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"""
Acceptance tests for Studio related to the split_test module.
"""
import math
from bok_choy.promise import Promise
from selenium.webdriver.support.ui import Select
from base_studio_test import StudioCourseTest
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.... | jolyonb/edx-platform | common/test/acceptance/tests/studio/test_studio_split_test.py | Python | agpl-3.0 | 47,048 | [
"VisIt"
] | 30859828626782b961ccfdf418557632918ae60a51b2d0fc4fbd16d5dacb7027 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/lbgpu_remove_total_momentum.py | Python | gpl-3.0 | 2,247 | [
"ESPResSo"
] | 2a34fe51d993211acf77a5e20c477e9a1f55e950ac6bd3c9f8e23102d74d5f00 |
# This file is part of PyImgur.
# PyImgur 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.
# PyImgur is distributed in the hope that i... | Damgaard/PyImgur | pyimgur/__init__.py | Python | gpl-3.0 | 64,541 | [
"VisIt"
] | 3e525fd778436c47e0148682302a81f5b28c323e7985126742eefb857f1cc2ca |
# !/usr/bin/env python
import sys
sys.path.append('/opt/lib/python2.7/site-packages/')
import math
import numpy as np
import pylab
import nest
import nest.raster_plot
import nest.topology as tp
import logging as log
from network_params import *
from sim_params import *
from user_params import *
# Implementation of ... | synergetics/potjans_2014 | microcircuit.py | Python | mit | 15,865 | [
"NEURON"
] | 5eca087cc4484bd21cc43a5c65c3ff565babfeaad73e16a3f23d76efdcaf5de1 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2016 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | crisely09/horton | horton/io/cp2k.py | Python | gpl-3.0 | 14,969 | [
"CP2K",
"Gaussian"
] | b46365eaefe5871acc9852c9d2b97f5e4fe916adfbfc3065169d50d27323e7b5 |
from typing import Any, Optional, Tuple
import numpy as np
import pytest
import tensorflow as tf
import gpflow
from gpflow import set_trainable
from gpflow.config import default_float
from gpflow.kernels import Kernel, SquaredExponential
from gpflow.likelihoods import Gaussian, Likelihood
from gpflow.models import GP... | GPflow/GPflow | tests/gpflow/optimizers/test_natural_gradient.py | Python | apache-2.0 | 5,685 | [
"Gaussian"
] | d5a86f6a9de252258adec9d634fa8f37ce93273ff42da05784eff23322848b6f |
import sys,os,unittest
from ctypes import *
from lammps import lammps, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR
try:
import numpy
NUMPY_INSTALLED = True
except ImportError:
NUMPY_INSTALLED = False
# add timestep dependent force
def callback_one(lmp, ntimestep, nlocal, tag, x, f):
lmp.fix_external_set_virial_... | akohlmey/lammps | unittest/python/python-fix-external.py | Python | gpl-2.0 | 7,469 | [
"LAMMPS"
] | 2fe6fef824ebee315776deb206bbd8d3a664eab4928d278ec8d2e74040220af8 |
'''
* Copyright (C) 2017 Music Technology Group - Universitat Pompeu Fabra
*
* This file is part of jingjuSingingPhraseMatching
*
* pypYIN 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 (FSF), e... | ronggong/jingjuSingingPhraseMatching | phoneticSimilarity/generalProcess.py | Python | agpl-3.0 | 14,591 | [
"Gaussian"
] | 376ce2274d289d3ff292c8dfa1aa49bb847d037ba10383bc85da1db1ad96de75 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/errors.py | Python | lgpl-3.0 | 832 | [
"VisIt"
] | 92fccb9281de3ec5639d7a6980bf878ef03f6c8a772b9494606ea4c88950f171 |
# Module wordnet.py
#
# Original author: Oliver Steele <steele@osteele.com>
# Project Page: http://sourceforge.net/projects/pywordnet
#
# Copyright (c) 1998-2004 by Oliver Steele. Use is permitted under
# the Artistic License
# <http://www.opensource.org/licenses/artistic-license.html>
"""Utility functions to use wit... | textioHQ/pattern | pattern_text/en/wordnet/pywordnet/wntools.py | Python | bsd-3-clause | 12,405 | [
"Amber"
] | e01d58cd4e48373ef08600e26278ada1cabf3c21bfda5e821c19e88496dbbd47 |
#!/usr/bin/env python
import Pyro.core
import Pyro.naming
import string
import MySQLdb
import time
import random
import threading
try:
from phamerator import *
except:
import sys, os
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
import alignmentDatabase
from errorHandler import *
import db_conf
... | byuphamerator/phamerator-dev | phamerator/phamServer_InnoDB.py | Python | gpl-2.0 | 16,847 | [
"BLAST"
