfec6b1b21ad545ed08 |
"""
Using otagrum
=============
"""
# %%
import openturns as ot
import pyAgrum as gum
from matplotlib import pylab as plt
import otagrum
# %%
def showDot(dotstring):
try:
# fails outside notebook
import pyAgrum.lib.notebook as gnb
gnb.showDot(dotstring)
except ImportError:
impo... | openturns/otagrum | python/doc/examples/plot_using_otagrum.py | Python | lgpl-3.0 | 5,402 | [
"Gaussian"
] | 60a5ce495dcb73bc9505e73fd28483fc85b93618c2c079ea962c5decca909be3 |
#!/usr/bin/env python
# Copyright (c) 2012 ARM Limited
# All rights reserved
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation... | prodromou87/gem5 | util/cpt_upgrader.py | Python | bsd-3-clause | 12,954 | [
"VisIt"
] | 245c973228a71047459f52d51f6cc4bddd5b4bedf77b42b1130973b8ce3768e8 |
# -*- coding: utf-8 -*-
# Dioptas - GUI program for fast processing of 2D X-ray diffraction data
# Principal author: Clemens Prescher (clemens.prescher@gmail.com)
# Copyright (C) 2014-2019 GSECARS, University of Chicago, USA
# Copyright (C) 2015-2018 Institute for Geology and Mineralogy, University of Cologne, Germany
... | Dioptas/Dioptas | dioptas/model/util/PeakShapes.py | Python | gpl-3.0 | 1,283 | [
"Gaussian"
] | 4749e9516f934e0fc3b6b35d3cc8d20e11accc4a294915518cb36bbcd1e34360 |
import os
import mimetypes
import copy
import tempfile
import shutil
import logging
import json
from django.core.urlresolvers import reverse
from django.core.exceptions import ObjectDoesNotExist, SuspiciousFileOperation
from django.http import HttpResponseRedirect
from django.shortcuts import redirect
from django.cont... | FescueFungiShare/hydroshare | hs_core/views/resource_rest_api.py | Python | bsd-3-clause | 48,034 | [
"Brian"
] | 3ec6b78fa4bf94835401dd5b0c0856c894a347abc7066123a1c928f7c63d08e0 |
"""
Backports. Mostly from scikit-learn
"""
import numpy as np
from scipy import linalg
###############################################################################
# For scikit-learn < 0.14
def _pinvh(a, cond=None, rcond=None, lower=True):
"""Compute the (Moore-Penrose) pseudo-inverse of a hermetian matrix.
... | emmaggie/hmmlearn | hmmlearn/utils/fixes.py | Python | bsd-3-clause | 6,917 | [
"Gaussian"
] | f90d527c8386cbb5458998411d0e2c1e84b5f17e13f57bdd12a66952441d7162 |
"""Mixture model for matrix completion"""
from typing import Tuple
import numpy as np
from scipy.special import logsumexp
from common import GaussianMixture
from scipy.special import logsumexp
from scipy.stats import multivariate_normal
def log_pdf_multivariate_gauss(x, mu, cov):
#assert(mu.shape[0] > mu.shape[1])... | xunilrj/sandbox | courses/MITx/MITx 6.86x Machine Learning with Python-From Linear Models to Deep Learning/project4/netflix/em.py | Python | apache-2.0 | 7,765 | [
"Gaussian"
] | 2b8c5bfbf5b94357dfd1f1c4d2936500a44405c2933fb6293fd729be7415dbe1 |
#!/usr/bin/python
#
# Copyright 2012 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | codeanu/flask-login-oauth2 | modules/oauth2.py | Python | bsd-3-clause | 12,286 | [
"VisIt"
] | 43abe0d819291ec4948b377aca4cdbc5ed67d6769de97640f6af86f2386afee7 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/gromacs/package.py | Python | lgpl-2.1 | 3,939 | [
"Gromacs"
] | f928db7daea4b4478b8089c14e17980fc1d38d8c1f207ac61757fcd5b271b103 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import numpy as np
import pandas as pd
from pymatgen import Element
