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# -*- coding: utf-8 -*-
#
# helpers.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, or
# (... | janhahne/nest-simulator | pynest/examples/Potjans_2014/helpers.py | Python | gpl-2.0 | 14,760 | [
"NEURON"
] | f0b979a562985dc9903ad442fb73275bfc23a8df646b30fa192bee2dfb6eadaf |
# Copyright (c) 2015 MaxPoint Interactive, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
# following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditi... | vishpat/Practice | python/puzzles/bayes_logistic.py | Python | gpl-3.0 | 19,763 | [
"Gaussian"
] | 069001c0b5fdf0ea6e311eada84fd043c11a2f4e4da0b1c105d8c1f08c4d11d0 |
#!/usr/bin/python
"""Test to verify bug #361167 is still fixed.
Add dynamic row and column header support in Orca for
StarOffice/OpenOffice calc.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
######################################################################
# 1. Start oocal... | h4ck3rm1k3/orca-sonar | test/keystrokes/oocalc/bug_361167.py | Python | lgpl-2.1 | 8,958 | [
"ORCA"
] | 2997e334647f0462b4cbf3cb1f661c8842d66d72748d343b41ddca25f0e7efa4 |
#! /usr/bin/env python
"""
Cosmology + some useful functions
This module contains various functions to compute distances and
times in a Universe with a given cosmology.
List of functions:
set_cosmology(): lets user specify a cosmology.
cosmology_set(): determines wheter an input cosmology
has... | cosmodesi/desibgsdev | mocks/MXXL/generate_ascii_randoms/randoms/check_randoms/Cosmology.py | Python | bsd-3-clause | 18,619 | [
"Galaxy"
] | 1b7efc7232d356194ea3d88a47a767647f8e3b290fbbf6848032a22c8cf349fe |
# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for the Earth and Planetary Sciences
# Copyright (C) 2012 - 2017 by the BurnMan team, released under the GNU
# GPL v2 or later.
from __future__ import absolute_import
from __future__ import print_function
import operator
import bisect
import o... | tjhei/burnman | burnman/tools.py | Python | gpl-2.0 | 28,683 | [
"Avogadro",
"Gaussian"
] | fe4e7378a6058c22b4f3a64405d3a9af57b1688de41d100e483b2143c5a0eb4d |
# (C) British Crown Copyright 2014 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | davidnmurray/iris | lib/iris/tests/integration/test_grib2.py | Python | gpl-3.0 | 11,750 | [
"Gaussian",
"NetCDF"
] | 0ca5fb568a06ee780b10051307dc0a4200b86de637ac9d83e0b13e1f0e996d2d |
# -*- coding: utf-8 -*-
# Copyright © 2012-2022 Roberto Alsina and others.
# 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 t... | getnikola/nikola | nikola/plugins/command/plugin.py | Python | mit | 13,634 | [
"VisIt"
] | 8b900b6f298dce5b3284d76dc0b34fb6ca9598604b8160a689dae5c8ab8ef99e |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/logging.py | Python | gpl-3.0 | 1,382 | [
"Brian"
] | c0f2820777b3e88369cfa26b37d944f882f2e52eb4fcd53bf08cc8e627dd113c |
"""Tornado handlers for 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, distributed as p... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/frontend/html/notebook/handlers.py | Python | lgpl-3.0 | 25,750 | [
"Brian"
] | db06c9fd91832f9526c09615a3a4bde25bd2bbd90a3a0338e249f9e89a6cc818 |
import unittest
import os
import glob
import numpy as np
import fitsio
import healpy
from picca.utils import userprint
from picca.tests.test_helpers import AbstractTest
class TestDelta(AbstractTest):
"""
Test case for picca_deltas.py
"""
def produce_folder(self):
"""
Create ... | igmhub/picca | py/picca/tests/test_1_deltas.py | Python | gpl-3.0 | 17,417 | [
"Gaussian"
] | 3f2f8e0ab1f0de8986176e7a0697725faffa3872e7a9afbd6dedf9b45d4f9be9 |
#!/usr/bin/env python
# Run most of AmberTools serial tests
''' Require: AMBERHOME
You need to call amber.setup_test_folders first (only do once)
amber.setup_test_folders
Then run test (anywhere)
amber.run_tests
Adjust the test by updating env TEST_TASK (please lookt at the code)
'''
from time import tim... | hainm/ambertools-binary-test | devtools/ci/ci_test.py | Python | mit | 6,648 | [
"Amber"
] | 74191ebd74b8feb77a29de8babe174eb697f6a2d00bb0cde738a477f0116763c |
#!/usr/bin/env python3
import tempfile
import pkg_resources
from Mikado.exceptions import InvalidParsingFormat
from ..parsers import blast_utils
import unittest
import os
import gzip
import subprocess
from ..serializers.blast_serializer import xml_utils as seri_blast_utils
from ..serializers.blast_serializer.tabula... | lucventurini/mikado | Mikado/tests/test_blast_related.py | Python | lgpl-3.0 | 17,393 | [
"BLAST"
] | c6e52ea5c705c7e97a97d26c9c652739d214c5df942dad22824e5da287a40ed6 |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import Directive, directives
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.domains.std import Cmdoption
from sphinx.util import logging
... | kawamon/hue | desktop/core/ext-py/Django-1.11.29/docs/_ext/djangodocs.py | Python | apache-2.0 | 10,974 | [
"VisIt"
] | d147346e7e243dbb522285539f8914d3bf6d6ce8017356e5839aa0aeabe07542 |
# -*- coding: utf-8 -*-
"""
The MIT License (MIT)
Copyright (c) 2017 SML
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... | smlbiobot/SML-Cogs | crprofile/crprofile.py | Python | mit | 64,820 | [
"VisIt"
] | 4f2d7db565a341ea4d429bc958a69f66fa429873d9b2ab1dbd420f50abd3ad5a |
"""
Reads from input file or writes to the output file.