] | e9112117b38111d8c77b29813a9c331740dd4ea3a8da214f3e8d910920e062f2 |
# -*- coding: utf-8 -*-
# This file is part of AudioLazy, the signal processing Python package.
# Copyright (C) 2012-2014 Danilo de Jesus da Silva Bellini
#
# AudioLazy 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 Foun... | antiface/audiolazy | audiolazy/lazy_synth.py | Python | gpl-3.0 | 17,869 | [
"Gaussian"
] | 478e5aa4761115661b7d423a5a7b517fe413e5f6515801622b982afd7d6ff599 |
import numpy as np
from itertools import izip
from multiprocessing import Pool
from scipy.linalg import inv
import emcee as mc
from pearce.mocks.kittens import TrainingBox
from collections import OrderedDict
import h5py
def lnprior(theta, param_names, param_bounds, *args):
"""
Prior for an MCMC. Default is to... | mclaughlin6464/pearce | bin/vdf_mcmc/hod_recovery_test.py | Python | mit | 8,063 | [
"Gaussian"
] | ed4f96cb83cfc6218bcdee51e0b17a321f82a3b600644a06c736a45bbc0866c5 |
../../../../../../../share/pyshared/orca/scripts/apps/Banshee/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Banshee/__init__.py | Python | gpl-3.0 | 73 | [
"ORCA"
] | b9b084693a0710e1c5003a711a5c0cb3a65ccf5c41bab0d234b68b9895f33af8 |
# -*- coding: utf-8 -*-
import base64
import datetime
import json
import time
import mock
from nose.tools import eq_, ok_
from nose.plugins.attrib import attr
from pyquery import PyQuery as pq
from urlparse import urlparse
from django.conf import settings
from django.contrib.sites.models import Site
from django.core... | cindyyu/kuma | kuma/wiki/tests/test_views.py | Python | mpl-2.0 | 167,438 | [
"VisIt"
] | 752a693ca68f6bd83a3e48ec2d2c880b9b41919fa64508bb9ac622aeef9db74a |
"""
Module holds JMX handlers implementations
Copyright 2017 BlazeMeter 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 appli... | greyfenrir/taurus | bzt/jmx/tools.py | Python | apache-2.0 | 30,351 | [
"Gaussian",
"VisIt"
] | f3eed78b3814bfdd0062a09e1a10f114d06934d2270c9655d7938b8444c82b5c |
from __future__ import print_function
# Copyright 2008, 2009
# CAMd (see accompanying license files for details).
from __future__ import print_function
import sys
from optparse import OptionParser
import ase.gui.i18n
from gettext import gettext as _
# Grrr, older versions (pre-python2.7) of optparse have a bug
# whic... | suttond/MODOI | ase/gui/ag.py | Python | lgpl-3.0 | 5,523 | [
"ASE"
] | 5a3486c814ba853eab75eb81387f0a62c613ad2c09b8c382a79e4f1c00a2864b |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c8064Smooth/Generate8064Centreline.py | Python | gpl-2.0 | 1,020 | [
"VTK"
] | dfac248af049118743b38d34428d31de63568aa411887c8e7ea0a0430aad27fc |
import numpy as np
from numpy.testing import (assert_equal, assert_almost_equal,
assert_array_almost_equal)
from skimage.filters._gabor import gabor_kernel, gabor_filter, _sigma_prefactor
def test_gabor_kernel_size():
sigma_x = 5
sigma_y = 10
# Sizes cut off at +/- three sigma ... | michaelpacer/scikit-image | skimage/filters/tests/test_gabor.py | Python | bsd-3-clause | 2,901 | [
"Gaussian"
] | b4dbe5ccc3e53d9c56950dc84a831a1428a11a6180dda5987e71a90c79a1eb04 |
import os
import numpy as np
import pandas as pd
import xarray as xr
from . import randint, randn, requires_dask
try:
import dask
import dask.multiprocessing
except ImportError:
pass
os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
class IOSingleNetCDF:
"""
A few examples that benchmark reading... | shoyer/xarray | asv_bench/benchmarks/dataset_io.py | Python | apache-2.0 | 14,824 | [
"NetCDF"
] | 70e84ffbedfa9cf7d752dc6c8ba1103bf215ae81d01251eb1b557c3232a04ed9 |
from setuptools import setup, find_packages
import bioframes
setup(
name = bioframes.__projectname__,
version = bioframes.__release__,
packages = find_packages(),
author = bioframes.__authors__,
author_email = bioframes.__authoremails__,
description = bioframes.__description__,
license = ... | VDBWRAIR/bioframes | setup.py | Python | gpl-2.0 | 552 | [
"Biopython"
] | e463cedc1f689566bc08dc4db8e57f5a55262a65ebff9782eddf27ffdd7fde1c |
import json,code
def make_original_json():
JSON_DATA_FILE = 'last_backup.json'
json_data = json.load(open(JSON_DATA_FILE))
data = {}
for d in json_data:
model = d['model'].split('.')[1]
pk = d['pk']
fields = d['fields']
fields['pk'] = pk
if model == 'client... | I-TECH-UW/mwachx | tools/make_json.py | Python | apache-2.0 | 1,621 | [
"VisIt"
] | 7ee7ee96f2cca7110de48ca277c215779d94927335a69f325f592d2c8392e741 |
# If this code is slow, I think some simple improvements can be made to greatly increase speed.
# For example, allocate all memory at the start of the function.
import sys
import numpy as np
from numpy.linalg import det
from scipy.signal import butter, lfilter
from copy import deepcopy
ANG = 1/1.889725989
##########... | bbusemeyer/busempyer | busempyer/cubetools.py | Python | gpl-2.0 | 14,521 | [
"CRYSTAL",
"Gaussian"
] | 0e9bf7cbb429660f6d06c26d251f3a8bb57d96629e5947493a3328634ac5cca5 |
""" DIRACAccountingCommand
The DIRACAccountingCommand class is a command class to
interrogate the DIRAC Accounting.
