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#
# Copyright (C) 2017-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | testsuite/python/auto_exclusions.py | Python | gpl-3.0 | 2,327 | [
"ESPResSo"
] | 917f98909bcf8455d1d454855bea9ed1402cec46d65ab1ec89f8ae12761fbc6c |
#!/usr/bin/python
# (c) 2013, Cove Schneider
# (c) 2014, Joshua Conner <joshua.conner@gmail.com>
# (c) 2014, Pavel Antonov <antonov@adwz.ru>
#
# 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... | haad/ansible-modules-core | cloud/docker/_docker.py | Python | gpl-3.0 | 74,792 | [
"VisIt"
] | 9dd00378c998d6af4eb583fc75ccd836c409238fe775db480444fa4107991f7d |
#
# Classify Template
#
# Finish the code for the method, nearestNeighbor
#
# Code file for the book Programmer's Guide to Data Mining
# http://guidetodatamining.com
#
# Ron Zacharski
#
class Classifier:
def __init__(self, filename):
self.medianAndDeviation = []
# reading the dat... | ChaoSBYNN/Tools | Data Mining/A Programmer's Guide to Data Mining/code/chapter-4/classifyTemplate.py | Python | gpl-3.0 | 5,128 | [
"CRYSTAL"
] | a02a7c558ddb953ce3ac17c8de09c4ff35777c110eef618cd984394be7fedde0 |
#!/usr/bin/env python3
"""
Demo of using monte-carlo vs linearization to approximate
a transformed random variable's probability distribution.
Automatic differentiation is used to find jacobians.
The "state" terminology comes from the field of stochastic processes.
"""
from autograd import numpy as np, jacobian # htt... | jnez71/demos | methods/montecarlo_vs_linearization.py | Python | mit | 3,593 | [
"Gaussian"
] | ae7100c3488ff3238ad30b11c14595b25eee7d833246d4cca4af8e5c0dcf16bd |
import pynet,netext,percolator
import random
import numpy as np
def mst(net,maximum=False):
"""Find a minimum/maximum spanning tree
"""
return mst_kruskal(net,True,maximum)
def mst_kruskal(net,randomize=True,maximum=False):
"""Find a minimum/maximum spanning tree using Kruskal's algorithm
If ran... | lkovanen/TMFinder | python/netpython/transforms.py | Python | gpl-3.0 | 16,557 | [
"VisIt"
] | 58c10fd14a0a1a444f6f8621a5d39dafb6401e89c5a809fe270a25f1a549e3dc |
#
# Code by Alexander Pruss and under the MIT license
#
#
from mine import *
import colors
import sys
import os
from PIL import Image
from fonts import FONTS
import random
import text
mc = Minecraft()
pos = mc.player.getTilePos()
filename = sys.argv[1]
if not os.path.isfile(filename):
filena... | arpruss/raspberryjam-pe | p2/scripts3/dither.py | Python | mit | 1,836 | [
"Gaussian"
] | e41216f3fb259a8446ce980a482c4923056c41f37f2fc84ee6f6c7144ad8f88d |
#!/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.
'''Unit tests for grit.xtb_reader'''
import os
import sys
if __name__ == '__main__':
sys.path.append(os.path.join(os.path.dirna... | guorendong/iridium-browser-ubuntu | tools/grit/grit/xtb_reader_unittest.py | Python | bsd-3-clause | 3,988 | [
"xTB"
] | decdcab1669d5a0301add2d32f35e42ac1f43a610f6855a87046e6db84af24ad |
# -*- coding: utf-8 -*-
from findspam import FindSpam
import pytest
@pytest.mark.parametrize("title, body, username, site, body_is_summary, match", [
('18669786819 gmail customer service number 1866978-6819 gmail support number', '', '', '', False, True),
('18669786819 gmail customer service number 18... | NickVolynkin/SmokeDetector | test/test_regexes.py | Python | apache-2.0 | 7,899 | [
"VisIt"
] | d53742a1704292c8999cf9d51140d749ef268de04b56a449b59c8943e3eb65b6 |
# -*- coding: utf-8 -*-
# This file as well as the whole tsfresh package are licenced under the MIT licence (see the LICENCE.txt)
# Maximilian Christ (maximilianchrist.com), Blue Yonder Gmbh, 2016
# Thanks to Andreas W. Kempa-Liehr for providing this snippet
import logging
import numpy as np
import pandas as pd
_lo... | blue-yonder/tsfresh | tsfresh/examples/driftbif_simulation.py | Python | mit | 6,531 | [
"Gaussian"
] | 20c90af673cae0e4e841e1dc0094acdf775e542af5b66c6fb565ad851984719a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import runpy
from setuptools import setup
import os
here = os.path.abspath(os.path.dirname(__file__))
with open(os.path.join(here, "README.rst")) as readme_file:
readme = readme_file.read()
with open(os.path.join(here, "HISTORY.rst")) as history_file:
history = h... | catmaid/catpy | setup.py | Python | mit | 1,825 | [
"NEURON"
] | b25a727d8aef1948265389b83fa3e965d6340962b446993a79b6d80c69eac4e4 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
from odoo.addons.account.tests.account_test_classes import AccountingTestCase
from odoo import fields
class ValuationReconciliationTestCase(AccountingTestCase):
""" Base class for tests checking interim accounts re... | t3dev/odoo | addons/stock_account/tests/test_anglo_saxon_valuation_reconciliation_common.py | Python | gpl-3.0 | 6,417 | [
"MOOSE"
] | f3facc7e473e87cb994157b4a5355a85ca345c84747ad67bbbad42d5cd1f4bee |
# Import OVITO modules.
from ovito.io import *
from ovito.modifiers import *
from ovito.data import *
# Import standard Python and NumPy modules.
import sys
import numpy
# Load the simulation dataset to be analyzed.
node = import_file("../data/NanocrystallinePd.dump.gz")
# Create bonds.
node.modifiers.append(CreateB... | srinath-chakravarthy/ovito | examples/scripts/cna_bond_analysis.py | Python | gpl-3.0 | 2,214 | [
"OVITO"
] | 1383ae8d0e45f297e952ce8f91f3ed16f7d218bc5fffef3baf7a39a259d97cef |
"""
Author: Aaron MacDonald
Date: June 14, 2007
Description: An implementation of the precise permissive field
of view algorithm for use in tile-based games.
