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########################################################################
# File : JobCleaningAgent.py
# Author : A.T.
########################################################################
""" The Job Cleaning Agent controls removing jobs from the WMS in the end of their life cycle.
This agent will take care... | petricm/DIRAC | WorkloadManagementSystem/Agent/JobCleaningAgent.py | Python | gpl-3.0 | 10,062 | [
"DIRAC"
] | 266cff17220f0f4c1013ae6c7810f319fab71da7a942fffb5f971019f202a5a3 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkUnstructuredGridAlgorithm(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkUnstructuredGridAlgorithm.py | Python | bsd-3-clause | 527 | [
"VTK"
] | ab51b8672d06d4c68a3751c71bbcdedc5c9a25db148c6dbb55f5dc9ab5037bf9 |
import sys, os
try:
from setuptools import setup
kw = {'entry_points':
"""[console_scripts]\nvirtualenv = virtualenv:main\n""",
'zip_safe': False}
except ImportError:
from distutils.core import setup
if sys.platform == 'win32':
print('Note: without Setuptools installed you wi... | nanonyme/trivial-buildpack-python | virtualenv/setup.py | Python | mit | 2,155 | [
"Brian"
] | 151708cef87f3dcf8b006e81787b58d48b2fe13c3e58301097b650fa9e1d1693 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
from os import path
import sys
ON_POSIX = 'posix' in sys.builtin_module_names
try:
from subprocess import Popen
except ImportError:
from os import popen3
else:
def popen3(cmd):
from subprocess import PI... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/svnversion_io.py | Python | gpl-2.0 | 1,429 | [
"ASE"
] | 057bd09ed36d2e7af29ffd1757275ff3af9ff555e8a77b846ba3695340c73373 |
"""
This module is used to create an appropriate object which can be used to insert records to the Monitoring system.
It always try to insert the records directly. In case of failure the monitoring client is used...
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_... | yujikato/DIRAC | src/DIRAC/MonitoringSystem/Client/ServerUtils.py | Python | gpl-3.0 | 1,086 | [
"DIRAC"
] | 2597cdb3d29eaecedce7b9fbc1407a4916ad222c4d028b40575e322876a58bf4 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import logging
plainLogger = logging.getLogger(__name__)
from container.utils.visibility import getLogger
logger = getLogger(__name__)
import base64
import datetime
import functools
import time
import inspect
import json
import os
import re
import shutil... | chouseknecht/ansible-container | container/docker/engine.py | Python | lgpl-3.0 | 53,581 | [
"Galaxy"
] | 008b70cfee43f387fbfb0aefd55d52f7713a4ddfe7e6af3cfd28870f5a54384f |
#!/usr/bin/env python2
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2015, Kovid Goyal <kovid at kovidgoyal.net>'
import ctypes, ctypes.wintypes as types, _winreg as winreg, struct, datetime... | songfj/calibre | src/calibre/utils/winreg/lib.py | Python | gpl-3.0 | 14,668 | [
"MOOSE"
] | f741d8dd7316718d97ce99516324fbf6494896c8040209929d64ef10e37501bf |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/Thunderbird/script_settings.py | Python | gpl-3.0 | 1,210 | [
"ORCA"
] | 86de4716a9ebdabfb6e43da164156cd0355c49c743f2c5fcbe96ffb98bc629ae |
from sfepy.base.base import *
import sfepy.base.ioutils as io
from sfepy.fem import ProblemDefinition
from sfepy.base.conf import get_standard_keywords
##
# c: 03.07.2007, r: 27.02.2008
def save_only( conf, save_names, problem = None ):
"""Save information available prior to setting equations and
solving them... | certik/sfepy | sfepy/solvers/generic.py | Python | bsd-3-clause | 6,822 | [
"VTK"
] | 83b5bf4188c0c0b5175f279da7188e4e7391813bf6b18b2909f60b071ce5018b |
from datetime import datetime, timedelta
import logging
from django.core.urlresolvers import reverse
from django.http import Http404
from django.utils import html
from django.utils.safestring import mark_safe
import pytz
from corehq import Domain
from corehq.apps import reports
from corehq.apps.app_manager.models impor... | SEL-Columbia/commcare-hq | corehq/apps/reports/models.py | Python | bsd-3-clause | 32,904 | [
"VisIt"
] | efff56c3a09af3ce3008638028ecd85d9a8c9b0b1d8f45d905a7a72fcf9359c1 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | bgoli/pysces | pysces/core2/InfixParser.py | Python | bsd-3-clause | 18,506 | [
"PySCeS"
] | 22dc76a4e755186afa81bd2ad729b2e97aa40aaa4fc922e54f913c617024fba0 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2015 by Tobias Houska
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Tobias Houska
This class holds the LatinHyperCube algorithm based on McKay et al. (1979):
McKay, M. D., Beckman, R. J. and Conover, W. J.: Comparison of Three Methods for Sel... | gitporst/spotpy | spotpy/algorithms/lhs.py | Python | mit | 5,271 | [
"Gaussian"
] | b5bfc23c1df2c71eee3be339030bbeb605ff5fb8b1474141f217df8f07fad4f9 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageWrapPad(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | nagyistoce/devide | modules/vtk_basic/vtkImageWrapPad.py | Python | bsd-3-clause | 487 | [
"VTK"
] | 8b3e7e56dea9eb7af11bddbabb62ce61a512314c4b7a134d5e99474ce96e12ac |
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
# check checkpointing for Regression with IRLSM.
def testGLMCheckpointGaussianLambdaSearch():
print("Checking checkpoint for regression with la... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_PUBDEV_7890_glm_checkpoint_IRLSM_gaussian_lambda_search.py | Python | apache-2.0 | 2,128 | [
"Gaussian"
] | 7c10cf96ceda1481448eafebacbb5a04c39bdd34d04446b2223353456c285476 |
""" A set of common tools to be used in pilot commands
"""
__RCSID__ = '$Id$'
import sys
import time
import os
import pickle
import getopt
import imp
import urllib2
import signal
def printVersion(log):
log.info("Running %s" % " ".join(sys.argv))
try:
with open("%s.run" % sys.argv[0], "w") as fd:
pick... | chaen/DIRAC | WorkloadManagementSystem/PilotAgent/pilotTools.py | Python | gpl-3.0 | 18,093 | [
"DIRAC"
] | 9264a279e2e2e67d87b6064feeaa296877134ed7dd02c91fb75a5b7713a0909b |
"""Read and write ASE2's netCDF trajectory files."""