from veidt.potential.abstract import Potential
from veidt... | czhengsci/veidt | veidt/potential/snap.py | Python | bsd-3-clause | 6,745 | [
"LAMMPS",
"pymatgen"
] | 7cc01bdcce2cbd34d6c7a28c05e2ea96940241cc42adaa356fae03be7caf0ffd |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import numpy as np
from roppy.sample import sample2D, sample2DU, sample2DV
from roppy.depth import sdepth
class Section(object):
"""Class for handling sections in a ROMS grid
The section is defined by a sequence of nodes, supposedly quite close... | bjornaa/roppy | roppy/section.py | Python | mit | 3,550 | [
"NetCDF"
] | ecf80360922e32b32b41c6388c2b0eada571ec1885136faf56fca7fd158538c9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
lineColor = colors.GetColor3d("peacock")
modelColor = colors.GetColor3d("silver")
backgroundColor = colors.GetColor3d("wheat")
modelSource = vtk.vtkSphereSource()
plane = vtk.vtkPlane()
cu... | lorensen/VTKExamples | src/Python/PolyData/ExtractPolyLinesFromPolyData.py | Python | apache-2.0 | 2,569 | [
"VTK"
] | 2f92fe1e6681bce8e89d6f6eaea68f786ad6be6c26bb2bf07a07151338c49fef |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
n0 = 25
n1 = 25
numLambdas = 3
startLambda = ... | mcopik/Elemental | examples/interface/BPDN.py | Python | bsd-3-clause | 2,579 | [
"Gaussian"
] | b14bbe0ef1cf43282d256a5879f581554aa2a7fed7ba37cc6d01462b2472edac |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import random
from .node import Input, Output, Neuron
class Network(dict):
'''
A network composed of input, neuron, and output nodes. It can be modeled
as a unidirectional directed graph with edge weights.
'''
def __init__(self):
... | CtrlC-Root/cse5526 | spark/network.py | Python | mit | 1,768 | [
"NEURON"
] | 5224f60d62ce73de4fde9bf70486dfa7ac2df643d11f5b91627ce5621bd6d426 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from scipy._lib._util import getfullargspec_no_self as _getfullargspec
import sys
import keyword
import re
import types
import warnings
import inspect
from itertools import zip_longest
from collections import namedt... | mdhaber/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 146,733 | [
"Gaussian"
] | 441bf37fd74362c06e7e59ec233ca7cfa89a609867004d68855df6dafe1a87c7 |
import gpflow
import numpy as np
import tensorflow_probability as tfp
from gpflow.utilities import set_trainable, to_default_float
from . import BranchingTree as bt
from . import VBHelperFunctions, assigngp_dense, assigngp_denseSparse
from . import branch_kernParamGPflow as bk
def FitModel(
bConsider,
GPt,
... | ManchesterBioinference/BranchedGP | BranchedGP/FitBranchingModel.py | Python | apache-2.0 | 9,710 | [
"Gaussian"
] | ce02b829a0e68780b30a4e129d33c7068511cc7de1d957c84dc0892f70c10078 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWi... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/cursor3D.py | Python | bsd-3-clause | 2,339 | [
"VTK"
] | dd68995bea2e405e6288569e81e3aea556b5077f23587457aa9916798ca2deb3 |
#coding: utf8
import numpy as N
from traits.api import Int, Float, Tuple, Range
from traitsui.api import View, VGroup, Item
from enable.api import ColorTrait
from DisplayPlugin import DisplayPlugin
class BeamProfiler(DisplayPlugin):
# These traits control the calculation of the Gaussian fit
background_percen... | ptomato/Beams | beams/BeamProfiler.py | Python | mit | 6,347 | [
"Gaussian"
