text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
# pylint: disable=missing-docstring
from lettuce import step
from lettuce import world
from lettuce import before
from pymongo import MongoClient
from nose.tools import assert_equals
from nose.tools import assert_in
REQUIRED_EVENT_FIELDS = [
'agent',
'event',
'event_source',
'event_type',
'host',
... | MakeHer/edx-platform | lms/djangoapps/courseware/features/events.py | Python | agpl-3.0 | 2,247 | [
"VisIt"
] | 8eacddcd21bea1d1be605cd725484213756aa5a3e4f449caa718eaca23ec99d2 |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
def main():
myscreen = camvtk.VTKScreen()
focal = cam.Point(50, 0, 0)
r = 300
theta = (float(45)/360)*2*math.pi
fi=45
campos = cam.Point( r*math.sin(theta)*math.cos(fi), r*math.sin(theta)*math.sin... | aewallin/opencamlib | examples/python/kdtree_debug_1.py | Python | lgpl-2.1 | 3,691 | [
"VTK"
] | f5530311e2b765db0cb18d2675f2e0c6187937d600f45575cd9529d4e772c054 |
###
# Copyright (c) 2002-2005, Jeremiah Fincher
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list of co... | mazaclub/mazabot-core | test/test_ircutils.py | Python | bsd-3-clause | 16,070 | [
"COLUMBUS"
] | af10bc33094301be48c2b622e76441de3553085f6859ee9ea5254d1c64ebcd9f |
'''
Created on 2013-3-31
pysa - reverse a complete computer setup
Copyright (C) 2013 MadeiraCloud Ltd.
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 Li... | VisualOps/pysa | pysa/scanner/actions/file.py | Python | gpl-3.0 | 2,386 | [
"VisIt"
] | dc7b48aab5fa4dbb411c296fc580ce8503d7293de663ba577123344bc5cff580 |
"""The optimizer tries to constant fold expressions and modify the AST
in place so that it should be faster to evaluate.
Because the AST does not contain all the scoping information and the
compiler has to find that out, we cannot do all the optimizations we
want. For example, loop unrolling doesn't work because unrol... | pallets/jinja2 | src/jinja2/optimizer.py | Python | bsd-3-clause | 1,418 | [
"VisIt"
] | 3bb69340f8164218ff896e574950bfeccb7afccbda1c327c2bcbc546f3368c04 |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2012 OpenStack 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
#
# Unless required by... | gold3bear/swift | test/unit/proxy/test_server.py | Python | apache-2.0 | 403,114 | [
"MOOSE"
] | 859f9846dc60a7cde8f7daa9b3537333f0e58ba5e989af3aa8d14e0232e5cc9a |
from django.db import models
from django.dispatch import receiver
from django.utils import timezone
from django.utils.translation import ugettext_lazy as _
from supersalon.purchases.models import ServicePurchase, ProductPurchase
class Visit(models.Model):
# Customer
customer = models.ForeignKey('customers.C... | dogukantufekci/supersalon | supersalon/visits/models.py | Python | bsd-3-clause | 2,022 | [
"VisIt"
] | 645ca171fb8cd8f2a2f0b791e65b4dcd810f60f96da4cff62be6f33ebc3fad38 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | CodeMonkeyJan/hyperspy | hyperspy/signal_tools.py | Python | gpl-3.0 | 40,200 | [
"Gaussian"
] | 283eefc94b69c935ac14c9cec30b733b7307058724dfb1e7b8de9b4b2483d343 |
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Kenneth Hoste
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>
# License:: MIT/GPL
# $Id... | omula/easybuild-easyblocks | easybuild/easyblocks/b/bwa.py | Python | gpl-2.0 | 2,400 | [
"BWA"
] | a8ccecd3ab78a47bc6d40764c4b1bb4450f68f0fab4c9f29c295cf53b8757afb |
from octopus.modules.es.testindex import ESTestCase
from service.models import Record, SpreadsheetJob, OAGRLink
import time
class TestModels(ESTestCase):
def setUp(self):
super(TestModels, self).setUp()
def tearDown(self):
super(TestModels, self).tearDown()
def test_01_spreadsheet(self):
... | CottageLabs/oacwellcome | service/tests/unit/test_models.py | Python | apache-2.0 | 11,345 | [
"Octopus"
] | 7c6cb6cb0d05fad94141fcdd4c8d69a4bcba08d8434a694e268d22ee07f0418c |
#!/usr/bin/env python
"""
Read the Dimer Vector from CP2K.
The vector is read from the cp2k-1.restart file.
"""
import sys,re
#Read the cp2k-1.restart file
if ( len(sys.argv) < 2):
print "Usage: %s cp2k-1.restart" %(sys.argv[0])
exit()
CP2KFileName = sys.argv[1]
DimerFileName = "NEWMODECAR"
inp=open(CP2KFileNam... | zevanzhao/TCCL-Code | CP2K/GetCP2KDimerVector.py | Python | gpl-3.0 | 1,370 | [
"CP2K"
] | 9e98ee4bb6dcad4d84755a93899d0cfb3ac5385065c30fe49d9689da6b2f0fee |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0021_auto_20150515_0131'),
]
operations = [
migrations.AddField(
model_name='visit',
name='... | koebbe/homeworks | visit/migrations/0022_visit_no_show.py | Python | mit | 401 | [
"VisIt"
] | c96ef4dea901d60b8b27b7e26dab714bd4a0d24232da221ede6ad070be7fa90f |
# -*- coding: utf-8 -*-
"""
=====================
Cython related magics
=====================
Magic command interface for interactive work with Cython
.. note::
The ``Cython`` package needs to be installed separately. It
can be obtained using ``easy_install`` or ``pip``.