Author: Mateusz Malinowski
Email: mmalinow@mpi-inf.mpg.de
"""
###
# Helpers
###
def _dirac(pred, gt):
return int(pred==gt)
###
# Main functions
###
def file2list(filepath):
with open(filepath,'r') as f:
lines =[k for k in
[k.strip()... | mateuszmalinowski/visual_turing_test-tutorial | kraino/utils/read_write.py | Python | mit | 4,953 | [
"DIRAC"
] | cf1353a906c36f5e57d2b8451515e47e2a6343fff06f32c6523e01b30c7dcf10 |
'''
Module for retrieving RSTN/Penticton quiet Sun flux densities and evaluating
expected solar flux densities expected for 2.1-m antennas, as a function of
frequency. '''
#
# History:
# 2014-Dec-13 DG
# Written earlier, but updated for changes to NOAA ftp location and new
# archive file with ... | dgary50/eovsa | rstn.py | Python | gpl-2.0 | 22,686 | [
"Gaussian"
] | 2e14f15cce6bdc271026028c7a5a92453e8dd70a727f6d20eca7136e799e90c1 |
#!/usr/bin/env python
import os
import sys
import subprocess
import unittest
from operator import mul
import numpy
try:
import pysam
except:
pass
from hifive import hic_data
import h5py
class HiCData(unittest.TestCase):
def setUp(self):
self.data = h5py.File('test/data/test_import.hcd', 'r')
... | bxlab/HiFive_Paper | Scripts/hifive-1.1.3/test/test_hic_data.py | Python | bsd-3-clause | 4,331 | [
"pysam"
] | bd4e885f94d5b557ded807e9bb367201b2a0fabce80589f6be8932c44d8566fd |
__author__ = "Nitin Kumar, Rick Sherman"
__credits__ = "Jeremy Schulman"
import unittest
from nose.plugins.attrib import attr
from jnpr.junos import Device
from jnpr.junos.facts.switch_style import facts_switch_style as switch_style
@attr('unit')
class TestSwitchStyle(unittest.TestCase):
def setUp(self):
... | JamesNickerson/py-junos-eznc | tests/unit/facts/test_switch_style.py | Python | apache-2.0 | 1,620 | [
"Firefly"
] | 23bf43285ccd0af9c826491d75d7749da3205f39e8a9cf253da822b0f2462ff4 |
#!/usr/local/sci/bin/python
#*****************************
#
# Frequent Value Check (FVC)
#
#
#************************************************************************
# SVN Info
#$Rev:: 55 $: Revision of last commit
#$Author:: rdunn ... | rjhd2/HadISD_v2 | qc_tests/frequent_values.py | Python | bsd-3-clause | 12,392 | [
"Gaussian"
] | 4dbbdfb64ca7cff14710f518530a464d85d6d41f794c1a7ae6dcbef729ab6693 |
from Firefly.helpers.events import Command
def command_from_dict(ff_id:str, source:str, command_dict:dict) -> Command:
""" Create command from dict
Args:
ff_id: ff id of device to send command to
source: source sending command
command_dict: dict of command
Returns: (Command) the command object
"... | Firefly-Automation/Firefly | Firefly/util/firefly_util.py | Python | apache-2.0 | 524 | [
"Firefly"
] | ab21fdd9ed7c13859fc2d79afb033be85c10f5dafe2f7a31baa611ee2ff26c70 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import os, os.path
import csv
import numpy as np
import concurrent.futures
from itertools import groupby
# <codecell>
def fasta_reader(handle, check_lens = True):
outseqs = {}
clen = None
for key, lines in groupby(handle, lambda x: x.s... | JudoWill/ResearchNotebooks | CorProcess.py | Python | mit | 17,704 | [
"VisIt"
] | 754f8c90c525a87fd55262047cd1be23ab94b3b515203709e09b5f813b0b3577 |
"""
Basic enumeration, providing ordered types for collections. These can be
constructed as simple type listings, ie:
::
>>> insects = Enum("ANT", "WASP", "LADYBUG", "FIREFLY")
>>> insects.ANT
'Ant'
>>> tuple(insects)
('Ant', 'Wasp', 'Ladybug', 'Firefly')
with overwritten string counterparts:
::
>>> pe... | meganchang/Stem | stem/util/enum.py | Python | lgpl-3.0 | 4,712 | [
"Firefly"
] | 21f38fee7290e0b1e381dd65c4efe87fc7a59518cc41990ac34dcb429b3e5fbb |
# -*- coding: utf-8 -*-
"""
Default MEEP launch-file for arbitrary PICwriter components.
MCTS = "Meep Compute Transmission Spectra"
Launches a MEEP simulation to compute the transmission/reflection spectra from each of the component's ports when light
enters at the input `port`.
How this function maps the GDSII laye... | DerekK88/PICwriter | picwriter/mcts.py | Python | mit | 16,597 | [
"Gaussian"
] | 8bac9565c453896247270d91166d3d53fb1e48d0c6c5252d3851e381d9e8d1e0 |
"""Provide classes related to widgets."""