Based on the algorithm presented at
http://roguebasin.roguelikedevel... | jwvhewitt/dmeternal | pbge/scenes/pfov.py | Python | gpl-2.0 | 15,400 | [
"VisIt"
] | 2c5952a21d4bce1a5838eabdf8486fa657f3a6ace957e5ae57f872808dfd95a3 |
from __future__ import print_function, division
import sys, numpy as np
from pyscf.nao.tddft_iter import tddft_iter
from pyscf.scf import hf, uhf
from copy import copy
from pyscf.nao.m_pack2den import pack2den_u
from pyscf.nao.m_vhartree_coo import vhartree_coo
from timeit import default_timer as timer
#
#
#
class scf... | gkc1000/pyscf | pyscf/nao/scf.py | Python | apache-2.0 | 6,479 | [
"PySCF",
"SIESTA"
] | 63368fbbc0acb993e023a8258d0a0a6fa8786cacdc065a3d4df0d31fe401169a |
#------------------------------------------------------------------------------
# askmail.py - mail and mailbox related classes
#
# (C) 2001-2006 by Marco Paganini (paganini@paganini.net)
#
# This file is part of ASK - Active Spam Killer
#
# ASK is free software; you can redistribute it and/or modify
# it under t... | celer/ask | askmail.py | Python | gpl-2.0 | 22,110 | [
"VisIt"
] | 3f9205ea08825c357ee5369e50cedd43544878747b9010e2d907d49feaadcb41 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
File: sync_metadata_spreadsheets.py
Intent: get data from several spreadsheet sources, glean relevant, output to
new sample, dnaprep(&? raw and trimmed) sheets.
Author: Benjamin Leopold
Date: 2016-07-25 10:46:07-0400
"""
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~... | TheJacksonLaboratory/osdf_submit | scripts/sync_metadata_spreadsheets.py | Python | gpl-3.0 | 16,449 | [
"VisIt"
] | e89cf3d1b09e667c85957f95390ecb40222c8b1f411c0337e07b8ad99d0f32e1 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of t... | psiwczak/openstack | nova/tests/network/test_manager.py | Python | apache-2.0 | 73,308 | [
"FEFF"
] | ad6ccb6b51d42e11b3d5f01b49fcef37f573a153cf99eac662d82537afc41aca |
from syned.util.json_tools import load_from_json_file
from syned.storage_ring.electron_beam import ElectronBeam
from syned.storage_ring.magnetic_structures.undulator import Undulator
from syned.beamline.optical_elements.ideal_elements.screen import Screen
from syned.beamline.optical_elements.ideal_elements.lens impor... | srio/shadow3-scripts | extract_from_syned_json.py | Python | mit | 3,157 | [
"CRYSTAL"
] | de9037c29c785f1418c56f038aa1b857a5a6909e9b42daeec072ba6c822a683f |
# coding=utf-8
# Copyright 2020 The Real-World RL Suite Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | google-research/realworldrl_suite | realworldrl_suite/environments/realworld_env.py | Python | apache-2.0 | 24,716 | [
"Gaussian"
] | 353567779db83ed43ac8a43d213bac85be27d8caaa6aa70b96fc1f442c2cfa4c |
"""Sphinx configuration for lsst/pipelines_lsst_io (pipelines.lsst.io).
To use this configuration in a Sphinx project, write a conf.py::
from documenteer.conf.pipelines import *
For additional documentation, see:
https://documenteer.lsst.io/pipelines/configuration.html#pipelines-conf
"""
# This configuratio... | lsst-sqre/sphinxkit | documenteer/conf/pipelines.py | Python | mit | 13,515 | [
"Firefly"
] | 694c435cfa908a048b77b40c22e072cb4646f61a450760f3e954448a50c8b987 |
# -*- coding: utf-8 -*-
"""
flaskbb.utils.helpers
~~~~~~~~~~~~~~~~~~~~
A few helpers that are used by flaskbb
:copyright: (c) 2014 by the FlaskBB Team.
:license: BSD, see LICENSE for more details.
"""
import re
import time
import itertools
import operator
from datetime import datetime, timedelta
... | Aaron1992/flaskbb | flaskbb/utils/helpers.py | Python | bsd-3-clause | 12,048 | [
"VisIt"
] | ea9f2004dff96fb72d93f08e1c395f10c6ff271fba11fd3ba3839508a4cb2105 |
import os.path
import numpy as np
import matplotlib
import matplotlib.pylab as plt
import healpy as hp
import string
import yt
import os
import glob
from PIL import Image as PIL_Image
from scipy.stats import chi2
import time
#import beatbox.universe
import beatbox
# ==================================================... | rogerblandford/Music | beatbox/multiverse.py | Python | mit | 31,376 | [
"Gaussian"
] | 2761bd5a37a07357eb929bb910b125c023e7f38cd8abbb6673e5b42704705d4b |
#!/usr/bin/env python
"""Compartment.py:
A compartment in moose.