Usage
=====
To enable the magics below,... | fabianrost84/cython | Cython/Build/IpythonMagic.py | Python | apache-2.0 | 12,985 | [
"Brian"
] | 8d5e5c65b951cf0f7531746cb45e02ae18507e04b2bb81ca381e0d608a1eaaed |
#!/usr/bin/env python
#encoding=utf8
#Copyright [2014] [Wei Zhang]
#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 ... | anthonylife/EventRecommendation | src/WMF/model.py | Python | apache-2.0 | 14,466 | [
"Gaussian"
] | 48db89893d36383560dab357fb0255421a04138b242aacc7c32a23e3d5c80e82 |
"""
Title: Probabilistic Bayesian Neural Networks
Author: [Khalid Salama](https://www.linkedin.com/in/khalid-salama-24403144/)
Date created: 2021/01/15
Last modified: 2021/01/15
Description: Building probabilistic Bayesian neural network models with TensorFlow Probability.
"""
"""
## Introduction
Taking a probabilist... | keras-team/keras-io | examples/keras_recipes/bayesian_neural_networks.py | Python | apache-2.0 | 14,079 | [
"Gaussian"
] | ee1f504c050bbad2fa668aea163f5c56283f054ac766ae7c3d6039b4be1f2770 |
# -*- coding: utf-8 -*-
# TODO: Port to pytest
# PEP8 asserts
from copy import deepcopy
import httplib as http
import time
import mock
import pytest
import pytz
import datetime
from nose.tools import * # noqa
from tests.base import OsfTestCase, fake
from osf_tests.factories import (
UserFactory, NodeFactory, Pr... | erinspace/osf.io | addons/wiki/tests/test_wiki.py | Python | apache-2.0 | 62,693 | [
"VisIt"
] | 32a67cf1c32511ffe1313c41b4d4edc77bd3e6d3fdd7ce3b6b9f9441186ae683 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-ampliqueso/package.py | Python | lgpl-2.1 | 2,383 | [
"Bioconductor"
] | 4abd3c3012166b86a2b60f8e9d78641c79a487204f7197150af10444a25d8dfd |
#!/usr/bin/env python
#String in Pi, stringinpi.py v1.01
#Copyright (c) 2015 by Brian Mikolajczyk, brianm12@gmail.com
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Lic... | bmikolaj/stringinpi | stringinpi.py | Python | gpl-3.0 | 2,823 | [
"Brian"
] | 1168f6568ed4a194dd75c6d7bc49945ff0f583a11b1dc66dbfa0d10ade6584af |
import types
import base64
from RESTDIRAC.RESTSystem.Base.RESTHandler import WErr, WOK, RESTHandler
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.Utilities import List, Time
class BaseFC( RESTHandler ):
@property
def rpc( self ):
return RPCClient( "DataManagement/FileCatalog" )
def decod... | DIRACGrid/RESTDIRAC | RESTSystem/API/FileCatalog/BaseFC.py | Python | gpl-3.0 | 1,716 | [
"DIRAC"
] | 3e7bc5e780cc14190db95b61fd842054ae3e3bd70cd7eb58a97e62ffb959a32c |
# -*- coding: utf-8 -*-
"""
Implements Monte Carlo Reinforcement Learning for iterSemiNFG objects
Created on Mon Feb 18 09:03:32 2013
Copyright (C) 2013 James Bono
GNU Affero General Public License
"""
from __future__ import division
import time
import copy
import numpy as np
import matplotlib.pylab as plt
from pyn... | jwbono/PyNFG | pynfg/levelksolutions/mcrl.py | Python | agpl-3.0 | 12,877 | [
"VisIt"
] | 42793810114e2c7c39d72fd040ade46bc2bd0742bf561d17e0bbbf0d6648c8cb |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for the
IDL version is:
... | gLENTNER/SLiPy | astrolibpy/mpfit/mpfit.py | Python | gpl-2.0 | 78,437 | [
"Gaussian"
] | 1fc2a5aa285e7f1af90eb503016960d3fefadce18b8586636eb066fb51beb1b0 |
# 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... | BackupTheBerlios/espressopp | src/integrator/__init__.py | Python | gpl-3.0 | 2,344 | [
"ESPResSo"
] | 7013c954a1622cc3efbc10718f9d9af68d5cb7912cfe600960af2eaa0a866081 |
"""
Async helper function that are invalid syntax on Python 3.5 and below.
This code is best effort, and may have edge cases not behaving as expected. In
particular it contain a number of heuristics to detect whether code is
effectively async and need to run in an event loop or not.
Some constructs (like top-level `r... | sserrot/champion_relationships | venv/Lib/site-packages/IPython/core/async_helpers.py | Python | mit | 4,998 | [
"VisIt"
] | 66fa8e2f2c754cb0087a89e08a1e739131f0eb82668d0c7f125cf188b03f41fb |
#
#-*- coding:utf-8 -*-
"""
Gentoo-keys - gkey.py
Holds GKEY class and related values
@copyright: 2012-2015 by Brian Dolbec <dol-sen@gentoo.org>
@license: GNU GPL2, see COPYING for details.
