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# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | alisonken1/openlp-projector-2.0 | openlp/projectors/error_codes.py | Python | gpl-2.0 | 8,670 | [
"Brian"
] | fcdb77ca4fef53905af42681142f78058c5f9dc121daebbbe2a0d58476d065a1 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import copy, sys
class Visitor:
def defaultVisit(self, node):
raise Exception, "INTERNAL ERROR: no visitor ... | Yukarumya/Yukarum-Redfoxes | ipc/ipdl/ipdl/cxx/ast.py | Python | mpl-2.0 | 23,105 | [
"VisIt"
] | bf4bc6bf0dddb3168bc0978d76ae379a12ef78c9b37ea41890927dcd5e211f4f |
from jinja2 import Environment, FileSystemLoader
import subprocess
import os.path
import shutil
from PIL import Image
import win32gui
import glob
import time
import uuid
import os
from subprocess import *
#TODO: Create new Zero template for sprite-based playback
#they said it couldn't be done
#and they were wrong!
#w... | milkey-mouse/Nada | ZeroLossless/ZeroVideo/ZeroVideo/ZeroVideo.py | Python | mit | 11,524 | [
"Gaussian"
] | 9ab01d85d7deff78797f0606a78359c7a5e36e5b25925ae6d13043be4d391629 |
"""
It is a helper module used to create a certain plot...
"""
from DIRAC import S_OK, S_ERROR
def _convertToSeconds(interval):
"""
Converts number of minutes, hours, days, weeks, months, years into seconds
"""
# unit symbols
units = ["s", "m", "h", "d", "w", "M", "y"]
# this is the number of ... | DIRACGrid/DIRAC | src/DIRAC/MonitoringSystem/private/DBUtils.py | Python | gpl-3.0 | 5,663 | [
"DIRAC"
] | 1217d2b8c269d934a7a8ea2d5fdc3844cadc64e1348e44a019c464fc156edca8 |
"""
PHYLIP multiple sequence alignment format (:mod:`skbio.io.phylip`)
==================================================================
.. currentmodule:: skbio.io.phylip
The PHYLIP file format stores a multiple sequence alignment. The format was
originally defined and used in Joe Felsenstein's PHYLIP package [1]_,... | Achuth17/scikit-bio | skbio/io/phylip.py | Python | bsd-3-clause | 10,543 | [
"BioPerl",
"scikit-bio"
] | af52feead40963498be3441e3981f5f564d8183f014f38e4041ff66ee52e55f7 |
'''
single crystal Bragg reflection
'''
from ocelot.optics.elements import *
# from ocelot.optics.wave import TransferFunction
from ocelot.optics.bragg import *
from ocelot.optics.ray import Ray, trace as trace_ray
from ocelot.gui.optics import *
class Signal(object):
def __init__(self, n=100):
self.t = ... | ocelot-collab/ocelot | ocelot/optics/utils.py | Python | gpl-3.0 | 2,866 | [
"CRYSTAL"
] | a324cc5541d99eb1c3b762a1b3d8996857616f740b9573444de3622a4ce36efb |
#!/usr/bin/env python
# This example demonstrates the use of multiline 2D text using
# vtkTextMappers. It shows several justifications as well as
# single-line and multiple-line text inputs.
import vtk
font_size = 14
# Create the text mappers and the associated Actor2Ds.
# The font and text properties (except jus... | b3c/VTK-5.8 | Examples/Annotation/Python/multiLineText.py | Python | bsd-3-clause | 6,586 | [
"VTK"
] | f3d8eb56654ae6bd0874347f717908af1199bda94a00fbafa710efc21da32955 |
#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
def heliumDetectorEff(workspace):
''' Calculate the corrected Helium detector values. '''
ac= 6.022169e23 # Avogadro's constant mol-1
vm= 2.24136e4 # Mo... | wdzhou/mantid | scripts/LargeScaleStructures/ReflectometerCors.py | Python | gpl-3.0 | 2,907 | [
"Avogadro"
] | 2f663d31f74c36a4f82a0874e256144664e0cae772072602de05b35ad7518310 |
import enum
import inspect
import pydoc
import unittest
from collections import OrderedDict
from enum import Enum, IntEnum, EnumMeta, Flag, IntFlag, unique, auto
from io import StringIO
from pickle import dumps, loads, PicklingError, HIGHEST_PROTOCOL
from test import support
try:
import threading
except ImportError... | yotchang4s/cafebabepy | src/main/python/test/test_enum.py | Python | bsd-3-clause | 93,588 | [
"MOE"
] | 514af0f4bd089d15564d81638f94dae367c920c92a92758978e93b4276b561df |
"""
=================================================
Deterministic Tracking with EuDX on Tensor Fields
=================================================
In this example we do deterministic fiber tracking on Tensor fields with EuDX
(Garyfallidis, PhD thesis, 2012).