Last modified: Tue May 13, 2014 06:03PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ ... | dilawar/moose-full | moose-core/tests/python/Rallpacks/compartment.py | Python | gpl-2.0 | 4,032 | [
"MOOSE"
] | 0ddedacd44533af5dcc6319eb96f2a3895d0531bd41bebd8da8c3da88755c2ce |
# -*- coding: utf-8 -*-
import numpy as np
import scipy.special
from bokeh.plotting import *
mu, sigma = 0, 0.5
measured = np.random.normal(mu, sigma, 1000)
hist, edges = np.histogram(measured, density=True, bins=50)
x = np.linspace(-2, 2, 1000)
pdf = 1/(sigma * np.sqrt(2*np.pi)) * np.exp(-(x-mu)**2 / (2*sigma**2))... | the13fools/Bokeh_Examples | plotting/file/histogram.py | Python | bsd-3-clause | 3,662 | [
"TINKER"
] | b9a8c47040fcd352d1e3caf5472c536ce064eb3964cfd0be35f699c1aef34128 |
#!/usr/bin/python
#Python script to analyze dihedrals. Usage: "python dihedral_analyze.py (list of files to plot). D. Mobley, 5/16/07"
#from numpy import zeros, ones, arange, outer, inner, float32, float64, int16, sqrt, floor, mean, std, log, add, average, nonzero, cov, transpose, resize, array, reshape, repeat, transp... | chris-lee-mc/MutInf | dihedral_mutent_2_2010.py | Python | gpl-3.0 | 219,455 | [
"Gaussian",
"Gromacs"
] | 5cef7f8f239d4d4d1cbdff0f1b0a31ca35d244a7f39303275e077fc024472a0f |
# this script is based on RADIANCE sun.c script
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Ladybug is free software; you can redistribute ... | samuto/ladybug | src/Ladybug_SunPath.py | Python | gpl-3.0 | 41,384 | [
"EPW"
] | c8661e4b330c2f529c888d4d8e20196269197c72b594b6581edbe0e726a6ad8d |
import numpy as np
class Neuron:
def __init__(self, nInputs):
self.nInputs = nInputs + 1
#Generate random weights including bias neuron
self.weight = np.random.rand(self.nInputs,) | holandajunior/ExtremeLearningMachine | src/Neuron.py | Python | mit | 188 | [
"NEURON"
] | c7e0e7ca85ec5fcd3fdc276d5d860aac31f4ab61a765e37e694e00d552cb94df |
#!/usr/bin/env python
argv="/storage/home/mglee/source/THF/tophat-2.0.14.Linux_x86_64/tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /storage3/Project/mglee/Bt1index/hg19"
"""/storage/home/mglee/source/THF/tophat_ref
tophat-fusion-post
Created by Daehwan Kim on 2011-05-05.
Copyr... | demittsse/ChimerDB3 | LUAD/post.py | Python | apache-2.0 | 106,197 | [
"BLAST",
"Bowtie"
] | 6424958e2951c280dc1739845317bfdda55332886dd631565714592289cccb4d |
import time, re # time.sleep, re.split
import sys # some prints
from selenium import webdriver # for running the driver on websites
from datetime import datetime ... | tadatitam/info-flow-experiments | AdFisher/core/web/google_search.py | Python | gpl-3.0 | 4,726 | [
"VisIt"
] | aaa629f22d7486caeea85bc5c5249441dc1e75b45f4541e459fed648ce43d3e9 |
#!/usr/bin/env python
from ARMI_Lt import GeneSeekr
from Bio.Blast.Applications import NcbiblastnCommandline
__author__ = 'mike knowles'
class GeneSeeker(GeneSeekr):
def _blast(self, (fasta, db)):
self.yeah()
blastn = NcbiblastnCommandline('/usr/local/bin/blastn',
... | adamkoziol/pythonGeneSeekr | GeneSeekrOOP.py | Python | mit | 2,830 | [
"BLAST"
] | e40573d6676652f03ee59834f19894d3af84701003a76fac3105aaa06b933e9e |
# -*- coding: utf-8 -*-
from collections import namedtuple
from itertools import product
import os
import shutil
import tempfile
from mock import patch
from django.conf import settings
from django.contrib.auth.models import User
from django.core.files.base import File
from django.core.files.storage import FileSystemS... | sinergatis/pathagar | books/tests/test_permissions.py | Python | gpl-2.0 | 13,883 | [
"VisIt"
] | d4eeb854e50e35d3c5a564edca5c38c55847793671911ea964c149a2a5b7210b |
r"""``sphobjinv`` *CLI parser definition module*.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
15 Nov 2020
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
https://github.com/bsk... | bskinn/sphobjinv | src/sphobjinv/cli/parser.py | Python | mit | 11,911 | [
"Brian"
] | 9ebfc3409637960b40c6517d3838b50a761cf6cc2a77f860f8c8f0a2dda3af90 |
"""
Python package for tidal computations. Main components:
Tides - class of objects for tidal calculations. Provided with amplitudes and
phases it computes the tidal signal
harmonic_analysis - function to compute harmonic analysis on a
signal. Reconstructs amplitudes and phases of specified... | stephankramer/uptide | uptide/__init__.py | Python | lgpl-3.0 | 1,196 | [
"NetCDF"
] | c9e51b6f62184d579577cc54565eeec0e036adcd48ea4876c5a89cb040fbe2e1 |
"""
This class is being called whenever there is need to send data operation to Accounting or Monitoring, or both.
Created as replacement, or rather semplification, of the MonitoringReporter/gDataStoreClient usage for data operation to handle both cases.