"""
from collections import namedtuple
GKEY_STRING = ''' ----------
Name.........: %(name)s
Nick... | gentoo/gentoo-keys | gkeys/gkeys/gkey.py | Python | gpl-2.0 | 2,466 | [
"Brian"
] | 21f9d1325d35129ce727fd7f46c33fa4a35b57aa730e5b8a1cf5626c9aca4231 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/line/tracer.py | Python | lgpl-2.1 | 841 | [
"MOOSE"
] | e364d9b91bc05e029ee3380d1a1da290cd07ab12568dadc0d6315458d33a03f4 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/espresso/package.py | Python | lgpl-2.1 | 5,930 | [
"ESPResSo"
] | 1f681545527306d312bed598d29185e9cf317903451467ffdc9dfa9d8c1488b2 |
# 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 Exciting(MakefilePackage):
"""
exciting is a full-potential all-electron density-funct... | LLNL/spack | var/spack/repos/builtin/packages/exciting/package.py | Python | lgpl-2.1 | 6,878 | [
"exciting"
] | 86476bc45f9fb864f82ef0d6b30fbeafab331e7eb13977bdc3345c11b75bccf4 |
import codecs
import contextlib
import io
import locale
import sys
import unittest
import encodings
from unittest import mock
from test import support
try:
import _testcapi
except ImportError as exc:
_testcapi = None
try:
import ctypes
except ImportError:
ctypes = None
SIZEOF_WCHAR_T = -1
else:
... | kikocorreoso/brython | www/src/Lib/test/test_codecs.py | Python | bsd-3-clause | 131,220 | [
"FEFF"
] | c113d81aff0dfd47b192c9dd9daf2b7423c9fe17e96f4a70679d79b954fc8246 |
#WCS response decoder.
#Decodes response from a WCS (either a Coverages XML document or a Multipart MIME) and extracts the urls of the coverage data.
#Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#Author: Dominic Lowe, STFC
#contact email: d.lowe@rl.ac.uk
#
# Multipart MIME decoding based on http://aspn.activestate.... | sebastic/QGIS | python/ext-libs/owslib/coverage/wcsdecoder.py | Python | gpl-2.0 | 3,839 | [
"NetCDF"
] | 76c41e0090c526305c274dddb2d96ffc4ffee4a6a310fcd78156429813307405 |
from django.utils.translation import ugettext_lazy as _
from django.forms import ValidationError # noqa
from django.core.urlresolvers import reverse
from horizon import exceptions
from horizon import forms
from horizon import messages
from crystal_dashboard.dashboards.crystal import exceptions as sdsexception
from cr... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/regions/forms.py | Python | gpl-3.0 | 2,968 | [
"CRYSTAL"
] | 9d912cc9a5f09bc971cb999d0ce87b515258342c2e25ad492522e63b94e2b0de |
#!/usr/bin/env python
from __future__ import print_function
import numpy as np
import sys
import mdtools.constants as const
import mdtraj as md
import itertools
from tqdm import tqdm
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import seaborn as sns
### setup ###
# example...
target_pair... | TaizoAyase/mdtools | min_dist/calc_mindist.py | Python | gpl-2.0 | 3,430 | [
"MDTraj"
] | 2c075f4541b5e3a774c48f44942d78769b5dda4d291c90ac142864042af4ea72 |
from Firefly import logging
from Firefly.helpers.device_types.switch import Switch
from Firefly.const import SWITCH, LEVEL, AUTHOR
CAPABILITIES = {
LEVEL: True,
SWITCH: True
}
TITLE = 'Virtual Switch'
def Setup(firefly, package, **kwargs):
logging.message('Entering %s setup' % TITLE)
switch = Virt... | Firefly-Automation/Firefly | Firefly/components/virtual_devices/dimmer.py | Python | apache-2.0 | 794 | [
"Firefly"
] | 608df4c87fb13b6ed77dd115059a0e071a4b0291884f49adf0751f3c9e33b0d1 |
from __future__ import with_statement
import os
import time
import tempfile
from latex import latex
def preview(expr, output='png', viewer=None, euler=True, **latex_settings):
"""View expression or LaTeX markup in PNG, DVI, PostScript or
PDF form.
If the expr argument is an expression, it will be ... | ichuang/sympy | sympy/printing/preview.py | Python | bsd-3-clause | 7,314 | [
"VisIt"
] | d4c71728fa107742e5a083228fe5c3a66da43407e11a21e48c4bff442d815e38 |
# 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/tpt.py | Python | gpl-2.0 | 36,692 | [
"MDTraj"
] | ac8943cae6fb0639d7a6157f749d3f2c52ac4992a9eade08f6c8500cbfc4fe82 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import re
import pyte... | Lujeni/ansible | test/units/galaxy/test_api.py | Python | gpl-3.0 | 37,758 | [
"Galaxy"
] | becd90f73001169cb499c5794217cfd7cb8b5a6b61705a33302531b460d3b1ba |
"""
Single Bubble Model: Inert particles
=====================================
Use the ``TAMOC`` `single_bubble_model` to simulate the trajectory of an inert
particle (e.g., a dead oil) rising through the water column. This script
demonstrates the typical steps involved in running the single bubble model.