This example requires to import example `reconst_dt... | maurozucchelli/dipy | doc/examples/tracking_eudx_tensor.py | Python | bsd-3-clause | 3,725 | [
"VTK"
] | 99bdbbcc61813415f0d5529a461c6e13541bd105889abcc05d82eef74b71763e |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyEspresso(CMakePackage):
"""ESPResSo is a highly versatile software package for performi... | LLNL/spack | var/spack/repos/builtin/packages/py-espresso/package.py | Python | lgpl-2.1 | 1,821 | [
"ESPResSo"
] | 3cc9ae87e7f4961bb7f76a1acccc63280b43162a347cbf31f5476e66570d9226 |
##############################################################################
# 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 | lib/spack/spack/test/cmd/url.py | Python | lgpl-2.1 | 5,814 | [
"NetCDF"
] | c33dca9a17eaa68786e6f68f377ac98c0d71b1ac2f64a26e499662b04223e652 |
## Automatically adapted for numpy.oldnumeric Mar 26, 2007 by alter_code1.py
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Ge... | ostrokach/biskit | Biskit/AmberEntropyMaster.py | Python | gpl-3.0 | 25,612 | [
"Amber"
] | 7daf1d2edc6057c082d23298479ffcd58b388cb13d568eb3e198621311e20d97 |
from __future__ import print_function
from rdkit import RDConfig
import os.path
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Descriptors
descrs = ['SMR_VSA1', 'SMR_VSA10', 'SMR_VSA2', 'SMR_VSA3', 'SMR_VSA4', 'SMR_VSA5', 'SMR_VSA6',
'SMR_VSA7', 'SMR_VSA8', 'SMR_VSA9', 'Slo... | jandom/rdkit | rdkit/Chem/test_data/BuildDescrsTestSet.Crippen.py | Python | bsd-3-clause | 1,610 | [
"RDKit"
] | c55c3d7cc0745ae1a877cc4151a369a44ce8c8b0e0c2c4c01c6c98ed403b19ff |
########################################################################
# #
# Cyprium is a multifunction cryptographic, steganographic and #
# cryptanalysis tool developped by members of The Hackademy. #
# French White Hat Hackers... | underloki/Cyprium | app/cli/root/crypto/text/brainfuck.py | Python | gpl-3.0 | 15,009 | [
"Octopus"
] | 61c671a0fb08c25e9062349819d31ccd80cb73c82294927ea6daace65b527ce0 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
""" unit tests for the model and descriptor packager """
from rdkit import RDConfig
from rdkit.ML.Data import DataUtils
import unittest,os,sys
import io
from rdkit.six.moves import ... | soerendip42/rdkit | rdkit/ML/ModelPackage/UnitTestPackage.py | Python | bsd-3-clause | 4,877 | [
"RDKit"
] | bd091908324400be0fd6ad0b40280713315bb17a554a04def6f408ec5f16aeba |
# Copyright 2019 Brian Quinlan
#
# 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 law or agreed to in writin... | brianquinlan/learn-machine-learning | lunarlander/model.py | Python | mit | 880 | [
"Brian"
] | 46a9cbec2ca0ded626c4e32f1d5dc1633d645c771602b2f9ab327feacc5da785 |
#! /usr/bin/env python2
# -*- coding: utf-8 -*-
#======================================================================
#
# emake.py - emake version 3.6.9
#
# history of this file:
# 2009.08.20 skywind create this file
# 2009.11.14 skywind new install() method
# 2009.12.22 skywind implementation execute int... | skywind3000/collection | script/emake.py | Python | mit | 95,752 | [
"VisIt"
] | b492e8440595e2528427cd6d75ed0ed9d3fc80dae64616b51fb5750ec59ace58 |
'''
***************************************************************.
GOOGLE PHONE TECHNICAL INTERVIEW TIPS:
Please be prepared for the engineers to ask you questions in the following areas:
- Google products (i.e. what you use)
- Coding ability (you will code in a Google Doc)
- Algorithm Design/Analysis.
- System Des... | UmassJin/Leetcode | Experience/May/Google_Interview_prepare_lists(recruiter).py | Python | mit | 11,670 | [
"VisIt"
] | a0dc36491de276d4cd2ace0b8974e63a09e896bd29f436f77e87485b9cf9c7ac |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Classes for reading/manipulating/writing VASP input files. All major VASP input
files.
"""
__author__ = "Shyue Ping Ong, Geoffroy Hautier, Rickard Armient... | sonium0/pymatgen | pymatgen/io/vasp/inputs.py | Python | mit | 64,386 | [
"VASP",
"pymatgen"
] | 493cd86047a7a28f70d4c4ffe07cc3e34d94ee09e7faed5c9aba60a2a638a4e1 |
"""
This module contains a method for easy ShakeMap creation using
string-parameters.
"""
from eqep.interpolation.rbf_pgvinterpolator import RbfPGVInterpolator
from eqep.shakemap.display.scales import *
from eqep.shakemap.display.styles import *
from eqep.shakemap.preinitialized_shakemap import PreinitializedShakeMap... | TGM-HIT/eqep-api | eqep/shakemap/shakemap_factory.py | Python | mit | 4,257 | [
"Gaussian"
] | e3c8f78e8e23c480644ecb0a4093d89f9559e6e3c70cf76ea2da04df97332ecc |
# -*- coding: utf-8 -*-
import operator
import pyjsparser
from autojsdoc.parser import jsdoc, parser
params = operator.attrgetter('name', 'type', 'doc')
def parse(s, source=None):
tree = pyjsparser.parse(s)
mods = parser.ModuleMatcher(source).visit(tree)
post(mods)
return mods
def post(mods):
... | t3dev/odoo | doc/_extensions/autojsdoc/parser/tests/support.py | Python | gpl-3.0 | 1,767 | [
"VisIt"
] | ad8d16fd15505c575676ab821f2deca2727ddb21aa8d8e1b358f1df56834004d |
from aiida import load_dbenv
load_dbenv()
from aiida.orm import Code, DataFactory, WorkflowFactory
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
import numpy as np
# Silicon structure
a = 5.404
cell = [[a, 0, 0],
[0, a, 0],
[0, 0, a]]
symbols=['Si'] * 8
scaled_pos... | abelcarreras/aiida_extensions | workflows/launcher/launch_phonon_qe_si.py | Python | mit | 2,789 | [
"phonopy"
] | dddfca638c787a1554674977852e3548f3ed77d02957c56db499a932fe49a521 |
#!python
#############################################################################
# cubit2specfem3d.py #
# this file is part of GEOCUBIT #
# #... | komatits/specfem3d | CUBIT_GEOCUBIT/geocubitlib/cubit2specfem3d.py | Python | gpl-2.0 | 62,504 | [
"NetCDF"
