text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""
This is the File StorageClass, only meant to be used localy
"""
import os
import shutil
import errno
import stat
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Storage.Utilities import checkArgumentFormat
from DIRAC.Resources.Storage.StorageBase import StorageBase
from DIRAC.Core.Utilities.Adler i... | DIRACGrid/DIRAC | src/DIRAC/Resources/Storage/FileStorage.py | Python | gpl-3.0 | 21,805 | [
"DIRAC"
] | 0d6e52e50daaa608e2f0ef8aa6a7af05ed7a511b7e716506aa48ef3979290094 |
from pyscf.gto import Mole
from pyscf.scf import RHF, RKS
from pyscf.gw import GW
from pyscf.gw.gw_slow import GW as GW_slow
from pyscf.tdscf import TDRHF, TDRKS
from pyscf.tdscf.rhf_slow import TDRHF as TDRHF_slow
from pyscf.tdscf.proxy import TDProxy
import numpy
from numpy import testing
import unittest
from test_... | gkc1000/pyscf | pyscf/gw/test/test_gw.py | Python | apache-2.0 | 5,418 | [
"PySCF"
] | 1fc476eb864afbb0dbadca18092d4824e1accad54a062598076f19a41c2548ad |
"""
Tinker Tank V : Python Meetup
Description : Simple Flask app + with GPIO usage
Contact: lgobaira@gmail.com
MAY 2016
"""
# Import necessary external libraries
import time
import RPi.GPIO as GPIO
import requests
from flask import Flask
# Lets create an instance of a Flask app
app = Flask(__name__)
# Setup the GP... | lmgobaira/tinkerTankExamples | app.py | Python | mit | 2,365 | [
"TINKER"
] | 39ff7b16a8adbb5ea40451f151361b4efdc190bae1152caf6e5ca048b9324adf |
# -*- coding: utf-8 -*-
"""
Suntans temporal filtering code
Created on Tue May 14 09:49:38 2013
@author: mrayson
"""
import numpy as np
from netCDF4 import Dataset
import matplotlib.pyplot as plt
from sunpy import Spatial, unsurf
from timeseries import timeseries
from suntans_ugrid import ugrid
import othertime
c... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/sunfilter.py | Python | mit | 4,764 | [
"NetCDF"
] | 9af3c26ae43e690f2a68610eee55b94aaa7e053c289f2bf0dd3e7752e8e95b6d |
# Copyright 2017 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | duftler/spinnaker | unittest/buildtool/bom_command_test.py | Python | apache-2.0 | 14,861 | [
"ORCA"
] | 54d7dd1343dc719df4403d425eeeb55ec898a06317085d28fecdf8b7b12baff9 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_http_client,
compat_urllib_error,
compat_urllib_parse_urlparse,
compat_urlpa... | kthordarson/youtube-dl-ruv | youtube_dl/extractor/common.py | Python | unlicense | 33,599 | [
"VisIt"
] | a6ee99fd1636c2e02f01e62a715d179d9a92f31c8c3c9337899bf03dfac81d24 |
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Supplies a class for worki... | rvianello/rdkit | rdkit/Chem/Fingerprints/DbFpSupplier.py | Python | bsd-3-clause | 4,448 | [
"RDKit"
] | ad01e0c11b5fa6a5ce923713e46340c9ede12333542f6c071ffd0844e302b961 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | ramondelafuente/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 12,503 | [
"Brian",
"Galaxy"
] | 3c2c3abd25ef0b3a8711317df0a85209fa2c60cc7dfbc2851bbc898a96c78f27 |
#! /usr/bin/python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Version: 0.7+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
For developers who work from a V... | waytai/doto | versioneer.py | Python | mit | 25,372 | [
"Brian"
] | 47e175217b60882e976243fa5bab7931224041598a8bb99fa227613c851d997e |
r"""
This module is a VTK Web server application.
The following command line illustrate how to use it::
$ vtkpython .../vtk_web_phylogenetic_tree.py --tree /.../data.phy --table /.../data.csv
Set of expected arguments:
--tree /file/path/to/anolis.phy
--table /file/path/to... | hlzz/dotfiles | graphics/VTK-7.0.0/Web/Applications/PhylogeneticTree/server/vtk_web_phylogenetic_tree.py | Python | bsd-3-clause | 5,429 | [
"VTK"
] | 3835224d8d570ea9f544d23db824f8fea55f6c68d55d8dfcdd949398731d39b0 |
# Turta IoT HAT Helper for Raspbian
# Distributed under the terms of the MIT license.
# Python Driver for NXP MMA8491Q 3-Axis Accelerometer & Tilt Sensor
# Version 1.02
# Updated: June 25th, 2019
# Visit https://docs.turta.io for documentation.
import time
import RPi.GPIO as GPIO
from smbus import SMBus
class MMA84... | Turta-io/IoTHAT | DriverSource/Raspbian/Python/Turta_MMA8491Q.py | Python | mit | 4,446 | [
"VisIt"