"""
import DIRAC
from DIRAC import S_OK, gLogger
from DIRAC.Co... | DIRACGrid/DIRAC | src/DIRAC/MonitoringSystem/Client/DataOperationSender.py | Python | gpl-3.0 | 4,285 | [
"DIRAC"
] | 6da365cf26c68206a17102887f5114dd1615152f0ff3794d6e0e4a454ea1e9fd |
"""
Multi set model
"""
from renderers import VTKRenderController
from enaml.application import deferred_call
import vtk
class RenderViewController(VTKRenderController):
def __init__(self, view=None, bgColor=None, callbacks=None, actors=None):
"""
default init
"""
super(RenderVie... | viz4biz/PyDataNYC2015 | tutorial/multi_set_model.py | Python | apache-2.0 | 3,538 | [
"VTK"
] | a3921347d8550c3e20a5d14510567f7cdfdc70c37d7593308a2c18ca95afd51a |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/soffice/speech_generator.py | Python | gpl-3.0 | 18,953 | [
"ORCA"
] | 9cb32091d9835352e2f9d5732cdecaa6c237909f0f0200c0ff358b56efe99b1a |
#!/usr/bin/env python
# Copyright 2014-2019 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/scf/ghf.py | Python | apache-2.0 | 21,143 | [
"PySCF"
] | a291957479e9ae5c4a5af0d03efe936f9a51a7a3ee839493fb9ba435a6688135 |
import numpy as np
import matplotlib.pyplot as plt
from tilitools.profiler import print_profiles
from tilitools.ssad_convex import ConvexSSAD
from tilitools.lp_mkl_wrapper import MKLWrapper
from tilitools.utils_kernel import get_kernel, center_kernel, normalize_kernel
if __name__ == '__main__':
"""
MKL is a ... | nicococo/tilitools | scripts/exm_mkl.py | Python | mit | 4,072 | [
"Gaussian"
] | 077106e6127fa61fa2b23dcd2f213ae357fba1b48c93a0fc8d70d062d0a83f37 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('test_app', '0001_initial'),
]
operations = [
migrations.CreateModel(
name='TestInlineModel',
fields=... | benzkji/django-formfieldstash | formfieldstash/tests/test_app/migrations/0002_auto_20160714_0808.py | Python | mit | 3,385 | [
"Octopus"
] | e59ed41cadc63165e079c7ac0819e4a4c66801a97cf3fdbd9bf3ce42f4e9bf73 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | xsm110/Apache-Beam | sdks/python/apache_beam/runners/runner.py | Python | apache-2.0 | 14,562 | [
"VisIt"
] | 6f173adf7eb6fa11b29666dc81883af3510c02974f41329bb184f84cf2ba0d1a |
import threading
import functools
from DIRAC.Core.Utilities.DIRACSingleton import DIRACSingleton
class ThreadConfig( threading.local ):
__metaclass__ = DIRACSingleton
def __init__( self ):
self.reset()
def reset( self ):
self.__DN = False
self.__group = False
self.__deco = False
self.__set... | Sbalbp/DIRAC | Core/DISET/ThreadConfig.py | Python | gpl-3.0 | 1,439 | [
"DIRAC"
] | d2573633ef86f8d60694db5af968ac019e7b054477c55b48305554aaae557776 |
# ----------------------------------------
# USAGE:
# ----------------------------------------
# python res_res_correlation.py config_file
# ----------------------------------------
# PREAMBLE:
# ----------------------------------------
import sys
import numpy as np
from numpy.linalg import *
import MDAnalysis
from ... | rbdavid/DENV-NS3h | Correlation_analysis/res_res_correlation.py | Python | gpl-3.0 | 13,303 | [
"MDAnalysis"
] | 1bc15ce5e1625ee4ece1ba34d26d3ebca61baf49d5598829d73e02b6e7586896 |
""" DIRAC FileCatalog Security Manager mix-in class with full access checks
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.SecurityManager.Sec... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/SecurityManager/FullSecurityManager.py | Python | gpl-3.0 | 2,411 | [
"DIRAC"
] | aad944035e4acffc7b7d2d14ecbbd43f3b5b3f09eaa32aae85dabda6748503b5 |
#!/usr/bin/env python
helptext='''This script will use bwa and samtools to determine the depth of coverage
across a sequence generated by HybPiper. Reads will be mapped against the coding
sequence. The coding sequence will be aligned to the reference gene, and depth estimates
will be relative to the reference.
By de... | mossmatters/HybPiper | depth_calculator.py | Python | gpl-3.0 | 6,095 | [
"BWA"
] | baaeebe76e2fb35044a41579977a39e61e43917e41d2701a2e17232df91b3ff4 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAffydata(RPackage):
"""Affymetrix Data for Demonstration Purpose
Example datasets... | LLNL/spack | var/spack/repos/builtin/packages/r-affydata/package.py | Python | lgpl-2.1 | 1,138 | [
"Bioconductor"
] | c7103daa80f68d5c777ae762fb91af749d079c76fb550c645adccbdecae7c282 |
### ====================================================================
### Python-file
### author: Ethan T. Coon
### filename: solution_reader.py
### version:
### created: 25 January 2011
### on: 10:53:33 MST
### last modified: 30 March 2011
###... | ecoon/Taxila-LBM | src/testing/solution_reader.py | Python | lgpl-2.1 | 5,524 | [
"VTK"
] | 47f21f19fa4c2410f5ebaae7ac26ef3ae4a47993bccaf5b7d979e06bc28a6fda |
#!/usr/bin/env python
# Copyright 2014-2019 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/prop/magnetizability/uhf.py | Python | apache-2.0 | 6,175 | [
"PySCF"
] | 0ab772f34a2c84204c52df325e7f5b29363b80764391c2059b5afc72279817fc |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/wrapper_autofrag.py | Python | gpl-2.0 | 5,232 | [
"Psi4"
] | 0706954ae413a6a1d734778904a4a2d9658e90c9f477db9f4a14a5357f06f047 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | ldirer/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 30,796 | [
"Gaussian"
] | 07f2e5ba44c8f8f111955bdfaf0fb879cdb550ecd78f1017d28a05c4e989e293 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A. Beauchamp
#
# MDTraj i... | tcmoore3/mdtraj | mdtraj/geometry/__init__.py | Python | lgpl-2.1 | 2,415 | [
"MDTraj"
] | f95791246ea2ef61b5ee1a3ea1d72802bc9427de117f310e83cd658f3ae3a902 |
r"""
Stokes equations for incompressible fluid flow.