] | 57b871002acdb37b4e504dd4fb36d1ce6a4fedddc805897f31e0b7cf747e586c |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 07 13:37:47 2016
@author: Greeff
"""
import numpy as np
import cv2
import matplotlib.pyplot as plt
from math import sqrt as math_sqrt
from QtLoadSaveObjects import make_config_dict
np.seterr(invalid='raise')
#=========================================================... | gpgreeff/filament_vision_sensing | ROIAtesting.py | Python | mit | 99,127 | [
"Gaussian"
] | bbb03a72810ad48b9fd851706c6d302d65d0e8937bf6d80f625e17a3272017b7 |
""" DIRAC FileCatalog Security Manager base class
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security.Properties import FC_MANAGEMENT
_readMethods = [
"exists",
"isFile",
"getFileSize",
"getFileMetadata",
"getReplicas",
"getReplicaStatus",
"getFileAncestors",
"getFileDescendent... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/SecurityManager/SecurityManagerBase.py | Python | gpl-3.0 | 2,826 | [
"DIRAC"
] | 7be7b8176c38a1cddb0e8b14a376ccdd42625129c4f671002e704e3202fc8589 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | Nick-Hall/gramps | gramps/plugins/webreport/basepage.py | Python | gpl-2.0 | 142,223 | [
"Brian"
] | 3fd7438bb640ecce31fb0777f5e80495def034661faae751dc00d52803605198 |
########################################################################
# $HeadURL$
# File : ModuleFactory.py
# Author : Stuart Paterson
########################################################################
""" The Module Factory instantiates a given Module based on a given input
string and set of argumen... | sposs/DIRAC | Core/Utilities/ModuleFactory.py | Python | gpl-3.0 | 1,836 | [
"DIRAC"
] | 8d7f9298ababfbe823173d4e3d12cd4711d6f43d0cee97b3d8e403c7f3a6084f |
import sys
from ast import literal_eval
from itertools import islice, chain
from . import nodes
from ._compat import text_type
from .compiler import CodeGenerator, has_safe_repr
from .environment import Environment, Template
from .utils import concat, escape
def native_concat(nodes):
"""Return a native Python typ... | facelessuser/sublime-markdown-popups | st3/mdpopups/jinja2/nativetypes.py | Python | mit | 7,279 | [
"VisIt"
] | 38242398fef030a9d3a8a66e2c243ee79a31dbec4823179b2e86191a22146384 |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/df/incore.py | Python | apache-2.0 | 10,276 | [
"PySCF"
] | d74154fd29db02bf37aa9d9ffc3ca663d74b1ff01c879c05dd45e8fbb192947f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
import warnings
import numpy as np
from monty.json import MontyDecoder
from pymatgen.analysis.xas.spectrum import XAS, site_weighted_spectrum
from pymatgen.core import El... | gmatteo/pymatgen | pymatgen/analysis/xas/tests/test_spectrum.py | Python | mit | 5,998 | [
"pymatgen"
] | c43b0d02edadd075732c8e338358eece930740945dfaa29c29bdf7f3062b3f2a |
########################################################################
# $HeadURL: svn+ssh://svn.cern.ch/reps/dirac/DIRAC/trunk/DIRAC/DataManagementSystem/DB/FileCatalogComponents/UserAndGroupManager.py $
########################################################################
__RCSID__ = "$Id$"
""" DIRAC FileCatalo... | Sbalbp/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DirectoryFlatTree.py | Python | gpl-3.0 | 9,231 | [
"DIRAC"
] | 179544fd80b98802aa33173b85503a2d0b66fede7e49fb1788fe9ac8eb80564c |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | seq2act/data_generation/common.py | Python | apache-2.0 | 14,083 | [
"VisIt"
] | bfcc0bc134a1de499569cbcf032e4706dd1a443ab87b23149dbcc8357a01201b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2016 Andi Albrecht, albrecht.andi@gmail.com
#
# This setup script is part of python-sqlparse and is released under
# the BSD License: http://www.opensource.org/licenses/bsd-license.php
import re
from setuptools import setup, find_packages
def get_versi... | vmuriart/sqlparse | setup.py | Python | bsd-3-clause | 3,154 | [
"VisIt"
] | e25bf683d4b13bb56e494663c95c758075ee274667c47ec10e12758da1312df0 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | iemejia/incubator-beam | sdks/python/apache_beam/transforms/ptransform.py | Python | apache-2.0 | 36,031 | [
"VisIt"
] | 7aae1a623717a54b90fe0ae7dab080a87e48fedffdfc1581f417d53ea09fd8a3 |
#! /usr/bin/env python
# This version uses NEST's RandomConvergentConnect functions.
from scipy.optimize import fsolve
import cynest as nest
#import cynest.raster_plot
import time
from numpy import exp
def ComputePSPnorm(tauMem, CMem, tauSyn):
"""Compute the maximum of postsynaptic potential
for a sy... | QJonny/CyNest | cynest/examples/brunel-alpha-nest.py | Python | gpl-2.0 | 4,644 | [
"NEURON"
] | 41500a0fa5236ec4607fb7d761464c12ec7312536de3579c7e18f68b9e9c1c11 |
import numpy as np
import pandas as pd
import time
import simtk.openmm.app as app
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
n_steps = 10000
temperature = 300. * u.kelvin
data = {}
for cutoff in np.linspace(0.8, 1.3, 10):
testsystem = testsystems.DH... | kyleabeauchamp/HMCNotes | code/old/benchmark_dhfr.py | Python | gpl-2.0 | 1,019 | [
"OpenMM"
] | 41516398e05728aedc629fba91d3501b9d4dcc07412cdbca422aead7500316ce |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAdsplit(RPackage):
"""Annotation-Driven Clustering
This package implements cluste... | LLNL/spack | var/spack/repos/builtin/packages/r-adsplit/package.py | Python | lgpl-2.1 | 1,528 | [
"Bioconductor"
] | 314018c80a55ba1af304e9376a72054fc3fac99baae7152e9c4204dc5b5abd2d |
"""
This module contains the CharmmWriter class and associated methods,
which outputs a psf/pdb file with CHARMM names and parameters.
