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# -*- coding: utf-8 -*-
r"""
.. _disc-filtering:
===================================
Background information on filtering
===================================
Here we give some background information on filtering in general, and
how it is done in MNE-Python in particular.
Recommended reading for practical applications ... | rkmaddox/mne-python | tutorials/preprocessing/25_background_filtering.py | Python | bsd-3-clause | 48,286 | [
"Gaussian"
] | 1b01f4e5898bf3bd3fa9aa40a5d1b148f4a75a2acea49d92c74cb9db7b081da0 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | scripts/AbinsModules/GeneralAbInitioProgram.py | Python | gpl-3.0 | 11,064 | [
"CASTEP"
] | 0e2a78a5254621739f85f3ce21170fbd928dc13c1ea211f460f06c82e69a5736 |
import pytest
from events import renderers
from events.models import Location, CustomEvent
@pytest.fixture
def simple_component_renderer(mocker):
mocker.patch.multiple(
'events.renderers',
render_event=str,
render_block_location=lambda v: '{} '.format(v),
)
@pytest.fixture
def time_... | pycontw/pycontw2016 | src/events/tests/renderers/test_render_block.py | Python | mit | 4,987 | [
"Amber"
] | 9952fc50057c4d09e1a7699403441f4f36362f4f60fa6a3edc893374a77b36ae |
from __future__ import print_function
import os
import boto
from boto.s3.key import Key
import assaytools.version
if assaytools.version.release:
# The secret key is available as a secure environment variable
# on travis-ci to push the build documentation to Amazon S3.
AWS_ACCESS_KEY_ID = os.environ['AWS_AC... | MehtapIsik/assaytools | devtools/travis-ci/update-versions.py | Python | lgpl-2.1 | 1,078 | [
"MDTraj"
] | 5178f4eec837c801e3d2ff056cd5fe0495108b754461a8a685856c00f3f11d1e |
"""
Multilayer Perceptron
"""
__authors__ = "Ian Goodfellow"
__copyright__ = "Copyright 2012-2013, Universite de Montreal"
__credits__ = ["Ian Goodfellow", "David Warde-Farley"]
__license__ = "3-clause BSD"
__maintainer__ = "LISA Lab"
import logging
import math
import operator
import sys
import warnings
import numpy ... | goodfeli/pylearn2 | pylearn2/models/mlp.py | Python | bsd-3-clause | 166,284 | [
"Gaussian"
] | d73bd79c5792f44a4e515d55736a712e6e72daf92be5d6b01fc25d473facc3ad |
import nglview
import tempfile
import os
import mdtraj as md
import numpy as np
import tempfile
from rdkit import Chem
from rdkit.Chem import Draw
from itertools import islice
from IPython.display import Image, HTML, display
def combine_mdtraj(protein, ligand):
chain = protein.topology.add_chain()
residue = protei... | deepchem/deepchem | contrib/visualization/utils.py | Python | mit | 2,568 | [
"MDTraj",
"RDKit"
] | 8ec14f6d92f87a6ec5af7f2ce40414b4c4917b8695b426e4a6e42f7d674d2a08 |
"""models for the ``group_messaging`` app
"""
from askbot.mail import send_mail #todo: remove dependency?