This example demonstrates fields defined on subdomains as well as use of
periodic boundary conditions.
Find :math:`\ul{u}`, :math:`p` such that:
.. math::
\int_{Y_1 \cup Y_2} \nu\ \nabla \ul{v} : \nabla \ul{u}
- \int_{Y_1 \cup Y_2} p\ \nabla \cdot \ul{v}
... | RexFuzzle/sfepy | examples/navier_stokes/stokes.py | Python | bsd-3-clause | 4,420 | [
"VTK"
] | 4587ca94649f9ef2629d2d7b35c5a5c0f2f8a89a1a69629971ec24dfefec4872 |
#!/usr/bin/env python3
import argparse
import sys
import getpass
import shutil
import os
import zipfile
try:
import requests
except ImportError:
print("Python3 requests is not installed. Please use e.g. pip3 install requests")
sys.exit()
BASE_URL = "{{ base_url }}/"
def login(user, password):
"""Lo... | bit-bots/imagetagger | src/imagetagger/images/templates/images/download.py | Python | mit | 8,382 | [
"VisIt"
] | ed488ca218970e7610f1dd320b7cb92dd8aad81c5b69b3decad1c3b72bfdc91e |
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input dimension
of D, a hidden dimension of H, and perform classification over C classes.
The architecu... | machinelearningnanodegree/stanford-cs231 | solutions/kvn219/assignment2/cs231n/classifiers/fc_net.py | Python | mit | 17,858 | [
"Gaussian"
] | d6ba20467a4f1406e12653ade2c878c8a415ae170aecf9e5d60a697612b2602d |
from __future__ import print_function
from intermol.forces.forcedata import *
from intermol.forces.forcefunctions import *
"""To add another bonded force interacton, add to forcedata.py in one of the
existing categories:
1. add it to the appropriate forcelist
2 define the parameters
3. define the units for the para... | shirtsgroup/InterMol | intermol/forces/make_forces.py | Python | mit | 8,894 | [
"Gromacs"
] | a61089a93057084765e867375a1d58b6ae760dac7d17c6a22b3a781c034b6833 |
# -*- coding: utf-8 -*-
import logging
from tipfy import (abort, app, get_config, HTTPException, import_string, local,
request, RequestHandler, Response, Tipfy, url_for)
from tipfy.ext import i18n
from tipfy.ext import jinja2
from tipfy.ext import session
from tipfy.ext import auth
from tipfy.ext.auth import acl
... | ac001/moe | project/app/moe/base/handlers.py | Python | bsd-3-clause | 4,709 | [
"MOE"
] | 2cdada3f32ea4754e5743999d81c521e410f62483633f0d5b685ffa432e6f217 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkHierarchicalDataSetGeometryFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manag... | nagyistoce/devide | modules/vtk_basic/vtkHierarchicalDataSetGeometryFilter.py | Python | bsd-3-clause | 536 | [
"VTK"
] | db933741576bab27e4c6b82353b9653aed3254c8dc7dbe6d0938a54711ae938e |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/convolution/matching.py | Python | agpl-3.0 | 3,283 | [
"Gaussian"
] | 18479b7cb4fa9e1761640af39da5d01cd7b52bc21c917e8794ea680412466951 |
#Internet Archive ROM Launcher
#Zach Morris
#https://github.com/zach-morris/plugin.program.iarl
import os, sys, re, shutil, json, zipfile, urllib, glob, difflib
import xbmc, xbmcaddon, xbmcvfs, xbmcgui
# from resources.lib.xbmcswift2b import xbmcgui
from descriptionparserfactory import *
from webutils import ... | zach-morris/plugin.program.iarl | resources/lib/util.py | Python | gpl-2.0 | 206,429 | [
"ADF",
"Jaguar"
] | ba8ab4d885e1260c6f651e0792b705bf2160dde97b71e97b2fc5b645d29c25a9 |
# Copyright (c) 2015 Tobias Neumann, Philipp Rescheneder.
#
# This file is part of Slamdunk.
#
# Slamdunk is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your o... | t-neumann/slamdunk | setup.py | Python | agpl-3.0 | 6,388 | [
"Biopython",
"pysam"
] | d10d718c8f22c2dc2dd3cb1ae31c9236b7879236d718230d90aaf80a4207b56a |
"""
FEniCS tutorial demo program: Poisson equation with Dirichlet conditions.
Test problem is chosen to give an exact solution at all nodes of the mesh.
-Laplace(u) = f in the unit square
u = u_D on the boundary
u_D = 1 + x^2 + 2y^2
f = -6
"""
from __future__ import print_function
from dolfin i... | jintonic/gefica | examples/fenics/minippc.py | Python | mit | 6,322 | [
"VTK"
] | a049ec497c37685b20091641a95fa174874b036950f9b36132f634d2708d7ce2 |
#=====================================================================================================================================
#Copyright
#=====================================================================================================================================
#Copyright (C) 2014 Alexander Blaessle... | mueller-lab/PyFRAP | pyfrp/modules/pyfrp_vtk_module.py | Python | gpl-3.0 | 18,585 | [
"VTK"
] | a286b313f5a04280680216540a48c8a52a544ada89fcb3a59a863118fac667ca |
############################################################################
##
## Copyright (C) 2006-2010 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software F... | VisTrails/vistrails-contrib-legacy | vtksnl/hasher.py | Python | bsd-3-clause | 1,769 | [
"VTK"
] | 8b56a5b24288af5b30ef75c24e8d267e51f57b8f3f7d6f707173e9eeafb2ae83 |
########################################################################
# File: FTSManagerHandler.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/08 14:24:08
########################################################################
"""
:mod: FTSManagerHandler
.. module: FTSManagerHandler
:synopsis: handl... | vmendez/DIRAC | DataManagementSystem/Service/FTSManagerHandler.py | Python | gpl-3.0 | 18,109 | [
"DIRAC"
] | 1b8d76b5eda8ac3953b29ef13bd05a34f536396b5c796a8c66f41bd17773da3d |
"""pytest configuration file for Z2Pack tests."""