It does this by converting atom names to CHARMM names, writing
intermediate files as necessary to invoke the vmd psfgen plugin.
Author: Robin Betz
Copyright (C) 2019 Robin Betz
"""
#... | Eigenstate/dabble | dabble/param/charmm.py | Python | gpl-2.0 | 37,819 | [
"Amber",
"CHARMM",
"NAMD",
"VMD"
] | 58da9753e5554f1dfe4c83368de2bd721a57e18b152f7c465e2367114fc1076c |
import numpy as np
from .network import Network
from . import losses
from . import activations
class VAE:
'''Variational Autoencoder'''
def __init__(self, dimensions, latent_dim, params):
self.latent_dim = latent_dim
self.encoder = Network(dimensions[0] + [2], params)
self... | FaustineLi/Sta663-Project | vae/vae_class.py | Python | mit | 3,993 | [
"Gaussian"
] | f3156f6fce5a1a9062a54d90a8069919df2f4b5b386d865991364026c6067323 |
import sys
import ast
import inspect
import textwrap
from collections import defaultdict
from itertools import count
from byteplay import Code, LOAD_GLOBAL, LOAD_CONST
from funcy import (
walk_keys, zipdict, merge, join, project, flip, ikeep,
post_processing, unwrap, none, cached_property, cut_prefix
)
__all... | Suor/rebind | rebind.py | Python | bsd-2-clause | 10,827 | [
"VisIt"
] | eddb73ba9d7d487d8e6015177d935290779577ed254f8f2c5ff592df5ff9a588 |
"""
Constructs added to allow easy switching between PyCSP implementations.
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp.greenlets.exceptions import *
de... | runefriborg/pycsp | pycsp/greenlets/compat.py | Python | mit | 3,124 | [
"Brian"
] | f8054f24233ae11c363afb3054eb2a6d35870fe19fe5b24b7cffa42b27095630 |
# -*- coding: utf-8 -*-
# pylint: disable=
"""
Created on Tue May 3 18:34:45 2016
@author: P. Rodriguez-Mier and T. Teijeiro
"""
import random
from operator import attrgetter
def bound_value(v, min_v, max_v):
return min(max(min_v, v), max_v)
def recombinate(pairs, gene_props, mutation_probability=0.1, effect... | citiususc/citius-invaders | python/evolution.py | Python | mit | 2,775 | [
"Gaussian"
] | fd89e2a9d9f2bab3075ec216c298e435b8e7943babddb3095f46dc6a1fcad035 |
import contextlib
import collections
import pickle
import re
import sys
from unittest import TestCase, main, skipUnless, SkipTest, skip
from copy import copy, deepcopy
from typing import Any, NoReturn
from typing import TypeVar, AnyStr
from typing import T, KT, VT # Not in __all__.
from typing import Union, Optional,... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.8.0/Python-3.8.0/Lib/test/test_typing.py | Python | apache-2.0 | 124,018 | [
"VisIt"
] | 916a51ff68a027840b069e73c4346e112488bab5fe779c44afc1f0b9f77c076b |
import sys
tests=[
("testExecs/testFeatures.exe","",{}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| soerendip42/rdkit | Code/Features/test_list.py | Python | bsd-3-clause | 233 | [
"RDKit"
] | efcf79a56c4178189595d06830b7ab8dc9d360e99c68c98f923bca31e3de69a1 |
# Copyright: 2005 Gentoo Foundation
# Author(s): Brian Harring (ferringb@gentoo.org)
# License: GPL2
import errno
import re
import stat
import sys
from portage import os
from portage import _encodings
from portage import _unicode_encode
from portage.cache import cache_errors, flat_hash
import portage.eclass_cache
from... | Neuvoo/legacy-portage | pym/portage/cache/metadata.py | Python | gpl-2.0 | 4,361 | [
"Brian"
] | 11d1ebae737a3a76c3316a1f80afb378590b691b1b26c1a1d4aa0b8f297b79c9 |
"""
Generate a synthetic dataset of Hodgkin-Huxley style neurons.
We'll use this to test our classification algorithms.
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import gamma
import cPickle, gzip
from hips.plotting.sausage import sausage_plot
from hh_dynamics import forward_euler, impli... | HIPS/optofit | optoclassify/generate_classification_data.py | Python | gpl-2.0 | 5,928 | [
"NEURON"
] | a6af520fc028d7fcd5310cb737118eaa9a19664b9ac891c5d00a309dfec6e64d |
#!/usr/bin/env python
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | kaarolch/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 10,835 | [
"Galaxy"
] | 709dc01459f8debb57ad069a653092cabfdc19b00394f38c7383632534fa6a23 |
import logging
from collections import namedtuple
from .refs import extract
from .nodes import NodeVisitor
from .utils import Buffer
from .parser import parse
from .errors import UserError, WARNING, ERROR, Errors
from .compat import _exec_in
from .checker import def_types, split_defs, Environ, check, collect_defs
from... | vmagamedov/kinko | kinko/lookup.py | Python | bsd-3-clause | 7,960 | [
"VisIt"
] | 26e5e2ee7e6c1dc15af409e4a7a5575ddab942d8ad0c7877452a836d4decdbe9 |
#!/usr/bin/env python
import matplotlib.pyplot as plt
import scipy.signal as ss
import numpy as np
class GetFeatures(object):
'''Class to extract features from step-current soma traces'''
def __init__(self, tvec, traces):
'''Initialize object. Input tvec is global time vector,
traces an n x tve... | espenhgn/NSGAII | feature.py | Python | gpl-2.0 | 6,768 | [
"Gaussian"
] | a3c9018cb97247478177cb9c5204976d02f13d82f4403d824506649f892a562f |
r"""
=======================================
Robust vs Empirical covariance estimate
=======================================
The usual covariance maximum likelihood estimate is very sensitive to the
presence of outliers in the data set. In such a case, it would be better to
use a robust estimator of covariance to guar... | manhhomienbienthuy/scikit-learn | examples/covariance/plot_robust_vs_empirical_covariance.py | Python | bsd-3-clause | 6,490 | [
"Gaussian"
] | bf38b9411fcabd15dfb5c157d78f36a58ad81133b7384f47a2c8b01dbc49659d |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck
... | toastedcornflakes/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 46,488 | [
"Gaussian"
] | 31b6a4d2b7f809abe519e1dbdf42c0d96f9d3d1c8fcfed9040d31db2e95e39a6 |
from __future__ import (absolute_import, division, print_function)
import AbinsModules
import io
import numpy as np
from mantid.kernel import Atom
class LoadGAUSSIAN(AbinsModules.GeneralDFTProgram):
"""
Class for loading GAUSSIAN ab initio vibrational data.