from askbot.mail.messages import GroupMessagingEmailAlert
from django.conf import settings as django_settings
from django.contrib.auth.models import Group
from django.contrib.auth.models import User
from django.con... | openpgh/askpgh | askbot/deps/group_messaging/models.py | Python | gpl-3.0 | 20,920 | [
"VisIt"
] | d32df48a3ff72fdc5b1ad30eb81111ef40cb9fdb2dd92c6355f7eeb3ec18c8c3 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | baselines/toxic_comments/sngp.py | Python | apache-2.0 | 43,600 | [
"Gaussian"
] | 568f362b79e39307c1e5c64c4b246bb87a3636e7e0c93af2f07a480b7e525798 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# nicechart.py
#
# Copyright 2011-2016
#
# Christoph Sterz
# Florian Weber
# Maren Hachmann
#
# 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 Found... | danieljabailey/inkscape_experiments | share/extensions/nicechart.py | Python | gpl-2.0 | 32,218 | [
"Gaussian"
] | 84aaa9ca6a1c48324e55bba4e72c89ff24dcedfef897a043b45257abea692edc |
import demistomock as demisto
from CommonServerPython import *
from CommonServerUserPython import *
''' IMPORTS '''
import requests
import json
import collections
# Disable insecure warnings
requests.packages.urllib3.disable_warnings()
''' GLOBALS/PARAMS '''
USERNAME = demisto.params().get('credentials').get('iden... | demisto/content | Packs/Perch/Integrations/Perch/Perch.py | Python | mit | 17,486 | [
"Amber"
] | 03bd8df2e7b09e38b0d8c15315c6b41e2a58993b74275918908942cd19f622d5 |
#!/usr/bin/env python
'''CREATED:2014-05-22 16:43:44 by Brian McFee <brm2132@columbia.edu>
Pitch-shift a recording to be in A440 tuning.
Usage: ./adjust_tuning.py [-h] input_file output_file
'''
from __future__ import print_function
import argparse
import sys
import librosa
import soundfile as sf
def adjust_tuning... | carlthome/librosa | examples/adjust_tuning.py | Python | isc | 1,703 | [
"Brian"
] | 7837439649bc5b25e63ee43010332f472d2acadf3f9cbc32a4adfe8ef0126cea |
from __future__ import absolute_import, division, print_function
import functools
import warnings
from distutils.version import LooseVersion
from io import BytesIO
import numpy as np
from .. import Variable
from ..core.indexing import NumpyIndexingAdapter
from ..core.pycompat import OrderedDict, basestring, iteritem... | jcmgray/xarray | xarray/backends/scipy_.py | Python | apache-2.0 | 9,010 | [
"NetCDF"
] | c1a84a87aa0fe9429bd90fdd8c3760723f22f048f8a608524d9db2ad2de4be57 |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | andrewcbennett/iris | lib/iris/fileformats/cf.py | Python | gpl-3.0 | 44,920 | [
"NetCDF"
] | 595068e20d7b21d3cddbf91cc6030f5b5e0b1857516e97abcd3263c6fbdf79bf |
# The MIT License
#
# Copyright (c) 2008
# Shibzoukhov Zaur Moukhadinovich
# szport@gmail.com
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without ... | intellimath/pyon | dump.py | Python | mit | 13,023 | [
"VisIt"
] | 211c18a86c43df01d4801f1fd94f6fdb211ee7bc0805ff4b27ec59f6c298af5e |
"""Utilities for configuring ansible runtime environment."""
import json
import logging
import os
import pathlib
import re
import subprocess
import sys
from functools import lru_cache
from typing import Any, Dict, List, Optional, Tuple, Type, Union
import packaging
import tenacity
from packaging import version
from a... | ansible/ansible-lint | src/ansiblelint/prerun.py | Python | mit | 17,947 | [
"Galaxy"
] | 27752ea5348cd6a119b9979f7beec1cb9a9b4c3972b2b6780ba281cab3017175 |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option... | tbereau/espresso | testsuite/python/coulomb_cloud_wall.py | Python | gpl-3.0 | 4,540 | [
"ESPResSo"
] | f1cbc6ab397724bf9b13d53632a510c8732dbf10adc992c135289d556e3aa1d2 |
# sql/elements.py
# Copyright (C) 2005-2018 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
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | fernandog/Medusa | ext/sqlalchemy/sql/elements.py | Python | gpl-3.0 | 150,021 | [
"VisIt"
] | ac917603eb8039a1fba78e9f2dca9b8459d77013bcd8c0a68627b4b418f32121 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | abel-von/commons | tests/python/twitter/common/metrics/test_metrics.py | Python | apache-2.0 | 3,717 | [
"Brian"
] | 3f753a6af642ea9e0f81a60244beafb33b048e99ac1b078c8f7669a94bb4c431 |
"""
Node classes (`Apply`, `Variable`) and expression graph algorithms.
