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import ast
from jaspyx.visitor import BaseVisitor
class AugAssign(BaseVisitor):
def visit_AugAssign(self, node):
attr = getattr(self, 'AugAssign_%s' % node.op.__class__.__name__, None)
if attr is None:
# Rewrite the expression as an assignment using a BinOp
self.visit(ast.A... | iksteen/jaspyx | jaspyx/visitor/augassign.py | Python | mit | 1,209 | [
"VisIt"
] | d4888a47755b2e87a3b068c8dab897b8be7af40612fee78b01661ab2e70de54d |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2... | Excito/audiotools | test/test_utils.py | Python | gpl-2.0 | 208,131 | [
"Brian"
] | 24dd36ef639c0754c6367253d7bcf339e65ef5045b98be503560b18b58a4b36a |
# -*- coding: utf8 -*-
# $Id: __init__.py 6385 2010-08-13 12:17:01Z milde $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributions from several people include... | bancek/egradebook | src/lib/docutils/writers/latex2e/__init__.py | Python | gpl-3.0 | 111,472 | [
"VisIt"
] | 430ff96b79be70b4e0c86abebfff48c47912f2f6c11866ee29a41f45873707aa |
#!/usr/bin/env python
"""
Populates the database with the current installations of components
This script assumes that the InstalledComponentsDB, the
ComponentMonitoring service and the Notification service are installed and running
"""
__RCSID__ = "$Id$"
import sys
from datetime import datetime
from DIRAC import ex... | vmendez/DIRAC | FrameworkSystem/scripts/dirac-populate-component-db.py | Python | gpl-3.0 | 7,273 | [
"DIRAC"
] | 95c8a9e818e0e08a386b6ec3b3b626f65c0c3047f658dee5a6fb78498e73f4cc |
import io
import os
import sys
from aussieaddonscommon import session
from aussieaddonscommon import utils
from aussieaddonscommon.exceptions import AussieAddonsException
from pycaption import SRTWriter
from pycaption import WebVTTReader
import resources.lib.classes as classes
import resources.lib.comm as comm
impo... | andybotting/xbmc-addon-abc-iview | resources/lib/play.py | Python | gpl-3.0 | 4,342 | [
"VisIt"
] | e2fea17879ef65a121d9b8ce28decd2848c2bc3f4436df2a608f32fde3dc5c27 |
# Copyright (c) 2012, James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core.sparse_gp_mpi import SparseGP_MPI
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference import VarDTC
from GPy.core.parameterization.variational import Nor... | befelix/GPy | GPy/models/sparse_gp_regression.py | Python | bsd-3-clause | 2,664 | [
"Gaussian"
] | 5b368d8c3c32b2e23cba86b593edbdb882169563fdcd97d8307b3524566e670e |
"""
Job Base Class
This class provides generic job definition functionality suitable for any VO.
Helper functions are documented with example usage for the DIRAC API. An example
script (for a simple executable) would be::
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.Interfaces.API.J... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/API/Job.py | Python | gpl-3.0 | 50,982 | [
"DIRAC"
] | 4bc178237b348d8f73362fed71ea133b439892d35fd02b8407f3c5cb03c91e53 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division
import petl as etl
from petl.compat import text_type
from petl.util.base import Table
def fromtabix(filename, reference=None, start=None, stop=None, region=None,
header=None):
"""
Extract rows from a tabix... | alimanfoo/petlx | petlx/bio/tabix.py | Python | mit | 3,291 | [
"pysam"
] | 883849e8c9917972c5f81c115c394b010365a81dd7bb11a501f8c78145bfe6e2 |
########################################################################
# $HeadURL$
########################################################################
""" ProxyManagementAPI has the functions to "talk" to the ProxyManagement service
"""
__RCSID__ = "$Id$"
import os
import datetime
import types
from DIRAC.Core.U... | Sbalbp/DIRAC | FrameworkSystem/Client/ProxyManagerClient.py | Python | gpl-3.0 | 19,823 | [
"DIRAC"
] | 344f109708710b7f3835f03762d0d534c53bbbd56c82e674aa895cd48cfa4a30 |
# -*- coding: utf-8 -*-
#
# network_params.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | tobikausk/nest-simulator | pynest/examples/Potjans_2014/network_params.py | Python | gpl-2.0 | 8,234 | [
"NEURON"
] | b5089d1fb35b393014824b7e5fef980759cdb60589b160104fc667d559bc0b07 |
# -*- coding: utf-8 -*-
'''Programme to clone galaxies from a catalogue and generate a random,
unclustered catalogue to examine the effects of clustering on galaxy properties.
This is the full interface version, with a text prompt to generate a catalogue
when run as the main program. Note that this is currently set up ... | jmoore06/Large-scale-galaxy-clustering-code | rand_cat_gen.py | Python | mit | 39,049 | [
"Galaxy"
] | d3381724a3a6a55ed94c49362aad8426d42cd5e14edbc4b1bb7f738e12825a4e |
import logging
import urllib
from functools import partial
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User
from django.contrib.auth.decorators i... | EduPepperPD/pepper2013 | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 33,478 | [
"VisIt"
] | e64f5b476ebee3653f63091dcb3ee6207b00200f100bc5802a64d567e914c40b |
# 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/log_mesh.py | Python | apache-2.0 | 6,338 | [
"GPAW",
"Gaussian",
"PySCF",
"SIESTA"
