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# -*- coding: utf-8 -*-
"""QGIS Unit tests for QgsProviderUtils.
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
"""
... | timlinux/QGIS | tests/src/python/test_qgsproviderutils.py | Python | gpl-2.0 | 9,083 | [
"ADF"
] | 26e7b6f2dacbad5cac85bfd8ba55a679619567203861b3683557040f59099ecd |
# -*- coding: utf-8 -*-
'''auto reduce test mixins'''
from inspect import ismodule
from twoq.support import port
class AMathQMixin(object):
def test_max(self):
self.assertEqual(self.qclass(1, 2, 4).max().end(), 4)
from stuf import stuf
stooges = [
stuf(name='moe', age=40),
... | lcrees/callchain | callchain/tests/mixins/auto/reducing.py | Python | mit | 4,836 | [
"MOE"
] | 1f8299dee335b531254f0c87430a800fb5073862218fa87b70b38b188f0b48b1 |
# This file is part of Checkbox.
#
# Copyright 2013 Canonical Ltd.
# Written by:
# Zygmunt Krynicki <zygmunt.krynicki@canonical.com>
#
# Checkbox 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 versio... | zyga/debian.plainbox | plainbox/impl/commands/analyze.py | Python | gpl-3.0 | 9,549 | [
"VisIt"
] | 8238349352ea131a0dd5c3fa87e08753d7cb5dcd05248ea1801b54d0ccd120f9 |
# wildcard.py ---
#
# Filename: wildcard.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Tue Jun 4 11:20:57 2013 (+0530)
# Version:
# Last-Updated: Tue Jun 4 12:27:42 2013 (+0530)
# By: subha
# Update #: 143
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
... | dilawar/moose-full | moose-examples/snippets/wildcard.py | Python | gpl-2.0 | 5,085 | [
"MOOSE"
] | 90a1b4d9329270e023fe6de85acd4c3164eb6424f7f66acd1012378026727793 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
class ICPTransform(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
... | nagyistoce/devide | modules/filters/ICPTransform.py | Python | bsd-3-clause | 3,099 | [
"VTK"
] | 017c0a4a1960fb4b05aa3185ac960963d89e758d1bfe9fd3563df67238202d19 |
# -*- mode: python; -*-
##
## sashimi_plot
##
## Utility for visualizing RNA-Seq densities along gene models and
## for plotting MISO output
##
import os
import sys
import glob
import matplotlib
# Use PDF backend
matplotlib.use("pdf")
from scipy import *
from numpy import *
import pysam
import shelve
import misopy
... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/misopy/sashimi_plot/sashimi_plot.py | Python | apache-2.0 | 10,725 | [
"pysam"
] | 2e6025359c60fdbc14df910b776eaf1d86e0f0e7e258a2f12d67ae64057b2eeb |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | gusai-francelabs/datafari | windows/python/Lib/site-packages/setuptools/command/easy_install.py | Python | apache-2.0 | 86,204 | [
"VisIt"
] | 9b1f9bb607b3f851523ecc4901bf845bd604ecc5861e902a235b5c1db50bca15 |
# 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.
"""Information about the IUPAC alphabets."""
__docformat__ = "restructuredtext en"
protein_letters = "ACDEFGHIKLMNPQRSTVWY"
extended_protein_letters... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Data/IUPACData.py | Python | gpl-2.0 | 9,160 | [
"Biopython",
"PyMOL"
] | be093c200e648dc2632640039b3020084302329ebea49e5e947ff805077c1cf0 |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2005 CCLRC Daresbury Laboratory
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 ... | alexei-matveev/ccp1gui | interfaces/smeagolio.py | Python | gpl-2.0 | 9,939 | [
"VTK"
] | 226a7d2873e28f8952a838a02bd9fe354e0d56d4b091ad66b904f51d2404a576 |
"""
Workflow class is the main container of Steps and Modules
"""
import os, re, types
import xml.sax
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Workflow.Module import *
from DIRAC.Core.Workflow.Step import *
from DIRAC.Core.Workflow.Utility import *
from DIRAC import S_OK, S_ERROR
__RCSID__ = "$... | arrabito/DIRAC | Core/Workflow/Workflow.py | Python | gpl-3.0 | 14,627 | [
"DIRAC"
] | c0b2fe1c8e01d16f3ac7175fe8f46ab798a21930c09c3fa1f721f2b99be8e150 |
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import numpy as np
import sys, time
from astropy.table import Table
from . import loki
def prob(sub1 = None, sub2 = None, RAs1 = None, DECs1 = None, RAs2 = None, DECs2 = None,
dists1 = None, dists2 = ... | ctheissen/LoKi | loki/binary_probability.py | Python | mit | 14,320 | [
"Galaxy"
] | 8b90b6bbbff064515c2fd438349c8b42e1695b976062507e2536bd0dc70c73a0 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
dataobject.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
****************************... | michaelkirk/QGIS | python/plugins/processing/tools/dataobjects.py | Python | gpl-2.0 | 16,205 | [
"NetCDF"
] | 9b50dcc6766b8ae30403352096282f5ee9bcfb67f8631d6859ea7cc655318fa2 |
# $Id$
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import wx # need this for wx.SAVE
class metaImageWRT(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__ini... | chrisidefix/devide | modules/writers/metaImageWRT.py | Python | bsd-3-clause | 2,731 | [
"VTK"
