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#!/usr/bin/env vpython
# Copyright 2017 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Utilities for checking for disallowed usage of non-Blink declarations.
The scanner assumes that usage of non-Blink code is always n... | ric2b/Vivaldi-browser | chromium/third_party/blink/tools/blinkpy/presubmit/audit_non_blink_usage.py | Python | bsd-3-clause | 59,398 | [
"VisIt"
] | 2a1cf7c0873607262e346d020889eda5ee01ed59dacc0a4931e98b5302b493c8 |
# Copyright 2003 Iddo Friedberg. 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.
"""A parser for the NCBI blastpgp version 2.2.5 output format. Currently only supports
the '-m 9'... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Blast/ParseBlastTable.py | Python | gpl-2.0 | 3,717 | [
"Biopython"
] | bb703ff99c68487b833c196e7a4d6edd656b297507d55ddd433bd149679241e4 |
"""
Tests for discussion pages
"""
import datetime
from pytz import UTC
from uuid import uuid4
from nose.plugins.attrib import attr
from .helpers import BaseDiscussionTestCase
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.courseware import CoursewarePage
from... | simbs/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 46,784 | [
"VisIt"
] | 5857c0951df397e5184ce10eeab465725c585de77b2ad7e41510895a1c702c98 |
from charm.toolbox.enum import *
OpType = Enum('OR', 'AND', 'ATTR', 'THRESHOLD', 'CONDITIONAL', 'NONE')
class BinaryNode:
def __init__(self, value, left=None, right=None):
self.value = value
self.left = left
self.right = right
def getLeft(self):
return self.left
def getR... | denniss17/charm | charm/toolbox/node.py | Python | lgpl-3.0 | 4,318 | [
"VisIt"
] | 2c99ddf43dbdbc6e8b33afdf32eb6e195e0804b9f04fd0ec8038800034dc1982 |
# encoding: utf-8
"""
A payload based version of page.
Authors:
* Brian Granger
* Fernando Perez
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# ... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/core/payloadpage.py | Python | lgpl-3.0 | 2,912 | [
"Brian"
] | 2036d2b3eb82010b2f4955d70e28f5d7d3747d8eeb51c74e89b0bd2e5061a419 |
# -*- coding: utf-8 -*-
#
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
# Oleh Kozynets <ok7mailbox@gmail.com>
#
# License: Simplified BSD
imp... | wmvanvliet/mne-python | mne/viz/_brain/tests/test_brain.py | Python | bsd-3-clause | 40,665 | [
"VTK"
] | 43a91c4e27a00dc894ef39d21e696c5a9494e1296479bbfb84922419b398b22a |
#!/usr/bin/env python3
########################################################################
# Solves problem 53 from projectEuler.net.
# Determines the amount of, not necessarily distinct, values of,
# combinations of n taken by r for 1 n 100, are greater than one-million?
# Copyright (C) 2010 Santiago Al... | sanSS/programming-contests | project-euler/problem053.py | Python | gpl-3.0 | 1,427 | [
"VisIt"
] | 7c4679c6538e3396dc6d22a05e02d90244751bafcd03c589a367a4c0a3305d3e |
#
# 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... | spektom/incubator-airflow | tests/plugins/test_plugin.py | Python | apache-2.0 | 3,646 | [
"Galaxy"
] | d78ae5da109a2892c4567349f26f2fc7a41ac8dbef0df5c9033b5969acb47f28 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | lahnerml/espresso | samples/python/visualization.py | Python | gpl-3.0 | 6,984 | [
"ESPResSo",
"Mayavi"
] | f93843bf4f65f959b71ed7cfe1071e5203b3e095bf6f99cc9c3a573d84bf27c0 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Run writer unit tests for cclib."""
import sys
import unittest
sys.path.append('io')
from testccio import *
from test... | Schamnad/cclib | test/test_io.py | Python | bsd-3-clause | 478 | [
"cclib"
] | 1370dc9608be094da3e35da30f85cfefc652bb91303e4263d8124cd0ee4a10f3 |
# DIALS_ENABLE_COMMAND_LINE_COMPLETION
"""
This program is used to integrate the reflections on the diffraction images. It
is called with an experiment list outputted from dials.index or dials.refine and
a corresponding set of strong spots from which a profile model is calculated.
The program will output a set of integ... | dials/dials | command_line/integrate.py | Python | bsd-3-clause | 25,755 | [
"CRYSTAL"
] | beb953dc1295b50d3ad8e9cab86afd55af45b7f19d9ac82e70162e91798015f2 |
#!/usr/bin/env python
"""
Make plots of the chi-squared distribution for different degrees of freedom
"""
import matplotlib.pyplot as pl
from scipy.stats import norm
from scipy.stats import chi2
import numpy as np
mu = 0. # the mean, mu
nus = [1., 3, 5., 10., 15.] # standard deviations, sigma
markers = ['b-', 'r-', ... | mattpitkin/GraWIToNStatisticsLectures | figures/scripts/chisquared.py | Python | mit | 1,029 | [
"Gaussian"
] | 6d584cec4aaeca9c780dae55e936c9227fb3b1376d6163c22ec2362f3f2af027 |
import os
import mdtraj as md
import glob
stride = 1
min_num_frames = 400
filenames = glob.glob("/home/kyleb/dat/FAH/munged/protein/10470/*.h5")
for k, filename in enumerate(filenames):
print(filename)
trj = md.formats.HDF5TrajectoryFile(filename, mode='r')
n_frames = len(trj)
trj.close()
if n_fra... | kyleabeauchamp/PMTStuff | code/subsample_trajectories.py | Python | gpl-2.0 | 495 | [
"MDTraj"
] | 92da619df74a153c36266244d8a5e325d79996376c85f06a08ef498003801066 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Kongsea/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 40,444 | [
"VisIt"
] | 049d681d5c579e71fa7887c4223ad150052f3b14fcbe17aa41c1dc646931a3ef |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Execute computations asynchronously using threads or processes."""