] | bfa8f0a495ec8ab3ad7b05d85eed7db2f17ef9ba50b3dc6226b1f9ebc6fe40cc |
# Import the necessary modules.
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
# For easily grabbing several file names
import glob
# For image processing functions
import skimage.io
import skimage.exposure
import skimage.filters
import skimage.morphology
# In this script, we will compute t... | RPGroup-PBoC/gist_pboc_2017 | code/ecoli_growth_phase.py | Python | mit | 8,724 | [
"Gaussian"
] | 221827c896c9c19e85301df909b996b8a05e279e723f9938fb287bebe3b12544 |
import math
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
import cv2
def grayscale(img):
"""Applies the Grayscale transform
This will return an image with only one color channel
"""
return cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
def canny(img, low_threshold, ... | shivamsardana/Simple-Lane-Detection-System | main.py | Python | mit | 7,667 | [
"Gaussian"
] | 8de455a389630f9a63dceb3672eaabf10c03946c2142f8fa1810156412438131 |
import re
from os.path import basename
import sys
import argparse
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
# When the user supplies an invalid sort key
class InvalidSortKey(Exception): pass
def main():
args = parse_args()
srpf = s... | VDBWRAIR/bio_bits | bio_pieces_old/cat_sequences.py | Python | gpl-2.0 | 5,801 | [
"Biopython"
] | 343b428a800af08d66fb667ce64bd4fcac994f2e5cf0a98f3f1b8ff8be637861 |
import numpy
import chainer
from chainer import cuda
def exponential_decay_noise(xp, shape, dtype, hook, opt):
"""Time-dependent annealed Gaussian noise function from the paper:
`Adding Gradient Noise Improves Learning for Very Deep Networks
<https://arxiv.org/pdf/1511.06807>`_.
"""
std = numpy.... | pfnet/chainer | chainer/optimizer_hooks/gradient_noise.py | Python | mit | 2,840 | [
"Gaussian"
] | a214ffec191518eed59e288e8f59e1d38a2b4fc495e9fa59b21ed7b78ea4add2 |
"""
Dist Plot
=========
_thumb: .2, .8
_example_title: Plot distribution.
"""
import matplotlib.pyplot as plt
import numpy as np
import arviz as az
az.style.use("arviz-darkgrid")
a = np.random.poisson(4, 1000)
b = np.random.normal(0, 1, 1000)
_, ax = plt.subplots(1, 2, figsize=(10, 4))
az.plot_dist(a, color="C1", ... | arviz-devs/arviz | examples/matplotlib/mpl_plot_dist.py | Python | apache-2.0 | 415 | [
"Gaussian"
] | 63bd23cc0e5b3a3771229373806c33e98199d45efaf19f2a3a6c735df1cb2d05 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/Sound.py | Python | gpl-3.0 | 7,387 | [
"ORCA"
] | ee5c4b6b04d8c06a8d4ac3cfa4c62939ccb9459d198b8734d8dda1e7e78b1992 |
"""Simple test for the ImageDataProbe filter.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from io import BytesIO
import copy
# Local imports.
from common import TestCase, get_... | dmsurti/mayavi | integrationtests/mayavi/test_labels.py | Python | bsd-3-clause | 4,116 | [
"Mayavi",
"VTK"
] | ed2a914d15fc4fb000533c52e020fb65f5d78810d876fc5ba00684da91a5de6d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2018-2019, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# f... | nupic-community/nupic.audio | SpeechRecognition/cochlea-encoder/cochlea_encoder.py | Python | gpl-3.0 | 6,805 | [
"NEURON"
] | 60d861c4ca892169cbc7fb5ab2b6d063b1c908cbff9e7df41eb648d15017e16b |
# -*- coding: utf-8 -*-
# module pyparsing.py
#
# Copyright (c) 2003-2019 Paul T. McGuire
#
# 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 limitatio... | rouge8/pip | src/pip/_vendor/pyparsing.py | Python | mit | 263,468 | [
"VisIt"
] | b89b85bff5282e628e1e5094f8484888a8d8a984b63828fe1a6afeb11902ce65 |
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# t... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/ete2/tools/phylobuild_lib/task/cog_creator.py | Python | mit | 22,294 | [
"BLAST"
] | 31545cc3bd20244841b34955b9ad47e4a117056965fb06038a68be7910e9b81e |
#! /usr/bin/env python
import setuptools # necessary for install_requires
from setuptools import find_packages
from distutils.core import Command
from numpy.distutils.core import Extension
from numpy.distutils.command.build_clib import build_clib
from numpy.distutils.command.build_ext import build_ext
from numpy.distu... | nickhand/pyRSD | setup.py | Python | gpl-3.0 | 9,322 | [
"Galaxy"
] | 71d7b73445cecee934caf2a7343f68f27bf407ee4277ceb9c96e6583b9ed6e35 |
#!/usr/bin/env pvbatch
from paraview.simple import *
import pviz
import sys
oviz = pviz.viz(sys.argv) # instantiate viz object (and load data)
part = pviz.makeSlice( y = 0. ) # make slice
oviz.view.CameraViewUp = [0,0,1]
oviz.view.CameraPosition = [0,1,0]
ResetCamera() # auto-adapt ca... | ruizanthony/pviz | examples/simple/cut_y0.py | Python | lgpl-3.0 | 573 | [
"ParaView"
] | f4a02944720e331eb0c7e65fe0255018f191de8455ae4d330b8e473b57f1071b |
#!/usr/bin/env python
"""
Unwrap fasta file so that each sequence takes up only one line.
Usage:
%program input_file output_file
"""
import sys
try:
from Bio import SeqIO
except:
print "This program requires the Biopython library"
sys.exit(0)
try:
in_file = open(sys.argv[1], "rU")
out_file... | wkh124/wkh124 | fasta_unwrap.py | Python | gpl-3.0 | 600 | [
"Biopython"
] | e7dd70ecedebdd0bd2782229142fc9d3a6a8587533f0b2e2cfdbfba20f67cf91 |
"""compctl
Usage:
compctl halt
compctl usage
compctl schedule (lunch | league | knockout | open | briefing | photo | prizes | tinker) <time>
compctl unschedule <id>
compctl show-schedule <from> <to>
compctl add-team <tla> <name> <college>
compctl del-team <tla>
compctl set-team-name <tla> <name>
comp... | prophile/compd | src/control.py | Python | mit | 3,010 | [
"TINKER"
] | b6931f65462edf76a41aa64ea6c237be7da0fb34bd8b44a50f786b4c71249344 |
# -*- coding: utf-8 -*-
# +---------------------------------------------------------------------------+
# | pylstar : Implementation of the LSTAR Grammatical Inference Algorithm |
# +---------------------------------------------------------------------------+
# | Copyright (C) 2015 Georges Bossert ... | gbossert/pylstar | src/pylstar/automata/Automata.py | Python | gpl-3.0 | 9,152 | [
"VisIt"
] | 59b6c63ac48cd16a3083d990a3c4ddfd51f9a2dd654421f48bf8ba44d6a37dba |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This file is part of the web2py Web Framework
Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
License: LGPLv3 (http://www.gnu.org/licenses/lgpl.html)
The widget is called from web2py.
