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#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, Ve... | sparkslabs/kamaelia_ | Sketches/MPS/Stats/zipf.py | Python | apache-2.0 | 8,103 | [
"Gaussian"
] | 5f82a8390bb5e316f99d1a70e5cbbdadaf238d93dcc2da6209a67eeca7d23b36 |
# Copyright 2012 the rootpy developers
# distributed under the terms of the GNU General Public License
from __future__ import absolute_import
from math import sqrt
import ROOT
from . import log; log = log[__name__]
from . import MIN_ROOT_VERSION
from ...extern.six import string_types
from ...memory.keepalive import ... | mverzett/rootpy | rootpy/stats/histfactory/histfactory.py | Python | gpl-3.0 | 36,348 | [
"Gaussian"
] | e2afe16cf13e187aaf40ca526dd7a2ccd46b4159d4786b8108fe706bd3142955 |
import urllib2
import json
from pprint import pprint
followedChannels = []
liveChannels = []
offset = 0;
#Get twitch.tv username as user input
username = raw_input("Enter your twitch.tv username: ")
#Create an html file to write to and initialize headers for .html
file = open('twitchyFollowers.html', 'w')
file.write... | jamesjlee/twitchy | twitchyFollowing.py | Python | mit | 3,096 | [
"VisIt"
] | 0f2296ba4d59a8815e3d30ed9a35d243e5b955fdf5df25a001589bac7feb8ff5 |
# Copyright 2013-2020 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 RGenomeinfodbdata(RPackage):
"""for mapping between NCBI taxonomy ID and species. Used by ... | iulian787/spack | var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py | Python | lgpl-2.1 | 1,208 | [
"Bioconductor"
] | e73567977aa1aa0ebaf116b2e416921dab8a5c51e06e94d8fd29a5c21aaafee1 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/letters/views.py | Python | gpl-3.0 | 7,091 | [
"Brian"
] | c1fd7ac483b745d4be2657ed35a3201355f5a595dcd2d4d34c7041b48b55f1a2 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import os
import re
import webapp2
import jinja2
import logging
import StringIO
from markupsafe import Markup, escape # https://pypi.python.org/pypi/MarkupSafe
import parsers
from google.appengine.ext import ndb
from google.appengine.ext import blobstore
from google.ap... | pwz3n0/schemaorg | sdoapp.py | Python | apache-2.0 | 78,319 | [
"VisIt"
] | cbbcca0a91579cf303b697b950c414934147218e0abd7a75032ceb4a204fa92e |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-cpu-normalization
# Author : Ricardo Graciani
########################################################################
"""
Determine Normalization for current CPU
"""
__RCSID__ = "$Id$"
import DIRAC
f... | avedaee/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-cpu-normalization.py | Python | gpl-3.0 | 1,989 | [
"DIRAC"
] | 4504a8bac34739a9f1c0cc2701d224c3ee4f055c69486f25367c7cefa0eb5794 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | xtiankisutsa/MARA_Framework | tools/androguard/androguard/decompiler/dad/writer.py | Python | lgpl-3.0 | 25,752 | [
"VisIt"
] | 85d6a8a2341b919b5c390427ac065f479491f82cb27f5718c59ff141b9ee399d |
from __future__ import division
"""
Module: spectrum.py
Contains SourceSpectrum and SpectralElement class defnitions and
their subclasses.
Also contains the Vega object, which is an instance of a FileSourceSpectrum
that can be imported from this file and used for Vega-related calculations.
Dependencies:
============... | martindurant/starclassifier | ui/pysynphot/spectrum.py | Python | mit | 62,915 | [
"Gaussian"
] | fac9c08c32a9620f98986e4e9e8b67934ffb55784e3d9bf23dde57d41013860b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | Forage/Gramps | gramps/gen/filters/rules/person/_regexpname.py | Python | gpl-2.0 | 2,430 | [
"Brian"
] | 9b812e294f1930c8506ebb189920dacc04c2181e62f6118856bdb1f07c8b69ed |
#!/usr/bin/env python
'''Analysis mdtraj test'''
import os
import mdtraj as md
import numpy as np
import matplotlib
import scipy.cluster.hierarchy
from pylab import *
from math import pi
from sklearn.decomposition import PCA
from itertools import combinations
import mdtraj.testing
import itertools
#loading and printi... | mkuiper/MD_workflow_py | Analysis/analysis_mdtraj.py | Python | bsd-3-clause | 4,143 | [
"MDTraj"
] | 0a6dd424cab45455044be1d04bea1dd9b6daead8236e5b462a7fbe7b33584601 |
# coding: utf-8
"""Python bindings for 0MQ."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, d... | ellisonbg/pyzmq | zmq/sugar/context.py | Python | lgpl-3.0 | 6,210 | [
"Brian"
] | 5f7f36cc477aab501b6eeb1ac2fdd8b1b88415dc13390c9ccd60856a5429b847 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Unit tests for grit.xtb_reader'''
import os
import sys
if __name__ == '__main__':
sys.path.append(os.path.join(os.path.dirna... | JoKaWare/WTL-DUI | tools/grit/grit/xtb_reader_unittest.py | Python | bsd-3-clause | 3,105 | [
"xTB"
] | aae23d4662bfc59a2541882bed6f0b25b46c0d78074b511fe3f6d21af5c8110b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Craig J. Anderson
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Matt Keenan (matt.keenan@... | Forage/Gramps | gramps/plugins/textreport/descendreport.py | Python | gpl-2.0 | 17,656 | [
"Brian"
] | a998f6fb6a30b94f3a5a23f60cbb76c7a2a3a5ef46c4226f9b67b8c020d39a7b |
#!/usr/bin/python
from contacts.models.interactions import Message, PhoneCall, Note
from contacts.models.visit import Visit, ScheduledPhoneCall
from contacts.models.misc import Connection, Practitioner, EventLog
from contacts.models.contact import Contact, StatusChange, get_contact_model
| I-TECH-UW/mwachx | contacts/models/__init__.py | Python | apache-2.0 | 290 | [
"VisIt"
] | a8fa88d584d6af429fb4458920921f7fb93b7367825e220b965cfca510b5f622 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 18 14:57:46 2013
Author: Josef Perktold
"""
from __future__ import print_function
import numpy as np
from statsmodels.genmod.generalized_estimating_equations import GEE, GEEMargins
from statsmodels.genmod.families import Gaussian, Binomial, Poisson
from statsmodels.ge... | rgommers/statsmodels | statsmodels/examples/try_gee.py | Python | bsd-3-clause | 2,980 | [
"Gaussian"
] | c3e24679684c5acce6f61dfabfa1b08bd5af9c93dc9dd7ec0328c9fa8c0a7cc5 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
class Migration(DataMigration):
def forwards(self, orm):
"Write your forwards methods here."