from ase.io.pupynere import NetCDFFile
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
def read_netcdf(filename, index=-1):
nc = NetCDFFile(filename)
dims = nc.dimensions
vars = nc.variables
positions = va... | grhawk/ASE | tools/ase/io/netcdf.py | Python | gpl-2.0 | 2,930 | [
"ASE",
"NetCDF"
] | 286fa9fdbe9f5678bca65e9397f0b66f8a5059f68c5501c9759945b071b9b9b0 |
# Lint as: python3
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | tensorflow/lingvo | lingvo/core/inference_graph_exporter_test.py | Python | apache-2.0 | 16,688 | [
"Gaussian"
] | b449737446b4dd774bc3418b6180cf953a1e38a826cdd232e735cdc502bfca96 |
# -*- coding: utf-8 -*-
"""Warnings for old TSV conversion module."""
import warnings
from ..triples import to_edgelist
from ..triples import to_triples_file as to_tsv
__all__ = [
"to_tsv",
"to_edgelist",
]
warnings.warn(
"""Use pybel.io.triples module instead. Changes in PyBEL v0.15.0:
- pybel.to_t... | pybel/pybel | src/pybel/io/tsv/__init__.py | Python | mit | 423 | [
"Pybel"
] | e9a3565a4c2b43aa24782e2f253898d4f89a836a5e39bb6c14828848220d469d |
from setuptools import setup
from argparse2tool import __version__
with open("README.rst") as fh:
readme = fh.read()
setup(
name="argparse2tool",
version=__version__,
description="Instrument for forming Galaxy XML and CWL tool descriptions from argparse arguments",
author="Helena Rasche, Anton Kh... | erasche/argparse2tool | setup.py | Python | apache-2.0 | 1,174 | [
"Galaxy"
] | 1bb1dc108f26ffc5de47a790357dd9dd36ee69ed1bce993771d19e6694dd86f7 |
"""
StdoutBackend wrapper
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import logging
import sys
from DIRAC.Resources.LogBackends.AbstractBackend import AbstractBackend
from DIRAC.FrameworkSystem.private.standardLogging.Formatter.... | ic-hep/DIRAC | src/DIRAC/Resources/LogBackends/StdoutBackend.py | Python | gpl-3.0 | 1,650 | [
"DIRAC"
] | 15b8841040b06e0e5926ddc8fb1a886bcefd249f368c2592dca933dd535468c1 |
#!/usr/bin/python2.7
"""
Returns a bed-like translation of a CDS in which each record corresponds to
a single site in the CDS and includes additional fields for site degenaracy,
position ind CDS, and amino acid encoded.
usage: %prog nibdir genefile [options]
-o, --outfile=o: output file
-f, --format=f: ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/bx_python-0.7.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/gene_fourfold_sites.py | Python | apache-2.0 | 7,678 | [
"Amber"
] | 8f76f17ebefbd7816a5ce2603d72b6bdab4c3ac848d568413881cd9fec0978de |
from pyrates.frontend import CircuitTemplate
from pyrates.utility.grid_search import grid_search
from pyrates.utility.visualization import plot_connectivity
import matplotlib.pyplot as plt
import numpy as np
# parameter definition
dt = 1e-3
dts = 1e-2
cutoff = 100.0
T = 200.0 + cutoff
start = int((0 + cutoff)/dt)
dur ... | Richert/BrainNetworks | CMC/analysis/spinal_cord_delay_fitting.py | Python | apache-2.0 | 2,866 | [
"NEURON"
] | f1bd7df12234daeb4cfd1d0e46f437c2351e2d32284b7e67ff7aaf900f2f3f90 |
from collections import OrderedDict
import os
import itertools
import re
import numpy as np
from copy import deepcopy
from collections import Iterable
from scipy.spatial.distance import cdist
from chargetools import constants, grids
from chargetools.exceptions import InputError
from chargetools.utils.utils import in... | jincheng95/charges-tools | chargetools/entities.py | Python | mit | 20,327 | [
"Gaussian"
] | fe0a6905440ede1ac6cd1fb8041721289668b46df31b6fd6bb58a12cb158679b |
"""BWA (https://github.com/lh3/bwa)
"""
import os
import signal
import subprocess
from bcbio.pipeline import config_utils
from bcbio import bam, utils
from bcbio.distributed import objectstore
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
from bcbio.ngsalign import alignprep, novoalign, postali... | lbeltrame/bcbio-nextgen | bcbio/ngsalign/bwa.py | Python | mit | 17,449 | [
"BWA"
] | 8bef8e0648eedf78715ae544d3c7baaa675a5d5781f05658c1539383a54806f8 |
#Ver. 0.1.0
#Authors: Dylan Wise & Zach Almon
import urllib.request
import re
import os
import platform
import sys
import string
import html
platformType = platform.system()
#Check All .re Expressions DONE
#Fix Chapter Names DONE
#Make Sure Titles are Good. DONE
#BUG: Manga doesnt have Chapte... | DylanTheWise/MangaMine | MangaMine (Bato).py | Python | gpl-2.0 | 29,387 | [
"Gaussian"
] | 6c4b9028489f8b8c62f37ba2cb472010575f700d1d60f2373723dc93ee699308 |
#!/usr/bin/python
# script extract a particular genome region
# version 3 - 4-12-2012 to simplify the previous 27-12-2011 version with "usine a gaz" class
# Usage bowtie_window_extraction.py <bowtie input> <geneID> <Upstream_coordinate> <Downstream_coordinate> <output> <minsize> <maxsize> <output_format>
import sys, ... | JuPeg/tools-artbio | unstable/local_tools/bowtie_window_extraction.py | Python | mit | 3,382 | [
"Bowtie"
] | 7d9a04763a3988c7cb9db4eac286e3ea5000378b3e92f43e36de92d58c0b0635 |
"""
This is a very simple service performance test. It calls the service with a message. The service
return the same message.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import time
from DIRAC.Core.Base.Client import Client
from DIRAC.Core.Base.Scr... | ic-hep/DIRAC | tests/Performance/Service/test_scripts/service.py | Python | gpl-3.0 | 946 | [
"DIRAC"
] | 2ddcdfec8dbf1ac956acfc609fd7fc335274ce3661914cbcad1a8aeca43d7180 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/delegates/currencydelegate.py | Python | gpl-2.0 | 1,203 | [
"VisIt"
] | 562f2b582b8d5f373258dfbe5e2f507f09820709b1995254234a8c780f9ce9bc |
#!/usr/bin/env python2.7
# coding=utf-8
""" _ + _ . .