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
from concurrent.futures._base import (FIRST_COMPLETED,
FI... | ychen820/microblog | y/google-cloud-sdk/platform/google_appengine/lib/concurrent/concurrent/futures/__init__.py | Python | bsd-3-clause | 800 | [
"Brian"
] | e8aaaf62976a6f64efb7b1e338cb775abab16ee46e3d7ac7f2a67efbde2abded |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Break spin symmetry for UHF/UKS by initial guess.
See also examples/dft/32-broken_symmetry_dft.py
'''
import numpy
from pyscf import gto
from pyscf import scf
mol = gto.Mole()
mol.verbose = 4
mol.atom = [
["H", (0., 0., 2.5)],
["H", ... | gkc1000/pyscf | examples/scf/32-break_spin_symm.py | Python | apache-2.0 | 969 | [
"PySCF"
] | 86a01e065cb6b9d4824ce27738517b85f24e46ddbfb10bddc0bba7909c099ec8 |
#!/usr/bin/env python
import argparse
parser = argparse.ArgumentParser(prog='smooth_traj.py',
formatter_class=argparse.RawDescriptionHelpFormatter,
description='''version1''')
parser.add_argument("top", help="A prmtop file", type=str)
parser.add_argumen... | jeiros/Scripts | AnalysisMDTraj/superpose_ctf.py | Python | mit | 1,895 | [
"MDTraj",
"NetCDF"
] | 731c902d05290db242097fb030c654293e47eec798cbac9db5d425959db28684 |
"""Go through a BAM file made from alignments on a FASTQ and do the following:
1. BADBAM: Create a bam file containing only the misaligned reads. The read (CHROM, POS, CIGAR) are set to be the correct alignment
and the original alignment (CHROM, POS, CIGAR) is encoded in extended tags (see below).
The reason for setti... | latticelabs/Mitty | mitty/benchmarking/perfectbam.py | Python | gpl-2.0 | 10,257 | [
"pysam"
] | 25a5fdb1fcdba5d73eb82ab4ac68cb6c7ad1e26aac009697896158865cd16cd9 |
# Copyright (C) 2014-2015 Kate Cook, 2016-2017 Kevin Ha
#
# This file is part of rnascan.
#
# rnascan 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 the License, or
# (at your optio... | morrislab/rnascan | rnascan/rnascan.py | Python | agpl-3.0 | 21,409 | [
"Biopython"
] | d83968d3f979e0bfc66c98c4b143d3cbd076209c2679bf148a65b380d2cdbea6 |
# -*- coding: utf-8 -*-
import datetime
import json
import os
import shutil
from django.conf import settings
from django.core.files.storage import default_storage as storage
import mock
from nose.tools import eq_, ok_
from pyquery import PyQuery as pq
import amo
import amo.tests
from addons.models import (Addon, Add... | robhudson/zamboni | mkt/submit/tests/test_views.py | Python | bsd-3-clause | 38,483 | [
"exciting"
] | c9120086dea06fed63ef16b032493327c60c0cdd5caf1354522b7cc021a808f1 |
import os
from setuptools import setup, find_packages
__version__ = (0, 0, 1)
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name = "netcdf-pycli",
version='.'.join(str(d) for d in __version__),
author = "Basil Veerman",
author_email = "bveerman@uvi... | basilveerman/netcdf-pycli | setup.py | Python | gpl-3.0 | 588 | [
"NetCDF"
] | 058654104f74f4674e4e9effdb568212f28834fc18e98c178dc41b36893e678f |
import sys
import os
import traceback
import unittest
from antlr4 import * # type: ignore
from c2p.grammar.antlr.SmallCLexer import SmallCLexer
from c2p.grammar.antlr.SmallCParser import SmallCParser
from c2p.grammar.ast.visitor import ASTVisitor
from c2p.grammar.ast.visualize import Visualizer
from .environment impor... | Sibert-Aerts/c2p | src/c2p/codegen/test_semantic_errors.py | Python | mit | 2,939 | [
"VisIt"
] | b071e3c77bb8a0d59d217192ab973804bc57988a8d1a1bd1f096c685f96d9781 |
#!/usr/bin/env python
"""
dirac-rss-set-status
Script that facilitates the modification of a element through the command line.
However, the usage of this script will set the element token to the command
issuer with a duration of 1 day.
"""
__RCSID__ = '$Id$'
from datetime import datetime, timedelta
f... | andresailer/DIRAC | ResourceStatusSystem/scripts/dirac-rss-set-status.py | Python | gpl-3.0 | 8,219 | [
"DIRAC"
] | 4049089350b3497d86c93dfd2694b544ad85ac084a7d5b3c0fe98ebff3607cef |
""" :mod: SRM2Storage
=================
.. module: python
:synopsis: SRM v2 interface to StorageElement
"""
# # imports
import os
import re
import time
import errno
from types import StringType, StringTypes, ListType, IntType
from stat import S_ISREG, S_ISDIR, S_IMODE, ST_MODE, ST_SIZE
# # from DIRAC
from ... | vmendez/DIRAC | Resources/Storage/SRM2Storage.py | Python | gpl-3.0 | 84,297 | [
"DIRAC"
] | db4d1d55db8d4b15635e6ff7febafc02a38759022e52f4acf80b5d64acd0b447 |
u"""
setup.py: Install ODIN
"""
import os, sys,re
from os.path import join as pjoin
from glob import glob
#try:
#from setuptools import Extension, setup
#except:
from distutils.extension import Extension
from distutils.core import setup
from Cython.Distutils import build_ext
import numpy
import subprocess
fro... | tjlane/odin | setup.py | Python | gpl-2.0 | 7,114 | [
"MDTraj"
] | facb8bbc2705ca00e4416313ad634cf2339a438bdee2f04498777cce3c2876f6 |
# CREATED:2013-08-13 12:02:42 by Brian McFee <brm2132@columbia.edu>
'''
Evaluation criteria for structural segmentation fall into two categories:
boundary annotation and structural annotation. Boundary annotation is the task
of predicting the times at which structural changes occur, such as when a verse
transitions to... | urinieto/hier_eval | segment_tree.py | Python | gpl-3.0 | 51,887 | [
"Brian"
] | 90c4c800da71e731e5212ec65b373376ef791e9675c74c2da3115c9ecadc273b |
"""
Transfer functions with more complex dependencies.
