text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
''' CEAvailabilityPolicy module
'''
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
class CEAvailabilityPolicy(PolicyBase):
'''
The CEAvailabilityPolicy checks if the CE is in 'Production' or not on the BDII.
'''
@staticmethod
def _eva... | andresailer/DIRAC | ResourceStatusSystem/Policy/CEAvailabilityPolicy.py | Python | gpl-3.0 | 1,449 | [
"DIRAC"
] | a88a8f9975c72bbefbd56f708eace7b4af8b9d309760668bd7f016a037683f3e |
#
# OpenMX.py
#
# Interface to OpenMX (http://openmx-square.org)
#
# Copyright (c) 2018 Yuto Tanaka
#
# This file is distributed under the terms of the MIT license.
# Please see the file 'LICENCE.txt' in the root directory
# or http://opensource.org/licenses/mit-license.php for information.
#
import numpy as np
"""Op... | ttadano/ALM | tools/interface/OpenMX.py | Python | mit | 13,780 | [
"OpenMX"
] | 6153aaca5f23a3a3fbc4c14dbc0b92ff11d873d5574249a101fba780def126ba |
# Copyright (c) 2012 Spotify AB
#
# 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 writing, s... | soxofaan/luigi | setup.py | Python | apache-2.0 | 3,637 | [
"VisIt"
] | bc552fffa5752956a90c52fccb1f43ff91ff0d216e730d33b522c7e386adab24 |
# pmx Copyright Notice
# ============================
#
# The pmx source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# pmx is Copyright (C) 2006-2015 by Daniel ... | dseeliger/cmdline | cmdline/options.py | Python | bsd-2-clause | 17,268 | [
"Gromacs"
] | b29cbd60ff09ad03d229183b7f6eea4b8584be062e271259ab1dbc63c58132a6 |
# -*- coding: utf-8 -*-
# This code is part of Qiskit.
#
# (C) Copyright IBM 2019.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any modif... | QISKit/qiskit-sdk-py | test/python/visualization/test_pulse_visualization_output.py | Python | apache-2.0 | 5,760 | [
"Gaussian"
] | 048f366655d056dcd1a1b64431876b96a921ff10547933d69e69d413b3261fad |
""" Callback when a staging operation is finished """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import S_OK
from DIRAC.RequestManagementSystem.private.OperationHandlerBase import OperationHandlerBase
from DIRAC.WorkloadM... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/StagingCallback.py | Python | gpl-3.0 | 1,577 | [
"DIRAC"
] | 62da8c1722c7881bfd03754c93a552c6e6138746f53769d71e4cd7da00fb133f |
import yt
from yt import derived_field
import numpy as np
import matplotlib.pyplot as plt
from galaxy_analysis import Galaxy
import glob
from collections import OrderedDict
from yt.visualization.base_plot_types import get_multi_plot
import matplotlib.colorbar as cb
from matplotlib.colors import LogNorm
import sys, os
... | aemerick/galaxy_analysis | plot/plot_metal_evolution_panel.py | Python | mit | 10,848 | [
"Galaxy"
] | fe9b025d181eef93ab37a72ca8e83c09e88fc9ee5f78bf26decb9e33cfeaa52e |
#!/usr/bin/env python
# AUTHOR: Shane Gordon
# CREATED: 2015-06-16 21:46:32
import mdtraj as md
import numpy as np
def compute_rmsd(fname, topname, sel="name CA", step=1):
rmsd = []
atom_indices = md.load(topname).topology.select(sel)
top = md.load(topname)
for chunk in md.iterload(fname, ... | s-gordon/MD-TAT | mdtat/analysis/rmsd.py | Python | mit | 490 | [
"MDTraj"
] | 6e5d375eb3ac816d0bede1d859831771b9b7cf0d784ac31f830e8085ded1ef4e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Contains functions and classes for generating 3D geometries using Open Babel.
Also contains functionality for estimating thermo using group additivity and
RMG database values.
"""
from __future__ import division
import os
import numpy as np
from scipy import optimiz... | cgrambow/AutomaticReactionDiscovery | ard/gen3D.py | Python | mit | 35,110 | [
"Open Babel",
"Pybel"
] | 5e01568d77e076d7c443b041428b6bd687ad5f06a4588b471c1802b09ea9da99 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/dbproc.py | Python | gpl-2.0 | 3,968 | [
"Psi4"
] | 4f7917b0c234c43c08f96951dd0267fb2d2c41a4331ff1712180aad97582e239 |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from codecs import open
from os import path
from setuptools import setup
here = path.abspath(path.dirname(__file__))
# Get the long de... | dieterich-lab/FUCHS | setup.py | Python | gpl-3.0 | 5,082 | [
"pysam"
] | 38d3bee6fe90bec2b62c32406714508a45121dd28c8cd2d941f0a46747c48290 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | lonerr/ansible | lib/ansible/utils/__init__.py | Python | gpl-3.0 | 41,234 | [
"VisIt"
] | a9e70679154a620992b9008864d0b08240b1e074f4296c7eac9cd69ef7a3b4a8 |
##############################################################################
# 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-a4core/package.py | Python | lgpl-2.1 | 1,696 | [
"Bioconductor"
] | 0f9b1f8f68cff1fd029a5f93c0f2846806ad600ed0498915578e0411752df61a |
"""Support for package tracking sensors from 17track.net."""