] | f9db167bc4e6dace30bb9afcdedc31c3d662316ddb2a267ff3967df9e91a902b |
# Copyright 2010-2019 Kurt McKee <contactme@kurtmckee.org>
# Copyright 2002-2008 Mark Pilgrim
# All rights reserved.
#
# This file is a part of feedparser.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistrib... | LukeMurphey/splunk-syndication-input | src/bin/syndication_app/feedparser/http.py | Python | gpl-3.0 | 10,778 | [
"NetCDF"
] | 9a620eb5f3d0eeb4417eb7b3a578208656e21f5cc80bca9a73cf199362fcd219 |
def agts(queue):
co = queue.add('co.py', ncpus=4, walltime=5 * 60)
queue.add('co.agts.py', deps=co)
if __name__ == '__main__':
import numpy as np
from ase.io import read
configs = read('co.traj@:')
e = [config.get_potential_energy() for config in configs]
a = np.array([config.cell[0, 0] ... | robwarm/gpaw-symm | gpaw/test/big/stress/co.agts.py | Python | gpl-3.0 | 778 | [
"ASE"
] | 9895c37113c50091695877b5362167f428ff51db347f20756a806d17f84b3451 |
#!/usr/bin/env python
from os import sys, path
p = path.dirname(path.dirname(path.abspath(__file__)))
sys.path.append(p)
sys.path.append(p+'/utilities')
from neuron import h
import numpy as np
import argparse
import matplotlib.pyplot as plt
import os
import lims_orca_utils
# Load the morphology
def load_morphology(... | XiaoxiaoLiu/morphology_analysis | model_fitting/neuron_passive_fit.py | Python | gpl-3.0 | 4,219 | [
"NEURON"
] | 959291cdb963daa0ae2beff11436e1fd99f56c9b6f3bf4760bebe34bff7ab541 |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
account = "ACXXXXXXXXXXXXXXXXXXXXX... | teoreteetik/api-snippets | notifications/rest/credentials/create-fcm-credential/create-fcm-credential.6.x.py | Python | mit | 510 | [
"VisIt"
] | 693b70f29c14873991e066e365e6d2c0d7193d0a419772a9610b68e682bdf4c6 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Carlos Hernande... | gph82/mdtraj | mdtraj/formats/pdb/pdbfile.py | Python | lgpl-2.1 | 30,853 | [
"MDTraj",
"OpenMM"
] | 545d61eaadddb1a9ad9ae1abfbb6b5e7afb8a89b239dc2df5e58fb7148331b63 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2015-2019 Bitergia
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This ... | grimoirelab/GrimoireELK | tests/test_elk_elsticsearch.py | Python | gpl-3.0 | 3,366 | [
"Amber"
] | 21db066e8d3112ae0a1b540dacbb669c09b91058ec2c1688f850d390e0bc7338 |
import re, os
import util
from InputParameters import InputParameters
from MooseObject import MooseObject
class Tester(MooseObject):
@staticmethod
def validParams():
params = MooseObject.validParams()
# Common Options
params.addRequiredParam('type', "The type of test of Tester to crea... | backmari/moose | python/TestHarness/testers/Tester.py | Python | lgpl-2.1 | 18,823 | [
"VTK"
] | ef3cbdb93759936a7c526c5b06f3063e38e2996e138e685e3772102dae8b2643 |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits, load_iris
from sklearn.externals.six.moves import zip
from sklearn.model_selection import cross_val_score
from sklearn.model_selection import train_test_split
from sklearn.naive_bayes import GaussianNB... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/tests/test_naive_bayes.py | Python | mit | 17,905 | [
"Gaussian"
] | 91964fb1f2de08a1eb68f59fcdfc59379c28ff3412508897832c75ec4ac96de3 |
import sys
from paraview.simple import *
print 'Number of files to be converted:', len(sys.argv) - 1
for x in range(1, len(sys.argv)):
inputFile = str(sys.argv[x])
outputFile = inputFile[:-1] + 'u'
print x,': Converting ', inputFile, ' -> ', outputFile
reader = LegacyVTKReader( FileNames= in... | phirus/vtk2vtu | conversion.py | Python | unlicense | 470 | [
"ParaView"