To read about what theano graphs are from a user perspective, have a look at
`graph.html <../doc/graph.html>`__.
"""
from __future__ import print_function
from collections import deque
from copy import copy
from itertools import count
import th... | cmdunkers/DeeperMind | PythonEnv/lib/python2.7/site-packages/theano/gof/graph.py | Python | bsd-3-clause | 42,523 | [
"VisIt"
] | 0afa9beef3bdb339d17fea272c16136d91998a0f8d691eff4fc2bbb018425526 |
midi_instruments = {
"Piano": [
"1.Acoustic Piano",
"2.BrtAcou Piano",
"3.ElecGrand Piano",
"4.Honky Tonk Piano",
"5.Elec.Piano 1",
"6.Elec.Piano 2",
"7.Harsichord",
"8.Clavichord",
],
"Chromatic Percussion": [
"9.Celesta",
"10... | pepitogithub/PythonScripts | musica/midi_instruments.py | Python | gpl-2.0 | 5,031 | [
"CRYSTAL"
] | d6da945bfad97982ff90b8e15f2fc93d774806bea226b0c70dbfc30ee2dc7d17 |
"""
GENERAL ARTIFICIAL INTELLIGENCE FOR GAME PLAYING
JAN KLUJ, 2017.
For more information on models or documentation how to use them, please visit:
https://github.com/Honkl/general-ai
"""
from __future__ import division
from __future__ import print_function
import random
import numpy as np
from evolu... | Honkl/general-ai | Controller/controller.py | Python | mit | 4,720 | [
"VisIt"
] | 1c613c60770952361c41eb90314efea263c8da991fb94dad93d83512bcd96eee |
# -*- coding: UTF-8 -*-
## Copyright 2012-2013 Luc Saffre
## This file is part of the Lino project.
## Lino 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 y... | MaxTyutyunnikov/lino | lino/utils/demonames.py | Python | gpl-3.0 | 101,531 | [
"Amber"
] | 949989b78423afc29f29f28f8581cbf6a2c604826257c7158c163705eed1e841 |
"""
Unit tests for the `blowout` module of ``TAMOC``
Provides testing of the class definition, methods, and functions in the
`blowout` module of ``TAMOC``. These tests check the behavior of the class
object, the results of simulations, and the related object methods.
The ambient data used here are from the `ctd_BM54... | socolofs/tamoc | tamoc/test/test_blowout.py | Python | mit | 42,041 | [
"NetCDF"
] | 78c4f3526fe738b36dc2417b7adaef49f7cd8c4f11aefe034b687279a151ff56 |
"""Tool for calculating RDFs
"""
from __future__ import print_function
import numpy as np
from MDAnalysis.lib.distances import distance_array
from analysisbase import AnalysisBase, blocks_of
class InterRDF(AnalysisBase):
"""Analysis object for calculating intermolecular RDF.
See the init method for argume... | richardjgowers/MDA-RDFTool | rdftool.py | Python | gpl-2.0 | 3,827 | [
"MDAnalysis"
] | 54db7262ec2e459139e54586aa29903605d10ce30dc6f380fc17757e9fe8904d |
#!/usr/bin/env python
"""
"""
import cocos
from ui.utils.factories import GCLabelFactory
from ui.menu import GCMenu, GCMenuItem
from ui.scenes.main import GCMainScene
from ui.scenes.options import GCOptionsScene
__all__ = ['GCTitleScene']
label_factory = GCLabelFactory()
class _TitleLayer(cocos.layer.Layer):
... | GalaxyCrawl/GalaxyCrawl | galaxycrawl/ui/scenes/title/title_scene.py | Python | mit | 1,093 | [
"Galaxy"