|_||!_' Y
| ||._! |
Simple GR1 synthesizer from
[AIGER-like](http://fmv.jku.at/aiger/) GR1 format.
The format is described [here](https://github.org/5nizza/spec-framework).
Gmail me: ayrat.khalimov
"""
import argparse
from logging import Logger... | 5nizza/aisy | aisy.py | Python | mit | 21,602 | [
"VisIt"
] | 8158785254ab4a208eea93530d07d363e74da0453e7b2ac8e88d301a011dcc43 |
"""Window manager which controls any pop up windows from MPF. Used to display
game information, status, tests, keyboard-to-switch mapping, on screen DMD,
etc."""
# window.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
... | jabdoa2/mpf | mpf/media_controller/core/window.py | Python | mit | 5,616 | [
"Brian"
] | 6467a86fa7e9f4e1080f35800def87cea7fdad12d8d37a8f5a03f97b2b7e9085 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkQuadricDecimation(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkQuadricDecimation.py | Python | bsd-3-clause | 495 | [
"VTK"
] | 86bcc13a38173be75f9b0dbd08b1a2ef9979ecbf970312d305838394dab5bda3 |
# Copyright (C) 2014 Sereina Riniker
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Torsion Fingerprints (Deviation) (TFD)
According to a paper from Schulz-Gasch et a... | bp-kelley/rdkit | rdkit/Chem/TorsionFingerprints.py | Python | bsd-3-clause | 24,514 | [
"RDKit"
] | ab3bfbd8050301230994443e5cef7c28149aad0e5c2e0839f717a80ce39d4f0e |
# -*- coding: utf-8 -*-
# Copyright (C) 2005-2006 Joe Wreschnig
# Copyright (C) 2006-2007 Lukas Lalinsky
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
import struct
from mutage... | jetskijoe/headphones | lib/mutagen/asf/_util.py | Python | gpl-3.0 | 10,716 | [
"CRYSTAL"
] | 9bd2437e13ccd05417c55c410266327e175555ecd169a85c6b609adc62f0891d |
import unittest
import datetime
from kev import (Document,CharProperty,DateTimeProperty,
DateProperty,BooleanProperty,IntegerProperty,
FloatProperty)
from kev.exceptions import ValidationException, QueryError
from kev.query import combine_list, combine_dicts
from kev.testcase import k... | armicron/kev | kev/tests/documents.py | Python | gpl-3.0 | 12,189 | [
"Brian"
] | da41b6efd54d6b3f1a608ce0ae7f2c12cc0947ceb0aa63e9a8d4862fab9d14bc |
from numpy.testing import TestCase, run_module_suite, assert_,\
assert_raises
from numpy import random
from numpy.compat import asbytes
import numpy as np
class TestMultinomial(TestCase):
def test_basic(self):
random.multinomial(100, [0.2, 0.8])
def test_zero_probability(self):
random... | lthurlow/Network-Grapher | proj/external/numpy-1.7.0/numpy/random/tests/test_random.py | Python | mit | 23,877 | [
"Gaussian"
] | b889a1cf44aa08b030c2d935421dba83092ccb11482c3b14ac3883184ce66b0f |
# -*- coding: utf-8 -*-
## Copyright (c) 2015-2022, Exa Analytics Development Team
## Distributed under the terms of the Apache License 2.0
"""
Tests for :mod:`~exatomic.interfaces.cube`
#############################################
"""
import numpy as np
from unittest import TestCase
from exatomic.base import resource... | exa-analytics/exatomic | exatomic/interfaces/tests/test_cube.py | Python | apache-2.0 | 2,188 | [
"ADF"
] | d06566dae053882c2e0a2bfd64cb1139d679c76e4b08fed1c52e56af07831f9d |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
This ... | gadsbyfly/PyBioMed | PyBioMed/PyMolecule/PubChemFingerprints.py | Python | bsd-3-clause | 53,803 | [
"RDKit"
] | ff9e49d1fac82ec5b797f55a0aa681355bab3cdec473c93ca366bf43f453a818 |
import sys
import os
import numpy as np
import h5py
import multiprocessing
import cPickle
import ephem
import matplotlib.pyplot as plt
import types
from sklearn.gaussian_process import GaussianProcess
from sklearn.cross_validation import train_test_split
from sklearn import metrics, linear_model, tree, ensemble
# NOTE... | acbecker/solar | regress_bk.py | Python | mit | 10,580 | [
"Gaussian"
] | 76ff629a88fd89e509781c01bb3484be48b6b7e7d2671c343881bc929c97949a |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | yorvic/.vim | bundle/python-mode/pylibs/pylama/checkers/pylint/utils.py | Python | gpl-3.0 | 23,922 | [
"VisIt"
] | d7013a0628ceb5c390d38fa40b25a72255166a3b703a3da68ac00268a367feec |
from dulwich.repo import *
from dulwich.objects import *
import yaml
import os
import argparse
import shutil
import time
import datetime
from dateutil.tz import tzlocal
import uuid
from user import User
import hashlib
# Man is this ugly
from crypto.asymencdata import ASymEncData
from crypto.asymenc import ASymEnc
from... | jimktrains/freebooks | ledger.py | Python | gpl-3.0 | 8,782 | [
"ASE"
] | 0b246762607b4cdf5456749da0c2bcd2f176c825899ee32587d1d08a06e251f6 |
# AddHeaderForEdgeR/AddHeaderForEdgeR.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called AddHeaderForEdgeR
# User mika.yoshimura@riken.jp at 30/01/2015 16:38:14
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# c... | myoshimura080822/tools_of_rnaseq_on_docker_galaxy | AddGroupIdForDEGAnalysis/AddGroupIdForDEGAnalysis.py | Python | mit | 32,429 | [
"Galaxy"
] | 0ef8420231c2897b8d9f237c854de8738dddb4d82108a824d98cca59dc92d999 |
import pytest
from ethereum import tester