] | 2957b96e3feba9f2e1a25973f62211b6b1e77d1fa3579f0b226c69199a42f999 |
# This file is part of MSMBuilder.
#
# Copyright 2011 Stanford University
#
# MSMBuilder is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version... | msmbuilder/msmbuilder-legacy | MSMBuilder/msm_analysis.py | Python | gpl-2.0 | 29,438 | [
"MDTraj"
] | e75db13e855d16f5d2b438ce2ce9c9c9100d33c53ddc0d9818e35a069f1ed203 |
# author: brian dillmann
# for rscs
from Devices.Input import Input
from Devices.Timer import Timer
from Devices.AnalogInput import AnalogInput
from Devices.Output import Output
class DeviceManager:
def __init__(self):
self.inputs = {}
self.outputs = {}
def addSimpleInput(self, name, location, invert = False):
... | dillmann/rscs | lib/DeviceManager.py | Python | mit | 1,683 | [
"Brian"
] | 9bdce5e257015818d0f254759665d81c6c8559203b4ef3e50d1d4888bbf496b0 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/tools/catalogs.py | Python | agpl-3.0 | 38,029 | [
"Galaxy"
] | 455160d91bb2e2f1ca06bca972985e3e47224e7bf6a047b809db3b53993868ff |
from setuptools import setup, find_packages
setup(
name='orcalib',
version='0.1',
description='AWS Tools and Utilities for Operational Simplification',
long_description=__doc__,
url='https://github.com/bdastur/orca.git',
author='Behzad Dastur',
packages=find_packages(exclude=('tests*','... | bdastur/orca | setup.py | Python | apache-2.0 | 714 | [
"ORCA"
] | 07e5fdb1f8b0c1da35c3d8db347f8ddef39ed0e5d44b897b3c887c3428ae9d49 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | ramondelafuente/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 33,832 | [
"VisIt"
] | e88d456fa6f0315c703baae0412d7f9d189e1dbbeb6f0f0882f9f12dc2b2c15b |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from contextlib import contextmanager
from datetime import datetime
from nose.plugins.attrib import attr
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage... | fintech-circle/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 34,903 | [
"VisIt"
] | 5e16bd226a550151d476524e400d128dbf59567aaf8d6082a11be44f79d07425 |
"""
# Majic
# Copyright (C) 2014 CEH
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This pr... | NERC-CEH/jules-jasmin | job_runner/job_runner/utils/land_cover_editor.py | Python | gpl-2.0 | 6,071 | [
"NetCDF"
] | dc968d2002119e282a7558f8ef6d654d839385727cf2b3bbd9ad90c3318b64fc |
from distutils.core import setup
setup(name='PyBIND',
version='0.1.0',
description='Python package for writing ISC BIND files',
author='Brian L. Brush',
author_email='rhubarbsin@gmail.com',
classifiers=['Development Status :: 4 - Beta',
'Intended Audience :: Information... | RhubarbSin/PyBIND | setup.py | Python | mit | 603 | [
"Brian"
] | f27bf90f9d81d5e8f5b2480d1cfd7182db26dcc805237f03c924b286cdb2e22e |
# Copyright 2002 by Katharine Lindner. 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.
"""
Module to represent the NDB Atlas structure (a minimal subset of PDB format).
Hetero,... | zjuchenyuan/BioWeb | Lib/Bio/Crystal/__init__.py | Python | mit | 8,654 | [
"Biopython",
"CRYSTAL"
] | c98ac0d9cb4e9ed6c970e95834b05f7f44499765e3937e5b2df911fe97e550ae |
"""
Various bayesian regression
"""
from __future__ import print_function
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from scipy.linalg import pinvh
from .base import LinearModel
from ..base import RegressorMixin
from ..util... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/linear_model/bayes.py | Python | mit | 19,750 | [
"Gaussian"
] | 1f4b623995d61a00b7d82bf9f995a363b2b6b594fce26007d5c09ee9df6ec187 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018 Piero Dalle Pezze
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the ... | pdp10/sbpipe | sbpipe/snakemake/ps1_postproc.py | Python | mit | 6,622 | [
"COPASI"
] | 7bcccfee9dbc72e736440ea1aea2bc47d0cf7ae51783785f53a3b0cff67ca1c0 |
#__Author = 'Jongmin Yu' @ Ph.D Candidate @ GIST-MLV
#__Laboratory of Machine Learning and Computer Vision
#
#--Title.Gaussian probability density function for image file
#__data format = numpy
#
from math import sqrt
from parser import st2list
import matplotlib
from matplotlib import pyplot as plt
import numpy as n... | jminyu/PatternRecognition_library | MarkovModel.py | Python | gpl-3.0 | 393 | [
"Gaussian"
] | 9c139614a044adc558d1e25d8a6a78c63fd858f33cef247d9b75ac3f9b314eff |
#!python
# Load libraries
import numpy as np
import sys, csv
import getopt
import libPipeline
HELP_MSG = '''
SYNOPSIS
readsToChromCounts
readsToChromCounts [OPTIONS] [FILE]
#
DESCRIPTION
readsToChromCounts.py
Parses Bowtie alignments into paired-end read summaries.
Prints results to stdout.
... | awblocker/paired-end-pipeline | readsToChromCounts.py | Python | apache-2.0 | 1,489 | [
"Bowtie"
] | d729d3af8480b38d50c9441b1ec3147568abf69e163d863af099d2320e93f4ea |
import pdb
import numpy as np
import matplotlib.pyplot as plt
import math
import itertools
import operator
######################################################################
#
# Data
#
######################################################################
# Uses data set from Chapter 1 of Bishop, stored in file
#... | LYZhelloworld/Courses | 50.021/10/learn_nn/learn.py | Python | mit | 11,839 | [
"Gaussian"
] | 8b2dbbe901e3419bd29a41664590d34e3be48fd848dac13484e769f8c27f345f |
""" Test class for agents
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access, missing-docstring, invalid-name, line-too-long
# imports
import datetime
import pytest
from mock import MagicMock
from DIRAC import gLogger
#... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Agent/test/Test_Agent_TransformationSystem.py | Python | gpl-3.0 | 11,345 | [
"DIRAC"
] | 0fb2fb9ceef634a589d2f73f098b00a3eee064d5e7bfa5e5263a7fc69cd9e5f1 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from .settings.common import INSTALLED_APPS
urlpatterns ... | giantryansaul/easy_blog_django | config/urls.py | Python | bsd-3-clause | 1,433 | [
"VisIt"
] | bd48aa91128b4cda26f99d3b80d353dd78ce4af56d6b4296d226b3ce75736a79 |
########################################################################
# File: RegisterOperation.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/19 13:55:14
########################################################################
""" :mod: RegisterFile
==================
.. module: RegisterFile
... | Sbalbp/DIRAC | DataManagementSystem/Agent/RequestOperations/RegisterFile.py | Python | gpl-3.0 | 3,590 | [
"DIRAC"
] | d556994f31ff0840cf9a0f7310e9a256750e7d71eff5e4040e17244b44d3c10a |
from skbuild import setup
import subprocess
from packaging.version import LegacyVersion
from skbuild.exceptions import SKBuildError
from skbuild.cmaker import get_cmake_version
import packaging
import os
def get_installed_gdal_version():
try:
version = subprocess.run(["gdal-config","--version"], stdout=sub... | Chrismarsh/mesher | setup.py | Python | gpl-3.0 | 3,168 | [
"VTK"
] | 3f197442d532c51d6637ada8439ddb4094ed788f25406f1594cca664e44750a5 |
""" GOCDBClient module is a client for the GOC DB, looking for Downtimes.
