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"""
Acceptance tests for studio related to the outline page.
"""
import json
from datetime import datetime, timedelta
import itertools
from pytz import UTC
from bok_choy.promise import EmptyPromise
from nose.plugins.attrib import attr
from ...pages.studio.settings_advanced import AdvancedSettingsPage
from ...pages.stu... | B-MOOC/edx-platform | common/test/acceptance/tests/studio/test_studio_outline.py | Python | agpl-3.0 | 77,904 | [
"VisIt"
] | 5777528e51749235ca125b09074909252569ab0942e7eaf6dd05d6286abf7c2b |
__author__ = 'robswift'
__project__ = 'blastnfilter'
import os
from BlastNFilter.PreRelease import ParsePreRelease
from BlastNFilter.Blast import ParseAlignment
import OutPut
def run(options):
non_polymer = options.non_polymer
polymer = options.polymer
out_dir = options.out
blast_dir = os.path.abspat... | rvswift/BlastNFilter | BlastNFilter/Utilities/Run.py | Python | bsd-3-clause | 840 | [
"BLAST"
] | 8679ac1a524735f374246a0251ccb9b87b062152490aa2944e4d9d4d6c1821b9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# (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, either version 3 of the Licen... | milad-soufastai/ansible-modules-extras | notification/jabber.py | Python | gpl-3.0 | 4,578 | [
"Brian"
] | b02df74224de9e72993010013a0b572f73b7356fac7624f37829f7e19d8f06f7 |
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (a... | andrebellafronte/stoq | stoqlib/gui/widgets/accounttree.py | Python | gpl-2.0 | 7,546 | [
"VisIt"
] | ca2b385fbfae2433ccdfd5ba770510afae9d9b6896cce4da1d71f8046e63f257 |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
#
# @file matplotlib-ref-zernike.py -- plot zernike functions with matplotlib
# Copyright (C) 2011--2013 Tim van Werkhoven (timvanwerkhoven@gmail.com)
#
# This work is licensed under the Creative Commons Attribution-Share Alike
# 3.0 Unported License. To view a copy of ... | tvwerkhoven/pretty-plots | matplotlib-ref-zernike.py | Python | gpl-2.0 | 3,558 | [
"VisIt"
] | 6a472e06ddbcdabf73b9895319f163eb3e79612a601f769ae768a7b8a93f8447 |
#!/usr/bin/env python3
import os, sys, time, traceback
import argparse, multiprocessing
if sys.version_info < (3,7):
sys.exit('Sorry, Python < 3.7 is not supported')
# get the path of this script and add it to the "pythonpath"
SCRIPT_PATH = os.path.split(os.path.realpath(os.path.abspath(__file__)))[0]
sys.pa... | jhcepas/eggnog-mapper | emapper.py | Python | gpl-2.0 | 40,600 | [
"Biopython"
] | 0221474c0e1240c43d190900f23e96d73dff93cc14499ba381a136024f1efdd5 |
from mc_objects import (ENCHANT_WEAPONS, ENCHANT_ARMOR, ENCHANT_HELMETS,
ENCHANT_BOOTS, ENCHANT_TOOLS, ENCHANT_BOWS, ENCHANT_SHIELDS,
ENCHANT_ELYTRA, MCEnchant, register_enchant, register_item, MCItem,
WEAPONS, BOOTS, HELMETS, ARMOR, TOOLS, BOWS, SHIELDS, ELYTRA, AXES,
ENCHANT_AXES, register_attribute,... | Kovak/KivyNBT | mc_data/minecraft/__init__.py | Python | mit | 18,812 | [
"BLAST"
] | 252484b6935720bc14698e172c0ecd96f24c2cad4752fafb147ab0e755eacd68 |
import shutil
import CxDataHandler
import numpy as np
from pyusound.dicom.recloader import DicomRecordingBMode2dCompounding
import os
import sys
from collections import defaultdict
def RemoveRect(nav_acq):
if nav_acq[-1]=='/':
nav_acq=nav_acq[:-1]
if os.path.isdir(nav_acq+"_removed_rect"):
pri... | Danielhiversen/pyCustusX | CxDataHandler/examples/RemoveRect.py | Python | mit | 2,075 | [
"VTK"
] | a7a6bf8d1296a5174e62064a78a76493904e62e7849df2d75d69f417705e7444 |
# This file is part of cldoc. cldoc 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the ... | jessevdk/cldoc | cldoc/nodes/cclass.py | Python | gpl-2.0 | 3,144 | [
"VisIt"
] | 2b9b76cc4992d43d00ec78bc4cef91ab18df6e7294b8f552dbc9ad961be93f53 |
import re
import copy
import os
import tempfile
import logging
import subprocess
import shlex
import time
from threading import Timer
from pycparser import parse_file, c_generator
from pycparser.c_ast import Break
_ENV_ORIG_SRC = 'MUTATE_ORIG_SRC'
_ENV_MODIFIED_SRC = 'MUTATE_MODIFIED_SRC'
def _node_to_str(node):
... | Juzley/Fawkes | mutate/mutator.py | Python | mit | 10,400 | [
"VisIt"
] | 54c371c4af6f02f6c2c02a60b88f50c0e3f80ba402b9d5f0517bf5e23da21d8a |
"""
This module implements a Resource Allocating Vector Quantizer (RAVQ) and
described by Linaker and Niklasson, 2006
Adapted for FoREST-cat by Emily Dolson from code from the pyrobot project,
originally modified for CS81 at Swarthmore College
Spring 2012, by Lisa Meeden
Copyright 2012-2013, Emily Dolson, distribu... | emilydolson/forestcat | netGNGRegion.py | Python | agpl-3.0 | 9,880 | [
"Gaussian"
] | b085e01fb3f0ecf21d7cbd8f0b7a73bc6b89307a2bae0b88e2c16d5a023f18bc |
'''
Superclass to extract yield data from tables
and from mppnp simulations
Christian Ritter 11/2013
Two classes: One for reading and extracting of
NuGrid table data, the other one for SN1a data.