from ethereum import utils
from ethereum._solidity import get_solidity
solidity_currency = open('currency.sol').read()
serpent_currency = open('currency.se').read()
@pytest.mark.skipif(get_solidity() is None, reason="'solc' compiler not available")
def test_currency_apis():
... | LianaHus/dapp-bin | standardized_contract_apis/test.py | Python | mit | 7,672 | [
"MOOSE"
] | 9d6c8f81ca2e63f9b61d437f8c5e858c613afd6535f3718f9a92049c80fc1804 |
#!/usr/bin/env python2.5
#
# Copyright 2008 the Melange 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 applic... | MatthewWilkes/mw4068-packaging | src/melange/src/soc/views/helper/access.py | Python | apache-2.0 | 58,088 | [
"VisIt"
] | 1b2864d460fa5a4f3b1946b2fb13c024fbcfbbdb8b392663d4f87b58abd4f6ba |
import time
import os.path
import tensorflow as tf
import numpy as np
import networkDef as nn
import sys
from fiberfileIO import *
flags = tf.app.flags
FLAGS = flags.FLAGS
flags.DEFINE_integer('num_hidden', 1024, 'Number of hidden layers.')
flags.DEFINE_string('data_dir', '',
'Directory with the t... | PrinceNgattaiLam/Trafic | TraficLib/runClassification.py | Python | apache-2.0 | 9,752 | [
"VTK"
] | e23aabd00d2e021a62dd0788b4f82c7ff19e278066ec10a7bf799724cd1f89f3 |
""" Module that holds the ReportGeneratorHandler class
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN ReportGenerator
:end-before: ##END
:dedent: 2
:caption: ReportGenerator options
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/Service/ReportGeneratorHandler.py | Python | gpl-3.0 | 9,358 | [
"DIRAC"
] | 919db86b7bda5190c52df8cced924cea6df462fea0611470144b68ffd9b9a951 |
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to handle XML-RPC requests in a CGI
environment using CGIXMLRPCRequestHandler.
A list of possibl... | antb/TPT----My-old-mod | src/python/stdlib/SimpleXMLRPCServer.py | Python | gpl-2.0 | 25,681 | [
"Brian"
] | 30648bdf3db31b43b87f8c4b7ad723b49aef2364c841b6309cf77b0321e69301 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | kain88-de/mdanalysis | package/MDAnalysis/topology/ExtendedPDBParser.py | Python | gpl-2.0 | 2,608 | [
"MDAnalysis"
] | 6af94f32e7c9ddb25a9c25426a0f23b412e48ba40c9f3e91c043aa8f58d9cab5 |
#!/usr/bin/env python
# file parse.py: parsers for map file, distance matrix file, env file
__author__ = "Rob Knight"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Daniel McDonald", "Greg Caporaso",
"Justin Kuczynski", "Cathy Lozupone", "Jens Reeder",
"... | antgonza/qiime | qiime/parse.py | Python | gpl-2.0 | 32,670 | [
"BLAST"
] | ae5fd9871c10bf5c5d33ac725b71a9753c0c01d92b546ad2792496bdeadd2128 |
#!/afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs4/bin/python2.7
"""
Returns a bed-like translation of a CDS in which each record corresponds to
a single site in the CDS and includes additional fields for site degenaracy,
position ind CDS, and amino acid encoded.
usage: %prog nibdir genefile [options]
-o,... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/EGG-INFO/scripts/gene_fourfold_sites.py | Python | gpl-3.0 | 7,729 | [
"Amber"
] | 43ed4b1f8cb029767bd710dc7dd48f43ddb7df6f9deec1075f6eadc7752c6307 |
import os,md5,sys
from PyQt4.QtGui import *
from DisasmWin import *
import sqlite3
import json
import pefile
sys.path.append("distorm-read-only/build/lib/")
#sys.path.append("distorm-read-only/build/lib")
#from pydasm import *
BASE_ADDR = 0x0;
import distorm3
import mmap
from utils import *
import re
labels = {}
tovi... | drgowen/GarethDisasm-Python | garethdisasm.py | Python | gpl-3.0 | 11,800 | [
"VisIt"
] | 57d8d48d02a26c862880668cdebc99856903e08c7553b71eeb110f491e3670e6 |
# -*- coding: utf-8 -*-
__license__ = 'GPL v3'
__copyright__ = '2009, John Schember <john at nachtimwald.com>'
__docformat__ = 'restructuredtext en'
'''
Generic USB Mass storage device driver. This is not a complete stand alone
driver. It is intended to be subclassed with the relevant parts implemented
for a partic... | jelly/calibre | src/calibre/devices/usbms/driver.py | Python | gpl-3.0 | 23,538 | [
"VisIt"
] | c7882b1f5566e35830f40e6b49c5625b607c8f4b4e67587ad5b450e6428c766f |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/ferret/package.py | Python | lgpl-2.1 | 4,431 | [
"NetCDF"
] | 9cce4c6acddd1f8beb7be6073279b475b6b42c50845c9e0149c136596bd36c38 |
from __future__ import print_function
from string import Template
import neuroml
from .channel import Channel
from .biology import BiologyType
from .dataObject import DatatypeProperty, ObjectProperty, This
from .cell_common import CELL_RDF_TYPE
__all__ = ["Cell"]
# XXX: Should we specify somewhere whether we have N... | gsarma/PyOpenWorm | PyOpenWorm/cell.py | Python | mit | 6,111 | [
"BLAST",
"NEURON"
] | 364fb03e0ea6a8bbbd79d0b7f8c90965f18c0b9d4a3964ed0050970c87d45a1f |
__author__ = 'esteinig'
"""
seqD3
Version 0.1
Multiple Sequence Comparison Tool for interactive visualization in D3
Idea with reference to the BLAST Ring Image Generator (BRIG) by
Alikhan et al. (2012): http://sourceforge.net/projects/brig/
Manual and tutorials for seqD3: https://github.com/esteinig/seqD3.