] | 247cc1dafb7167565dcdfcd6047b102a3c86a7ef6153a15f2c7020c40043e78b |
#!/usr/bin/env python
#
# displace.py
#
# Simple script to generate input files of given displacement patterns.
# Currently, VASP, Quantum-ESPRESSO, and xTAPP are supported.
#
# Copyright (c) 2014 Terumasa Tadano
#
# This file is distributed under the terms of the MIT license.
# Please see the file 'LICENCE.txt' in the... | ttadano/ALM | tools/displace.py | Python | mit | 10,240 | [
"ESPResSo",
"LAMMPS",
"OpenMX",
"VASP"
] | 5a806ff06a41649c1928e09330e54a76740718577823fde4b393ebd7a2d05a7a |
#!/usr/bin/env python
import numpy
import itertools
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from crystal import fillcell, tikz_atoms
def SiMn_Isite():
a = 5.43
fcc = Lattice([[a/2,a/2,0],[a/2,0,a/2],[0,a/2,a/2]])
isite = Structure(fcc,['Si']*2,[[0.00,0.00,0... | ldamewood/figures | scripts/SiMn_sites.py | Python | mit | 1,478 | [
"CRYSTAL",
"pymatgen"
] | a4fe42cc5bfff4119fd306cad46a86cb8134c0b2b4382f7c938bf88b8b761146 |
'''
This application uses Flask as a web server and jquery to trigger
pictures with SimpleCV
To use start the web server:
>>> python flask-server.py
Then to run the application:
>>> python webkit-gtk.py
*Note: You are not required to run the webkit-gtk.py, you can also
visit http://localhost:5000
'''
print __doc__... | vdt/SimpleCV | SimpleCV/examples/web-based/webdisplay/flask-server.py | Python | bsd-3-clause | 1,451 | [
"VisIt"
] | 25eb6efee748465cace6224beb30dc39c28dfada5b6f1cca3d5efbe72980160a |
##
# Copyright 2009-2012 Ghent University
# Copyright 2009-2012 Stijn De Weirdt
# Copyright 2010 Dries Verdegem
# Copyright 2010-2012 Kenneth Hoste
# Copyright 2011 Pieter De Baets
# Copyright 2011-2012 Jens Timmerman
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://u... | JensTimmerman/easybuild-easyblocks | easybuild/easyblocks/n/netcdf.py | Python | gpl-2.0 | 4,802 | [
"NetCDF"
] | 594b1b0861b5f1cfb80bbd72759645312cc6ad6514dbb20a1f4d66dd170e5486 |
#coding: utf-8
# Hungarian Phrasebook, <https://www.youtube.com/watch?v=G6D1YI-41ao>
# Use with Pythonista
# The MIT License
#
# Copyright © 2014 Mia Sinno Smith and Steven Thomas Smith
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation f... | essandess/HungarianPhrasebook | HungarianPhrasebook.py | Python | mit | 17,363 | [
"Octopus"
] | 58ef927670c37d943e75c38e898a8900ce2a128de8ab4d50814751fc895f361d |
import numpy as np
import scipy
from .math import strictly_positify, positify, clip01
def psf(img, sx, sy=None, angle=0):
"""
Return a Gaussian PSF of the same size as img.
img: image (reference for the output size)
sx: sigma value for the long axis
sy: sigma value for the short axis. If None take... | scholi/pySPM | pySPM/utils/restoration.py | Python | apache-2.0 | 6,930 | [
"Gaussian"
] | 01376e9632b70dc5b59ea602839df546353c36fb7fe44c209beaa53fc92acfec |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | Chuban/moose | python/MooseDocs/tests/bibtex/test_bibtex.py | Python | lgpl-2.1 | 4,046 | [
"MOOSE"
] | 3afc084f60d748efa6690e888e1335f421410460f01965d2fb5664b7b561439a |
#
# This file is part of postpic.
#
# postpic 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.
#
# postpic is distributed in the hope th... | skuschel/postpic | postpic/datareader/openPMDh5.py | Python | gpl-3.0 | 12,725 | [
"VisIt"
] | fcaa1c55c154b40d576d220b701b99bd9cc991fe679ffffef91177a8b78bc69e |
import inspect
from functools import wraps
from motherbrain import conf
class Unauthorized(Exception):
def __init__(self, entity_name, entity_value, detail=None):
self.entity_name = entity_name
self.entity_value = entity_value
self.detail = detail
def __str__(self):
msg = 'A... | urlist/urlist | motherbrain/workers/decorators.py | Python | gpl-3.0 | 2,243 | [
"MOE"
] | fec97d96a763629917dc4e7cb4ac9a87f032b05e388efc7c2268b75d48c383b2 |
from calendar import monthrange
from itertools import product
import multiprocessing
import os
import time
import numpy as np
import pandas as pd
from scipy import spatial
import xarray as xr
from gsee.climatedata_interface.pre_gsee_processing import resample_for_gsee
from gsee.climatedata_interface import util
def... | renewables-ninja/gsee | gsee/climatedata_interface/interface.py | Python | bsd-3-clause | 17,053 | [
"NetCDF"
] | 32e7e4d99447582dff10d576a6f9302b577d372f9bf3306a55f9b49b0bddfe5a |
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Author: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort
# License: BSD 3 clause
import num... | cdegroc/scikit-learn | sklearn/decomposition/fastica_.py | Python | bsd-3-clause | 12,450 | [
"Gaussian"
] | d009d763b9b5ec22e3dae1f30c778ef49bd1fae48670bf1a0f3634a339859c30 |
"""
Spatial Error Models with regimes module
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
import multiprocessing as mp
import regimes as REGI
import user_output as USER
import summary_output as SUMMARY
from pysal import lag_spatial
from ols import BaseOLS... | spreg-git/pysal | pysal/spreg/error_sp_regimes.py | Python | bsd-3-clause | 64,257 | [
"COLUMBUS"
] | f47f1f3fc1957246cd8b38636dbff796b4f0a3cee3296102ee407f315fd85e57 |
from __future__ import division, unicode_literals
import unittest
import os
import json
import scipy
from io import open
from pymatgen.phonon.dos import CompletePhononDos
from pymatgen.phonon.plotter import PhononDosPlotter, PhononBSPlotter, ThermoPlotter
from pymatgen.phonon.bandstructure import PhononBandStructureS... | czhengsci/pymatgen | pymatgen/phonon/tests/test_plotter.py | Python | mit | 3,708 | [
"pymatgen"
] | 1aa4c5d37525c26c10d4a28e3c93a1a4750eb5b2939b1739fd369f1885f44fe7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2009 Benny Malengier
#
# 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 2 of the License, or
# (at your option) ... | Fedik/gramps | gramps/plugins/graph/graphplugins.gpr.py | Python | gpl-2.0 | 3,139 | [
"Brian"
] | bddfb8324d8d5f2058294aa98aa195fc4e8e07180bc705f6800428d4a5b4cb32 |
# -*- coding: utf-8 -*-
from lxml import etree
from lxml import html
import requests
#doesn't work
def main():
url = 'http://lispon.moe/cdn/activity/act161108/index.html?aUserId=1494366573'
page = requests.get(url)
tree = html.fromstring(page.content)
print(page.content)
xpath_selector = "//a/@hre... | umyuu/Sample | src/Python3/Q102431/exsample.py | Python | mit | 478 | [
"MOE"
] | 6b06cfac3e6511c5937fa846fad95de1d83ed523485cb30d90de533f3dad582d |
#!/bin/env python
"""
Illustrate how to combine a SMIRNOFF parameterized small molecule with an AMBER parameterized protein using ParmEd.
"""
#
# Load and parameterize the small molecule
#
# Load the small molecule
from openff.toolkit.utils import get_data_file_path
ligand_filename = get_data_file_path('molecules/t... | open-forcefield-group/openforcefield | examples/deprecated/mixedFF_structure/generate_mixedFF_complex.py | Python | mit | 2,220 | [
"Amber",
"CHARMM",
"OpenMM"
] | a14b5069845aae1ee5c9e858cee047475db2f15bb0438bdac9c61dbc1e1c679a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual 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 L... | iwm911/plaso | plaso/formatters/firefox.py | Python | apache-2.0 | 4,092 | [
"VisIt"
] | 6b0e821657c9f2951052233a855fa346cb746abdf621b5afeec2efaf414d9c05 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-resource-manager | tests/unit/gapic/resourcemanager_v3/test_tag_keys.py | Python | apache-2.0 | 115,667 | [
"Octopus"
] | 3a60c2f2da1efb46c362677d7bb47679d82b73823bb61358f8a1118ff1f1d38a |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | marmyshev/transitions | resources/__init__.py | Python | gpl-2.0 | 2,272 | [
"Brian"
] | 2124b5facd659ad24c34345d1fabfb3703acac72789f792f4e4e55db65bea20d |
import unittest
from __main__ import vtk, qt, ctk, slicer
import SimpleITK as sitk
import sitkUtils
#
# LabelObjectStatistics
#
class LabelObjectStatistics:
def __init__(self, parent):
import string
parent.title = "Label Object Statistics"
parent.categories = ["Microscopy"]
parent.contributors = ["B... | blowekamp/Slicer-IASEM | LabelObjectStatistics/LabelObjectStatistics.py | Python | apache-2.0 | 19,184 | [
"VTK"
] | b99b33d197f55a8fc9d49f976990ad0c5902f851a11d6f79fd473d591722be52 |
from django import forms
from django.contrib.localflavor.cz.forms import CZBirthNumberField
from django.utils.translation import ugettext_lazy as _
from djcode.reservations.models import Examination_kind, Patient, Visit_reservation
class Patient_form(forms.ModelForm):
label_suffix = ":"
class Meta:
model = Patien... | mmincikova/medobs | djcode/reservations/forms.py | Python | gpl-3.0 | 1,292 | [
"VisIt"
] | 635d5f48b4da9e023d70d26c349a8abdff0dff76a8c21e827f66e9ea15822940 |
# 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... | prakritish/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 100,223 | [
"VisIt"
