text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
#!/usr/bin/env python
#
# Copyright (c) 2010 Brian E. Granger
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, o... | takluyver/pyzmq | setup.py | Python | lgpl-3.0 | 7,400 | [
"Brian"
] | c9a98280116f95dd3fcc334e420d0de9aba61c1dc001af838a9678f605383859 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Classes for reading/manipulating/writing VASP input files. All major VASP input
files.
"""
__author__ = "Shyue Ping Ong, Geoffroy Hautier, Rickard Armiento, " + \
"Vincent L Chevrier, Stephen Dacek"
__copyright__ = "Copyright 2011, Th... | rousseab/pymatgen | pymatgen/io/vasp/inputs.py | Python | mit | 64,220 | [
"VASP",
"pymatgen"
] | 91059153e84a4f9828799140fd53dc447b4d5803c56a640fb53106d1e56da315 |
"""Setup script for Bokeh."""
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2014, Continuum Analytics, Inc. All rights reserved.
#
# Powered by the Bokeh Development Team.
#
# The full license is in the file LICENCE.txt, distributed with this software.
#---------... | abele/bokeh | setup.py | Python | bsd-3-clause | 19,338 | [
"GULP"
] | 3bb8bcceed7beafba37de86245ca8404be40def30ee7c3977c2b76de4db099f0 |
import ast
import os
import sys
import json
import logging
import pprint
import pytest
import mock
from requests_oauthlib import OAuth2Session
from mock import Mock
from bioblend import galaxy
from bioblend.galaxy.objects import (GalaxyInstance, Library, Folder, client)
from bioblend.galaxy.objects.wrappers import Lib... | phac-nml/irida-galaxy-importer | irida_import/tests/unit/test_irida_import.py | Python | apache-2.0 | 16,794 | [
"Galaxy"
] | cf851f436dbfa07479edd3f5b68d3ac75f72f1c72d50b3870a8be88aa226ed90 |
# Copyright 2003 by Bartek Wilczynski. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parsing AlignACE files: AlignAceParser
"""
from Bio.Motif import Motif
from Bio.Alphab... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/AlignAce.py | Python | gpl-2.0 | 1,715 | [
"Biopython"
] | 0ddf560fbb64a706e96bee7bb20333f6c08293fa1a16fc085fe7b60fed29677d |
from django.conf.urls import patterns, include, url
# Uncomment the next two lines to enable the admin:
from django.contrib import admin
admin.autodiscover()
# these have to be in the right order, specific to general
urlpatterns = patterns('',
url(r'^$', 'vasp.views.index'),
url(r'^(?P<path>.*)/fi... | jboes/jasp | jasp/www/vasp_django/vasp_django/urls.py | Python | gpl-2.0 | 915 | [
"VASP"
] | 7f477259c5d8de72cf2a2cd9ee93137dc519f3cf46f84d52afc15aa667c567a5 |
#!/usr/bin/env python
###############################################################################
#
# __init__.py
#
# Copyright (C) 2011 Christopher Davoren
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to de... | PapenfussLab/MHC-clogs | lib/massivetools/__init__.py | Python | artistic-2.0 | 3,353 | [
"BWA"
] | 5e73c478f94e53ebf6cb47e4110d48690bb734fe0eb5cb45ac4607068a103d9f |
#! /usr/bin/env python
import numpy as np
import os, sys
import cPickle as pickle
from shutil import copyfile
import sim, pickleTraj
import makeProtein as mp
LastNFrames = 20000
# user input
# Only for ala peptides
NRes = int(sys.argv[1])
# ala15 peptides are kept in a different place
if NRes == 15:
TrajDir = ... | tanmoy7989/idp | data/conv_zamtrj.py | Python | gpl-3.0 | 3,280 | [
"Amber",
"LAMMPS"
] | 55644129fcd0ac215cd71e74529e780404fbab63c380f350c3e5aab73fea33ac |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup
with open('README.rst') as readme_file:
readme = readme_file.read()
with open('HISTORY.rst') as history_file:
history = history_file.read()
requirements = [
'Click>=6.0',
'future',
'pandas>=0.19.1',
'Biopython>=1.6'
]... | tbrittoborges/protein_motif_encoder | setup.py | Python | mit | 1,769 | [
"Biopython"
] | 7ceaac91000c00f8679bf17317c1da564b60405714681f5c967350b351edc7ff |
import sys
import taxon
## run this as a script
if __name__ == "__main__":
ids=['1211997']
if len(sys.argv) == 1:
print("Supply your own id for the tree. Here is an example")
print("""
1211997 name: Cimicodes sp. BOLD:AAW5588 blast name: Cimicodes sp. BOLD:AAW5588 rank: speci... | linsalrob/EdwardsLab | ncbi/taxonomy.py | Python | mit | 3,870 | [
"BLAST"
] | bfaffbaed88f8da3bfb7a46bf8d356dbd73b472025e254b7c7881af11556ed87 |
#!/usr/bin/python
"""
Copyright 2017 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/delCreatureResource.py | Python | gpl-3.0 | 3,459 | [
"Galaxy"
] | f565dd218f16c1cb43d08857110749e6bfe6364fc9b7603333a0c271ab050c78 |
#!/usr/bin/env python3
import netCDF4 as nc
import sys
import argparse
import numpy as np
from utilities import partialMatchFromList
debug = True
# =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
def asciiEncode(uList, uStr):
n = len(uList)
if(n > 0):
uList = list(uList) # This might be a tuple coming... | mjsauvinen/P4UL | pyLib/netcdfTools.py | Python | mit | 12,076 | [
"NetCDF"
] | e7be4fa6c71897bd688cb49ac45265797cab950055b9c82fa27082991cf1b9e0 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_null.py | Python | gpl-2.0 | 1,399 | [
"MDAnalysis"
] | bfb04f155dc8792f77b260e4fbedc529bc0b08827441a746a51f05ac79de4745 |
# -*- coding: utf-8 -*-
"""
Jinja2
~~~~~~
Jinja2 is a template engine written in pure Python. It provides a
`Django`_ inspired non-XML syntax but supports inline expressions and
an optional `sandboxed`_ environment.