Eike J.... | esteinig/seqD3 | seqD3.py | Python | gpl-2.0 | 42,067 | [
"BLAST",
"Biopython"
] | d2244033b13d47397ad93ff21caedbb32582381c02c382a29f2f310c69187625 |
"""
Tools for analysing the relationship between tidal stresses and tectonics on
icy satellites.
Written by U{Zane Selvans <http://zaneselvans.org>}
(C{U{zane.selvans@colorado.edu <mailto:zane.selvans@colorado.edu>}}) as part of
his Ph.D. dissertation research.
C{satstress} is released under GNU General Public Licens... | zaneselvans/satstress | satstress/__init__.py | Python | gpl-3.0 | 8,848 | [
"NetCDF"
] | 60c4d9e8dbd062f1899c0bbdc5faaaefe59f918df3954ee8d8fda866f28e89a7 |
from cached_property import cached_property
from .cigar import (
cigartuples_to_cigarstring,
cigar_to_tuple,
cigartuples_to_named_cigartuples
)
from collections import namedtuple
class BaseTag(object):
"""Generate class template for tags."""
def __new__(cls, header):
"""Return a Tag class... | bardin-lab/readtagger | readtagger/tags.py | Python | mit | 7,468 | [
"pysam"
] | a09595349f9bfdd0f1818df377ee8995070416786553bd6652d12d29bf54f4e0 |
"""
#python -c "import cyth, doctest; print(doctest.testmod(cyth.cyth_benchmarks))"
"""
from __future__ import absolute_import, division, print_function
import utool
import doctest
import ast
import astor
from cyth import cyth_helpers
def get_bench_text_fmt():
bench_text_fmt_ = r'''
" Autogenerated by cyth on... | aweinstock314/cyth | cyth/cyth_benchmarks.py | Python | apache-2.0 | 12,648 | [
"VisIt"
] | b164c927e64c4785b219468318f71109c6bd0175896e5c2df067774ab0ec970b |
"""
Test support for the HANDLE_OWNERS_NOT_AVAILABLE group flag, and calling
GetHandleOwners on MUC members.
By default, MUC channels should have the flag set. The flag should be unset
when presence is received that includes the MUC JID's owner JID.
"""
import dbus
from gabbletest import make_result_iq, exec_test, ... | jku/telepathy-gabble | tests/twisted/muc/test-muc-ownership.py | Python | lgpl-2.1 | 4,034 | [
"Brian"
] | 4d7a88013dd33b970cd03d8ca55df483dcaa7cd4df6513563a6912d2dfe8dde9 |
#!/usr/bin/env python
__description__ =\
"""
Parses the output from calc-rmsd.tcl and makes it pretty and R-readable.
"""
__author__ = "Michael J. Harms"
__date__ = "101122"
__usage__ = "calc-rsmd.py vmd_output_file"
import sys
HEADER = ["frame","ca_rmsd","lig_rmsd"]
class ParseVmdError(Exception):
"""
Gene... | harmsm/md-analysis-tools | global-rmsd/global-rmsd.py | Python | unlicense | 1,599 | [
"VMD"
] | 3cff9226b4b435a82d0370c944a03c1781fc0f6d9e071bd4ccdafdc35f7e214f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This is the entry point for the command-line interface (CLI) application.
.. note::
To learn more about Click visit the `project website <http://click.pocoo.org/5/>`_. There is
also a very helpful `tutorial video <https://www.youtube.com/watch?v=kNke39OZ2k0>`... | mndarren/Code-Lib | Python_lib/cliff/cli.py | Python | apache-2.0 | 4,674 | [
"VisIt"
] | f364d77041aee19170f502e230b570c55d7405b1c4528b2c26899b34228e1264 |
# Copyright (C) 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 versio... | KaiSzuttor/espresso | testsuite/scripts/test_importlib_wrapper.py | Python | gpl-3.0 | 15,753 | [
"ESPResSo",
"VisIt"
] | bf7167c306fffc28140a6005db7468b2630de0ef434b7a885c035523ed61ac15 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
###########################################################################
# Given the output of the vsearch-pipe after the BLAST this will create
# a SLRUM file to parse the BLAST data so as to create a single entry for
# each sequence. Based upon the BLAST data it will try a... | colford/nbgw-plant-illumina-pipeline | bin/vsearch-blast-summary.py | Python | gpl-3.0 | 9,724 | [
"BLAST"
] | d7ee1878da92d41a42a7a7523dd31ff37893c93a4e843e9b08fa2419a6da75b3 |
"""
A serial module for accessing data from a vehicles OBD-II port
For more documentation, visit:
https://github.com/brendanwhitfield/python-OBD/wiki
"""
########################################################################
# #
# python-OBD: ... | cloud-rocket/python-OBD | obd/__init__.py | Python | gpl-2.0 | 2,488 | [
"VisIt"
] | 67d668f787e34793d85cc76554c9253a9801afac3764bd66aa6db9f244c0f80c |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Classes corresponding to phyloXML elements.