] | 0de0f3299cf14c3716687614eb1ef904475ae6fbfc63a77f4ab337c0389f6497 |
# $Id$
#
# Copyright (C) 2004-2006 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.
#
from rdkit import RDConfig
from rdkit im... | soerendip42/rdkit | rdkit/Chem/ChemUtils/SDFToCSV.py | Python | bsd-3-clause | 4,077 | [
"RDKit"
] | 81d4a1878fddab427da4a172049cb8882fe824bbf3f7acca98b4aafe2c2192fb |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..compat import (
compat_str,
compat_HTTPError,
)
from ..utils import (
ExtractorError,
find_xpath_attr,
lowercase_escape,
smuggle_url,
unescapeHTML,
)
class NBCIE(InfoExtractor):
_VALID_URL = r'... | Oteng/youtube-dl | youtube_dl/extractor/nbc.py | Python | unlicense | 10,298 | [
"Brian"
] | 7209fad7effb1883c09d95e6dd8f6054a7fd346d8470349d69094544d13d53b4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# eclipses.py
# Waqas Bhatti and Luke Bouma - Feb 2017
# (wbhatti@astro.princeton.edu and luke@astro.princeton.edu)
'''Light curve fitting routines for eclipsing binaries:
- :py:func:`astrobase.lcfit.eclipses.gaussianeb_fit_magseries`: fit a double
inverted gaussian ec... | lgbouma/astrobase | astrobase/lcfit/eclipses.py | Python | mit | 17,004 | [
"Gaussian"
] | 7024c2d3f344a090e1fae27374830924347b228be6d376f8601d9841e700b08a |
#!/usr/bin/env python
#JSON {"lot": "RKS/6-31G(d)",
#JSON "scf": "CDIISSCFSolver",
#JSON "er": "cholesky",
#JSON "difficulty": 7,
#JSON "description": "Basic RKS DFT example with hybrid MGGA exhange-correlation functional (TPSS)"}
import numpy as np
from horton import * # pylint: disable=wildcard-import,unused-wi... | theochem/horton | data/examples/hf_dft/rks_water_hybmgga.py | Python | gpl-3.0 | 3,761 | [
"Gaussian"
] | 9adba042d7e460c70dd63bde21d0c0b492eb5c923cd71d174b61f64da268cc17 |
#!/usr/bin/env python
from setuptools import setup, find_packages
version = '0.1dev'
print '''------------------------------
Installing RNAseq version {}
------------------------------
'''.format(version)
setup(
name='rnaseq',
version=version,
author='lx Gui',
author_email='guilixuan@gmail.com',
... | bioShaun/OMrnaseq | setup.py | Python | gpl-3.0 | 1,031 | [
"Biopython",
"HTSeq"
] | 3106d783ef72895961475ed9447b36edc48971bb3cdc7332b775936b8c5562ee |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/interaction/LennardJonesGromacs.py | Python | gpl-3.0 | 9,198 | [
"ESPResSo"
] | eff898a3d95c8386971a9608c87b24188c95ddc4f98b6b55136f8a584145110b |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/tools/c60struct.py | Python | apache-2.0 | 3,727 | [
"PySCF"
] | 6beecba7e60d344837ce4aed5335628084c4bdca47cdb56b7afafc1b530b3847 |
import re
import json
import typing as t
from dataclasses import dataclass
from functools import partial
from collections import OrderedDict
from ..graph import Graph, Root, Node, Link, Option, Field, Nothing
from ..graph import GraphVisitor, GraphTransformer
from ..types import (
TypeRef,
String,
Sequenc... | vmagamedov/hiku | hiku/introspection/graphql.py | Python | bsd-3-clause | 22,919 | [
"VisIt"
] | 5dfb7f5f2f7c869146e37e88241918c6e32eee99c34366f4ba3f97521bd23d07 |
#!/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/web/getaudiotracks.py | Python | gpl-2.0 | 6,042 | [
"VisIt"
] | 836752fb95eb42bb0914c9af21ed3b1a012b2b3d08875f57b7243d807d326bbd |
import pytest
import betterbib
@pytest.mark.parametrize(
"string,ref",
[
(
"The Magnus expansion and some of its applications",