"""
import datetime
import sys
import cStringIO
import time
import threa... | pouyana/teireader | webui/gluon/widget.py | Python | mit | 44,631 | [
"VisIt"
] | 45ef0088ddbf8414e31e371e624ff8ddda4e927b3dc7375657a675c8486ded1c |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/input_tab/ParameterInfo/test_ParameterInfo.py | Python | lgpl-2.1 | 3,778 | [
"MOOSE"
] | fbfe55fa31f352ebb4876a3972a2081a0aacb0e26cdd444b689032a5d3ed816b |
"""
This example demonstrates using Mayavi as a component of a large Qt
application.
For this use, Mayavi is embedded in a QWidget. To understand this
example, please read section :ref:`builing-applications`.
"""
# First, and before importing any Enthought packages, set the ETS_TOOLKIT
# environment variable to qt4, ... | dmsurti/mayavi | examples/mayavi/interactive/qt_embedding.py | Python | bsd-3-clause | 3,934 | [
"Mayavi",
"VTK"
] | 5c530fd13185b90309559c8a48728f9017e38dd2614aa30a09441fbff95728e9 |
from ..utils import *
##
# Hero Powers
# Lesser Heal (Anduin Wrynn)
class CS1h_001:
activate = Heal(TARGET, 2)
##
# Minions
# Northshire Cleric
class CS2_235:
events = Heal(ALL_MINIONS).on(Draw(CONTROLLER))
# Lightwarden
class EX1_001:
events = Heal().on(Buff(SELF, "EX1_001e"))
EX1_001e = buff(atk=2)
# Ca... | amw2104/fireplace | fireplace/cards/classic/priest.py | Python | agpl-3.0 | 3,116 | [
"BLAST"
] | 9d8ea706b9774273e1185130b842118880a27f458a92b227717d594e6e467628 |
from distribute_jobs import (
SLURM, format_slurm_parameters, write_python_script)
from os.path import join
from qmflows import Settings
import fnmatch
import h5py
import os
def main():
# Current Work Directory
cwd = os.getcwd()
# ========== Fill in the following variables
# Varaible to define... | felipeZ/nonAdiabaticCoupling | scripts/distribution/merge_job.py | Python | mit | 3,235 | [
"CP2K"
] | 74041d26cb7e16ccc4e19fc23917106bc8075db6d770617f93c4f25de4463ac6 |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/method/fragments.py | Python | lgpl-2.1 | 5,424 | [
"cclib"
] | 4310bb9d162b46e4c41b8d65a8148832cf9a1995a6a8be00e77dbc9d8347f6f8 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | WangWenjun559/Weiss | summary/sumy/sklearn/cluster/k_means_.py | Python | apache-2.0 | 54,694 | [
"Gaussian"
] | 2912b2ab6bd732b699a8f3512b5bc2da328c22c7b608f0a244bb2c0ef0b35ee4 |
vocab1k = [
"a",
"ability",
"able",
"about",
"above",
"accept",
"according",
"account",
"across",
"act",
"action",
"activity",
"actually",
"add",
"address",
"administration",
"admit",
"adult",
"affect",
"after",
"again",
"against",
... | HazyResearch/metal | synthetic/words1k.py | Python | apache-2.0 | 13,536 | [
"VisIt"
] | 12e78dcd667a1940afc64ed0a4a45f24809dab4a8ed1e77744a918edd06d185d |
import sys, pysam, gzip, pdb, argparse, pdb
parser = argparse.ArgumentParser()
parser.add_argument("-p", action='store_true', dest='is_paired_end', default=False)
parser.add_argument("orig_bam")
parser.add_argument("remap_bam")
parser.add_argument("keep_bam")
parser.add_argument("orig_num_file")
options= parser.parse... | PrincetonUniversity/WASP | mapping/filter_remapped_reads.py | Python | apache-2.0 | 2,576 | [
"pysam"
] | 9bdffb5a5d2d12fa4d4656ed4d50af2b100e69df16a8d9a0e20efabb7622dc9a |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (http://w... | geimer/easybuild-easyblocks | easybuild/easyblocks/f/foldx.py | Python | gpl-2.0 | 2,924 | [
"FoldX"
] | 7468b6ba35187f0400f5135973e40acae3312e2d72fe8ea7eb8b79f3ed035fbc |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getp... | Ballz0fSteel/Umeko | lib/youtube_dl/extractor/common.py | Python | gpl-3.0 | 121,355 | [
"VisIt"
] | 8b38a59a96781f4b2462721ef87750129051b72c8d983d78c0cd69aa8677c508 |
from __future__ import absolute_import
import os.path as op
import numpy as nm
import sfepy
from sfepy.discrete import FieldVariable
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.base.base import assert_
from sfepy.base.testing import TestCommon
class Test(TestCommon):
@staticmethod
def fr... | lokik/sfepy | tests/test_projections.py | Python | bsd-3-clause | 6,322 | [
"VTK"
] | d209273effc198302a575d8c98116b74dc0f22b8a20bf0210f045567d68bb27c |
import sys
msg = "\nThe matplotlib python module is missing or not installed properly.\n"
msg += "Is the PYTHONPATH environment variable set correctly?\n"
msg += "Please verify your installation by running on the command line:\n"
msg += "python -c 'import matplotlib'\n"
msg += "\n"
msg += "This module is optional and ... | grhawk/ASE | tools/ase/test/dependency_matplotlib.py | Python | gpl-2.0 | 1,052 | [
"ASE"
] | 7791dded95e1bc63479bb2b44d3a4f132d4f869b2a317a4792e83d57a99ba1fe |
# -*- coding: utf-8 -*-
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""This module defines a Hamiltonian."""