It uses th... | socolofs/tamoc | bin/sbm/particle.py | Python | mit | 1,951 | [
"NetCDF"
] | cc31855f5087662882b010e950155a643e08ea28bb4d39c575bcb77524f9d5b0 |
import numpy as np
from scipy.ndimage.filters import gaussian_filter1d
class TestStatistic(object):
"""Base test statistic class
"""
use_pmf_cache = True
statistic_name = 's'
n_trials = int(1e4) # Number of trials used in monte carlo training of p(s|mu) for a given mu
mu_dependent = False ... | JelleAalbers/plunc | plunc/statistics/base.py | Python | mit | 4,325 | [
"Gaussian"
] | 31293c16f6e8e9d37f2514f8da3c8877b3dec9447bad6a22618280b1851aa98c |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# vizplotgui_vmd.py
# Purpose: viz running LAMMPS simulation via VMD with plot and GUI
# Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data point and viz sha... | SGenheden/lammps | python/examples/vizplotgui_vmd.py | Python | gpl-2.0 | 4,473 | [
"LAMMPS",
"VMD"
] | 63fa46e38c7e86b0842aa52a375f09609ffc8e894cf2e34186eaf9ea7af97a6b |
from __future__ import print_function
import sys
import argparse
from collections import Counter, defaultdict
import operator
import itertools
import warnings
import traceback
import os.path
import multiprocessing
import pysam
import HTSeq
class UnknownChrom(Exception):
pass
def invert_strand(iv):
iv2 = iv... | simon-anders/htseq | python2/HTSeq/scripts/count_with_barcodes.py | Python | gpl-3.0 | 25,733 | [
"HTSeq",
"pysam"
] | be9259b9ed1683315c40206d570a1d11faad032c98f10b6b49691c0ff937b1dc |
from .Singleton import Singleton
from kalliope.core.Models.settings.Resources import Resources
from .Brain import Brain
from .Synapse import Synapse
from .Neuron import Neuron
from .Signal import Signal
| kalliope-project/kalliope | kalliope/core/Models/__init__.py | Python | gpl-3.0 | 203 | [
"NEURON"
] | 1a6591786da9b02b0dbcf52c554e11ca54cbef2cb31343fcf86dc5ab89948649 |
from __future__ import division
from warnings import warn
from collections import Iterable
import numpy as np
import PIL.Image as PILImage
from menpo.compatibility import basestring
from menpo.base import (Vectorizable, MenpoDeprecationWarning,
copy_landmarks_and_path)
from menpo.shape import ... | grigorisg9gr/menpo | menpo/image/base.py | Python | bsd-3-clause | 128,607 | [
"Gaussian"
] | b3f39d2098959d98f70be553f77ce5ed9d42857f94d29c49bf9468dc8df3895e |
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 15 15:46:50 2016
@author: camacho
"""
import numpy as np
#import matplotlib.pyplot as pl
#pl.close("all") #fecha todas as figuras anteriores
from time import time
import george
from george.kernels import *
from Kernel import *
def lnlike(K, r):
from scipy.linalg imp... | jdavidrcamacho/Tests_GP | 01 - Trials and attempts/03_nova_likelihood.py | Python | mit | 2,428 | [
"Gaussian"
] | a4eaae6df0529b9ef0b6216ab4f79e40b4efa24064900e4053e06a3cd4c59496 |
# Copyright 2012 OpenStack Foundation
# 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 requ... | waltBB/neutron_read | neutron/tests/unit/test_linux_ip_lib.py | Python | apache-2.0 | 44,577 | [
"Brian"
] | 09c6384bb95c6a98200090ed766abd6bd18ba74727aee0ecc4edf4a68287ddba |
"""
Utility functionality (:mod:`skbio.util`)
=========================================
.. currentmodule:: skbio.util
This package provides general exception/warning definitions used throughout
scikit-bio, as well as various utility functionality, including I/O and
unit-testing convenience functions.
Testing functio... | Achuth17/scikit-bio | skbio/util/__init__.py | Python | bsd-3-clause | 2,160 | [
"scikit-bio"
] | c28d7b281e6118d6357dc7e811d65b1671b4278b678581437ae0d654e134a4c5 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
print "hello world"
# <codecell>
from apiclient.discovery import build
# <codecell>
from oauth2client.client import OAuth2WebServerFlow
# <codecell>
import httplib2
# <codecell>
import gflags
import httplib2
from apiclient.discovery import build... | nakul225/Scheduler | Scheduler.py | Python | gpl-2.0 | 5,308 | [
"VisIt"
] | 6c7de8a5350b69412d5e96ce91a47254ad58e10fa91cc5393e324dee6d3371be |
# -*- Mode: python; coding: utf-8 -*-
from __future__ import division
#from __future__ import with_statement
LAYOUT_ALGORITHM = 'neato' # ['neato'|'dot'|'twopi'|'circo'|'fdp'|'nop']
REPRESENT_CHANNELS_AS_NODES = 1
DEFAULT_NODE_SIZE = 2.0 # default node size in meters
DEFAULT_TRANSMISSIONS_MEMORY = 5 # default number o... | srene/ndnSIM-inrpp | src/visualizer/visualizer/core.py | Python | gpl-2.0 | 62,118 | [
"FLEUR"
] | 9ee74f367db211aad330f138870b379375fd281159756828c881b2612f522b9d |
class node(object):
"""
This class represents a node in the AST built while parsing command lines.
It's basically an object container for various attributes, with a slightly
specialised representation to make it a little easier to debug the parser.