See Also
--------
Official specification... | LyonsLab/coge | bin/last_wrapper/Bio/Phylo/PhyloXML.py | Python | bsd-2-clause | 47,107 | [
"Biopython"
] | b3cf7de19fac886cf705403bb5f175338d7ab46649e641131ba92b5b05177f90 |
# Copyright 2009 by Cymon J. Cox. 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.
"""Command line wrapper for the multiple alignment program PRANK.
"""
from __future__ import pr... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Align/Applications/_Prank.py | Python | gpl-2.0 | 10,752 | [
"Biopython"
] | f9b0cc772b4d4696c0c0ebf10610a8162929227c8ac0308120b681110e1b378b |
#/usr/bin/python3
__author__ = 'johannes'
import numpy as np
import functools
class SRM:
""" SRM_0 (Spike Response Model) """
def __init__(self, neurons, threshold, t_current, t_membrane, eta_reset, simulation_window_size=100, verbose=False):
"""
Neurons can have different threshold, t_current... | johannesmik/neurons | neurons/spiking.py | Python | bsd-2-clause | 10,482 | [
"NEURON"
] | a8fc128434061f7f9723b87cd5900790b71d82dd23d47ce31ff2d4d8c9642a6b |
from nose.tools import *
from nose.plugins.attrib import attr
import json
import shutil
import os
import tempfile
import logging
import copy
import stat
from mock import patch
from optparse import OptionParser
from biomaj.bank import Bank
from biomaj.session import Session
from biomaj.workflow import Workflow, Upd... | markiskander/biomaj | tests/biomaj_tests.py | Python | agpl-3.0 | 38,862 | [
"BLAST"
] | 481af5c41b23113442d2456f992c6e576122a4d3d665c32ffd75d8740e09d645 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*
# Name: isodump3.py
# Purpose: Module to list and extract iso files.
# Authors: LiQiong Lee (written exclusively for multibootusb)
# Licence: This file is a part of multibootusb package. You can redistribute it or modify
# under the terms of GNU General Public Licens... | alindt/multibootusb | scripts/isodump3.py | Python | gpl-2.0 | 29,132 | [
"VisIt"
] | 1d2329d75dbcbbdff4dfc4edc74c509e477c82566701cf7f8b5c6f4d3db72c08 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008-2011 Kees Bakker
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Softw... | pmghalvorsen/gramps_branch | gramps/plugins/importer/importprogen.py | Python | gpl-2.0 | 55,893 | [
"Brian"
] | 7da37b305073aad3f8135b68c5bea80b15b0834c3d49e69de34fb0b3073cb2d7 |
#!/usr/bin/env python3
import argparse
import os
import csv
import datetime
import getpass
from selenium import webdriver
from scraper import Page
DATA_DIR = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data')
parser = argparse.ArgumentParser()
parser.add_argument(
'-b', '--browser',
choices=... | skamsie/facebook-friends-tracker | scrutinize.py | Python | mit | 2,264 | [
"VisIt"
] | cff068235f59ce37203e393da2bd8b9fec633369917c5a2bca10054e5af5ba58 |
import os
import sys
import glob
import shutil
import subprocess
def cmd(c):
x = os.system(c)
assert x == 0, c
def fail(subject, email=None, filename='/dev/null', mailer='mail'):
assert mailer in ['mailx', 'mail', 'mutt']
import os
if email is not None:
if filename == '/dev/null':
... | robwarm/gpaw-symm | tools/niflheim-agts.py | Python | gpl-3.0 | 5,426 | [
"ASE",
"GPAW"
] | 2cb540b0e4b3aba10705d24149ec7dccb632b244f97d0515391ea0a2c97c1a6a |
#!/usr/bin/env python2
import numpy,re,sys
def pyscf2QP(cell,mf, kpts=[], int_threshold = 1E-15):
# The integral will be not printed in they are bellow that
PBC=False
ComputeMode= re.split('[. ]', str(mf))
print 'ComputeMode=',ComputeMode
for n in ComputeMode:
if n in ("UHF","KUHF","UKS"):
... | TApplencourt/quantum_package | plugins/tapplencourt/pyscf/PyscfToQp.py | Python | gpl-3.0 | 4,289 | [
"PySCF"
] | 8979760b24548690a50e310b500aeab5955515dd2e8bd6cd35aaa696d3181e88 |
"""
Test Levels
"""
__RCSID__ = "$Id$"
import unittest
from DIRAC.FrameworkSystem.private.standardLogging.test.TestLoggingBase import Test_Logging, gLogger
class Test_Levels(Test_Logging):
"""
Test get and set levels.
"""
def test_00shown(self):
"""
Test the validity of the shown method
"""
... | andresailer/DIRAC | FrameworkSystem/private/standardLogging/test/Test_Levels.py | Python | gpl-3.0 | 6,874 | [
"DIRAC"
] | 5df9c368b58bc09e4a29f2c4834d199f205ca91e9ee54e5c589baf50e5b12aa0 |
"""
Support for running a tool in Galaxy via an internal job management system
"""
from abc import ABCMeta
from abc import abstractmethod
import time
import copy
import datetime
import galaxy
import logging
import os
import pwd
import random
import re
import shutil
import subprocess
import sys
import traceback
from ga... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/__init__.py | Python | gpl-3.0 | 87,953 | [
"Galaxy"