WARN: the URL of the GOC DB API is hardcoded, and is: https://goc.egi.eu/gocdbpi/public/
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
import... | yujikato/DIRAC | src/DIRAC/Core/LCG/GOCDBClient.py | Python | gpl-3.0 | 13,708 | [
"DIRAC"
] | 0c81c34109d7b049355b23d5663190c438389bed9e38550c82ad4d2ccf621dad |
import os
import subprocess
from subprocess import CalledProcessError
from functools import partial
from collections import namedtuple
Project = namedtuple('Project', ['name', 'versions'])
# all projects using condaci along with the Python version they
# need. Note that for non-python projects we can choose any singl... | menpo/menpo-admin | utils.py | Python | bsd-3-clause | 4,704 | [
"Mayavi",
"VTK"
] | bacd9284934e2143b72f9e0de711bb50b9dde36d6a1f158e6d5fd865260e6afe |
"""
Functionality for dealing with tool errors.
"""
import string
from galaxy import model, util, web
error_report_template = """
GALAXY TOOL ERROR REPORT
------------------------
This error report was sent from the Galaxy instance hosted on the server
"${host}"
-------------------------------------------------------... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/errors.py | Python | gpl-3.0 | 5,587 | [
"Galaxy"
] | 24432b802705efb25b8853642da66d30589af4119bc47d6bebee00532afc472f |
"""Show information about the test environment."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import datetime
import functools
import os
import platform
import re
import signal
import sys
import time
from .config import (
CommonConfig,
TestConfig,
)
from .io impor... | ilpianista/ansible | test/lib/ansible_test/_internal/env.py | Python | gpl-3.0 | 9,965 | [
"Octopus"
] | 34fbba7a0c47f9c10231e28c657a1db5c8a822605961f9cd086eac76c3766c2a |
import numpy as np
import cv2
from matplotlib import pyplot as plt
'''
Helper functions for batch.py
Uses OpenCV 3.0.0
'''
def inverte(imagem, name):
'''
Performs a bitwise NOT to convert image to its negative.
It does exist in CV2 but I didn't trust the code in the beta version - it looked sloppy.
'''
image... | abhinavrk/Circle-Detection | cdet.py | Python | mit | 8,444 | [
"Gaussian"
] | 450ba2d571ccba66ec245332015b708462d1fec2eaf6e5367694f857418099df |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
i... | nuclear-wizard/moose | python/peacock/utils/ExeFinder.py | Python | lgpl-2.1 | 4,041 | [
"MOOSE"
] | f10e8b4ca56e943307020f693f7cf63a78ef4d4f3734209c7d19dca3dae2d1d5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from pymatgen.core.structure import Molecule
from pymatgen.electronic_structure.core import Spin
from pymatgen.io.gaussian import GaussianInput, GaussianOutput
from pymatgen.util.test... | gmatteo/pymatgen | pymatgen/io/tests/test_gaussian.py | Python | mit | 15,819 | [
"Gaussian",
"pymatgen"
] | 8002cdd24979fa59c1d4b61d31bb9f8c54baa0624dd8013c63139a4861075a7e |
"""Catgirl cog. Send random cute catgirls to a channel."""
import asyncio
import random
import discord
import requests
from redbot.core import checks, Config, commands
from redbot.core.bot import Red
# Global variables
KEY_CATGIRL = "catgirls" # Key for JSON files.
KEY_CATBOY = "catboys" # Key containing other imag... | ARG-TLQ/Red-DiscordBot | cogs/catgirl/catgirl.py | Python | gpl-3.0 | 13,608 | [
"MOE"
] | 1e95a36092356edbb8c0246ad2f93dd6cc29d9ad163715c705adcf67e9dc1a05 |
#!/usr/bin/env python3
"""
-------------------------------------------------------------------------------
This script generates relavant top BLAST hits, which we refer as outlier hits,
for each query sequence.
Written by N. R. Shah [nidhi@cs.umd.edu] for WABI/AMB submission 2017.
-------------------------------------... | shahnidhi/outlier_in_BLAST_hits | src/score_blast.py | Python | mit | 11,859 | [
"BLAST"
] | 57a141e4df7b047703bdff8f1735c5a79d0e61ae26c689d823f61c06c0c8dd07 |
import dataset_adapter as dsa
import numpy
from vtk.util import numpy_support
import vtk
def _cell_derivatives (narray, dataset, attribute_type, filter):
if not dataset :
raise RuntimeError, 'Need a dataset to compute _cell_derivatives.'