from __future__ import annotations
from datetime import timedelta
import logging
from py17track import Client as SeventeenTrackClient
from py17track.errors import SeventeenTrackError
import voluptuous as vol
from homeassistant.components import persistent_... | rohitranjan1991/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | mit | 11,161 | [
"VisIt"
] | 4e7d4b9ebd362c76025ff425f948d65407e0d67825baaab5016b093aee1698cb |
from setuptools import setup
setup(
# general meta
name='ebs-deploy',
version='1.9.9',
author='Brian C. Dilley',
author_email='brian.dilley@gmail.com',
description='Python based command line tools for managing '
'Amazon Elastic Beanstalk applications.',
platforms='any',
... | cfeduke/ebs-deploy | setup.py | Python | mit | 805 | [
"Brian"
] | cfe6013b5a058129b42d5d7b281d6cbb21567d6061506d5b9075cc6400301c1d |
#!/usr/bin/python3.5
# -*- coding: utf-8 -*-
# @package MODULES_SEB.py
# @author Sebastien Ravel
#__docformat__ = "restructuredtext en"
"""
The MODULES_SEB module
======================
:author: Sebastien Ravel
:contact: sebastien.ravel@cirad.fr
:date: 28-06-2017
:version: 0.2
Use it to import very handy functi... | sravel/scripts | modules/MODULES_SEB.py | Python | gpl-3.0 | 47,524 | [
"Biopython"
] | 6a9e840b6cb8d9e48f62b4b2b4dcfbf8cc36caad436818c5d480178562fee6e1 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
This shows an example of a bare-bones distributed web set up. The "master" and
"slave" parts will usually be in different files -- they are here together only
for brevity of illustration. In normal usage they would each run in a separate
pro... | EricMuller/mynotes-backend | requirements/twisted/Twisted-17.1.0/docs/web/examples/silly-web.py | Python | mit | 805 | [
"VisIt"
] | ffb4f1cbcf5e0a478ed7836c756a84bbe163069f0426d8b780728e7adec1e13a |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without res... | f0rki/cb-multios | original-challenges/HeartThrob/poller/for-release/machine.py | Python | mit | 2,486 | [
"Brian"
] | 84b2aaee642c4130e4012de0f413f33e081ace0b6ec048536c6688768a3a0dd2 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
GrassAlgorithm.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
************************... | NINAnor/QGIS | python/plugins/processing/algs/grass/GrassAlgorithm.py | Python | gpl-2.0 | 21,872 | [
"NetCDF"
] | bfb14fc3862dea58662487be50488b6b25420f02e46c23a9b00b7037a686a2c2 |
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 24 09:54:37 2017
@author: tih
"""
def API(output_folder, DownloadType, string1, string2, string3, string4, string5, string6, string7, string8, string9, string10):
import os
from ecmwfapi import ECMWFDataServer
os.chdir(output_folder)
server = ECMWFDat... | wateraccounting/wa | Collect/ECMWF/ECMWFdownload.py | Python | apache-2.0 | 1,854 | [
"NetCDF"
] | 0b22c6565d1d99bd7a390140075dd5480b82290f3c3aaaad1fb8c45c78754fd5 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, 2013, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License... | zenoss/ZenPacks.zenoss.CloudStack | ZenPacks/zenoss/CloudStack/Host.py | Python | gpl-2.0 | 3,499 | [
"VisIt"
] | e8c8e40a3a6dd3c8fc7341ec5d844277127e396965a3b34dc9e3778f25ba6c96 |
# -*- 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-dialogflow | tests/unit/gapic/dialogflow_v2/test_fulfillments.py | Python | apache-2.0 | 64,897 | [
"Octopus"
] | a7d0ece72c63bceb47cfc15c1235737703fc22605bf8671a729f829361908c52 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/extras/mbd/_mbd.py | Python | apache-2.0 | 1,511 | [
"PySCF"
] | b8b57d2b6fa6f3980a13c7d6dc0414ed24952f8a3834952b1562749b4f5c6a58 |
__author__ = 'algol'
import cherrypy
from jinja2 import Environment, PackageLoader
import memin.core as mc
from configparser import ConfigParser
class Menu:
def __init__(self):
self.menu = [
{'name': 'Главная', 'link': '/'},
{'name': 'Персоны', 'link': '/persons'},
{'n... | migihajami/memin | memin/frontend.py | Python | bsd-3-clause | 10,715 | [
"VisIt"
] | 6db07ade3dd3975299b83a5961d494ff071d5b6190efb755eada756c00cf5de1 |
# !/usr/bin/env python
__author__ = 'NishantNath'
'''
Using : Python 2.7+ (backward compatibility exists for Python 3.x if separate environment created)
Required files : hdf5_getters.py, find_second_max_value.py
Required packages : numpy, pandas, matplotlib, sklearn, pickle
Steps:
1.
# Uses k-means method for clas... | nishantnath/MusicPredictiveAnalysis_EE660_USCFall2015 | Code/Machine_Learning_Algos/10k_Tests/ml_classification_kmeans_training.py | Python | mit | 9,358 | [
"Gaussian"
] | 54bd26f57db63d7df510f298f837f86660a4cf649fcaa925ad0bb1dfe7b84136 |
"""Code to transcribe DNA into RNA or back (DEPRECATED).
You are now encouraged to use the Seq object methods or the functions
in Bio.Seq instead.
This module is now deprecated, and will be removed in a future release of
Biopython.