"""
# FIXME: NOT Usable ATM
# missing doNew, doCache, doMaster
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.JEncode import strToIntDict
from D... | ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/Command/DIRACAccountingCommand.py | Python | gpl-3.0 | 10,229 | [
"DIRAC"
] | 1ec1501d15d097cf25c68774b49dbf4047c891197efd940621dd5eb9e511b61b |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import json
import os.path
import random
import re
import traceback
from .common import InfoExtractor, SearchInfoExtractor
from ..compat import (
compat_chr,
compat_HTTPError,
compat_parse_qs,
compat_str,
compat_urllib_parse... | rg3/youtube-dl | youtube_dl/extractor/youtube.py | Python | unlicense | 142,967 | [
"ADF"
] | 450e3a31e37bbf846ab8390311f2cead3edaf26dc03b05ed0939c3c347e406b4 |
# mooseplots.py ---
#
# Filename: mooseplots.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Mon Jul 5 21:35:09 2010 (+0530)
# Version:
# Last-Updated: Fri Jun 17 12:39:59 2011 (+0530)
# By: Subhasis Ray
# Update #: 615
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#... | BhallaLab/moose-thalamocortical | pymoose/gui/qt/mooseplot.py | Python | lgpl-2.1 | 14,089 | [
"MOOSE"
] | 62e39ba18a63db411270803db5a4a35b7dd9627ebe3074224fee09dd8c029f63 |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | sn-amber/mylpp | src/plotview.py | Python | gpl-2.0 | 5,880 | [
"LAMMPS"
] | 9f1684ac32f44ae7da1b5aed4d3bd15299c9d888c3be8a2664fe5ade73a07988 |
#!/usr/bin/env python3
# Version 1.1
# Author Alexis Blanchet-Cohen
# Date: 09/06/2014
import argparse
import glob
import os
import os.path
import pandas
import subprocess
import util
# Read the command line arguments.
parser = argparse.ArgumentParser(description="Generates GATK RealignerTargetCreator scripts.")
par... | blancha/abcngspipelines | exomeseq/realignertargetcreator.py | Python | gpl-3.0 | 2,858 | [
"BWA"
] | 60317ccdb3cd49cc6b94fad1515a18c93137b8d02191cc86dbca6a50758b6587 |
"""
Inline-optimized Sheet classes
$Id$
"""
__version__='$Revision$'
import param
from topo.base.cf import MaskedCFIter
from topo.base.projection import NeighborhoodMask
from topo.misc.inlinec import inline,provide_unoptimized_equivalent,c_header
from topo.sheet.lissom import LISSOM
from topo.sheet.basic import comp... | jesuscript/topo-mpi | topo/sheet/optimized.py | Python | bsd-3-clause | 5,510 | [
"Gaussian"
] | 72ca9cbdc8d2dddd72558d3c2c6f380cd33a57f61b06b607384785426d4b9054 |
########################################################################
# $HeadURL$
########################################################################
""" NotificationDB class is a front-end to the Notifications database
"""
__RCSID__ = "$Id$"
import time
import types
from DIRAC import gConfig, gLogger, S_OK,... | sposs/DIRAC | FrameworkSystem/DB/NotificationDB.py | Python | gpl-3.0 | 34,490 | [
"DIRAC"
] | 1f6d6a5c74f510f87e9400bda3f99139b6602bf4c587a50f7bea0bffa488ecae |
r"""
Biot problem - deformable porous medium with the no-penetration boundary
condition on a boundary region enforced using Lagrange multipliers.
The non-penetration condition is enforced weakly using the Lagrange
multiplier :math:`\lambda`. There is also a rigid body movement
constraint imposed on the :math:`\Gamma_{... | RexFuzzle/sfepy | examples/multi_physics/biot_npbc_lagrange.py | Python | bsd-3-clause | 4,049 | [
"VTK"
] | 4d9510be66d9debe18282c9ddf8996855b7e0b7ec04fc8daf5e00f61a4b32953 |
#!/usr/bin/env python
'''
Purpose:
non-coding sequence retrieval surrounding a gene or sequence of interest
from large genomic scaffolds.
This script uses BLAST, so the exact location of the gene is not required.
Because there may be multiple matching HSPs (high scoring segment pairs)
produced by BLAST for each ge... | juswilliams/bioscripts | non-coding-retrieval/ncd_run.py | Python | gpl-3.0 | 8,656 | [
"BLAST",
"Biopython"
] | 4fbf7add048a65f9728733ffc50eb72338a50942f4b78c6e9f4e8fe638ade4bd |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/core/ui/maindisplay.py | Python | gpl-2.0 | 26,442 | [
"Brian"
] | 4439b4fa67ecde092b03e439696c1b9e5378605e5a696426a95a4d067ec33807 |
import pytest
import os
import glob
import tempfile
import filecmp
import numpy.testing.utils as nptu
from abipy.abio.input_tags import *
from abipy.abio.factories import dte_from_gsinput
from fireworks.core.rocket_launcher import rapidfire
from abiflows.fireworks.workflows.abinit_workflows import DteFWWorkflow
from a... | davidwaroquiers/abiflows | abiflows/fireworks/integration_tests/itest_dte.py | Python | gpl-2.0 | 6,183 | [
"ABINIT"
] | 8cca117bdc0545cf9418c91294147ef3363833ad104967a4d50d742bfb4bb8d6 |
"""
GWAS association graphing Galaxy Wrapper
Mark Einon <mark.einon@gmail.com>
"""
import optparse
import os
import subprocess
import sys
def __main__():
cmd = 'plot_assoc.R'
# Local args are options not passed on, but processed in this file
local_args = ['output', 'output_id', 'new_file_path', 'run_di... | einon/galaxy-tools | plink2/plot_assoc.py | Python | gpl-3.0 | 1,926 | [
"Galaxy"
] | 9c35a95fe53596c0499b28925cf00b458161a48a2be1b8e31c13512f5dee0c89 |
import functools
import json
import logging
import random
import re
import string # pylint: disable=W0402
import fnmatch
from textwrap import dedent
from external_auth.models import ExternalAuthMap
from external_auth.djangostore import DjangoOpenIDStore
from django.conf import settings
from django.contrib.auth ... | rationalAgent/edx-platform-custom | common/djangoapps/external_auth/views.py | Python | agpl-3.0 | 38,612 | [
"Brian"
] | 52172fc29d6030e00ade1150e8c4a2733a23ff81dba91274411c12e89af0b17e |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/hybpiper/package.py | Python | lgpl-2.1 | 2,426 | [
"BLAST",
"BWA",
"Biopython"
] | a45d3cd62a8f5a11ed4195a1e6efe8083c15af319a8ae3bdfc89aeafcab9d7ca |
""" GraphData encapsulates input data for the DIRAC Graphs plots
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import time
import datetime
import numpy
from matplotlib.da... | petricm/DIRAC | Core/Utilities/Graphs/GraphData.py | Python | gpl-3.0 | 17,727 | [
"DIRAC"
] | b450ebeab2a4f5ec00819f96af2080437378f036bad21724b990af869987ae17 |
"""Utilities used in the Kadenze Academy Course on Deep Learning w/ Tensorflow.