Nutshell
--------
Here a small example of a Jinja template::
{% extends 'base.html' %}
{% b... | brstew/MBED-BUILD | Jinja2-2.8/setup.py | Python | apache-2.0 | 2,392 | [
"VisIt"
] | 320e35c10b7050540afe96b5c7495de1a22bc622b1eff2b9b67376e07eb9b4a5 |
# coding: utf-8
"""
django informer commands
"""
from django.conf import settings
from django.core.management.base import BaseCommand
from informer.checker.base import BaseInformer, InformerException
class Command(BaseCommand):
help = 'Check all Informers.'
def add_arguments(self, parser):
parser.... | rodrigobraga/informer | informer/management/commands/checkinformer.py | Python | mit | 3,004 | [
"VisIt"
] | 2660e0138cbfe5d632ecfc1d6d9bff46e2678a85974b4d27cc22a7272ee1c1d2 |
class Node(object):
#a binary search tree has a left node (smaller values) and a right node (greater values)
def __init__(self, data):
self.data = data;
self.left_child = None;
self.right_child = None;
class BinarySearchTree(object):
def __init__(self):
self.root = None;
#inserting ite... | prk327/CoAca | Algo - DataStru/bst.py | Python | gpl-3.0 | 4,916 | [
"VisIt"
] | a224e5d85aa41c04b2c1a12c4fbebf679bb02f0e266b30fe656c277bc2ad43cb |
#! A simple Psi 4 input script to compute a SCF reference using Psi4's libJK
import time
import numpy as np
import psi4
psi4.set_output_file("output.dat", False)
# Benzene
mol = psi4.geometry("""
0 1
O
H 1 1.1
H 1 1.1 2 104
symmetry c1
""")
psi4.set_options({"basis": "aug-cc-pVDZ",
"scf_ty... | amjames/psi4 | tests/psi4numpy/rhf/input.py | Python | lgpl-3.0 | 3,453 | [
"Psi4"
] | efcee6c50c86c74645d32ce9776b7f2a891878d23ddf86dcb311d2cc8aa00979 |
# This file is part of Sequana software
#
# Copyright (c) 2016-2021 - Sequana Development Team
#
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.r... | sequana/sequana | sequana/kraken/analysis.py | Python | bsd-3-clause | 48,466 | [
"ASE"
] | 4be29d7915457cf0dc0502b9b894fc0367f8eb844d300321c5e0baf3717e792a |
import sys
import os
from os.path import join
from SpectraStackingSDSSOnly import *
import glob
hdus_eb67 = fits.open("/uufs/chpc.utah.edu/common/home/u0936736/stack_eBOSSELG/elg270_eboss67summaryTable_stack_comparison.fits")
hdus_eb17 = fits.open("/uufs/chpc.utah.edu/common/home/u0936736/stack_eBOSSELG/elg270_eboss... | JohanComparat/pySU | galaxy/bin_stack/inDev/stack_spectra_SDSS.py | Python | cc0-1.0 | 7,789 | [
"Galaxy"
] | 0d93a2c8d5df1022e9edadb869352803915ddc0d99ee353cc2796132ad305bc0 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import with_statement
import collections
import errno
import filecmp
import os.path
import re
import tempfile
import sys
# A minimal memoizing d... | fceller/arangodb | 3rdParty/V8/v7.1.302.28/tools/gyp/pylib/gyp/common.py | Python | apache-2.0 | 20,746 | [
"VisIt"
] | 33d86a77faa9f22a83deb066c20e96b28c723bf9cf80d0c64dae44dc2d9fed6c |
# -*- coding: utf-8 -*-
#############################################################################
#
# VoiceID, Copyright (C) 2011-2012, Sardegna Ricerche.
# Email: labcontdigit@sardegnaricerche.it, michela.fancello@crs4.it,
# mauro.mereu@crs4.it
# Web: http://code.google.com/p/voiceid
# Authors: Michela Fanc... | ais-recognition/recognizer | voiceid/db.py | Python | mit | 21,273 | [
"Gaussian"
] | 2c63ef1aa44e25a5c9a106c9a5a5dda74d5a647c01857e079615f1dc233cb51f |
#!/usr/bin/env python
# File created on 17 Feb 2010
from __future__ import division
import re
import sys
from setuptools import setup
from stat import S_IEXEC
from os import (chdir, getcwd, listdir, chmod, walk, rename, remove, chmod,
stat, devnull, environ)
from os.path import join, abspath
from subpr... | adamrp/qiime | setup.py | Python | gpl-2.0 | 15,026 | [
"Brian",
"scikit-bio"
] | 60c7c4e82d142d9db65ec295d20cef89e213f2931b52c843e82137fddca8030b |
import numpy as np
from .. import _base
class AnimalsInResearch(_base.DatasetCI2):
def _set_values(self):
self.www = 'http://onlinestatbook.com/2/estimation/difference_means.html'
self.datafile = 'http://onlinestatbook.com/2/case_studies/animal_research.html'
self.YA = np.array([5, 5, 5, 2, 3, 7,... | 0todd0000/spm1d | spm1d/data/uv0d/ci2.py | Python | gpl-3.0 | 680 | [
"VisIt"
] | 7425da51a386754e9f8edc0f792717e95e94eb2ad0df31fa506e6f8375433dbf |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
================================================================================
mingus - Music theory Python package, Instrument module
Copyright (C) 2008-2009, Bart Spaans
This program is free software: you can redistribute it and/or modify
it under the... | spiderbit/canta-ng | mingus/containers/Instrument.py | Python | gpl-3.0 | 7,070 | [
"CRYSTAL"
] | 002a0b9ab92a85b83074c132643971eec8cd5609aaaff8052e0a437e6075eebf |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes and methods related to the Structure Notation Language (SNL)
"""
import datetime
import json
import re
import sys
from collections import namedtuple
from io import StringIO
from monty.json import ... | davidwaroquiers/pymatgen | pymatgen/util/provenance.py | Python | mit | 14,145 | [
"pymatgen"
] | aef04794fed542e65dbb5c1934509251656a4508544a02a2258b72bf512d849e |
"""This module implements functions for manipulating the annotated image,
in order to make annotation more efficient."""