"""
def __init__(self, **kwargs):
asse... | blurrymoi/bashlex | bashlex/ast.py | Python | gpl-3.0 | 7,001 | [
"VisIt"
] | 6cca36aee97a4b32651794c9211b1e27cb4064c4eefd2d2608d0efe925b7d4bf |
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 2 14:42:50 2015
@author: timmonen
"""
#####################33
'''
Iterate over sam-file in read pairs
-------------------------------------
0.a Get the reference positions of each (fwd and bwd) primer (only once)
0.b Make dictionary of fragment and beginning and end... | timmonen/pipeline | pipeline/trim_and_divide.py | Python | mit | 14,762 | [
"pysam"
] | e7f5e8526ce61928d2576f929f28f7cd3587eca0f1caf2a513292cc8d4ac2627 |
#!/usr/bin/env python 3
from olctools.accessoryFunctions.accessoryFunctions import make_path, run_subprocess
from genemethods.sipprCommon.bowtie import Bowtie2CommandLine, Bowtie2BuildCommandLine
from sipprverse.sippr.method import Method
import genemethods
from Bio.Sequencing.Applications import SamtoolsFaidxCommandli... | adamkoziol/geneSipprV2 | tests/test_method.py | Python | mit | 13,128 | [
"BLAST",
"Biopython",
"Bowtie"
] | 5f89cf90e436170b37dbb902290dbb6f7224b4227f29612a1c2bb45869b2f442 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | fingeronthebutton/RIDE | src/robotide/lib/robot/reporting/resultwriter.py | Python | apache-2.0 | 6,011 | [
"VisIt"
] | 2c06a360cfe32691b0ba919a5300c53805c8bb4140ce87d3cd9a63c74f7ecd45 |
#!/usr/bin/env python
import sys, os, pysam
from optparse import OptionParser
from jobTree.scriptTree.target import Target
from jobTree.scriptTree.stack import Stack
from jobTree.src.bioio import fastqRead, fastaRead, setLoggingFromOptions, logger
from subprocess import Popen, PIPE
from itertools import izip
"""
An... | mitenjain/nanopore | scripts/muscle_compare_2d/muscle_compare_2d.py | Python | mit | 7,051 | [
"pysam"
] | 607c868259044dcd44e1656fcddb169313638b59c0a7ada989c33e6224730629 |
#
# Copyright 2014-2015, 2017, 2020-2021 Lars Pastewka (U. Freiburg)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GN... | libAtoms/matscipy | tests/test_supercell_calculator.py | Python | lgpl-2.1 | 2,641 | [
"ASE",
"Matscipy"
] | 807ba18a463feba659bb91d6740b48436ebbfd106b2c3d3c9016a38c6071dd55 |
""" Base Storage Class provides the base interface for all storage plug-ins
exists()
These are the methods for manipulating files:
isFile()
getFile()
putFile()
removeFile()
getFileMetadata()
getFileSize()
prestageFile()
getTransportURL()
These are the methods for... | vmendez/DIRAC | Resources/Storage/StorageBase.py | Python | gpl-3.0 | 10,756 | [
"DIRAC"
] | 5bf1507cc037bf8d8dc48f696bd42f90138ff0c9c58ed32a49d8464ea1efaa19 |
# 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 PyParmed(PythonPackage):
"""ParmEd is a general tool for aiding in investigations of
b... | LLNL/spack | var/spack/repos/builtin/packages/py-parmed/package.py | Python | lgpl-2.1 | 753 | [
"Amber",
"CHARMM",
"OpenMM"
] | 3686d595c435394681e54626beaf76cb1b20a08f549823065c287411624e8d14 |
"""
How to get a particular Neuron's gap junctions from the database.
"""
from __future__ import absolute_import
from __future__ import print_function
import PyOpenWorm as P
from PyOpenWorm.worm import Worm
from PyOpenWorm.context import Context
from OpenWormData import BIO_ENT_NS
# Connect to existing database.
P.co... | gsarma/PyOpenWorm | examples/gap_junctions.py | Python | mit | 968 | [
"NEURON"
] | 8ba05d01c3449eac34592cd82637d4e91fac26d364a5d717235b225029d53daf |
"""
Test utils for CCX
"""
import datetime
import pytz
from django.conf import settings
from student.roles import (
CourseCcxCoachRole,
CourseInstructorRole,
CourseStaffRole
)
from student.tests.factories import (
UserFactory
)
from xmodule.modulestore.django import modulestore
from xmodule.modulestor... | ampax/edx-platform | lms/djangoapps/ccx/tests/utils.py | Python | agpl-3.0 | 4,160 | [
"VisIt"
] | 8ea59661a55286b832fa74f551f480e49ab014f1c9b8273d93193263837becad |
# Copyright (C) 2012 Mathias Brodala
#
# 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, or (at your option)
# any later version.
#
# This program is distributed in the hope that... | Zarokka/exaile | plugins/osd/__init__.py | Python | gpl-2.0 | 12,804 | [
"FLEUR"
] | e2e9f37fe9f747fe2b2a52f5f86a1c0aba7203c7a52e3e124dd37e560caa9343 |
from iminuit import Minuit
from probfit import BinnedLH, Extended, AddPdf, gen_toy
from probfit.pdf import HistogramPdf
from probfit.plotting import draw_pdf
import numpy as np
bound = (0, 10)
np.random.seed(0)
bkg = gen_toy(lambda x : x**2, 100000, bound=bound) # a parabola background
sig= np.random.randn(50000)+5 #... | mtresch/probfit | doc/pyplots/pdf/histogrampdf.py | Python | mit | 899 | [
"Gaussian"
] | 1e942f0a175b064b8f33aae192bd6b8061a053902a34efbcc5f570f2da710f32 |
#!/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... | sunqm/pyscf | pyscf/pbc/scf/test/test_uhf.py | Python | apache-2.0 | 4,007 | [
"PySCF"
] | 627ee54614fbdd463041ea75cf87ce07016b17d4568365b071eefa433b210b67 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 9 18:38:07 2018
Handler for the big nasty integrals pertaining to generating correlation models
from CAMB.
The model desired here is:
omega_{DM}(theta) = pi times integral of (z = 0 to infinity)
times integral o... | cassandra-sh/corrset | camb_model_new.py | Python | mit | 14,255 | [
"Gaussian"
] | 1fdbb1e11dc06b0468f8bfb18cbae0d9e2ab1086dfde0a1fe3aad7dde3b0cb40 |
# -*- coding: utf-8 -*-
from pymol.cgo import *
from pymol import cmd ... | yorzh86/Step1 | scripts/drawBox.py | Python | gpl-2.0 | 5,047 | [
"PyMOL"
] | 5198bd864b5190d2bcdfcbe2b6ee7dcb055b8441964b9b35c129d4f14ff87e25 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/xyz.py | Python | gpl-2.0 | 3,096 | [
"ChemPy",
"PyMOL"
] | f8f82abc5919082d1b11fbb39aa891d4ea569e4551faf500223771f1c6035ad4 |
"""
Sample problems on which to test algorithms.