] | fef4f17c2d341f981a667889edc61484aaebd46bb6427d82ab03c2e9e53c964d |
# copyright 2003-2013 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of astroid.
#
# astroid is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
#... | JetChars/vim | vim/bundle/python-mode/pymode/libs/astroid/rebuilder.py | Python | apache-2.0 | 37,747 | [
"VisIt"
] | ef2264458e0685db04fc53e148babbc324523863430398022a4256fb06be5cac |
"""
Dict with the emojis of osm tyles
"""
typeemoji = {
'aerialway:cable_car': '\xF0\x9F\x9A\xA1',
'aerialway:station': '\xF0\x9F\x9A\xA1',
'aeroway:aerodrome': '\xE2\x9C\x88',
'aeroway:terminal': '\xE2\x9C\x88',
'amenity:ambulance_station': '\xF0\x9F\x9A\x91',
'amenity:atm': '\xF0\x9F\x92\xB3'... | Xevib/osmbot | bot/typeemoji.py | Python | gpl-3.0 | 7,711 | [
"CASINO"
] | 87858ae92b5da940cdb448c7954ba47e436af2cbff9ab91b249d6be3dd4d3454 |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
##!/mnt/lustre_fs/users/mjmcc/apps/python2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
import sys
import numpy as np
from numpy.linalg import *
import MDAnalysis
from distance_fun... | rbdavid/Distance_matrix | Test_Case1/test_matrix_calc.py | Python | gpl-3.0 | 1,966 | [
"MDAnalysis"
] | 8158a74e7eb836347be632d862320a3334d4990f544f88b6f8744329cbcbd5dc |
from __future__ import print_function, division, absolute_import
import os
import re
from collections import defaultdict
from operator import itemgetter
import logging
import sys
from scipy.interpolate import InterpolatedUnivariateSpline as spline
from scipy.integrate import quad
from scipy.optimize import minimize_s... | kgullikson88/gullikson-scripts | kglib/cross_correlation/CCF_Systematics.py | Python | mit | 37,521 | [
"Gaussian"
] | 3a68bb74f604ed59cdb696c25a2991a462f840ffde342b7b11ce9f90b4f10773 |
import topo
import param
import imagen
from topo import projection, responsefn, learningfn, transferfn, sheet, optimized
import topo.transferfn.misc
from topo.submodel import Model, ArraySpec, order_projections # pyflakes:ignore (API import)
from topo.submodel.earlyvision import EarlyVisionModel
@Model.definition
c... | ioam/topographica | topo/submodel/gcal.py | Python | bsd-3-clause | 9,576 | [
"Gaussian"
] | 6b57c5671eb675c35598e233e491d820f6e4d2cb00e3516380ba3159260951bc |
from distutils.core import setup
setup(
name='spfem',
packages=['spfem'],
version='2016.1',
install_requires=[
"numpy",
"scipy",
"matplotlib",
"sympy",
"mayavi",
],
description='Finite elements in pure SciPy'... | kinnala/sp.fem | setup.py | Python | agpl-3.0 | 620 | [
"Mayavi"
] | 2f97266cfda86ad86e197e0b2bdf453f063fee4d95afcb6e758e2caeeece291d |
from copy import deepcopy
from argparse import ArgumentParser
import time
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import galsim
import emcee
import triangle
from astropy.utils.console import ProgressBar
def walker_ball(alpha, spread, nwalkers):
return [alpha+np.r... | jmeyers314/mcgalsim | mcgalsim.py | Python | bsd-3-clause | 8,223 | [
"Galaxy"
] | f057b311a25df61ca85a616b58f1a99095a6fed1caca0c4c6d9c8af358ca2662 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from authlib.oauth2.base import OAuth2Error
from authlib.oauth2.rfc6749.grants import RefreshTokenGrant as _RefreshTokenGrant
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getUsernameForDN, wra... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/private/authorization/grants/RefreshToken.py | Python | gpl-3.0 | 2,809 | [
"DIRAC"
] | 6c7e575dc919f3d9f85cc049aaf04eca0e887edef4eebbdf27109a6189d1b6bc |
#==================================================================================================