Creative Applications of Deep Learning w/ Tensorflow.
Kadenze, Inc.
Parag K. Mital
Copyright Parag K. Mital, June 2016.
"""
import matplotlib.pyplot as plt
import tensorflow as tf
import urllib
import numpy as np
import zipfile
import os
... | niazangels/CADL | session-2/libs/utils.py | Python | apache-2.0 | 10,004 | [
"Gaussian"
] | a987086c0767e9ff9a392cc398b2cbe014721b11cbfc68e8996b8e0674ba26b3 |
../../../../../../../share/pyshared/orca/scripts/apps/gnome-panel/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gnome-panel/script.py | Python | gpl-3.0 | 75 | [
"ORCA"
] | 11946c725b662b8b26b0d7d49624b5c079a8bc6e7b4442ce6568caad83303e66 |
# -*- coding: utf-8 -*-
# ---
# jupyter:
# jupytext:
# formats: ipynb,py:percent
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.2'
# jupytext_version: 1.2.3
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# --... | buzmakov/tomography_scripts | misc/reconstructor-v-2.1a.py | Python | mit | 36,458 | [
"Gaussian"
] | f285d49713b7b28e232d546f690b4e0232d6f8e6bf0efc6f07ef99d27d360329 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/learn/ray/tf/test_tf_ray_estimator.py | Python | apache-2.0 | 25,253 | [
"ORCA"
] | 42d5b50791b46dec717c23fe1ce1c4fd1e91e96738ccbe238e8e6d62c4a879c2 |
#! /usr/bin/env python
###############################################################################
# Copyright 2016 Adam Jackson
###############################################################################
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GN... | WMD-group/kgrid | kgrid/cli.py | Python | gpl-3.0 | 3,963 | [
"ASE",
"CASTEP",
"VASP"
] | 614bdf3421c3eb041dacc74e8e9f5a6562706e0621d095d85a7d855ac4fa252a |
# Copyright 2017 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 a... | jiaphuan/models | research/lfads/synth_data/synthetic_data_utils.py | Python | apache-2.0 | 11,355 | [
"Gaussian"
] | 97b42161864927645b86d40320f4f5aa89993f093a84e9a0228624aef86c51c5 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-pilot-summary
# Author : Stuart Paterson
########################################################################
from __future__ import print_function
__RCSID__ = "$Id$"
# pylint: disable=wrong-imp... | fstagni/DIRAC | Interfaces/scripts/dirac-admin-pilot-summary.py | Python | gpl-3.0 | 663 | [
"DIRAC"
] | 82e11cbed8e41ec5d9d4f3778ed0e3029b8aa21ad1902dfc3d2345aa7a320eb0 |
from abc import ABCMeta, abstractmethod
import pandas as pd
import numpy as np
from bids.variables import BIDSRunVariableCollection
from bids.utils import convert_JSON
def create_model_spec(collection, model):
kind = model.get('type', 'glm').lower()
SpecCls = {
'glm': GLMMSpec
}[kind]
return... | INCF/pybids | bids/analysis/model_spec.py | Python | mit | 11,942 | [
"Gaussian"
] | 172dc780e12dc266f73acff6bf5fd8a7d70d10f418daf1f551b048715c3363ec |
""" Basic unit tests for the Job API
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from os.path import dirname, join
import pytest
from six import StringIO
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Core.Utilities.ClassAd... | yujikato/DIRAC | src/DIRAC/Interfaces/API/test/Test_JobAPI.py | Python | gpl-3.0 | 2,970 | [
"DIRAC"
] | b4c3411c1746e1754cfbfd8068a3cce2a133f11f4e11b3d04c852338213c1dd2 |
from unittest import TestCase
from webob import Response
from webob.dec import wsgify
from maitai.prunecookies import PruneCookiesMiddleware
from .utils import FixedTestApp
@wsgify
def bare_app(req):
s = '\n'.join(['%s: %s' % (k, v)
for k, v in req.cookies.items()])
return Response(s)
... | storborg/maitai | maitai/tests/test_prunecookies.py | Python | mit | 2,184 | [
"MOE"
] | 766dd18d0ae3d66a5eab5aeeb398191839c80829fc2d6597cad71e5a2ed3ea5d |
"""
Read and write [fasta format](http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml)
"""
from itertools import groupby
class FastaReader(object):
"""
Read fasta files into tuples (header, seq).