# Note: Don't use "from appname.models imp... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0012_wait_time.py | Python | bsd-2-clause | 13,101 | [
"VisIt"
] | df96056d032dd8a1019bf55c1d38337934da9302a28ee00baa557d9b4df7063d |
# -*- coding: utf-8 -*-
import os
import swc2vtk
import swcfilelist
# input_dir = '/home/nebula/git/LAL-VPCmapping/converted_swc'
input_dir = './swc'
output_dir = '/home/nebula/work/paraview/standardbrain20170131/'
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
filelist = swcfilelist.filelist_lalvpc
fo... | DaisukeMiyamoto/swc2vtk | examples/convert_allswc.py | Python | apache-2.0 | 840 | [
"ParaView",
"VTK"
] | 0fc5086f4908a25a01873eb6478f5f4ebcd845d2b3c42c6d4bde32843e06d422 |
from unittest import TestCase
import sys
from os import path
from PyContact.core.ContactAnalyzer import *
from PyContact.exampleData.datafiles import DCD, PSF, TPR, XTC
import MDAnalysis as mda
import multiprocessing
multiprocessing.log_to_stderr()
sys.path.append(path.dirname(path.dirname(path.abspath(__file__))))
... | maxscheurer/pycontact | tests/test_basic.py | Python | gpl-3.0 | 3,256 | [
"MDAnalysis"
] | 4393e0f8aaab06584467666e8d3f5b5be33fd6cd67aa187b764907e0b5bfbefe |
""" Entry points into the antlr4 parser.
"""
import sys
from antlr4 import FileStream, InputStream, CommonTokenStream
from ..antlr4.PLambdaLexer import PLambdaLexer
from ..antlr4.PLambdaParser import PLambdaParser
from .Visitor import Visitor
def main():
if len(sys.argv) != 2:
print(f'Usage: {sys.argv... | SRI-CSL/PLambda | plambda/visitor/Parser.py | Python | mit | 897 | [
"VisIt"
] | e7ffff993db19b8ce30ee503b81d80729b0bf1dc12bb10537cc8c8529bcf832b |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | kevclarx/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 39,218 | [
"VisIt"
] | d42f08a5e13516de1c699d756723b413a7ebbf646c9a9585e300b5968b606972 |
"""
This module contains code for generating toy examples
"""
#############################################################################################
# #
# This program is free software; you can redistribute it and/or mo... | AzamYahya/shogun | applications/easysvm/esvm/datafuncs.py | Python | gpl-3.0 | 6,419 | [
"Gaussian"
] | c0b76b743f502425f84ad106350909f07a06eed10ae2732425f673d900ab0fa2 |
from ..base import TestBase
from ..mocking.community import MockCommunity
from ...community import _DEFAULT_ADDRESSES
from ...peerdiscovery.discovery import RandomWalk
class TestRandomWalk(TestBase):
def setUp(self):
super(TestRandomWalk, self).setUp()
while _DEFAULT_ADDRESSES:
_DEFAU... | qstokkink/py-ipv8 | ipv8/test/peerdiscovery/test_random_discovery.py | Python | lgpl-3.0 | 4,806 | [
"VisIt"
] | 2f9a19ce9715f052024efbea40390dbc3914d89d7aacfc71b2b4c89ef2684b30 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
from nose.plugins.attrib import attr
from ..helpers import UniqueCourseTest, get_modal_alert, EventsTestMixin
from ...pages.common.logout import LogoutPage
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.instructor_da... | shubhdev/openedx | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 20,765 | [
"VisIt"
] | 346454e146d8ace70e61b8e28346cf9f9d19f94aab93fd448a7a6f7cba493c99 |
# -*- coding: utf-8 -*-
#
# This file is part of PyGaze - the open-source toolbox for eye tracking
#
# PyGazeAnalyser is a Python module for easily analysing eye-tracking data
# Copyright (C) 2014 Edwin S. Dalmaijer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GN... | esdalmaijer/PyGazeAnalyser | pygazeanalyser/gazeplotter.py | Python | gpl-3.0 | 14,526 | [
"Gaussian"
] | f9caa5bef67b98139fe4f1a65cf1e521db252dab073a50bf6d38fa48d71af884 |
#!/usr/bin/env python
"""
reid14_rotcurve.py
Utilities involving the Universal Rotation Curve (Persic+1996) from
Reid+2014.