"""
def __init__(self, input_dft_filename):
... | dymkowsk/mantid | scripts/AbinsModules/LoadGAUSSIAN.py | Python | gpl-3.0 | 8,008 | [
"Gaussian"
] | 5b9bebec1088482d918e3fcdcb3b8b80e5452b712bc9302a70a05edee98f210e |
""" DIRAC JobDB class is a front-end to the main WMS database containing
job definitions and status information. It is used in most of the WMS
components
The following methods are provided for public usage:
getJobParameters()
getJobParametersAndAttributes()
setJobParameter()
"""
from __future__ import a... | petricm/DIRAC | WorkloadManagementSystem/DB/ElasticJobDB.py | Python | gpl-3.0 | 7,057 | [
"DIRAC"
] | d2f99736e415115da834f62898269b64e46706bf1998bcd374897545bb8cdc7c |
#!/usr/bin/env python
# coding: utf-8
from datetime import datetime
from HTMLParser import HTMLParser
import argparse
import json
import os
import sys
import urllib2
###############################################################################
# Options
#############################################################... | mdxs/gae-init-babel | magic.py | Python | mit | 6,224 | [
"VisIt"
] | f6d038bfa16b63b9eba564e31b8d7bb72b2861c920d811ffb889fe9eaba0966e |
""" Frontend to FTS3 MySQL DB. Written using sqlalchemy
"""
# We disable the no-member error because
# they are constructed by SQLAlchemy for all
# the objects mapped to a table.
# pylint: disable=no-member
import datetime
import errno
from sqlalchemy.orm.exc import NoResultFound
from sqlalchemy.exc import SQLAlchem... | fstagni/DIRAC | DataManagementSystem/DB/FTS3DB.py | Python | gpl-3.0 | 24,062 | [
"DIRAC"
] | 1b355fe740eeb06b4aabcf5df00bbefce0e133adaae17661efc6fa63a0abeb7e |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to generate point defect structures
"""
import logging
from abc import ABCMeta, abstractmethod
from monty.json import MSONable
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymat... | vorwerkc/pymatgen | pymatgen/analysis/defects/generators.py | Python | mit | 10,953 | [
"pymatgen"
] | 49379804b95d51f03bd46284561f1711684fa53fe0efd5476a57204d1dd8c713 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | tests/jobfolder/test_jobfolder.py | Python | gpl-3.0 | 4,660 | [
"CRYSTAL",
"VASP"
] | ac9fc456f2fdd0e5daa4176566a8429095444f3f98e581d84969b951d2cd3681 |
"""
Service class implements the server side part of the DISET protocol
There are 2 main parts in this class:
- All useful functions for initialization
- All useful functions to handle the requests
"""
# pylint: skip-file
# __searchInitFunctions gives RuntimeError: maximum recursion depth exceeded
import os
i... | fstagni/DIRAC | Core/DISET/private/Service.py | Python | gpl-3.0 | 24,377 | [
"DIRAC"
] | 7a863144af249c0e8f9e4da90dca3a7a74b0a4925624370051ab1afa9d394234 |
from django.test import TestCase
from django.test import Client
from django.urls import reverse
# Import Some Django models that we use
from django.contrib.auth.models import User, Group
# Import some models
from .models import ActivityGenerator
from .models import ActivitySet
from .models import ActivityType
from... | profcturner/WAM | loads/tests.py | Python | agpl-3.0 | 26,483 | [
"exciting"
] | 42a9e1f048f0de47d777cb6b6c296d4f99c2acd06210e838f29e273539e23354 |
#!/usr/bin/env python
# Copyright 2014-2019 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
#
# U... | gkc1000/pyscf | pyscf/lo/pipek.py | Python | apache-2.0 | 9,347 | [
"PySCF"
] | c32ea7623459fa74d26e11022cc2eb4da24608f0323cc2dc55249677369fa1ed |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
# Copyright (C) 2010-2016 Bastian Kleineidam
#
# 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 o... | wummel/patool | setup.py | Python | gpl-3.0 | 9,029 | [
"ADF"
] | 8c143a74429223af05abb2a5b56de62314fdaac54f365146ccb4ab7811e72e61 |
# -----------------------------------------------------------------------------
#
# Copyright (C) 2021 CERN & University of Surrey for the benefit of the
# BioDynaMo collaboration. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance w... | BioDynaMo/biodynamo | test/unit/core/visualization/paraview/validate_diffusion_grid.py | Python | apache-2.0 | 2,985 | [
"ParaView"
] | 413a6fe9015011833b9c5705118f21be638b7e4bdadaf9be3903f2dd05303264 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | alisonken1/openlp-projector-2.0 | openlp/projectors/projectoritem.py | Python | gpl-2.0 | 2,490 | [
"Brian"
] | d293a53e3965bbe65ff0aaf775f7e69e0cf9966a4b7ba4c412b723d5697bd2e9 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | sxjscience/tvm | vta/python/vta/top/graphpack.py | Python | apache-2.0 | 18,326 | [
"VisIt"
] | 2d39d25a80e1d09a90e570cee041a971e0e2c4d78b76d1ab355c1414f26571e9 |
#!/usr/bin/env python
# -*- Mode: Python; py-indent-offset: 4 -*-
# vim: tabstop=4 shiftwidth=4 expandtab
#
# Copyright (C) 2010 Red Hat, Inc., John (J5) Palmieri <johnp@redhat.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License a... | davibe/pygobject | demos/gtk-demo/demos/combobox.py | Python | lgpl-2.1 | 11,098 | [
"COLUMBUS"
] | 37fc134b130a4fc6ed76287b6bc18181b1dfb70cfaff885417e476d9d07bbebe |
#!/usr/bin/env python
'''
Optimize the geometry of the excited states
Note when optiming the excited states, states may flip and this may cause
convergence issue in geometry optimizer.