import os.path
from json import dumps, JSONEncoder
from ...const import API_PATH
from ...util.cache import cachedproperty
from ..base import PRAWBase
from ..list.base import BaseList
class Button(PRAWBase):
"""Class to represent a single button inside a :class:`.ButtonW... | leviroth/praw | praw/models/reddit/widgets.py | Python | bsd-2-clause | 67,053 | [
"exciting"
] | 84b10522e13393dd2be4b20a7b5d1378775eb1ba6e16c6ffd5650585b1e87a43 |
# Module to compare PYPIT vs. LowRedux
# v0.1 -- First look [Kast_red only]
# v0.2 -- With improved trace
# v0.3 -- With improved skysub and airtovac 9 Nov 2015
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as np
import sys, os
import yaml
import pdb
from scipy impor... | PYPIT/PYPIT | doc/comparisons/pypit_vs_lowredux.py | Python | gpl-3.0 | 15,098 | [
"Gaussian"
] | b769740132724f47e7b1337db7c9583405d4123e7dedaded28dee7810d87a7a9 |
import random
import numpy as np
from . import make_sequence_from_gate_lists
# TODO: pulse_mod
# TODO: use or delete decompose matrix
clifford_rotations = [
['I'],
['X'],
['Y'],
['X/2'],
['-X/2'],
['Y/2'],
['-Y/2'],
['Y', 'X'],
['X/2', 'Y/2'],
['X/2', '-Y/2'],
['-X/2', 'Y/2... | QCoDeS/Qcodes-contrib | qdev_transmon_helpers/sequencing/benchmarking.py | Python | mit | 3,285 | [
"Gaussian"
] | 745ecaeed7c3920c917bdb99e37c83ef6974b2378e162a9f231f98f317b7ba5f |
from typing import Text
def is_reserved_subdomain(subdomain: Text) -> bool:
if subdomain in ZULIP_RESERVED_SUBDOMAINS:
return True
if subdomain[-1] == 's' and subdomain[:-1] in ZULIP_RESERVED_SUBDOMAINS:
return True
if subdomain in GENERIC_RESERVED_SUBDOMAINS:
return True
if sub... | mahim97/zulip | zerver/lib/name_restrictions.py | Python | apache-2.0 | 26,751 | [
"Octopus"
] | 9e19633d5d821c31debfe10e01e449fd381994787eec964bba3364fc8a98930e |
"""pgas.py
2D square lattice Gaussian MRF using Particle Gibbs with Ancestor sampling.
"""
import numpy as np
from scipy import misc
from numpy.random import random_sample
import time
def main():
# Size of problem
M = 10
# Number of particles - N, number of iterations of PGAS - R
N = 15
R = ... | can-cs/smc-pgm | gmrf/pgas.py | Python | mit | 10,015 | [
"Gaussian"
] | cce1f53cdd964d613569e2cf3188d11e4c092e03d77bdc87c8dce90129c1f806 |
'''
Created on Jul 6, 2011
@author: mkiyer
'''
'''
Created on Apr 28, 2011
@author: mkiyer
'''
import os
import tempfile
import logging
from chimerascan.lib.fastq_to_bam import fastq_to_bam, bam_to_fastq
from chimerascan.lib.config import JOB_SUCCESS, JOB_ERROR
from chimerascan import pysam
def sort_fastq_files(fa... | madhavsuresh/chimerascan | chimerascan/deprecated/fastq_sort.py | Python | gpl-3.0 | 1,078 | [
"pysam"
] | a2616091023c4fc2b53621f06c766511dba07452057dbe68be5b5c3f7ded00ec |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/util.py | Python | lgpl-3.0 | 53,439 | [
"NetCDF"
] | ddfcdc8f52f368818b048bb6ff989f73de6c9654b1d43c29fcae36507dab9fbd |
#
# co_co_no_shapes_except_in_convolve.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, or
... | kperun/nestml | pynestml/cocos/co_co_no_shapes_except_in_convolve.py | Python | gpl-2.0 | 5,073 | [
"NEURON"
] | f663a09d4bf27a5d8d873a1fceaa929e1d9d661bd49b3d8779a1f9756f4a893f |
import os
from setuptools import setup, find_packages
setup(name='pyatactools',
version='0.0.1',
#packages=find_packages(),
description='pyatactools is a Python module to analyze ATAC-seq NGS data',
author='Patrick Lombard',
author_email='ptk.lmb55@gmail.com',
packages=['pyatactools... | pdl30/pyatactools | setup.py | Python | gpl-2.0 | 1,075 | [
"pysam"
] | 38fcc926165db1cc16132483a6dd23fe15b15304eb4b0b56bbd82e634de802ee |
# Copyright 2016 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... | ppwwyyxx/tensorflow | tensorflow/python/autograph/converters/call_trees.py | Python | apache-2.0 | 7,543 | [
"VisIt"
] | 77a292f8fb378ab08b5503cab64228fe30a0dae592dcb53fbc2e4623ce69539f |
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 25 14:22:29 2014
@author: cbarbosa
Make simulations to derive errors on Lick indices including both noise and the
error on the determined velocity.
"""
import os
import numpy as np
import multiprocessing as mp
from scipy.stats import nanmedian
from config import *
imp... | kadubarbosa/hydra1 | mc_lick.py | Python | gpl-2.0 | 4,147 | [
"Galaxy"
] | 520262caba703c24e9baaf7f428025cff7215c3d2950c4fb109796fa4f3c509c |
import sys
from rpython.rlib.objectmodel import specialize, we_are_translated
from rpython.rlib.rstring import StringBuilder, UnicodeBuilder
from rpython.rlib.rarithmetic import r_uint, intmask
from rpython.rlib.unicodedata import unicodedb
from rpython.rtyper.lltypesystem import lltype, rffi
from rpython.rlib import j... | jptomo/rpython-lang-scheme | rpython/rlib/runicode.py | Python | mit | 64,823 | [
"FEFF"
] | 7ccff8b2e720287a821444bcd364ad93be89b7fd12de27315d3f1d0c5cae6816 |
'''
Created on 2013/06/11
Author: Duong Nguyen
Email: nguyen@sg.cs.titech.ac.jp
Simple implementation of projection pursuit and demo.