] | d8d1021ff6bd006310fb1ed158478494e52846d88d7898fcffa8dda2eeafb744 |
# -*- coding: utf-8 -*-
# Copyright (C) 2009 Canonical
#
# Authors:
# Michael Vogt
#
# 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; version 3.
#
# This program is distributed in the hope that... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/software-center/softwarecenter/backend/reviews.py | Python | gpl-3.0 | 46,555 | [
"exciting"
] | 5c0f7fbdb9e37dabd072831535aea81d66314db9db032c41f570531421c31987 |
# -*- 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 import defaults as default_views
from django.views.generic import TemplateView
from fi... | TejasM/Personal | config/urls.py | Python | bsd-3-clause | 2,482 | [
"VisIt"
] | 6c8ff3c3a79a2b080e5d33bc855a5cdacff916e64f08906523a3507e8e17ac9f |
#!/usr/bin/python
import csv
import glob
from numpy.distutils import cpuinfo
from optparse import OptionParser
import os
import re
from subprocess import Popen, call, check_call
import subprocess
import sys
import time
parser = OptionParser( usage = "%prog [otions] number" )
parser.add_option( "--spec-config", help =... | eschulte/goa | bin/collect_model_data.py | Python | gpl-3.0 | 6,660 | [
"GAMESS",
"Gromacs",
"NAMD"
] | 86c1f32cd00dcd7d304dea4d80d0761b4833a1c4398c22a087c25792cb847b8a |
# Orca
#
# Copyright 2014 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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 o... | h4ck3rm1k3/orca-sonar | src/orca/spellcheck.py | Python | lgpl-2.1 | 9,432 | [
"ORCA"
] | 6a6c92088b053aab5d751b43c77dbcd9f755e0a2ef4804dcad39f4844a1f1693 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# XCode Project Creator
#
import os, sys, re, shutil, codecs
from shutil import copyfile
from os.path import join, splitext, split, exists
from datetime import date
template_dir = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
from tools import *... | gianina-ingenuity/titanium-branch-deep-linking | testbed/x/mobilesdk/osx/5.5.1.GA/iphone/projector.py | Python | mit | 8,529 | [
"VisIt"
] | 15792612048a6d3c7808280083f64e66998392614a7546cac47806ac002674a4 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/aliases.py | Python | lgpl-3.0 | 7,396 | [
"Psi4"
] | 4be739119ed3da23a197a8fe13737cafddd4c5e74c95e173cb7e16986b38d062 |
import numpy as np
import theano
import theano.tensor as T
from theano.tensor.signal import pool
from lasagne import init
from lasagne import nonlinearities
from lasagne import layers
from lasagne.theano_extensions import padding
from lasagne.utils import as_tuple
floatX = theano.config.floatX
# Duplicate of conv1d ... | ciaua/clip2frame | clip2frame/layers.py | Python | isc | 32,463 | [
"Gaussian"
] | e2344c0e4a7708d704e56ea1473b4bbfa65d1a1e814e20063c5bb0ac7ef481b2 |
#!/usr/bin/env python
#
# Data manager for reference data for the 'mothur_toolsuite' Galaxy tools
import json
import optparse
import os
import shutil
import sys
import tarfile
import tempfile
import urllib2
import zipfile
# When extracting files from archives, skip names that
# start with the following strings
IGNORE_... | blankclemens/tools-iuc | data_managers/data_manager_mothur_toolsuite/data_manager/fetch_mothur_reference_data.py | Python | mit | 18,096 | [
"Galaxy"
] | 6ddc0232fb6f7dc9876a7163149707e8b1ab353d7f306b0ce567d6c462a5f421 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max-Planck-Institute of Neurobiology, Munich, Germany
# Authors: Philipp Schubert, Joergen Kornfeld
import copy
import re
from typing import Union, Tuple, List, Optional, Dict, Generator, Any, Iterator
import netw... | StructuralNeurobiologyLab/SyConn | syconn/reps/segmentation.py | Python | gpl-2.0 | 73,145 | [
"NEURON"
] | afa72548310be5c73c86d846f408a6d7ca4d92d72a763edfde359959bd2d9609 |
#!/usr/bin/env python
# Copyright (C) 2012 Tianyang Li
#
# 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... | tianyang-li/meta-transcriptome | trans-len/get_SAM_aligned_query_ids.py | Python | gpl-3.0 | 1,493 | [
"HTSeq"
] | 238e496c291e8a4aceb12587e876d687bffa937f3a958bdec37d88123d2533aa |
#! /usr/bin/python
# -*- coding: utf-8 -*-
#
# Vladimír Slávik 2010 - 2011
# Python 2.6
#
# for Simutrans
# http://www.simutrans.com
#
# code is public domain
#
#
# creates a timeline chart for given objects
#-----
from __future__ import print_function
#-----
paksize = 128 # default only
stop_year = 2050 # d... | simutrans/pak128 | tools/timeline-chart.py | Python | artistic-2.0 | 13,461 | [
"VisIt"
] | ea477654921c5a4ba5b48a779635433bff0417cc5e1c78cd6569b556e3cb4611 |
from math import pi, cos, sin, sqrt, acos
from ase.atom import Atom
from ase.atoms import Atoms
from ase.parallel import paropen
def read_I_info(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
lines = fileobj.readlines()
del lines[0]
finished = False
s = Atoms(... | freephys/python_ase | ase/io/cmdft.py | Python | gpl-3.0 | 585 | [
"ASE"
] | ceed440997ec050cdaf499324b8d828685780610f98af5019e41d1cd615cb15d |
"""Parsing functions for Binvox files.
https://www.patrickmin.com/binvox/binvox.html
Exporting meshes as binvox files requires binvox CL tool to be on your path.