from math import pi, sqrt
import numpy as np
from gpaw.poisson import PoissonSolver
from gpaw.transformers import Transformer
from gpaw.lfc import LFC
from ... | ajylee/gpaw-rtxs | gpaw/hamiltonian.py | Python | gpl-3.0 | 19,793 | [
"GPAW"
] | 39041006141a777b05d2aea590abd092b921a303b366caba2928768e8cdae8ff |
""" Test cktapps """
import pytest
from StringIO import StringIO
from collections import OrderedDict
from textwrap import dedent
from cktapps import core
from cktapps import Ckt
from cktapps.formats import spice
class TestSpiceReadLine:
def test_simple(self):
f = StringIO("a b\n"
"* ... | r-rathi/ckt-apps | cktapps/tests/test_cktapps.py | Python | mit | 24,777 | [
"MacroModel"
] | 545151c424ab8e40c147a29806c543d175dba98321b4cf521a0991df75aeca20 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
import warnings
from math import ceil
from math import cos
from math import sin
from math import tan
from math import pi
from warnings impor... | Bismarrck/pymatgen | pymatgen/symmetry/bandstructure.py | Python | mit | 30,212 | [
"pymatgen"
] | ef5e514c9e4e04a80c1d8abe7733af113d233599535b2c684d8ba401c4f85df0 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def loop_waterline(zh, cutter,s):
range=2
Nmax = 200
yvals = [float(n-float(Nmax)/2)/Nmax*range for n in xrange(0,Nmax+1)]
xvals = [float(n-float(Nmax)/2)/Nmax*range for n in xrange(0,Nmax+1)]
bpc = ocl.BatchPushCutter()
... | AlanZatarain/opencamlib | scripts/fiber_12_waterline_onetriangle.py | Python | gpl-3.0 | 2,999 | [
"VTK"
] | c201af6f2ed2c44981dce56e2b866356f46dae34e010e770fd9417c7f95c3ae0 |
from __future__ import print_function
import os,sys
import unittest
import math
from rdkit import RDConfig
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Chem import rdMolAlign
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdShapeHelpers as rdshp
from rdkit.Chem import rdMolTran... | soerendip42/rdkit | Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py | Python | bsd-3-clause | 3,827 | [
"RDKit"
] | e3008261c8907150d327040a9d70afaa3e4c8311a63aa522f400f206223b2820 |
#!/usr/bin/python
#
# Python script to read bluetooth serial data from USB Smart Chargers
# from http://briandorey.com/post/usb-smart-charger-with-bluetooth-le.aspx
#
# run every 5 mins with cron
# sudo crontab -e
# */5 * * * * python /home/pi/processchargers.py &
#
import urllib2
import serial
import time
# url for p... | briandorey/USB-Smart-Charger-with-BluetoothLE | serverscripts/processchargers.py | Python | mit | 3,614 | [
"Brian"
] | a214ad61480b2518ac9b3e1bcb347156c1c51f979d61634692640890929407f6 |
'''
File: fibonacci_heap_mod.py
Author: Keith Schwarz (htiek@cs.stanford.edu)
Ported to Python by Dan Stromberg (strombrg@gmail.com)
An implementation of a priority queue backed by a Fibonacci heap, as described
by Fredman and Tarjan. Fibonacci heaps are interesting theoretically because
they have asymptotically goo... | AminFadaee/8_Puzzle_Solver | fibonacci_heap_mod.py | Python | mit | 24,049 | [
"VisIt"
] | 296ca4d9f47dafbe032537fb9ee4cf340c3cc1e2ccd7d0f234f4e400488a19b1 |
"""
Contains a class for containing multiple replica Universes in a single object.
This module defines a class that will contain Universes for each replica in a
replica exchange simulation.
While each replica can be defined individually, this adds a convenient
container for logically similar trajectories and allows ea... | theavey/ParaTemp | paratemp/re_universe.py | Python | apache-2.0 | 11,993 | [
"MDAnalysis"
] | b28dc7323ee5b03d31d9424aa8c9588ecee5b93cffc3c1569c635460afa547b9 |
"""Read and write treebanks."""
from __future__ import generator_stop
import os
import re
import sys
import gzip
from glob import glob
from itertools import count, chain, islice
from collections import defaultdict
import xml.etree.ElementTree as ElementTree
from collections import OrderedDict
from .tree import (Tree, P... | andreasvc/disco-dop | discodop/treebank.py | Python | gpl-2.0 | 44,624 | [
"VisIt"
] | ad8200ba096784139d9fcc1345f82985595f4d4c737218388e234f378952838a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2011 Adam Stein <adam@csh.rit.edu>
#
# This program is free software; you... | arunkgupta/gramps | gramps/plugins/docgen/rtfdoc.py | Python | gpl-2.0 | 21,154 | [
"Brian"
] | 6d400c46a2eaedfe2929953c455b74e5e9a6fb3cf0422dd8da5e995c4397c25e |
import re
import tensorflow as tf
# If a model is trained with multiple GPUs, prefix all Op names with tower_name
# to differentiate the operations. Note that this prefix is removed from the
# names of the summaries when visualizing a model.
TOWER_NAME = 'GPU0'
def conv_layer(name, input, shape, weight_decay=0.0, s... | peerdavid/social-neural-network | neural_network/model.py | Python | gpl-3.0 | 8,655 | [
"Gaussian"
] | dc7fe27853d31683d9b39367e0ff437ed50d0d39561ddd679eb4dd18eff45a64 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import warnings
from abc import abstractmethod
from math import acos, cos, exp, floor, inf, log, pi, sin, sqrt
from numbers import Number
import numpy as np
import astropy.constants as const
import astropy.units as u
from astropy.utils.compat.optional_d... | pllim/astropy | astropy/cosmology/flrw.py | Python | bsd-3-clause | 113,801 | [
"Galaxy"
] | a563c44ea373606c2aa93c54655c2c69444c59dea5b4678d57d02e363f4b431e |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to build a CG or AA/CG dual-resolution
system from an AA system. Converts AA residues
automatically to CG using dictionary of conversions.