'''
import matplotlib.pyplot as plt
import numpy as np
import os
color=['r'... | jan-rybizki/Chempy | Chempy/input/yields/NuGrid/read_yields.py | Python | mit | 29,284 | [
"Brian"
] | c7898342a9672215f81177eda23993e3d8ef909be120e5c6b0ae44416e00134a |
"""Echo module based on the GFAL2_StorageBase class."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger, S_ERROR, S_OK
class EchoStor... | yujikato/DIRAC | src/DIRAC/Resources/Storage/EchoStorage.py | Python | gpl-3.0 | 3,832 | [
"DIRAC"
] | 8a03aa86045706a96d193d544e3c9bb54d4bb68860d972bc963cd7e8ec8d43be |
__author__ = "John D. Chodera, Frank Noe"
__copyright__ = "Copyright 2015, John D. Chodera and Frank Noe"
__credits__ = ["John D. Chodera", "Frank Noe"]
__license__ = "LGPL"
__maintainer__ = "John D. Chodera, Frank Noe"
__email__="jchodera AT gmail DOT com, frank DOT noe AT fu-berlin DOT de"
import copy
import numpy a... | bhmm/legacy-bhmm-force-spectroscopy-manuscript | bhmm/output_models/discrete.py | Python | lgpl-3.0 | 14,241 | [
"Gaussian"
] | fbfaa92928761c39fd3e5cca6980828adb1d4403bf63aea0d559b9e8d17d7fa9 |
# 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 u... | kkk669/mxnet | python/mxnet/gluon/model_zoo/vision/vgg.py | Python | apache-2.0 | 9,301 | [
"Gaussian"
] | f5b5541caa9bea4fd9e5f086261354ff6141444eaad9865df3e5e3641ae41b46 |
########################################################################
# File: FTSClient.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/08 14:29:43
########################################################################
"""
:mod: FTSClient
.. module: FTSClient
:synopsis: FTS client
.. moduleauthor::... | miloszz/DIRAC | DataManagementSystem/Client/FTSClient.py | Python | gpl-3.0 | 16,128 | [
"DIRAC"
] | 16f9b915abc662d7ef06e3b6d493823f075a6af82f0a53cddadacf574fc9cd6f |
'''
lofar_source_sorter.py
the main code for the decision tree
'''
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from astropy.table import Table, join, Column
import astropy.units as u
import astropy.coordinates as ac
import utils.plot_util as pp
import os
class Mask:
'''Mask store a boolea... | wllwen007/lofar-sources | flowchart/lofar_source_sorter.py | Python | gpl-3.0 | 51,851 | [
"Galaxy",
"Gaussian"
] | 11695ccb22034eb0b7073222498dea1fd2106c27fe6b1a57eb0adc4ab6df408c |
# proxy module
from __future__ import absolute_import
from mayavi.filters.cut_plane import *
| enthought/etsproxy | enthought/mayavi/filters/cut_plane.py | Python | bsd-3-clause | 93 | [
"Mayavi"
] | fcc1a73f8c2ebc89839cf2654f61e6ca9a1c97a384608b090057c55ac920d3df |
# Autodetecting setup.py script for building the Python extensions
#
__version__ = "$Revision: 60581 $"
import sys, os, imp, re, optparse
from distutils import log
from distutils import sysconfig
from distutils import text_file
from distutils.errors import *
from distutils.core import Extension, setup
from distutils... | TathagataChakraborti/resource-conflicts | PLANROB-2015/seq-sat-lama/Python-2.5.2/setup.py | Python | mit | 69,044 | [
"VisIt"
] | eebc37d2c4cb0cfa26462bfabff9f9fcf58d75c3d87cdf1537d08a559ac414b9 |
#!/usr/bin/python3
# coding: utf-8
# # Initialization
#
# Welcome to the first assignment of "Improving Deep Neural Networks".
#
# Training your neural network requires specifying an initial value of the weights. A well chosen initialization method will help learning.
#
# If you completed the previous course of ... | jinzishuai/learn2deeplearn | deeplearning.ai/C2.ImproveDeepNN/week1-hw/Initialization/Initialization.py | Python | gpl-3.0 | 17,528 | [
"NEURON"
] | 7c44cdeae07f4850de4555055a427b602237962681af0a04a76e4acd2acb923e |
#!/usr/bin/env python
#pylint: disable-msg=C0301,C0103,R0914,R0903
"""
DAS command line tool
"""
__author__ = "Valentin Kuznetsov"
import sys
if sys.version_info < (2, 6):
raise Exception("DAS requires python 2.6 or greater")
DAS_CLIENT = 'das-client/1.0::python/%s.%s' % sys.version_info[:2]
import os
import r... | rovere/utilities | das.py | Python | mit | 15,924 | [
"VisIt"
] | af291784c58443d11cbecc674ad566a68a7bf5fc57e240e624cf657a63c02e54 |
# Shifter will be a strictly 2-dimensional game. It will have a start menu when first loaded,
# music, sounds, and graphics.
import pygame
from pygame import *
import CONST
from CONST import *
import random
screen = display.set_mode(WINSIZE)
clock = pygame.time.Clock()
caption("SHIFTER")
pygame.font.init()
#=========... | iPatso/PyGameProjs | PYex/RunnerEx/main.py | Python | apache-2.0 | 106,750 | [
"BLAST"
] | 345c065b176f67fa1cbed66c4da826b27a20616397a984d5c661dfb6e754f88c |
""" This is the admin interface to the LFC. It exposes the functionality not available through the standard
LcgFileCatalogCombinedClient """
from DIRAC.Resources.Catalog.LcgFileCatalogCombinedClient import LcgFileCatalogCombinedClient
class LcgFileCatalogAdminClient(LcgFileCatalogCombinedClient):
LcgFileCa... | Sbalbp/DIRAC | Resources/Catalog/LcgFileCatalogAdminClient.py | Python | gpl-3.0 | 578 | [
"DIRAC"
] | dffc1438cba4775c6f6b19d8bd9a71743238981c2fc257fc99564cd123b5db3c |
# -*- coding: utf-8 -*-
## src/disco.py
##
## Copyright (C) 2005-2006 Stéphan Kochen <stephan AT kochen.nl>
## Copyright (C) 2005-2007 Nikos Kouremenos <kourem AT gmail.com>
## Copyright (C) 2005-2008 Yann Leboulanger <asterix AT lagaule.org>
## Copyright (C) 2006 Dimitur Kirov <dkirov AT gmail.com>
## Copyright (C) 20... | sgala/gajim | src/disco.py | Python | gpl-3.0 | 67,696 | [
"VisIt"
] | 9ef668918b570fd875d4593939c9f388fa2936d88fb3aeeb255231e84a7deb57 |
# Copyright 2013 by Kamil Koziara. 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.
"""
I/O operations for NeXO.