Copyright(C) 2017-2020 by
Trey V. Wenger; tvwenger@gmail.com
GNU General Public License v3 (GNU GPLv3)
This program is free software: you can redistribute it and/or modify
it under the terms o... | tvwenger/kd | kd/reid14_rotcurve.py | Python | gpl-3.0 | 4,782 | [
"Gaussian"
] | e344518cc2fb31eaf1e33957c73d6c9ed9bba8942b082f7b4bca94f617ff9fd9 |
import sys
import pytest
import numpy as np
from numpy.testing import (
assert_, assert_raises, assert_equal,
assert_warns, assert_no_warnings, assert_array_equal,
assert_array_almost_equal, suppress_warnings)
from numpy.random import Generator, MT19937, SeedSequence
random = Generator(MT19937())
@pyt... | MSeifert04/numpy | numpy/random/tests/test_generator_mt19937.py | Python | bsd-3-clause | 86,873 | [
"Gaussian"
] | 550e9386874e28ac40902a8ba49f1d4d7355f78788bfd59b53f29dd48b85ea03 |
# coding=utf-8
# Copyright 2020 The SimCLR Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | google-research/simclr | data_util.py | Python | apache-2.0 | 18,042 | [
"Gaussian"
] | 798d9c22fa98748b606c073f77d3285738c2faba1a58f15c8581f9997edcc71c |
from brian import *
N = 5
duration = 100 * ms
Vr = -60 * mV
Vt = -50 * mV
tau = 10 * ms
Rmin = 1 * Mohm
Rmax = 10 * Mohm
freq = 50 * Hz
k = 10 * nA
eqs = '''
dV/dt = (-(V-Vr)+R*I)/tau : volt
R : ohm
I : amp
'''
G = NeuronGroup(N, eqs, reset='V=Vr', threshold='V>Vt')
G.R = linspace(Rmin, Rmax, N)
t = linspace(0 * se... | mac389/mayer | timed-array.py | Python | gpl-2.0 | 586 | [
"Brian"
] | 5662f1a78df181f924c85fa6e89e8eeaaa373ccd01e6787cd02d9f33416f794c |
from setuptools import setup, find_packages
from codecs import open
from os import path
__version__ = '0.0.9'
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
# get the dependen... | MaxInGaussian/GPoFM | setup.py | Python | bsd-3-clause | 1,363 | [
"Gaussian"
] | f0e75696d4ada27dcf40d8e697bf1181e6c8e335d2dbea0a641b82203f0d1ee3 |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
QtCore.QString = str
except ImportError:
raise ImportError("Cannot load either PyQt or PySide... | gleicher27/Tardigrade | moose/gui/vtk/ExodusResultRenderWidget.py | Python | lgpl-2.1 | 49,289 | [
"VTK"
] | 7477eb73b6bc2e60849eff6437b103fa09e1b752a027ed20491bfff456fbcad0 |
import os, logging, threading, time
from Queue import Queue, Empty
from galaxy import model
from paste.deploy.converters import asbool
import pkg_resources
try:
pkg_resources.require( "DRMAA_python" )
DRMAA = __import__( "DRMAA" )
except:
DRMAA = None
log = logging.getLogger( __name__ )
if DRMAA is not... | dbcls/dbcls-galaxy | lib/galaxy/jobs/runners/sge.py | Python | mit | 13,180 | [
"Galaxy"
] | eeba1243cb9d20f0f6a50255e60259ef5dc40e958a651aa2b3dabb04893f98a9 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | testsuite/python/scafacos_dipoles_1d_2d.py | Python | gpl-3.0 | 5,192 | [
"ESPResSo"
] | b20fbfca6b245c1e2b818c4a6e133586a99419358fe3695ec8430197a409da6f |
from ase.atoms import Atoms
from ase.parallel import paropen
def read_xyz(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
lines = fileobj.readlines()
L1 = lines[0].split()
if len(L1) == 1:
del lines[:2]
natoms = int(L1[0])
else:
natoms = le... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/io/xyz.py | Python | gpl-2.0 | 1,231 | [
"ASE"
] | 4297e469f86df67c1195abb0493dc45c113af225d3910971bc4536b1353ae297 |
from ase import Atoms
from gpaw import GPAW
from gpaw.tddft import TDDFT
from gpaw.tddft.ehrenfest import EhrenfestVelocityVerlet
from gpaw.test import equal
d = 4.0
atoms = Atoms('NaCl', [(0,0,0),(0,0,d)])
atoms.center(vacuum=4.5)
gs_calc = GPAW(nbands=4, eigensolver='cg', gpts=(32, 32, 44), xc='LDA',
... | robwarm/gpaw-symm | gpaw/test/ehrenfest_nacl.py | Python | gpl-3.0 | 866 | [
"ASE",
"GPAW"
] | aa81226106bb9949b93d8ee1797b6bcf99a453f8d0ea8c68b57b6d947daba25a |
#! /usr/bin/env python2.7
"""
This script post-processes amplicon sequenced DBLa-tags basecalled using Multipass.
"""
import os, sys, time, copy
from optparse import OptionParser
import subprocess as Sp
from shlex import split as cmdsplit
# Constants
USEARCH = "/usr/local/bin/usearch_v5.2.32_i86osx32"
HMMSEARCH = "/us... | 454data/postprocess | postprocess_basecalls.py | Python | mit | 13,075 | [
"BLAST"
] | 47d978e7a341eca96867304d699abac405c921e3f7c179a0e35cc265337810d2 |
#!/usr/bin/python
# -- Content-Encoding: UTF-8 --
"""
Python modules repository
:author: Thomas Calmant
:license: Apache Software License 2.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
... | isandlaTech/cohorte-devtools | qualifier/deploy/cohorte-home/repo/cohorte/repositories/python/modules.py | Python | apache-2.0 | 21,139 | [
"VisIt"
] | 03527569ccaa82d2cc400de22398fd9e5707fff1d6cf7f93fa501c710c6b681a |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | demis001/scikit-bio | skbio/diversity/alpha/_gini.py | Python | bsd-3-clause | 3,694 | [
"scikit-bio"
] | 97a4cdc8fc481e51d86f0285e90e866c3df03410dd6a7e9813d4859325037657 |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# This 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 the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/planner/__init__.py | Python | gpl-3.0 | 1,007 | [
"ORCA"
] | 52431212b0f89f9c077b455327993b344a6d5ca0c56998cf4b7719ee3a104dc6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Module for Latent Semantic Indexing.