XXX: get some standard optimization problems from literature
"""
import numpy as np
import base
from pyll import as_apply
from pyll import scope
from pyll_utils import hp_choice
from pyll_utils import hp_uniform, hp_loguniform, hp_quniform, hp_qloguniform
from pyll_u... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/hyperopt-0.0.2/hyperopt/bandits.py | Python | bsd-3-clause | 3,342 | [
"Gaussian"
] | 3841e3762662dc1d537792304d045ae44a0e4ccc74cd39e621c2b0d5c95cc7f2 |
"""
This module provides the AST. Subclass :py:class:`Context` and override the
various methods to allow minivect visitors over the AST, to promote and map types,
etc. Subclass and override :py:class:`ASTBuilder`'s methods to provide alternative
AST nodes or different implementations.
"""
import copy
import string
imp... | markflorisson/minivect | minivect/miniast.py | Python | bsd-2-clause | 49,678 | [
"VisIt"
] | 368d73ae3f9ec8e8335725f7468550d9cc759ac0cb8368c0488a1877e6a44936 |
#\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\#
import os
from GangaGaudi.Lib.RTHandlers.RunTimeHandlerUtils import get_share_path, master_sandbox_prepare, sandbox_prepare, script_generator
from GangaDirac.Lib.RTHandlers.DiracRTHUtils import dirac_inputdata, dirac_ouputdata, mangle_job_n... | ganga-devs/ganga | ganga/GangaLSST/Lib/Im3ShapeApp/Im3ShapeRTHandler.py | Python | gpl-3.0 | 9,462 | [
"DIRAC"
] | 90db995d3e9d6f0a5c2d868b6e09c3ea5fcda6d9702e262805e72e2f9115f6af |
# IM - Infrastructure Manager
# Copyright (C) 2011 - GRyCAP - Universitat Politecnica de Valencia
#
# 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... | indigo-dc/im | IM/InfrastructureManager.py | Python | gpl-3.0 | 65,292 | [
"Galaxy"
] | 4c1867fa2f420b8c55c56e9c934a9e174080976b6ede28de10be5ace0a199760 |
# Copyright 2001 by Gavin E. Crooks. 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.
""" Handle the SCOP CLAssification file, which describes SCOP domains.
The file format is d... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SCOP/Cla.py | Python | apache-2.0 | 3,824 | [
"Biopython"
] | 5abaf20f57c89c1c31a4ab3f49e38fa8fc2d50169c2bc462a1c155bf044a1d68 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Complete pipeline for online processing using OnACID.
@author: Andrea Giovannucci @agiovann and Eftychios Pnevmatikakis @epnev
Special thanks to Andreas Tolias and his lab at Baylor College of Medicine
for sharing their data used in this demo.
"""
from copy import dee... | agiovann/Constrained_NMF | demos/obsolete/1_1/demo_OnACID_mesoscope_1_1.py | Python | gpl-2.0 | 18,568 | [
"NEURON"
] | 8c1c2aeff042f137023138303aad056c907a826c9f3e2a9c1842f9de1692ea32 |
from traceHandler import *
from modelHandler import *
from optimizerHandler import *
from optionHandler import optionHandler
from scipy.interpolate import interp1d
from scipy import linspace
import time
import numpy
class coreModul():
"""
This class is responsible to carry out the main steps of the optimization proc... | KaliLab/optimizer | optimizer/Core.py | Python | lgpl-2.1 | 21,650 | [
"NEURON"
] | 663e035054da403abd7247357228cde09cc16fac1cac1b6411d3a141b0805731 |
import unittest,zlib
from DIRAC.WorkloadManagementSystem.DB.SandboxDB import SandboxDB
class JobDBTestCase(unittest.TestCase):
""" Base class for the SandboxDB test cases
"""
def setUp(self):
print
self.sDB = SandboxDB('Test',20)
class SandboxCase(JobDBTestCase):
""" TestJobDB represents a te... | avedaee/DIRAC | WorkloadManagementSystem/DB/test/TestSandboxDB.py | Python | gpl-3.0 | 1,326 | [
"DIRAC"
] | 25fa3ab95dc73e8da44789520411b0c75c556ab18b8bf3e5c52b9d2780217eee |
# Copyright (C) 2013-2020 2ndQuadrant Limited
#
# Client Utilities for Barman, Backup and Recovery Manager for PostgreSQL
#
# Barman 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 Lice... | 2ndquadrant-it/barman | tests/test_barman_wal_archive.py | Python | gpl-3.0 | 12,267 | [
"BWA"
] | 5f56b12835873abed0c7c9c7c33430504907df3393ca269edcb3c1eb9bd57aed |
# Natural Language Toolkit: Expectation Maximization Clusterer
#
# Copyright (C) 2001-2011 NLTK Project
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
import numpy
from api import *
from util import *
class EMClusterer(VectorSpaceClusterer):
""... | tadgh/ArgoRevisit | third_party/nltk/cluster/em.py | Python | apache-2.0 | 9,501 | [
"Gaussian"
] | 4ebdd5745eb13a432f979be9ee83095f6d7440052b14699182f964dcca8795fa |
import logging
from django.core.urlresolvers import reverse_lazy
from django.http import HttpResponseRedirect
from django.views.generic.detail import DetailView
from django.views.generic.edit import CreateView, UpdateView
from django.views.generic.list import ListView
from api.models import GalaxyInstance
from regist... | erasche/galactic-radio-telescope | web/views.py | Python | agpl-3.0 | 2,279 | [
"Galaxy"
] | d1d4748cf1f1189c649727061eabc62239c7b6a75aa0ed1f4b314f33bd81c8d7 |
#!/usr/bin/python
# sim1: simulate effect of B/F on shape measurement if it's not accounted for
import numpy as np
import os
import sys
import math
import matplotlib
matplotlib.use('Pdf')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.backends.backend_pdf impor... | plazas/wfirst-detectors-vnl | code/nonlinearity.py | Python | mit | 11,762 | [
"Gaussian"
] | 3ae37aa4221ae0465ef079da3e9f169278f6e521d6e40bff631fcf01512b9e39 |
import json
import nose
import datetime
import pylons
import sqlalchemy.orm as orm
import ckan.plugins as p
import ckan.lib.create_test_data as ctd
import ckan.model as model
import ckan.tests.legacy as tests
import ckan.tests.helpers as helpers
import ckanext.datastore.db as db
from ckanext.datastore.tests.helpers ... | namgk/ckan-timeseries | ckanext/timeseries/tests/test_upsert_short.py | Python | agpl-3.0 | 3,333 | [
"Galaxy"
] | 7b7e2235f7b28a417ad0b409ad0189388e10c2fe4a34f40a7b5ce8ed5dd11c3c |
"""Test the JobInfo"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import sys
from six import StringIO
from mock import MagicMock as Mock
from parameterized import parameterized, param
from DIRAC import S_OK, S_ERROR, gLogger
import DI... | yujikato/DIRAC | src/DIRAC/TransformationSystem/test/Test_JobInfo.py | Python | gpl-3.0 | 25,699 | [
"DIRAC"
] | 9061650b38f2a9feccbb3e136c1611ed0e2d70d503264df853f7197bb94dd4ee |
#!/usr/bin/env python2
'''
description: Wrapper to create a single output file in LITTLE_R format from a
list of netcdf files defined in an input file.