] | 4f4a778ad6cd0df145cd154880e7c32ece7f06b954f6c7fde513a0742dd2074c |
# -*- coding: utf-8 -*-
#
# TGiT, Music Tagger for Professionals
# Copyright (C) 2013 Iconoclaste Musique Inc.
#
# 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... | Iconoclasteinc/tgit | tgit/countries.py | Python | gpl-3.0 | 11,846 | [
"BWA"
] | bfa2d627d195b693c66ac8936897364140b5c868b1e50b602b6221a3090b797a |
#!/usr/bin/env python
import sys
import os
import tempfile
sys.path.append('/usr/lib/freecad/lib')
import FreeCAD, Part
from pivy import coin
# create a test geometry and create an IV representation as string
box=Part.makeCone(10,8,10)
iv=box.writeInventor()
# load it into a buffer
inp=coin.SoInput()
#inp.setBuffer... | dwighthubbard/SimpleSolidPy | examples/image_dump.py | Python | gpl-2.0 | 1,385 | [
"CRYSTAL"
] | 0180990d238a6cb5f080539ae986919c58d62986e1f7fe1f4c74a992efa54b40 |
#!/usr/bin/env python
##########################################################################
#
# Copyright 2008 Tungsten Graphics, Inc., Cedar Park, Texas.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files ... | guorendong/iridium-browser-ubuntu | third_party/mesa/src/src/gallium/tools/trace/model.py | Python | bsd-3-clause | 5,795 | [
"VisIt"
] | 2451a435174d1a8800f5c3cfe0545db63897261996d3edbc451cba57630a613f |
from celery import shared_task, task
from django.core.mail import send_mail
from django.conf import settings
import logging
from django.template.loader import render_to_string
from let_me_app import models
from let_me_auth import models as auth_models
from django.core.mail.message import EmailMultiAlternatives
from le... | oleg-chubin/let_me_play | let_me_app/tasks.py | Python | apache-2.0 | 13,101 | [
"VisIt"
] | c3ab02ea28cbf6577dd16fdc25dbf2f345fef8a710a4b938fb3301bd7e0a91f4 |
# -*- coding: utf-8 -*-
import sys
from math import pi, exp, sqrt, log
import numpy as np
from scipy.optimize import fsolve
from scipy import __version__ as scipy_version
from ase.utils import prnt, devnull
from ase.units import Hartree
from ase.data import atomic_numbers, chemical_symbols
from gpaw.spline import Spl... | robwarm/gpaw-symm | gpaw/atom/generator2.py | Python | gpl-3.0 | 40,677 | [
"ASE",
"GPAW",
"Gaussian"
] | 1404f2cec100c1964a4adea0bd425c2a1bf5de264904d11c579b75bf1e185437 |
########################################################################
# $HeadURL $
# File: FTSStrategy.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/12 13:12:07
########################################################################
""" :mod: FTSStrategy
=================
.. module: FTSStrate... | vmendez/DIRAC | DataManagementSystem/private/FTS2/FTS2Strategy.py | Python | gpl-3.0 | 18,293 | [
"DIRAC"
] | ead0431e7949dea18652499bb743e7a663560545968fd989aeea3c4afa3fd8f9 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | paulojamorim/invesalius3 | invesalius/gui/dicom_preview_panel.py | Python | gpl-2.0 | 32,672 | [
"VTK"
] | 91dd7ede0a9209f583b604bd5cc4dfe2445e6dc313f88a75cafaf44fcef7b467 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | samples/visualization_cellsystem.py | Python | gpl-3.0 | 2,509 | [
"ESPResSo"
] | 2b47ceb874ccec219bb1fd7540f9ed4ce121a94481d97905deec5c96d43f3e64 |
from __future__ import print_function
import numpy as np
from theano.compat.six.moves import cStringIO, xrange
import theano.tensor as T
from theano.tests import disturb_mem
from theano.tests.record import Record, RecordMode
from pylearn2.compat import first_key
from pylearn2.costs.cost import Cost, SumOfCosts, Defau... | Refefer/pylearn2 | pylearn2/training_algorithms/tests/test_sgd.py | Python | bsd-3-clause | 59,375 | [
"VisIt"
] | 16bef8d11d9dc60671afc10f1a41a0263ec77a2fea9ba35eaa0943160c02d2f6 |
# -*- coding: utf-8 -*-
"""
@file
@brief Defines a sphinx extension to show :epkg:`DOT` graph
with :epkg:`viz.js` or :epkg:`graphviz`.
.. versionadded:: 1.9
"""
import os
import logging
import shutil
from docutils import nodes
from docutils.parsers.rst import directives
import sphinx
from docutils.parsers.rst import D... | sdpython/pyquickhelper | src/pyquickhelper/sphinxext/sphinx_gdot_extension.py | Python | mit | 10,979 | [
"VisIt"
] | 65fb74606b0ab81a273f24dabfebba8da38a7e61d2801fbf67f9ca572b2e3a73 |
# $Id$
from module_base import ModuleBase
from module_mixins import FilenameViewModuleMixin
import module_utils
import vtk
import os
class vtkPolyDataRDR(FilenameViewModuleMixin, ModuleBase):
def __init__(self, module_manager):
"""Constructor (initialiser) for the PD reader.
This is almost ... | chrisidefix/devide | modules/readers/vtkPolyDataRDR.py | Python | bsd-3-clause | 2,204 | [
"VTK"
] | 37286e78fdbab0783f5aefb4afaf5ec8cbb8fdc5ae67948d42dc93cd317c9619 |
# Copyright 2019 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... | aam-at/tensorflow | tensorflow/python/keras/layers/kernelized.py | Python | apache-2.0 | 11,195 | [
"Gaussian"
] | 12ee5ace425aaf584b9152dcce52c801e4fb716701f904abd45d862f7dc998aa |
"""
Histogram-related functions
"""
from __future__ import division, absolute_import, print_function
import operator
import warnings
import numpy as np
from numpy.compat.py3k import basestring
__all__ = ['histogram', 'histogramdd', 'histogram_bin_edges']
# range is a keyword argument to many functions, so save the ... | ryfeus/lambda-packs | Tensorflow_Pandas_Numpy/source3.6/numpy/lib/histograms.py | Python | mit | 36,704 | [
"Gaussian"
] | 2b07466660d76283ce2a3cbfe54759d1ac0e6a75a5dc440662437440b5e78904 |
from __future__ import print_function
import numpy as np
from ase.dft import Wannier
from gpaw import restart
atoms, calc = restart('poly.gpw', txt=None)
# Make wannier functions using (one) extra degree of freedom
wan = Wannier(nwannier=6, calc=calc, fixedenergy=1.5)
wan.localize()
wan.save('poly.pickle')
wan.trans... | misdoro/python-ase | doc/tutorials/wannier/wannier_polyacetylene.py | Python | gpl-2.0 | 868 | [
"ASE",
"GPAW"
] | a1420af8e6e54ac5d48ec42c31e142a4cd6e3163198a4590d4b495f52941ef4c |
"""
FoldX
=====
"""
import os
import logging
import shutil
import ssbio.utils
import os.path as op
import pandas as pd
from ssbio.core.object import Object
log = logging.getLogger(__name__)
class FoldX(Object):
"""Class to run various commands from the FoldX suite of tools on a protein structure file.