from __future__ import print_function, unicode_literals, division
from builtins import zip
from builtins import range
from builtins import object
import logging
import numpy
from skimage.filters im... | hajicj/MUSCIMarker | MUSCIMarker/image_processing.py | Python | apache-2.0 | 11,087 | [
"Gaussian"
] | dff8ce876f8bc35ede25e2f331483341621a8210e7c51829951e54d2a5239410 |
# -*- coding: utf-8 -*-
#
# test_parrot_neuron.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 Lice... | terhorstd/nest-simulator | pynest/nest/tests/test_parrot_neuron.py | Python | gpl-2.0 | 10,031 | [
"NEURON"
] | 20e3a834e35c25c4a8b786de6fccf253bc512d9f77e446112e178405a9d7ceb3 |
# -*- coding: utf-8 -*-
# --------------------------------------------------
# Plot temperature at 50 m, using the SGrid class
#
# Bjørn Ådlandsvik, <bjorn@imr.no>
# Institute of Marine Research
# Created: 2010-01-20
# --------------------------------------------------
# ---------
# Imports
# ---------
import numpy ... | chiluf/roppy | examples/plot_temp50.py | Python | mit | 1,736 | [
"NetCDF"
] | e3083e771b6f96e4292b5acc0f71dfd9fce304720a8a921684deb3494bf390f6 |
import sys
import re
import copy
import os
import shutil
import stat
import socket
import json
from contextlib import contextmanager
from pycparser import c_parser, c_ast, parse_file
#warning to python gurus. Ugly, goal-oriented, fiddly and improvised code.
class LibPS4Util:
@staticmethod
def copytree(src, d... | ps4dev/libps4-generator | generate.py | Python | unlicense | 19,601 | [
"VisIt"
] | 5aa007c5a886b32f93257dde7bd73f8e7eafbcb85ff2be67e8b046af05f40189 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Acehaidrey/incubator-airflow | airflow/providers/microsoft/azure/hooks/data_factory.py | Python | apache-2.0 | 32,292 | [
"ADF"
] | c97c40214392d34c29888c96ccafa5a62f36829ef2b1f621502a3c201a266759 |
#!/usr/bin/env python
#
# Copyright (C) 2014 Brian Caswell <bmc@lungetech.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights... | f0rki/cb-multios | tools/generate-polls/examples/dfars/dfars.py | Python | mit | 16,802 | [
"Brian"
] | 9bae39ceac57bf728897da246bc4d8f4fe6f4aaedc4ee6bc196c628afea61af6 |
#!/usr/bin/python
"""
BACnet Virtual Link Layer Service
"""
import sys
import struct
from time import time as _time
from .debugging import ModuleLogger, DebugContents, bacpypes_debugging
from .udp import UDPDirector
from .task import OneShotFunction, OneShotTask, RecurringTask
from .comm import Client, Server, bind... | JoelBender/bacpypes | py25/bacpypes/bvllservice.py | Python | mit | 48,799 | [
"ASE"
] | 7c07e6b16edc39179451949c2f2afdc13f12f8d0210e0beb85d47651c93ae029 |
from __future__ import print_function
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.deeplearning import H2ODeepLearningEstimator
from h2o.estimators.gbm import H2OGradientBoostingEstimator
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
from h2o.estima... | mathemage/h2o-3 | h2o-py/tests/testdir_jira/pyunit_pubdev_4702_algo_max_runtime_secs_large.py | Python | apache-2.0 | 9,499 | [
"Gaussian"
] | b458c0a74228651ee54ffcc6a2153d2610e7277e4c8cbecf0fb51e5806ea1625 |
# Name: vrt.py
# Purpose: Container of VRT classes
# Authors: Asuka Yamakawa, Anton Korosov, Knut-Frode Dagestad,
# Morten W. Hansen, Alexander Myasoyedov,
# Dmitry Petrenko, Evgeny Morozov
# Created: 29.06.2011
# Copyright: (c) NERSC 2011 - 2018
# Licence:
# This file is par... | nansencenter/nansat | nansat/vrt.py | Python | gpl-3.0 | 70,809 | [
"NetCDF"
] | 179b8e70a4c4aea2c8d44f2ed309ff81426710d7f01ce0bad64d46564b3fb8db |
########################################################################
# File : FC_Scaling_test
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Test suite for a generic File Catalog scalability tests
"""
from __future__ import print_function
__RCSID_... | fstagni/DIRAC | tests/Performance/DFCPerformance/FIXME_Test_FC_scaling.py | Python | gpl-3.0 | 10,587 | [
"DIRAC"
] | 58a29777b1a5886dffc534ebc8de4aa542dc8a808dbebfc68c07de9b4dc4701b |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.absp... | s6juncheng/Test | setup.py | Python | gpl-3.0 | 3,976 | [
"pysam"
] | a969f3779e36a43ee1269f396e14e68201907b88ec1f23bee0ab18e6f42019be |
from osgeo import gdal
from osgeo import osr
from datetime import datetime
import netCDF4
import os
import sys
import numpy as np
inFolder = sys.argv[1]
# create list of netcdf files
fileList = []
for f in os.listdir(inFolder):
if f.endswith(".nc"):
fileList.append(f)
scale_factor = 1.0
add_offset ... | MACBIO/GIS-Scripts | ConvertNCtoTIF.py | Python | gpl-3.0 | 2,038 | [
"NetCDF"
] | 79ffce0d56cc637ef759c0816af3d833d43e3d39fc73c139a523239e0283b6b7 |
from Menu import Menu
from BootMenuAction import BootMenuAction
from TopMenu import TopMenu
class BootMenu (Menu):
def __init__ (self):
self.actions = []
self.ledManager.oneOn(0,100,0)
self.actions.append(BootMenuAction(">>>MP3/WiFi/VoIP<<<"))
self.actions.append(BootMen... | tbdale/crystalfontz-lcd-ui | python/BootMenu.py | Python | mit | 572 | [
"Brian"
] | 99c41005bd4fa39a1a4ff84cb2000f789d71967ed23359883577e081b367622e |
# Copyright 2008-2014 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | userzimmermann/robotframework-python3 | src/robot/model/filter.py | Python | apache-2.0 | 3,521 | [
"VisIt"
] | cc38ea9a1932866db1d0cc694155f82037a273bbf339bbe15c43f35b8c8c94ed |
"""
A collection of back end subroutines (mostly SQL queries).