Time window is extracted from obsproc.namelist.
Uses external packages: convert_littler_single and cdo
license: ... | rvanharen/ERA_URBAN | scripts/wrapper_littler/wrapper_littler.py | Python | apache-2.0 | 5,397 | [
"NetCDF"
] | 24201d9b1ddcf39439ea79982b27b3ea1618dc068bcfa411a00a45b264fce9e5 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/basics/models.py | Python | agpl-3.0 | 69,727 | [
"Galaxy"
] | d20709532cb8d8e55e845a34c615325b2f633ec04f37d43afc0a23e538471ba0 |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# Denis A. Engemann <d.engemann@fz-juelich.de>
#
# License: BSD 3 clause
from math import log, sqrt
import warnin... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/sklearn/decomposition/pca.py | Python | apache-2.0 | 26,604 | [
"Gaussian"
] | 252e7747c9076ec8b6575c7a7c5b407bdc5aa61e60ea86c3cd237a5eeb1a39c4 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | thilbern/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 34,935 | [
"Brian"
] | 3450ad19e0ba2c9d47f0ac1dcac1a352b0de1a427fc329684e591b4fe787b311 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | jor-/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 208,122 | [
"Gaussian"
] | 5aaff20b2a145ac89c0296663520adc612d807ed58b71a533fa88499349a1c01 |
#!/usr/bin/env python
import sys
import gd_util
from Population import Population
################################################################################
if len(sys.argv) != 6:
gd_util.die('Usage')
input, input_type, ind_arg, pop_input, output = sys.argv[1:]
p_total = Population()
p_total.from_wrappe... | gigascience/galaxy-genome-diversity | tools/discover_familial_relationships/discover_familial_relationships.py | Python | gpl-3.0 | 2,516 | [
"Galaxy"
] | cbe4c440a8430ea34711424b20d530582d251cadfc53296108965a530528a28f |
"""Neighbour Exploring Routing (NER) algorithm from J. Navaridas et al.
Algorithm refrence: J. Navaridas et al. SpiNNaker: Enhanced multicast routing,
Parallel Computing (2014).
`http://dx.doi.org/10.1016/j.parco.2015.01.002`
"""
import heapq
from collections import deque
from ...geometry import concentric_hexagon... | project-rig/rig | rig/place_and_route/route/ner.py | Python | gpl-2.0 | 24,812 | [
"VisIt"
] | bf95ddb1b0c3f0d20021d5628d3b5bfea4eb96832d72ba9d15461ed871405e3a |
#!/usr/bin/env python
#===============================================================================
# Copyright 2015 Geoscience Australia
#
# 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
#... | ama-jharrison/agdc | agdc/deprecated/scene_kml_generator.py | Python | apache-2.0 | 18,633 | [
"NetCDF"