This module actually contains several algorithms for decomposition of large corpora, a
combin... | samantp/gensimPy3 | gensim/models/lsimodel.py | Python | gpl-3.0 | 33,211 | [
"Gaussian"
] | 8396917e8542aba744fb4c3d60305a32ca71e9660361be516081e7cb8b01c003 |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as ... | CopyChat/Plotting | Downscaling/global_change_rsds.cmip5.py | Python | gpl-3.0 | 5,099 | [
"NetCDF"
] | 7eadfea7af681201942a35d72c449768d3131a3b7a1afa012d191f51a109e022 |
# 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... | aam-at/tensorflow | tensorflow/python/eager/function_test.py | Python | apache-2.0 | 167,367 | [
"Octopus"
] | ca9be24d16b551f98262919dcec3e689c7285c95938908e39287a9f5020463a5 |
from datetime import datetime
import unittest
from pheme.util.config import Config
from pheme.util.pg_access import AlchemyAccess
from pheme.warehouse.tables import create_tables
from pheme.warehouse.tables import HL7_Dx
from pheme.warehouse.tables import HL7_Msh
from pheme.warehouse.tables import HL7_Nte
from pheme.w... | pbugni/pheme.warehouse | pheme/warehouse/tests/test_warehousedb.py | Python | bsd-3-clause | 19,638 | [
"VisIt"
] | eb615f33f249fdab9124e42d62744290ba1252e56ddfb11fa7f6658c93db9c2d |
import math
import numpy
from chainer import cuda, Function
def _as_mat(x):
return x.reshape(x.shape[0], x.size / x.shape[0])
class Linear(Function):
"""Implementation of a linear function (a.k.a. fully-connected layer or affine
transformation).
This function holds a weight matrix ``W`` and a bias ve... | nushio3/chainer | chainer/functions/linear.py | Python | mit | 3,511 | [
"Gaussian"
] | 995b88959edaf602a5a0c1e45b3207d39198bbc50888435685d6d8696a31a383 |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import urllib
import analytics
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.staticfiles.storage import staticfiles_storage
from django.core.mail import se... | lduarte1991/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 49,123 | [
"VisIt"
] | 61289f5d3275bb32549104e51f337e6c6d5d484cb15323f1c0797f87b2b8fc23 |
from polychartQuery.expr import ExprTreeVisitor
QUOTE = "'" # note: double quote does not work in postgres!
def escape(str): return str # TODO: implement
def quote(str): return QUOTE+escape(str)+QUOTE
def unquote(str):
if str[0] == QUOTE and str[-1] == QUOTE:
return str[1:len(str)-1]
return str
class ExprToGA... | Polychart/builder | server/polychartQuery/googleAnalytics/expr.py | Python | agpl-3.0 | 1,518 | [
"VisIt"
] | 7228f3ba3720ada3a6a51b82f5ab6f393887dedf6ee9b6e4eed17bfcf44fddcd |
"""
This module defines export functions for decision trees.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Dawe <noel@dawe.me>
# Satrajit Gosh <satrajit.ghosh@gmail.com>
# Licence: BSD 3 ... | soulmachine/scikit-learn | sklearn/tree/export.py | Python | bsd-3-clause | 4,427 | [
"Brian"
] | 85e38714bf5c7d7607601f4912eb0b76047194e092b0fb31208d546a277e2ddf |
#! PsiAPI pubchem access
import psi4
from psi4.driver.constants.physconst import hartree2ev
psi4.set_output_file("output.dat", False)
benz = psi4.geometry("""
pubchem:benzene
""")
psi4.set_options({"REFERENCE" : "RHF",
"MAX_ENERGY_G_CONVERGENCE" : 8,
"BASIS" ... | amjames/psi4 | tests/python/pubchem/input.py | Python | lgpl-3.0 | 1,465 | [
"Psi4"
] | af74b3aeffbe86f16a149741cdba5db2235597ef51d45723076449a73c6ba630 |
"""
Test the about xblock
"""
import datetime
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.core.urlresolvers import reverse
from django.test.utils import override_settings
from milestones.tests.utils import MilestonesTestCaseMixin
from mock import patch
from nose.plu... | procangroup/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 25,700 | [
"VisIt"
] | b4f4459bd43e1ce6909195a752b45731e3c0d782548cc969a63a340b1431b53e |
"""
Recurrent layers.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import copy
import theano
import theano.tensor as TT
# Nicer i... | kyunghyuncho/GroundHog | groundhog/layers/rec_layers.py | Python | bsd-3-clause | 81,816 | [
"Gaussian"
] | 73c61aba3b70edf356ba70416ab8043e97de5cb5567944d40e526756ab0ef97e |
#!/usr/bin/env python
# Copyright (c) 2011 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.
"""Does scraping for all known versions of IE."""
import pywintypes
import time
import types
from drivers import keyboard
from dr... | Chilledheart/chromium | tools/site_compare/scrapers/ie/ie7.py | Python | bsd-3-clause | 5,669 | [
"VisIt"
] | 4b4fa900da4c2a9c31c03d2c8889755a9a7e967bfa01035723c48791b9999889 |
from tvtk.api import tvtk
from animation import Stop
class Object(object):
"""Base class for objects that can be placed into the scene."""