Args... | SBRG/ssbio | ssbio/protein/structure/utils/foldx.py | Python | mit | 9,750 | [
"FoldX"
] | 3caa522e386c29eabc3b4bbc45bc3fcff797543462b59c6c6d0e1e4bccd4d34c |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009-2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | pmghalvorsen/gramps_branch | gramps/plugins/rel/rel_sl.py | Python | gpl-2.0 | 15,427 | [
"Brian"
] | 379a5d7462e7a91ba1bbde98ed2e8f684e7e03b495bbd845b144faf111658a89 |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 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... | sillvan/hyperspy | hyperspy/model.py | Python | gpl-3.0 | 78,500 | [
"Gaussian"
] | 57203b0bd6aa8e2490ca4f39531d57e54d50c4ca2bff839b823862e32d6ee8c1 |
import argparse, random
class randomizeFastq:
"""
Class Description:
User Notes:
Revision History: 2014.12.12 Brian Yu Created
2015.05.28 Changed file open syntax to with open() as f
"""
def __init__(self, fastq1, fastq2):
"""
Reads in both fastq files... | brianyu2010/Mini-Metagenomic_Analyses | randomizeFastq.py | Python | gpl-3.0 | 2,658 | [
"Brian"
] | a593516ba22f9dea26c3f11eba551332cb8a3a34c219504a3304099922a12042 |
#
# Copyright (C) 2019 Greg Landrum
# All Rights Reserved
#
from rdkit import RDConfig, rdBase
from rdkit import Chem
from io import BytesIO
import unittest
class TestCase(unittest.TestCase):
def setUp(self):
self.sdf = b"""
RDKit 2D
3 3 0 0 0 0 0 0 0 0999 V2000
0.8660 0... | ptosco/rdkit | Code/GraphMol/Wrap/testPropertyLists.py | Python | bsd-3-clause | 3,981 | [
"RDKit"
] | 8a662731bc2ec488ee7309bb18b0105ed92a1d2c7207972c3cc91c71deb74576 |
# -*- coding: utf-8 -*-
#
# MOOSE documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 1 19:05:47 2014.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | rahulgayatri23/moose-core | Docs/user/snippets_tutorial/conf.py | Python | gpl-3.0 | 8,275 | [
"MOOSE"
] | 1b4d407c7971265d0b7d58db45dcc9d3e6eafa05dd34e9417d7232fafe243c0a |
"""
==========================
Plotting tract profiles
==========================
An example of tracking and segmenting two tracts, and plotting their tract
profiles for FA (calculated with DTI). This example uses the Yeatman et al.
waypoint ROI approach, first described in [Yeatman2012]_ and further elaborated
in [Ye... | arokem/pyAFQ | examples/plot_tract_profile.py | Python | bsd-2-clause | 8,734 | [
"Brian"
] | 526fb5d881606b6c1ebf9d982b7a65bae27458a19578c40f33940840e2a5af05 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParallel import R... | zzyfisherman/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 40,131 | [
"MOOSE",
"VTK"
] | 65e0ebf55c239b3f46437a2f0cc561ed4f182c68eb70951ca5bdfef5dc667484 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Greyscale ℓ2-TV Denoising
=========================
This example demonstrates the use of class :class:`.tvl2.T... | alphacsc/alphacsc | alphacsc/other/sporco/examples/scripts/tv/tvl2den_gry.py | Python | bsd-3-clause | 2,745 | [
"Gaussian"
] | 090c121c4d2bb1e1a485953f158ec10fd0affa739f4225d04ea40b2100415dc9 |
# Copyright (c) 2010 OpenStack, LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | zaitcev/swift-lfs | test/unit/common/middleware/test_staticweb.py | Python | apache-2.0 | 32,705 | [
"VisIt"
] | cd21aea2931550c70ff2235975ec19cf53b4ab6ea408b9cbafc401cdf8694c44 |
import unittest
import os
import time
from AZutilities import dataUtilities
from AZutilities import getCinfonyDesc
import AZOrangeConfig as AZOC
class evalUtilitiesTest(unittest.TestCase):
def setUp(self):
smiDataPath = os.path.join(AZOC.AZORANGEHOME,"tests/source/data/mol.smi")
self.smi... | AZCompTox/AZOrange | tests/source/AZorngCinfonyTest.py | Python | lgpl-3.0 | 2,795 | [
"CDK"
] | 5ac9d6c5ddc5e4a89592f6ae78f539476e8fee161146d150a41cb917a202118b |
#!/usr/bin/env python
"""
After a library is mapped to the genome (using map_single_fragments.py or any
other mapper), the bam file is screened for reads that weren't mapped to the
genome or weren't concise and try to map wach of the ends to a different
location. This script report the reads that are chimeric in a tab... | asafpr/pro_clash | bin/map_chimeric_fragments.py | Python | mit | 7,982 | [
"BWA",
"pysam"