$Id: basic.py 10790 2009-11-21 17:51:33Z antolikjan $
"""
__version__='$Revision: 10790 $'
import copy
import numpy, numpy.random
from numpy import ones
import param
import topo
import topo.base.functionfamily
from topo.base.arrayutil import clip_lower,array_... | jesuscript/topo-mpi | topo/transferfn/misc.py | Python | bsd-3-clause | 13,244 | [
"Gaussian"
] | fbf59cd43595673f14161cd47c46e9b05878710ad445a80bca460462d4ca8f3b |
#!/usr/bin/env python
# ******************************************************************************
# Copyright 2017-2018 Intel Corporation
#
# 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
... | NervanaSystems/neon | examples/gan/mnist_dcgan.py | Python | apache-2.0 | 4,727 | [
"Gaussian"
] | 28c4299ba749dad2f4c5b7a03919d7f9e2dcf3d4bb7539af0b5b3210a7e89e60 |
import nose
from pandas import DataFrame
import numpy as np
import pandas.util.testing as tm
from pandas.io.json import json_normalize, nested_to_record
def _assert_equal_data(left, right):
if not left.columns.equals(right.columns):
left = left.reindex(columns=right.columns)
tm.assert_frame_equal(... | pjryan126/solid-start-careers | store/api/zillow/venv/lib/python2.7/site-packages/pandas/io/tests/test_json_norm.py | Python | gpl-2.0 | 7,841 | [
"COLUMBUS"
] | 2ddf68a871536293983ea3a7707d20cb7979880952a36e8d6b77148f4e5646df |
# Copyright 1999-2000 by Jeffrey Chang. 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.
"""
This module provides code to work with PubMed from the NCBI.
http://www.ncbi.nlm.nih.... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PubMed.py | Python | apache-2.0 | 12,647 | [
"Biopython"
] | f6d86d4ff998a49dc4151b5ac1060ea75225898d2ef7dfce5344162945699058 |
#!/usr/bin/python
import sys #need sys to use system variables
import numpy as np # need numpy for arrays and the like
import Bio.SeqIO
import Bio.Seq
#Array of single letter amino acid cods for use in arrays.
IDS = np.zeros([22,1],dtype=object)
IDS[:,0]=['G', 'P', 'A', 'V', 'L', 'I', 'M', 'C', 'F', 'Y', 'W', 'H', '... | bryanjjones/pyConsensusFinder | modules/analyze.py | Python | gpl-2.0 | 13,814 | [
"BLAST"
] | dc1f750b688ed61dc2b2ea094026530915c1d98e0ca556533d6c87ec86eae024 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##
## (C) 2007, 2008, 2013 Muthiah Annamalai,
## Licensed under GPL Version 3
##
## Module has elements of PARSE-TREE AST
## in the classes Expr, ExprCall, ExprList, Stmt, ReturnStmt,
## BreakStmt, ContinueStmt, ElseStmt, IfStmt, WhileStmt,
## ForStmt, AssignStmt, PrintStmt, E... | arcturusannamalai/Ezhil-Lang | ezhil/ast.py | Python | gpl-3.0 | 33,386 | [
"VisIt"
] | e9789f5f0f00af0b088a839a4169103ff60cdc15bbaa3adceaa4f71757c790da |
from __future__ import unicode_literals
from django.db import models
from django.conf import settings
import pprint
from Bio.Phylo.TreeConstruction import _DistanceMatrix, DistanceTreeConstructor
from Bio import Phylo
import StringIO
import json
STATUS = {'PENDING':1,'RUNNING':2,'ERROR':3,'COMPLETE':4}
STATUS_CHOICES... | lairdm/islandviewer-ui | webui/models.py | Python | gpl-3.0 | 17,795 | [
"BLAST"
] | 24e7b7f0064feaa64cf3dda319b95dfebdd167b8863a6011b7d9519c766f6c10 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | chrys87/orca-beep | src/orca/debug.py | Python | lgpl-2.1 | 17,180 | [
"ORCA"
] | 9ddf4f8cf945271e489c31637fee5a11ec82a6a09b3e1c582274cc54b4598064 |
import datetime
import sys
import numpy as np
import mygis
from bunch import Bunch
def write_file(date,info,erai):
"""writes ERAi input data to a netcdf file"""
filename=str(date).replace(" ","_")
dims = ("time", "level","lat","lon")
dims2dt = ("time", "lat","lon")
extra_vars=[]
# 3D var... | NCAR/icar | helpers/erai/output.py | Python | mit | 4,218 | [
"NetCDF"
] | 3c06cecd37199ba16383858082f315748fba25cd58d55ca61114997d9cbe65d1 |
########################################
# Read ECMWF netcdf files for heat fluxes
#
# Created by: Peter Willetts
# Created on: 12/06/2014
#
# ECMWF heat and radiation flux - Read from netcdf
# filter by date, latitude and longitude
# calculate mean and t... | peterwilletts24/Python-Scripts | era_interim/netcdf_fileread_heat_fluxes.py | Python | mit | 4,199 | [
"NetCDF"
] | 298c26bcb8c97ec3b5c2a467d5ab96b96a78807c4c02f93c73f5dfbc2c19258e |
import socket
import time
import sys
import subprocess
import codecs
from octopus.modules import dictdiffer
from unittest import TestCase
from octopus.lib import plugin
import os
class FunctionalTestServer(TestCase):
"""
FIXME: don't use this, it doesn't work. Leaving it here for later diagnosis.