Writes out LAMMPS datafiles and include file
for the force field, as well as a PDB-file.
"""
import sys
import mat... | SGenheden/Scripts | Lammps/aa2cg.py | Python | mit | 11,978 | [
"CHARMM",
"LAMMPS"
] | 1db94d924b93308acb8bc7934f9aacbeac88297e8e771a3abdb335e9d05bc5f3 |
import numpy as np
from sklearn.gaussian_process.gpr import GaussianProcessRegressor as GPR
def fit(kernel, sample_indices, X, y, n_restarts_optimizer, normalize_y):
"""Fits a Gaussian Process Regression model on a subset of X and y using
the provided covariance kernel and subset indices. This is used as a s... | lucaskolstad/rBCM | rBCM/gpr.py | Python | bsd-3-clause | 2,397 | [
"Gaussian"
] | f29c4bc606b54314ab1c81f695f3ed935b5920b6fd9d1085e0e71e9df03406f2 |
########################################################################
# $Id$
########################################################################
""" JobStateUpdateHandler is the implementation of the Job State updating
service in the DISET framework
The following methods are available in the Service i... | rajanandakumar/DIRAC | WorkloadManagementSystem/Service/JobStateUpdateHandler.py | Python | gpl-3.0 | 12,605 | [
"DIRAC"
] | 2f459ad54d9ceb979dc6e8c45f87cab84997e3dafcb03befeb4e71136e4f0f15 |
#!/usr/bin/env python
import cdsapi
import calendar
import os
#Time of dataset
year_start = var_year_start
year_end = var_year_end
month_start = var_month_start
month_end = var_month_end
# Area
north = var_north
south = var_south
west = var_west
east = var_east
# Output folder, i.e. re... | e5k/TephraProb | CODE/cdsapi-0.2.5/download_ERA5_tmp.py | Python | gpl-3.0 | 2,496 | [
"NetCDF"
] | b73803a0c5c73ca39c2f432d43301fee874c75125b88336aac75fe0f8f6b5db8 |
from textwrap import dedent
import psycopg2
import pytest
from unittest.mock import patch, MagicMock
from pgspecial.main import PGSpecial, NO_QUERY
from utils import run, dbtest, requires_json, requires_jsonb
from pgcli.main import PGCli
from pgcli.packages.parseutils.meta import FunctionMetadata
def function_meta_... | dbcli/pgcli | tests/test_pgexecute.py | Python | bsd-3-clause | 16,600 | [
"MOE"
] | 5ff905d3b79cb47626bfcbae3b833b9ef29e8dcf9950790cbeabe9ce25d992bf |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, print_function
import os
import sys
from tempfile import mkdtemp
from shutil import rmtree
import locale
import logging
import subprocess
from pelican import Pelican
from pelican.settings import read_settings
from pelican.tests.support import LoggedTest... | 0xMF/pelican | pelican/tests/test_pelican.py | Python | agpl-3.0 | 7,512 | [
"exciting"
] | dbcb0e8682ba2e710544fa214212dfd02c9eb74a0f82f90007cdd9a3523a74a1 |
# pyenchant
#
# Copyright (C) 2004-2011, Ryan Kelly
#
# 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 ... | meska/pyenchant | enchant/__init__.py | Python | lgpl-2.1 | 35,386 | [
"VisIt"
] | 86e3d80c0e82604132bab9503b38bd250e901428364996e9ce44aed7f1f6fddc |
import sys
import os
import json
import csv
import shutil
import subprocess
def createSimulationDirectory(simulationid):
# YZ: This directory is created by making a full copy of the 'Facade' folder in the jEPlus repository
directory = 'simulations/{0}'.format(simulationid)
if os.path.exists(directory):
sh... | nrgsim/nrgsim | scripts/runsimulation.py | Python | agpl-3.0 | 6,184 | [
"EPW"
] | 086a4ff9edd671e09dcf1708cfe564d3f2cd993c16ff39d43cbaee7ea0e80215 |
from __future__ import annotations
import copy
import os
import pickle
import random
import pytest
from cctbx import sgtbx
from dxtbx.model import Crystal, Experiment, ExperimentList
from dxtbx.serialize import load
from dials.array_family import flex
def test_accessing_invalid_key_throws_keyerror():
table = ... | dials/dials | tests/array_family/test_reflection_table.py | Python | bsd-3-clause | 50,591 | [
"CRYSTAL"
] | d6cbd2cb211a578a1489da2422a37e881fa6eedeb33e7fdf05b8eedb7b554841 |
import logging
import os
import subprocess
import sys
from galaxy import eggs
eggs.require( "decorator" )
eggs.require( "Tempita" )
eggs.require( "SQLAlchemy" )
eggs.require( "sqlalchemy_migrate" )
from migrate.versioning import repository
from migrate.versioning import schema
from sqlalchemy import create_engine
from ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py | Python | gpl-3.0 | 12,303 | [
"Galaxy"
] | 42a3d13fb7489866cba9a0b63028f1db4f49336ca611e8fd5c28c38a04c0a5ef |
import pytest
import re
from capybara.exceptions import ExpectationNotMet
class TestAssertCurrentPath:
@pytest.fixture(autouse=True)
def setup_session(self, session):
session.visit("/with_js")