# Reshape n dimensional vector to n by 1 matrix
if len(narray... | berendkleinhaneveld/VTK | Wrapping/Python/vtk/numpy_interface/internal_algorithms.py | Python | bsd-3-clause | 19,252 | [
"VTK"
] | c88a7d0eb45d64fa5d777427aa73c425e26ce78389e7908fa28b409e3df686cb |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#
# $Id: e8192a9e9900106561cd9a10220ad0521cfa1582 $
"""
sqlcmd - a simple SQL command interpreter
Requires:
- The Grizzled Python API (http://www.clapper.org/software/python/grizzled/)
- One or more Python DB API drivers. See the Grizzled "db" package.
- The enum pa... | adviti/melange | thirdparty/google_appengine/lib/sqlcmd/sqlcmd/__init__.py | Python | apache-2.0 | 61,014 | [
"Brian"
] | 68c5b4888b81a0bc6bd9c1c7050c70ab4a2d11c4f12b657146c8f85820ae27e4 |
# -*- coding: utf-8 -*-
#
# brunel_alpha_evolution_strategies.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... | luis-rr/nest-simulator | pynest/examples/brunel_alpha_evolution_strategies.py | Python | gpl-2.0 | 20,503 | [
"Gaussian",
"NEURON"
] | 8cdb95a3cc1b59df849ffdc20019516905b5ad0178e2956502338c8c18eb58d6 |
#!/usr/bin/env python
# Copyright 2016 Jim Pivarski
#
# 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 la... | diana-hep/transpiler-rules | transpiler/core.py | Python | apache-2.0 | 8,559 | [
"VisIt"
] | 72dae97a64e1d1cdf1c81167038aaacf3afbcd4d0ebbf20b5b369810b4e6d49e |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Hybrid/Testing/Python/depthSort.py | Python | gpl-3.0 | 2,477 | [
"VTK"
] | c4744f08403f639a3e64fa8a51c6a2937586aceff4c55afcafb24e02f9adbb7f |
#
# @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/share/psi4/databases/RSE42.py | Python | lgpl-3.0 | 77,098 | [
"Psi4"
] | 041196c812ba894e432ef60dd6626f684084bf575334a9aa0f0d7cea3138f850 |
import functools
from collections import defaultdict
from datetime import date, datetime
import dateparser
from lark import GrammarError, Lark, Transformer, Tree, Visitor, v_args
from lark.lexer import Token
from sqlalchemy import (
Boolean,
Date,
DateTime,
Float,
Integer,
String,
and_,
... | juiceinc/recipe | recipe/schemas/expression_grammar.py | Python | mit | 40,782 | [
"VisIt"
] | 4eaba61e0667bb7e75596cd8f9db002c1a841560212024c3cebcb3741e0969c7 |
from django.apps import AppConfig
class BowtieContentConfig(AppConfig):
label = 'bowtie-content'
name = 'bowtie_content'
verbose_name = 'bowtie_content'
BLOCK_TYPES = [
'Text',
'List',
'Quote',
'Image',
'Video',
'Tweet',
'Heading'
]
D... | django-bowtie/bowtie-content | bowtie_content/config.py | Python | mit | 405 | [
"Bowtie"
] | d050f75c380b6c42546fccbf3aef07f1e8390426733030aaac77202b180fd95c |
"""
Elite code -- no meaningful use/pure vanity
(c) Copyright 2005 Philip Jenvey
[See end of file]
"""
import random
from Hellanzb.Util import cmHella
__id__ = '$Id$'
class Codez:
allCodez = {}
aolSays = []
def __init__(self, name, codez):
self.codez = codez
Codez.allCodez[name] = self.... | ShaneMcC/hellanzb | Hellanzb/Elite.py | Python | bsd-3-clause | 21,757 | [
"MOE"
] | 046377daffa63d23cccbdf64bb94ea244f10cb54c6941884e3f4e89ff61405af |
# Copyright 2014-2016 by Marco Galardini. 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.
"""Growth curves fitting and parameters extraction for phenotype data
This module provi... | zjuchenyuan/BioWeb | Lib/Bio/phenotype/pm_fitting.py | Python | mit | 3,925 | [
"Biopython"
] | f4cf69b1e1c870305cefc332fd6359744a6cc8b8cd8a39c3ceb5a627d12c8804 |
import numpy as np
import matplotlib.pyplot as plt
from util import utils
from scipy import pi,sqrt,exp
from matplotlib.ticker import MultipleLocator
import matplotlib
### This program is used to create a plot showing the light curve of multiple different light bands on different days. It also has the ability to save ... | bmazin/ARCONS-pipeline | examples/Pal2012-sdss/plotFullData.py | Python | gpl-2.0 | 6,709 | [
"Gaussian"
] | 8466a0f6770881d52658e963c881b1d91d584b1770426cb79e38a4c521b4e598 |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of ngs_crumbs.