"""
... | JiscPER/magnificent-octopus | octopus/modules/test/helpers.py | Python | apache-2.0 | 4,753 | [
"Octopus"
] | 320ddea1842946a9e84a6f05ee017fdd8385f1383b00e15ccaa5791124ccbf87 |
# Orca
#
# Copyright 2011 The Orca Team.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is ... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/xfwm4/__init__.py | Python | gpl-3.0 | 830 | [
"ORCA"
] | 9a923140881b341155aaaa3cf78d55befc00473c877dbe2cab375dbbd4472085 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Reference-free tGBS related functions.
"""
import os.path as op
import logging
import sys
from collections import defaultdict
from itertools import combinations
from jcvi.formats.fasta import Fasta, SeqIO
from jcvi.formats.fastq import iter_fastq
from jcvi.formats.b... | sgordon007/jcvi_062915 | projects/tgbs.py | Python | bsd-2-clause | 16,624 | [
"pysam"
] | 78721f800f700801332ab0c1574bff74b96a899282f91a06df5c659e6b08e117 |
"""Tests for core.groups.requires decorator
"""
import numpy as np
from numpy.testing import (
assert_,
assert_raises,
)
from MDAnalysis.core.groups import requires
from MDAnalysis import NoDataError
from MDAnalysisTests import make_Universe
class TestRequires(object):
def test_requires_failure_singula... | alejob/mdanalysis | testsuite/MDAnalysisTests/core/test_requires.py | Python | gpl-2.0 | 1,949 | [
"MDAnalysis"
] | 3ba5c14abec2ff824eb71fdf2dd2eb72da08af244dfe6d304bec32b7e19d5dab |
from multiprocessing import Pool
import itertools
import time
import numpy as np
import os
import glob
import mdtraj as md
import fahmunge
import pandas as pd
import signal
import sys
# Reads in a list of project details from a CSV file with Core17/18 FAH projects and munges them.
projects = pd.read_csv("./projects.c... | steven-albanese/FAHMunge | scripts/munge_fah_data_parallel.py | Python | lgpl-2.1 | 1,726 | [
"MDTraj"
] | fe5f065e72b76a126c6321ac587c5875a8158528440638e34bcbc90e9370218e |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or later
Recommended: CJKCodecs... | ltucker/radarpost | radarpost/lib/feedparser.py | Python | gpl-2.0 | 157,161 | [
"NetCDF",
"VisIt"
] | 66af4b1ab3d489a2f68a15c45bf1abdaf315a068f73c2397993cb8bbb3e88801 |
path={0:{1:10},
1:{2:20},
2:{1:30},
3:{0:-60},
}
def dfs(start,visit):
for i in path[start]:
if str(i) in visit:
print(start,visit)
pathl=0
for x in visit[visit.index(str(i)):]:
pathl+=path[int(x)][start]
if pathl > pathl+path[start][int(visit[-1])]:
print('have')
else:
print('NO')
... | ytlai4851/Uva | Python/Q558.py | Python | gpl-2.0 | 390 | [
"VisIt"
] | 80c183a7cd44f56cdaf5598e553c439c19bdff6ec6dc4d3c1d2701d5e4893184 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/base/test_translator.py | Python | lgpl-2.1 | 1,188 | [
"MOOSE"
] | 7055cfe1e4ee4491f972637b57c55df5c508ae2447102a3e18429f8ed9bfc86d |
"""
audfprint_analyze.py
Class to do the analysis of wave files into hash constellations.
2014-09-20 Dan Ellis dpwe@ee.columbia.edu
"""
from __future__ import print_function
import os
import numpy as np
import scipy.signal
# For reading/writing hashes to file
import struct
# For glob2hashtable, localtester
impor... | piotrwicijowski/whistler | audfprint_analyze.py | Python | mit | 22,382 | [
"Gaussian"
] | 5fdd7dec0c190142e9159bdc1baa29cc2e2539019f7553bf07e24bc5f8fc8587 |
# 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/FixedPairDistList.py | Python | gpl-3.0 | 2,997 | [
"ESPResSo"
] | 97d2f01c3ce22e403f3855acf9343c9bf576bbcca193e6de047e49482a199c0d |
import os
import numpy as np
import mdtraj as md
from unittest import skipIf
import logging
from mdtraj.testing import eq
from openmoltools import utils
from openmoltools import amber
import simtk.unit as u
from simtk.openmm import app
import simtk.openmm as mm
import simtk.openmm.openmm as mmmm
from distutils.spawn im... | andrrizzi/openmoltools | openmoltools/tests/test_utils.py | Python | gpl-2.0 | 6,346 | [
"Amber",
"Gromacs",
"MDTraj",
"OpenMM",
"RDKit"