'''
import numpy as np
import matplotlib.pyplot as plt
from numpy.linalg import eigh
from sklearn.decomposition import PCA
def loadData(datfile, pre_process=True, plot=True):
""" L... | ntduong/ML | Projection-Pursuit/proj_pursuit.py | Python | mit | 5,918 | [
"Gaussian"
] | 23b8e5f57fa66da999a35304b2195c6c285be92b5431a956a3e05117242aa8c7 |
# Jython Database Specification API 2.0
#
# $Id: runner.py 4185 2008-02-28 16:55:33Z cgroves $
#
# Copyright (c) 2001 brian zimmer <bzimmer@ziclix.com>
"""
To run the tests, simply invoke this script from the commandline:
jython runner.py <xml config file> [vendor, ...]
If no vendors are given, then all vendors wi... | babble/babble | include/jython/Lib/test/zxjdbc/runner.py | Python | apache-2.0 | 7,148 | [
"Brian"
] | 43e6b8149fe18b79f57dd2e3ce22c9cfb0f5c861e341896fe57f37558ab8d7df |
import collections
InstrumentData = collections.namedtuple('InstrumentData', 'program min_pitch max_pitch family_idx')
class InstrumentDb(object):
_instrument_families = [
'None',
'Piano',
'Chromatic Percussion',
'Organ',
'Guitar',
'Bass',
'Strings',
... | klabble/pollution-music | instrumentdb.py | Python | gpl-3.0 | 8,597 | [
"CRYSTAL"
] | 0aad59a434e818125ccf8eb5e3674edf13dc3e02590ea558712af738875846bd |
#!/usr/bin/env python
# Copyright (c) 2012, Nick Harvey
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# - Redistributions of source code must retain the above copyright notice, this
# list... | bluemini/agenetic | network.py | Python | bsd-3-clause | 1,796 | [
"NEURON"
] | d3911b8e8e90cd53870841f2a2de33eb625ef04be607bcb1307e3cd57436c9fa |
#!/usr/bin/env python
from vtk import *
import os.path
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
dataRootDir = VTK_DATA_ROOT + "/Data/Infovis/XML/"
if not os.path.exists(dataRootDir):
dataRootDir = VTK_DATA_ROOT + "/Data/Infovis/XML/"
reader1 = vtkXMLTreeReader()
reader1.S... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/tree_map.py | Python | bsd-3-clause | 977 | [
"VTK"
] | 6a349483ce59d2dac9b06cc794a1dd2413fdd3b96dd8963565374ff7d991570d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 10 15:39:33 2017
@author: kostenko
*********** Pilot for the new tomo_wrap *************
"""
#%% Initialization
import matplotlib.pyplot as plt
#%%
from scipy import misc # Reading BMPs
import os
import numpy
import re
import pkg_resou... | cicwi/seashell_project | tomo_wrap.py | Python | mit | 46,343 | [
"Mayavi"
] | a92a1a6cc65547d9cee0cce5184fd17c507b9eee8c2fe1a681a770feccc28d23 |
'''
synbiochem (c) University of Manchester 2017
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
import io
import sys
from synbiochem.utils import ice_utils, dna_utils
import panda... | neilswainston/development-py | synbiochemdev/design/plasmid_writer.py | Python | mit | 2,207 | [
"VisIt"
] | 0b43776effd8f3c0b46eb83bc2a253a05e6172bb93acc1e14a7206e45de699dc |
'''
@author: lbergesio
Simple XML parser using minidom for this example
'''
from xml.dom import minidom
'''
SimpleXmlParser class.
'''
class SimpleXmlParser():
@staticmethod
def parse(xml):
self = SimpleXmlParser()
data = minidom.parseString(xml)
actions=list()
actiond=dict()
rspec=... | fp7-ofelia/pypelib | example/interface/SimpleXmlParser.py | Python | lgpl-3.0 | 1,413 | [
"VMD"