def test_does_not_raise_if_the_page_has_the_given_current_path(self, session):
session.assert_c... | elliterate/capybara.py | capybara/tests/session/test_assert_current_path.py | Python | mit | 2,570 | [
"VisIt"
] | eb6a66f8e5776081b7bc62e620fd701a86ba72891edf382f07288fdaf797280a |
import IPython
if IPython.release.version<'0.11':
raise ImportError,'this module requires at least v0.11 of IPython'
from rdkit.Chem import rdchem
from rdkit.Chem import Draw
from cStringIO import StringIO
import copy
import numpy
import Image
molSize=(450,150)
highlightSubstructs=True
kekulizeStructures=True
def... | rdkit/rdkit-orig | rdkit/Chem/Draw/IPythonConsole.py | Python | bsd-3-clause | 2,622 | [
"RDKit"
] | 7b0c594e9b939e794b4190c6b09bb987f10466494d0e13407542a85f3a387ad5 |
#! /usr/bin/env python
from ase import Atoms
from pyDFTutils.ase_utils import to_smallest_positive_pos,cut_lattice ,scaled_pos_to_pos
force_in_cell = to_smallest_positive_pos
from ase.lattice.cubic import SimpleCubicFactory
from ase.lattice.tetragonal import SimpleTetragonalFactory
from ase.lattice.triclinic import Tr... | mailhexu/pyDFTutils | pyDFTutils/perovskite/lattice_factory.py | Python | lgpl-3.0 | 8,373 | [
"ASE",
"CRYSTAL"
] | 9fc39257199a3b178aa92db2a1c9ca48598cb799f6b732c3585e754bd9ac2b95 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from bs4 import BeautifulSoup
from enum import Enum
import urllib
import galaxy
import general
import datetime
import traceback
from scraper import Scraper
from datetime import timedelta
class Messages(Scraper):
def __init__(self, browser, config):
self.gener... | yosh778/OG-Bot | ogbot/scraping/messages.py | Python | mit | 8,789 | [
"CRYSTAL",
"Galaxy"
] | 98648ea3cfae1b47152bc8aad55cc2fd18a30b92069c0acd69625ef3e16da34e |
# NeHe Tutorial Lesson: 44 - Lense Flare
#
# Ported to PyOpenGL 2.0 by Brian Leair 2004
#
# This code was created by Jeff Molofee 2000
#
# The port was based on the PyOpenGL tutorials and from
# PyOpenGLContext (tests/glprint.py)
#
# If you've found this code useful, feel free to let me know
# at (Brian Leair telcom_... | mgood7123/UPM | Sources/PyOpenGL-Demo-3.0.1b1/PyOpenGL-Demo/NeHe/lesson44/lesson44.py | Python | gpl-3.0 | 18,610 | [
"Brian"
] | 3b4f6fe7889b3580a48f308e153b0e0d2a63e6bb8048c473e77160bf27d1f635 |
# -*- mode: python; coding: utf-8 -*-
# Copyright 2018 Peter Williams <peter@newton.cx> and collaborators.
# Licensed under the MIT License.
"""This module helps you run the synchrotron code described in Fleischman &
Kuznetsov (2010; hereafter FK10) [`DOI:10.1088/0004-637X/721/2/1127
<https://doi.org/10.1088/0004-637X... | pkgw/pwkit | pwkit/fk10.py | Python | mit | 28,406 | [
"Gaussian"
] | 8808590f3d494a0f853250c61578ac8bfa3b4d8bfb6a06dd926d5c975449ccb7 |
from core.datacontainer import DataContainer
from bio.neuron import Neuron
from PyQt5 import QtGui, QtWidgets, QtCore
class NeuronGUI(QtWidgets.QGroupBox):
def __init__(self, data_container):
if not isinstance(data_container, DataContainer):
raise TypeError("the data container has the wrong type")
sup... | zibneuro/brainvispy | gui/neurongui.py | Python | bsd-3-clause | 1,786 | [
"NEURON"
] | 4077cb60d68571e7b9b79f3fbddaf4e2202bd41c9fbf442cb7c2c825e71897c6 |
from scipy import integrate
import numpy as np
print "Gaussian integral", np.sqrt(np.pi), integrate.quad(lambda x: np.exp(-x**2), -np.inf, np.inf)
| moonbury/notebooks | github/Numpy/Chapter10/gaussquad.py | Python | gpl-3.0 | 148 | [
"Gaussian"
] | 7463c870608a25b1c206f2d580f3f899b1e92acb212b6fa8612bb2e603f14ad3 |
import numpy as np
from pysisyphus.calculators.Calculator import Calculator
class LennardJones(Calculator):
# Corresponds to σ = 1 Å, as the default value in ASE, but
# pysisyphus uses au/Bohr.
def __init__(self, sigma=1.8897261251, epsilon=1, rc=None):
super().__init__()
self.sigma = s... | eljost/pysisyphus | pysisyphus/calculators/LennardJones.py | Python | gpl-3.0 | 2,628 | [
"ASE"
] | 1fd5f05844f44d93aa71eda30fde894210a8d3afdf73cb472d670f653a51f8e0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of OpenDrift.
#
# OpenDrift 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
#
# OpenDrift is distributed in the hope that it will b... | OpenDrift/opendrift | tests/readers/test_interpolation.py | Python | gpl-2.0 | 20,549 | [
"NetCDF"
] | 2d543f719f2192c4efc023a3e7dd260bc2f7f71e16d9fa9b3a5d549b3e98802d |
########################################################################
# File : InProcessComputingElement.py
# Author : Stuart Paterson
########################################################################
""" The simplest Computing Element instance that submits jobs locally.