"""
import warnings
import Bio
warnings.warn("Bio.Translate and Bio.Transcribe are dep... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Transcribe.py | Python | gpl-2.0 | 1,826 | [
"Biopython"
] | 4c29591d2dbea0bb86d9308e6d02a34efeda2c47b33247ce4279e7a272008c85 |
#!/usr/bin/env python
import argparse
import shutil
import icqsol_utils
# Parse Command Line.
parser = argparse.ArgumentParser()
parser.add_argument('--input', dest='input', help='Shape dataset selected from history')
parser.add_argument('--input_file_format_and_type', dest='input_file_format_and_type', help='Input f... | pletzer/galaxy-csg | tools/icqsol_solve_laplace/icqsol_solve_laplace.py | Python | mit | 2,585 | [
"VTK"
] | 3bd00f968300c5d12004c09b5c57aa4390ae882264e5a8b8bc79ad67f0639c0b |
"""
Install tigramite
"""
from __future__ import print_function
import pathlib
import os
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
# Handle building against numpy headers before installing numpy
class UseNumpyHeadersBuildExt(build_ext):
"""
Subclassed build_ex... | jakobrunge/tigramite | setup.py | Python | gpl-3.0 | 3,038 | [
"Gaussian"
] | 9bfd248224e2351cb2bc2e453216ae4e9606f63c753ed03878f2ef86d1547a51 |
"""Display the contents of the implementation cache."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _
import os, sys
import gtk
from zeroinstall.injector import namespaces, model
from zeroinstall i... | afb/0install | zeroinstall/gtkui/cache.py | Python | lgpl-2.1 | 20,757 | [
"VisIt"
] | 552481e0f154ff219bda8ee3ae6f5953b4f79495f8f7cdf4e95f93930586c0ff |
# 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 PyNetcdf4(PythonPackage):
"""Python interface to the netCDF Library."""
homepage = "h... | LLNL/spack | var/spack/repos/builtin/packages/py-netcdf4/package.py | Python | lgpl-2.1 | 2,747 | [
"NetCDF"
] | 500b6095ebbd62fb5d846e1677fa076578896f38f62dd92c9026fadcba4894cf |
# Copyright 2021, Google LLC. 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | google-research/federated | distributed_dp/distributed_discrete_gaussian_query_test.py | Python | apache-2.0 | 6,913 | [
"Gaussian"
] | 7e7fd8267b5603b282c021f3118251eaaa83d7cff451b2e91ae5b09e5ee41a85 |
from traits.api import HasTraits, Button, Instance, List, Str, Enum, Float, File, Int
from traitsui.api import View, Item, VGroup, HSplit, HGroup, FileEditor
from tvtk.pyface.scene_editor import SceneEditor
from mayavi.tools.mlab_scene_model import MlabSceneModel
from mayavi.core.ui.mayavi_scene import MayaviScene
from... | xinglunju/tdviz | TDViz3.py | Python | mit | 17,195 | [
"Mayavi"
] | 805a455a52215c6c37f781564577964ac9c1d159990ecb73f02b1dd1d7e9f882 |
"""
@name: PyHouse/src/Modules/Families/_test/test_UPB.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 29, 2015
@Summary:
Passed all tests - BK - 2018-02-13
"""
__updated__ = '2018-02-13'
# Import... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/_test/test_UPB.py | Python | mit | 814 | [
"Brian"
] | f01cb77d82bd3d313856366a0daf5d4653bf579d28d3e3649de7f1edeac479a7 |
'''
Copyright (C) 2013 Travis DeWolf
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope t... | sebastien-forestier/PLAY2017 | play/dmp/dmp_discrete.py | Python | gpl-3.0 | 4,452 | [
"Gaussian"
] | dcab3b46c0860239f6e01065d8876ca1162211653a698bffb0ae0fafbde612ad |
# (c) 2014, 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, either version 3 of the License, or
# (at your option) any later version.... | jotes/ansible | lib/ansible/runner/filter_plugins/math.py | Python | gpl-3.0 | 1,902 | [
"Brian"
] | 13f5d3e8e486c22fdf89b13578cc4b1566d52c840e0467365b1d5b6b4c438a35 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | johnchase/scikit-bio | skbio/alignment/_pairwise.py | Python | bsd-3-clause | 38,935 | [
"BLAST",
"scikit-bio"
] | 0a688b062a9d7aa9d2d35881229f34d9b9ef62dda3b6ea9bcebc8678fcc75254 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
import math
import statlib
import stats
from stats import find_repeats
import distributions
from numpy import isscalar, r_, log, sum, around, unique, asarray
from numpy import zeros, arange, sort, amin, amax, any, where, ... | lesserwhirls/scipy-cwt | scipy/stats/morestats.py | Python | bsd-3-clause | 44,067 | [
"Gaussian"