] | ea2fb6dcaef4543be93553b4ea927e05f5b16933a92a3bff425fea2d1fd7b1ae |
#!/usr/bin/env python
# coding: utf-8
# # Elements of Probability Theory and Statistical Data Analysis
#
#
# ## Domains and probabilities
# Consider the following simple example, namely the tossing of two dice, resulting in the following possible values
# $$
# \{2,3,4,5,6,7,8,9,10,11,12\}.
# $$
# These values are... | CompPhysics/MachineLearning | doc/LectureNotes/_build/jupyter_execute/statistics.py | Python | cc0-1.0 | 63,634 | [
"Gaussian"
] | 0615803dc99084f92272f292db45f925cd9d55fa71686592e81fe983b7ccc182 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import sys
import argparse
import re
import subprocess
if __name__ == '__main__':
# Arguments parsing
parser = argparse.ArgumentParser(description='')
# -i / --input_fastq
parser.add_argument('-i', '--input_fastq',
actio... | ppericard/matamog | scripts/sga_assemble.py | Python | agpl-3.0 | 8,095 | [
"BWA"
] | 888a3afcfdb19289d624c71d221167079ac44c3e521bbe8263c1a92c69840043 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
# @package parse_blast.py
# @author Lea Picard
#################### MODULES ####################
## Python modules
import argparse, requests, sys, os, subprocess
from Bio import Entrez, SeqIO
from collections import defaultdict, OrderedDict
from time import localtime, strfti... | leapicard/pipeline | G2P.py | Python | gpl-3.0 | 7,758 | [
"BLAST"
] | 455373cbf94e200788fb63a71036aded700f4b4f649801113af693e6785ea18d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# h5cube File Specification build configuration file, created by
# sphinx-quickstart on Tue Dec 6 21:10:22 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
... | bskinn/h5cube-spec | doc/source/conf.py | Python | mit | 16,625 | [
"Brian",
"Gaussian"
] | a1eedc1ee9e4ebaa77455e12785e8ecbfd61e25ff811a73a3fc7b710d2fdd08c |
import math
import json
from jmespath import exceptions
from jmespath.compat import string_type as STRING_TYPE
from jmespath.compat import get_methods, with_metaclass
# python types -> jmespath types
TYPES_MAP = {
'bool': 'boolean',
'list': 'array',
'dict': 'object',
'NoneType': 'null',
'unicode'... | gregbdunn/aws-ec2rescue-linux | lib/jmespath/functions.py | Python | apache-2.0 | 12,641 | [
"VisIt"
] | 06f8dd841d44fd94124b3f0147fca57453f21667ae054130e3472aa5d5849dde |
#encoding:utf8
import json
from aces.tools import *
import os,sys
import aces.config as config
import time
from aces.env import *
def genPbs(path,disp,queue,nodes,procs):
content="cd %s\n"%path
content+="ae app >aces.out\n"
s="""#!/bin/bash -x
#PBS -l nodes=%s:ppn=%s
#PBS -l walltime=240:00:00
#PBS -j oe
#PBS -q %s... | vanceeasleaf/aces | aces/pbs/toolsub.py | Python | gpl-2.0 | 4,564 | [
"LAMMPS"
] | ec816f983599cda004e3dab6be761a0ceb03e8a1864ba5f8e073c4595c089e28 |
# ***************************************************************************
# * Copyright (c) 2018 Bernd Hahnebach <bernd@bimstatik.org> *
# * *
# * This file is part of the FreeCAD CAx development system. *
# * ... | sanguinariojoe/FreeCAD | src/Mod/Fem/femtest/app/test_object.py | Python | lgpl-2.1 | 57,944 | [
"VTK"
] | 46b18f79f8692830b7943e84fe915d5fad35f9e86eae7744a337113833c6c75e |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
# Important note for the deprec... | waterponey/scikit-learn | sklearn/mixture/gmm.py | Python | bsd-3-clause | 32,575 | [
"Gaussian"
] | 65893a82f5408cd710970d15f16040a547f270686b78fc9aea7b4fc127389d5c |
# Definition for a binary tree node.
# class TreeNode(object):
# def __init__(self, x):
# self.val = x
# self.left = None
# self.right = None
from collections import Counter
class Solution(object):
def findFrequentTreeSum(self, root):
"""
:type root: TreeNode
:rtype: List[int]
"""
... | xiaonanln/myleetcode-python | src/508. Most Frequent Subtree Sum - 2.py | Python | apache-2.0 | 776 | [
"VisIt"
] | 8876d15113fd73a997b7b7a652e88ed6537be8d8e49beb44d6693811d6b557a1 |
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
# create planes
# Create the RenderWindow, Renderer
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer( ren )
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
pl... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/streamSurface.py | Python | bsd-3-clause | 2,108 | [
"VTK"
] | fdd65540c60bf728d31cb773965f3c13f79b15301781d1dea1acd414eeecbb4a |
#
# Copyright 2014-2015, 2021 Lars Pastewka (U. Freiburg)
# 2015 Till Junge (EPFL)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Lic... | libAtoms/matscipy | matscipy/contact_mechanics/Hertz.py | Python | lgpl-2.1 | 12,698 | [
"Matscipy"
] | fc702edd082446ac901561913eef7beb123a2bd51c880797aa6f10d4907f3e47 |
# Place file path to the dist folder generated by gulp here
# Do not include trailing slashes.
# Finally, rename this file to config.py to use
CLIENT_DIST_PATH='PATH_TO_DIST_FOLDER' | wangchulab/CIMAGE | cimage/cimage-clientpatches/source/cimage-preview/config.sample.py | Python | mit | 181 | [
"GULP"
] | dcc766440ea24c15c4d7a8ad038a0bb6524daec2c9374dcfdd37de4d3b4ee496 |
#!/usr/bin/env python
'''
GOAL:
- read catalog of spirals that is generated by LCSmergespiralscats.py
- make plots for paper
- run correlation/KS tests
- print latex tables with resulting KS statistics. these are written to SamplePlots directory
USAGE:
- in ipython
%run LCSanalysespirals.py
- all spirals are ... | rfinn/LCS | paper1code/LCSanalyzeblue.py | Python | gpl-3.0 | 412,953 | [
"Galaxy"
] | 596d71339ed6e2d7596b0bb9cb2003f593789dace0272fb868caa67fe8f59cff |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Brian Coca <briancoca+ansible@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/system/debconf.py | Python | bsd-3-clause | 5,418 | [
"Brian"
] | 74b92d9c8bfcc472bc5c2decdd4f5ed94763fd700e5441ccc3f6530f75fa9855 |
#!/usr/bin/env python
import matplotlib
matplotlib.rcParams['legend.fancybox'] = True
import matplotlib.pyplot as plt
import numpy as np
#data
x = [5000, 10000, 15000, 20000]
#define some data
pc_mean = [3.014, 3.903, 4.228, 4.539]
s3mini_mean = [59.412, 30.321, 86.975, 183.882]
s3_mean = [36.336, 16.471, 45.387, 97... | edlectrico/dissertation | graphics/pellet_abox_barchart.py | Python | apache-2.0 | 2,496 | [
"Galaxy"
] | a569a637d1d8f9fb53d33dc7cb88385c863703aa264f8d6b21cb143ccc669c37 |
# GromacsWrapper: cbook.py
"""
:mod:`gromacs.setup` -- Setting up a Gromacs MD run
===================================================
Individual steps such as solvating a structure or energy minimization
are set up in individual directories. For energy minimization one
should supply appropriate mdp run input files; o... | CTCNano/GromacsWrapper | gromacs/setup.py | Python | gpl-3.0 | 47,104 | [
"GROMOS",
"Gromacs"