In this module we collect together various routines
that don't fit into a more specific collection.
"""
import math
import logging
import itertools
import tkp.db
from tkp.utility.coordinates import eq_to_cart
from tkp.utility.coordinates import alpha_inf... | mkuiack/tkp | tkp/db/general.py | Python | bsd-2-clause | 13,884 | [
"Gaussian"
] | 2ddb6d77c525ed06c4e02ff6451adeebc83699cab05968810e227f3d3b09ab7e |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
import time
import numpy as np
import tables
from scipy import ndimage
from scipy.misc import imsave
import scipy.optimize as opt
from sklearn.cross_decomposition import PLSCanonical
from sklearn... | sealhuang/brainCodingToolbox | braincode/vim2/neomain.py | Python | bsd-3-clause | 42,086 | [
"Gaussian"
] | 2738034a6e9937084ed76b5ba417a66b0a0ac66f68cc7a6510343c043e06c8f2 |
# $HeadURL$
"""
DIRAC.Core.Utilities package
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Utilities.File import makeGuid, checkGuid, getSize, getGlobbedTotalSize, getGlobbedFiles, getCommonPath, getMD5ForFiles
from DIRAC.Core.Utilities.List import uniqueElements, appendUnique, fromChar, randomi... | Andrew-McNab-UK/DIRAC | Core/Utilities/__init__.py | Python | gpl-3.0 | 1,288 | [
"DIRAC"
] | 180d4a19f8f756cf24e0afe7b6d8a76346d566eb9c670f9e37996adefb41eeb8 |
#
# Copyright (C) 2013,2014 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KonradBreitsprecher/espresso | samples/reaction_ensemble.py | Python | gpl-3.0 | 2,741 | [
"ESPResSo"
] | 63f43e48d3e069abbd428669f6376ae5ff1039dc098490d943120a5d29d10c64 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | Chuban/moose | python/MooseDocs/common/__init__.py | Python | lgpl-2.1 | 1,922 | [
"MOOSE"
] | f5bd9c111ba848a7fcca356536d2a70b227e108b9ea288dc4238ac3c2f363246 |
#!/usr/bin/env python
# ViralGenome_Analysis.py
import os, cmath, math, sys, glob, subprocess, re, argparse, shutil, datetime, csv
import numpy as np
from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
import matpl... | ChangLab/FAST-iCLIP | fasticlip/ViralGenome_analysis.py | Python | gpl-2.0 | 9,958 | [
"Bowtie"
] | 7952e7213e6d49f632ff642af8c81efa392cc04f65fd242ecb75000237147913 |
"""Unit tests for PilotLoggerTools
"""
from __future__ import absolute_import, division, print_function
# pylint: disable=protected-access, missing-docstring, invalid-name, line-too-long
import sys
import json
import os
import unittest
import mock
from Pilot.PilotLoggerTools import generateDict, encodeMessage
from P... | DIRACGrid/Pilot | Pilot/tests/Test_PilotLoggerTools.py | Python | gpl-3.0 | 11,872 | [
"DIRAC"
] | 162df862ea8f3e757f008ca0563a0e059cbb3d7d2c20ebcdd6590f1745fb5f9d |
'''
A tool to calculate two proportion Z-test.
The two input files contain gene variants counts
for their corresponding populations.