"""
import os
import subprocess
import numpy as np
import collections
from distutils.spawn import find_executable
from .. import util
from ..base import T... | dajusc/trimesh | trimesh/exchange/binvox.py | Python | mit | 17,700 | [
"VTK"
] | dcfd2fed22458fa69deb9b1f2321cb8cf30fb7cfb031ee2b5f0f1016ec2e7715 |
from __future__ import print_function
from __future__ import absolute_import
import unittest
import csv
import PyOpenWorm
from PyOpenWorm.worm import Worm
from PyOpenWorm.cell import Cell
from PyOpenWorm.neuron import Neuron
from PyOpenWorm.connection import Connection
from PyOpenWorm.context import Context
from PyOpe... | gsarma/PyOpenWorm | tests/DataIntegrityTest.py | Python | mit | 19,722 | [
"NEURON"
] | 750487f8761916f06f1fed532dcd993930a4761ad8fd0585acf47adaed1ba45f |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authen... | ZLLab-Mooc/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 96,983 | [
"VisIt"
] | bf4a602fd3289a29db45a946abc597b2a7752123c8d164b198b28b28194ff712 |
# -*- coding: utf-8 -*-
# Copyright (C) 2015-2020 by Brendt Wohlberg <brendt@ieee.org>
# All rights reserved. BSD 3-clause License.
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""Signal and image processin... | bwohlberg/sporco | sporco/signal.py | Python | bsd-3-clause | 11,378 | [
"Gaussian"
] | 38d4c40f8db154a25158bd761c80226da6c1e2ccfacb58dbb4c13a94010fd11a |
from itertools import product
import os
import numpy as np
from openfermion.config import DATA_DIRECTORY
from openfermion.chem import MolecularData, make_reduced_hamiltonian
from openfermion.linalg import wedge
from openfermion.linalg.erpa import singlet_erpa, erpa_eom_hamiltonian
from openfermion.transforms.opconversi... | quantumlib/OpenFermion | src/openfermion/linalg/erpa_test.py | Python | apache-2.0 | 4,973 | [
"PySCF"
] | 6be074c09af6449204f5144cf9e3bcdfadd10dd583adb2f1a79dd544a696799c |
# -*- coding: utf-8 -*-
"""
Tests for user authorization password-related functionality.
"""
import json
import logging
import re
from datetime import datetime, timedelta
import ddt
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core import mail
from django.core.cache impor... | msegado/edx-platform | openedx/core/djangoapps/user_authn/views/tests/test_password.py | Python | agpl-3.0 | 13,150 | [
"VisIt"
] | 9d16636869e50f69d12a70b325e28efa943816ee0db60f74da8964290d9eaed3 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/eccodes/package.py | Python | lgpl-2.1 | 4,224 | [
"NetCDF"
] | 06c6a1a6dd8c88e6f509584d5824ab5a3f3ce6775ab05c283cc8e5e710f84b3c |
import numpy as np
from ase.utils import rotate, irotate
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
print(xyz)
print(ixyz)
#print np.around(a-a2, 5)
assert abs(a-a2).max() < 1e-10
test('10z')
test('155x,43y,190z')
test('55x,90y,190z')
test('180x,-90y... | suttond/MODOI | ase/test/rotate.py | Python | lgpl-3.0 | 644 | [
"ASE"
] | 2b782c9f8170e9af6552c04ca5a942999b1f1745ef097e99b8873800ba2eb235 |
# $HeadURL$
__RCSID__ = "$Id$"
import types
import os
import datetime
from DIRAC import S_OK, S_ERROR, rootPath, gConfig, gLogger, gMonitor
from DIRAC.AccountingSystem.DB.AccountingDB import AccountingDB
from DIRAC.AccountingSystem.private.Summaries import Summaries
from DIRAC.AccountingSystem.private.DataCache import... | avedaee/DIRAC | AccountingSystem/Service/ReportGeneratorHandler.py | Python | gpl-3.0 | 8,961 | [
"DIRAC"
] | a60f6c5dfe5f771b4cc32a8ab35b9db8bb12647b1d717fb35137accdec53ef15 |
# Copyright (C) 2018 Charlie Hoy, Collin Capano
# 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... | sfairhur/pycbc | pycbc/inference/models/marginalized_gaussian_noise.py | Python | gpl-3.0 | 25,814 | [
"Gaussian"
] | 9ef597cdca4778b4d21559863cbfb1bee4abda6c1bb096ba973a5f1eaf2edc98 |
# -*- coding: utf-8 -*-
#
# This file is part of Harvesting Kit.
# Copyright (C) 2013, 2014, 2015 CERN.
#
# Harvesting Kit is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or ... | jalavik/harvesting-kit | harvestingkit/elsevier_package.py | Python | gpl-2.0 | 49,386 | [
"VisIt"
] | 08b8964cd5d464fda0757ec3db7ad52c9626c5bec49e3ae7111126cf91bfe4a4 |
# Django
from django.conf import settings
from django.utils.translation import ugettext_lazy as _
# Tower
from awx.conf import fields, register
from awx.conf import settings_registry
# Define a conf.py file within your app and register each setting similarly to
# the example below. Any field class from Django REST Fr... | GoogleCloudPlatform/sap-deployment-automation | third_party/github.com/ansible/awx/awx/conf/conf.py | Python | apache-2.0 | 3,506 | [
"MOOSE"
] | 092025adf9fec34c20130f030e36b9e1c89168157a38bcc8b96e53417c06551b |
# Copyright 1999 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 the sprotXX.dat file from
SwissProt.
http://www.exp... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SwissProt/SProt.py | Python | apache-2.0 | 50,022 | [
"Biopython"
] | 62a9e3c7a5b038c8f0ad43042caa583fed78dbe6781e9e7bea7bfd6107c2692e |
# Copyright (c) 2007-2009 Pedro Matiello <pmatiello@gmail.com>
# Johannes Reinhardt <jreinhardt@ist-dein-freund.de>
# Rhys Ulerich <rhys.ulerich@gmail.com>
# Roy Smith <roy@panix.com>
# Salim Fadhley <sal@stodge.org>
# ... | cwacek/experimentor_tools | pygraph/algorithms/minmax.py | Python | mit | 15,697 | [
"VisIt"
] | 569e2906f03aacc1157a47d852c8c748c47a2d91cf14ba653f9cc53d6ad11eae |
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