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#!/usr/bin/env python
# Copyright (c) 2014 Michael Strosaker
# MIT License
# http://opensource.org/licenses/MIT
import sys
try:
import unittest2 as unittest
except ImportError:
import unittest
sys.path.insert(0, '..')
import hmm
class TestHMMConstructor(unittest.TestCase):
def test_simple_hmm(self):
... | mstrosaker/hmm | test/test.py | Python | mit | 5,887 | [
"VisIt"
] | 1f4bc6ea4dcf4980373c1fcc7382fb0e0048965947534d011b0a73e420834da3 |
"""This package contains irf items."""
from typing import List
import numpy as np
from glotaran.model import model_attribute, model_attribute_typed
from glotaran.parameter import Parameter
@model_attribute(has_type=True)
class IrfMeasured:
"""A measured IRF. The data must be supplied by the dataset."""
@model... | glotaran/glotaran | glotaran/builtin/models/kinetic_image/irf.py | Python | gpl-3.0 | 3,156 | [
"Gaussian"
] | 013056a1809b9cbf4878e6d3bd4f2c4bba909563c9e2547c08c526b7f69421e6 |
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Python
abstract syntax grammar. The abstract syntax itself might change with
each Python release; this module helps to find out programmatically what
the current grammar looks like and allows modifications of it.
... | brython-dev/brython | www/src/Lib/ast.py | Python | bsd-3-clause | 59,572 | [
"VisIt"
] | 82b49d8f184bdc8906f7e66231b05294d937ccfef9f3a53c13500e938f049f86 |
"""
Utility functions used across scripts.
"""
__author__ = "Shyue Ping Ong, Dan Gunter"
__copyright__ = "Copyright 2012-2014, The Materials Project"
__version__ = "1.1"
__maintainer__ = "Dan Gunter"
__email__ = "dkgunter@lbl.gov"
__date__ = "2012-12-01"
## Imports
import bson
import datetime
import json
import loggi... | materialsproject/pymatgen-db | pymatgen/db/util.py | Python | mit | 3,028 | [
"pymatgen"
] | 8c489597919c2a7973a4ea117fc6f76e75d5866ad20d290178bff552189a4d4b |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0079_auto_20150828_2156'),
]
operations = [
migrations.RenameField(
model_name='visit',
old... | koebbe/homeworks | visit/migrations/0080_auto_20150828_2201.py | Python | mit | 382 | [
"VisIt"
] | b7f87272b6b3bafa06c9fec934ca59702ff495596eb20ce0a6c5c80b58e2e218 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | code-sauce/tensorflow | tensorflow/contrib/distributions/python/ops/distribution.py | Python | apache-2.0 | 37,886 | [
"Gaussian"
] | 86b7fea2c7dddd2072f9190657bc3613a1f065cd03c4b9856c78c3e9d42f73db |
# coding=utf-8
"""Pasta enables AST-based transformations on python source code."""
# Copyright 2021 Google LLC
#
# 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
#
# https://www.apache.org/... | google/pasta | pasta/__init__.py | Python | apache-2.0 | 922 | [
"VisIt"
] | 3f3b13539ef8c72663c6e7e06c560ea4a66ef9b7ff0e8d30a01c1edebbb1bbb8 |
"""
Utility functions for atmospheric data wrangling / preparation.
- ndarrays
- netCDF files
- Lat-lon geophysical data
- Pressure level data and topography
"""
from __future__ import division
import numpy as np
import pandas as pd
import collections
import scipy.interpolate as interp
from mpl_toolkits import basema... | jenfly/atmos-tools | atmos/data.py | Python | mit | 62,848 | [
"NetCDF"
] | cac08302714764075c216c0d035855bc9f22ff19f6a16a7d89fdcea889bc2d13 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_cluster.py | Python | bsd-3-clause | 3,776 | [
"VisIt"
] | d3df8759a0634355d879adcbf97e36b9691b2f5d496b5188f87c2e033258bf9c |
# vim: set et ts=4 sw=4 fileencoding=utf-8:
'''
pycsync.auth
============
Module for authentication related functions.
'''
from os.path import join as pjoin
import flickr_api as fapi
def request_token(rootdir, input_func=raw_input):
'''
Request an auth token. Prompt the user to accept the client API key and... | shadowfax-chc/pycsync | pycsync/auth.py | Python | isc | 1,381 | [
"VisIt"
] | 4d929e2772c6569ed83964211a9d3c47f071caec11e6cd3c5cd24a77033def85 |
# Generated from java-escape by ANTLR 4.5
from antlr4 import *
# This class defines a complete generic visitor for a parse tree produced by ModelParser.
class ModelVisitor(ParseTreeVisitor):
# Visit a parse tree produced by ModelParser#model.
def visitModel(self, ctx):
return self.visitChildren(ctx)
... | SDXorg/ANTLR_collection | Compiled/Python_Vensim/ModelVisitor.py | Python | mit | 3,764 | [
"VisIt"
] | 31fd140b0a5f0aa6056d64d581b35e293b8a66755872561f947df502e8e5f528 |
"""
Most descriptor compounds selection
"""
# Author: Giuseppe Marco Randazzo gmrandazzo@gmail.com
# License: BSD 3 clause
from numpy import zeros, array
class MDC(object):
"""Perform Most-Descriptor-Compound object selection
Parameters
----------
dmx : array, shape(row,row)
A square distance... | zeld/scikit-optobj | optobj/mdc.py | Python | bsd-3-clause | 4,248 | [
"Brian"
] | 5a3b4d1c2fafd3ce4ae5fe27c9fd2e89030a962ea53f32fcc7fe2103b88e6883 |
'''
The settings for OSMC are handled by the OSMC Settings Addon (OSA).
In order to more easily accomodate future changes and enhancements, each OSMC settings bundle (module) is a separate addon.