Author: Khalid Mahmood
Contact: khalid.mahmood@unimelb.edu.au
Copyright: 2015
'''
#!/usr/bin/python
#from annotations import getTabixValCondel
#from annotations import getExAC
from math... | khalidm/ExAC_genes | src/calcProportion.py | Python | mit | 5,998 | [
"pysam"
] | 43a9c46b5ec84a3bfb9290a02961e029e63e06c67bea21dbf341adb79afec5ea |
"""
Javascript tests for the crowdsourcehinter xblock
"""
from __future__ import absolute_import
from textwrap import dedent
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.... | ESOedX/edx-platform | common/test/acceptance/tests/xblock/test_crowdsourcehinter_problem.py | Python | agpl-3.0 | 4,300 | [
"VisIt"
] | b7218495ce2269f5c7ada8c1c9d023e5d2055ba8678fe28676db01faf54a4b94 |
from openzwave.network import ZWaveNode
from openzwave.value import ZWaveValue
from Firefly import logging
from Firefly.components.zwave.device_types.contact_sensor import ZwaveContactSensor
TITLE = 'Ecolink Contact Sensor'
def Setup(firefly, package, **kwargs):
logging.message('Entering %s setup' % TITLE)
sens... | Firefly-Automation/Firefly | Firefly/components/zwave/ecolink/contact_sensor.py | Python | apache-2.0 | 940 | [
"Firefly"
] | 537d8e6cc9142b13ec15bb4ee3aa3c367495491c37680552e532d97d42dca451 |
import re
from subprocess import check_call
from future.moves.subprocess import check_output
def test_hadoop_build(tmpdir):
dest = tmpdir.mkdir('default_configs')
check_call([
'env2config',
'build',
'hadoop',
'2.7.0',
str(dest),
])
subpaths = list(dest.visit()... | dacjames/env2config | tests/test_hadoop.py | Python | mit | 1,060 | [
"VisIt"
] | b51fbb0debb70c2e239d1b58483a2bed05ef589e4285d76450d4ab9d55347624 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | samples/visualization_bonded.py | Python | gpl-3.0 | 2,333 | [
"ESPResSo",
"Mayavi"
] | ffd0f1b7592508ecfc07b7eae055801d5c8afb78938e10f08a2a04c5b4ed27fb |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck ... | marcocaccin/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 45,783 | [
"Gaussian"
] | 9b5c3835bd413f9503942f1370e8a3491cb4492cc77ee73e50cf8351fb54db03 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAnnotationfilter(RPackage):
"""Facilities for Filtering Bioconductor Annotation Resources... | rspavel/spack | var/spack/repos/builtin/packages/r-annotationfilter/package.py | Python | lgpl-2.1 | 1,214 | [
"Bioconductor"
] | 2f23a236acb7e3a993c6ab1acb9fb00225704e303ad4ab0b2c52a40127481d87 |
#!/usr/bin/python2.7
#Author: Eli Draizen
#File: hsp_viz.py
#Standard libraries
import sys
import argparse
from itertools import izip
import collections
import math
#Import other libraries
import prettyplotlib as ppl
import numpy as np
from prettyplotlib import plt
import matplotlib as mpl
#import matplotlib.pyplot ... | edraizen/hsp_tiler | hsp_tiler/hsp_viz.py | Python | bsd-3-clause | 15,049 | [
"BLAST"
] | 2ff31b3efde1a60ef800b9ce519313090c38479adbe304e08e9a482492f1fe6f |
#!/bin/sh
chmod 644 LICENSE
chmod 644 README.md
chmod 644 firefly.ico
chmod 644 .gitignore
chmod 644 *.py
chmod 644 *.css
chmod 644 local_settings.default
chmod 755 firefly.py
chmod 755 firefly.desktop
chmod 755 commit.sh
chmod 755 images
chmod 644 images/*.*
chmod 755 nx
chmod 644 nx/*.py
chmod 755 nx/common
chmo... | opennx/nx.client | fix_permissions.py | Python | gpl-3.0 | 341 | [
"Firefly"
] | 2328bf6ccdec50131effeda771b5e85eb15257daece8cae685dfd04d1e6fb370 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Input Generator and Parser
###############################
"""
from .editor import Editor
_template = """\
{seward}
{calc}
{postcalc}
"""
_seward = """\
&SEWARD &END
Title
... | avmarchenko/exatomic | exatomic/molcas/inputs.py | Python | apache-2.0 | 6,379 | [
"MOLCAS"
] | c0ad49a98feb708b2f47c8a61661b9c57e8b8ab1e3a99bfacf9715f2efcee194 |
import MPImfp
import MPLn23d
import cv2
import sys
import random
import numpy as np
import json
import math as m
from PyQt5 import QtCore, QtGui, QtWidgets
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
"""
Image Scene
"""
class ... | ksugio/MPImage | MPImage.py | Python | mit | 94,071 | [
"Gaussian"
] | 11c77a599f18b46259c0334a926c3db09efaa36bf23ff6e07019219a729d3f0f |
__all__ = ["KNN", "Kernel", "DistanceBand"]
__author__ = "Sergio J. Rey <srey@asu.edu>, Levi John Wolf <levi.john.wolf@gmail.com>"
from ..cg.kdtree import KDTree
from .weights import W, WSP
from .util import isKDTree, get_ids, get_points_array_from_shapefile,\
get_points_array, WSP2W
import copy
fro... | lixun910/pysal | pysal/lib/weights/distance.py | Python | bsd-3-clause | 30,382 | [
"COLUMBUS",
"Gaussian"
] | 0496c7532677c4183fd6178d5b0f05e55052a26dd5db54fd6a50092cc01faae4 |
# Copyright (c) 2012 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 ... | yanheven/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 56,480 | [
"exciting"
] | cdc7e41eac6f4fa97f097c2817190f5ef7092b0adf95a9fe21b61c2f3d1094de |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import matp... | nuclear-wizard/moose | modules/level_set/examples/rotating_circle/area.py | Python | lgpl-2.1 | 1,400 | [
"MOOSE"
] | 3f2dbfb0eab7e71c42792e36b6b898e448b9aaf938f86c07b0cee0b655f8701a |
#!/usr/bin/env python3
import argparse
import os
import os.path
from pathlib import Path
import semver
import subprocess
# Compatible with Python 3.4 due to travis using trusty as default.
def version_string(path=None, *, valid_semver=False):
version = None
try:
tag = subprocess.check_output('git desc... | adafruit/micropython | tools/preprocess_frozen_modules.py | Python | mit | 3,179 | [
"VisIt"