def _set_actor(self):
self.actor = tvtk.Actor(mapper=self.mapper)
self.actor.mapper.update()
def get_actor(self):
return self.actor
... | lukius/mlab-tools | mlab_tools/object.py | Python | mit | 2,005 | [
"VTK"
] | 63cf57d46b6769a16b6fcbc4c3de5e83dcd3139d71b40816d8dc25dc11773577 |
import pytest
import ert3
# The inverse cumulative normal distribution function evaluated at 0.995
CNORM_INV = 2.57582930
# The inverse cumulative uniform distribution function evaluated at 0.995
CUNI_INV = 0.005
def test_no_parameters():
with pytest.raises(ValueError):
ert3.algorithms.one_at_the_time(... | joakim-hove/ert | tests/ert_tests/ert3/algorithms/test_one_at_the_time.py | Python | gpl-3.0 | 7,614 | [
"Gaussian"
] | 7507f28ce5ec99ee8e0c90e866a2793f08845453ba60c6c96f4212b3d803aef5 |
#!/usr/bin/env python
###
# name : seqfiles.py
# description : Script for analyzing sequencing results
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# LICENSE:
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public Lice... | openpaul/DNApy | seqfiles5.py | Python | gpl-3.0 | 33,689 | [
"Biopython"
] | 6df362f6f7246b87c05f010325a84eebba09d5c3e351dc604753159b2b1cf1a3 |
#!/usr/bin/env python
# CREATED:2013-03-11 18:14:30 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.onset
from __future__ import print_function
import pytest
from contextlib2 import nullcontext as dnr
# Disable cache
import os
try:
os.environ.pop("LIBROSA_CACHE_DIR")
except:
pass
import war... | librosa/librosa | tests/test_onset.py | Python | isc | 9,085 | [
"Brian"
] | 26715e2acdac22144dd94f47db7f17cf58f8b28e5c8f9224932fd9ca4b6b9607 |
#!/usr/bin/env python
#============================================================================
# P Y I B E X
# File : test_thickPaving.py
# Author : Benoit Desrochers
# Copyright : Benoit Desrochers
# License : See the LICENSE file
# Created : Dec 28, 2015
#====... | benEnsta/pyIbex | pyibex/tests/test_SepPaving.py | Python | lgpl-3.0 | 1,117 | [
"VisIt"
] | fe1ad6bd6272ea90e26061446755ba6d77f8921f0398183a717206e06ca4ba7a |
#!/usr/bin/env python
# coding: utf-8
# # 4 - Medium Level Example - Debugging your Scene with Custom Objects
# ### Fixed Tilt 2-up with Torque Tube + CLEAN Routine + CustomObject
#
# This journal has examples of various things, some which hav ebeen covered before and some in more depth:
#
# <ul>
# <li> Running ... | NREL/bifacial_radiance | docs/tutorials/4 - Medium Level Example - Debugging your Scene with Custom Objects (Fixed Tilt 2-up with Torque Tube + CLEAN Routine + CustomObject).py | Python | bsd-3-clause | 12,836 | [
"EPW"
] | 2db723fb9b6283b5cff374619cb43c8aff47dac68a230c501df4ecd34f252a16 |
# -*- coding: utf-8 -*-
import itertools
import os
import re
import urllib
import logging
import datetime
import urlparse
from collections import OrderedDict
import warnings
import pytz
from flask import request
from django.core.urlresolvers import reverse
from modularodm import Q
from modularodm import fields
from m... | jolene-esposito/osf.io | website/project/model.py | Python | apache-2.0 | 123,650 | [
"VisIt"
] | b7ee5ed02c548a85f7a284a7cdabcec35bcae51d325a8e931367c6bb64c69f7d |
"""Read and write notebooks as regular .py files.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, dist... | Carreau/gistpynb | nbformat/v3/nbpy.py | Python | apache-2.0 | 7,569 | [
"Brian"
] | 87ea991c2a2bd4d65f695bfdc05d33f9a71a799422e7e420949edfbdaea8a96f |
"""Mayavi/traits GUI for averaging two sets of KIT marker points"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
import numpy as np
# allow import without traits
try:
from mayavi.core.ui.mayavi_scene import MayaviScene
from mayavi.tools.mlab_scene_model imp... | jniediek/mne-python | mne/gui/_marker_gui.py | Python | bsd-3-clause | 14,997 | [
"Mayavi"
] | 4fd459317dba3675ac68d59d842a828a2d4ff369e32d15208b8c00d0ca55862c |
import requests
import re
from bs4 import BeautifulSoup
from contextlib import closing
from cloudbot import hook
# This will match ANY we url including youtube, reddit, twitch, etc... Some additional work needs to go into
# not sending the web request etc if the match also matches an existing web regex.
blacklist = re... | bharaths/CloudBot | plugins/link_announcer.py | Python | gpl-3.0 | 1,826 | [
"Galaxy"
] | 1cc606411afa0ab9d5c18c1311a9040ad1716c399759a338414259da9ea99580 |
################################################################
#
# kim_compare_lammps
#
################################################################
#
# Copyright 2018 the potfit development team
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated doc... | potfit/potfit | util/kim/kim_compare_lammps/testrun.py | Python | gpl-2.0 | 3,676 | [
"LAMMPS"
] | 95b154dedfa5401af209b6d50af6c117f382353359cf164d84bd5d953fd0a00d |
#! /usr/bin/python
"""
Runs Lastz
Written for Lastz v. 1.01.88.
usage: lastz_wrapper.py [options]
--ref_name: The reference name to change all output matches to
--ref_source: Whether the reference is cached or from the history
--source_select: Whether to used pre-set or cached reference file
--input1:... | volpino/Yeps-EURAC | tools/sr_mapping/lastz_wrapper.py | Python | mit | 12,944 | [
"Galaxy"
] | 580a4b06a87e361ac957835272bd042c782aca61f834a4a2a20aab12eddab1c7 |
# -*- coding: utf-8 -*-
"""General functions supporting pRF fitting."""