"""
def __init__(self, file):
"""
Args:
file: The fasta file. Can either be a nam... | grst/microbio | microbio/formats/fasta.py | Python | mit | 2,049 | [
"BLAST"
] | 0210a0a6dd5ce95db8de7bba49634bc9d0fbeb422a07a6cdb2e8d0a33b8dc047 |
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.List import stringListToString, intListToString
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.FileManagerBase import FileManagerBase
class FileManagerFlat(FileManagerBase):
##########################################... | fstagni/DIRAC | DataManagementSystem/DB/FileCatalogComponents/FileManagerFlat.py | Python | gpl-3.0 | 13,782 | [
"DIRAC"
] | cbe095cde1e3c2b45f36b20e0a67d54a02cf763dbebd38fc1c6d4a13120e6101 |
#!/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/pbc/mp/__init__.py | Python | apache-2.0 | 1,289 | [
"PySCF"
] | 81ddc5d78ae48c09d9698357ca1c358b3697fdd122a8b8f3b057d72da0b7182f |
from unittest import skip
from datetime import date
import pytest
from . import GenericCalendarTest
from ..usa import (
UnitedStates,
Alabama, AlabamaBaldwinCounty, AlabamaMobileCounty, AlabamaPerryCounty,
Arkansas, Alaska, Arizona,
# California and others
California, CaliforniaEducation, Californ... | jaraco/calendra | calendra/tests/test_usa.py | Python | mit | 77,324 | [
"COLUMBUS"
] | d7d7cd8b29df335e7efa7e2380e02679e51a881eb55480278efbd8a3461d7c94 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_http_client,
compat_urllib_error,
compat_urllib_parse_urlp... | 0x7678/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 38,143 | [
"VisIt"
] | eff8e80f931e8167f9caf755995ec499017a4bc34c0e475b550a97e04fc674ec |
import logging
from kalliope import Utils, BrainLoader
from kalliope.core import NeuronModule
from kalliope.core.NeuronModule import MissingParameterException
logging.basicConfig()
logger = logging.getLogger("kalliope")
class Brain(NeuronModule):
def __init__(self, **kwargs):
super(Brain, self).__init_... | kalliope-project/kalliope | kalliope/neurons/brain/brain.py | Python | gpl-3.0 | 1,654 | [
"NEURON"
] | c0100dfe10fd6d64e50429b4eab3e53f5ced644efca8699416e0f3ae3c9dfaa7 |
#!/bin/env python
import inspect
import os
from collections import OrderedDict
"""
# shell
aws s3 ls s3://grizli-v1/Pipeline/j000200m5558/Prep/j000200m5558_visits.npy --request-payer requester
# Python
import boto3
s3 = boto3.resource('s3')
bkt = s3.Bucket('grizli-v1')
field = 'j000200m5558'
s3_file = '{0}_visits.np... | gbrammer/grizli | grizli/aws/aws_drizzler.py | Python | mit | 44,559 | [
"VisIt"
] | 93e6e2d2700de7aee371282fc58b93d7bd354a3b6b4270847303e30aadf50695 |
"""
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. module:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each univariate distribution is an insta... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/scipy/stats/__init__.py | Python | gpl-3.0 | 9,284 | [
"Gaussian"
] | 652141394d833d480cd345893b5813c22c21ddd4b43a06f57bfa5aa1162fe0dc |
import unittest
from bok_choy.web_app_test import WebAppTest
from pages import GitHubSearchPage, GitHubSearchResultsPage
class TestGitHub(WebAppTest):
"""
Tests for the GitHub site.
"""
def setUp(self):
"""
Instantiate the page object.
"""
super().setUp()
self.... | edx/bok-choy | docs/code/round_3/test_search.py | Python | apache-2.0 | 1,017 | [
"VisIt"
] | 97d3911d0ae969afa3f9369ea384132d6717f740a8a9689e39f439eef9016bb5 |
'''
Created on Apr 19, 2013
@author: bill
'''
import unittest
from pylab import *
from brian import *
import sys
sys.path.append('../../')
from MLI_PKJ_net import *
defaultclock.dt = .25*ms
class MLITest(unittest.TestCase):
def test_model_equivalency(self):
T = 200*msecond
# spike train mea... | blennon/MLI_PKJ_net | MLI_PKJ_net/tests/MLI_test.py | Python | mit | 1,768 | [
"Brian"
] | 283a62501a26dd9d79a13c6ae8380e280daf3c874dff2f4fd78a56f4fcc81bf0 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.StereoCapableWindowOn()
iren = vtk.vtkRenderWindowInte... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/EnSight/Testing/Python/EnSightBlow2Bin.py | Python | gpl-3.0 | 1,508 | [
"VTK"
] | d0af4e101782806b3a057dc5aaf67256dbb85db379a0b2a6b3e1ae791bd17d80 |
# Threshold functions
import os
import cv2
import math
import numpy as np
from matplotlib import pyplot as plt
from plantcv.plantcv import fatal_error
from plantcv.plantcv import params
from skimage.feature import greycomatrix, greycoprops
from scipy.ndimage import generic_filter
from plantcv.plantcv._debug import _de... | danforthcenter/plantcv | plantcv/plantcv/threshold/threshold_methods.py | Python | mit | 28,133 | [
"Gaussian"
] | 40cb99ea09aaa5639e374560e3f487e4e48345aac9298cc0eff36b936398c1b4 |
# $Id$
#
# Copyright (C) 2003-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | jandom/rdkit | rdkit/ML/UnitTestBuildComposite.py | Python | bsd-3-clause | 6,780 | [
"RDKit"
] | e030cd93f26e0176426071f68f0e4bc52185adc49c0f777198be4e0a21b8c9fc |
# ******************************************************************************
# pysimm.forcefield.charmm module
# ******************************************************************************
#
# ******************************************************************************
# License
# *****************************... | polysimtools/pysimm | pysimm/forcefield/charmm.py | Python | mit | 35,193 | [
"CHARMM",
"Gromacs"
] | a97b0396c218e2dda4c5f12e79c74860e1f3edb88208cfaaf75be97b25fdced0 |
#!/usr/bin/env python
# encoding: utf-8
"""
api.py
Created by Brian Whitman on 2010-06-16.