] | f6613ab5685d6eb7cd07cb4823d6f64c0160f98f5f7ce48ccc4fcedc5e298a06 |
#!/usr/bin/env python
# NOTE: multiprocessing import required for issues with nose tests.
# See: http://bugs.python.org/issue15881#msg170215
import multiprocessing
from setuptools import setup
setup(
name='optmage',
version='0.9',
author='Church Lab',
author_email='gleb@mit.edu',
maintainer='Gleb... | churchlab/optmage | setup.py | Python | mit | 598 | [
"Biopython"
] | b800a279290cd89ecb0d3339a241a0d1601c4ef50f948117817f5ace22c7a1e6 |
import numpy as np
from pyvisfile.vtk import (
UnstructuredGrid, DataArray,
AppendedDataXMLGenerator,
VTK_VERTEX, VF_LIST_OF_VECTORS, VF_LIST_OF_COMPONENTS)
from pyvisfile.vtk import write_structured_grid
def test_vtk_unstructured_points():
n = 5000
points = np.random.randn(n, 3)
data = [
... | inducer/pyvisfile | test/test_vtk.py | Python | mit | 1,867 | [
"VTK"
] | 6ed44903f6b9371f2ac16e4e392f8e7a0edcce8bcfbb6e48b343d7f8e5113b57 |
# Copyright (c) 2006-2011, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014-2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 BioGeek <jeroen.vangoey@gmail.com>
# Copyright (c) 2014 Google, Inc.
# Copyright (c) 2014 Eevee (Alex Munroe) <amunroe@yelp.com>
# Copyright (c) 2015... | PyCQA/astroid | astroid/manager.py | Python | lgpl-2.1 | 14,861 | [
"VisIt"
] | ae480e284841c88fa59d8623760752b0251e9b4fb88826011672bdaff5724c59 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | pdiazv/makaw | config/urls.py | Python | bsd-3-clause | 1,469 | [
"VisIt"
] | 85ecadf958ecad5a62123660b6d10a6c831ff0b3596b5901fa17c25279685ce5 |
#!/usr/bin/env python
# encoding: utf-8
# The MIT License (MIT)
# Copyright (c) 2014-2016 CNRS
# 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 limita... | pyannote/pyannote-algorithms | pyannote/algorithms/segmentation/hmm.py | Python | mit | 21,952 | [
"Gaussian"
] | c694e08755948b81900f6277d57a848cd1e3619a7ee949b9923ea7a179a3700c |
#!/usr/bin/env python
'''
Anh Nguyen <anh.ng8@gmail.com>
2016
'''
import os, sys
os.environ['GLOG_minloglevel'] = '2' # suprress Caffe verbose prints
import settings
sys.path.insert(0, settings.caffe_root)
import caffe
import numpy as np
from numpy.linalg import norm
import scipy.misc, scipy.io
import argparse
im... | philkuz/ppgn | sampling_class.py | Python | mit | 11,157 | [
"NEURON"
] | 913e37c3849ffd2d4409532aeb3a9f0a013a8372dec847b72014872ad3ec3923 |
# File: setup.py
# -*- coding: utf-8 -*-
# Import modules
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, 'README.rst'), encodin... | jkglasbrenner/sshcustodian | setup.py | Python | mit | 1,348 | [
"VASP"
] | 28cb6461a896231c922e054dae900a891f254be6f0518174134d1a6f9a5f36ab |
"""
**DEPRECATED**
A print function that pretty prints sympy Basic objects.
:moduleauthor: Brian Granger
Usage
=====
Once the extension is loaded, Sympy Basic objects are automatically
pretty-printed.
As of SymPy 0.7.2, maintenance of this extension has moved to SymPy under
sympy.interactive.ipythonprinting, any m... | sserrot/champion_relationships | venv/Lib/site-packages/IPython/extensions/sympyprinting.py | Python | mit | 1,075 | [
"Brian"
] | 3203842719b5fddab5b3e1201e6c09aba8797283f1aeba392a054e3e71f62471 |
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
plt.rcParams['image.cmap'] = 'viridis'
import numpy as np
import tensorflow as tf
from backend.networks import Model
from backend.weight_initializer import weight_initializer
#import backend.visualizations as V
from backend.simulation_tools impor... | davidbrandfonbrener/Project-Sisyphus | tasks/memory_tasks.py | Python | mit | 28,079 | [
"Gaussian",
"NEURON"
] | 429a6de53e4940e1d681acfa1329a05cc45ad18cfa95f501959497e5c28dbfe5 |
from distutils.core import setup
setup(
name='RainMaker',
version='0.1.0',
author='Grant R. Tremblay',
author_email='grant.tremblay@yale.edu',
packages=['rainmaker', 'towelstuff.test'],
scripts=['bin/stowe-towels.py','bin/wash-towels.py'],
url='https://github.com/granttremblay/RainMaker',
... | granttremblay/RainMaker | setup.py | Python | mit | 542 | [
"Galaxy"
] | bfdaf6c1bc1680a37c02bf6dbfc56994c0e88f228cf9e80e59ba000ec1c04143 |
#!/usr/bin/env python3
# Copyright (C) 2011-2012, 2014, 2016, 2017 The PISM Authors
# script to generate figure: results from SeaRISE experiments
# usage: if UAFX_G_D3_C?_??.nc are result NetCDF files then do
# $ slr_show.py -m UAFX
# try different netCDF modules
try:
from netCDF4 import Dataset as CDF
except:
... | pism/pism | examples/std-greenland/slr_show.py | Python | gpl-3.0 | 3,943 | [
"NetCDF"
] | 7b68052ba88c1313ad7287ebfd8104a60258265abe3e67ef0f62e792a9e33cc5 |
"""Contains code for a virtual hardware platform. At this point this is more
for testing before you have a P-ROC or FAST board installed. Eventually this
can be used to allow the MPF to drive PinMAME and Virtual Pinball machines.