"""
import xml.sax
import collections
impor... | arkatebi/SwissProt-stats | Ontology/IO/NexoIO.py | Python | gpl-3.0 | 4,401 | [
"Biopython"
] | 97dc1247a3d0343bd1a61ff37af2e94871af5e087750c858a09104d3e7dc330b |
"""Tests for the ArchiveFiles Operation"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access, redefined-outer-name
import six
from functools import partial
import logging
import os
import pytest
from mock import MagicMock a... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/test/Test_ArchiveFiles.py | Python | gpl-3.0 | 15,159 | [
"DIRAC"
] | 8b6b71957c5086b6bc19e294b339f3dae4dd13a156cc05ea9890989378965108 |
# -*- 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/test_api.py | Python | gpl-2.0 | 2,813 | [
"MDAnalysis"
] | 694c0ac52c9b334b41277f2ef3823c7152ebe4678b67919e5681f516b0d600c4 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/mp/test/test_kpoint.py | Python | apache-2.0 | 6,345 | [
"PySCF"
] | 054887ccf6ac1a8ba1677e855ba0de747cde0d5c91ab05bc2c820af284beb462 |
"""Copyright 2012 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'
import threading
from ctypes ... | danielsuo/mobot | src/move/PhidgetsPython/Phidgets/Devices/MotorControl.py | Python | mit | 35,542 | [
"VisIt"
] | 7ef7a122c43eaf49d9a8b955f6efb578d5d41cac46aafab5962cd68f61d6b99f |
import numpy as np
from . import sql_query
# SDSS primtarget codes
TARGET_QSO_HIZ = int('0x00000001', 16)
TARGET_QSO_CAP = int('0x00000002', 16)
TARGET_QSO_SKIRT = int('0x00000004', 16)
TARGET_QSO_FIRST_CAP = int('0x00000008', 16)
TARGET_QSO_FIRST_SKIRT = int('0x00000010', 16)
TARGET_GALAX... | astroML/astroML | astroML/datasets/tools/cas_query.py | Python | bsd-2-clause | 3,040 | [
"Galaxy"
] | 996a2288ad8765c36eacf7decc1aeae14e6f419852f5e22ae420a22e5358a896 |
#!/usr/bin/env python
""" update local cfg
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import os
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
from DIRAC.ConfigurationSystem.Client.CSAPI import CSAPI
Script.setUsageMessage("\n"... | ic-hep/DIRAC | tests/Jenkins/dirac-cfg-update-dbs.py | Python | gpl-3.0 | 2,992 | [
"DIRAC"
] | d98284082458ea32c2aef5de0a2a1d89c86e2e09e104cb9a8fa8aeb347d7491f |
#
# 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... | iemejia/incubator-beam | sdks/python/apache_beam/runners/direct/direct_runner.py | Python | apache-2.0 | 22,891 | [
"VisIt"
] | 1d7c1ff2ee3b003591d4922774b6f044f1e5bec8bf448b89eb38ed6b33373a86 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-05-19 17:00:49
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-07-30 19:23:16
from __future__ import print_function, division, absolute_import
from marvin.tests.api.co... | albireox/marvin | python/marvin/tests/api/test_modelcube.py | Python | bsd-3-clause | 2,900 | [
"Brian",
"Galaxy"
] | cd290efacd8223299c8af4e2380f0e61dffd320e2117f3a8a7de2821feb653ec |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2017-06-26 14:13:40
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-26 17:25:41
from aces.runners import Runner
from aces.runners.minimize import minimize as minimize_input
import aces.tools as tl
from aces.io.vasp import writevasp
import numpy as n... | vanceeasleaf/aces | aces/runners/z_strain.py | Python | gpl-2.0 | 1,308 | [
"ASE",
"VASP"
] | 15e4aa443ca15de46526b6b6868c3eaadf3162155af0b6a30852dc6bb8f0e7d7 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Final/results/objects/24/test10_cross_validate_objects_24_1200ms.py | Python | mit | 4,249 | [
"Mayavi"
] | b96dfda4e92a77ee3b754ce2f53cbd4416c33a6fd18f078dfdf76a4699dfd5ea |
"""
Support the ISY-994 controllers.