# Part of pyprf_feature library
# Copyright (C) 2018 Marian Schneider, Ingo Marquardt
#
# 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 Softwar... | MSchnei/py_pRF_motion | pyprf_feature/analysis/utils_general.py | Python | gpl-3.0 | 31,893 | [
"Gaussian"
] | 9fbfcbb9df9a2b0225e419a9c066ec1eb237f6fb060ff161db731c23e994a011 |
#!/usr/bin/env python
"""
Converts SAM data to sorted BAM data.
usage: sam_to_bam.py [options]
--input1: SAM file to be converted
--index: path of the indexed reference genome
--ref_file: Reference file if choosing from history
--output1: output dataset in bam format
"""
import optparse, os, sys, subproces... | jhl667/galaxy_tools | tools/sam_to_bam/sam_to_bam.py | Python | apache-2.0 | 8,364 | [
"Galaxy"
] | 13b52255e77ce53312f8e05d224b508fcb344bcd3e1e535229c5b88354cb7467 |
from insights.tests import context_wrap
from insights.parsers import tomcat_xml
from insights.parsers.tomcat_xml import TomcatWebXml
from insights.parsers.tomcat_xml import TomcatServerXml
import doctest
web_xml_content = """
<?xml version="1.0" encoding="ISO-8859-1"?>
<!--
Licensed to the Apache Software Foundation... | RedHatInsights/insights-core | insights/parsers/tests/test_tomcat_xml.py | Python | apache-2.0 | 55,650 | [
"NetCDF"
] | 1de98b93a165bd29916b9f49e40830dd6177aba73af9782552e554a6fb9e25b3 |
"""P65 Intermediate Representation
Classes for representing the Intermediate nodes upon which the
assembler passes operate."""
# Copyright 2002 Michael C. Martin.
# You may use, modify, and distribute this file under the BSD
# license: See LICENSE.txt for details.
from __future__ import nested_scopes
imp... | cacciatc/happiNES-dev | tools/assembler/Ophis-1.0/lib/Ophis/IR.py | Python | lgpl-2.1 | 4,970 | [
"VisIt"
] | b822dd2cd79da1e7eaf752209759d1526d6da24d514a19aab17341ad1d695199 |
"""Payload management for sending Ansible files and test content to other systems (VMs, containers)."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import atexit
import os
import tarfile
import tempfile
import time
from . import types as t
from .config import (
Integra... | aperigault/ansible | test/lib/ansible_test/_internal/payload.py | Python | gpl-3.0 | 4,646 | [
"Galaxy"
] | 00f828dcea6b1fe9187470f6d3ec71a52391ce72ad65219c416037cc0573cf51 |
from wsgiref.simple_server import make_server
__author__ = 'pahaz'
def application(environ, start_response):
assert environ.get('PATH_INFO') is not None, "environ['PATH_INFO'] is None"
status = "200 OK"
headers = [('Content-type', 'text/html; charset=utf-8')]
body = """<!DOCTYPE html>
<h1>Exampl... | pahaz/homework-simple-python-web-application | main.py | Python | gpl-3.0 | 682 | [
"VisIt"
] | db0c0ba262deb117690f8e6f0e3b2a1cd0b785570b4e20a63aa07f5096332759 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import json
import os
from monty.json import MontyDecoder
from pymatgen.analysis.defects.dilute_solution_model import *
import random
import sympy
test... | xhqu1981/pymatgen | pymatgen/analysis/defects/tests/test_dilute_solution_model.py | Python | mit | 4,601 | [
"pymatgen"
] | b6d35758868a544b76fb374ca285132e68dc2f50a92694d0170f83ddff8b7196 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Mesh Preview Generator.
Examples
--------
$ ./script/gen_mesh_prev.py meshes/2d/
"""
from optparse import OptionParser
import sys
sys.path.append('.')
import os
import vtk
from sfepy.discrete.fem import Mesh
def gen_shot(vtk_filename, png_filename):
"""
Gener... | RexFuzzle/sfepy | script/gen_mesh_prev.py | Python | bsd-3-clause | 3,376 | [
"VTK"
] | 875c55cd103fe130064b12ed894753e8c07579b3bfeb9e69911111b459c4178e |
"""
desispec.zfind.redmonster
=========================
Classes for use with the redmonster package.
"""
from __future__ import division, absolute_import
import os
import numpy as np
import time
from desispec.zfind import ZfindBase
from desispec.interpolation import resample_flux
from desispec.log import get_logger... | timahutchinson/desispec | py/desispec/zfind/redmonster.py | Python | bsd-3-clause | 6,150 | [
"Galaxy"
] | c1f6e71bbda18af43d40fbbac1f38e3a442a1838566451422ef14a7ad79d0b80 |
import datetime
import netCDF4
import numpy
import os
import re
from dateutil import relativedelta
from ece2cmor3 import cmor_target, cmor_utils
def get_table_path(tab_id=None):
directory = os.path.join(os.path.dirname(cmor_target.__file__), "resources", "tables")
return os.path.join(directory, "CMIP6_" + t... | goord/ece2cmor3 | test/test_utils.py | Python | apache-2.0 | 8,331 | [
"NetCDF"
] | b403f453a41b2c4aa4a754a773735b6988874fedd63361c8e78346d31746554e |
'''
Expresses the spherical harmonics as perturbations from
spherical symmetry, as used in my research.