"The {Magnus} expansion and some of its applications",
),
(
"On generalized averaged Gaussian formulas, II",
... | nschloe/betterbib | tests/test_bibtex_title.py | Python | gpl-3.0 | 1,535 | [
"Gaussian"
] | c0296b4ced3a6849f6db2a109cc84d031e243ff59fad42b7836ac89aa7c9cc83 |
# coding: utf-8
# # Machine Learning Engineer Nanodegree
# ## Supervised Learning
# ## Project: Finding Donors for *CharityML*
# Welcome to the second project of the Machine Learning Engineer Nanodegree! In this notebook, some template code has already been provided for you, and it will be your job to implement the ... | leizhipeng/ml | finding_donors/finding_donors.py | Python | gpl-3.0 | 28,896 | [
"Gaussian"
] | e151dcc5e97e0fa227b12b412939254ab7a83dd54774974734bbcf71d9392a5e |
#!/usr/bin/env python
"""
Status of DIRAC components using runsvstat utility
Example:
$ dirac-status-component
DIRAC Root Path = /vo/dirac/versions/Lyon-HEAD-1296215324
Name : Runit Uptime PID
WorkloadManagement_PilotStatusAgent : Run 4029 169... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_status_component.py | Python | gpl-3.0 | 1,658 | [
"DIRAC"
] | 29b3584b21cb66e79534b05b14736797b305e60591d894e27b5dc61fab6521f4 |
"""Tools for managing evaluation contexts. """
from sympy.utilities.iterables import dict_merge
from sympy.core.basic import PicklableWithSlots
__known_options__ = set(['frac', 'gens', 'wrt', 'sort', 'order', 'domain',
'modulus', 'gaussian', 'extension', 'field', 'greedy', 'symmetric'])
__global_options__ = []
... | ichuang/sympy | sympy/polys/polycontext.py | Python | bsd-3-clause | 1,887 | [
"Gaussian"
] | 572775101f63dda6e98a6250c509913fd022116b59aa922c1ed6dd23a34c7f93 |
"""
Test courseware search
"""
import os
import json
import uuid
from ..helpers import remove_file
from ...pages.common.logout import LogoutPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms.courseware_search import CoursewareSearchPage
from ...pages.lms.staff_view import StaffPage
from ...f... | adoosii/edx-platform | common/test/acceptance/tests/lms/test_lms_cohorted_courseware_search.py | Python | agpl-3.0 | 14,005 | [
"VisIt"
] | def31e25c0e12a2341aab74d216cf95442d9ed0e2e450c8f353d9a464142d9c4 |
"""
sphinx.ext.apidoc
~~~~~~~~~~~~~~~~~
Parses a directory tree looking for Python modules and packages and creates
ReST files appropriately to create code documentation with Sphinx. It also
creates a modules index (named modules.<suffix>).
This is derived from the "sphinx-autopackage" script... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/sphinx/ext/apidoc.py | Python | mit | 18,689 | [
"VisIt"
] | 1dab6220b857421526a7594b43faaf3c03ab8a5a3cd6c3539c067f09c9c283d6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
import csv
import collections
import itertools
from io import open
import math
from six.moves import zip
import warnings
from monty.json import MSON... | johnson1228/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 77,867 | [
"pymatgen"
] | 177883f020404416ac3f1748ab5470e189864c94159845a0767d77d73322c870 |
__author__ = 'brian'
import sys
my_paths = [
'/usr/local/pbs/default/python/lib/python2.5',
'/usr/local/pbs/default/python/lib/python2.5/plat-linux2',
'/usr/local/pbs/default/python/lib/python2.5/lib-tk',
'/usr/local/pbs/default/python/lib/python2.5/lib-dynload',
'/usr/local/pbs/default/python/lib/... | Karaage-Cluster/karaage-hacks | require_project.py | Python | gpl-3.0 | 1,951 | [
"Brian"