] | abbc84ad644bd2eeeeeee25f1cf729ef799837d26e8f8ebc83dad367dd5a49e6 |
# Copyright (C) 2017-2018 Michael Freitag, Shahin Amiriparian, Sergey Pugachevskiy, Nicholas Cummins, Björn Schuller
#
# This file is part of auDeep.
#
# auDeep 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,... | auDeep/auDeep | audeep/cli/upsample.py | Python | gpl-3.0 | 2,906 | [
"NetCDF"
] | 9338bf8bd32421fa2d7c007cc8ec8b4e49bed0a5442127ea4ed488ab9d4769e1 |
''' Semi-automated particle selection (LFCPick)
This script (`ara-lfcpick`) was designed to locate potential particles on a micrograph using template-matching. A user
should spend time tuning the number of particles returned to limit the number of noise windows found. Also, a manual
selection is generally performed to... | ezralanglois/arachnid | arachnid/app/lfcpick.py | Python | gpl-2.0 | 19,159 | [
"Gaussian"
] | 2e3dbc17b532630588160c05be724b9361e5f3f854025052dec23d2ad59f8705 |
# 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... | BackupTheBerlios/espressopp | src/tools/lammpsfilewrite.py | Python | gpl-3.0 | 4,096 | [
"ESPResSo",
"LAMMPS"
] | 9d620d2d5ab5ccbde46ac9055bb67e64232930d567fdbab408b2fd0d54365ad4 |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; you can redistribute it an... | d7415/merlin | Arthur/views/search.py | Python | gpl-2.0 | 13,533 | [
"Galaxy"
] | fa6b57d9a135b70cc10531f584fb6801f168ad52b32ad9e086c5e3610c11dacb |
'''
Doc...
@author: kmu
@since: 16. nov. 2010
'''
# Built-in
import time
import datetime
# Additional
from numpy import arange
from netCDF4 import Dataset, num2date, date2num
# Own
from pysenorge.tools.date_converters import iso2datetime
from pysenorge.set_environment import timeunit, default_UM4_width,\... | kmunve/pysenorge | pysenorge/tools/clone_netCDF.py | Python | gpl-3.0 | 3,835 | [
"NetCDF"
] | 96198150928d145a1ecfc47429b395fe167e6d052c6a24672612e5b8ce0b717b |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@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 ... | KyleJamesWalker/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 31,880 | [
"Galaxy"
] | 412f4ea1719e783ec09100e63a9af9862c950f25ca0373306387faf07b45ed4f |
import json
from datetime import datetime
from pymongo import MongoClient
from travel_penguin.model.place import Place
class PenguinDb():
PLACES = "places"
TIMESTAMP_FIELD = "visited"
def __init__(self, database_url):
"""
database_url: have to include database name (mongodb://localhost:27... | icoxfog417/TravelPenguinBot | travel_penguin/travel/penguin_db.py | Python | mit | 1,594 | [
"VisIt"
] | f733e09bdfe4959c819f43004eb4d837a23f1fc2085f7185ef7fcc7299a70fad |
# Copyright (c) 2002-2005 Bryce "Zooko" Wilcox-O'Hearn
# portions Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
# http://zooko.com/repos/pyutil/pyutil/pyutil/
"""
This m... | pombredanne/git-git.fedorahosted.org-git-pyrpm | pyrpm/database/lrucache.py | Python | gpl-2.0 | 27,083 | [
"VisIt"
] | 869e1636d7df1fc835e596032e6c1397aa41e9980f87c141852c47363b714b9d |
import datetime
from django.core.urlresolvers import reverse
from django.core import mail
from splinter import Browser
from situational.testing import BaseCase
class TestQuickHistory(BaseCase):
def test_happy_path(self):
with Browser("django") as b:
b.visit(reverse("quick_history:start"))
... | lm-tools/situational | situational/apps/quick_history/tests/test_feature.py | Python | bsd-3-clause | 1,970 | [
"VisIt"
] | 4491409133e8bdef25a7f3d67ae1c49512d77a4c5399ca3de463461b0c3dae9b |
# Copyright 2018 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... | ghchinoy/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2_test.py | Python | apache-2.0 | 92,347 | [
"Gaussian"
] | 0dab711f3e81879d4f42525ce425d1628588e9bd68feb9b9a0e3400b43e6bbb4 |
# coding: utf8
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an I... | blond-admin/BLonD | __EXAMPLES/main_files/EX_07_Ions.py | Python | gpl-3.0 | 6,437 | [
"Gaussian"
] | a021639b5b76a8fba86370b9c17363650bcfb7d8107d4d8fcac7e7a18c3b641f |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | sleuthkit/autopsy | pythonExamples/Aug2015DataSourceTutorial/RunExe.py | Python | apache-2.0 | 7,491 | [
"Brian"
] | dcc97476bece4a8352645ced9d107210392cfa7903b9bc90085a181bf5c29dfe |
# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this s... | sequana/sequana | sequana/isoseq.py | Python | bsd-3-clause | 22,371 | [
"pysam"
] | d1639f1b254bc60b1f75d6a5e95cc819dc895fa628d1641358b9d0f0792c4052 |
"""Module to read data from vasprun.xml.
Sometimes the OUTCAR file has formatting overflow errors. This module
provides an alternative approach to get the data.
"""
from jasp import *
import xml
from xml.etree import ElementTree
old_read_forces = Vasp.read_forces
def read_forces(self, atoms=None, all=False):
"... | jboes/jasp | jasp/read_vasprun.py | Python | gpl-2.0 | 3,770 | [
"VASP"
] | ffa7278cd1b6310b591f684cb8d45f582596b57e731132e725bebf72ff65f11e |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import socket
import time
import copy
import sys
import re
import os
import warnings
from astropy.io import ascii
from six.moves.urllib_error import URLError
from collections import OrderedDict
from ..query import BaseQuery
from ..utils import commons, pr... | imbasimba/astroquery | astroquery/besancon/core.py | Python | bsd-3-clause | 15,470 | [
"Galaxy"
] | 6c15a6f379983ebe252cba1a807b598050c789b42b14493dd6285c79dcb27b9e |
"""
K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
====================================================================
Provides routines for k-means clustering, generating code books
from k-means models and quantizing vectors by comparing them with
centroids in a code book.