The module can take the form of an xbmc service, an xbmc script, or an xbmc module, but it must be installed into the u... | mega-force/osmc | package/mediacenter-addon-osmc/src/script.module.osmcsetting.pi/resources/osmc/OSMCSetting.py | Python | gpl-2.0 | 33,044 | [
"VisIt"
] | e9bec3755055ad9b13897373f7fc2955fb675d47e34ddeeebcc20b0749f44b60 |
# sql/compiler.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.c... | davidfraser/sqlalchemy | lib/sqlalchemy/sql/compiler.py | Python | mit | 100,317 | [
"VisIt"
] | 138ed5856d2f5d38405f9b8bb82b3385f3fbe1fd11543d539cf33995886ef91a |
import ast
import inspect
import os
if __name__ == '__main__':
import django
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "sapl.settings")
django.setup()
if True:
from scripts.lista_urls import lista_urls
def get_decorators(cls):
target = cls
decorators = {}
def visit_functionDef(n... | interlegis/sapl | scripts/lista_permissions_in_decorators.py | Python | gpl-3.0 | 4,034 | [
"VisIt"
] | 6093053ca630bfe0f5d8d76ae33c7234e5caf4b2d530b0ae0e1f7aae85cfcb79 |
"""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... | tedkulp/bossogg | boss3/xmlrpc/SimpleXMLRPCServer.py | Python | gpl-2.0 | 17,480 | [
"Brian"
] | 6b871bc9e3dbd5fe6a1742a7a8d846606f8ad0633e54a4d35782b4907e9dd6f9 |
import enum
class OutputPort(enum.Enum):
"""Indicate the intended transmitting part of an executable."""
standard = 0
"""Standard, value-based, output port."""
class InputPort(enum.Enum):
"""Indicate the intended receiving part of an executable."""
standard = 0
"""Standard, value-based, outp... | project-rig/nengo_spinnaker | nengo_spinnaker/builder/ports.py | Python | mit | 778 | [
"NEURON"
] | 9f4db9df7675453306c6ba21ede6a84488c79f044fa9ea22eaf520e86583832a |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines standard transformations which transforms a structure into
another structure. Standard transformations operate in a structure-wide manner,
rather than site-specific manner.
All transformations should inherit the AbstractTransfor... | Dioptas/pymatgen | pymatgen/transformations/standard_transformations.py | Python | mit | 26,522 | [
"pymatgen"
] | d75ff902bb3f1c84137fc4d42970ed221d380e29c7e34891e57597855eaaead7 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
__RCSID__ = "$Id$"
from DIRAC import exit as DIRACExit
from DIRAC.Core.Base import Script
Script.setUsageMessage( """
Get the gi... | vmendez/DIRAC | DataManagementSystem/scripts/dirac-dms-replica-metadata.py | Python | gpl-3.0 | 1,519 | [
"DIRAC"
] | b03d431f659eee120c21c84c553985dc8b7900eca5b9f73ec0d7f6b563b90324 |
# Copyright (c) 2015-2017 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | kharkevich/molecule | molecule/config.py | Python | mit | 12,696 | [
"Galaxy"
] | c0249baaa7baa2a4352fdd983b6cc128b6c90c38f80eea1314f16e2eec957baa |
import ast
from unittest import (
TestCase,
)
from darglint.analysis.variable_visitor import (
VariableVisitor,
)
from .utils import (
reindent,
)
class VariableVisitorTests(TestCase):
def assertFound(self, program, *variables):
"""Assert that the return was found.
Args:
... | terrencepreilly/darglint | tests/test_variable_visitor.py | Python | mit | 2,326 | [
"VisIt"
] | 0c6edb15973464affd50ff9a9de709e8bbc40da0526541508f2f14a7147d6062 |
from __future__ import with_statement
import py
import sys
from rpython.rlib.parsing.tree import Nonterminal, Symbol, RPythonVisitor
from rpython.rlib.parsing.codebuilder import Codebuilder
from rpython.rlib.objectmodel import we_are_translated
class BacktrackException(Exception):
def __init__(self, error=None):
... | jptomo/rpython-lang-scheme | rpython/rlib/parsing/makepackrat.py | Python | mit | 24,419 | [
"VisIt"
] | 9e31109f473950a8f1ec9c0ef9b4e080b9c218a7b914bec451377630af9e26bf |
import os
import subprocess
from gpaw.test.big.agts import Cluster
class NiflheimCluster(Cluster):
def __init__(self, asepath='', setuppath='$GPAW_SETUP_PATH'):
self.asepath = asepath
self.setuppath = setuppath
def submit(self, job):
dir = os.getcwd()
os.chdir(job.dir... | ajylee/gpaw-rtxs | gpaw/test/big/niflheim.py | Python | gpl-3.0 | 2,816 | [
"GPAW"