For configuration details please visit the documentation for this component at
https://home-assistant.io/components/isy994/
"""
import logging
from urllib.parse import urlparse
import voluptuous as vol
from homeassistant.core import HomeAssistant # noqa
from homeassistant.const i... | Smart-Torvy/torvy-home-assistant | homeassistant/components/isy994.py | Python | mit | 8,368 | [
"VisIt"
] | 379ca9adc5775895421afb0702e7bc377262f96f85cfb6ceee708afe692aa9b6 |
##############################################################################
##
## nymp - a graphical xmms2 cli frontend
## Copyright 2010 Thammi
##
## nymp 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 Foundat... | thammi/nymp | src/nymp/gui/browser.py | Python | gpl-3.0 | 10,793 | [
"VisIt"
] | bce7294c8ac4fea2561b89b32c578b4a6690da194aacf83e447deba908073ae8 |
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime
import dateutil.parser
from xmodule.modulestore import Location
from xmodule.seq_module import Sequen... | rationalAgent/edx-platform-custom | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 41,972 | [
"VisIt"
] | 1daca23c553b9fa3007c458f3215e2dcaeaca382f9fc7514583684bfeb0c77b5 |
#! /usr/bin/env python
#import __main__
#__main__.pymol_argv = ['pymol','-qc']
##__main__.pymol_argv = ['pymol','']
#import sys,time,os
#import pymol
#
#pymol.finish_launching()
#pymol.cmd.feedback("disable","all","actions")
#pymol.cmd.feedback("disable","all","results")
#sys.path.append("/home/scratch/software/Pymol-... | demharters/git_scripts | dist_dna_4dnb_fragment_hme2.py | Python | apache-2.0 | 2,828 | [
"MDAnalysis",
"PyMOL"
] | 8d48be84e0b82d66d1e9e486628f52d32daaea6ee5249e3b643e00250bd9119b |
# -*- coding: utf-8 -*-
import numpy as np
import scipy.special
from bokeh.plotting import *
from bokeh.objects import Range1d
mu, sigma = 0, 0.5
measured = np.random.normal(mu, sigma, 1000)
hist, edges = np.histogram(measured, density=True, bins=50)
x = np.linspace(-2, 2, 1000)
pdf = 1/(sigma * np.sqrt(2*np.pi)) ... | sahat/bokeh | examples/plotting/file/histogram.py | Python | bsd-3-clause | 3,786 | [
"TINKER"
] | 683cd7771eed450a517014f1aad00009f97865c1b2ec4a739e6ede6398837b50 |
"""
Unit tests for the Voronoi renderer
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import unittest
import numpy as np
import vtk
from .. import voronoiRenderer
from ... import utils
from ....filtering import voronoi
from ....system import lattice
from six.moves import range
... | chrisdjscott/Atoman | atoman/rendering/renderers/tests/test_voronoiRenderer.py | Python | mit | 3,377 | [
"VTK"
] | f03e08eb7cdfd75bb05f3478fdbe413171f3c0c7ec07b852a0fcb4012d7f0054 |
"""Weight initializer."""
from __future__ import absolute_import, print_function
import re
import logging
import warnings
import json
import numpy as np
from .base import string_types
from .ndarray import NDArray, load
from . import random
# inherit str for backward compatibility
class InitDesc(str):
"""Descripto... | rishita/mxnet | python/mxnet/initializer.py | Python | apache-2.0 | 22,395 | [
"Gaussian"
] | c15973d0f07687f83e64d8b32a6c093cece422ff0b8eead6ca42dace1d461885 |
# -*- coding: utf-8 -*-
"""Some utility functions."""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)
import atexit
from collections import Iterable
from contextlib import contextmanager
from distutils.version import LooseVersio... | teonlamont/mne-python | mne/utils.py | Python | bsd-3-clause | 96,393 | [
"Mayavi"
] | ecf16f45ad300336ef68f456289c90f7ce154f6089318be91aa7cacde7e878a6 |
try: paraview.simple
except: from paraview.simple import *
def RequestDataDescription(datadescription):
"Callback to populate the request for current timestep"
if datadescription.GetForceOutput() == True:
for i in range(datadescription.GetNumberOfInputDescriptions()):
datadescription.GetIn... | openmichigan/PSNM | NavierStokes/Programs/NavierStokes3dFortranMPIParaView/cell-based/pipeline_images.py | Python | bsd-2-clause | 29,563 | [
"ParaView"
] | 4df40dc3e22400c37eab9614af4095a1f7b9d188dc73c02d630cb9431a168e78 |
""" Activations
A collection of activations fn and modules with a common interface so that they can
easily be swapped. All have an `inplace` arg even if not used.
Hacked together by / Copyright 2020 Ross Wightman
"""
import torch
from torch import nn as nn
from torch.nn import functional as F
def swish(x, inplace:... | rwightman/pytorch-image-models | timm/models/layers/activations.py | Python | apache-2.0 | 4,040 | [
"Gaussian"
] | 893fd64b078ad41d787c06a67c9385720a90e43a0123a16fb7e5f87d1b98b123 |
#! test QC_JSON Schema for response properties
import psi4
import numpy as np
import json
import os
from distutils import dir_util
# Generate JSON input
json_data = {
"schema_name": "qcschema_input",
"schema_version": 1,
"molecule": {
"geometry": [
0.0, 0.0, -0.1294769411935893, 0.0, ... | jturney/psi4 | tests/json/schema-1-response/input.py | Python | lgpl-3.0 | 5,134 | [
"Psi4"
] | 70923317cca4fede723d53c2477a4f817bd0e0f325f9a79cf84b3dd126a2b486 |
#!/usr/bin/env python
import os, sys
import re
if len(sys.argv) != 3:
print """
Usage: WhatModulesVTK.py vtkSourceTree applicationFile|applicationFolder
Generate a FindPackage(VTK COMPONENTS) that lists all modules
referenced by a set of files.
Additionally, two extra find_package( VTK COMPONENTS)... | timkrentz/SunTracker | IMU/VTK-6.2.0/Utilities/Maintenance/WhatModulesVTK.py | Python | mit | 9,635 | [
"VTK"
] | a59ef0de60282f95e67fb8885c289919e087aaea3a879808fef9400973aa7506 |
# 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... | gkc1000/pyscf | pyscf/nao/m_prod_talman.py | Python | apache-2.0 | 10,232 | [
"PySCF"
] | 6e441300ad69805eb061b33a3b92bc8c71e1714feeaf1ccb185401ba556f2beb |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Parameters for debugging
res = 1000
# create pipeline
#
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
pl3d.SetQFileName(VTK_DATA_R... | sumedhasingla/VTK | Filters/Points/Testing/Python/TestPointInterpolator.py | Python | bsd-3-clause | 6,099 | [
"Gaussian",
"VTK"
] | bd2c5b0286dc890f655cecbf74519c7c2c0d9873db8b0a3afc9b6c2696f295bc |
#
# 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... | astitcher/qpid-proton-old | tests/python/proton_tests/messenger.py | Python | apache-2.0 | 30,342 | [
"Galaxy"
] | 19984be246d43ea3259f734d7f375a2c855a6168caec4f8ede9a9d5e5be60b50 |
"""
:mod:`Mutators` -- mutation methods module
=====================================================================
In this module we have the genetic operators of mutation for each chromosome representation.