] | 82b50f57d9ccdb857d4a832f65918c14442cbb3fb9d4b7cceab27fd680faecaf |
#
# NAME
# problem_set2_solutions.py
#
# DESCRIPTION
# Open, view, and analyze action potentials recorded during a behavioral
# task. In Problem Set 2, you will write create and test your own code to
# create tuning curves.
#
#Helper code to import some functions we will use
from __future__ i... | sankar-mukherjee/EEG-coursera | problem/problem_set2/problem_set2.py | Python | mit | 7,304 | [
"NEURON"
] | 7ab4f41fee91e231a22cd60b5a0f9e42b7900802a83608c191d7b9cb3d4b4e58 |
#* 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 html
... | nuclear-wizard/moose | python/MooseDocs/tree/html.py | Python | lgpl-2.1 | 4,827 | [
"MOOSE"
] | c24cbd8ad1ac7f6566b38e99432ebc62dc7b2740283da03de97f41cf12bc012a |
# This file is part of xrayutilities.
#
# xrayutilities 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 program is distributed... | dkriegner/xrayutilities | examples/xrayutilities_io_cif_parser_bi2te3.py | Python | gpl-2.0 | 952 | [
"CRYSTAL"
] | 50e395cc695cfe539a1029d44c1ec04945677674a19e8b36f97ff83ddda08b24 |
#!/usr/bin/env python
import vtk
import vtk.test.Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Parameters for testing
res = 250
# Graphics stuff
ren0 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren0)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderW... | keithroe/vtkoptix | Filters/Points/Testing/Python/TestSPHInterpolator.py | Python | bsd-3-clause | 2,429 | [
"VTK"
] | 305d996381b37442cc0a2b11a5ac3ee63c0f61d5398067de627a61909dd96186 |
# -*- coding: utf-8 -*-
import html
from datetime import date, timedelta
from dateutil.relativedelta import relativedelta
from itertools import chain
import random
import reversion
from unittest.mock import patch
import urllib
from urllib.parse import urlparse
from django import forms
from django_comments import get_f... | WikipediaLibrary/TWLight | TWLight/applications/tests.py | Python | mit | 128,362 | [
"VisIt"
] | f68968e2c98eb2c5363a46e3990cec2f6353b65b00abd7f20dd152b7a8069700 |
# -*- coding: utf-8 -*-
#
# This file is part of couchapp released under the Apache 2 license.
# See the NOTICE for more information.
from __future__ import with_statement
import base64
import logging
import mimetypes
import os
import os.path
import re
import webbrowser
try:
import desktopcouch
except ImportErr... | rwaldron/couchapp | couchapp/localdoc.py | Python | apache-2.0 | 15,751 | [
"VisIt"
] | 8666939c532ab3df7733a40274d0be8c01d9e9c3feec63a4ba58e46a218af486 |
# -*- coding: utf-8 -*-
# Copyright (c) 2013 Spotify AB
import logging
import pdb
import random
import sys
from graphwalker import codeloader
from graphwalker import halting
# some ghetto enums
COST, PATH = 0, 1
# approximation of infinity(tm)
inf = 2 ** 31
log = logging.getLogger(__name__)
class Planner(object):
... | bartvanherck/python-graphwalker | graphwalker/planning.py | Python | apache-2.0 | 11,785 | [
"VisIt"
] | 3dc5ecca9a99a5e674651c237b7bb04b822c5dad1f5f053745b9c088f0c60d35 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/__init__.py | Python | apache-2.0 | 2,114 | [
"ORCA"
] | 8d04fbef442e346e0df91545b0b7db95cb038cfa4940cee5344888328eb11b9e |
#!/usr/bin/env python
"""
Copyright (c) 2006-2017 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import sys
sys.dont_write_bytecode = True
try:
__import__("lib.utils.versioncheck") # this has to be the first non-standard import
except ImportError:
exit("[!] wro... | zhinaonet/sqlmap-z | sqlmap.py | Python | gpl-3.0 | 13,026 | [
"VisIt"
] | ae6c3cfe56cd730700e92971d5e268f5c41a03fbc4bd9be8472e711d1e3179ba |
#!/usr/bin/env python
"""clustal_run.py
Example code to show how to create a clustalw command line, run clustalw
and parse the results into an object that can be dealt with easily."""
# standard library
from __future__ import print_function
import os
import sys
import subprocess
# biopython
from Bio.Alphabet import... | updownlife/multipleK | dependencies/biopython-1.65/Doc/examples/clustal_run.py | Python | gpl-2.0 | 2,053 | [
"Biopython"
] | 715ca8506051367739c03c8d26a71df2240a92c4848a6ceb14f39af749605658 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import datetime
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from django.utils import timezone
from mock import patch, MagicMock
from zerver.lib.test_helpers import MockLDAP
from confirmation.model... | dawran6/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 69,443 | [
"VisIt"
] | e1feac414f18002fb72c6f4f5db6e4d15f93415e9e4058e56fe653ae87b9b573 |
"""Module collecting functions dealing with the GLUE2 information schema
:author: A.Sailer
Known problems:
* ARC CEs do not seem to publish wall or CPU time per queue anywhere
* There is no consistency between which memory information is provided where,
execution environment vs. information for a share
* Some ... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/Glue2.py | Python | gpl-3.0 | 15,988 | [
"DIRAC"
] | 8aad73fa3970079459b08181fbe69ed4d42ce1960208e05f43f3511a3819ea5c |
from shadow4.sources.source_geometrical.source_gaussian import SourceGaussian
from shadow4.tools.graphics import plotxy
from srxraylib.plot.gol import plot_scatter
def example_point_source():
a = SourceGaussian.initialize_point_source(number_of_rays=10000,
sigmaXprime=3e-6,
sigma... | srio/minishadow | examples/sources/examples_source_gaussian.py | Python | mit | 2,703 | [
"Gaussian"