] | e815b4ee37188ce45cea05ece28524cd3e60e2dc43a7317e77344933933b4820 |
import os
from __main__ import slicer
import qt, ctk
from SampleData import *
#
# BenderSampleData
#
# To add new data, edit the ui file to add case to the tree.
# and fill the corresponding information in the BenderSampleDataLogic
# download data dictionnary.
class BenderSampleData:
def __init__(self, parent):
... | ricortiz/BenderCraniosynostosis | Modules/Scripted/BenderSampleData/BenderSampleData.py | Python | apache-2.0 | 10,423 | [
"VTK"
] | daa4154d5a5ff6aa395962e759e1943c9fd0f411a55f05a3c623b0c63facc47d |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
from __future__ import unicode_literals
import bindings as bi
import sys
PY3 = sys.version_info[0] == 3
str_type = str if PY3 else (str, unicode)
# We specify these not as real types, but as parameter annotations in the docstrings
class PythonTypeTranslatorForCheck(bi.T... | h2oai/h2o-dev | h2o-bindings/bin/gen_python.py | Python | apache-2.0 | 33,158 | [
"Gaussian"
] | 758d8501ab3687bf5ab94102cc4a0f7238173c0b6486a172eec7da55c002123b |
import csv
import getopt
import json
import logging
import os
import shutil
import sys
import time
from urllib.parse import urlencode
import numpy as np
import requests
class ONav_Profiling_Driver:
def __init__(
self,
base_url,
config_url,
csv_file,
prof_path,
user... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | scripts/profiling_scripts/api_profiling_driver.py | Python | gpl-3.0 | 22,858 | [
"Gaussian"
] | 34473d8ce78717bc4c000f705ea414c60e5aeac0addf9919735c3e950114659c |
from mptypes import (mp, mpf, mpmathify, inf,
eps, nstr, make_mpf, AS_POINTS, fdot)
from functions import pi, exp, log, ldexp
from libmpf import mpf_neg
import math
def NEG(x):
return make_mpf(mpf_neg(x._mpf_))
class Quadrature(object):
"""
Quadrature rules are implemented using this class, in order... | hazelnusse/sympy-old | sympy/mpmath/quadrature.py | Python | bsd-3-clause | 35,806 | [
"Gaussian"
] | 22505d80fc0c7a3ecbde859038d71be5e03eb4fdebb0b8244c73b3c8023cafef |
# -*- coding: utf-8 -*-
"""Parser for the Google Chrome History files.
The Chrome History is stored in SQLite database files named History
and Archived History. Where the Archived History does not contain
the downloads table.
"""
from plaso.events import time_events
from plaso.lib import timelib
from plaso.l... | 8u1a/plaso | plaso/parsers/sqlite_plugins/chrome.py | Python | apache-2.0 | 11,487 | [
"VisIt"
] | 25082c38533e1f7886d65ba2b35a7d21b3bedda0c5fbbae2c651bd7c68d67e6b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/diversity/tests/test_block.py | Python | bsd-3-clause | 8,358 | [
"scikit-bio"
] | 1a14a0767ace01da879c0e9c72cdffa7537b1bb84efa4097a2462626f620217e |
#!/usr/bin/env python3
"""This module provide Gaussian and Gauss-Jordan eliminations on numpy
array of floats since they are not provided by numpy.
Note that matrix operations are straightforward with numpy.array, namely
add (+ -), scalar ops (+ - * / **) and mul (@), so try to make use of
the library while doing your... | McSinyx/hsg | toys/gauss.py | Python | gpl-3.0 | 3,141 | [
"Gaussian"
] | 99ea3ced5c435aff4616c9d33e2aaeedf7f682e68c3b186ced0fb0a8303b8cbd |
#!/usr/bin/env python
from __future__ import division
###############################################################################
# #
# som.py #
# ... | Ecogenomics/GroopM | groopm/som.py | Python | gpl-3.0 | 29,810 | [
"Gaussian"
] | 74258a3b29a044ae14260353db65b2fe028e1e74b329212284f604c4dc76e6b3 |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
"""Simple protein analysis.
Example,
X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
print X.... | bryback/quickseq | genescript/Bio/SeqUtils/ProtParam.py | Python | mit | 10,895 | [
"Biopython"
] | 110426c6b33b77c1715246c242476e3bf3a40eb10409f131e78d7fc32a5b58ed |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Sof... | tiagocardosos/stoq | plugins/ecf/ecfui.py | Python | gpl-2.0 | 27,339 | [
"VisIt"
] | c84f2bae7eb112d1d3462289f8d031835bfcb3aa688816aed01f2459f6e4a9dd |
# $HeadURL$
__RCSID__ = "$Id$"
import types
from DIRAC.Core.DISET.private.BaseClient import BaseClient
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
class InnerRPCClient( BaseClient ):
def executeRPC( self, functionName, args ):
stub = ( self._getBaseStub(), functionName, args )
retVal = sel... | Sbalbp/DIRAC | Core/DISET/private/InnerRPCClient.py | Python | gpl-3.0 | 928 | [
"DIRAC"
] | 3a5a23043a40ea830bbcdcf2f84ea3147681df38e025a6497f020c0c1a8b35eb |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | dgasmith/psi4 | psi4/driver/procrouting/dft/libxc_functionals.py | Python | lgpl-3.0 | 12,746 | [
"Psi4"
] | 69cb4c23b266ed942bf151b8e7588abe6dea6e22a509902bf713a61dc043e9ce |
#!/usr/bin/env python3
import argparse
import sys
try:
from pycgtool.pycgtool import main, map_only
from pycgtool.interface import Options
from pycgtool.functionalforms import FunctionalForms
except SyntaxError:
raise RuntimeError("PyCGTOOL requires Python 3.2 or greater")
if __name__ == "__main__":
... | jag1g13/pycgtool | pycgtool.py | Python | gpl-3.0 | 2,519 | [
"Gromacs"
] | d811d997e84fe38adc35673dec663e74dbc85d3798eca7aca18a47033432dd60 |
#!/usr/bin/python
"""
# Created on Aug 12, 2016
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com) GitHub ID: grastogi23
#
# module_check: supported
#
# Copyright: (c) 2016 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
"""
... | tersmitten/ansible | lib/ansible/modules/network/avi/avi_gslbservice_patch_member.py | Python | gpl-3.0 | 10,419 | [
"VisIt"
] | 344299c818d4969c2bf230f4b88097e201f1969b060013c4c33488a4b6a8c0a4 |
"""
Test courseware search
"""
import json
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.lms.course_home import CourseHomeP... | edx-solutions/edx-platform | common/test/acceptance/tests/lms/test_lms_split_test_courseware_search.py | Python | agpl-3.0 | 4,593 | [
"VisIt"
] | f136d01f7bbf785d06a28a71a3a9569ad548bd5ef145cd716d1aeefa14d92ff0 |
# Authors: Lukas Breuer <l.breuer@fz-juelich.de>
# Juergen Dammers <j.dammers@fz-juelich.de>
# Denis A. Engeman <denis.engemann@gemail.com>
#
# License: BSD (3-clause)
import math
import numpy as np
from ..utils import logger, verbose, check_random_state, random_permutation
@verbose
def infomax(d... | jniediek/mne-python | mne/preprocessing/infomax_.py | Python | bsd-3-clause | 11,854 | [
"Gaussian"
] | f870ed9137f7374928b12d7528d02744766c501db3a7f1dd8d07960196bb2b0d |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.nozen.HPUXMon | ZenPacks/nozen/HPUXMon/modeler/plugins/nozen/snmp/HPUXProcessMap.py | Python | gpl-2.0 | 2,335 | [
"VisIt"
] | c95a28d88fcd4021b12b12ad845bd0bb063f36e9f1c4e0b743075a61b44ae5b5 |
"""Stateful programmatic WWW navigation, after Perl's WWW::Mechanize.