"""
import Util
from random import randint as rand_randint, gauss as rand_gauss, uniform as rand_uniform
f... | tapomayukh/projects_in_python | sandbox_tapo/src/AI/Genetic Algorithm/Mutators.py | Python | mit | 28,614 | [
"Gaussian"
] | 29ebc2cb23de011a19ca17f4be15126e850e2f3d5de793f33b5c8ac7358f5fba |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2014 Eficent (<http://www.eficent.com/>)
# <contact@eficent.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero... | Eficent/odoo-operating-unit | purchase_requisition_operating_unit/__openerp__.py | Python | agpl-3.0 | 2,941 | [
"VisIt"
] | 607fed54966f7426ec36788c3983555d7cbc1a945a569cd4b13370bb4567534b |
#! A test of the basis specification. A benzene atom is defined using a ZMatrix containing dummy atoms
#! and various basis sets are assigned to different atoms. The symmetry of the molecule is automatically
#! lowered to account for the different basis sets.
import psi4
psi4.set_output_file("output.dat", False)
b... | ashutoshvt/psi4 | samples/python/mints2/input.py | Python | lgpl-3.0 | 3,880 | [
"Psi4"
] | de1cfbcaed1e9287a2ab215ae8cba54eafede98fc2ccf2bd27cd8ecd71274ed0 |
from pele.storage.database import Database, Minimum, TransitionState
import time
import numpy as np
from simtk.openmm.app import AmberPrmtopFile
""" creates a sqlite database from min.data, ts.data, extractedmin, extractedts
Input:
coords.prmtop ( for number of atoms )
min.data, ts.data, extractedmin, extr... | kjs73/pele | playground/amber/aladipep/optim2sqlite.py | Python | gpl-3.0 | 2,319 | [
"OpenMM"
] | 754467a25e233e7c0f9797c8af241f77a92c072ae3b85343ec1a3842e837c606 |
""" This file contains custom checkers for pylint.
"""
from typing import List
import astroid.node_classes
import astroid.nodes
from pylint.checkers import BaseChecker
from pylint.interfaces import IAstroidChecker
from pylint.lint.pylinter import PyLinter
class NoFromImportChecker(BaseChecker):
"""This checker c... | RoboJackets/robocup-software | rj_gameplay/stp/pylint_stp.py | Python | apache-2.0 | 2,080 | [
"VisIt"
] | 478126b720c89ba58f76423559cca1e3a7e72d0f2011e60748a14e1293009acd |
""" DISET request handler base class for the ProductionDB.
"""
import six
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.Utilities.DEncode import ignoreEncodeWarning
from DIRAC.Core.Utilities.ObjectLoader import ObjectLoader
prodTypes = [six.string_... | DIRACGrid/DIRAC | src/DIRAC/ProductionSystem/Service/ProductionManagerHandler.py | Python | gpl-3.0 | 5,600 | [
"DIRAC"
] | 86535bdabe4c238b96eb9bbc20cd438486bef34818dbabe9a57232344026b18b |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/__init__.py | Python | gpl-2.0 | 3,742 | [
"VisIt"
] | fc30baf50ce1289fbf67d532c05f50aa5e590220d4ea038fcc593963d5a96c1b |
#!/usr/bin/env python
"""
Script that facilitates the modification of a element through the command line.
However, the usage of this script will set the element token to the command
issuer with a duration of 1 day.
"""
from datetime import datetime, timedelta
from DIRAC import gLogger, exit as DIRACExit, S_OK, version... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/scripts/dirac_rss_set_status.py | Python | gpl-3.0 | 8,316 | [
"DIRAC"
] | ea2dca519b8b298bc538ac666e269078dace5b90e8949bcfceedf0904a4beaa4 |
import re
import os
import six
class Compiler(object):
RE_INTERPOLATE = re.compile(r'(\\)?([#!]){(.*?)}')
doctypes = {
'5': '<!DOCTYPE html>'
, 'xml': '<?xml version="1.0" encoding="utf-8" ?>'
, 'default': '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR... | zeraien/pyjade | pyjade/compiler.py | Python | mit | 13,936 | [
"VisIt"
] | 27afe8092f2e34158baa003b33434924084102ab399e1191d4c1fc46adb4e924 |
#encoding:utf-8
from __future__ import division
from random import random, randint
from math import log, e, tan
'''
Various random generators, inspired from sources present in github.com/belangeo/pyo
'''
class MyRandoms:
def __init__(self):
self.RAND_MAX = 4294967295
self.PYO_RAND_SEED = randint(1, self.RAND_MA... | poifra/Creamuspython2 | MyRandoms.py | Python | mit | 7,071 | [
"Gaussian"
] | 81df7aa78514b1b3227571b6d5a05ae6e63ca1ef26f6279fea1986fa154016dc |
# -*- coding: utf-8 -*-
# More advanced SWIG module test script
#
# Import highlight.py, which is the interface for the _highlight.so module.
# See highlight.py for all available attributes and class members.
#
# Example: python2.7 testmod.py -Sperl -O odt testmod.pl testmod.pl.odt
import highlight
import sys
from opt... | ahmadaghazadeh/FastBook | src/FastBookCreator/highlight/examples/swig/testmod.py | Python | mit | 3,086 | [
"VTK"