] | b8cecef30db8e8695b6bab105cbe2a35f40ae4ad12d909e5bf59c99c161f9121 |
# Copyright (C) 2019 Brian McMaster
# Copyright (C) 2019 Open Source Integrators
# License AGPL-3.0 or later (http://www.gnu.org/licenses/agpl).
from odoo.tests.common import TransactionCase
class TestL10nUsForm1099(TransactionCase):
def test_on_change_is_1099(self):
"""
Test that supplier i... | OCA/l10n-usa | l10n_us_form_1099/tests/test_l10n_us_form_1099.py | Python | agpl-3.0 | 811 | [
"Brian"
] | 49c7494c17be3868ab389a553ac5c5e44e7d28e00effc31e5e3fd2e696bb1cff |
from __future__ import absolute_import, unicode_literals
from django.test import TestCase
from django.utils import six
from .models import (Building, Child, Device, Port, Item, Country, Connection,
ClientStatus, State, Client, SpecialClient, TUser, Person, Student,
Organizer, Class, Enrollment)
class Select... | waseem18/oh-mainline | vendor/packages/Django/tests/regressiontests/select_related_regress/tests.py | Python | agpl-3.0 | 6,599 | [
"Brian"
] | 0c61c11a4505fc96d94074c7db52ee43636f3ee06e85790a28c512dcc509d28f |
"""pyMOOSE
Python bindings of MOOSE simulator.
References:
-----------
- `Documentation https://moose.readthedocs.io/en/latest/`
- `Development https://github.com/BhallaLab/moose-core`
"""
# Notes
# -----
# Use these guidelines for docstring: https://numpydoc.readthedocs.io/en/latest/format.html
import sys
import... | BhallaLab/moose-core | python/moose/__init__.py | Python | gpl-3.0 | 23,812 | [
"MOOSE",
"NEURON"
] | 22f265a4ea99da192b5df79f9f99fabc572e54856ca0e1a20f4d52d18accf397 |
#! /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-kms | scripts/fixup_kms_v1_keywords.py | Python | apache-2.0 | 8,355 | [
"VisIt"
] | 4159793087504aff34959c2afed9e8ab7fcc66343d4453d8f32e959dbaadd117 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/speed/__init__.py | Python | mit | 1,175 | [
"VisIt"
] | 5db82b400bb7f81c14cfd2be5f8c8ab7f5b384f2270460711712a14820a41656 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | s-hertel/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 17,649 | [
"Brian",
"Galaxy"
] | b54bd525015a6ba5b9e9db92e3d17adde7db9834f45eed13d9a2311fa188f7e1 |
# Generated from antlr4-python3-runtime-4.7.2/src/autogen/Grammar.g4 by ANTLR 4.7.2
from antlr4 import *
if __name__ is not None and "." in __name__:
from .GrammarParser import GrammarParser
else:
from GrammarParser import GrammarParser
# This class defines a complete generic visitor for a parse tree produced ... | damorim/compilers-cin | 2020_3/projeto2/GrammarCheckerVisitor.py | Python | mit | 6,465 | [
"VisIt"
] | 23ecee7a205bba68d87700c4d8e923e6adb51fe70c6b548f69c2e77463ea987e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/core/test_segment.py | Python | gpl-2.0 | 2,949 | [
"MDAnalysis"
] | 44ef8ad2357f7e436a968688c0f897d9cbcb5632f12cbdf230936eef60d908ea |
"""
================
Neuropop Example
================
A demonstration of Neuropop using simulated data
"""
########################################################
import numpy as np
import matplotlib.pyplot as plt
from spykes.ml.neuropop import NeuroPop
from spykes.utils import train_test_split
################... | codekansas/spykes | examples/plot_neuropop_simul_example.py | Python | mit | 3,434 | [
"NEURON"
] | 19d6ca371847bd64a76ee9cf3d9dae6f16715df07b39eaea7ec7b9f6ed89172d |
from __future__ import division
import copy
import numpy
import random
import re
RUNNERS = [
["Adam", "0:05:47", "M"],
["Ali", "0:06:38", "F"],
["Andrew", "0:06:55", "M"],
["Blonde Megan", "0:08:38", "F"],
# ["Brian", "0:06:43", "M"],
# ["Brian Tall", "0:06:24", "M"],
# ["Collin", "0:06:14... | topher200/balanced-teams | balanced_teams.py | Python | mit | 4,353 | [
"Brian"
] | 5fdc6dafb0601337fc225d826dd51594537293ce9153e98087c31ad435dfc672 |
# -*- coding: utf-8 -*-
"""Specifies static assets (CSS, JS) required by the CATMAID front-end.