Copyright (c) 2010 The Echo Nest Corporation. All rights reserved.
"""
from __future__ import with_statement
import web
import fp
import re
try:
import json
except ImportError:
import simplejson as json
# Very simple... | hzlf/openbroadcast | website/apps/ep/API/api.py | Python | gpl-3.0 | 2,258 | [
"Brian"
] | 1decfac6bede59246af1cc3efc5d728d14e271414fc11c05727c88077b55dcbe |
from glob import glob
import fitsio
import sys
from astrometry.util.fits import *
from astrometry.util.file import *
from astrometry.util.starutil_numpy import *
from astrometry.libkd.spherematch import *
from collections import Counter
from legacypipe.oneblob import _select_model
from legacypipe.survey import wcs_for_... | legacysurvey/pipeline | py/legacyanalysis/fix-dup-data.py | Python | gpl-2.0 | 7,052 | [
"Galaxy"
] | e49cd23173c0f3ef974d50a0fdb8348e704f2d471c581d9fd9f07c42797f8615 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from monty.json import MSONable
import numpy as np
import warnings
from pymatgen.core.spectrum import Spectrum
from copy import deepcopy
from veidt.elsie.preprocessing import Preprocessing
from veidt.elsie import si... | materialsvirtuallab/veidt | veidt/elsie/spectra_similarity.py | Python | bsd-3-clause | 17,232 | [
"pymatgen"
] | 793b35c6eddcb249d44a4a395e9abeeb6780a2f705ca6fb2fad7aae0aa6458d9 |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | ryanmark/django-facebookconnect | facebookconnect/views.py | Python | gpl-3.0 | 13,397 | [
"Brian"
] | e9dc6636c09a821f7c1d5d8a2bd165f41c1dbc6e7594e8828308f99bbc9442b3 |
import os
import csv
import time
import json
import numpy as np
import logging as log
class Database():
""" Stores tables to respond to :meth:`API._feature_info`
Arguments
----------
path: str
The file path to store and access the database
_runtime: :class:`RUNTIME`
Gets stored as ... | Rhoana/butterfly | bfly/CoreLayer/DatabaseLayer/Database.py | Python | mit | 14,761 | [
"NEURON"
] | ce97ead7111a9ac055e90954f3aeae44ff325592d367506366008163819d19b8 |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO object to model a single database hit."""
from __future__ import print_fu... | zjuchenyuan/BioWeb | Lib/Bio/SearchIO/_model/hit.py | Python | mit | 16,260 | [
"BLAST",
"Biopython"
] | 3fc4534d824877ee956b4bf955274c17cfc205766636a54e3c5502eb37c9757c |
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework Foundation
#
# 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
... | alexandrul-ci/robotframework | src/robot/model/totalstatistics.py | Python | apache-2.0 | 2,319 | [
"VisIt"
] | ea0aef9579ab362a0f16a80faa2c01cf2e0f465be1f4470d4fed7adb477e67c0 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | testsuite/python/tabulated.py | Python | gpl-3.0 | 3,531 | [
"ESPResSo"
] | b580c6c6fec5413237667f5fcd07ae84491a297f2f00ffc21205fc8f0084df19 |
# -----------------------------------------------------------------------------
#
# Copyright (C) 2021 CERN & University of Surrey for the benefit of the
# BioDynaMo collaboration. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance w... | BioDynaMo/biodynamo | src/core/visualization/paraview/default_insitu_pipeline.py | Python | apache-2.0 | 13,744 | [
"ParaView",
"VTK"
] | b0a4ad51861000331d0f4e00a48f7f4a607f6f0fc46c6a951970b5df7c76fbd2 |
#!/usr/bin/env python
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2016, Numenta, Inc. Unless you have purchased from
# Numenta, Inc. a separate commercial license for this software code, the
# following terms and conditio... | marionleborgne/nupic.research | tests/nlp/integration/text_mapping_test.py | Python | agpl-3.0 | 10,290 | [
"NEURON"
] | 41daed32ecfd05e3fcad160fd57a1ecc3edc1c065468c2a32d5b09a1d5e38239 |
# coding: utf-8
"""Tools for the submission of Tasks."""
from __future__ import unicode_literals, division, print_function
import os
import time
import collections
import yaml
from six.moves import cStringIO
from datetime import timedelta
from monty.io import get_open_fds
from monty.string import boxed, is_string
fro... | yanikou19/pymatgen | pymatgen/io/abinitio/launcher.py | Python | mit | 29,690 | [
"ABINIT",
"pymatgen"
] | d41ff5d4f04e00267ac7f30728808b52e09165a477dd694a8b06b123041177e3 |
# pylint: disable=missing-docstring, useless-object-inheritance
from __future__ import print_function
from enum import Enum
class Aaaa(object): # [too-few-public-methods]
def __init__(self):
pass
def meth1(self):
print(self)
def _dontcount(self):
print(self)
# Don't emit for... | kczapla/pylint | pylint/test/functional/too_few_public_methods.py | Python | gpl-2.0 | 934 | [
"Octopus"
] | cc7b672e8ec23d6a0bfe1bb7dc4ab413d88e1f6c983a8da7e830044ac2f20d2f |
import rhomb
import reactivityModifier
import math
import log
import corr
import random
import os.path
import warnings
import numpy as np
from PIL import Image
from PIL import ImageDraw
class Kagome():
"""Creates a two-dimensional Kagome lattice and all tools for drawing on it."""