# Copyright (C) 2016 Olivier Mallet - All Rights Reserved
#==================================================================================================
import numpy as np
... | olmallet81/URT | Python/example.py | Python | mit | 1,247 | [
"ADF"
] | 68399c4e3c4bc6c1b5f91d80b9efa61cd3f7a25c2c668b13eebee8a813206ac7 |
import json
import pandas as pd
import requests
from py2cytoscape.data.network_view import CyNetworkView
from ..util import util_networkx as nx_util
from ..util import util_dataframe as df_util
from .util_http import check_response
from . import BASE_URL, HEADERS
import warnings
warnings.warn('\n\n\n**** data.cynet... | idekerlab/py2cytoscape | py2cytoscape/data/cynetwork.py | Python | mit | 12,242 | [
"Cytoscape"
] | ec02c729b116cd858360cfd935482e47a932565f6daa3d1f8e100da6b0d9c74a |
# $Id: nodes.py 7054 2011-06-07 15:05:58Z milde $
# Author: David Goodger <goodger@python.org>
# Copyright: This module has been placed in the public domain.
"""
Docutils document tree element class library.
Classes in CamelCase are abstract base classes or auxiliary classes. The one
exception is `Text`, for a text (... | chirilo/remo | vendor-local/lib/python/docutils/nodes.py | Python | bsd-3-clause | 64,968 | [
"VisIt"
] | 74fd6db8a00a8055d6862f8f23e7ec979f37e746e3ba6a9fe8e577986f6b6102 |
import numpy as np
from numpy import fft
from .plotter_utils_consts import n_pts_smooth, default_fourier_n_harm
def gauss(x, a, x0, sigma):
return a * np.exp(-(x - x0) ** 2 / (2 * sigma ** 2))
def gaussian_fit(x, y, x_smooth=None, n_pts=n_pts_smooth):
"""
Fits a Gaussian to some data - x and y. Returns... | ceos-seo/data_cube_utilities | data_cube_utilities/curve_fitting.py | Python | apache-2.0 | 7,564 | [
"Gaussian"
] | 0007202f0c82bbc38522ca2b46217826e962cfa8d851c5765d775bd8ba12e8af |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Stephane Charette <stephanecharette@gmail.com>
# Contribution 2009 by Bob Ham <rah@bash.sh>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013-2014 Paul Franklin
# Copyright (C) 2015 ... | beernarrd/gramps | gramps/plugins/graph/gvhourglass.py | Python | gpl-2.0 | 16,031 | [
"Brian"
] | ba07f4ac59519190b289aed08a3cf52878071e96158c84b5e4d2185dd3eb9396 |
from __future__ import division
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits, load_iris
from sklearn.model_selection import train_test_split
from sklearn.model_selection import cross_val_score
from sklearn.externals.six.moves import zip
from sk... | aflaxman/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 23,848 | [
"Gaussian"
] | 995593d0f76c4f2cc26b314fcfc7c51c5dfbea54aa360bbebe2126d6c4693991 |
#
# @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/p4util/exceptions.py | Python | lgpl-3.0 | 9,523 | [
"Psi4"
] | 4eaf1961aeb36483bf1fd600d251ee21de91b7c2d72e5bb5f827426ead87091c |
# -*- coding: utf-8 -*-
##################################################################################################
import logging
import sqlite3
import threading
from datetime import datetime, timedelta, time
import xbmc
import xbmcgui
import xbmcvfs
import api
import utils
import clientinfo
... | agentxan/plugin.video.emby | resources/lib/librarysync.py | Python | gpl-2.0 | 32,260 | [
"VisIt"
] | b8dc97ef9f27a6aaccc5fd97f42249f371cca5334fed67a9fd7ea9d6d806b39b |
# creates: ag.png water_divide_surf.png
from urllib import urlretrieve
def setup(app):
pass
urlretrieve('http://wiki.fysik.dtu.dk/ase-files/ag.png', 'ase/ag.png')
urlretrieve('http://wiki.fysik.dtu.dk/ase-files/water_divide_surf.png',
'ase/dft/water_divide_surf.png')
| slabanja/ase | doc/images.py | Python | gpl-2.0 | 284 | [
"ASE"