] | 159992f792f98cd1d14a9a620050332fa73cc12a8007cb73dfc4c71151673b9b |
## Copyright (c) 2012-2015 Aldebaran Robotics. All rights reserved.
## Use of this source code is governed by a BSD-style license that can be
## found in the COPYING file.
import os
import py
import qilinguist.worktree
from qisys.test.conftest import *
from qibuild.test.conftest import *
class QiLinguistAction(Test... | dmerejkowsky/qibuild | python/qilinguist/test/conftest.py | Python | bsd-3-clause | 3,893 | [
"Brian"
] | 2628f2273d9e6115eaa1e0e24700a799ad2298c733cf7f4dd390d7dd690ef141 |
from __future__ import division
import numpy as np
import scipy.sparse as sp
from sklearn.exceptions import DataDimensionalityWarning
from sklearn.metrics import euclidean_distances
from sklearn.random_projection import GaussianRandomProjection
from sklearn.random_projection import SparseRandomProjection
from sklearn.... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/tests/test_random_projection.py | Python | mit | 14,036 | [
"Gaussian"
] | bda4f1af983568ff09bba8ccb546e5828e2a8e335dbf5e592f7be1924a1d8073 |
"""
Clustering Interface For Galaxy
Date: January 2013
Author: James Boocock
"""
#Python Imports
import os
import sys
import logging
#Clustering Module Imports
import util
from grid import Grid
from tool_run import ToolRun
from ui_reader import UiReader
from elementtree import ElementTree
log = logging.g... | smilefreak/NesiGridSelection | grid_selection/clustering/interface.py | Python | mit | 2,833 | [
"Galaxy"
] | 631571ffebe239538a8a4fd502df240b5b3ced5228484409a183555fdf87071d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##################################################################################################
# module for the symmetric eigenvalue problem
# Copyright 2013 Timo Hartmann (thartmann15 at gmail.com)
#
# todo:
# - implement balancing
#
###########################... | JensGrabner/mpmath | mpmath/matrices/eigen_symmetric.py | Python | bsd-3-clause | 58,534 | [
"Gaussian"
] | 14f28f790af5706630e98e9e6b7d9ad587445900cb3fa265407100d967cd2d88 |
'''
Simulation data model for the EI network: in general a network of two
populations, E and I cells; more specifically, a grid cell network.
'''
import numpy as np
from ...analysis import spikes
def getNetParam(data, p):
'''Extract a network parameter (p) from the data dictionary'''
return data['net_attr'][... | MattNolanLab/ei-attractor | grid_cell_model/data_storage/sim_models/ei.py | Python | gpl-3.0 | 4,127 | [
"NEURON"
] | 0758de1452feb05f89aba4a1c59ebfb02317c83ac39a8aeeb59e259fdf2dddd0 |
import numpy as np
import sys, os
import nrrd
def sphere(shape, radius, position):
# assume shape and position are both a 3-tuple of int or float
# the units are pixels / voxels (px for short)
# radius is a int or float in px
semisizes = (radius,) * 3
#ignore divide by zero
np.seterr(divide='i... | Robbie1977/NRRDtools | swc2nrrd.py | Python | mit | 2,954 | [
"NEURON"
] | 1694ee444f781f48d8c8d7fea8c73fe2835de8ada8ffc8255ad27f7179113967 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | markovmodel/PyEMMA | pyemma/coordinates/tests/test_source.py | Python | lgpl-3.0 | 9,204 | [
"MDTraj"
] | 53241c2291c0081d9da75107e0d090c08f04b7a51d354b134e4423316f2e857b |
#-*- coding:utf-8 -*-
"""
PyHdust *poltools* module: polarimetry tools
History:
-grafpol working for *_WP1110....log files!
-grafpol working for log/out files with more than a single star
:co-author: Daniel Bednarski
:license: GNU GPL v3.0 (https://github.com/danmoser/pyhdust/blob/master/LICENSE)
"""
from __future_... | dbednarski/pyhdust | pyhdust/poltools.py | Python | gpl-3.0 | 201,725 | [
"Gaussian"
] | 1f70c6e4ca4bd07db633e9947133f70c5664d956bc92be63e113811814fb6857 |
"""
Note: This is a third-party package that was included
to adapt it to my needs. I'm not the author.
For the original source, please visit:
https://django-channels-presence.readthedocs.io/en/latest/
"""
| kkmsc17/smes | backend/channels_presence/__init__.py | Python | agpl-3.0 | 207 | [
"VisIt"
] | 44e6e1444e37843673742e8c763fb4d010823c35fc8f468f8e9c14f5e07a42a3 |
"""gro.py: Used for loading Gromacs GRO files.
"""
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Robert McGi... | mattwthompson/mdtraj | mdtraj/formats/gro.py | Python | lgpl-2.1 | 19,964 | [
"Gromacs",
"MDTraj",
"OpenMM"
] | 1ed8eb26f53e52e2b27d50105000c94cc7a399889b6449bb61541c681d21b928 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | sarvex/tensorflow | tensorflow/python/autograph/pyct/qual_names.py | Python | apache-2.0 | 8,237 | [
"VisIt"
] | 1094ed10f5374b93f377cd8853d3523086704504289f48f672d0ed2f9322c064 |
import keras
import tensorflow as tf
import numpy as np
import menpo.io as mio
import menpo
from scipy.interpolate import interp1d
import scipy as sp
from keras import backend as K
from matplotlib import pyplot as plt
from pathlib import Path
from scipy.io import loadmat
from menpo.image import Image
from menpo.shape i... | yuxiang-zhou/deepmachine | deepmachine/utils/tf.py | Python | mit | 12,823 | [
"Gaussian"
] | 2330d4b843c1557ecd79d31e5573363f6e7f00b46c2e96ade567ab507d3957e7 |
# -*- coding: utf-8 -*-
'''
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 later version.
This program is dis... | repotvsupertuga/repo | plugin.video.zen/resources/lib/sources/rlsbbonline_mv_tv.py | Python | gpl-2.0 | 5,095 | [
"ADF"
] | c22df191f61e4ea51f5709d45dc99f4ed91e493dd7f9145c27023796dbf6a6ac |
"""The post-processing module contains classes for image filtering mostly applied after a classification.
Image post-processing aims to alter images such that they depict a desired representation.