'''
from pyscf import gto
from pyscf import scf
from pyscf import ci, tdscf, mcscf
from pyscf import geomopt
mol = gto.Mole()
mol.... | gkc1000/pyscf | examples/geomopt/12-excited_states.py | Python | apache-2.0 | 959 | [
"PySCF"
] | 03f9b4c655301fbf74a8e13b30917677bffe93d9310531cf2ba12064155d2fa9 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Alex Grigorevskiy
# Licensed under the BSD 3-clause license (see LICENSE.txt)
"""
Main functionality for state-space inference.
"""
import collections # for cheking whether a variable is iterable
import types # for cheking whether a variable is a function
import numpy a... | SheffieldML/GPy | GPy/models/state_space_main.py | Python | bsd-3-clause | 143,832 | [
"Gaussian"
] | 9617358dd6529d963e7043acea4de04e185367efcfb2f6960331a6e76dcf86d8 |
"""
@name: Modules/Web/web_computerMenu.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2020y D. Brian Kimmel
@license: MIT License
@note: Created on Jun 21, 2015
@Summary:
"""
# Import system type stuff
import os
from nevow import loaders
from nev... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Web/web_computerMenu.py | Python | mit | 1,022 | [
"Brian"
] | 9b3bff5e4fb68e19c2f069e311434eea47fd6199daeface9749e03fdc61cd2c9 |
import numpy as np
from scipy import optimize
import matplotlib.pylab as plt
import collections, copy, itertools
class TrajectorySource(object):
"""
Class to generate initial trajectories for linkage inference as well as for continued production
of trajectories feeding into a "live" linking process... | Hamstard/AtomStalker | AtomStalker/TrajectorySimulator.py | Python | mit | 9,717 | [
"Gaussian"
] | 0de368bf6043bdf1bdef0068141a3e0c895586f9ce5e703f62a517fa835c590a |
"""
Comparison of Dimension Reduction Techniques
--------------------------------------------
A comparison of several different dimension reduction
techniques on a variety of toy datasets. The datasets
are all toy datasets, but should provide a representative
range of the strengths and weaknesses of the different
algo... | lmcinnes/umap | examples/plot_algorithm_comparison.py | Python | bsd-3-clause | 4,675 | [
"Gaussian"
] | e2742d59592e066c8d7485eae1eaf964599663e47fe9d5fe560739c2b70c40fb |
# ============================================================================
#
# 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/wizard/pages/backup_page.py | Python | gpl-2.0 | 9,943 | [
"VisIt"
] | 3beedee8d29e48027ab538adbbcb7cec854303a6bdd26e53635b1acd2a2e0b40 |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
def pubdev_random_cv():
cars = h2o.import_file(path=pyunit_utils.locate("smalldata/junit/cars_20mpg.csv"))
response_col = "economy"
distribution = "gaussian"
predictors = ["displacement","power","weight","acceleration... | madmax983/h2o-3 | h2o-py/tests/testdir_jira/pyunit_pubdev_1752_random_cv.py | Python | apache-2.0 | 992 | [
"Gaussian"
] | b84fea55749b2a20ec0c2e98373d9e301d213ed64482fcc0405bd6e49182947e |
#
# Author: Henrique Pereira Coutada Miranda
# Check the convergence of the coulomb cutoff for a BSE calculation using yambo
#
from __future__ import print_function
from yambopy import *
from qepy import *
from schedulerpy import *
from functools import partial
import multiprocessing
import argparse
import sys
prefix ... | henriquemiranda/yambopy | tutorial/bn/bse_cutoff.py | Python | bsd-3-clause | 7,445 | [
"Quantum ESPRESSO",
"Yambo"
] | b2c8170331403a5a606867a8595e09db6cc402369250a1484a5142c91075f652 |
"""
Test Display Options
"""
__RCSID__ = "$Id$"
import unittest
import thread
from DIRAC.FrameworkSystem.test.testLogging.Test_Logging import Test_Logging, cleaningLog
from DIRAC.FrameworkSystem.test.testLogging.Test_Logging import gLogger, oldgLogger
class Test_DisplayOptions(Test_Logging):
"""
Test the creat... | hgiemza/DIRAC | FrameworkSystem/test/testLogging/Test_DisplayOptions.py | Python | gpl-3.0 | 11,122 | [
"DIRAC"
] | f57f1aaf77f78e96737b4bc1cf5cf71c75a8e266c512dbb179426703e4e2c8cd |
# The MIT License (MIT)
#
# Copyright (c) 2015 Brian Wray (brian@wrocket.org)
#
# 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
# ... | wrocket/Tulip-Chess | tests/basic-tests/test_book.py | Python | mit | 1,837 | [
"Brian"
] | af1b88de3972c3c5b28952a30c73406d67e4bff5e78c52d1bdb0c2f58321a8fe |
#### import the simple module from the paraview
from paraview.simple import *
#from paraview_find_arrayname import get_Para_Array_name
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
# create a new 'PVD Reader'
#import os
#terminal_path=os.getcwd() + "\n"
#cSF_Subdomains_... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/Visualization_files/Paraview_adapted.py | Python | gpl-3.0 | 7,006 | [
"ParaView"
] | 7580e844a13dbe9248ac0688f3de73421e4629a53b47f9f45a899340c53901e7 |
from util import devlib
from color import yuvlib
texshearlib = devlib(defs=r'''
// Filter directions specified in degrees, using image/texture addressing
// [(0,0) is upper left corner, 90 degrees is down].