] | 847ad8828b404018fae8721b9f6e83cad6642ba55befbda7f633ba4589c403d1 |
# Kevin van Rensburg 11/20/2021
# Copyright 2001
# Testing Startup Script version 0.19
# kstart19.py
# Working on Kvep8.
# added def's ALL(), ALI(), COMCODE(), core(), cipl() and AnotherCode().
# Adding rd(), Or(),bfot(),srr(),cft(),st(),ct(),rat(),wst(),fep(), esot(),seor()
# fixed, reworked, and added scipt to Kvep8 ... | kurg/KendyVerse | kstart19adapted.py | Python | gpl-3.0 | 95,308 | [
"BLAST"
] | 0bdc49de4952e2fce15808b49cdde1ed9f2e223f3222f13d46ee5120baaa72ce |
#!/usr/bin/env python
# coding: utf-8
"""
"""
from __future__ import absolute_import
from puliclient.server.server import Server
from puliclient.server.queueHandler import QueueHandler
from octopus.core import enums
qh = QueueHandler(Server("localhost", 8004))
allJobsList, summary = qh.getAllJobs()
for job in allJo... | mikrosimage/OpenRenderManagement | scripts/examples/request-edit/02_request_jobs.py | Python | bsd-3-clause | 1,145 | [
"Octopus"
] | 60610a250c32ed16584f1317c5163fe753cdb7b1b26aaead2eda59f69cd294ba |
'''
More generic version of the logisitic function
Read in a fasta sequences, scan for every motif in a tamo file, produce numpy matrix as a result
'''
__author__="Sara JC Gosline, Chris W Ng"
__email__="sgosline@mit.edu"
from optparse import OptionParser
#import chipsequtil.Fasta as Fasta
import cPickle
import nu... | agitter/OmicsIntegrator | scripts/motif_fsa_scores.py | Python | bsd-2-clause | 11,275 | [
"Galaxy"
] | 6e6d4b1bf5c94874830eb587ad9fbe8a52e8c554799383d2f052c82a93ef2d89 |
import numpy as np
from ase.dft import Wannier
from gpaw import restart
atoms, calc = restart('poly.gpw', txt=None)
# Make wannier functions using (one) extra degree of freedom
wan = Wannier(nwannier=6, calc=calc, fixedenergy=1.5)
wan.localize()
wan.save('poly.pickle')
wan.translate_all_to_cell((2, 0, 0))
for i in r... | grhawk/ASE | tools/doc/tutorials/wannier/wannier_polyacetylene.py | Python | gpl-2.0 | 824 | [
"ASE",
"GPAW"
] | a4fbf1f650d35fb72055a8cc2063536e7eff4d4a27e6b33e9063fbdacc8ec7e3 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.StereoCapableWindowOn()
iren = vtk.vtkRenderWindowInte... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/EnSight/Testing/Python/EnSight6Elements.py | Python | gpl-3.0 | 1,601 | [
"VTK"
] | 03c8312b0a154f59ffb5709075530397a8091950069d2d620bd4d25090935840 |
#!/usr/bin/env python
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the fol... | wizmer/NeuroM | examples/get_features.py | Python | bsd-3-clause | 6,771 | [
"NEURON"
] | 1f1a112bfd6fa52f111e43cb6a628a41a87fc7192f22f64d5d7e0de65841fdb4 |
import arrow
from datetime import datetime
from django.test import TestCase
from edc_base import get_utcnow
from edc_facility.import_holidays import import_holidays
from edc_visit_schedule.site_visit_schedules import site_visit_schedules
from ..constants import (
NEW_APPT, INCOMPLETE_APPT, IN_PROGRESS_APPT, CANCE... | botswana-harvard/edc-appointment | edc_appointment/tests/test_unscheduled.py | Python | gpl-2.0 | 6,055 | [
"VisIt"
] | 9ffea62daa0aaf83cafe352e64126d56343c24a660827b330ad6e57ecb3bdae9 |
# 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 PyAngel(PythonPackage):
"""ANGEL: Robust Open Reading Frame prediction"""
homepage = ... | LLNL/spack | var/spack/repos/builtin/packages/py-angel/package.py | Python | lgpl-2.1 | 857 | [
"Biopython"
] | 80d75892baabc7f9eabd0d187eb5085d4120305af855444d254fde1705ddf980 |
# Copyright: (c) 2018, 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 ast
from itertools import islice, chain
from jinja2.runtim... | nitzmahone/ansible | lib/ansible/template/native_helpers.py | Python | gpl-3.0 | 4,731 | [
"VisIt"
] | 6407e9e7a8d71e465df5b57f8f159b9cf84cdf7e229cb9a7307dc1d3dde79699 |
import catmap
from catmap import ReactionModelWrapper
from catmap.model import ReactionModel
from catmap.functions import get_composition, add_dict_in_place
try:
from scipy.optimize import fmin_powell
except ImportError:
fmin_powell = None
import warnings
from mpmath import mpf
from math import exp, log
IdealG... | montoyjh/catmap | catmap/thermodynamics/enthalpy_entropy.py | Python | gpl-3.0 | 38,144 | [
"ASE"
] | 18eaa88e974e16d476011e436dee7dc0e07df97d1a566d5c0944f57be8ed62b3 |
"""
This module must define the following objects:
- a dictionary P with keys. The value of every key is a tuple with the
same length (the number of model parameters)
name : parameter names
min : minimum allowed parameter values
max : maximum allowed parameter values
- a model(*par) function that g... | nhmc/LAE | python_modules/run_emcee/examples/model.py | Python | mit | 5,763 | [
"Gaussian"
] | 5b1a46a064644651ff3445ae5e07b88b53acacc65d1afcb981fa8ae19811d384 |
# Author: Prabhu Ramachandran
# License: BSD style
# Copyright (c) 2004, Enthought, Inc.
"""Tests class_tree.py. Uses the vtk module to test the code. Also
tests if the tree generation works for the __builtin__ module.