# pylint: disable=protected-access,redefined-outer-name,unused-argument
import os
import json
import logging
import operator
from collections.abc import Iterable
import pytest
from ctrl_base_tester import test_ctrl_base # pylint: disable=unused-import
import z2pack
... | Z2PackDev/Z2Pack | tests/conftest.py | Python | gpl-3.0 | 4,196 | [
"ABINIT",
"Quantum ESPRESSO",
"VASP"
] | 1a9cd2bcab2aeceb39f6632beddad7596e00858c5c124a0cb782f9341db8ae6e |
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import absolute_import
from __future__ import division
from threedi_wms.threedi import config
from threedi_wms.threedi import tasks
from threedi_wms.threedi import utils
from gislib import rasters
fr... | nens/threedi-wms | threedi_wms/threedi/responses.py | Python | gpl-3.0 | 51,416 | [
"NetCDF"
] | ac7009f7175ae1582cf536e6269d61406cd4f4b4deceec6396d42397308fad02 |
#!/usr/bin/env python
from setuptools import setup
# Modified from http://stackoverflow.com/questions/2058802/
# how-can-i-get-the-version-defined-in-setup-py-setuptools-in-my-package
def version():
import os
import re
init = os.path.join('dark', '__init__.py')
with open(init) as fp:
initDat... | bamueh/dark-matter | setup.py | Python | mit | 3,733 | [
"BLAST",
"Biopython"
] | 8bff87533b5edb6b0a3232264f1d3c471a67cf46e5105f10edfd6f5eb7314494 |
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | andela-angene/coursebuilder-core | coursebuilder/common/schema_fields.py | Python | apache-2.0 | 28,167 | [
"VisIt"
] | 88a1c6d2f6fd4d54be699b0479506f603a0c2ffd029a4ae33e71c37edde45cda |
# $HeadURL$
__RCSID__ = "$Id$"
import time
import copy
import os.path
import GSI
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Utilities.Network import checkHostsMatch
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.Core.Security import Locations
from DIRAC.Core.Security.X50... | calancha/DIRAC | Core/DISET/private/Transports/SSL/SocketInfo.py | Python | gpl-3.0 | 13,035 | [
"DIRAC"
] | 90589203cc3920e3d674b385bd3870c6e79c5524afa4d839313e974bbe674e35 |
from pytest_bdd import scenario, given, when, then
@scenario('template.feature', 'Publishing the article')
def test_publish():
pass
@given("I'm an author user")
def author_user(auth, author):
auth['user'] = author.user
@given('I have an article')
def article(author):
return create_test_article(author=author)... | cappetta/SecDevOps-Toolkit | tooling/slack/bootstrap/template.py | Python | mit | 947 | [
"VisIt"
] | 64ac8dbf8b3ada258beeef869dd7fcee352bb641adfed4ef29374456d365835f |
#!/usr/bin/env python
import datetime
import subprocess
import pysam
import os
import sys
from collections import Counter
from shutil import move
from re import sub
def now():
return str(datetime.datetime.now())
def majorbase(basepile):
"""returns tuple: (major base, count)
"""
return Counter(bas... | MischaLundberg/bamsurgeon | bamsurgeon/common.py | Python | mit | 4,487 | [
"pysam"
] | 30e48acdd70ed3330b97d2e97c7bbcf103954ede50ca7c5c29c1a756793322c0 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
from functools import reduce
import unittest
import numpy
from pyscf import lib
from pyscf import gto
from pyscf import scf
from pyscf import mcscf
from pyscf import ao2mo
from pyscf import fci
from pyscf.tools import molden
from pyscf.grad import ... | sunqm/pyscf | pyscf/grad/test/test_casscf.py | Python | apache-2.0 | 10,469 | [
"PySCF"
] | fbafe06e118e1e35bc548de6e00cc0174411bcdc66d2fe11e1c2723d88aad4dd |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | lidakanari/NeuroM | neurom/view/_dendrogram.py | Python | bsd-3-clause | 11,020 | [
"NEURON"
] | 2cbe0d7e39bf774d7b54369fcda0d60b06f1b97fc38eb2b26b4cfb733f16fa12 |
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | thonkify/thonkify | src/lib/oauth2client/tools.py | Python | mit | 9,144 | [
"VisIt"
] | c40fa9273b13b43489644be69fc6dc9f6a096086402d194f7d8bf31159e9be59 |
# Copyright (C) 2008 Novell, Inc.
# Written by Brian G. Merrell <bgmerrell@novell.com>
# THIS FILE IS LICENSED UNDER THE MIT LICENSE
from tempfile import mkstemp
from shutil import move, rmtree
from os import remove, close, rename, path, listdir
from subprocess import Popen
import re
LZMA_PATTERN = 'chromium\.[0-9]+... | bgmerrell/novellium | replace.py | Python | mit | 3,003 | [
"Brian"
] | 8389f1c262b0cb6c684b7fbbabf37b4f78f3c705d1dff2908f7a70584e4c6e5d |
""" pylase Example: Calculate phase-matching and walk-off angles of LBO for SHG
In this pylase example we use the materials module to calculate the
phase-matching angles and the corresponding walk-off angle for second harmonic
generation in lithium triborate with a fundamental wavelength of 1064 nm.