] | 1f95b781ce89ffd7569d59902b511f3ad0957d09d691806b9d64c893b594ad34 |
# Copyright (C) 2019 Brian McMaster
# License AGPL-3.0 or later (http://www.gnu.org/licenses/agpl).
from . import account_payment_1099_report
| OCA/l10n-usa | l10n_us_form_1099/reports/__init__.py | Python | agpl-3.0 | 143 | [
"Brian"
] | a9dbdbc881dd7ed580ddc9dc207b2c3763b589e3802a2a1aabc77c3157a53b05 |
#!/usr/bin/env python
"""Copyright 2010 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
#Basi... | danielsuo/mobot | src/move/Python/PHSensor-simple.py | Python | mit | 3,775 | [
"VisIt"
] | 6cfc1ebb11d67d8a26fbd1e1a07715a5cbda11ec72ae16a395ed4273fb256543 |
import cv2
import numpy as np
import math
cap = cv2.VideoCapture(0)
while(cap.isOpened()):
# read image
ret, img = cap.read()
# get hand data from the rectangle sub window on the screen
cv2.rectangle(img, (300,300), (100,100), (0,255,0),0)
crop_img = img[100:300, 100:300]
# convert to graysc... | livalencar/beethoven | libras.py | Python | mit | 3,771 | [
"Gaussian"
] | 7fb8c14f2a195b444fd1db825aad7585cf6e69cac2d73b2edb80bf3185048b50 |
#!/usr/bin/env python2.7
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redis... | jtulach/mx | mx.py | Python | gpl-2.0 | 623,804 | [
"VisIt"
] | c19c967c2be10c948dbe58d097d94195a41bbefe0e51dcb589f656f9f2cb3108 |
# Recorded script from Mayavi2
from numpy import array
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
# -------------------------------------------
from mayavi.modules.iso_surface import Is... | FreeON/spammpack | spammsand/stabilized_paper_1/tube_dual_c6_x128_b64/x_18_33tube_x128_c5.py | Python | bsd-3-clause | 3,916 | [
"Mayavi",
"VTK"
] | 3b8f92c980cc6d014d3ceeebd2171c90cd94355b258a582a019abe8d73ff0211 |
#
# Copyright 2015, 2017, 2021 Lars Pastewka (U. Freiburg)
# 2020 Johannes Hoermann (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/o... | libAtoms/matscipy | tests/matscipytest.py | Python | lgpl-2.1 | 4,902 | [
"Matscipy"
] | 4daf0b90ca967988bbd1bc2462e70136e47a3fce87e9480843401516f31b09e9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements input and output processing from Gaussian.
"""
import re
import numpy as np
import warnings
from pymatgen.core.operations import SymmOp
from pymatgen import Element, Molecule, Comp... | mbkumar/pymatgen | pymatgen/io/gaussian.py | Python | mit | 60,532 | [
"Gaussian",
"pymatgen"
] | 903cf75ce28265654cd1d8d8f76d07f67a902f642aa9da31a3201e4d4ab25986 |
# Copyright 2015 PerfKitBenchmarker 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 appli... | akshara775/PerfKitBenchmarker-master-2 | tests/linux_benchmarks/speccpu2006_benchmark_test.py | Python | apache-2.0 | 11,728 | [
"GAMESS",
"Gromacs",
"NAMD"
] | 8855dd23281f1cc9793ffda55a8ab4a7bfb2c99f719203582f9415a9b7fe8a84 |
# Psychrometric Chart
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify
# it under the terms of t... | samuto/ladybug | src/Ladybug_Psychrometric Chart.py | Python | gpl-3.0 | 117,677 | [
"EPW"
] | eb32c9fd9a85182a20553aea5f5eb51b43b681fcb97912abc7858bd2cbafd0bb |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | olexiim/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 20,582 | [
"VisIt"
] | 8762017831dc80d736101ef51bd2c1bab090e9f5da45301b2095fd32659ca934 |
# Copyright (C) 2016-2018 The ESPResSo project
# Copyright (C) 2014 Olaf Lenz
#
# 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... | hmenke/espresso | src/python/espressomd/gen_code_info.py | Python | gpl-3.0 | 1,817 | [
"ESPResSo"
] | a9a72a685dd00ceba4c731095b181aade782363fb3ca8b66aa9fac0260369a42 |
# vi: ts=8 sts=4 sw=4 et
#
# visitor.py: visits nodes in a model
#
# This file is part of Draco2. Draco2 is free software and is made available
# under the MIT license. Consult the file "LICENSE" that is distributed
# together with this file for the exact licensing terms.
#
# Draco2 is copyright (c) 1999-2007 by the Dr... | geertj/draco2 | draco2/model/visit.py | Python | mit | 2,117 | [
"VisIt"
] | 473f218a3c0f0a29be11b54e958ee1773b33d3595acad9e4c9121289504c88d5 |
# Izhikevich.py ---
#
# Filename: Izhikevich.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri May 28 14:42:33 2010 (+0530)
# Version:
# Last-Updated: Wed Aug 4 20:34:46 2010 (+0530)
# By: Subhasis Ray
# Update #: 985
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/izhikevich/Izhikevich.py | Python | lgpl-2.1 | 22,803 | [
"MOOSE",
"NEURON"
] | 07e5f088dbc85036c2ffa9c745feebd2dd4fb78c360dfc861c60e81c32afb6dd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This is a very simple way to culculate the famous number of Pi, which is very use in mathematics ans science. We can call this 'the magical number', because it appears naturally in a lot of formulas and scopes.
# With this program we calculate Pi with a technique based o... | xoancosmed/Calculate-Pi | Basel/Basel.py | Python | gpl-3.0 | 1,512 | [
"VisIt"
] | 579981db38b88e83dbf3b73ecf24dedded53e368a0a1d17e056411de540b5587 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
import os
from rmgpy import getPath
from rmgpy.qm.main import QMSettings, QMCalculator
from rmgpy.molecule import Molecule
import qmdata
class TestQMSettings(unittest.TestCase):
"""
Contains unit tests for the QMSettings class.