Created on 30 Jan 2013
@author: chris
'''
import numpy as np
from my_real_sph_harm import my_real_sph_harm
# import scipy.misc as sc
def main():
l = 4
m = 2
r, theta, phi = pert_sphere(l,m)
... | chrisjdavie/ws_cross_project | general_maths/sph_harms/pert_sphere.py | Python | mit | 1,287 | [
"Mayavi"
] | 95eccf1a9f3d8592c95b936e1b16d898e140a9f915db2662ac5a95a7bea7a551 |
"""
HPHF
"""
import numpy as np
from frankenstein.sgscf import sphf
class HPHF(sphf.SPHF):
def __init__(self, pymol, **kwargs):
self.eta = 1
sphf.SPHF.__init__(self, pymol)
self.__dict__.update(kwargs)
if np.abs(self.eta) != 1:
raise ValueError("eta must be eithe... | hongzhouye/frankenstein | sgscf/hphf.py | Python | bsd-3-clause | 1,250 | [
"PyMOL",
"PySCF"
] | 91242a844c33540bb3fe6e6123c5a2ecabd237ac9cd5321e6011a9eadc1f4463 |
import numpy as np
import matplotlib.pyplot as plt
def compute_pose_iter(beta, X, Y, W, iters):
for iter in range(iters):
residuals = abs(np.dot(X, beta) - Y)
res_scale = 6.9460 * np.median(residuals)
W = residuals / res_scale
W.shape = (W.shape[0],1)
outliers = (W > 1)... | CoffeRobot/fato | pose_estimation/src/lsq.py | Python | bsd-3-clause | 6,923 | [
"Gaussian"
] | 4871a93420f8e89889ac65cb3b8f78be9bcdb6598263399616bd9f24384e9675 |
# Copyright (c) 2015 Uber Technologies, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publ... | ianmabie/uberpy | venv/lib/python2.7/site-packages/uber_rides/auth.py | Python | mit | 20,155 | [
"VisIt"
] | 47c59b7918ec9837e794cd588229643cec57bacd82c4dd509cd74a2b39df2bed |
# creates: metric.png
import numpy as np
import matplotlib
matplotlib.use('Agg')
import pylab as plt
from math import pi, cos
# Special points in the BZ of a simple cubic cell
G = pi * np.array([0., 0., 0.])
R = pi * np.array([1., 1., 1.])
X = pi * np.array([1., 0., 0.])
M = pi * np.array([1., 1., 0.])
# The path fo... | qsnake/gpaw | doc/documentation/densitymix/metric.py | Python | gpl-3.0 | 1,634 | [
"GPAW",
"VASP"
] | 0450756255f19ff92e8aa2fe52f08b1ab36f1df298e840d9de56fa4cf3b50bee |
# -*- coding: utf-8 -*-
# Copyright 2017 GIG Technology NV
#
# 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... | threefoldfoundation/app_backend | plugins/tff_backend/bizz/nodes/hoster.py | Python | bsd-3-clause | 23,717 | [
"VisIt"
] | 85dec08b240cdfa7684d22b55dfcc9d2b2855469a3d4d3e4644c410af7ebdfcb |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageQuantizeRGBToIndex(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkImageQuantizeRGBToIndex.py | Python | bsd-3-clause | 509 | [
"VTK"
] | 2df5ad4ce14384350460c2a90706b83fbf620ebcb781605c47a6c54640b41ca9 |
# coding: utf-8
from datetime import datetime
from django.core import mail
from django.core.urlresolvers import reverse
from django.test import TestCase
import os.path
from Simplan import settings
from Simplan.account.factories import UserFactory
from Simplan.event.factories import EventGuestFactory, EventUserFactory,... | meuhia/Simplann | Simplan/event/tests.py | Python | gpl-3.0 | 51,991 | [
"FLEUR"
] | c11093b57d63caaba8283f0ba08b813d9015b6d100bddd4c0bbc65c936859aa3 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | jaidevd/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 44,488 | [
"Brian"
] | 1074137e9f5050192145163684d20885c9c03fd9aab4c7eb42d39215e7516785 |
"""Manage IPython.parallel clusters in the notebook.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, d... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/html/services/clusters/clustermanager.py | Python | bsd-3-clause | 5,952 | [
"Brian"
] | e17083802710640351d0dfb3687a7b9df102a2cf268505f0ee287f0945b86f36 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
# vim:ai:sta:et:ts=4:sw=4:sts=4
"""kernelng 0.x
Tool for maintaining customized overlays of kernel-ng.eclass-based ebuilds
Copyright 2005-2014 Gentoo Foundation
Copyright (C) 2005 Colin Kingsley <tercel@gentoo.org>
Copyright (C) 2008 Zac Medico <zmedico@ge... | gmt/kernel-ng-util | kernelng/kngclick.py | Python | gpl-2.0 | 14,411 | [
"Brian"
] | aa9fa42fa8611243ac564068f47a10981cee18dd0fdabdb122e9fd1e10bbe93a |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from common import *
from terrain.steps import reload_the_page
from selenium.common.exceptions import InvalidElementStateException
from opaque_keys.edx.locations import SlashSeparatedCourseKey
from contentstore.utils import reverse_course_... | carsongee/edx-platform | cms/djangoapps/contentstore/features/grading.py | Python | agpl-3.0 | 7,202 | [
"VisIt"
] | c2fd0311fb2ecf0aa00f49bf15527440d8650922da5ba7784696eaed2a0edc65 |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# ... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/molecule/resonance.py | Python | mit | 36,175 | [
"RDKit"
] | 0cd9f41ff23d6324bc7cb18bb393390293a4a0d5a19724fdb8cf06423cb6860c |
"""
Functions for explaining classifiers that use tabular data (matrices).
"""
import collections
import copy
from functools import partial
import json
import warnings
import numpy as np
import scipy as sp
import sklearn
import sklearn.preprocessing
from sklearn.utils import check_random_state
from pyDOE2 import lhs
f... | marcotcr/lime | lime/lime_tabular.py | Python | bsd-2-clause | 34,542 | [
"Gaussian"
] | 60dc96c70fa448df9a38f0bb857b7f9624527474d05f16beefb56d35c605afa8 |
import lb_loader
import simtk.openmm.app as app
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems, integrators
from sys import stdout
platform_name = "CUDA"
platform = mm.Platform.getPlatformByName(platform_name)
properties = {'CudaPrecision': "mixed"}
precision... | kyleabeauchamp/HMCNotes | test_mts_conservation2.py | Python | gpl-2.0 | 1,797 | [
"OpenMM"
] | 30d21343e9f1be52db218fab5461711bbc2eadad5538f95e550b81a844ad7a34 |
""" Define allowed quantities for FRB galaxies
Uncertainty is valid for any quantity with '_err' add-on, eg. W1_err
Am also likely to add _flg for each as well
"""
##############################################################
# Redshift
valid_z = [
'z', # Preferred redshift, may derived from one of sev... | FRBs/FRB | frb/galaxies/defs.py | Python | bsd-3-clause | 6,396 | [
"Galaxy"