] | 418a02d3f383c354671c6dce42f8c21773da46cf4621c4be9c556cd5fac4cd9a |
# Test executable #5 to exercise the Gauss-Hermite class
# Here, we fit two Gauss-Hermite expansions to a donut shaped profile
# (Each one forces one of the zero'th order coefficients to be zero)
# The SciPy least squares method is used.
#
# Copyright (c) 2013 RadiaBeam Technologies. All rights reserved
# python impor... | radiasoft/radtrack | experimental/hermite/testHermite05.py | Python | apache-2.0 | 9,777 | [
"Gaussian"
] | 7880f46a0cfebc589846c2c17a131046f1b92fbd71df50dffea0f50a7da41e05 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | src/python/espressomd/lbboundaries.py | Python | gpl-3.0 | 2,658 | [
"ESPResSo"
] | 88b3a541eb1fedb318975553278cd15ca35e06ed4291c14dcd8065565f83b52a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
#Author: Read AUTHORS file.
#License: Read COPYING file.
import gettext
from PyQt4 import *
from constants import const
from ui_main import Ui_Dialog
from lib import stripFilename, stripPath, getPardusRelease, ratioCalc
from about import aboutDialog
from options import opt... | alierkanimrek/pog | src/main.py | Python | gpl-3.0 | 7,150 | [
"VisIt"
] | 20cc795b6126984344dc5c01fd98beae6a7aa0ba1bc839c5187c3fd7ace91367 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_billiard.py | Python | gpl-3.0 | 1,318 | [
"ESPResSo"
] | 4f7277112f50cf4da150089eb726312633614a8a4d5b8fa6c9bd0a328ff6d881 |
"""
Tests for IPython.config.application.Application
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, d... | marcoantoniooliveira/labweb | oscar/lib/python2.7/site-packages/IPython/config/tests/test_application.py | Python | bsd-3-clause | 6,352 | [
"Brian"
] | 660dfaa412754427964b02b82064af123b532a2da50c7accb220e2a141354be0 |
import argparse
import sys, traceback
import os
from os import path
sys.path.append(path.abspath(path.join(path.dirname(__file__), "..")))
import csv, math
#import rasterio
import ogr, gdal, gdalconst, osr
#import fiona
import numpy
from lib.sitkaAPI import downloadUnzipTopo
from lib.loghelper import Logger
from lib.e... | SouthForkResearch/CHaMP_Metrics | tools/hydro_gis_export_gdal.py | Python | gpl-3.0 | 12,099 | [
"VisIt"
] | cd0d0f02aa39e3aab5068f92de09a734af26d8034cb96d7f45aa7e5686af3264 |
"""
python-can requires the setuptools package to be installed.