] | 24fa1cd7addcd705d0977e2fde97e67fae3c2ecf5be5ebcd30605bf5063db76a |
#
# Copyright (C) 2000 Stephen Davies
# Copyright (C) 2000 Stefan Seefeld
# All rights reserved.
# Licensed to the public under the terms of the GNU LGPL (>= 2),
# see the file COPYING for details.
#
from Synopsis.Processor import Parameter
from Tree import Tree
from Synopsis.Formatters.HTML.Tags import *
import os
... | stefanseefeld/synopsis | Synopsis/Formatters/HTML/Views/FileTree.py | Python | lgpl-2.1 | 2,018 | [
"VisIt"
] | 07fd3490c438bb820236c6ecad5507075fa1db90eeac936c4e877700d746dc4e |
# -*- coding: utf-8 -*-
"""
==========================================================
Structure data I/O (:mod:`sknano.io`)
==========================================================
.. currentmodule:: sknano.io
Contents
========
Base I/O classes to inherit from when creating new I/O classes
-----------------------... | androomerrill/scikit-nano | sknano/io/__init__.py | Python | bsd-2-clause | 1,324 | [
"LAMMPS"
] | 0362a36a095ae633383c80c159aec7e439e8e94a9df5dc48a1a051251cecafd4 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_paymentcategoryeditor.py | Python | gpl-2.0 | 2,817 | [
"VisIt"
] | 7615dac8966702c41eb0083adbb679025a8436ca99966956de8009d56dc155bd |
#!/usr/bin/env python
#PBS -m ae
#PBS -q verylong
#PBS -l nodes=2:ppn=8
#!/usr/bin/env python
from ase import Atom, Atoms
from ase.optimize.bfgslinesearch import BFGSLineSearch
from ase.io import read
from gpaw import GPAW
#Relax the Au 55 atoms cluster with both lcao and paw modes
cluster = read('Au55.xyz')
cell = ... | qsnake/gpaw | gpaw/test/big/CO_Au55_cluster/Au55_cluster.py | Python | gpl-3.0 | 2,345 | [
"ASE",
"GPAW"
] | 083e5dcafc52eefef5f3e224ae2fcc1d4eadd09a66e2f77abe93d4a92f70a7ab |
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#
# Okinawa Institute of Science and Technology, Japan.
#
# This script runs on STEPS 2.x http://steps.sourceforge.net
#
# H Anwar, I Hepburn, H Nedelescu, W Chen and E De Schutter
# Stochastic calcium mechanisms cause dendritic calcium spike... | CNS-OIST/STEPS_Example | publication_models/API_2/Anwar_J_Neurosci_2013/HybridCaburst_detchannels.py | Python | gpl-2.0 | 18,841 | [
"Avogadro"
] | fc6daf96d1372d85813efb5e9cd2c7ec1a48c14956ffc03a444272b858088ebf |
"""Generate the storage netcdf file for Iowa Flood Center Precip"""
import datetime
import sys
import os
import numpy as np
from pyiem.util import ncopen, logger
LOG = logger()
def init_year(ts):
"""
Create a new NetCDF file for a year of our specification!
"""
fp = "/mesonet/data/iemre/%s_ifc_dail... | akrherz/iem | scripts/iemre/init_daily_ifc.py | Python | mit | 2,453 | [
"NetCDF"
] | 6b9bae98e4a34abc8bb12661da6db883dd8a5eff1a34927d23782d4e08795585 |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
"""
Gaussian Processes regression examples
"""
try:
from matplotlib import pyplot as pb
except:
pass
import numpy as np
import GPy
def olympic_marathon_men(optimize=True, plot=True):
"""Ru... | avehtari/GPy | GPy/examples/regression.py | Python | bsd-3-clause | 18,747 | [
"Gaussian"
] | ed7ccef629281dc97a6a298c321da9a144a735584d84e42d0045ec736599018d |
#!/usr/bin/env python3
"""diffout
Usage:
diffout [options] [--] <commandline> <infile>...
diffout -s
diffout -h | --help
diffout --version
Runs a command on a list of input files, then compares the resulting outputs with copies stored from a previous run.
Examples:
diffout <commandline> <infile>...
Optio... | davem2/diffout | diffout/diffout.py | Python | mit | 12,520 | [
"FEFF"
] | a5a3df3308f772054ed4ee1616a1d1c72c298e7be7e10e4c6d0f5c08a7f0d357 |
"""URL opener.
Copyright 2004-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt included with the distribution).
"""
from __future__ import absolute_import
import bisect
import os
import temp... | Masood-M/yalih | mechanize/_opener.py | Python | apache-2.0 | 14,735 | [
"VisIt"
] | db25a3ec600f7f7206b8485f75e2cb0db4debf59d5d29eac2b2817d83cd144d8 |
"""
@name: PyHouse/src/Modules/Drivers/_test/test_Null.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2018 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 30, 2015
@Summary:
"""
__updated__ = '2018-02-12'
# Import system type stuff
from twisted.tria... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Drivers/_test/test_Null.py | Python | mit | 813 | [
"Brian"
] | f12b7c86c10083717426bfadf1fd29ffca3eb7fb322b79384c01e6cf98e8cc3f |
import unittest
import numpy as np
from spglib import get_symmetry
from vasp import read_vasp
from os import listdir
class TestGetSymmetry(unittest.TestCase):
def setUp(self):
lattice = [[4, 0, 0], [0, 4, 0], [0, 0, 4]]
positions = [[0, 0, 0], [0.5, 0.5, 0.5]]
numbers = [1, 1]
magm... | sauliusg/cod-tools | src/externals/spglib/python/test/test_collinear_spin.py | Python | gpl-2.0 | 1,389 | [
"VASP"
] | f9bbaf6ce88d79571053c2e56ea58c671e5a94bcee77789dc7943fe3e53e7968 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/external.py | Python | gpl-2.0 | 5,656 | [
"VisIt"
] | 876ea510e11f0182672346047c5c02c455816e175eec4fcd3f25c95fac682b49 |
"""Module documentation goes here."""