] | c3419a2c884b43ec2aac6f7fa36c74ed199d5e3586e7bffdeb2411e539115f13 |
#!/usr/bin/env python3
#-*- coding: utf-8 -*-
# Copyright 2017, National University of Ireland and The James Hutton Insitute
# Author: Nicholas Waters
#
# This code is part of the riboSeed package, and is governed by its licence.
# Please see the LICENSE file that should have been included as part of
# this package.
"... | nickp60/riboSeed | riboSeed/riboScore.py | Python | mit | 24,260 | [
"BLAST"
] | a2c23051fdcd6d7dc64b5c772e2269c1df7e95c00538f7a055216b165627b96d |
#ImportModules
import ShareYourSystem as SYS
#Definition
MyBrianer=SYS.BrianerClass(
).set(
'-Populations',
[
(
'ManagingBeforeSetVariable',
{
'NeurongroupingBrianKwargDict':
{
'model':
'''
dv/dt = (ge+gi-(v+49*mV))/(20*ms) : volt
dge/dt = -ge/(5*ms) : volt
dg... | Ledoux/ShareYourSystem | Pythonlogy/draft/Simulaters/Brianer/draft/01_ExampleDoc.py | Python | mit | 1,386 | [
"Brian"
] | 9ef1d86a69149e29639bb1489d65f8a4c37673ad54af40852922d71e37a967ea |
from distutils.core import setup
setup(
name='RMQ-Utils',
version='0.0.5',
author='Brian Hines',
author_email='brian@projectweekend.net',
packages=['rmq_utils'],
url='https://github.com/projectweekend/RMQ-Utils',
license='LICENSE.txt',
description='Utilities for managing RabbitMQ.',
... | projectweekend/RMQ-Utils | setup.py | Python | mit | 452 | [
"Brian"
] | be68ed3a85a70cd66546b367aeccad58aab82b83d0623160202e37b2f266c1d2 |
from octopus.modules.es.testindex import ESTestCase
from service import licences
class TestModels(ESTestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_01_variations(self):
vars = licences.make_variations(["a", "b", "c"])
assert "a b c" in vars
asser... | CottageLabs/oacwellcome | service/tests/unit/test_licences.py | Python | apache-2.0 | 926 | [
"Octopus"
] | 480cec6b7623059255f0101a73755c03061e7de6ba538a02166813bb5466e75c |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/peacock/tests/utils/test_FileCache.py | Python | lgpl-2.1 | 1,899 | [
"MOOSE"
] | cdf9a31ab1682b8b338c01356139c5789a5d8a636af688d634c0ecf6c4dd8699 |
from __future__ import absolute_import
from . import TypeSlots
from .ExprNodes import not_a_constant
import cython
cython.declare(UtilityCode=object, EncodedString=object, BytesLiteral=object,
Nodes=object, ExprNodes=object, PyrexTypes=object, Builtin=object,
UtilNodes=object)
from . imp... | madjar/cython | Cython/Compiler/Optimize.py | Python | apache-2.0 | 182,733 | [
"VisIt"
] | 9dbaaf411ff0d515362857d112ea32f0193ab442008c1b567684d1e6e0a2efb0 |
#!/usr/bin/python
#
# Copyright (c) 2012, Psiphon Inc.
# All rights reserved.
#
# 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 v... | MewX/Psiphon3-for-Linux | pyclient/psi_client.py | Python | gpl-2.0 | 6,909 | [
"VisIt"
] | 3c0b4c25db017a7f11c62cf24410f139e141dafc491c8711fd81e6dbff598c78 |
"""
Acceptance tests for Studio related to course reruns.
"""
import random
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..pages.studio.index import DashboardPage
from ..pages.studio.course_rerun import CourseRerunPage
from ..pages.studio.overview import CourseOutlinePage
from .... | epam-mooc/edx-platform | common/test/acceptance/tests/test_studio_rerun.py | Python | agpl-3.0 | 4,115 | [
"VisIt"
] | ed05acd520abe00fcbf99652478ca9210247260f50213b0c4bf579f95557d683 |
"""
A program to solve the 2D Klein Gordon equation using a
second order semi-explicit method
More information on visualization can be found on the Mayavi
website, in particular:
http://github.enthought.com/mayavi/mayavi/mlab.html
which was last checked on 6 April 2012
"""
import math
import numpy
from mayavi impor... | openmichigan/PSNM | PythonPrograms/Programs/PythonCode/KleinGordon2D.py | Python | bsd-2-clause | 4,657 | [
"Mayavi"
] | e7d9ae5de1fc4574202b230b9ac8c244873703fce4791b5fed196d77b15be910 |
#
# 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, time
m = 500
n = 250
display = True
worldRan... | justusc/Elemental | examples/interface/NNLSDense.py | Python | bsd-3-clause | 1,406 | [
"Gaussian"
] | 1411467af6c482986daf7a2d5776e22826e74c51b6255156cae869bbd18390ab |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | zak-k/iris | lib/iris/tests/test_netcdf.py | Python | gpl-3.0 | 42,650 | [
"NetCDF"
] | 41e1ce50522f4e5ed69df79cc2dab0cdedaf04763f4ff5521cde8daead1afd92 |
"""
This module calculates corrections for the species listed below, fitted to the experimental and computed
entries given to the CorrectionCalculator constructor.
"""
import os
import warnings
from typing import Dict, List, Optional, Tuple, Union
import numpy as np
import plotly.graph_objects as go
from monty.serial... | materialsproject/pymatgen | pymatgen/entries/correction_calculator.py | Python | mit | 20,358 | [
"pymatgen"
] | 67537230563733f2a79e9209acdffefb412021dbc4a9dff54e9746ce8f4faee3 |
# -*- coding: utf-8 -*-
# Copyright (C) 2019 - 2020 by Pedro Mendes, Rector and Visitors of the
# University of Virginia, University of Heidelberg, and University
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc.,... | copasi/COPASI | copasi/bindings/python/unittests/Test_CCopasiVector.py | Python | artistic-2.0 | 2,748 | [
"COPASI"
] | d90bd092b1a59d249317fb1fdce725830bf0da10b1ada5cef60b58629ade7c0e |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements input and output processing from Nwchem.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date_... | Dioptas/pymatgen | pymatgen/io/nwchemio.py | Python | mit | 26,194 | [
"Gaussian",
"NWChem",
"pymatgen"
] | 4db58270fbbd571e4dffab64cff3dfa14cb05984b0a095e3643436cfcb084541 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015-2016 Nervana Systems 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
#... | guoxuesong/deepstacks | examples/neon/mnist_mergesum.py | Python | mit | 4,240 | [
"Gaussian"
] | c1b5167ecaf1f4b171d7ed0f8f81a43ca0940c30f794b94411d68c4225b9aedc |
import POVME.packages.binana.peel as peel
import POVME.packages.pymolecule.pymolecule as pymolecule
my_params = peel.defaultParams
trp = pymolecule.Molecule()
trp.fileio.load_pdb_into( 'trp.pdb', bonds_by_distance=True, serial_reindex = True, resseq_reindex=False)
my_peel = peel.peel(trp, my_params)
my_peel.write_vmd_s... | POVME/POVME | POVME/packages/binana/tests/peel_trp_basic/trpTest.py | Python | mit | 613 | [
"VMD"
] | 68fdca0e615db5978754f2fa3a0a9843558fcbe33c6978fd9e107e1e6952a708 |
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