"""
import sys
import unittest
from contextlib import contextmanager
from tvtk import class_tre... | dmsurti/mayavi | tvtk/tests/test_class_tree.py | Python | bsd-3-clause | 6,404 | [
"VTK"
] | dca306bc619dcb16466383149015ee7d9041b63b704d3bbc924fcafe6e9bc012 |
'''<b>Example2b</b> - Handling masked images
<hr>
This example deconvolves the image with a Gaussian. Given a point spread
function that is an accurate representation of how optics aberations map
a point to pixels in an image, the deconvolution with that point spread
function uses the information in the blurred image t... | LeeKamentsky/CellProfiler | tutorial/example2b_mask.py | Python | gpl-2.0 | 8,523 | [
"Gaussian"
] | 054ae9341ea2421569534e596f113ad91c04a0366ca278b12c45261df21f53f9 |
# -*- coding: utf-8 -*-
"""
.. class:: Network
This module contains the class that defines the neuronal network
"""
import PyOpenWorm
import rdflib as R
from PyOpenWorm import DataObject
class Network(DataObject):
def __init__(self, conf=False):
DataObject.__init__(self,conf=conf)
def identifier... | mwatts15/PyOpenWorm | PyOpenWorm/network.py | Python | mit | 2,848 | [
"NEURON"
] | b871b69b5d595cedbbe95c6622d688028467fe0ac2d41c7b592a2f511335183d |
"""A quick DOM implementation.
Python's xml.dom is very slow. The xml.sax module is also slow (as it imports urllib2).
This is our light-weight version.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from xml.parsers import expat
import zeroinstall
from zer... | afb/0install | zeroinstall/injector/qdom.py | Python | lgpl-2.1 | 5,597 | [
"VisIt"
] | 67f354c307a6f43e6e35414f4e7d088328684923636d7bc8359437a63c765ca3 |
from __future__ import absolute_import
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr, Callable, Iterable
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.mode... | verma-varsha/zulip | zerver/models.py | Python | apache-2.0 | 82,712 | [
"VisIt"
] | 16779f1882f10f68057a5ee9276d4bd8e67a74f98bdbce7b0836532773d46307 |
import sys
import numpy as np
msg = "\n'TypeError: array cannot be safely cast to required type'\n"
msg += "means you are probably using a broken ScientficPython, \n"
msg += "see: https://bugs.launchpad.net/ubuntu/+source/python-scientific/+bug/1041302\n"
import Scientific.IO.NetCDF as netcdf
import Scientific
versi... | grhawk/ASE | tools/ase/test/scientificpython_bug.py | Python | gpl-2.0 | 765 | [
"NetCDF"
] | beb1ad9d233dfd8451d4f5b17b682bb4d6d97a888342eb254c13e70133436400 |
import random
FIRST_NAMES = [
"JAMES",
"JOHN",
"ROBERT",
"MICHAEL",
"WILLIAM",
"DAVID",
"RICHARD",
"CHARLES",
"JOSEPH",
"THOMAS",
"CHRISTOPHER",
"DANIEL",
"PAUL",
"MARK",
"DONALD",
"GEORGE",
"KENNETH",
"STEVEN",
"EDWARD",
"BRIAN",
"RON... | PHB-CS123/graphene | gp-scripts/names.py | Python | apache-2.0 | 6,628 | [
"Brian"
] | 70a9784e1e4ed16263eb95f9865f2c6b77aebbe2099413ff61a7db7866d99f79 |
"""
Tests for Pose Generation
"""
import os
import tempfile
import unittest
import logging
import numpy as np
import deepchem as dc
import pytest
class TestPoseGeneration(unittest.TestCase):
"""
Does sanity checks on pose generation.
"""
def test_vina_initialization(self):
"""Test that VinaPoseGenerator ... | miaecle/deepchem | deepchem/dock/tests/test_pose_generation.py | Python | mit | 4,928 | [
"RDKit"
] | efd6818c086ff2d7855aaac4fc98432346f4cdc87ebccd1d3ac124edf38b38a6 |
import Sofa
import os, os.path
import sys
import json
import glob
import units
import numpy as np
def listToStr(x):
""" concatenate lists for use with data.
"""
# Sofa.msg_deprecated("SofaPython.Tools.listToStr", "In Node.createObject: no need to explicitely convert a list to string")
return ' '.join(... | Anatoscope/sofa | applications/plugins/SofaPython/python/SofaPython/Tools.py | Python | lgpl-2.1 | 11,783 | [
"VTK"
] | 85d26141efc01c3b391f55bb75efb75a3788658a8b2bf50e4a2b3155d1ea1e12 |
#! ===========================================
#! NEST Topology Module: A Case-Based Tutorial
#! ===========================================
#!
#! :Author: Hans Ekkehard Plesser
#! :Institution: Norwegian University of Life Sciences, Simula
#! Research Laboratory, RIKEN Brain Sciences Institute
#! :Versio... | gewaltig/cython-neuron | cynest/examples/hill_tononi_Vp.py | Python | gpl-2.0 | 36,305 | [
"Gaussian",
"NEURON"
] | 0671c9bf412f7f0dc210eced1aa8e2d04f20c2a715d3a801031f0e582892a892 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | jax_dft/jax_dft/utils.py | Python | apache-2.0 | 9,508 | [
"Gaussian"
] | 1823453c84973b16d3decb3a2adcce69609c5ac00c2bc206eadcbe8ba276c854 |
"""
Script to calculate per-residue RSCCs for a model versus an EM map with an
arbitrary origin.
"""
from __future__ import division
from mmtbx import real_space_correlation
import iotbx.phil
from cctbx import crystal
from cctbx import maptbx
from scitbx.array_family import flex
import sys
master_phil_str = """
mo... | fraser-lab/EMRinger | Phenix_Scripts/em_rscc.py | Python | bsd-3-clause | 4,393 | [
"CRYSTAL"
] | d766e5222a6c191fb4c98de23b5703b2b37cbfd3865034fe76e0aff8f094bb3d |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Aug 9 14:10:39 2017
NAME;
Monthly time series of precipitation from May 2000 - March 2017 for the Rondonia region
PURPOSE;
This program processes monthly precipitation data (mm/hr) for the Rondonia region (11S,63W).