# Enthought library imports.
from traits.api import Instance
from traitsui.api import View, Group, Item
from tvtk.api import tvtk
# Local imports
from mayavi.core.module import Module
from mayavi.components.actor import Actor
####################################################... | dmsurti/mayavi | mayavi/modules/skeleton_module.py | Python | bsd-3-clause | 2,822 | [
"Mayavi",
"VTK"
] | 34c1765733810c8aabc7c6d756cef675b92339d5d94a2ef94182802dcb46e928 |
# -*- coding: utf-8 -*-
from .body import GeoBody
from .point import Point
from .solver import solve
from .vector import Vector
class Plane(GeoBody):
"""A Plane (not the flying one)"""
def __init__(self, *args):
"""Plane(Point, Point, Point):
Initialise a plane going through the three given poi... | Kingdread/sgl | sgl/plane.py | Python | gpl-3.0 | 8,095 | [
"VTK"
] | 0ff931a25faca78d5b8a29b96f709929eaf8680968aa61f3904ba595c3ea7a2e |
#!/usr/bin/python
""" Functions to calculate the mean-square displacement from a LAMMPS trajectory
Usage:
#Must be in pythonpath or working directory
from msd import msd
msd_df = msd(atom_type,first_frame,last_frame)
Requirement:
python2
numpy
dump_dataframe.py
pandas
TODO:
Parallelisation
Add a function for a traje... | EtiCui/Msc-UdeS | dataAnalysis/msd.py | Python | mit | 3,196 | [
"LAMMPS"
] | a971285f73a2fb626b1fa38ded466f5e60ebd48e4a72cdc33187b6a74ed290f3 |
#!/usr/bin/env python
# qm.py -- A Quine McCluskey Python implementation
#
# Copyright (c) 2006-2013 Thomas Pircher <tehpeh@gmx.net>
#
# 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 ... | alexgorbatchev/node-crc | test/pycrc/qm.py | Python | mit | 20,761 | [
"ESPResSo"
] | 2981c11d9a6bb9ff883d44da7a554799c5f1485aa83e75a021c32e0ca37fccce |
import numpy as np;
import calconscious_lib as ccl;
"""
This test, since I don't have any real data, so I simply use numpy's
random function to generate Gaussian-like signals to test the correction of implementation.
Xt here is a 8*64 array which consists of 8 samples (X^t)
Xt_tau is a 8*64 array which consists of 8... | duguyue100/pycalconscious | calconscious_main.py | Python | gpl-3.0 | 2,704 | [
"Gaussian"
] | e13a4553db8be05564911687140af5826cc3c6e7f0fa1f9d5a4a5c1674f55e5e |
from __future__ import absolute_import
from __future__ import unicode_literals
import logging
from functools import reduce
from docker.errors import APIError
from .config import ConfigurationError
from .config import get_service_name_from_net
from .const import DEFAULT_TIMEOUT
from .const import LABEL_ONE_OFF
from .... | charleswhchan/compose | compose/project.py | Python | apache-2.0 | 13,153 | [
"VisIt"
] | 8a3bcb79af4e1a3c919e9305c6823ca15ebc2dc6ec097ffa29bae72f890a197d |
# -*- coding: utf-8 -*-
# Akvo RSR is covered by the GNU Affero General Public License.
# See more details in the license.txt file located at the root folder of the Akvo RSR module.
# For additional details on the GNU license please see < http://www.gnu.org/licenses/agpl.html >.
from django.core.exceptions import Va... | akvo/akvo-rsr | akvo/rsr/models/project_document.py | Python | agpl-3.0 | 6,058 | [
"VisIt"
] | f1369704702dc1d824b6f56ebd98ff28671627905f9daea380884fd34e70583e |
import extractor as ex
from sklearn.svm import LinearSVC
from sklearn import linear_model
from sklearn.naive_bayes import MultinomialNB
from sklearn.naive_bayes import GaussianNB
from sklearn.linear_model import LogisticRegression
from sklearn.tree import DecisionTreeClassifier
from sklearn.neighbors import KNeighborsC... | krishnasumanthm/Quora_Answer_Classifier | execute.py | Python | mit | 4,202 | [
"Gaussian"
] | 58df2eb8bf375c99dfdb4046df3e7fb531100e90e501a4aefe38f98ab90d75a1 |
import numpy
from tkp.utility import nice_format
from scipy.stats import norm
from sqlalchemy.sql.expression import desc
from tkp.db.model import Image
from tkp.db.quality import reject_reasons
def rms_invalid(rms, noise, low_bound=1, high_bound=50):
"""
Is the RMS value of an image outside the plausible range... | transientskp/tkp | tkp/quality/rms.py | Python | bsd-2-clause | 5,118 | [
"Gaussian"
] | 59e5c882cfbb8cf6b607bb76520c3de76c0ce30e6f5c1b0621db998e0cfed413 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Brian Coca <brian.coca+dev@gmail.com>
#
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.... | tszym/ansible | lib/ansible/modules/system/getent.py | Python | gpl-3.0 | 4,071 | [
"Brian"
] | 1a723a9830b213d8a76ec6f8f036574ccb36de858c96ef491035c928a5fecdb9 |
import argparse
import json
import sys
import numpy as np
import vtk
#### import the simple module from the paraview
import paraview.simple as pv
description = "ParaView python script to generate 3D event displays from 3D spacepoint data created with pixy_roimux."
parser = argparse.ArgumentParser(description=descript... | 70rc/pixy_roimux | display.py | Python | gpl-3.0 | 5,824 | [
"ParaView",
"VTK"
] | 53c5dc6eb493c5754266f2250382b272f92b55a5d0b2e44e28b8a55ddb6b3099 |
# author: brian dillmann
# for rscs
from context import DeviceManager
import unittest
import RPi.GPIO as GPIO
class device_manager_test(unittest.TestCase):
def setUp(self):
GPIO.setmode(GPIO.BCM)
GPIO.setwarnings(False)
def test_not_found_errors(self):
m = DeviceManager()
with self.assertRaises(KeyError)... | dillmann/rscs | test/devicetests/device_manager_test.py | Python | mit | 1,558 | [
"Brian"
] | 7167e325be1d798758a013d94e79f5f13c7c913fabbdc30a5272e79e1da6a0fe |
# Copyright 2017 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... | snnn/tensorflow | tensorflow/python/autograph/pyct/static_analysis/live_values.py | Python | apache-2.0 | 5,662 | [
"VisIt"
] | 4c9d510eeba132c5ea33d5486e172b543e87c966c2839ed2b65affaaea57423a |
# plugin: com.py
# Copyright (c) 2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Centre of mass
==============
Calculate the centre of mass of index groups.