The calculation a... | chrisark7/pylase | Examples/shg_lbo.py | Python | gpl-3.0 | 1,601 | [
"CRYSTAL"
] | 96e8f946caa529e7cfbcb12cc0bfb60e7cd4f798c713097195473008ca843264 |
import collections
import logging
# import multiprocessing
import time
# import numpy
import math
from svviz.multiprocessor import Multiprocessor
from svviz.utilities import reverseComp, Locus
from svviz.alignment import Alignment, AlignmentSet, AlignmentSetCollection
from svviz.pairfinder import PairFinder
from svviz... | gatoravi/svviz | src/svviz/remap.py | Python | mit | 8,794 | [
"pysam"
] | deefa03d4cb9d237074e29f9d44cb00ffd249474ed9ad26eee12aa54fb49c507 |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
except ImportError:
raise ImportError("Cannot load either PyQt or PySide")
import vtk
from vtk.util.... | amburan/moose | gui/vtk/ExodusRenderWidget.py | Python | lgpl-2.1 | 5,095 | [
"VTK"
] | 24c95bb67dc67fa3fd82a0b74d7b5e8564b22e853a8454149c53a4ad4fcd3403 |
"""Factor Analysis.
A latent linear variable model.
FactorAnalysis is similar to probabilistic PCA implemented by PCA.score
While PCA assumes Gaussian noise with the same variance for each
feature, the FactorAnalysis model assumes different variances for
each of them.
This implementation is based on David Barber's B... | yanlend/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 11,948 | [
"Gaussian"
] | 7b89c0a86710c1824555b5933eddb5c81b1f1940a04b46a443fdd3a4b054c32e |
from __future__ import print_function
import numpy as np
import mdtraj as md
from mdtraj.testing import eq
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS, PPM, SHIFTX2
from mdtraj.utils import six
import pytest
import os
@pytest.mark.skipif(not find_executable(SPARTA_PLUS),
rea... | leeping/mdtraj | tests/test_nmr.py | Python | lgpl-2.1 | 3,466 | [
"MDTraj"
] | a12ba60a2cf7d8dac461032f0d54f78ff9d06d272c8d80aadcced3946ed6a557 |
from __future__ import print_function
from ImageD11.columnfile import columnfile
from ImageD11.parameters import read_par_file
from ImageD11.unitcell import unitcell_from_parameters
from ImageD11.grain import read_grain_file, write_grain_file
from ImageD11 import transform
import numpy as np
# idea:
# Rota... | jonwright/ImageD11 | ImageD11/rotdex.py | Python | gpl-2.0 | 7,650 | [
"CRYSTAL"
] | e81c3927df055f7b28df2a8c13796aeced43150a3d05978a46ab9aa9f0e0d548 |
#!/usr/bin/env python
import vtk
def main():
fileName = get_program_parameters()
colors = vtk.vtkNamedColors()
# Read the CT data of the human head.
reader = vtk.vtkMetaImageReader()
reader.SetFileName(fileName)
reader.Update()
cast = vtk.vtkImageCast()
cast.SetInputConnection(read... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/ImageGradient.py | Python | apache-2.0 | 3,398 | [
"VTK"
] | d0e2f916122ad0136f73776e1beb12bafed03a9e4f983f2c3871106f34cbee3b |
"""This module contains the tools needed for satellite detection
within an ACS/WFC image as published in
`ACS ISR 2016-01 <http://www.stsci.edu/hst/acs/documents/isrs/isr1601.pdf>`_.
.. note::
Only tested for ACS/WFC FLT and FLC images, but it should
theoretically work for any instrument.
Requires skimag... | jhunkeler/acstools | acstools/satdet.py | Python | bsd-3-clause | 36,787 | [
"Gaussian"
] | 9eea431ba1bf5f862b953fc59e4484be97a11f6ebc0553e69a2597cb10371f84 |
"""Effective medium theory potential."""
from math import sqrt, exp, log, pi
import numpy as np
import sys
from ase.data import chemical_symbols
from ase.units import Bohr
from ase.calculators.neighborlist import NeighborList
from ase.calculators.calculator import Calculator
parameters = {
# E0 s0 ... | conwayje/ase-python | ase/calculators/emt.py | Python | gpl-2.0 | 7,231 | [
"ASE"
] | 7a0a59bd101daa69e42ba2b8e44ec92e8dd4a05f0da452be01325ac0c353f954 |
# -*- coding: utf-8 -*-
from __future__ import print_function
import collections
from itertools import chain
import json
import logging
import os
import pathlib
import pykwalify.core
import SimpleITK as sitk
import six
from radiomics import generalinfo, getFeatureClasses, getImageTypes, getParameterValidationFiles, ... | Radiomics/pyradiomics | radiomics/featureextractor.py | Python | bsd-3-clause | 31,662 | [
"Gaussian"
] | 6759cc4779c32941098a7eeba1c7e64e0c52eef25e645f9dc3c46520efdecc73 |
from scipy import stats
import numpy as np
from numpy.testing import (assert_almost_equal, assert_,
assert_array_almost_equal, assert_array_almost_equal_nulp, assert_allclose)
import pytest
from pytest import raises as assert_raises
def test_kde_1d():
#some basic tests comparing to normal distribution
np.... | person142/scipy | scipy/stats/tests/test_kdeoth.py | Python | bsd-3-clause | 15,786 | [
"Gaussian"
] | 3ed973f1bd797c551a24c54ad3aaf223d8a39435e49efd4eab52acaed7b8f491 |
import copy
import sys
from django.apps import apps as django_apps
from django.utils.module_loading import import_module, module_has_submodule
class RegistryNotLoaded(Exception):
pass
class AlreadyRegisteredVisitSchedule(Exception):
pass
class SiteVisitScheduleError(Exception):
pass
class SiteVisitS... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/site_visit_schedules.py | Python | gpl-2.0 | 6,993 | [
"VisIt"
] | bd8987c6cbf53200141df0fad2246a1590850648c4fed87068342d5eb4a9247d |
# Python Siesta
#
# Copyright (c) 2008 Rafael Xavier de Souza
#
# Modified by Eric Busboom
#
# 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... | treyhunner/databundles | databundles/client/siesta.py | Python | bsd-3-clause | 10,700 | [
"SIESTA"
] | e21d3111901dd5148389c5eec2406ee7630507bb208aefe628d652be8f80cfa8 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | JulienMcJay/eclock | windows/Python27/Lib/random.py | Python | gpl-2.0 | 32,129 | [
"Gaussian"
] | 1d161a5d0e746b7582b6e26ffca99218d3a1aa70b663104d7439aa750232583b |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rabipanda/tensorflow | tensorflow/contrib/py2tf/converters/logical_expressions.py | Python | apache-2.0 | 2,559 | [
"VisIt"
] | bb342dbb7387fb06346d7b787598a6c2af7ba62d1f8af54a7690b5be162f7db5 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | snerg/snerg/params.py | Python | apache-2.0 | 7,913 | [
"Gaussian"
] | 5e2b11461c9d7d7e24e365f5c87d6b96ef36721d6c9f61f8724becd3b8e3fe17 |
#!/usr/bin/env python
########################################################################
# File : dirac-proxy-info.py
# Author : Adrian Casajus
########################################################################
"""
Print information about the current proxy.