Copyright 2003-2006 John J. Lee <jjl@pobox.com>
Copyright 2003 Andy Lester (original Perl code)
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file COPYING.txt
included w... | deanhiller/databus | webapp/play1.3.x/samples-and-tests/i-am-a-developer/mechanize/_mechanize.py | Python | mpl-2.0 | 25,221 | [
"VisIt"
] | a78c18bfcc4125478bbac813bdf9997a8b1bfd36349964a8aff0be1d8cb21fbd |
__author__ = 'max'
import nest
import numpy as np
import pylab as pl
import nest.raster_plot
#neuron_model = "iaf_psc_alpha"
#neuron_model = "iaf_psc_delta"
neuron_model = "iaf_psc_exp"
#neuron_model = "iaf_cond_exp" -
#neuron_model = "iaf_cond_alpha" -
#neuron_model = "aeif_cond_alpha" -
#neuron_model = "mat2_psc_ex... | vitaliykomarov/NEUCOGAR | nest/dopamine/test_files/multimeter.py | Python | gpl-2.0 | 3,758 | [
"NEURON"
] | 3f10960cd2556f0b4f7bbdf3a4d037c37f76a8b5ebb5277268b126cd269efe44 |
"""
PyOTP, the Python One-Time Password module.
AppendixB.py: the standard dictionary for RFC2889 one-time passwords
encoded as six word sequences.
<insert Python license here>
"""
__version__ = '$Revision: 1.4 $'
DefaultDictionary = [
"A", "ABE", "ACE", "ACT", "AD", "ADA", "ADD",
"AGO", ... | gnperumal/exscript | src/Exscript/external/otp/AppendixB.py | Python | gpl-2.0 | 18,613 | [
"Elk",
"MOE"
] | 0aad660fb7184f9c5de9959e76cba8539927247d78d6f31ed6daf402a829185e |
import py
import pytest
import tox
import os
import sys
from py.builtin import _isbytes, _istext, print_
from fnmatch import fnmatch
import time
from .config import parseconfig
from .venv import VirtualEnv
from .session import Action
from .result import ResultLog
def pytest_configure():
if 'TOXENV' in os.environ:... | jcb91/tox | tox/_pytestplugin.py | Python | mit | 10,497 | [
"VisIt"
] | 44f0b7d24f02c40ff4ebb2cfd03909032906b093102973de18402fa0efeb282b |
#
# @file TestReadSBML.py
# @brief Read SBML unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestReadSBML.py | Python | bsd-3-clause | 55,324 | [
"VisIt"
] | fb4f264ede11a1a6342222f625bce65f8f5bdf8eedbae6cad8932809fce2b4ff |
#!/usr/bin/env python
#
# $File: accessIndividual.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redist... | BoPeng/simuPOP | docs/accessIndividual.py | Python | gpl-2.0 | 2,761 | [
"VisIt"
] | 15cea799304c97228fdb0074460e10de0fdda155b4a090d2eb205fcfd41134a4 |
"""
**************
Synapse Client
**************
The `Synapse` object encapsulates a connection to the Synapse service and is used for building projects, uploading and
retrieving data, and recording provenance of data analysis.
~~~~~
Login
~~~~~
.. automethod:: synapseclient.client.login
~~~~~~~
Synapse
~~~~~~~
..... | thomasyu888/synapsePythonClient | synapseclient/client.py | Python | apache-2.0 | 186,244 | [
"VisIt"
] | 2145b9c72e94c6beb8564eb3b0b15cb9e6474a21993000e70c78373ba559ff97 |
# Orca
# Copyright (C) 2014-2015 Synthicity, LLC
# Copyright (C) 2015 Autodesk
# See full license in LICENSE.
from __future__ import print_function
import inspect
import logging
import time
import warnings
from collections import Callable, namedtuple
from contextlib import contextmanager
from functools import wraps
... | SANDAG/orca | orca/orca.py | Python | bsd-3-clause | 55,236 | [
"ORCA"
] | 475efd189f0a444a13f391f6924ab1c0ef1fab12e1b447c548b3434cc07305ab |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/postSchematic.py | Python | gpl-3.0 | 22,282 | [
"Galaxy"
] | 570ce68a3bd604b040fb48403c6e56ffe86f96d926cff219bd315b390203f2a2 |
""" There is some shared logic between matching/multiplying inputs in workflows
and tools. This module is meant to capture some general permutation logic that
can be applicable for both cases but will only be used in the newer tools case
first.
Maybe this doesn't make sense and maybe much of this stuff could be replac... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/util/permutations.py | Python | gpl-3.0 | 3,656 | [
"Galaxy"
] | 631eb5ab20d346bed0e00dc571347699ff7a6001ddfd4ebe4acd22e4c97a91be |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
from brian import *
# Parameters
g0 = 0.5*siemens*meter**-2.
sigma = 0.002*siemens*meter**(-2.)*second**(0.5)
tg = 3*msecond
g_Ein = 1.*siemens*meter**(-2)
# Model equations
eqs="""
dV/dt = 0*volt/second: volt
dg/dt = (-g + g0 + sigma * xi)/tg : siemens*me... | neuro-lyon/multiglom-model | src/tests/test_noise.py | Python | mit | 688 | [
"Brian"
] | 105a2eeaf5d8798a3c3bcc36ce60742d66aaa50b250a4b4cc13d6b0774356a45 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import sys
... | nuclear-wizard/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 51,742 | [
"MOOSE",
"VTK"
] | 760f9be0e92bcc5c7447ebbe3630a92ecc4baba30f0c5aacad5120b3dc7ccfff |
"""
Base Classes and Infrastructure Supporting Concret Manager Implementations.