def deprecated(func):
... | k-eks/AceOfDiamonds | kagome_lattice.py | Python | gpl-3.0 | 17,964 | [
"CRYSTAL"
] | c9537f6c2b9f289952449149624fde9a60c794b349c879c52137607a32fd5782 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/rigid_bond.py | Python | gpl-3.0 | 2,148 | [
"ESPResSo"
] | 700705f1cd431c9c3977835e47da91abbe6c0ed79b0b48880b6a1315920f4946 |
#!/usr/bin/env python
# THIS FILE IS PART OF THE CYLC SUITE ENGINE.
# Copyright (C) 2008-2018 NIWA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at yo... | jonnyhtw/cylc | lib/cylc/scheduler.py | Python | gpl-3.0 | 72,789 | [
"BLAST"
] | 6d224f952c48d2cdebeb826cb24eec19f826dab921f0caa3bd7af251ae371241 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/bibles/lib/http.py | Python | gpl-2.0 | 31,053 | [
"Brian"
] | 25a839847d10e12c29f03e068cac25610caaee59c687b9443208cc9a177c1031 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | don-github/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 28,494 | [
"VisIt"
] | bc40e046ee6b669b636cf745aaafbcf0e332da57be33ec68850f731f94a9d9d9 |
# Orca
#
# Copyright 2008 Sun Microsystems Inc.
# Copyright 2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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
# ve... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/logger.py | Python | gpl-3.0 | 2,014 | [
"ORCA"
] | 8cd56add5b06c951b2a0d94f5ed731fb2ffdd0611d9274024e10dc586a50323e |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following d... | chatcannon/scipy | scipy/ndimage/filters.py | Python | bsd-3-clause | 40,512 | [
"Gaussian"
] | 7cae5bb21baaea3118ce79fcd9accde07d716c3291695abc064e4c269fa2f757 |
# 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 PyCrossmap(PythonPackage, SourceforgePackage):
"""CrossMap is a program for convenient con... | LLNL/spack | var/spack/repos/builtin/packages/py-crossmap/package.py | Python | lgpl-2.1 | 1,249 | [
"pysam"
] | f05e58daa96f24fcfc47918a8562039b92078124fd2fc423f8d94120f6672100 |
from collections import defaultdict, Counter
from dark.utils import median
from dark.filter import ReadSetFilter
from dark.intervals import ReadIntervals
def titleCounts(readsAlignments):
"""
Count the number of times each title in a readsAlignments instance is
matched. This is useful for rapidly discove... | bamueh/dark-matter | dark/titles.py | Python | mit | 18,728 | [
"BLAST"
] | 8537bd9165fe09d5cebed08c742c7ee592abf9e285f4a2d795c492466610f77f |
# coding: utf-8
#!/usr/bin/env python
"""
Created on Nov 12, 2011
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date__ = "Nov 12, 2011"
import itertools
import argparse
from pymatgen.io.va... | rousseab/pymatgen | scripts/diff_incar.py | Python | mit | 1,616 | [
"VASP",
"pymatgen"
] | ac05386fd219d663a0db9e45a13598a78afd91251fd70599514dfd310315ed00 |
from rdflib.namespace import Namespace
import csv
import re
import traceback
from ..utils import normalize_cell_name
from ..channel import Channel, ExpressionPattern
from ..evidence import Evidence
from ..muscle import Muscle
from ..network import Network
from ..neuron import Neuron
from ..website import Website
from ... | gsarma/PyOpenWorm | PyOpenWorm/data_trans/wormbase.py | Python | mit | 9,822 | [
"NEURON"
] | 7f727d1e8d34a5f27f9a54a3350877a910346fc1e5b6832c5ae18695b3c6ac2d |
#!/usr/bin/env python
from distutils.core import setup
setup(
name="housepy",
version="0.0.1",
description="Personal utility library for Python 3",
author="Brian House",
url="https://github.com/brianhouse/housepy",
py_modules=['housepy'],
package_dir={'housepy': ""},
packages=['housepy... | brianhouse/housepy | setup.py | Python | mit | 1,078 | [
"Brian"
] | a095f8c2262278a3b9c605500fae3d93748e4551f68c4d90249158cc93e7a727 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-06-12 19:13:30
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-06-12 19:23:07
from __future__ import print_function, division, absolute_import
from marvin.core import ... | sdss/marvin | tests/core/test_marvin_pickle.py | Python | bsd-3-clause | 1,519 | [
"Brian"