# ngs_crumbs 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, ... | JoseBlanca/ngs_crumbs | crumbs/utils/optional_modules.py | Python | gpl-3.0 | 7,537 | [
"BLAST",
"Biopython",
"pysam"
] | 2564bbebfbd48c13a53810ffd06d7d46b9b70b9b1ec2c7e9f9450b5baa10fe31 |
#!/usr/bin/env python
#
# Copyright (C) 2008 Sylvain
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | AloneRoad/Inforlearn | tools/images_uploader/config.py | Python | apache-2.0 | 1,579 | [
"VisIt"
] | 75683eaee21e61d050f445de9c2a5288adbb2ae0121b22f7f5d1e6aedef406b1 |
# 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... | kevin-coder/tensorflow-fork | tensorflow/contrib/distributions/python/ops/mvn_tril.py | Python | apache-2.0 | 7,944 | [
"Gaussian"
] | cf231bfae5e5366e575f53f784fd611843cb6a0fdd40fa50b8966caeec2a248b |
#!/usr/bin/python
#
# @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... | susilehtola/psi4 | doc/sphinxman/document_plugins.py | Python | lgpl-3.0 | 15,221 | [
"Psi4"
] | ec853f1476ddb1fb134479d44eb8b720de586b2b8da0fdec30d93965a42dfca5 |
"""
Bok choy acceptance and a11y tests for problem types in the LMS
See also lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
import random
import textwrap
from abc import ABCMeta, abstractmethod
from nose.plugins.attrib import attr
from selenium.webdriver import ActionChains
from capa.tests.... | Emergya/icm-openedx-educamadrid-platform-basic | common/test/acceptance/tests/lms/test_problem_types.py | Python | agpl-3.0 | 26,434 | [
"VisIt"
] | c612baa73a4675b4161e83931456d48101ce46d19b6cc78ab69a7d545a533d2b |
"""Debugger
This module contains wrapper classes of lldb objects for convenience
"""
import lldb
import re
from lldb import SBDebugger, SBStringList,\
SBCommandReturnObject, SBError, SBStream
import logging
class Debugger(object):
"""This class represents a SBDebugger with some util functions"""... | c0deforfun/LLL | debugger/__init__.py | Python | mit | 8,176 | [
"VisIt"
] | 49456ca640162142a60e990522d4b19305c56f22ca22573cc3641228275f5fa6 |
# -*- coding: utf-8 -*-
# <Lettuce - Behaviour Driven Development for python>
# Copyright (C) <2010-2012> Gabriel Falcão <gabriel@nacaolivre.org>
#
# 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 Foundatio... | yangming85/lettuce | tests/integration/test_dill.py | Python | gpl-3.0 | 3,802 | [
"Octopus"
] | 6e178701bf297d9ebcf132f47e8c5e2b80856b18e3a14e2d97e24af92b704132 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Example Updater."""
# Import the C++ module.
from hoomd.example_plugin import _example_plugin
# Import the hoomd Python package.
import hoomd
class Exampl... | joaander/hoomd-blue | example_plugin/example_plugin/update.py | Python | bsd-3-clause | 879 | [
"HOOMD-blue"
] | 42a1c398e88a2f4bfa6bd3b22fdc3f6b9012a6b8c3eabf9d810ac44d360175f2 |
# 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... | ghchinoy/tensorflow | tensorflow/python/autograph/converters/lists.py | Python | apache-2.0 | 8,339 | [
"VisIt"
] | 3737982f5a3c683b351947808d80b93c73907e759f53833d3c3ee93cafb9a6e9 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | rishikksh20/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 68,211 | [
"Gaussian"
] | 460906081f858e03283650fea5ec4f65031756632ddb8e45f3f67f8bf72c855c |
import re
def show_result_message(inputString, output, expected):
print "-------------------------"
print OKGREEN+"PASS"+ENDC if output == expected else FAIL+"FAIL"+ENDC,
print "input:", "'"+inputString+"'",
print "output:", "'"+output+"'",
print "expected:", "'"+expected+"'"
def strip_chars(inp... | kszynter/DailyChallenges | Challenge111_easy_star-delete/solution_regex.py | Python | mit | 741 | [
"ADF"
] | 24a1b3322b34e3611170402940412c800ef1e95d79c37eaa4c7527dabd4023d0 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alxgu/ansible | lib/ansible/modules/network/avi/avi_cloud.py | Python | gpl-3.0 | 10,722 | [
"VisIt"
] | ad6d4be9cff2e44557b8de1427da194380557d1f4b8769cf9a9bf192f2640bd5 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Unit tests for data_ingestion.py"""
__version__ = '$Id: test_userlib.py 9043 2011-03-13 10:25:08Z xqt $'
import os
import unittest
import test_utils
import pywikibot
import data_ingestion
class TestPhoto(unittest.TestCase):
def setUp(self):
self.obj = data_... | pywikibot/core-migration-example | scripts/tests/test_data_ingestion.py | Python | mit | 2,768 | [
"CRYSTAL"
] | 88d2bc96e85d5eb5d616dabdecfb18ade945a31ffe85657f94a072d6c29674ce |
import math
from itertools import product
from functools import wraps
import numpy as np
from bayesian.factor_graph import Node
from bayesian.gaussian import make_gaussian_cdf
from bayesian.utils import get_args
def conditional_covariance_matrix(sigma_11, sigma_12, sigma_22, sigma_21):
return sigma_11 - sigma_1... | kamijawa/ogc_server | bayesian/gaussian_node.py | Python | mit | 3,173 | [
"Gaussian"
] | 68d309bb0050564f9614bd52b8f5a14bbe026bc9319bf7376ae3bba627d76bc2 |
"""
SIRV_Experiment_Evaluator.py
This script calls cufflinks, calls the individual scripts and generates the outputs
updated: 27 Oct 2016 Patrick Schagerl,
Last revision: IH181011
(c)2016-2018 Lexogen GmbH
Examples commandline:
python SIRV_Experiment_Evaluator.py -anno_input_type "use_existing_files" -anno_id hg... | sirvsuite-support/sirvsuite | tools/SIRV_Experiment_Evaluator.py | Python | gpl-3.0 | 44,144 | [
"Galaxy"
] | b4bd9107fd9028777c3dd8ae095121d0164b77bf43223b6358b5b113aa79c1fc |
from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d
from numpy.core.numeric import (
ones, zeros, arange, concatenate, array, asarr... | jonathanunderwood/numpy | numpy/lib/function_base.py | Python | bsd-3-clause | 143,962 | [
"Gaussian"
] | e97082ee9f8ef944aef91d38390bd3db46c2ab8ac63ceadf748ef7501c881a0e |
# Adaptive Comfort Chart
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify
# it under the terms o... | boris-p/ladybug | src/Ladybug_Adaptive Comfort Chart.py | Python | gpl-3.0 | 85,820 | [
"EPW"
] | faf6e97ade02b572a916ffcacd54d1fbdb7bc911fe1999d5e23f0ae0ae06096c |
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as spio
from mayavi import mlab
import pdb
deg_to_rad = np.pi/180.