"""
import warnings
# import numpy as np
# import pydensecrf.densecrf as crf
# import pydensecrf.utils as crf_util
import... | istb-mia/MIALab | mialab/filtering/postprocessing.py | Python | apache-2.0 | 5,501 | [
"Gaussian"
] | b050c44d8aac9190f7364a07f5ca6793a38b01d8518eca621cd908ee06183d9d |
#!/usr/bin/env python
"""Module to create command references for DIRAC."""
from concurrent.futures import ThreadPoolExecutor
import logging
import os
import shutil
import textwrap
from collections import namedtuple
from diracdoctools.Utilities import writeLinesToFile, runCommand, makeLogger
from diracdoctools.Config i... | DIRACGrid/DIRAC | docs/diracdoctools/cmd/commandReference.py | Python | gpl-3.0 | 8,645 | [
"DIRAC"
] | 9db3cfee27def5e8070afea3155a08eb5f832b880b4b9b7a4e5210c3e666a3b9 |
# -*- coding: utf-8 -*-
"""
Created on Sat Feb 9 19:13:58 2019
@author: lyh
"""
import numpy as np
from oceansar import constants as const
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 7 17:09:40 2019
Create the directional swell spectrum by both generating the spread
and the directional distribution based on Gaus... | pakodekker/oceansar | oceansar/swell_spec/dir_swell_spec.py | Python | gpl-3.0 | 1,471 | [
"Gaussian"
] | 49154b1663ff32738ff7b1d35be992cde633888446623d3f67ebce9017cebdbc |
#!/usr/bin/env python
# Copyright (C) 2014 Swift Navigation Inc.
# Contact: Colin Beighley <colin@swift-nav.com>
#
# This source is subject to the license found in the file 'LICENSE' which must
# be be distributed together with this source. All other rights reserved.
#
# THIS CODE AND INFORMATION IS PROVIDED "AS... | henryhallam/piksi_tools | piksi_tools/console/update_view.py | Python | lgpl-3.0 | 22,270 | [
"VisIt"
] | e6450cb3e3f246a96bc35f620e9924a15573ef506a751a94a7b2b447ec2fb9d4 |
"""
This file is part of Giswater 3
The 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 later version.
"""
# -*- coding: utf-8 -*-
import csv
import... | Giswater/giswater_qgis_plugin | core/shared/psector.py | Python | gpl-3.0 | 100,688 | [
"VisIt"
] | aaaeed0daa48afa021c35c5c2ba8592a81fb69400e58a7f6a8fc30539dbb8f6b |
import os
import ntpath
import json
from math import sqrt
#from json_utils import create_json_file
def get_files_mol2(mypath):
only_mol2_file = []
for root, dirs, files in os.walk(mypath):
for file in files:
if file.endswith(".mol2"):
f_path = os.path.join(root,... | rodrigofaccioli/drugdesign | virtualscreening/vina/spark/vina_utils.py | Python | apache-2.0 | 9,638 | [
"Gromacs"
] | 796f869cb78aec2f0436fe0e17033f1ce33beff85c23f4420b96a03640c7c054 |
import xml.etree. ElementTree as ET
import numpy as np
from uncertainties import ufloat
import openmc
import pytest
from tests.unit_tests import assert_unbounded
from openmc.data import atomic_mass, AVOGADRO
def test_contains():
# Cell with specified region
s = openmc.XPlane()
c = openmc.Cell(region=+s... | walshjon/openmc | tests/unit_tests/test_cell.py | Python | mit | 8,229 | [
"Avogadro"
] | 8cd8f3cf42dce03918937f1aa87063c687409bb048781a26f1daf0c86fdd4888 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | yanlend/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 62,656 | [
"Brian"
] | 373a46165512f9daaab85d890647c0960a4abcfe0626cb2a3fc34bb8afe97b94 |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import operator
import threading
import sys
import timeit
from . import sigtools, dlti
from ._upfirdn import upfirdn, _output_len
from scipy._lib.six import callable
from scipy._lib._version import NumpyVersion
... | Eric89GXL/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 119,638 | [
"Gaussian"
] | 93ccaa6c04ddb10e5d2abf6e9fb015fec0e733ea63e6720565e8630befecd20c |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | NAMD/pypln.web | pypln/web/core/tests/utils.py | Python | gpl-3.0 | 2,062 | [
"NAMD"
] | e49c9a5e100023131a0fd8f28c4f3d769bb062a5707dd0c46c9b32b1c0aeca82 |
from django.core.exceptions import ValidationError
from cyder.base.tests import ModelTestMixin, TestCase
from cyder.cydns.soa.models import SOA
from cyder.cydns.domain.models import Domain
class SOATests(TestCase, ModelTestMixin):
@property
def objs(self):
"""Create objects for test_create_delete."""... | akeym/cyder | cyder/cydns/soa/tests/test_models.py | Python | bsd-3-clause | 4,623 | [
"ADF"
] | 9c15154f16c32bd269edb0bf1b861c2b2f0bdcb545081ff87502c0bd929a6755 |
#
# Copyright 2010 Suinova Designs Ltd.
#
__author__ = "Ted Wen"
__version__ = "$Revision: 1 $"
# $Source$
import logging, time, cgi, hashlib, os, base64, re, hmac, urllib
from datetime import datetime, timedelta
from google.appengine.ext import webapp
from google.appengine.ext.webapp.util import run_wsgi_app
from... | tedwen/suicomics | src/main.py | Python | apache-2.0 | 43,823 | [
"VisIt"
] | be0b821cc1f6f9348e61a65b6ab89acf10825ae7697038e4ca8a9568419a29a5 |
# -*- coding: utf-8 -*-
from pd_make import entry_data, aq_correction, stable_entr, form_e, mke_pour_ion_entr
def pd_entries(mtnme_1,mtnme_2):
"""
Creates the entry objects corresponding to a binaray or single component
Pourbaix diagram
Args:
mtnme_1: Name of element 1
mtnme_2: Name of element 2
"... | raulf2012/pourbaix_pymatgen | pourdiag.py | Python | mit | 2,551 | [
"pymatgen"