] | dd9024d48cd57cd8477cd2f38a7a06ac8cac2da98b3e017ed81b852868f5166f |
# Copyright (C) 2012 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
# (at your option) any later version.
#
# ESPR... | icimrak/espresso | config/gen_doxyconfig.py | Python | gpl-3.0 | 1,620 | [
"ESPResSo"
] | b3ec8725192c422e5953ba075c11ac10e5638ae3ecf06dac532cd0ea9e3aa186 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# 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.
# ---------------------... | demis001/scikit-bio | setup.py | Python | bsd-3-clause | 4,795 | [
"scikit-bio"
] | f6d1aee4fc025ae45d2251747eeaf4ed47ed4643720d81865813de7a7d18c87f |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | moto-timo/robotframework | src/robot/model/filter.py | Python | apache-2.0 | 3,481 | [
"VisIt"
] | 32815fc7c038f8df832735443c4ac61917892c6b865fab76d0dec096553a7184 |
#!/usr/bin/env python
"""packetradio, module for use with the RFM69HCW packet radio
created Dec 19, 2016 OM
work in progress - Mar 21, 2018
work in progress - Jan 18, 2020"""
"""
Copyright 2017, 2018, 2019, 2020 Owain Martin
This program is free software: you can redistribute it and/or modify
it under the terms of t... | owainm713/RFM69HCW-Python-Module | packetradio.py | Python | gpl-3.0 | 53,281 | [
"Gaussian"
] | 961674f20f77dce83f459adb267d7179af4f331828e5ec38d06d4ec6e94e291d |
#!/usr/bin/env python
# vim: ai ts=4 sts=4 et sw=4 encoding=utf-8
import errors, traceback, message
import re, datetime, time
import StringIO
import pytz
from smshandler import SmsHandler
class TextSmsHandler(SmsHandler):
SCTS_FMT = "%y/%m/%d,%H:%M:%S"
CMGL_MATCHER=re.compile(r'^\+CMGL: (\d+),"(.+?)","(.+?)",... | rapidsms/pygsm | lib/pygsm/textsmshandler.py | Python | bsd-3-clause | 10,014 | [
"FEFF"
] | d0f9c087042ad86d72e0306a439926f5a2c38ab7990b3ba64787021e206817e9 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/python/keras/optimizer_v2/learning_rate_schedule.py | Python | apache-2.0 | 38,548 | [
"Gaussian"
] | 21964ad42acaa512efe64ea47b041c239bfa57d53d1e1905617ba595ab4ea79f |
from django.db import models
from shortuuidfield import ShortUUIDField
from datetime import date
import datetime
from utils import parse_date , generate_weekend_list_of_range , generate_holidays_list , generate_day_list_of_range
from random import randint
from datetime import timedelta
LAST_NAME = [
'SMITH',
... | R3SWebDevelopment/HappyDogs | HappyDogs/HappyDogs/apps/HappyDogs/models.py | Python | mit | 12,617 | [
"MOOSE",
"VisIt"
] | 24e504f547de7f8819ec6ef3497d4d1168e77fb4d852f881c712a7e2791f0d72 |
from __future__ import absolute_import, division, print_function
import sys
from py._code.code import FormattedExcinfo
import py
import warnings
import inspect
import _pytest
from _pytest._code.code import TerminalRepr
from _pytest.compat import (
NOTSET, exc_clear, _format_args,
getfslineno, get_real_func,
... | hoehnp/navit_test | lib/python2.7/site-packages/_pytest/fixtures.py | Python | gpl-2.0 | 45,173 | [
"VisIt"
] | 2edbd9841f7071068a78cab4b6e06a3799706170c8c27077e1c2a91079e670dd |
# coding: utf-8
from __future__ import unicode_literals, division
from custodian.custodian import Validator
from pymatgen.io.vasp import Vasprun
class VasprunXMLValidator(Validator):
"""
Checks that a valid vasprun.xml was generated
"""
def __init__(self):
pass
def check(self):
... | davidwaroquiers/custodian | custodian/vasp/validators.py | Python | mit | 422 | [
"VASP",
"pymatgen"
] | b6e781d524dcf42ac8b9252336380cbb0ad50981a379f9a5e75b000d3da78b30 |
## file for parsing blast
## need to see those that are kept and those that are not kept.
from Bio.Blast import NCBIXML
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.SeqIO.FastaIO import FastaWriter
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
import sys
blast_xml=sys.argv[1]
original_... | jooolia/phylo_temporal_jericho | sequence_processing/parse_blast_results_for_good_and_bad.py | Python | mit | 2,314 | [
"BLAST"
] | 8ae948089c488d541bd26c7743fb4b6f01863b50a5039b675a560150a8150e69 |
import numpy as np
import mayavi.mlab as mlab
import moviepy.editor as mpy
duration = 2 # duration of the animation in seconds (it will loop)
# MAKE A FIGURE WITH MAYAVI
fig = mlab.figure(size=(500, 500), bgcolor=(1,1,1))
u = np.linspace(0,2*np.pi,100)
xx,yy,zz = np.cos(u), np.sin(3*u), np.sin(u) # Poin... | solvery/lang-features | python/use_lib/video_1/mayavi_2.py | Python | gpl-2.0 | 1,037 | [
"Mayavi"
] | 1c9467498229aa354341904d21049f3d4b7587a9dd9da35ea94ace8fbcd35406 |
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