"""
def setUp(self):
"... | KEHANG/RMG-Py | rmgpy/qm/mainTest.py | Python | mit | 10,699 | [
"Gaussian",
"MOPAC",
"Molpro"
] | 53672b685d92c0a8dfeaded33172509b0f2a779897ca503e72af66c938df22d8 |
''' This is a test of the chain
ResourceManagementClient -> ResourceManagementHandler -> ResourceManagementDB
It supposes that the DB is present, and that the service is running
The DB is supposed to be empty when the test starts
'''
# pylint: disable=invalid-name,wrong-import-position
import datetime
im... | arrabito/DIRAC | tests/Integration/ResourceStatusSystem/Test_ResourceManagement.py | Python | gpl-3.0 | 12,411 | [
"DIRAC"
] | ddfff1a30eb242803a20dabc1e414e566e83521325cd4a29ad50a023ac6ed284 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2015 Christian Bahati cbahati@luc.edu
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwar... | cbahati/FoxCatcher | build/lib.linux-x86_64-2.7/foxcatcher/FoxcatcherWindow.py | Python | gpl-3.0 | 14,209 | [
"VisIt"
] | 6d6a1b45b75bfb4306bcf68a396e0465b4611591d8086dbfffe33fdc37bf08cb |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | pkreissl/espresso | samples/minimal-charged-particles.py | Python | gpl-3.0 | 3,386 | [
"ESPResSo"
] | 2a9e7f80cfe8c6a82f66604d134f3f541ba766ef9f63046daa59f045272c0a7c |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2013 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | DeadBugEngineering/myHDL_shenanigans | ssd1306_8x64bit_driver/myhdl_10dev/lib/python2.7/site-packages/myhdl-1.0.dev0-py2.7.egg/myhdl/conversion/_analyze.py | Python | lgpl-2.1 | 46,368 | [
"VisIt"
] | 7c17bc86fa92f6ae0223f8cf33aef44518746be8eb16d317579e0ec44742293b |
"""Tests for the mycroft skill's get_response variations."""
from os.path import dirname, join
from threading import Thread
import time
from unittest import TestCase, mock
from lingua_franca import load_language
from mycroft import MycroftSkill
from mycroft.messagebus import Message
from test.unittests.mocks import... | MycroftAI/mycroft-core | test/unittests/skills/test_mycroft_skill_get_response.py | Python | apache-2.0 | 8,685 | [
"Octopus"
] | f67faf4b2aa24dd690dc8d20318d63fd52601aba6f57f8be51cfd3d0a2a070f1 |
#!/usr/bin/env python
# Copyright 2013 National Renewable Energy Laboratory, Golden CO, USA
# This file is part of NREL MatDB.
#
# NREL MatDB 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... | ssullivangh/nrelmat | nrelmat/readVasp.py | Python | gpl-3.0 | 12,830 | [
"VASP"
] | 63a18bc5c47debe0d2777f38a3edff5f550e682b540280d9b3894ad79b035aed |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Note: To use the 'upload' functionality of this file, you must:
# $ pip install twine
import io
import os
import sys
from shutil import rmtree
from setuptools import find_packages, setup, Command
# Package meta-data.
NAME = 'funannotate'
DESCRIPTION = 'funannotate: ... | nextgenusfs/funannotate | setup.py | Python | bsd-2-clause | 3,704 | [
"Biopython"
] | 7320e3c837d55c576b5c9f1b359d9f437ed78c50db694f167740860d163ece48 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
# Based on the exercise q7.occ from the source distribution of kroc-1.4
#
# This is an e... | runefriborg/pycsp | examples/Dining-Phil.py | Python | mit | 2,835 | [
"Brian"
] | 0850683c71e80b6b97f22d9cba3f45fe0f4471fe88f20a97a37bce3868e69088 |
from octopus.core import app
from octopus.lib import plugin
class AccountFactory(object):
@classmethod
def get_model(cls):
path = app.config.get("ACCOUNT_MODEL")
klazz = plugin.load_class(path)
return klazz
@classmethod
def get_user_formcontext(cls, acc=None, form_data=None):
... | JiscPER/magnificent-octopus | octopus/modules/account/factory.py | Python | apache-2.0 | 1,605 | [
"Octopus"
] | 2fdc67196db4a68d58c6f3ffc90993371c5c2274ac01311d294e54c8c992fe6e |
from graph.graph import Graph_Mat
DEBUG = 0
def DFS(g, start='a'):
visited = []
stack = []
visited.append(start)
stack.append(start)
c = 0
while stack != []:
c += 1
v = stack[-1]
print (c, v, stack)
vNeighbors = g.neighbors(v)
for neighbor in vNeighbors:
if neighbor not in visited:
next = nei... | xyvab/graphTheory | DFS.py | Python | gpl-3.0 | 851 | [
"VisIt"
] | 18b974f3417e78c8e6f37884fb3c99553baa8325911f7fe27a41c40ad7839ae7 |
#!/usr/bin/env python
# Copyright 2017 Informatics Matters Ltd.
#
# 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... | InformaticsMatters/pipelines | src/python/pipelines/rdkit/cluster_butina.py | Python | apache-2.0 | 10,427 | [
"RDKit"
] | ff43484d8ccf9ab49dc632f2f7880df8e34d5e41a348a43a11b5c0fd2162ac94 |
# -*- coding: utf-8 -*-
from datetime import datetime
from ellen.utils import JagareError
from celery.schedules import crontab
from celery.task import periodic_task
from vilya.libs.store import store
from vilya.models.project import CodeDoubanProject
from vilya.models.doc import DocBuilder
from vilya.models.sphinx_do... | xtao/code | tasks.py | Python | bsd-3-clause | 4,264 | [
"ADF"
] | 5750fbe5e3eacd9761a7ed6587a41184e5324927b7c5fc4ed678b1db7b297b8f |
"""OAuth2.0 user credentials."""