] | 6dbd4a00af49ff75bd31cca531e2b52cb454890988aa9c003321b343d61680e1 |
#
# QE.py
#
# Interface to Quantum ESPRESSO (http://www.quantum-espresso.org)
#
# Copyright (c) 2014-2020 Terumasa Tadano
#
# This file is distributed under the terms of the MIT license.
# Please see the file 'LICENCE.txt' in the root directory
# or http://opensource.org/licenses/mit-license.php for information.
#
from... | ttadano/alamode | tools/interface/QE.py | Python | mit | 37,994 | [
"CRYSTAL",
"ESPResSo",
"Quantum ESPRESSO"
] | 81b33e32d2f8e32f807058ab06f58eba2ab222f9a3fab960538e4410b14494dd |
import logging
logger = logging.getLogger('parse_cdr3.py')
from .all_genes import all_genes, gap_character
def get_cdr3_and_j_match_counts( organism, ab, qseq, j_gene, min_min_j_matchlen = 3,
extended_cdr3 = False ):
#fasta = all_fasta[organism]
jg = all_genes[organism][j_gene... | phbradley/tcr-dist | tcrdist/parse_cdr3.py | Python | mit | 4,891 | [
"BLAST"
] | f759d0c93de25265b042a966076f814bf7ad4d8e50b6df63fcb1383eabbbd152 |
from time import localtime, sleep, time
import paho.mqtt.client as mqtt
from blinkt import set_pixel, show, clear
# The callback for when the client receives a CONNACK response from the server.
def on_connect(client, userdata, flags, rc):
print("Connected with result code "+str(rc))
# Subscribing in on_conne... | dansmith9/MQTT-Blinkt-Countdown | MQTTcountdowntimer.py | Python | gpl-3.0 | 5,433 | [
"Amber"
] | bfa23cb44644226b5f5b5c6649de45239d21cff0bccfb32677b877422a485bed |
# vim: fileencoding=utf-8 et ts=4 sts=4 sw=4 tw=0
"""
A base class for RPC services and proxies.
Authors:
* Brian Granger
* Alexander Glyzov
* Axel Voitier
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2012-2014. Brian Granger, Min Ragan-Kelley, Alexander Glyzov,... | srault95/netcall | netcall/base.py | Python | bsd-3-clause | 15,103 | [
"Brian"
] | 31433d6358d34e711662f5049c396bb0d149978992398573b04bb117a44c3a25 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/commoncode/ignore.py | Python | apache-2.0 | 12,598 | [
"VisIt"
] | 27a489dd40da44a15d65a30a8d2673403e65a1b001edcb64c31f3da7db4ae7d0 |
import os
import numpy as np
import mmap
import dynaphopy.dynamics as dyn
import warnings
# VASP OUTCAR file parser
def read_vasp_trajectory(file_name, structure=None, time_step=None,
limit_number_steps=10000000, # Maximum number of steps read (for security)
last_ste... | abelcarreras/DynaPhoPy | dynaphopy/interface/iofile/trajectory_parsers.py | Python | mit | 16,636 | [
"LAMMPS",
"VASP"
] | 48965cabac27a57ff80c02f4165fa9184ce529fac9bd0b3f2608ca2634ec4fb1 |
# coding: utf-8
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | NAMD/pypln.backend | pypln/backend/workers/trigrams.py | Python | gpl-3.0 | 2,181 | [
"NAMD"
] | 4064ae0905bebf35c68d57851163d2f62479dc21caa7cb36c4ba8629351668e2 |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import, division, print_function
import ast
import _ast
import errno
import itertools
import imp
import marshal
import os
import re
import struct
import sys
import types
import py
from _pytest.assertion import util
# pytest ca... | flub/pytest | _pytest/assertion/rewrite.py | Python | mit | 36,227 | [
"VisIt"
] | 3d884ea19b2bc8855298dc2183db9f11356227a7ba34e536471a01bd8e495777 |
# 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... | capoe/espressopp.soap | src/integrator/BerendsenThermostat.py | Python | gpl-3.0 | 3,904 | [
"ESPResSo"
] | 373911c11e751ed1d3182ac17149c119849b1120d922b7f6859f63ee947625c7 |
#!/usr/bin/env python3.2
'''
The goal here is to take any VCF file output by VCFannotator and summarize the SNPs
contained there by type.
INPUT
The input expected is from the VCFannotator documentation:
An example output line transposed to a column format would look like so (taken from
the sample data):
0 TY-... | jonathancrabtree/biocode | sandbox/jorvis/summarize_vcfannotator.py | Python | gpl-3.0 | 4,385 | [
"Brian"
] | a7b9567d313298d594e472f4fd79fe742062e69b6174bcea065f701a37006e3b |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_nosyn_compiled_0032.py | Python | gpl-3.0 | 3,482 | [
"Brian"
] | 627cc15e91c947e6c4a5ecc657860a9d808ea83cedd790d27983154325058202 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/mooseutils/tests/test_run_executable.py | Python | lgpl-2.1 | 1,293 | [
"MOOSE"
] | 98c5b648bce5aa9e102698c70dd520e5171390e61a9c315bcecfdd69ca9167fb |
# Copyright 2020 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/python/distributions/exponentially_modified_gaussian.py | Python | apache-2.0 | 8,896 | [
"Gaussian"
] | ca79173a9d0f3c2b1e7519c7b78c19ba949c72ab354ee156cc9bcd2fc21f47a4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Generated from FHIR 3.0.0.11832 on 2017-03-22.