Plugin class
------------
.. autoclass:: COM
:members:... | pslacerda/GromacsWrapper | gromacs/analysis/plugins/com.py | Python | gpl-3.0 | 9,964 | [
"Gromacs"
] | 6713fbfa2c00f3ec43d1a4d3d12ecb930c044c82bc334f4c7542f779682f1d06 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-get-wn
# Author : Philippe Charpentier
########################################################################
"""
Get WNs for a selection of jobs
"""
import datetime
from functools import cmp_to_key
... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_wms_get_wn.py | Python | gpl-3.0 | 7,558 | [
"DIRAC"
] | 6c5e05e7b9e08181e8770775f994607f7db73eb61a5333c8e94fc7a82376f2fb |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | testsuite/python/domain_decomposition.py | Python | gpl-3.0 | 2,297 | [
"ESPResSo"
] | 0d80f5ce7a5a65c1cac28c973b66f194c651ddb473184f783944819f912abc43 |
# Copyright 2017 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... | drpngx/tensorflow | tensorflow/contrib/autograph/pyct/cfg.py | Python | apache-2.0 | 23,771 | [
"VisIt"
] | 11a8aa482e3d33aa05d819ab4e2047e771b76a2b30150644bc7a5339f78e7e5f |
#!/usr/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================
"""
environment.py
Lightweight module for validating SMIRKS using Open Force Field ToolkitWrappers.
AUTHORS
Cait... | open-forcefield-group/openforcefield | openff/toolkit/typing/chemistry/environment.py | Python | mit | 9,601 | [
"RDKit"
] | e41b2b358ecbe45439fdc6bdea8fac60e43d9cc0c6335df1de89267008ce2289 |
#! /usr/bin/env python
###############################################################################
# Copyright 2016 Adam Jackson
###############################################################################
# This program is free software: you can redistribute it and/or modify
# it under the terms of the G... | WMD-Bath/kgrid | kgrid/series.py | Python | gpl-3.0 | 5,183 | [
"ASE",
"CASTEP",
"CRYSTAL",
"VASP"
] | ef8907945443d5ab555f4cbf0bc80dc52f65be4e0d330cb0588cad7c4db1365c |
"""
Read data from ECMWF MACC Reanalysis.
"""
import threading
import pandas as pd
try:
import netCDF4
except ImportError:
class netCDF4:
@staticmethod
def Dataset(*a, **kw):
raise ImportError(
'Reading ECMWF data requires netCDF4 to be installed.')
try:
from e... | alorenzo175/pvlib-python | pvlib/iotools/ecmwf_macc.py | Python | bsd-3-clause | 11,452 | [
"NetCDF"
] | 4141874f9239557a18a62c2c1d7f42dd1fef291125b135c05f635516991c6915 |
import os
from uuid import uuid4
from pulsar import __version__ as pulsar_version
from .util import filter_destination_params
REMOTE_SYSTEM_PROPERTY_PREFIX = "remote_property_"
def build(client, destination_args):
""" Build a SetupHandler object for client from destination parameters.
"""
# Have define... | natefoo/pulsar | pulsar/client/setup_handler.py | Python | apache-2.0 | 4,404 | [
"Galaxy"
] | 9300ba7e008a8700fb23f55760acc7de73a3ad224f8b7961b49b3e0a998edce1 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
bonds_by_type.py reads a LAMMPS data file (or an excerpt of... | jag1g13/lammps | tools/moltemplate/src/bonds_by_type.py | Python | gpl-2.0 | 15,426 | [
"LAMMPS"
] | 7d3f285494ff2519ccda6ae9aa613a642ed386bb0956bcb676c663cfbc8c81a4 |
# -*- coding: utf-8 -*-
## Ranking of records using different parameters and methods on the fly.
##
## This file is part of Invenio.
## Copyright (C) 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public... | pamoakoy/invenio | modules/bibrank/lib/bibrank_record_sorter.py | Python | gpl-2.0 | 41,048 | [
"Octopus"
] | 25aa9cfdc2f15da292b959cfaca4bf726f702e7bb77504418896f72189de4a80 |
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import atexit
import logging
from pylib import android_commands
from pylib.device import device_utils
class PerfControl(object):
"""Provides methods for ... | mohamed--abdel-maksoud/chromium.src | build/android/pylib/perf/perf_control.py | Python | bsd-3-clause | 6,344 | [
"Galaxy"
] | cd34d9b86e90010fee4880b54174176e8cc321b23918e106e7756279bf52d4bc |
#!/usr/bin/env python3
import torch
from ..distributions import MultivariateNormal
from ..lazy import InterpolatedLazyTensor
from ..utils.broadcasting import _mul_broadcast_shape
from ..utils.interpolation import Interpolation, left_interp
from ..utils.memoize import cached
from ._variational_strategy import _Variati... | jrg365/gpytorch | gpytorch/variational/grid_interpolation_variational_strategy.py | Python | mit | 4,836 | [
"Gaussian"
] | 753bf71274402e3f22b1c66c8fd780288bc28a0c590009cacd44fa6b0a5bd22f |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# 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.
import re
def parse_ng86(lines, results):
""" Parse the Nei & Gojobori (1986) sectio... | zjuchenyuan/BioWeb | Lib/Bio/Phylo/PAML/_parse_yn00.py | Python | mit | 5,743 | [
"Biopython"
] | 3da1a25e0a045daea31e51e7471509350d4d4e1a8227a0c4f5c3248dbf5aa74f |
#!/usr/bin/env python
## -*- Mode: python; py-indent-offset: 4; indent-tabs-mode: nil; coding: utf-8; -*-
import cairo
import sys
import re
import gtk
class DataRange:
def __init__(self, start = 0, end = 0, value = ''):
self.start = start
self.end = end
self.value = value
class EventStri... | venzozhang/GProject | utils/grid.py | Python | gpl-2.0 | 39,708 | [
"FLEUR"
] | 460955e77c4505b1a5a45f9cdb1096a6cb93657df3ccebb6237c82d5f29c23bd |
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