"""
import errno
import logging
import os
from os.path import exists, isdir, join, basename
from os.path import relpath
from os import curdir
from os import listdir
from os import makedirs
from os import sep
from os import getenv
from os i... | natefoo/pulsar | pulsar/managers/base/__init__.py | Python | apache-2.0 | 13,462 | [
"Galaxy"
] | 15c0e0b194207c56f989b530e4c252b293384279d75db45282ab3437473f7ff9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Extract fasta sequences that are at or above a minimal length.
Usage:
%program <input_file> <output_file>"""
import sys
try:
from Bio import SeqIO
except:
print "This program requires the Biopython library"
sys.exit(0)
try:
fasta_file = sys.argv[... | enormandeau/Scripts | fasta_longer_nb.py | Python | gpl-3.0 | 681 | [
"Biopython"
] | a130d5d30ebcba4347fd639a597f5358cc7f69d97e83d0558f65b8cff2203c40 |
""" The Notification service provides a toolkit to contact people via email
(eventually SMS etc.) to trigger some actions.
The original motivation for this is due to some sites restricting the
sending of email but it is useful for e.g. crash reports to get to their
destination.
Another use-case is... | chaen/DIRAC | FrameworkSystem/Service/NotificationHandler.py | Python | gpl-3.0 | 10,712 | [
"DIRAC"
] | c35584625157496dfa5e19e10c6e7e6ec246e03888fb861572477654d95e4470 |
#!/usr/bin/env python3
import numpy as np
import pyboof as pb
import time
# This example shows how you can adjust the number of threads that BoofCV will use in the JVM
original = pb.load_single_band('../data/example/outdoors01.jpg', np.uint8)
gaussian = original.createSameShape()
# Let's warm up the JVM.
for i in r... | lessthanoptimal/PyBoof | examples/concurrency.py | Python | apache-2.0 | 1,127 | [
"Gaussian"
] | fba957d3b130fc9b06495f15d9a5ba350ed0f246c7a1689570f29c4416c141fa |
"""
Create a synthetic dataset
"""
import logging
import numpy as np
import os
import sys
sys.path.insert(0, '..')
from chronostar.synthdata import SynthData
from chronostar.component import SphereComponent as Component
from chronostar import tabletool
from chronostar import traceorbit
PY_VERS = sys.version[0]
"... | mikeireland/chronostar | create_synthetic_data/create_synthetic_dataset_spherical.py | Python | mit | 4,051 | [
"Gaussian"
] | 08b5b968550d1177892771249c29feb064bd21cf217f287608c8a2b09d829187 |
# coding=utf-8
# Copyright 2020 The TF-Agents 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable la... | tensorflow/agents | tf_agents/policies/gaussian_policy.py | Python | apache-2.0 | 3,367 | [
"Gaussian"
] | 7db7f55e24978e9fff5555f0fc5e68be14815f45a7a8f4af4842020e9254807d |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | samples/dpd.py | Python | gpl-3.0 | 2,474 | [
"ESPResSo"
] | 9d4f4248803ff9d1a08ab07a8bcf1051b3f491dd7c4c6ebad5c83e9ea9c2cfc6 |
"""Implementation of magic functions for interaction with the OS.
Note: this module is named 'osm' instead of 'os' to avoid a collision with the
builtin.
"""
from __future__ import print_function
#-----------------------------------------------------------------------------
# Copyright (c) 2012 The IPython Developmen... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/IPython/core/magics/osm.py | Python | gpl-3.0 | 28,952 | [
"VisIt"
] | a66f4653d2f1e42e498fd5e324565eabecb19ac763c90d46f217a3d5dccf888c |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def metric_accessors():
cars = h2o.import_file(path=pyunit_utils.locate("smalldata/junit/cars_20mpg.csv"))
r = cars[0].runif()
train = cars[r > .2]
valid = car... | h2oai/h2o-3 | h2o-py/tests/testdir_misc/pyunit_metric_accessors.py | Python | apache-2.0 | 43,027 | [
"Gaussian"
] | ce349c3bc1f5c41b5bab4fb191b3b69a241245963bca0d064e821dc9028d8423 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from flaky import flaky
from contextlib import contextmanager
from datetime import datetime
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from ...pages.common.logout import LogoutPage
from ...pages.lms.acc... | kxliugang/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 31,827 | [
"VisIt"
] | 740b8f6fce91b271734bf600a9cf712ecf747661c4812cb183a29d08ef73a022 |
from __future__ import print_function
from datetime import datetime
import moose
def time_creation(n=1000):
elist = []
start = datetime.now()
for ii in range(n):
elist.append(moose.Neutral('a_%d' % (ii)))
end = datetime.now()
delta = end - start
print('total time to create %d Neutral e... | subhacom/moose-core | tests/python/benchmark.py | Python | gpl-3.0 | 469 | [
"MOOSE"
] | 540de55c07ee9cdce20fee29cd788eb98db27233279492d35c67679e1923c3f4 |
import numpy as np
import thermoplotting as tp
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
#Use structure score and lattice score to bin structures as FCC, BCC or HCP.