import datetime
import ipaddress
import json
import multiprocessing
import os
import re
from socket import gethostbyname
import sys
from time import sleep
import threading
from urllib.parse import urlencode, urlparse, parse_qs
import wsgiref.simple_server
import wsgiref.util
import web... | GAM-team/GAM | src/gam/auth/oauth.py | Python | apache-2.0 | 27,660 | [
"VisIt"
] | d95ced07ad3c7e400627ededce246903934c8cff250eddfa54f575d67b400dea |
import pylab as pyl
from astLib import astStats
import cPickle as pickle
from scipy import stats
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I >30., galaxies)
f = pyl.figure(1, figsize=(6,4))
f1s1 = f.add_subplot(111)
icd = pyl.asarray([galaxy.ICD_IH*100 for gala... | boada/ICD | sandbox/plot_sfr_ratio.py | Python | mit | 893 | [
"Galaxy"
] | 8b109bc6e1544339cce71e32c989e8b5b2fac17bbb3192e68bb6bb35213e3bb6 |
import os
import ctypes
import numpy
_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build')))
#_cint4 = ctypes.cdll.LoadLibrary('libcint.so.4')
from pyscf import gto, lib
mol = gto.M(atom='''H 0 0 0;
H .2 .5 .8;
H 1.9 2.1 .1;
H 2.0 .... | sunqm/libcint | testsuite/test_int3c2e.py | Python | bsd-2-clause | 4,309 | [
"PySCF"
] | 58a52323d1c2640e9b181adff04a1c3e8f0ae02c4e38c23634446540b2274989 |
#!/usr/bin/env python
from traits.api import HasTraits, List, Instance, Bool, Str, File, Dict, Int
from traitsui.api import View, Item, VGroup, HGroup, Group, \
RangeEditor, TableEditor, Handler, Include,HSplit, EnumEditor, HSplit, Action, \
CheckListEditor, ObjectColumn
from ..streamlines.track_dataset impor... | mattcieslak/DSI2 | dsi2/database/mongo_track_datasource.py | Python | gpl-3.0 | 12,981 | [
"Mayavi"
] | 6ec209b7bc2ecf4fc1096fda574b3e79847bfcf52d6b3519c52f656c9e0b2037 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2015 Francois Beaune, The appleseedhq Organizatio... | Vertexwahn/appleseed | scripts/rendermanager.py | Python | mit | 21,708 | [
"VisIt"
] | 1e7b944660194da6e61bfc80245e98daf07cfdb41d0ec1edd9828141db7f77d1 |
"""
Views for user API
"""
import six
from django.contrib.auth.signals import user_logged_in
from django.shortcuts import redirect
from django.utils import dateparse
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import UsageKey
from rest_framework import generics, views
from rest_framework.decorat... | msegado/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 13,754 | [
"VisIt"
] | eba9fc345e8fbef4b5749fcd36059594a85ecef12f93d953322e0519c880e0c0 |
"""Oral Argument Audio Scraper for Court of Appeals for the Sixth Circuit
CourtID: ca6
Court Short Name: 6th Cir.
Authors: Brian W. Carver, Michael Lissner
Reviewer: None
History:
2014-11-06: Started by Brian W. Carver and wrapped up by mlr.
"""
import re
from datetime import datetime
from urlparse import urlparse, ... | brianwc/juriscraper | oral_args/united_states/federal_appellate/ca6.py | Python | bsd-2-clause | 2,477 | [
"Brian"
] | 02af08fb32b42919690eea5c1e24dd25b27d92598ac7a239da56c1b940ea1a95 |
from nanopore.mappers.abstractMapper import AbstractMapper
from sonLib.bioio import system, fastaRead
from nanopore.analyses.utils import normaliseQualValues
import pysam
import os
class Lastz(AbstractMapper):
def run(self, args=""):
tempFastqFile = os.path.join(self.getLocalTempDir(), "temp.fastq")
... | mitenjain/nanopore | nanopore/mappers/lastz.py | Python | mit | 1,384 | [
"pysam"
] | 9c5cddaf84316cc4e6e52ad23c7873cf8d810a0231596e4a1e1b8be565a8abf5 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | michalsenkyr/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 50,284 | [
"Gaussian"
] | aff953e40478d779c74313a872ca607250e0f8b852d33c20bf7045125928ddec |
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
from galaxy import datatypes, config, jobs
from shutil import move
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
output_data = out_data.items()[0][1]
history = output_data.history
if hi... | volpino/Yeps-EURAC | tools/maf/maf_to_bed_code.py | Python | mit | 2,386 | [
"Galaxy"
] | 24358d7ff22c68c2ebf21b90e00587792b497210c4678e65292fd55f13858343 |
import datetime
from custom.bihar import getters, BIHAR_DOMAINS
from custom.bihar.calculations.homevisit import DateRangeFilter
from custom.bihar.calculations.utils import filters
from casexml.apps.case.models import CommCareCase
from couchforms.models import XFormInstance
from custom.bihar.calculations import homevisi... | qedsoftware/commcare-hq | custom/bihar/models.py | Python | bsd-3-clause | 4,659 | [
"VisIt"