rad_to_deg = 180./np.pi
class OTA(object):
def __init__(self,theta,phi,R=0.66,H=1.5):
theta = theta*deg_to_rad
phi = phi*deg_to_rad
x = (R*np.sin(theta[:,Non... | dialounke/pylayers | pylayers/measures/OTA.py | Python | mit | 4,748 | [
"Mayavi"
] | 158d9af86ebd223d5efeab84e13e199fa67967ee9d63fed4f148fb7afe71cbe9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/encore/utils.py | Python | gpl-2.0 | 12,180 | [
"MDAnalysis"
] | 3e34a6c1bb3e4e7d244a638e6b9b81bb79559cbc8b38a5471f6ee23c5d58a9fd |
#!/usr/bin/env python3
import os
import logging
import re
import itertools
import argparse
import multiprocessing
import gzip
import subprocess
import uuid
import pysam
import tempfile
COSMIC_STRING = 'GENE,CDS,AA,CNT'
DBSNP_STRING = 'RSPOS,GENEINFO,dbSNPBuildID,SAO,SSR,VC,PM,MUT,KGPhase1,KGPhase3,OM,CDA,CAF,COMMON'
... | bioinform/somaticseq | somaticseq/utilities/variant_annotation.py | Python | bsd-2-clause | 3,255 | [
"pysam"
] | dc0fa4b80911a05cd9693bc7200dd0bd70ef5492128d5f8c676083d1aecd7048 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
import collections
"""Parser for Turbomole output files."""
import re
import numpy
from cclib.parser impo... | cclib/cclib | cclib/parser/turbomoleparser.py | Python | bsd-3-clause | 85,359 | [
"Gaussian",
"TURBOMOLE",
"cclib"
] | a6b236bf42ded65912ffc70b0e5dfeddf4c72223930c8efeefe1475b40ef523b |
import logging, string
from time import time, gmtime, strftime
from dirac.lib.base import *
from dirac.lib.diset import getRPCClient
from DIRAC.Core.Utilities.List import sortList
from DIRAC import gConfig, gLogger
import DIRAC.Core.Utilities.Time as Time
import dirac.lib.credentials as credentials
log = logging.getL... | DIRACGrid/DIRACWeb | dirac/controllers/jobs/ProductionMonitor.py | Python | gpl-3.0 | 22,484 | [
"DIRAC"
] | d258530a71d00b10c7b2b0cf3bc8fd9121e7d94ae33da946d060e1a6aaa0904d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 02 2017
The goal of this script is to vizualised the reponse of the filter of the
different convolution of the network
@author: nicolas
"""
import scipy
import numpy as np
import tensorflow as tf
import Style_Transfer as st
from Arg_Parser import ... | nicaogr/Style-Transfer | NoiseOrigin.py | Python | gpl-3.0 | 16,008 | [
"Gaussian"
] | dfd4251eeb0153d921adbc417edea9e0d329887e8548f8677505c395ff0acbf0 |
#!/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.
"""This script generates an rc file and header (setup_strings.{rc,h}) to be
included in setup.exe. The rc file includes translation... | keishi/chromium | chrome/installer/util/prebuild/create_string_rc.py | Python | bsd-3-clause | 9,618 | [
"xTB"
] | d001b59dd442de67f88b749f97a5997dc73fce76a96c92d33086ed9220a2f9e8 |
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
""" unit testing code for knn models """
import doctest
import os.path
import unittest
from rdkit import RDConfig
from rdkit import RDRandom
from rdkit.ML.Data import DataUtils
from rdkit.ML.KNN import CrossValidate, DistFunctions
from rdkit.ML.KN... | rvianello/rdkit | rdkit/ML/KNN/UnitTestKNN.py | Python | bsd-3-clause | 4,565 | [
"RDKit"
] | 435fc3066d2d0b9bd66ce89e7d1a69f2e9dbad63508cc155315111828e785e12 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 2000
n = 4000
testMehrotra = ... | sg0/Elemental | examples/interface/QPDirect.py | Python | bsd-3-clause | 4,313 | [
"Gaussian"