.. autosummary::
... | pizzathief/scipy | scipy/cluster/vq.py | Python | bsd-3-clause | 27,088 | [
"Gaussian"
] | 90debdcae3c61a4da4863dfd85094a8510edc817b150ad43ccf9793dea7a4bb0 |
import os
from collections import defaultdict
import numpy as np
try:
import matplotlib
if not os.environ.get('DISPLAY'):
# Use non-interactive Agg backend
matplotlib.use('Agg')
import matplotlib.pyplot as plt
except ImportError:
import platform
if platform.python_implementation() =... | terrycojones/dark-matter | dark/mutations.py | Python | mit | 16,447 | [
"BLAST"
] | 8e259dcb2163e960e91cffddfaee9e188b46a589ffdc5d71f97b1ad9a9379b74 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core.spectrum import Spectrum
"""
This module defines an excitation spectrum class.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "1.0"
... | montoyjh/pymatgen | pymatgen/analysis/excitation.py | Python | mit | 845 | [
"pymatgen"
] | a1a97ec60f22e5f5279df1ce63488572e3cd596ef83072b85630a16fd0456037 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
from pymatgen.core.structure import Molecule
from monty.io import zopen
"""
Module implementing an XYZ file object class.
"""
__author__ = "Shyue P... | matk86/pymatgen | pymatgen/io/xyz.py | Python | mit | 3,960 | [
"pymatgen"
] | 4c3a9182f20135d1071788461bceada4ce5b1d1880a26f19b7a75e8fac84e88e |
# ==================================================================================================
#
# Copyright (c) 2016, Chen Kian Wee (chenkianwee@gmail.com)
#
# This file is part of py4design
#
# py4design is free software: you can redistribute it and/or modify
# it under the terms of the GNU General ... | chenkianwee/envuo | py4design/buildingformeval.py | Python | gpl-3.0 | 63,177 | [
"EPW"
] | bcbf103c1159313a2859fc747e4de96508e19b405f15bbba6ceb5a6997f70d87 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/alignment/_alignment.py | Python | bsd-3-clause | 45,400 | [
"scikit-bio"
] | f6c2addb86f20c99158c356a2a789769a2ffcd2278c721609e30f779fd15dfdb |
import ase.db
c = ase.db.connect('results.db')
failed = ', '.join(d.name for d in c.select(ok=0))
assert not failed, 'Failed to converge: ' + failed
| robwarm/gpaw-symm | gpaw/test/big/scf/trouble/analyse.py | Python | gpl-3.0 | 150 | [
"ASE"
] | e6874adaa2ebaf047de233901b98d5fac4f36c69a452697a28f4325d9e54f559 |
"""
Routines for computing integrals.
"""
import numpy as np
import nomad.core.timings as timings
import nomad.integrals.centroid as centroid
class Integral:
"""Class constructor for the Bundle object."""
def __init__(self, kecoef, ansatz, numerical_eval):
self.kecoef = kecoef
self.ansatz ... | mschuurman/FMSpy | nomad/integrals/integral.py | Python | lgpl-3.0 | 8,573 | [
"DIRAC"
] | 5fd0674ac67f42366fa3de163730a213c103e3ab8720146efae56f15b9f6d56d |
'''
Groups.tests.models
'''
from MyPidge.Users.models import User, Membership
from MyPidge.Groups.models import GroupCategory, GroupTag, Group, Service, GroupService, ServiceProperty, GroupServiceProperty, MembershipInvitation
from MyPidge.Groups.forms import GroupForm
from django.core import mail
from django.test imp... | fergusrossferrier/mypidge.com | MyPidge/Groups/tests/models.py | Python | agpl-3.0 | 8,259 | [
"exciting"
] | 67c6e6b3e662aa42f69195e8a4202f76c70848d99f17dcb37fa4baaaed0c12ea |
import unittest
from builtins import str
from singa import tensor
from singa import singa_wrap as singa
from singa import device
from singa import autograd
import numpy as np
autograd.training = True
CTensor = singa.Tensor
gpu_dev = device.create_cuda_gpu()
cpu_dev = device.get_default_device()
dy = CTensor([2, 1... | kaiping/incubator-singa | test/python/test_operation.py | Python | apache-2.0 | 10,523 | [
"Gaussian"
] | b51d8577d9d653ea6ff3fa646504d76a8e08dcbe333def136d38a5f45c73fd4f |
#!/usr/bin/python
""" Classes and functions for fitting tensors """
from __future__ import division, print_function, absolute_import
import warnings
import functools
import numpy as np
import scipy.optimize as opt
from dipy.utils.six.moves import range
from dipy.utils.arrfuncs import pinv, eigh
from dipy.data impo... | JohnGriffiths/dipy | dipy/reconst/dti.py | Python | bsd-3-clause | 59,994 | [
"Gaussian"
] | 178d4e7fbbab7eedcb3c2514a91c7b71aa55b290f467823876e39228af9b4d2c |
import numpy as np
WHITE = -1
BLACK = +1
EMPTY = 0
class GameState(object):
"""State of a game of Go and some basic functions to interact with it
"""
def __init__(self, size=19):
self.board = np.zeros((size, size))
self.board.fill(EMPTY)
self.size = size
self.turns_played = 0
self.current_player = BLACK... | ttrine/AlphaGo | AlphaGo/go.py | Python | mit | 7,356 | [
"VisIt"
] | c334b29669561fd0eda46bc28d61811439e935b721b67e3dd998b2516182a25c |
import ast
from sys import _getframe
from lazy.transformer import LazyTransformer
from lazy._thunk import thunk
def run_lazy(src, name='<string>', globals_=None, locals_=None):