] | 3d20196ed17ad15d7726fcd634e6f47fc96bb6d66aa8a9d9d2eb38968a00328f |
# 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 DEScription file.
The file format is described in the scop
"release no... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/SCOP/Des.py | Python | mit | 2,863 | [
"Biopython"
] | 39e53abba06023eee856895372ec2e0db9241ee643d7148323679e5f2166eeac |
def CNOT(experimentResults, site1, site2):
a11 = experimentResults['iterations/0/analysis/loading_retention/atoms']
a10 = experimentResults['iterations/1/analysis/loading_retention/atoms']
a01 = experimentResults['iterations/2/analysis/loading_retention/atoms']
a00 = experimentResults['iterations/... | QuantumQuadrate/CsPyController | documentation/tex/AQuA_cost_functions.py | Python | lgpl-3.0 | 9,436 | [
"Gaussian"
] | 076b52cc09ceeb876f4b4d56622fd4812d2f90ff748efa60004d22dfebf5575b |
"""
Acceptance tests for the Import and Export pages
"""
from datetime import datetime
from abc import abstractmethod
from bok_choy.promise import EmptyPromise
from .base_studio_test import StudioLibraryTest, StudioCourseTest
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.import_export import E... | Semi-global/edx-platform | common/test/acceptance/tests/studio/test_import_export.py | Python | agpl-3.0 | 13,412 | [
"VisIt"
] | 588238f9874054a94e5f0a26af5b063df0a487de0a49304f43781e24de91d352 |
__author__ = 'Ivan Mahonin'
from gettext import gettext as _
from argparse import ArgumentParser
import os
import subprocess
import datetime
import pwd
class Launcher:
def __init__(self):
self.pidFile = ""
self.logFile = "-"
self.outputFile = "-"
self.sourceDir = ""
self.r... | morevnaproject/RenderChan | renderchan/launcher.py | Python | bsd-3-clause | 16,394 | [
"VisIt"
] | 4de87041b1514fc551d4df45a109908cb99abfbb249f8393daec23b346b6a94b |
# Moogul.py: MOOSE Graphics Using Lines
# This is a fallback graphics interface for displaying neurons using
# regular matplotlib routines.
# Put in because the GL versions like moogli need all sorts of difficult
# libraries and dependencies.
# Copyright (C) Upinder S. Bhalla NCBS 2018
# This program is licensed under... | dilawar/moose-core | python/rdesigneur/moogul.py | Python | gpl-3.0 | 12,667 | [
"MOOSE"
] | 8f0e9450b535833303a65af817a18d4bbd7677af1aeafe1694f42d04fcd2e0ac |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
# System stuff.
import argparse
import math
import os
import random
import sys
# Third-party stuff.
try:
import yaml
except ImportError:
print("Missing library 'pyyaml'.")
print()
print('clang-format uses yaml as its... | jaredgrubb/fit-clang-format | fit-clang-format.py | Python | mit | 19,654 | [
"VisIt"
] | fdf461793ef75e4810177db2e0a9bb2ed0903384b17469b24b4fea0c28348811 |
'''
Run entire analysis. The cube should already have been exported into a FITS
file from CASA.
This script includes deriving the signal mask and moment arrays for the VLA
and VLA + GBT HI cubes. The feathering and comparisons should already have
been run.
Paper 1 investigates the ensemble of HI properties:
- usin... | e-koch/VLA_Lband | paper1_analysis_pipeline.py | Python | mit | 3,226 | [
"Galaxy"
] | 47026ef570d707319f23d6ebbb8d1e5b35bb8a85cf9e72132d9e1e121a81df96 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/sgx/test/test_sgx_jk.py | Python | apache-2.0 | 4,704 | [
"PySCF"
] | 986e30450a145c70f0f5b3af13edc4a7fbd1f15278b8dac00905613b0891ef04 |
import galaxy.model
from galaxy.model.orm import *
from galaxy.model.mapping import context as sa_session
from base.twilltestcase import *
not_logged_in_as_admin_security_msg = 'You must be logged in as an administrator to access this feature.'
logged_in_as_admin_security_msg = 'You must be an administrator to access ... | volpino/Yeps-EURAC | test/functional/test_user_info.py | Python | mit | 8,765 | [
"Galaxy"
] | 016a93ad980459d4251f5ab586a40c85d727e3f9c5dddd84d484f8f1a01d12d0 |
#!/usr/bin/env python
import argparse
import binascii
import copy
import datetime
import hashlib
import json
import logging
import os
import shutil
import struct
import subprocess
import tempfile
import xml.etree.ElementTree as ET
from collections import defaultdict
from Bio.Data import CodonTable
logging.basicConfig(... | bimbam23/tools-iuc | tools/jbrowse/jbrowse.py | Python | mit | 44,787 | [
"BLAST",
"Galaxy"
] | ae827d9fa8242fdb6c87619371c980e1330e7f3812deeeebb8237b9fab82b94c |
from . import make_readout_wf, get_calibration_dict, \
cos_array, sin_array, flat_array, gaussian_array, \
make_time_varying_sequence
from . import Segment, Waveform, Element
def make_floquet_dur_sequence(start, stop, step, amp=1, floquet_freq=1e6,
channels=[1, 4], form='cos'):
... | QCoDeS/Qcodes-contrib | qdev_transmon_helpers/sequencing/floquet_new.py | Python | mit | 6,619 | [
"Gaussian"
] | 4a6f252ef74d20f529d3e01a5f01968903dc5516ea72f759404fab0632be4425 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/topology/test_xpdb.py | Python | gpl-2.0 | 1,643 | [
"MDAnalysis"