Example:
$ dirac-proxy-info
subject ... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_proxy_info.py | Python | gpl-3.0 | 6,734 | [
"DIRAC"
] | ffbc07d51e4eb1f460ecf6bf678517091a885287671328c1e3337998265714ee |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
# pylint: disable=E1111
import unittest
import json
import requests
import datetime
import ddt
import random
from urllib import quote
from django.test import TestCase
from nose.tools import raises
from mock import Mock, patch
from django.conf import... | kuiwei/kuiwei | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 114,894 | [
"VisIt"
] | c549cf2d45bbfcfbc3eab1da6099a0560d46dd401837a7866ff3d7b47c3101b1 |
#!/usr/bin/env python
#
# pKarun - scripts for running pKa calculations
# Copyright (C) 2010 Jens Erik Nielsen
#
# 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, ... | dmnfarrell/peat | pKarun/pKarun_base.py | Python | mit | 38,041 | [
"CRYSTAL"
] | d398459cede7bae7c2c1d4abcfa1d0867c7256accf5a3cc1c81090c41899d6e0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | dgasmith/psi4 | psi4/driver/driver_nbody.py | Python | lgpl-3.0 | 34,436 | [
"Psi4"
] | 8c9ff9213c394b193055e8f01ea35455a4cb30a88927bf613fb4a0573b0d7128 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0011_ao_eval_nao.py | Python | apache-2.0 | 1,826 | [
"PySCF"
] | 040279d833a12b2401b6e84631cf83f9baf67f6c060512fe6c558bd7bb9ff506 |
#!/usr/bin/env python
"""
Given an API, load all the forms, count up their non-NA values, and mark their missing/complete status.
"""
import argparse
import pandas as pd
import pdb
import redcap as rc
import sys
from load_utils import load_form_with_primary_key
from qa_utils import chunked_form_export, get_items_match... | sibis-platform/ncanda-data-integration | scripts/qc/make_redcap_inventory.py | Python | bsd-3-clause | 8,361 | [
"VisIt"
] | 9e60d76b37d0a8a0f91f687a4aa31d0026963fe33cc4e0deef6491c66fab304f |
from datetime import date
import datetime
from django.contrib.auth.models import User
from django.test import TestCase
from pagetree.models import Hierarchy, Section, UserPageVisit
from pagetree.tests.factories import HierarchyFactory, ModuleFactory
from factories import SchoolGroupFactory
from nepi.main.models impor... | coati-00/nepi | nepi/main/tests/test_models.py | Python | gpl-2.0 | 11,699 | [
"VisIt"
] | fbace45e6c57c71c5517416178188bab222479d453ef31cdd6a43b3d38950137 |
import MDAnalysis
import numpy as np
try:
from MDAnalysisTests.datafiles import (GRO, TPR, XTC,
PSF, DCD,
TRZ_psf, TRZ)
from MDAnalysis.exceptions import NoDataError
except:
pass
class AtomGroupMethodsBench(object):
... | MDAnalysis/mdanalysis | benchmarks/benchmarks/ag_methods.py | Python | gpl-2.0 | 12,035 | [
"MDAnalysis"
] | de7ca4b6d68e8a30424a2e77f3c863e8c53a9121d18c7b2a611d7d191e54fa5b |
from distutils.core import setup
from glob import glob
from os.path import join
import os
import sys
long_description = """\
Jacapo is a python package providing an interface to Dacapo that
is compatible with the open source Atomic Simulation
Environment in the python scripting language."""
if sys.version_info < (2,... | grhawk/ASE | tools/ase/calculators/jacapo/setup.py | Python | gpl-2.0 | 977 | [
"ASE"
] | 54fed162fb4dc4b9defc9527f6e9ff62da180c24c34aa8193538764d9a51e2df |
__author__ = "HarshaRani"
__credits__ = ["Upi Lab"]
__license__ = "GPL3"
__version__ = "1.0.0"
__maintainer__ = "HarshaRani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
__updated__ = "Oct 27 2018"
'''
2018
Oct 27 : When group is moved within another grou... | BhallaLab/moose | moose-gui/plugins/kkitViewcontrol.py | Python | gpl-3.0 | 75,008 | [
"MOOSE"
] | 844eae3862e5aeda21054accf516516a7299d275e25c14db014108edc44dbf4e |
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