__constant__ float2 addressing_patterns[16] = {
{ 1.0f, 0.0f}, { 0.0f, 1.0f}, // 0, 1: 0,... | stevenrobertson/cuburn | cuburn/code/filters.py | Python | gpl-2.0 | 12,956 | [
"Gaussian"
] | 722818e80524621bfac4732af2cfc7f32e78ef51cc1cd02fc0946ab7f8484453 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# License: BSD 3 clause
from itertools import chain, combinations
import numbers
import numpy as np
f... | mehdidc/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 39,855 | [
"Gaussian"
] | 5cdff2f06b44c91842b1363fa4029150bbefcd1c517ca0ae8b8af065595330e4 |
import os, re, sys, glob, logging
from bx.seq.twobit import TwoBitFile
from galaxy.util.json import loads
from galaxy import model, util
from galaxy.util.bunch import Bunch
log = logging.getLogger( __name__ )
# FIXME: copied from tracks.py
# Message strings returned to browser
messages = Bunch(
PENDING = "pending... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/visualization/genomes.py | Python | gpl-3.0 | 12,963 | [
"Galaxy"
] | 905dce6796eda60e69ffd57a8e06fe0a0236d63a45a941b86a9a17231618b295 |
""" Threaded implementation of service interface
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import time
import threading
from concurrent.futures import ThreadPoolExecutor, as_completed
from DIRAC import gLogger
from DIRAC.ConfigurationSystem.privat... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/private/ServiceInterface.py | Python | gpl-3.0 | 2,024 | [
"DIRAC"
] | e149abeaaa67250ee5eb8de5d27fc100edb0b8e00db659ff190476b19bf2b955 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License... | krull/docker-zenoss4 | init_fs/usr/local/zenoss/ZenPacks/ZenPacks.zenoss.MySqlMonitor-3.0.7.egg/ns/tests/util.py | Python | gpl-3.0 | 3,042 | [
"VisIt"
] | a7f207fdee620923c3b08b3d7c915297db4cbbc8bcf631359a02c1c097beca5b |
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 15 08:33:32 2016
@author: GDM
"""
##### Importing modules #####
import HTSeq
import cPickle as pickle
import pandas as pd
from collections import Counter
import os
from HaSAPPy.HaSAPPY_time import *
import itertools
#######################... | gdiminin/HaSAPPy | HaSAPPy/IIDefinition.py | Python | mit | 6,622 | [
"HTSeq"
] | 9688776358d4658cfb4e69bc94cb583a2eb57deecb932a7e3edb708913bd3ef7 |
#./parallel_manager.sh ./create_skysub_delink_para.sh ${SUBARUDIR}/${cluster}/${filter} SCIENCE ${ending} ".sub" TWOPASS
global tmpdir
import os
#os.system('mkdir -p ' + tmpdir)
astrom = 'solve-field'
import traceback, tempfile
def describe_db_long(c,db=['illumination_db']):
if type(db) != type([]):
db =... | deapplegate/wtgpipeline | non_essentials/calc_test/calc_test_save.olddb.py | Python | mit | 314,806 | [
"Galaxy"
] | ab37ad6f100514910432d311911e84a16455176f32c8ccff52c578e377348722 |
#!/usr/bin/env python3
import itertools as it
import logging
import os
from pathlib import Path
import re
from natsort import natsorted
import numpy as np
from pysisyphus.calculators.Gaussian09 import Gaussian09
from pysisyphus.calculators.Gaussian16 import Gaussian16
from pysisyphus.calculators.ORCA import ORCA
fro... | eljost/pysisyphus | deprecated/overlaps/Overlapper.py | Python | gpl-3.0 | 14,208 | [
"ORCA",
"TURBOMOLE"
] | 3e4de9bb42d37547e9dee4e8776cf888d5a15d21d7f3a421cee1499c543aa755 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/procrouting/dft_funcs/superfuncs.py | Python | lgpl-3.0 | 11,064 | [
"Psi4"
] | 3fd71ca9880a0dafc101c80fad5db7cd77c0c1f1ec03e7d6e0db07b9645d6509 |
# -*- mode: python; -*-
##
## sashimi_plot
##
## Utility for visualizing RNA-Seq densities along gene models and
## for plotting MISO output
##
import os
import sys
import glob
import warnings
with warnings.catch_warnings():
warnings.filterwarnings("ignore",category=UserWarning) ### hides import warnings
import... | nsalomonis/AltAnalyze | misopy/sashimi_plot/sashimi_plot.py | Python | apache-2.0 | 11,370 | [
"pysam"
] | 177ff41be26f8de615e2231518679a8c7d45ed67b25d3adcd54458358762c5bf |
"""Utilities to help Computing Element Queues manipulation
"""
from __future__ import absolute_import
from __future__ import division
import six
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.List import fromChar
from DIRAC.Core.Utilities.ClassAd.ClassAdLight import ClassAd
from DIRAC.ConfigurationSystem.C... | fstagni/DIRAC | WorkloadManagementSystem/Utilities/QueueUtilities.py | Python | gpl-3.0 | 8,673 | [
"DIRAC"
] | b3862e5006069c940ebd5da32ee42695cb29df0b6b5809f8cb1af61ad9a95554 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0071_auto_20150826_2053'),
]
operations = [
migrations.AlterField(
model_name='participantt... | koebbe/homeworks | visit/migrations/0072_auto_20150826_2057.py | Python | mit | 436 | [
"VisIt"
] | 61171113baadc6bd484f9259d781c7aaddb06d581dab7d884ea0253388ef79f5 |
# -*- coding: utf-8 -*-
###############################################################################
# Name: arpeggio.py
# Purpose: PEG parser interpreter
# Author: Igor R. Dejanović <igor DOT dejanovic AT gmail DOT com>
# Copyright: (c) 2009-2015 Igor R. Dejanović <igor DOT dejanovic AT gmail DOT com>
# License: MI... | renatav/GraphDrawing | GraphLayoutDSL/target/classes/modules/arpeggio/__init__.py | Python | mit | 57,497 | [
"VisIt"
] | 5af597d77d3c858c513f6ce3206bb4bbada4e9a14178796e31b691db1d98c399 |
"""
Test atomic coordinates and neighbor lists.