This is also the standard "CE" ... | Andrew-McNab-UK/DIRAC | Resources/Computing/InProcessComputingElement.py | Python | gpl-3.0 | 4,942 | [
"DIRAC"
] | 84fe396d7357ce5fe35a7fb69a52185b2887d02f5c224304a6e7fcfefc53bf82 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-biobase/package.py | Python | lgpl-2.1 | 1,894 | [
"Bioconductor"
] | 43eae646b0fed80c6531cbb930d4027834b5fefa5409cbc2f986d7add2820fcc |
import numpy as np
import FittingUtilities
import HelperFunctions
import matplotlib.pyplot as plt
import sys
import os
from astropy import units
import DataStructures
from scipy.interpolate import InterpolatedUnivariateSpline as interp
from scipy.interpolate import UnivariateSpline as smooth
import MakeModel
import Hel... | kgullikson88/Chiron-Scripts | Smooth.py | Python | gpl-3.0 | 13,289 | [
"Gaussian"
] | 3ec891169805017832c3067f59892179a3bacdb0bd4f9d829820b5c6411c0c19 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | junghans/espressopp | src/analysis/OrderParameter.py | Python | gpl-3.0 | 3,528 | [
"ESPResSo"
] | 8d8757c8d17d6b4778665010b5a9f41cf52afab8c8d6128f5a69f06729fca612 |
# Copyright 2013 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requ... | kfwang/Glance-OVA-OVF | glance/api/v2/image_members.py | Python | apache-2.0 | 13,892 | [
"Brian"
] | c87e3bc95bdc25517f042b266854e0b779e88090f973fc6f290b7693481ed312 |
"""
Set of objects to manage triggers streams.
A trigger is an audio signal with a value of 1 surrounded by 0s.
TrigXXX objects use this kind of signal to generate different
processes with sampling rate time accuracy.
"""
"""
Copyright 2009-2015 Olivier Belanger
This file is part of pyo, a python module to help di... | wang1986one/pyo | pyolib/triggers.py | Python | gpl-3.0 | 113,883 | [
"Gaussian"
] | 094d5ac6edcf1e7d49d93520ea4a0d330ef3aaf836be4c3b4e13a1fc703cdd72 |
"""
__init__.py
State Estimation and Analysis for PYthon
Module for working with oceanographic data and models
Copyright (c)2017 University of Hawaii under the MIT-License.
Requires the following packages: joblib
Import classes include:
- :class:`~seapy.environ.opt`
- :class:`~seapy.progressbar.... | ocefpaf/seapy | seapy/__init__.py | Python | mit | 1,333 | [
"NetCDF"
] | 82cef707a4e8baa9cc6ce1c379befd4b0a568ec33dd6251c1fbacc97cb9c7507 |
"""Restricted Boltzmann machine module"""
# TODO:
# REGULARIZATION
# MULTINOMIAL
# ADD JOINT CATEGORY MODELING
import numpy as np
from params import SGDParams, RBMParams
from batches import Batches
import time
def draw_normal(mu):
return np.random.normal(mu)
def draw_bernoulli(p):
return (p > np.random.ran... | ZenDevelopmentSystems/pedal | models/rbm.py | Python | bsd-2-clause | 8,322 | [
"Gaussian"
] | 161a88dae2516e8c9a1fd0252e4e620ba857030465cd8607410108229113e474 |
# Copyright: 2005-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# Author(s): Brian Harring (ferringb@gentoo.org)
__all__ = ["Mapping", "MutableMapping", "UserDict", "ProtectedDict",
"LazyLoad", "slot_dict_class"]
import sys
import weakref
class Mapping(object):
"""
In p... | devurandom/portage | pym/portage/cache/mappings.py | Python | gpl-2.0 | 10,177 | [
"Brian"
] | 599e2c8fb6b787a83ec5fc23571473b44eceec3b5a090d1d2bbdb0bffae41fca |
# This Python file uses the following encoding: utf-8
# Here we initialize the collection of all possible names.
# You might want to add or delete names before starting to seriously use idmas32.
# If you ruled out a gender/nationality in config.py, then the corresponding names are irrelevant.
import config
for na in c... | cjbauer/idmas | names.py | Python | agpl-3.0 | 198,168 | [
"Amber",
"Brian",
"CRYSTAL",
"Dalton",
"Desmond",
"Jaguar"
] | b98cdcce74ce8e2c7d69a3ebe011dfaaa377ecb36d7a373d2499614cc3bb56f7 |
# -*- coding: utf-8 -*-
"""INI simulator with time-to-first-spike code and a dynamic threshold.