This is similar to the P-ROC's 'FakePinPROC' mode of operation, though unlike
that it doe... | qcapen/mpf | mpf/platform/virtual.py | Python | mit | 7,687 | [
"Brian"
] | 7a2820f874547d86b8b19488816552bbdc5aa25e629ecf70190e9709677c5b66 |
""" An utility to load modules and objects in DIRAC and extensions, being sure that the extensions are considered
"""
__RCSID__ = "$Id$"
import re
import imp
import pkgutil
import collections
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import List, DIRACSingleton
from DIRAC.ConfigurationSystem.... | hgiemza/DIRAC | Core/Utilities/ObjectLoader.py | Python | gpl-3.0 | 7,789 | [
"DIRAC"
] | 0107afafb9b040e98982b93e9f8e733ceaf162a5d947c576ff9bacf4fed8bca5 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'cancelar' irá indicar que a entrada de log de ativo não ocorreu",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a bou... | devinbalkind/eden | languages/pt-br.py | Python | mit | 271,535 | [
"VisIt"
] | d08b550389f59b7527c1568078a5ef75f00cde596cf6938a12d65b68d485cfff |
### AUTHOR: Evan H. Baugh
### Affiliation: New York University
import wx
import wx.grid
import wx.lib.scrolledpanel
import os
import os.path
import time
import platform
import multiprocessing
import Bio.PDB
import webbrowser
import datetime
from threading import Thread
from tools import *
from io_tools import *
class... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/biotools.py | Python | gpl-2.0 | 36,895 | [
"Biopython",
"PyMOL"
] | 5ae6a2fb0b5724fdcdcde860f0e874a6148a747b39443279e9ed18aebdfbafb1 |
#!/usr/bin/env python
# Copyright (C) 2011 Tianyang Li
# tmy1018@gmail.com
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | tianyang-li/meta-transcriptome | single/simple_est.py | Python | gpl-3.0 | 881 | [
"HTSeq"
] | afc480c2afab4e8d4a6d1dabf61f89010c58ff77aa199161a11419de0834f782 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import os
import re
import json
import datetime
from copy import deepcopy
from monty.json import MontyDecoder
from pymatgen.core.structure import Structure
from pymatg... | xhqu1981/pymatgen | pymatgen/alchemy/materials.py | Python | mit | 14,267 | [
"VASP",
"pymatgen"
] | f770ac1e166bde2af260405a0c1818e4335f201966a03d293d1a3a35ce64c73b |
# Functions for instrumental resolution corrections and area of illumination
# these are to be included in the Models class and Refl class
# Note that these function assumes a Gaussian spread in both the angular as well
# as in real space
# THis one really needs scipy
from scipy import *
from numpy import *
from scipy... | joshp123/genx | models/lib/instrument.py | Python | gpl-3.0 | 4,676 | [
"Gaussian"
] | ac83ebc55dea3301c993c5ea5461e46e50be0928fb95375424f6af6bfe1d4329 |
#!/usr/bin/python
#
# Copyright (C) 2017 Quantum ESPRESSO group
# This file is distributed under the terms of the
# GNU General Public License. See the file `License'
# in the root directory of the present distribution,
# or http://www.gnu.org/copyleft/gpl.txt .
#
# Written by Lorenzo Paulatto 2017
#
from os.path impor... | dceresoli/ce-espresso | PW/tools/cell2ibrav.py | Python | gpl-2.0 | 7,153 | [
"Quantum ESPRESSO"
] | ce6d362098a918b88ccb8ec60fd350cc6d6dbe23906ed275b7abdb416e9a236d |
# -*- coding: utf-8 -*-
#
# RDKit documentation build configuration file, created by
# sphinx-quickstart on Sun Aug 7 18:51:45 2011.
#
# 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
# autogenerated file.
#
# All c... | bp-kelley/rdkit | Docs/Book/conf.py | Python | bsd-3-clause | 7,500 | [
"RDKit"
] | 00a46a4d85d364e9d88c8d08e9779d85e273f109e84dce17936f7311edb6ceeb |
"""to_graphviz.py:
Convert model to graphviz
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__ema... | dilawar/moose-chemical | utils/to_graphviz.py | Python | gpl-2.0 | 1,995 | [
"MOOSE"
] | ad930190ec08c301a9a89e9632ddfcc3331343f084d023ff39a8db3ebebc333f |
#
# Author: Henrique Pereira Coutada Miranda
# Tests for the yambopy library
# scheduler
#
import unittest
import sys
import os
import argparse
import subprocess
import filecmp
import json
from schedulerpy import *
from qepy import *
from textwrap import dedent
#name of the configuration file to be created when runnin... | henriquemiranda/yambopy | tests/test_scheduler.py | Python | bsd-3-clause | 6,455 | [
"ABINIT",
"ESPResSo"
] | 669131fa688744a6dcfc7eb5a40c4c81a53cd5e6f1fcf257c1d52f4b3cae4354 |
""" GOCDBClient module is a client for the GOC DB, looking for Downtimes.
"""
__RCSID__ = "$Id$"
import urllib2
import time
import socket
from datetime import datetime, timedelta
from xml.dom import minidom
from DIRAC import S_OK, S_ERROR, gLogger
def _parseSingleElement( element, attributes = None ):
"""
Given... | rajanandakumar/DIRAC | Core/LCG/GOCDBClient.py | Python | gpl-3.0 | 11,314 | [
"DIRAC"
] | 6b7937d7349bfaf4f6e444f869902f2756e39c94d7e54816b6ff533dabb702dd |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/interface_gcp.py | Python | lgpl-3.0 | 11,878 | [
"Psi4"
] | 5ca3a839e4ca3cdd6716349357f7d861d57f58dfc888042a6d616f4cdc615943 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/reporting/inventory.py | Python | gpl-2.0 | 1,539 | [
"VisIt"
] | 4ea2062aa677fc8e01897fe1fda3f3f43c184ce84c2b393c21314fd73e4b02b5 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list ... | LaoZhongGu/kbengine | kbe/src/lib/python/Lib/mimetypes.py | Python | lgpl-3.0 | 20,429 | [
"NetCDF"
] | d11b51ba865d62f9417e8ad2a854a96483904483f4b409dbce5a48595fb5beda |
#!/usr/bin/python
import numpy as np
import os
import sys
import math
import matplotlib
matplotlib.use('Pdf')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.font_manager as fm
## 7-20-15
## Simple code to ... | plazas/wfirst-detectors-vnl | code/bias_nonlinearity_vs_beta_version2_vs_magnitude.py | Python | mit | 27,257 | [
"Gaussian"
] | 0e4ff6dfdd311872ce9c469f84856f42432d5f132fed6fb79e356003019ff2d2 |
"This module implements the dual FSI solver."