This module specifies all the static files that are required by the
CATMAID front-end. The configuration is separated in libraries and CATMAID's
own files:
Libraries: To add a new library, add a new entry into the librari... | tomka/CATMAID | django/projects/mysite/pipelinefiles.py | Python | gpl-3.0 | 9,206 | [
"Cytoscape"
] | 6c474875998aa5b49296a4eee5a00dd669a5b984c3cdec4482b7ab918619b6e5 |
from ase.structure import molecule
from gpaw import GPAW
from gpaw import dscf
from gpaw.test import equal
# Ground state calculation
calc = GPAW(mode='lcao',
basis='dzp',
nbands=8,
h=0.2,
xc='PBE',
spinpol=True,
convergence={'energy': 100,
... | robwarm/gpaw-symm | gpaw/test/dscf_lcao.py | Python | gpl-3.0 | 1,095 | [
"ASE",
"GPAW"
] | 77346e218b24dc7e954f723a93bb44fbbdc7d46a3305ddf3c89e5470a64be9d0 |
""" :mod: GFAL2_GSIFTPStorage
=================
.. module: python
:synopsis: GSIFTP module based on the GFAL2_StorageBase class.
"""
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger
from DIRAC.Core.Utilities.Pfn import pfnparse, pfnunparse
cl... | Andrew-McNab-UK/DIRAC | Resources/Storage/GFAL2_GSIFTPStorage.py | Python | gpl-3.0 | 2,107 | [
"DIRAC"
] | 3343e8b44ea2a6c11381e3f582d6236ec5049549013788c57ea24075f1a8fd49 |
from ovito import *
import sys
sys.exit(2) | srinath-chakravarthy/ovito | tests/scripts/test_suite/system_exit.py | Python | gpl-3.0 | 43 | [
"OVITO"
] | ebea722074486e35c9197c95b00a4e54da47fbbd0a10a4c1453d8d812006ff9c |
#!/usr/bin/env python
"Check binaries configuration"
#
# Copyright (C) 2012-2021 ABINIT Group (Yann Pouillon)
#
# This file is part of the ABINIT software package. For license information,
# please see the COPYING file in the top-level directory of the ABINIT source
# distribution.
#
from __future__ import unicode_lite... | abinit/abinit | abichecks/scripts/check-binaries-conf.py | Python | gpl-3.0 | 3,229 | [
"ABINIT",
"NetCDF",
"Wannier90"
] | b90bb834904d8568fc7c042b1f626f645d4b02abebb0eb977b37e0d6160f3735 |
from contextlib import contextmanager
from django.utils.crypto import get_random_string
from ..ga_helpers import GaccoTestMixin, SUPER_USER_INFO
from ...pages.biz.ga_contract import BizContractDetailPage, BizContractPage
from ...pages.biz.ga_dashboard import DashboardPage
from ...pages.biz.ga_invitation import BizInv... | nttks/edx-platform | common/test/acceptance/tests/biz/__init__.py | Python | agpl-3.0 | 8,798 | [
"VisIt"
] | f32ce8d5f97112eb8a621f711a5dba680cdb880bdf7204a492dedc45752f5cae |
# -*- coding: utf-8 -*-
#
# recording_demo.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 the License,... | stinebuu/nest-simulator | pynest/examples/recording_demo.py | Python | gpl-2.0 | 2,234 | [
"NEURON"
] | 057c7271fa4f253260a1bf290aada572a531776ed2b840fea7a585f7970ef492 |
import os
from Bio.Nexus import Nexus
def check_taxa(matrices):
'''Checks that nexus instances in a list [(name, instance)...] have
the same taxa, provides useful error if not and returns None if
everything matches
From: http://biopython.org/wiki/Concatenate_nexus
'''
first_taxa = m... | Tagliacollo/Phyloworks | py_scripts/conc_nexus_aln.py | Python | gpl-3.0 | 2,208 | [
"Biopython"
] | c32c049c06a85980d81e9bac7d1245648bd65cc11097cdd2dc2e23da6161961d |
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