#Uses struclat_scores.txt, generated through
#casm query -k 'struc_score(PRIM,basis_score)' 'struc_score(PRIM,lattice_score)'... | goirijo/thermoplotting | old/scripts/strucbin.py | Python | mit | 2,695 | [
"VASP"
] | 25bd7f755b6a2f3f65bb31e64c373a6b882884576a9e965cfd733daad492f35a |
#!/usr/bin/env python
"""A kernel that creates a new ASCII file with a given size and name.
"""
__author__ = "The ExTASY project <vivek.balasubramanian@rutgers.edu>"
__copyright__ = "Copyright 2015, http://www.extasy-project.org/"
__license__ = "MIT"
from copy import deepcopy
from radical.ensemblemd.exceptions... | radical-cybertools/ExTASY | examples/grlsd-on-stampede/kernel_defs/gromacs.py | Python | mit | 3,411 | [
"Gromacs"
] | 73013517aa361405eeedde5c9ace95f99cb4f4dbb940f99a9fe996f52200ae66 |
# Copyright 2018 Google LLC. 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 applicable law or a... | PAIR-code/interpretability | text-dream/python/dream/similar_embedding_activation.py | Python | apache-2.0 | 6,200 | [
"NEURON"
] | bca79bc3ac884f5a923043e700922a8f03a94324e6898374bb6dacc9d3f22822 |
import sys,logging,os,time,re,threading,hashlib
import xml.dom.minidom
import tokens
from datetime import datetime
SPLUNK_HOME = os.environ.get("SPLUNK_HOME")
RESPONSE_HANDLER_INSTANCE = None
SPLUNK_PORT = 8089
STANZA = None
SESSION_TOKEN = None
REGEX_PATTERN = None
#dynamically load in any eggs in /etc/apps/snmp_ta... | damiendallimore/SplunkModularInputsPythonFramework | implementations/rest/bin/rest.py | Python | apache-2.0 | 36,297 | [
"VisIt"
] | 5e70c447fee6f92b22861f6ed92bf10a1909fe9992928ccacbfccc38718ba0dc |
##############################################################################
# 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... | TheTimmy/spack | var/spack/repos/builtin/packages/octopus/package.py | Python | lgpl-2.1 | 5,165 | [
"BerkeleyGW",
"NetCDF",
"Octopus"
] | 8462f4ba7d034c5f2c477a92dd895c09173961666c82b8bb70886a2ddde3a46a |
# Copyright (C) 2021 Alex Nitz
#
# 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 distributed in the ... | ligo-cbc/pycbc | test/test_infmodel.py | Python | gpl-3.0 | 6,723 | [
"Gaussian"
] | ac0464e8bc176bc80f2485406455c806a8d52e424e2b6b7b63f677d74f870710 |
import h5py
import numpy
from rdkit import Chem
from steps.featuregeneration.shared import substructure_feature_generator
from steps.featuregeneration.mossfeaturegeneration import moss_integration
from util import data_validation, misc, file_structure, file_util, logger, process_pool, constants, \
hdf5_util, multi... | patrick-winter-knime/mol-struct-nets | molstructnets/steps/featuregeneration/mossfeaturegeneration/moss_feature_generation.py | Python | gpl-3.0 | 6,288 | [
"RDKit"
] | f1bbafe49fdfac4033949a9f2b1ef6e2878c1a64caa3579c80083c4a044a4e0b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Run this test like so:
# vtkpython TestParallelCoordinatesColors.py -D $VTK_DATA_ROOT \
# -B $VTK_DATA_ROOT/Baseline/Charts/
import os
import vtk
import vtk.test.Testing
import math
class TestParallelCoordinatesColors(vtk.test.Testing.vtkTest):
def testLinePlot(se... | arnaudgelas/VTK | Charts/Testing/Python/TestParallelCoordinatesColors.py | Python | bsd-3-clause | 3,083 | [
"VTK"
] | 89180431cacca8d1bc5e36ab3fa345cdead560f5ebfb98c4db5d3a2659b12690 |
__script__.title = 'KKB Measurement Script'
__script__.version = '1.0'
from gumpy.commons import sics
from org.gumtree.gumnix.sics.control import ServerStatus
from pickle import Pickler, Unpickler
import time
from math import log as ln
from math import exp, isnan, isinf
from __builtin__ import max as bu... | Gumtree/Kookaburra_scripts | Internal/VariableStepSize.py | Python | epl-1.0 | 46,921 | [
"CRYSTAL"
] | 724b1dd21678752122bb10197f98f2e8e4519652aa01b599d9433037b94e2c1b |
import logging
from dirac.lib.base import *
from DIRAC import S_OK, S_ERROR
log = logging.getLogger(__name__)
class MessageController(BaseController):
def index(self):
return self.retrieve()
@jsonify
def retrieve( self ):
#return S_OK( { 'i' : 1 , 'content' : 'HELLO!' } )
return S_OK()
@jso... | DIRACGrid/DIRACWeb | dirac/controllers/systems/message.py | Python | gpl-3.0 | 477 | [
"DIRAC"
] | 2214f57ff342337a1c67a93c0297587476986d9cf554a055b7c3954ceed2080c |
'''
PropagationCommand module
This command gets all the elements that exist under a given site and applies the following logic:
if even one element is 'Active' for the given site then it marks the site as 'Active', if all elements
are set in a different status (like banned or error) then it marks the site as 'Banned'
'... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Command/PropagationCommand.py | Python | gpl-3.0 | 2,160 | [
"DIRAC"
] | 78abf79d5dbb0d956991521789977bc29e3263912d62560246e5703201ff03c3 |
# Copyright 2008, 2009 CAMd
# (see accompanying license files for details).
"""Atomic Simulation Environment."""