__author__ = "Kristoffer Selim and Anders Logg"
__copyright__ = "Copyright (C) 2010 Simula Research Laboratory and %s" % __author__
__license__ = "GNU GPL Version 3 or any later version"
# Last changed: 2011-08-31
from time import time as python_time
from dolfin import ... | Juanlu001/CBC.Solve | sandbox/aipcs/dualsolver.py | Python | gpl-3.0 | 4,359 | [
"VTK"
] | daa913d0edd9c310788ceb4a9ef99df83186d94f9944087ace8c55940aba78c4 |
#!/usr/bin/env python
# CREATED:2014-01-18 14:09:05 by Brian McFee <brm2132@columbia.edu>
# unit tests for util routines
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import matplotlib
matplotlib.use('Agg')
import numpy as np
import scipy.sparse
np.set_printoptions(precision=... | craffel/librosa | tests/test_util.py | Python | isc | 23,716 | [
"Brian"
] | 55eccadf6f94b1ced8a0e53ef04a7b0c898570d95d7cb79acfd874c7d59d37db |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Nccmp(CMakePackage):
"""Compare NetCDF Files"""
homepage = "http://nccmp.sourceforge.ne... | LLNL/spack | var/spack/repos/builtin/packages/nccmp/package.py | Python | lgpl-2.1 | 730 | [
"NetCDF"
] | ff16a65e154c1bfbf94c81f53efb88ea8becc85fb9bcd2d3ec0b60b330964fb1 |
#!/usr/bin/env python
#JSON {"lot": "RHF/cc-pvtz",
#JSON "scf": "PlainSCFSolver",
#JSON "er": "dense",
#JSON "difficulty": 1,
#JSON "description": "Basic RHF example with dense matrices, includes export of Hamiltonian"}
import numpy as np
from horton import * # pylint: disable=wildcard-import,unused-wildcard-imp... | tovrstra/horton | data/examples/hf_dft/rhf_n2_dense.py | Python | gpl-3.0 | 4,326 | [
"Gaussian"
] | 4ce36e875278a66f95962fe42fa556a28be3ddbe9e1fbefc1eb2c59bcf58e539 |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD 3 clause
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_rand... | BiaDarkia/scikit-learn | sklearn/cluster/spectral.py | Python | bsd-3-clause | 19,031 | [
"Brian",
"Gaussian"
] | 1679776d011afdb1fb1a037bc1d3b41966c1808f6a6d110f107199bc7388b673 |
from __future__ import unicode_literals
import base64
import json
import re
from .common import InfoExtractor
from .theplatform import ThePlatformIE
from .adobepass import AdobePassIE
from ..compat import compat_urllib_parse_unquote
from ..utils import (
smuggle_url,
try_get,
update_url_query,
int_or_... | rrooij/youtube-dl | youtube_dl/extractor/nbc.py | Python | unlicense | 18,728 | [
"Brian"
] | 06e71043de3b8a25e5e8ae84a2deb815f12ab1536187e9ca9e12a7d20e9115b4 |
#!/usr/bin/env python
import vtk, random
g = vtk.vtkMutableDirectedGraph()
init_v = g.AddVertex()
# Create this list of leaves + append inital
leaf_list = []
leaf_list.append(init_v)
# Randomly Pick a Termination number
total_nodes = random.randint(1,1000)
created_nodes = 0
# While don't exede the limit + run ou... | espinm2/interactive-vtk | pysrc/OrbitalTree.py | Python | mit | 1,115 | [
"VTK"
] | 4d8be8506af44e3d98b96d62c1965f692fa1f4e7fa67a2f4ac91e4bffc34d78e |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | bgrant0607/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 31,519 | [
"CDK"
] | c9852cec5de3e470d21c1b4fc465fb7a6cf35fbf0174ec9d2e48b72903e8b18b |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/sequence/_iupac_sequence.py | Python | bsd-3-clause | 16,572 | [
"scikit-bio"
] | 8d375722e42e7c35a2acb3052f0ac4559ad4ff4648adb5a90141758232ef280a |
''' config.py '''
DEBUG = False
SQLALCHEMY_ECHO = False
BCRYPT_LEVEL = 12 # Configuration for the Flask-Bcrypt extension
MAIL_FROM_EMAIL = "test@flask.touko.moe" # For use in application emails
| HoshinoTouko/ActivityRoomReservationSystem | config.py | Python | gpl-3.0 | 194 | [
"MOE"
] | 0845a6149d288961834cdab1c9dad93a8a85c92b3e1503ef585cac40426cd829 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/signals.py
#
# 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, t... | hdemeyer/king-phisher | king_phisher/server/signals.py | Python | bsd-3-clause | 10,838 | [
"VisIt"
] | 0033fa4f7989cc6d74f56ddd3265cf563a97f936362c0220cb88dae5393e533e |
#!/usr/bin/env python
# coding: utf-8
"""
.. module:: BUSCO
:synopsis: BUSCO - Benchmarking Universal Single-Copy Orthologs.
.. moduleauthor:: Felipe A. Simao <felipe.simao@unige.ch>
.. moduleauthor:: Robert M. Waterhouse <robert.waterhouse@unige.ch>
.. moduleauthor:: Mathieu Seppey <mathieu.seppey@unige.ch>
.. vers... | nextgenusfs/funannotate | funannotate/aux_scripts/funannotate-BUSCO2.py | Python | bsd-2-clause | 144,417 | [
"BLAST",
"VisIt"
] | f44852688731cecb5483e41e22fa0b5ea26fb14993e69f54e0ef36cb6f6cedc8 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.