@author: rbodo
"""
import sys
from tensorflow import keras
import numpy as np
from snntoolbox.simulation.target_simulators.\
INI_temporal_mean_rate_target_sim import SNN as SNN_
remove_classifier = False
class SNN(... | NeuromorphicProcessorProject/snn_toolbox | snntoolbox/simulation/target_simulators/INI_ttfs_dyn_thresh_target_sim.py | Python | mit | 6,562 | [
"NEURON"
] | dc9a6a527dfce3cb22d6b09cc2332ead5ff361d3fab2f1317bd90cc16ade2f3c |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Peek StdOut of the given DIRAC job
"""
__RCSID__ = "$Id$"
import DIRAC
fr... | avedaee/DIRAC | Interfaces/scripts/dirac-wms-job-peek.py | Python | gpl-3.0 | 1,156 | [
"DIRAC"
] | 8f89846ad1cf0fbfcc853267f954f5056711a0746b720ff87a106c8825035513 |
#!/usr/bin/python
'''
Created on Oct 23, 2013
@author: drnorris
'''
from Star import *
import random
import math
class Galaxy():
def __init__(self, position, velocity, centerMass):
self.position = position
self.velocity = velocity
self.centerMass = centerMass
self.stars = []
... | a8ksh4/solar | Rev-1/Galaxy.py | Python | gpl-3.0 | 1,805 | [
"Galaxy"
] | 9636e91398d231b4e01cd4cd333223d0b8327f3ccedaef1929c8e84467348eba |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
# Copyright (C) 2011 Doug Blank <doug.blank@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
... | SNoiraud/gramps | gramps/gen/filters/rules/person/__init__.py | Python | gpl-2.0 | 6,985 | [
"Brian"
] | 1ba4ad9c395f84bb01fa93f3e54774c1ab5aca38b947334795cce69cecf7d4be |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# 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; either version 2 of the License, or
# (at your... | arunkgupta/gramps | gramps/gen/proxy/living.py | Python | gpl-2.0 | 11,584 | [
"Brian"
] | 5f3ee601f0261c36f6c3ccec744a9c7bde5045a2a4d63c1646d272ed121c8958 |
# Copyright 2021 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/distributions/mvn_low_rank_update_linear_operator_covariance.py | Python | apache-2.0 | 14,579 | [
"Gaussian"
] | 5ce89038c585e3b677235633be81ab910109c23a23c536e547a5ccb54f8e72f5 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/main/__init__.py | Python | gpl-3.0 | 860 | [
"ESPResSo"
] | 66778dbba81c5f7280a103200a443c4f93c071147f18d2b2a24f8d31aca86cc2 |
# Copyright (c) 2017 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
Four Panel Map
===============
By reading model output data from a netCDF file, we can create a four panel plot showing:
* 300 hPa heights and winds
* 500 hPa heights and absol... | metpy/MetPy | v1.1/_downloads/d506add257ad1ffd2447607d972a8e31/Four_Panel_Map.py | Python | bsd-3-clause | 4,731 | [
"NetCDF"
] | 2ba7a313031cff690d7b2c84507202d847052e2fc59ecaaf057a37b936aeb243 |
#
# Copyright (c) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" utility functionality for fingerprinting s... | ptosco/rdkit | rdkit/Chem/Fingerprints/FingerprintMols.py | Python | bsd-3-clause | 17,388 | [
"RDKit"
] | 84a5884ac53c59e6e2b992322e799484cc94c6ced3ea902ff23ef154235bd1e0 |
"""Metrics to assess performance on classification task given class prediction
Functions named as ``*_score`` return a scalar value to maximize: the higher
the better
Function named as ``*_error`` or ``*_loss`` return a scalar value to minimize:
the lower the better
"""
# Authors: Alexandre Gramfort <alexandre.gramf... | chrsrds/scikit-learn | sklearn/metrics/classification.py | Python | bsd-3-clause | 91,448 | [
"Brian"
] | eb3603623d1c7dcea03e94998c0671364a1d4f60c5979635ec287b8fafda2394 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
class Openmm(CMakePackage, CudaPackage):
"""A high performance toolkit for molecular simulation. Use it as... | LLNL/spack | var/spack/repos/builtin/packages/openmm/package.py | Python | lgpl-2.1 | 1,948 | [
"OpenMM"
] | d4eaa5511659dfed1ed71a800ebf0a61c30dbd00098112e3fa8fc3baeb6fa253 |
# -*- coding: utf-8 -*-
"""Release data for the IPython project."""
#-----------------------------------------------------------------------------
# Copyright (c) 2008, IPython Development Team.
# Copyright (c) 2001, Fernando Perez <fernando.perez@colorado.edu>
# Copyright (c) 2001, Janko Hauser <jhauser@zscout.de>... | bgris/ODL_bgris | lib/python3.5/site-packages/IPython/core/release.py | Python | gpl-3.0 | 4,386 | [
"Brian"
] | d48b436a07528dc501534381d1717809699d18bd7b5275a3316c164762a645e5 |
import json
from simstream import PikaAsyncConsumer
settings = {}
with open("../settings.json", 'r') as f:
settings = json.load(f)
settings["routing_key"] = "openmm.log"
def print_log_line(body):
try:
lines = json.loads(body.decode())
if lines is not None:
for line in lines:
... | machristie/airavata | sandbox/simstream/example/openmm_example/openmm_log_consumer.py | Python | apache-2.0 | 1,030 | [
"OpenMM"
] | 9f3d40f3d784ac5977472f8e386d2b69e14dce7a5eb26f5b0826b20a0b3637a4 |
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 07 14:13:18 2013
@author: Shreejoy
"""
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 20 09:54:11 2012
@author: Shreejoy
"""
import os
import os.path
import re
import struct
import gc
from matplotlib.pylab import *
from xml.etree.ElementTree i... | neuroelectro/neuroelectro_org | article_text_mining/deprecated/db_add_full_text_wiley.py | Python | gpl-2.0 | 10,680 | [
"NEURON"
] | 9b7eb5c68dc71cf1b13b0d5df27158b3cc2a0f2c9b1e05f5769b5d01f3593843 |
"""Traits-based GUI for head-MRI coregistration"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from ..externals.six.moves import queue
import re
from threading import Thread
import warnings
import numpy as np
from scipy.spatial.distance import cdist
# allow import... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/mne/gui/_coreg_gui.py | Python | bsd-3-clause | 53,959 | [
"Mayavi"
] | 4da167cbcee14bde26ff6cc75ebd8fe86fee9d089a96677a8c3e56757377548c |
import operator, os, socket
from datetime import *
from time import mktime, strftime, localtime
import calendar
from galaxy.webapps.reports.base.controller import *
import galaxy.model
import pkg_resources
pkg_resources.require( "SQLAlchemy >= 0.4" )
import sqlalchemy as sa
import logging
log = logging.getLogger( __nam... | volpino/Yeps-EURAC | lib/galaxy/webapps/reports/controllers/jobs.py | Python | mit | 30,355 | [
"Galaxy"
] | fbbb523b869cdf78bd514c5ee0410ede6800abd9b333c5ee299a2ca7763840a8 |
import json
import logging
from datetime import datetime
import ddt
from django.core.urlresolvers import reverse
from django.http import Http404
from django.test.client import Client, RequestFactory
from django.test.utils import override_settings
from django.utils import translation
from mock import ANY, Mock, call, p... | miptliot/edx-platform | lms/djangoapps/discussion/tests/test_views.py | Python | agpl-3.0 | 76,837 | [
"VisIt"
] | 5e96f28d0445ebb2c96118d048d4f77f53e40496dc3c180e559a8695836e028b |
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