transformer = LazyTransformer()
code_obj = compile(transformer.visit(ast.parse(src)), name, 'exec')
globals_ = _getframe().f_ba... | wrobell/lazy_python | lazy/runtime.py | Python | gpl-2.0 | 823 | [
"VisIt"
] | a187afc7f5ffe2cf58555fcdf57865821c94f770f8492c750d4802c1fce70245 |
"""Test automatically write out of restart files"""
import os
import sys
import time
from gpaw import GPAW
from ase import Atom, Atoms
from gpaw.test import equal
from ase.parallel import rank, barrier, size
endings = ['gpw']
try:
import Scientific.IO.NetCDFXXXX
endings.append('nc')
except ImportError:
pa... | qsnake/gpaw | gpaw/test/wfs_io.py | Python | gpl-3.0 | 1,470 | [
"ASE",
"GPAW"
] | 2b3aaa18724b16bf8e5031f34873cc2d8908252c93447358589cb2af308c620d |
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not... | nudles/incubator-singa | examples/mlp/native.py | Python | apache-2.0 | 2,988 | [
"Gaussian"
] | f91a6c287b1c425c36d92609f32c358d4c37384dee727615df796bcc6d46b0e1 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/learn/pytorch/pytorch_ray_estimator.py | Python | apache-2.0 | 25,069 | [
"ORCA"
] | ca3814c72c8b780e490116e0e1a04151219a9f128d34a566376f2c1ed8fcc9ad |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/one2manyeditor.py | Python | gpl-2.0 | 6,903 | [
"VisIt"
] | f1c957dfb64ddebff1b651c6a5267e4ce90182b1b6131c22675a2bfabda21d38 |
"""
O(1) information test for equality of two bitstrings from Interactive Information Complexity [Braverman '11].
"""
from random import randint
import unittest
import argparse
import numpy as np
def is_invertible_F2(a):
"""
Determine invertibility by Gaussian elimination.
Via http://stackove... | crm416/equality | equality.py | Python | mit | 2,858 | [
"Gaussian"
] | 10a0be740b57df88ec9bd6a52e19f0f2c17572309cb5fb53f49300d3b7339b91 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | scripts/AbinsModules/LoadCRYSTAL.py | Python | gpl-3.0 | 24,552 | [
"CRYSTAL"
] | 860a7da34baacefdbf8315f971dad98ae3dd9dd9bd8b3a4c32898d595f36e15b |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Parsers for Qchem output files.
"""
import copy
import logging
import math
import os
import re
import warnings
from typing import Union, List, Dict, Any
import networkx as nx
import numpy as np
import pandas as pd
from m... | vorwerkc/pymatgen | pymatgen/io/qchem/outputs.py | Python | mit | 76,741 | [
"Q-Chem",
"pymatgen"
] | 5ed976152d67aca6aba9acc1a79eb837fa5f32dc008171244234f3dec766c552 |
import operator
import threading
import functools
import itertools
import contextlib
import collections
import numpy as np
from ..autoray import (
get_lib_fn,
infer_backend,
get_dtype_name,
register_function,
astype,
)
_EMPTY_DICT = {}
class LazyArray:
"""A lazy array representing a shaped... | jcmgray/autoray | autoray/lazy/core.py | Python | apache-2.0 | 35,799 | [
"VisIt"
] | aa9c11ec95f423f8dc6c604b6a89d0c8fbe9079042615c5a227751501d7daec7 |
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of source c... | arokem/PyEMMA | pyemma/coordinates/tests/test_cluster_samples.py | Python | bsd-2-clause | 3,273 | [
"MDTraj"
] | 62a7ec5e2284c9590e4b4f8ec6e9a7a13e0b8caa30d6983092ec090e881c4ff6 |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import unicode_literals
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from bok_choy.promise import EmptyPromise
from ...fixtures.course import XBlockFixtureDesc
from ..helpers import create_user_par... | AkA84/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 19,781 | [
"VisIt"
] | f4749b08c28d033d7f33155f6dffa4b2715212a4dc3a1ebbd91fc084aa00439e |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements WebWorkerExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +----------+ ... | Hasimir/brython | www/src/Lib/concurrent/futures/webworker.py | Python | bsd-3-clause | 17,561 | [
"Brian"
] | e7bd68e01f46f505141c8d2ef395c72e451f72773c7a227c6ecd33a3883bcaaa |
"""
Wrappers for calls to Mayavi2's `mlab` module for plotting
:mod:`fatiando.mesher` objects and automating common tasks.
.. warning::
This module will be **removed** in v0.7.
**Objects**
* :func:`~fatiando.vis.myv.prisms`
* :func:`~fatiando.vis.myv.polyprisms`
* :func:`~fatiando.vis.myv.points`
* :func:`~fat... | cmeessen/fatiando | fatiando/vis/myv.py | Python | bsd-3-clause | 33,222 | [
"Mayavi",
"VTK"
] | 981841477d53a717491f3046c019760c08a6cc05dfd4ce7f706d35df33503863 |
"""Support for package tracking sensors from 17track.net."""
from datetime import timedelta
import logging
from py17track import Client as SeventeenTrackClient
from py17track.errors import SeventeenTrackError
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA
from homeassistant.const... | tchellomello/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | apache-2.0 | 10,851 | [
"VisIt"
] | bb523546a80b021cf96c28cb2ac20e88452ac7ed3eda961ad73b55f63c80877c |
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