] | 84d53832a7129f15c5e2bfb9d90292fdb3879563db786a0acf13bc7d728024f2 |
# Copyright 2008 Canonical Ltd.
# This file is part of launchpadlib.
#
# launchpadlib is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, version 3 of the License.
#
# launchpadlib is distributed in the ho... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/launchpadlib/credentials.py | Python | gpl-3.0 | 22,081 | [
"VisIt"
] | 16ab50a76a1d4ccbbf5d150c4f706031ca4a7be0601dc377f6970363366af37d |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 t... | mozts2005/OuterSpace | client-pygame/lib/osci/res.py | Python | gpl-2.0 | 14,514 | [
"Galaxy"
] | c4bc3719374bbffd371cf07fac4a491ee3c196b55f9b92cb16ff97d6ba63a309 |
#
# build a samfile with bowtie or other aligner
#
import os
import sys
import bio
import config
if __name__ == "__main__":
if len(sys.argv) != 6:
print "Usage: %s [baseline|bowtie2|bwa|soap] reference.fasta reads.fastq output.sam seed_length" % sys.argv[0]
sys.exit(0)
bio.get_mapper( config, sys.argv[1]... | supernifty/mgsa | mgsa/mapper_selector.py | Python | mit | 377 | [
"BWA",
"Bowtie"
] | 10d6dffb22c9c0a4469dd3e9e3cabc69f8e97d11072370fd4b7d080a3ced70b4 |
../../../../../../../share/pyshared/orca/scripts/apps/pidgin/speech_generator.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/pidgin/speech_generator.py | Python | gpl-3.0 | 80 | [
"ORCA"
] | bff53ecfe82754dfbf035117f8aea01b47cf2ad86d5a1bf22a34a1efa6e9268c |
#!/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/riboStack.py | Python | mit | 15,469 | [
"BWA"
] | b99fd772baa992c9e3639e692f5c3eb0488d9b68c455f33c179f447c376751a6 |
""" DIRAC Workload Management System utility module to get available memory and processors from mjf
"""
import os
import urllib2
__RCSID__ = "$Id$"
def getJobFeatures():
features = {}
if 'JOBFEATURES' not in os.environ:
return features
for item in ('allocated_cpu', 'hs06_job', 'shutdowntime_job', 'grace_se... | petricm/DIRAC | WorkloadManagementSystem/Utilities/JobParameters.py | Python | gpl-3.0 | 1,026 | [
"DIRAC"
] | 4f34f3c0ea58bba2d7f0635e49c076d010fb86d34138221f4e2822e96976d7de |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Paul Franklin, Nicolas Adenis-Lamarre, Benny Malengier
#
# This program is free software; you can redistribute it... | Forage/Gramps | gramps/plugins/drawreport/fanchart.py | Python | gpl-2.0 | 31,763 | [
"Brian"
] | 8e17854133a1033ca5eaaa0af6fcba1e869743b0180e340c666c256ec847a98f |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a EnergyModel abstract class and some basic
implementations. Basically, an EnergyModel is any model that returns an
"energy" for any given structure.
"""
import abc
from monty.json import MSONable
... | materialsproject/pymatgen | pymatgen/analysis/energy_models.py | Python | mit | 5,996 | [
"GULP",
"pymatgen"
] | 4af930fd7f4580ebed9a20180678c6cee24282264987d310b82bf62adfa3a16e |
"""
YANK is a testbed for experimenting with algorithms for the efficient computation of small molecule binding free energies to biomolecular targets using alchemical methods.
YANK is built on OpenMM, the API for molecular simulation, and uses its GPU-accelerated library implementation for hardware acceleration.
"""
fr... | andrrizzi/yank | setup.py | Python | mit | 4,960 | [
"OpenMM"
] | 570f586219d638d3ff48ec0d88ba79babe4dbc350fff0a1f484f53c4400a936a |
#* 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
from .Facto... | nuclear-wizard/moose | python/FactorySystem/__init__.py | Python | lgpl-2.1 | 560 | [
"MOOSE"
] | 10d08f98bc8ae2ff750cf9168197f88b67a4c1317d2f406e2673047645ae121e |
#!/usr/bin/env python
# vim: fileencoding=utf-8 et ts=4 sts=4 sw=4 tw=0 fdm=marker fmr=#{,#}
""" A simple RPC server that shows how to run multiple RPC services
asynchronously using Eventlet cooperative multitasking
"""
#-----------------------------------------------------------------------------
# Copyright (C... | srault95/netcall | examples/eventlet/server_eventlet.py | Python | bsd-3-clause | 2,457 | [
"Brian"
] | a9ee46402756450e2fd50f279d78d2433b29b1bc7c1b978911f47358c675e60d |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/rotational_inertia.py | Python | gpl-3.0 | 6,381 | [
"ESPResSo"
] | 198940403962dcaa5072fa9d3cdcd35068249600a5f13f421c543e89210815c6 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/procrouting/roa.py | Python | lgpl-3.0 | 6,471 | [
"Psi4"
] | 2566f010364625d829b98a3c9ba1e68e2308142b010cd4f9e86519af4f6b935f |
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