# 2017, SMART Health IT.
import io
import json
import os
import unittest
from . import questionnaireresponse
from .fhirdate import FHIRDate
class QuestionnaireResponseTests(unittest.TestCase):
def instantiate_fro... | all-of-us/raw-data-repository | rdr_service/lib_fhir/fhirclient_3_0_0/models/questionnaireresponse_tests.py | Python | bsd-3-clause | 68,284 | [
"Brian"
] | b628f2b6275b310f9fc609318486f80e543b8e65897fe8cf202f16ca3e61774d |
"""
Tests for enthought/tvtk/misc.py
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
import unittest
import tempfile
import os.path
import os
from tvtk.api import tvtk, write_data
class TestMisc(unittest.TestCase):
def setUp(self):
d... | dmsurti/mayavi | tvtk/tests/test_misc.py | Python | bsd-3-clause | 2,910 | [
"VTK"
] | d742f92f9acfeb508a90f3712dda7570ce42851f9ce9e90494d824715a717201 |
# -*- encoding: utf-8
from sqlalchemy.testing import eq_, engines, pickleable
import datetime
import os
from sqlalchemy import *
from sqlalchemy import types, exc, schema, event
from sqlalchemy.orm import *
from sqlalchemy.sql import table, column
from sqlalchemy.databases import mssql
from sqlalchemy.dialects.mssql im... | rclmenezes/sqlalchemy | test/dialect/test_mssql.py | Python | mit | 80,949 | [
"ASE"
] | d8e36c745082e51bcf4a5af65931764ee76eb8586532cd7ea94f4552ce6e535c |
"""
It used to create several plots
"""
import time
import copy
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.MonitoringSystem.private.DBUtils import DBUtils
from DIRAC.Core.Utilities.Plotting import gDataCache
from DIRAC.Core.Utilities.Plotting.Plots import (
generateNoDataPlot,
generateTimedStackedBarP... | DIRACGrid/DIRAC | src/DIRAC/MonitoringSystem/private/Plotters/BasePlotter.py | Python | gpl-3.0 | 15,548 | [
"DIRAC"
] | 657716eaa0c5bf54e20208c40c0adfc32124525a2a55f1c7a5f6fa68979397eb |
import logging
import wx
from service.fit import Fit
from gui.bitmap_loader import BitmapLoader
import gui.globalEvents as GE
from gui.preferenceView import PreferenceView
from service.settings import EOSSettings
import gui.mainFrame
from wx.lib.intctrl import IntCtrl
logger = logging.getLogger(__name__)
class PFF... | blitzmann/Pyfa | gui/builtinPreferenceViews/pyfaEnginePreferences.py | Python | gpl-3.0 | 7,074 | [
"CRYSTAL"
] | 08a14e9cfa707694d17ce82e589742e3ffbaf739bd9ff9ace6acfc43b69a62a0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import copy
import numpy as np
from scipy.stats import linregress
from matplotlib import cm
import itertools
import warnings
from pymatgen.core.structure imp... | setten/pymatgen | pymatgen/analysis/surface_analysis.py | Python | mit | 21,488 | [
"VASP",
"pymatgen"
] | 58100e48c361e5c223591b3f1d9a10c8cf71fe07c03e86cbb44c7b856698e883 |
#!/usr/bin/env python
# -*- Mode: Python; py-indent-offset: 4 -*-
# vim: tabstop=4 shiftwidth=4 expandtab
#
# Copyright (C) 2010 Red Hat, Inc., John (J5) Palmieri <johnp@redhat.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License a... | nzjrs/pygobject | demos/gtk-demo/demos/combobox.py | Python | lgpl-2.1 | 12,201 | [
"COLUMBUS"
] | 985b7f86f7c7c10f022f994a6f9a0f6add08d2b3337ee3365b82df023ce45c64 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Simple script that tests CytoscapeGraphDrawer.
This script is kept separate from the unit tests as it is very
hard to test for the correctness of CytoscapeGraphDrawer without
a working instance of Cytoscape.
Prerequisites for running this test:
1. Start Cytoscape
... | nickeubank/python-igraph | test/cytoscape_test.py | Python | gpl-2.0 | 2,627 | [
"Cytoscape"
] | daaaecfdfabebd0c71b68d4fe6e738c56c1a1ace26557b07ce56567acd55b6f8 |
import os
from sfepy import data_dir
from sfepy.base.base import debug, nm
from sfepy.homogenization.micmac import get_homog_coefs_linear
from sfepy.homogenization.recovery import save_recovery_region, recover_micro_hook
def post_process( out, pb, state, extend = False ):
from sfepy.base.base import Struct
if... | olivierverdier/sfepy | examples/homogenization/linear_elastic_mM.py | Python | bsd-3-clause | 3,181 | [
"VTK"
] | 14fefedb258944ac895d0e732fe38d3f6c93792e6a1768a9c747e3086741fa0e |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2017 Francois Beaune, The appleseedhq Organi... | Aakash1312/appleseed | scripts/appleseed.package.py | Python | mit | 29,530 | [
"VisIt"
] | 1b103c4b2e54e9109377c8cb939525742957f555a2d4fc6952684eb659700da7 |
# ******************************************************************************
# Copyright 2014-2018 Intel Corporation
#
# 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.apa... | NervanaSystems/neon | tests/test_mergesum_layer.py | Python | apache-2.0 | 5,273 | [
"Gaussian"
] | 008d4051d7221e5e14b3654e298696f6f23bf9c2c485254e248561fb421878e7 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Run bridge unit tests for cclib."""
import sys
import unittest
sys.path.insert(1, "bridge")
if sys.version_info[0] =... | cclib/cclib | test/test_bridge.py | Python | bsd-3-clause | 899 | [
"cclib"
] | 71c69db7b6065d82ca382a63f6e93daf4720446d43b5de2a3d1f9507a5ffe1d6 |
#!/usr/bin/python
#
# Copyright (C) 2015, Jaguar Land Rover
#
# This program is licensed under the terms and conditions of the
# Mozilla Public License, version 2.0. The full text of the
# Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
#
#
# Register a service specified by command line with an RVI nod... | lillialexis/rvi_core | python/rvi_service.py | Python | mpl-2.0 | 3,035 | [
"Jaguar"
] | 041332edb5067b984405af2b7767cc63af761069a275f2683ed37f4a9df34466 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | bnaul/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 46,904 | [
"Gaussian"
] | 9ab6c8e119eb74a0e124176451551efd712a400815f710a4f2f817440da1c61e |
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