Plots:
1. Precipitation rate vs mon... | fe114/CCI_LAND | precipitation.py | Python | gpl-3.0 | 6,560 | [
"NetCDF"
] | 3e49a33b84a165db0e19335cd8b13e22305e026ea1b5c89d35b6b673f6e072ce |
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2008 Toon Verstraelen <Toon.Verstraelen@UGent.be>
#
# This file is part of MolMod.
#
# MolMod 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... | woutersmet/Molmodsummer | lib/molmod/constants.py | Python | gpl-3.0 | 955 | [
"Avogadro"
] | 67ec05a924adf87a31878088358fe9f80a9ad35626c0a8982d899e5f415e5e89 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-webrisk | tests/unit/gapic/webrisk_v1beta1/test_web_risk_service_v1_beta1.py | Python | apache-2.0 | 68,970 | [
"Octopus"
] | 47b9277cdbce259c390b6209531680ae1993e8d6f61196fc50bc487455adce51 |
import sympy
from sympy.functions import DiracDelta, Heaviside
from sympy.simplify.simplify import simplify
from sympy.solvers import solve
from sympy.utilities.misc import default_sort_key
def change_mul(node, x):
"""change_mul(node, x)
Rearranges the operands of a product, bringing to front any simple
... | devs1991/test_edx_docmode | venv/lib/python2.7/site-packages/sympy/integrals/deltafunctions.py | Python | agpl-3.0 | 4,953 | [
"DIRAC"
] | e35a360b7fc4143f6640d07617ce3155042a0e563c33b699526631507227c86d |
#
# Copyright 2015 Universidad Complutense de Madrid
#
# This file is part of Numina
#
# Numina 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 ... | Pica4x6/numina | numina/array/peaks/findpeaks1D.py | Python | gpl-3.0 | 4,703 | [
"Gaussian"
] | cb40975873deb6dec3da742b0f38097a63321feb871fbc1556868a0abb470c9c |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
from django.conf import settings
from django.core.exceptions import SuspiciousOperation
from django.core.urlresolvers import reverse
from django.template import... | chrisfranzen/django | tests/regressiontests/test_client_regress/tests.py | Python | bsd-3-clause | 48,296 | [
"VisIt"
] | 7f4aa6b1fca7ff4c1c685233825cd822bf389c07ca0e9f4afe2af337a142a71a |
import os, platform
import argparse
import sys
import tempfile
from Bio import SeqIO
from Bio.SeqFeature import FeatureLocation
from Bio.SeqFeature import SeqFeature
def createParser():
parser = argparse.ArgumentParser(
prog='TermGen',
usage='\n%(prog)s <input_file> <output_file> [option... | nikolaichik/SigmoID | Python/TermGen.py | Python | gpl-3.0 | 20,536 | [
"Biopython"
] | 5fc8bd14c6be09a01bb57d786230713fd08b8ee694a11aebccdd5c88c168e8c3 |
"""
Acceptance tests for Studio.
"""
from unittest import skip
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from ..pages.studio.asset_index import AssetIndexPage
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.studio.checklists import ChecklistsPage
from ..pages.stu... | xiandiancloud/edxplaltfom-xusong | common/test/acceptance/tests/test_studio_general.py | Python | agpl-3.0 | 5,378 | [
"VisIt"
] | 29009050cdad55ccace8f234aeaae94c30474df2f0016b261f99daa6e37a5053 |
from unittest import TestCase, expectedFailure
from autodepgraph import visualization as vis
import autodepgraph as adg
import networkx as nx
from autodepgraph.graph import AutoDepGraph_DAG
import yaml
import os
test_dir = os.path.join(adg.__path__[0], 'tests', 'test_data')
class Test_Graph(TestCase):
@classmeth... | AdriaanRol/AutoDepGraph | autodepgraph/tests/test_graph.py | Python | mit | 7,160 | [
"VisIt"
] | 464e2932f6c909fd70e9af575331dd879ea807bdf0095b5b9046142a65e7cbf1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# MEASURE - Master Equation Automatic Solver for Unimolecular REactions
#
# Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to... | jwallen/MEASURE | measure/input.py | Python | mit | 26,506 | [
"ChemPy"
] | 6d635b5cf3fd54ea93b07b6102b4f058d5ae9469afac602d0779b3d6a06c3efa |
import mxnet as mx
import logging
import os
import time
def _get_lr_scheduler(args, kv):
if 'lr_factor' not in args or args.lr_factor >= 1:
return (args.lr, None)
epoch_size = args.num_examples / args.batch_size
if 'dist' in args.kv_store:
epoch_size /= kv.num_workers
begin_epoch = args.load_epoch if ... | yancz1989/lr_semi | common/fit.py | Python | mit | 6,993 | [
"Gaussian"
] | af425bb7a6d32f1c521b452bc64678224c2dcf6584b9ab7a837e2496bfd575ca |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.PostgreSQL | ZenPacks/zenoss/PostgreSQL/__init__.py | Python | gpl-2.0 | 3,841 | [
"VisIt"
] | 42d9512cb6e6e071a814ab731814dca7dd765c9a51ff2d66db22a6e158da36e6 |
from .orca import *
version = __version__ = '1.6'
| UDST/orca | orca/__init__.py | Python | bsd-3-clause | 51 | [
"ORCA"
] | e7f3fe5f75bec29ea5fceb3a413f607d3f27617c20cd74823d12058b03a9fb7a |
import logging
import logging.config
import sys
import threading
import traceback
import time
import os
from amberdriver.common.message_handler import MessageHandler
from amberdriver.dummy import dummy_pb2
from amberdriver.dummy.dummy import Dummy
from amberdriver.null.null import NullController
from amberdriver.tool... | showmen15/testEEE | src/amberdriver/dummy/dummy_controller.py | Python | mit | 5,111 | [
"Amber"
] | 29484c4b67c3bb9f814387e7ce2ca4593479a2db2dde5a3ec0100534bafc734d |
#!/usr/bin/env python
"""
Reduced Gravity Shallow Water Model
based Matlab code by: Francois Primeau UC Irvine 2011