] | 57179036a1de2c3dfe18cdee66ab198defbc0ab5d7af42154d8ba8aa1b464574 |
# BurnMan - a lower mantle toolkit
# Copyright (C) 2012, 2013, Heister, T., Unterborn, C., Rose, I. and Cottaar, S.
# Released under GPL v2 or later.
#system libs:
import numpy
import scipy.optimize as opt
import scipy.integrate as integrate
import math
import matplotlib.pyplot as pyplot
#own libs:
import os, sys
if ... | tjhei/burnman_old2 | burnman/partitioning.py | Python | gpl-2.0 | 3,876 | [
"Avogadro"
] | 4ba6e6994b7f086c6d11c82af451c6453083d58ca605508389838934f0cd74c0 |
########################################################################
# File : Utilities.py
# Author : Federico Stagni
########################################################################
"""
Utilities for Transformation system
"""
import ast
import random
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.... | Andrew-McNab-UK/DIRAC | TransformationSystem/Client/Utilities.py | Python | gpl-3.0 | 17,682 | [
"DIRAC"
] | 8757bd2ee0d43d18833945946789de2f0f7cd7f2cdb72f9337ac305e8e9a0ad8 |
#-------------------------------------------------------------------------------
# Name: netcdf_builder
# Purpose: Selection of functions to open, create and manage netCDF
# objects and files. These routines have been developed and
# tested with netCDF3 and netCDF4 file formats.
#
# Author: M... | GeoscienceAustralia/gdf | gdf/netcdf_builder.py | Python | apache-2.0 | 27,813 | [
"NetCDF"
] | 655491ba4e98edb9ee3fa0fd33a780d5725eb3c93e227ee1b1bdcf5ff4b5b9c7 |
# 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 RBiocfilecache(RPackage):
"""Manage Files Across Sessions
This package creates a p... | LLNL/spack | var/spack/repos/builtin/packages/r-biocfilecache/package.py | Python | lgpl-2.1 | 1,588 | [
"Bioconductor"
] | 3ddcfdf11ccb8369c776b36afb356544284adc269a11a19807d468bf2c0dc387 |
from pyfcm import FCMNotification
import feedparser
''' === important constants === '''
tags = ['A Song of Ice and Fire', 'Ace Attorney', 'Ace of Diamond', 'Addams Family', 'Agents of SHIELD', 'Aldnoah.Zero',
'Alex Rider', 'Alias', 'Almost Human', 'American Horror Story', 'Angel: The Series', 'Animorphs', 'Arrow (TV... | michelleran/FicFeed | server/fcm.py | Python | mit | 15,355 | [
"Galaxy"
] | defed5f5cb2bb385edab88e946ba18c7a4e3c077875a851b609c5c50d0e6e406 |
#
# @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/pytest/utils.py | Python | lgpl-3.0 | 1,848 | [
"Psi4"
] | dce4abfd6e68cd93eee5a2131028c148e37d98df2a5dddec581ce42a4013fde5 |
#
# Copyright (C) 2001 greg Landrum
#
# unit testing code for the composite model COM server
from __future__ import print_function
from rdkit import RDConfig
import unittest
from rdkit.ML.Composite import Composite
from win32com.client import Dispatch
from Numeric import *
class TestCase(unittest.TestCase):
def s... | adalke/rdkit | rdkit/ML/Composite/UnitTestCOMServer.py | Python | bsd-3-clause | 2,667 | [
"RDKit"
] | 8873175491027e9682c91e30a3a24d549ea04b4f33b0c5d772f11dff7c767296 |
from typing import Any, Tuple, Type
import numpy as np
import pytest
import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow_probability.python.bijectors import Exp
from tensorflow_probability.python.distributions import Uniform
import gpflow
from gpflow.base import PriorOn
from gpflow.config imp... | GPflow/GPflow | tests/gpflow/test_base_prior.py | Python | apache-2.0 | 4,957 | [
"Gaussian"
] | f3f33e13c1d7663e0fef6d1ceb4d14451aecd96ad812493a605f446036a3df3a |
# 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... | fedepad/espressopp | src/standard_system/LennardJones.py | Python | gpl-3.0 | 5,605 | [
"ESPResSo"
] | 0f74aab96fb743f615d7de2e99a76d9a9ac824c30272455d966ee2fec8d5d513 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep... | nisse3000/pymatgen | pymatgen/util/tests/test_string_utils.py | Python | mit | 2,686 | [
"pymatgen"
] | 17a68d2ad1650f21a1ac5f4422bdf1e58c99149bea5af0056cd7e207e47ce895 |
#!/usr/bin/env python3
import matplotlib.pyplot as plt
import numpy as np
from td.peakdetect import peakdetect
NM2EV = 1240.6691
class Spectrum:
def __init__(self, name, excited_states, gs_energy=None, nm_range=None):
self.name = name
self.excited_states = excited_states
wavelengths = ... | eljost/td | td/Spectrum.py | Python | gpl-3.0 | 5,178 | [
"Gaussian"
] | 6454753b6d592f34f92eeeb2c4989424a687fae92cafc945689b6a2fdaa1ca67 |
from mock import *
from gp_unittest import *
from gppylib.operations.package import IsVersionCompatible
class IsVersionCompatibleTestCase(GpTestCase):
def setUp(self):
self.gppkg_mock_values = \
{'main_rpm': 'plperl-1.1-2.x86_64.rpm',
'postupdate': [],
'pkgname': 'plp... | lintzc/gpdb | gpMgmt/bin/gppylib/test/unit/test_unit_package.py | Python | apache-2.0 | 3,737 | [
"ORCA"
] | 3f2e9f3c48a73d9a1817b0f5bbd1832e17cf800c0ccd56b4d66346afe4322017 |
# -*- coding: utf-8 -*-
import datetime
import json
import mock
import pytest
import requests_mock
from constance.test import override_config
from django.conf import settings
from django.contrib.sites.models import Site
from django.core import mail
from django.template.loader import render_to_string
from django.utils.... | jwhitlock/kuma | kuma/wiki/tests/test_views.py | Python | mpl-2.0 | 116,810 | [
"VisIt"
] | b984e474afa3dbcccb2b910c3779857c9c9ffae7dffeb965c40ac93ea20a67c2 |
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