from ase.utils import memory
from ase.atom import Atom
from ase.atoms import Atoms
from ase.units import *
from ase.io import read, write
from ase.io.trajectory import PickleTrajectory
from ase.dft import ... | freephys/python_ase | ase/__init__.py | Python | gpl-3.0 | 957 | [
"ASE",
"SIESTA",
"VASP"
] | 37c2cc08a4b8a4210c061ca6c9ebeedf399846bdb2677b6966fbde52b2fb776c |
#! /usr/bin/env python
from openturns import *
TESTPREAMBLE()
RandomGenerator.SetSeed(0)
try:
# Log::Show(Log::ALL)
# observations
size = 10
realDist = Normal(31., 1.2)
data = realDist.getSample(size)
# calibration parameters
calibrationColl = [CalibrationStrategy()] * 2
# propos... | sofianehaddad/ot-svn | python/test/t_PosteriorRandomVector_std.py | Python | mit | 1,785 | [
"DIRAC"
] | 262dde44694c06f7286ffc8a62db0b356394d6fc0dae2237946e9beaa61c9b19 |
# Generated by Django 2.1.7 on 2019-08-09 09:36
from django.db import migrations, models
def migrate_public_event(apps, schema_editor):
"""Migrate options previously with no contents (displayed as "Other:")
to a new contents ("other").
The field containing these options is in CommonRequest abstract model... | pbanaszkiewicz/amy | amy/workshops/migrations/0191_auto_20190809_0936.py | Python | mit | 3,995 | [
"VisIt"
] | a4dd50001ca5fb94f10aa1905445faca6dc89bfa2a0fa8cd2b8591012202ce09 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from collections import defaultdict, OrderedDict
import numpy as np
from monty.io import zopen
from monty.json import MSONable
from pymatgen import Orbital,... | Bismarrck/pymatgen | pymatgen/io/feff/outputs.py | Python | mit | 12,025 | [
"FEFF",
"pymatgen"
] | 1de73478423fa406e78bce7d2759500009a6076188a8d0db5931f0c04b855a41 |
"""Excitation lists base classes
"""
from math import sqrt
import numpy as np
import gpaw.mpi as mpi
from gpaw.output import initialize_text_stream
class ExcitationList(list):
"""General Excitation List class.
"""
def __init__(self, calculator=None, txt=None):
# initialise empty list
l... | qsnake/gpaw | gpaw/lrtddft/excitation.py | Python | gpl-3.0 | 2,982 | [
"GPAW"
] | 49e3d03a57263cc8f0885cfd2cdc257b780afeae6171dc5a3bdc157103990504 |
########################################################################
# File : SiteDirector.py
# Author : A.T.
########################################################################
""" The Site Director is a simple agent performing pilot job submission to particular sites.
"""
try:
import hashlib
md5 =... | miloszz/DIRAC | WorkloadManagementSystem/Agent/SiteDirector.py | Python | gpl-3.0 | 46,757 | [
"DIRAC"
] | ffdb4f7068be374f634c7b9460324be0d220595b4f8d8fd299fe488753c48f44 |
# -*- coding: iso-8859-15 -*-
"""
routes.
======
This module establishes and defines the Web Handlers and Websockets
that are associated with a specific URL routing name. New routing
associations must be defined here.
Notes
-----
For more information regarding routing URL and valid regular expressions
visit: http:/... | andfoy/spyder-terminal | spyder_terminal/server/routes.py | Python | mit | 1,104 | [
"VisIt"
] | edc086d4ad74e65102dfaa0cdd2d7b7531feb308ff14a8ed6af988cbd024110b |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/r-affyio/package.py | Python | lgpl-2.1 | 1,746 | [
"Bioconductor"
] | e832bd14314dffde06b99b2956b066779c4e6c39f37a455d2787467d951eddeb |
class Settings:
# Each neuron is represented by a sphere. This is its radius:
neuron_sphere_radius = 3.0
# A synaptic connection (between two neurons) is represented by a line with a cone at the end (arrow).
# These are the paremeters.
neural_connection_cone_length = 5.0
neural_connection_cone_radius = 1.8
... | zibneuro/brainvispy | core/settings.py | Python | bsd-3-clause | 852 | [
"NEURON"
] | c3305dfc68d505ad1ecce34a7e012ee0839b7a86ee4776ddf381112e6ac08bdc |
#!/usr/bin/env python
#Dan Blankenberg
"""
Removes blocks that fall outside of specified size range.
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.align.maf
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
input_maf_filename = sys.argv[1].stri... | dbcls/dbcls-galaxy | tools/maf/maf_limit_size.py | Python | mit | 1,099 | [
"Galaxy"
] | 45df688f1a02a1c660107d7eca63297bee2c8264487ce7ec82e6ed62886e63c9 |
import rdkit.Chem as Chem
import rdkit.Chem.AllChem as AllChem
from global_config import USE_STEREOCHEMISTRY
class SmilesFixer():
'''
This class stores RDKit reactions which help turn molecules with
weird representations into ones with common ones (so they will match
a template)
'''
def __init__(self):
self.rx... | connorcoley/ochem_predict_nn | utils/canonicalization.py | Python | mit | 3,264 | [
"RDKit"
] | c7c6e0d21ab16577a29ef38c2c776b4094dca2d8f36c3cabf61fea8a52597487 |
allverbs = ["bird's-nest",
'abandon',
'abase',
'abash',
'abate',
'abbreviate',
'abdicate',
'abduct',
'abet',
'abhor',
'abide',
'abirritate',
'abjure',
'ablate',
'abnegate',
'abolish',
'abominate',
'abort',
'abound',
'about-ship',
'about-turn',
'aboutface',
'abrade',
'abreact',
'abridge',
'abrog... | interrogator/corpkit | corpkit/dictionaries/verblist.py | Python | mit | 99,966 | [
"BLAST",
"GULP",
"TINKER",
"VisIt"
] | 243fb1085561d6f35de61ba0c0183570d9e368fccb1a58194d5ad2261e4daedc |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Peek StdOut of the given DIRAC job
Example:
$ dirac-wms-job-peek 1
"""
import DIRAC
... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_peek.py | Python | gpl-3.0 | 1,068 | [
"DIRAC"
] | e9dbc069a8bb6c19185c08f0eb161ea6e3ac89218534df7eda0b7ce71ba7d7a2 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/chronos/forecaster/utils.py | Python | apache-2.0 | 3,394 | [
"ORCA"
] | cab23f044af27c689218c8f1a5d2861a4dbc3707a0c84a6b46a9f08d319b9e9c |
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright INRIA
# Contributors: Wahiba Taouali (Wahiba.Taouali@inria.fr)
# Nicolas P. Rougier (Nicolas.Rougier@inria.fr)
#
# This software is governed by the CeCILL license under French law and abidin... | rougier/Neurosciences | superior-colliculus/taouali-et-at-2014/model.py | Python | bsd-3-clause | 5,734 | [
"Gaussian"