Kelsey Jordahl
kjordahl@enthought.com
Time-stamp: <Sun Apr 15 15:35:37 EDT 2012>
"""
from scipy.io.netcdf import netcdf_file
from ocean_model import OceanModel
from image_plot import ImagePlot
from trai... | kjordahl/swm | wind_model.py | Python | bsd-3-clause | 879 | [
"NetCDF"
] | 1d569e8c75d8b49043162b8ca8d803c32436ff93975c67b8b0be9b8e4d1f1cd7 |
from math import sqrt
import numpy as np
__all__ = ['FixCartesian', 'FixBondLength', 'FixedMode', 'FixConstraintSingle',
'FixAtoms', 'UnitCellFilter', 'FixScaled', 'StrainFilter',
'FixedPlane', 'Filter', 'FixConstraint', 'FixedLine',
'FixBondLengths']
def slice2enlist(s):
"""Con... | slabanja/ase | ase/constraints.py | Python | gpl-2.0 | 22,881 | [
"ASE"
] | 09abf0ab0e0e7576f2f8226927d96885de8a48e0a0c5c22b07db02e38e1a7470 |
"""Test TorsionFitModel"""
from torsionfit.tests.utils import get_fun, get_files
import torsionfit.TorsionScanSet as torsionset
from torsionfit.TorsionFitModel import TorsionFitModel
from pymc import MCMC
import glob
import pymc
from numpy.testing import assert_
from cclib.parser import Gaussian
from cclib.parser.util... | jchodera/Torsions | torsionfit/tests/test_torsionFitModel.py | Python | gpl-2.0 | 2,499 | [
"CHARMM",
"Gaussian",
"OpenMM",
"cclib"
] | c4b621557f460b06b32ef5392a8922ab9a20a598af552b807ae8abe95e22ab9e |
"""
Save per-interface and per-feed configuration information.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import os
from xml.dom import minidom, XMLNS_NAMESPACE
from zeroinstall.support import basedir
from zeroinstall.injector ... | pombredanne/zero-install | zeroinstall/injector/writer.py | Python | lgpl-2.1 | 2,331 | [
"VisIt"
] | 45e4958d51792b03e33dc497b9f75e0a9c778dfb0a15ea61469baad0c3aeebc4 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib
import urllib2
import urlparse
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStri... | splbio/openerp-web | addons/web/controllers/main.py | Python | agpl-3.0 | 68,977 | [
"VisIt"
] | e22d22c2c18424ff3c80f1539fa435b480f554be57ec39e53a4453ed1d43db8e |
# Copyright 2013-2015 James S Blachly, MD and The Ohio State University
#
# This file is part of Mucor.
#
# Mucor 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,... | blachlylab/mucor | inputs.py | Python | gpl-3.0 | 16,428 | [
"BWA",
"HTSeq"
] | 6428b54654e0ef856026b43d7c03e6147ace3162c792a2fa8a9e3508f6857ff4 |
# Copyright 2015 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... | ryfeus/lambda-packs | Keras_tensorflow_nightly/source2.7/tensorflow/python/ops/control_flow_grad.py | Python | mit | 9,093 | [
"VisIt"
] | 8e22f40de3773ccc83c44cc4eef2a567aab91168bf22c7c4626e664a6c802707 |
# -*- coding: utf-8 -*-
#
# This file is part of PyBuilder
#
# Copyright 2011-2020 PyBuilder Team
#
# 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/l... | pybuilder/pybuilder | src/unittest/python/plugins/python/vendorize_plugin_tests.py | Python | apache-2.0 | 2,534 | [
"VisIt"
] | 8784a2b458acbb429f1d68e36ee6537334faada9c4107e435c94034f820c3b97 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
# vim:ai:sta:et:ts=4:sw=4:sts=4
"""kernelng 0.x
Tool for maintaining customized overlays of kernel-ng.eclass-based ebuilds
Copyright 2005-2014 Gentoo Foundation
Copyright (C) 2005 Colin Kingsley <tercel@gentoo.org>
Copyright (C) 2008 Zac Medico <zmedico@gentoo.org>
Cop... | gmt/kernel-ng-util | kernelng/version.py | Python | gpl-2.0 | 1,275 | [
"Brian"
] | 2e9f63875f9466d4bcfe57158c25326bca4f8a72e381d9eadd07070952dbcbf9 |
# sql/elements.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | davidfraser/sqlalchemy | lib/sqlalchemy/sql/elements.py | Python | mit | 141,433 | [
"VisIt"
] | 785c0287fedcf498e7630c2dfb00c5085295856380562a5b20907d7bd487a2bc |
########################################################################
# $HeadURL $
# File: StorageElementProxyHandler.py
########################################################################
"""
:mod: StorageElementProxyHandler
.. module: StorageElementProxyHandler
:synopsis: This is a service which represe... | Sbalbp/DIRAC | DataManagementSystem/Service/StorageElementProxyHandler.py | Python | gpl-3.0 | 12,103 | [
"DIRAC"
] | 3e8bc990e227ec8747eab5b3e5c9d19a9750be9de53cece706ffffefba215aa1 |
"""TransformationPlugin is a class wrapping the supported transformation plugins
New plugins can be created by defining a function.
The function name has to be ``_MyPlugin``, and the plugin is then call ``'MyPlugin'``. Do not forget to enable new
plugins in the ``Operations/Transformation/AllowedPlugins`` list.
The re... | andresailer/DIRAC | TransformationSystem/Agent/TransformationPlugin.py | Python | gpl-3.0 | 10,512 | [
"DIRAC"
] | 27c1f2a98ae06902de4b0a3ec81a2caeb4215348431492335ad3393abf4bee63 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import itertools
import pytest
import numpy as np
from numpy.testing import assert_allclose, assert_almost_equal
from astropy.convolution.convolve import convolve, convolve_fft
from astropy.convolution.kernels import (AiryDisk2DKernel, Box1DKernel, Box... | astropy/astropy | astropy/convolution/tests/test_kernel_class.py | Python | bsd-3-clause | 21,083 | [
"Gaussian"
] | 1afb6c448764e7e12c2c9d8e984da28248e6ec680679de78bf697ad2789c8154 |
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