"""
import os
import logging
import numpy as np
import unittest
from deepchem.utils import conformers
from deepchem.feat import AtomicCoordinates
from deepchem.feat import NeighborListAtomicCoordinates
from deepchem.feat import NeighborListComplexAtomicCoordinates
logger... | lilleswing/deepchem | deepchem/feat/tests/test_atomic_coordinates.py | Python | mit | 7,286 | [
"RDKit"
] | 85b6ccdc6c0f7eb015015d9ebfb1f0adfe192daef0d746df14e33dacb295aef0 |
import cPickle, gzip, numpy as np
#py 3
# u = pickle._Unpickler(f)
# train_set, valid_set, test_set = u.load()
f = gzip.open('mnist.pkl.gz', 'rb')
f2 = open('matplot-text.txt', 'w+')
train_set, valid_set, test_set = cPickle.load(f)
f.close()
print 'train_set length: ', len(train_set[0])
perceptron_layer = []
epochs... | xR86/ml-stuff | labs-neural-networks/hw-lab4/mnist-perceptron.py | Python | mit | 4,852 | [
"NEURON"
] | 831086f11ad059bf73303ed892a554391181ddfbbeb114f24a950859eddc407e |
"""
gene_server_dump v0.01
gene server dump
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot 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, ... | OndroNR/ga-bitbot | gene_server_dump.py | Python | gpl-3.0 | 2,672 | [
"Brian"
] | accaf3426cdc5990975bce0dd6d6bc38d1f6cc8f07791ff902a62f3f941e860f |
# -*- coding: utf-8 -*-
"""
Created on Wed Aug 1 18:05:48 2018
@author: davch
"""
#%%
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
from sklearn.datasets import make... | DoWhatILove/turtle | programming/python/library/scikit-learn/classifiers_comparison.py | Python | mit | 4,273 | [
"Gaussian"
] | ff766419b1a7b249f58810eac64f15b0004c1661b21e367b7e0dad1f71c0a50a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
from collections import defaultdict
def read_tab_file_handle_sorted(tab_file_handle, factor_index=0):
"""
Parse a tab file (sorted by a column) and return a generator
"""
previous_factor_id = ''
factor_tab_list = list()
# Reading ... | ppericard/matamog | scripts/generate_scaffolding_blast.py | Python | agpl-3.0 | 5,040 | [
"BLAST"
] | 35a86630e61c65d4b6bccedad8f6a42ee016096f1e4c95cf95c691e20a2792ab |
#
# ICRAR - International Centre for Radio Astronomy Research
# (c) UWA - The University of Western Australia, 2016
# Copyright by UWA (in the framework of the ICRAR)
# All rights reserved
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser G... | steve-ord/daliuge | daliuge-engine/dlg/deploy/pawsey/scale_test.py | Python | lgpl-2.1 | 25,117 | [
"Galaxy"
] | c1a22855f42db281a670e1e1bb18068c5eabd501f78b15e7f768d25bbde44f15 |
#coding:utf-8
import re
TLD_NAME = (
'ac.at',
'ac.cn',
'ac.id',
'ac.jp',
'ac.th',
'adv.br',
'ae',
'ag',
'ah.cn',
'ai',
'am',
'appspot.com',
'ar',
'art.pl',
'as',
'asia',
'at',
'au',
'ba',
'bd',
'be',
'bg',
'biz',
'bj.cn',
'bl.uk',
'blog.br',
'bo',
'br',
'br.com',
'by',
'bz',
'ca',
'cat',
'cc',
'cd',
'ch',
'cl',
'club.... | tonghuashuai/42qu-notepad | lib/tld_name.py | Python | mit | 2,993 | [
"Elk"
] | 0b60021e783abdb5f3db039b5bd4db03a3d7aa20c0c7631cea146c88ff608f31 |
'''
Created on Nov 27, 2011
@author: cryan
'''
import unittest
from PySim.SystemParams import SystemParams
from PySim.Simulation import simulate_sequence
from PySim.QuantumSystems import SCQubit, Hamiltonian
from PySim.OptimalControl import optimize_pulse, PulseParams
import numpy as np
import matplotlib.pyplot as p... | BBN-Q/PySimulator | tests/GRAPETests.py | Python | apache-2.0 | 4,491 | [
"Gaussian"
] | 8d264086a17c810c82111007246518e5378e13550efb0d00951b78a4b39ea2d0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# fpblockaverager.FPBlockAverager.py
#
# Copyright (C) 2012-2017 Karl T Debiec
# All rights reserved.
#
# This software may be modified and distributed under the terms of the
# BSD license. See the LICENSE file for details.
"""
Command-line tool to estimate standard e... | KarlTDebiec/FPBlockAverager | FPBlockAverager.py | Python | bsd-3-clause | 21,910 | [
"Gaussian"
] | dacce42dedab6f1e0373c3bccafc184a009f2e8ca6dc78a879be6450e4ce15f3 |
#!/usr/bin/python
'''
GARNET primary script executes 5 sub scripts according to provided configuration file. We provide vertebrate motif data and gene/xref data for hg19 and mm9.
--------------------------------------------------------------------
Config file:
---------------------------------------------------------... | Mkebede/OmicsIntegrator | scripts/garnet.py | Python | bsd-2-clause | 11,577 | [
"Galaxy"
] | 5e4944cd6a236e9417a5fcd21e3a1eb08dc068c790a7ad7bf0d4325b904327a7 |
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