] | e4fff3d2891430fb0b46c13eacd4933cd9a4719fb40ef10e51174b35b4f0ccc6 |
# pyWebGraph, a bridge between WebGraph an {J,P}ython
# Copyright (C) 2009 Massimo Santini
#
# This file is part of pyWebGraph.
#
# pyWebGraph 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... | aftab90/py-web-graph | pywebgraph/examples/breadth_first_raw.py | Python | gpl-3.0 | 1,729 | [
"VisIt"
] | 39970c10fc7f9a2712089756052d1da323acbc97de37fd4a630034e9f4397a7c |
#!/usr/bin/env python
# This example demonstrates the use of 2D text.
import vtk
# Create a sphere source, mapper, and actor
sphere = vtk.vtkSphereSource()
sphereMapper = vtk.vtkPolyDataMapper()
sphereMapper.SetInputConnection(sphere.GetOutputPort())
sphereMapper.GlobalImmediateModeRenderingOn()
sphereActor = vtk.v... | hjanime/VisTrails | examples/vtk_examples/Annotation/TestText.py | Python | bsd-3-clause | 1,504 | [
"VTK"
] | 4f6dd6da3060d604bbf476affe2b5fde6a0d7799f8cca16b93d4d59a62aa2b54 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0078_vhartree_pbc_water.py | Python | apache-2.0 | 2,208 | [
"PySCF",
"SIESTA"
] | 21e6061b9fc4087e21ffd8718c41080d26472be56ca6c71c598812d5f414439c |
import os
from subprocess import call
from shutil import copyfileobj
from Bio import SeqIO
from Bio.Alphabet import generic_dna
from Bio.Seq import Seq
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import colors
try :
import seaborn
sns = True
except :
sns = False
try :
from sklearn.neighb... | QCaudron/genepy | genepy/genepy.py | Python | mit | 9,289 | [
"Biopython"
] | f683be44504d18358a2280659d5bc60a608bed7bd7760b1ed89b3f6da9fc520b |
# 2-electron VMC code for 2dim quantum dot with importance sampling
# Using gaussian rng for new positions and Metropolis- Hastings
# No energy minimization
from math import exp, sqrt
from random import random, seed, normalvariate
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes... | CompPhysics/ComputationalPhysics2 | doc/Programs/ConjugateGradient/python/qdotnint.py | Python | cc0-1.0 | 4,670 | [
"Gaussian"
] | 9b5fb010089875eb90051bd4c9c649023e6bcece03cc007fae4bcb57e3c04fd2 |
# 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... | TakayukiSakai/tensorflow | tensorflow/python/ops/template.py | Python | apache-2.0 | 11,230 | [
"VisIt"
] | a7c07a0c66deb7e1efc4072a8a130acf154d9fd6edecd59d0d176c7bba8ddbf7 |
#!/usr/bin/env python
"""
Reformat spectra into a single fits file per object, combining all necessary
pieces from spPlate, spCFrame, spFrame, spFlat, and spZbest
Stephen Bailey, Summer 2011
Bugs/Features:
- Assumes RUN1D=RUN2D, and gets them from specObj (not env vars), assuming
that specObj has one and only ... | jgagneastro/FireHose_OLD | 3-XIDL/23-XIDL/idlspec2d/bin/reformat_sdss_spectra.py | Python | gpl-2.0 | 26,896 | [
"Galaxy"
] | e6a24044a6972ae63fd329b0ae05b5cf55a8ae24e4b1d7ce814c978d484c9826 |
# Python Scripts for the Star Wards LCG definition for OCTGN
# Copyright (C) 2013 Konstantine Thoukydides
# This python script 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 ... | db0/Doomtown-Reloaded-OCTGN | o8g/Scripts/customscripts.py | Python | agpl-3.0 | 127,061 | [
"CASINO"
] | c6d679d10beb503bb343db4dffb2643bc9713436c6764fa2362bf9f9c8f2cb9e |
import typing
import binascii
import themis.cbuild
import themis.auto
import themis.channel
import themis.codegen
import themis.codehelpers
import themis.joystick
import themis.pwm
import themis.timers
Mode = themis.channel.Discrete("DISABLED AUTONOMOUS TELEOP TESTING")
JOYSTICK_NUM = 6
AXIS_NUM = 12
MAX_BUTTON_NUM ... | celskeggs/themis | themis/frc.py | Python | mit | 8,259 | [
"Jaguar"
] | c09ecb69fa569b43e64c7e55bddb8f6314b4446bd6b2f55ab883e2acee9e0375 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | Forage/Gramps | gramps/gen/filters/rules/event/_hasgallery.py | Python | gpl-2.0 | 1,834 | [
"Brian"
] | 9fd1f77379075432991abaad0ad28d7ab69aa5e180d4c741e5b8a607b325d692 |
# store.py - repository store handling for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms
# of the GNU General Public License, incorporated herein by reference.
from i18n import _
import os, stat, osutil, util
_sha = util.sha1
def _bui... | pombredanne/SmartNotes | mercurial/store.py | Python | gpl-3.0 | 10,359 | [
"VisIt"
] | 37b3166575debb7c92a538691c062acfdb7baed5bef31c4491e36facd3c69de8 |
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