] | 85f7e8e2624946af6f0a96b2eaf4674f53bb1a7d29b855b3e7ec9ec3fd636c2f |
# Copyright 2000 by Jeffrey Chang. 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.
# Gavin E. Crooks 2001-11-03
# Minor extensions, some bug fixes, and major changes to the inte... | zjuchenyuan/BioWeb | Lib/Bio/SCOP/Residues.py | Python | mit | 2,939 | [
"Biopython"
] | 66d1e1aaa87eb744171e1b32f4c77b4bc6165c442b2c3efd44890618abcca4c6 |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa core (__init__.py)
#
# Run me as follows:
# cd tests/
# nosetests -v --with-coverage --cover-package=librosa
#
from __future__ import print_function
# Disable cache
import os
try:
os.environ.pop(... | r9y9/librosa | tests/test_core.py | Python | isc | 41,303 | [
"Brian"
] | 144d729cfd544469593bbeaa85548227afd5cc00365b860c90fb4ea594691011 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-
"""
============
obiwan
============
A package for injecting artificial stars and galaxy-targets (ELGs, LRGs, and QSOs) into the individual images of the DESI Legacy Surveys, DECALS, MzLS, and BASS. The legacypipe/Tractor pipeline ... | legacysurvey/obiwan | py/obiwan/__init__.py | Python | bsd-3-clause | 686 | [
"Galaxy"
] | d13a519db5127a12479eba242fd4f2f0f8718d38b5e3fbe4b9f19ac84d46520a |
#!/usr/bin/env python3
from selenium import webdriver
from selenium.webdriver import FirefoxOptions
from webdriver_manager.firefox import GeckoDriverManager
from splinter import Browser
class google:
def __init__(self, search_for):
ff_options = FirefoxOptions()
ff_options.add_argument("--headless... | dfsmith/dfsmith-public | utils/search.py | Python | gpl-2.0 | 1,019 | [
"VisIt"
] | 22e0628d5b14aa5d76b30bfe359ce488ea84bfab3d7a1b84c3e8137b8309f891 |
"""Common functions and classes.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2015, Enthought, Inc.
# License: BSD Style.
import os
import string
import sys
import re
import vtk
vtk_major_version = vtk.vtkVersion.GetVTKMajorVersion()
vtk_minor_version = vtk.vtkVersion.GetVTKMinorVers... | dmsurti/mayavi | tvtk/common.py | Python | bsd-3-clause | 4,227 | [
"VTK"
] | 2adb64dcf7b4b37c19d0a2151a44bdb43ff4113666829556a803133bdcefb83a |
""" Functions for working with tabix dosages in pandas dataframes
"""
import gzip
import numpy as np
import pandas as pd
import pysam
import statsmodels.api as sm
class Dosage(object):
def __init__(self, dosages, annotations, gene_name):
# Match up the annotation dataframe with the dosage dataframe
... | jeffhsu3/genda | genda/formats/dosages.py | Python | bsd-3-clause | 4,160 | [
"pysam"
] | 12139e6c9b021364a7822ae3f1b1b9234b1648fb4bb597b6c197b9bf4ab59a2f |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | experimental/single_model_uncertainty/models/util.py | Python | apache-2.0 | 7,452 | [
"Gaussian"
] | c188525b99c788c621195b6ba6ab1c7ac867432321cc4da52e006ec8da1939a5 |
import vigra
from vigra import graphs
# parameter:
filepath = '12003.jpg' # input image path
sigmaGradMag = 2.0 # sigma Gaussian gradient
superpixelDiameter = 10 # super-pixel size
slicWeight = 10.0 # SLIC color - spatial weight
gamma = 0.15 # exp(-gamma * edgeIndicator)
edgeThreshold = 2.5... | capturePointer/vigra | vigranumpy/examples/graph_smoothing.py | Python | mit | 2,198 | [
"Gaussian"
] | 0436cd94fcda7fb2ed14fce829c6e8ee90071e1318287e179710bf1d3cd42cbc |
"""
Container page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise, Promise
from common.test.acceptance.pages.common.utils import click_css, confirm_prompt
from common.test.acceptance.pages.studio import BASE_URL
from common.test.acceptance.pages.studio.utils import... | ahmedaljazzar/edx-platform | common/test/acceptance/pages/studio/container.py | Python | agpl-3.0 | 24,826 | [
"VisIt"
] | a5233f66d7e16f7d5a4053ff89b3a8761e8c476f144e3a4410e52d8e52a5b956 |
#!/usr/bin/env python
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as publishe... | bhdouglass/agui | setup.py | Python | gpl-3.0 | 1,822 | [
"Brian"
] | 221b64c53ce01cf6852b669d6035610ad6001c2637f0e49021f69a13d708377b |
#!/usr/bin/env python
# Copyright 2014-2021 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/cc/eom_gccsd.py | Python | apache-2.0 | 26,800 | [
"PySCF"
] | 99fa4970abd65e589cd8fb5d130fd1622f916dd3dd4e950617cf8c7e56c007ba |
"""Core implementation of the testing process: init, session, runtest loop."""
import argparse
import fnmatch
import functools
import importlib
import os
import sys
from typing import Callable
from typing import Dict
from typing import FrozenSet
from typing import Iterator
from typing import List
from typing import Opt... | The-Compiler/pytest | src/_pytest/main.py | Python | mit | 31,849 | [
"VisIt"
] | cdbf2defedd26c0769acb93e9d649dedead8c67207fa59bcefab76cba5fedcf6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import io
import os
import pprint
import re
import shutil
import subprocess
import sys
import warnings
from setuptools import setup, Extension
try:
import cython
except ImportError:
_HAVE_CYTHON = False
else:
_HAVE_CYTHON = True
assert cython # silence pe... | chemreac/chemreac | setup.py | Python | bsd-2-clause | 8,157 | [
"ChemPy"
] | 2cad4a997cd46c8ab837cd6288ab179ac13d8860e63bd65a7f87a433427fd026 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You s... | ghutchis/cclib | test/writer/testfilewriter.py | Python | lgpl-2.1 | 1,180 | [
"ADF",
"cclib"
] | f4f9296716c841fe12e35f05bb20d22c195dbd855b66af1dc75bda25aa93b945 |
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