"""
from setuptools import setup, find_packages
__version__ = "1.5.2"
import logging
logging.basicConfig(level=logging.WARNING)
setup(
name="python-can",
url="https://bitbucket.org/hardbyte/python-can",
version=__version__,
packages=fin... | luminize/python-can | setup.py | Python | lgpl-3.0 | 822 | [
"Brian"
] | fa99022286a1f5367435aafc57e6ede85379aec8b53e9e47c0aa108d8f9e66f2 |
import os
import unittest
import numpy as np
from deepchem.utils import rdkit_utils
from deepchem.utils.fragment_utils import get_contact_atom_indices
from deepchem.utils.fragment_utils import merge_molecular_fragments
from deepchem.utils.fragment_utils import get_partial_charge
from deepchem.utils.fragment_utils impor... | deepchem/deepchem | deepchem/utils/test/test_fragment_utils.py | Python | mit | 2,474 | [
"RDKit"
] | b4356910a4160a4d8a19fb9ed3b79d73a66d617c10e7a357006b79632d971c03 |
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
import sys
if not (sys.version_info.major == 3 and sys.version_info.minor > 5):
print("Python version %s.%s not supported version 3.6 or above required - exiting" % (sys.version_info.major,sys.version_info.minor))
sys.exit(1)
import os
for path in [os.getcwd(),"so... | schemaorg/schemaorg | software/tests/test_graphs.py | Python | apache-2.0 | 22,992 | [
"ASE"
] | a7d659a9a5fa17f0625adc7ded425b971588c0e125f66e17e0293c68f29d793b |
#!/usr/bin/env python
#
# File Name : ptbtokenizer.py
#
# Description : Do the PTB Tokenization and remove punctuations.
#
# Usage :
#
# Creation Date : 29-12-2014
# Last Modified : Feb 25 2015
# Author : Hao Fang and Tsung-Yi Lin
# Modified by: Desmond Elliott
import os
import sys
import subprocess
# import tempfil... | elliottd/GroundedTranslation | util/ptbtokenizer.py | Python | bsd-3-clause | 2,065 | [
"Desmond"
] | 2e6bdb044feb32b595a6390452e0e3e9930130f738167cb3449d3c3570af5464 |
"""
==================================
Advanced interactive visualization
==================================
In DIPY_ we created a thin interface to access many of the capabilities
available in the Visualization Toolkit framework (VTK) but tailored to the
needs of structural and diffusion imaging. Initially the 3D vis... | FrancoisRheaultUS/dipy | doc/examples/viz_advanced.py | Python | bsd-3-clause | 8,973 | [
"VTK"
] | ad86df2a36d8abfafa7bd29e07af2fccc367333acdb03b8ed913b09cf8a1e494 |
import cStringIO
import logging
import operator as op
from antlr3.tree import CommonTree as AST
from lib.typecheck import *
import lib.const as C
import lib.visit as v
from .. import util
from . import method_nonce, register_method, class_lookup
import statement as st
class Method(v.BaseNode):
def __init__(self... | plum-umd/pasket | pasket/meta/method.py | Python | mit | 8,739 | [
"VisIt"
] | 11d20fda75d66e5f6cd11a6f6832e828ce78f16ccce80b78fab3727f74bc9eda |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | ctk3b/mdtraj | mdtraj/geometry/tests/test_sasa.py | Python | lgpl-2.1 | 5,058 | [
"Gromacs",
"MDTraj"
] | 55acdb9008ddcdd7e1383cd4dfb6a00ed5e6f029abbfc93c43282bfe6f556d07 |
#!/usr/bin/env python
try:
import netCDF4 as netCDF
except:
print "netCDF4 is not installed!"
sys.exit(1)
from matplotlib import pyplot as pp
from matplotlib import colors as mc
from optparse import OptionParser
from siple.reporting import endpause
import numpy as np
usage = """Usage: %prog [options]
Exam... | talbrecht/pism_pik06 | examples/inverse/tauc_compare.py | Python | gpl-3.0 | 2,393 | [
"NetCDF"
] | dc7306c12b5f28d562d756d1097313f4e08081dde4087e01f83eb420577b99b6 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-rbgl/package.py | Python | lgpl-2.1 | 1,741 | [
"Bioconductor"
] | 525b9200a194b131e56c0491bf15ec136cc29aa9d61290e3d0463de5c382f136 |
#!/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_snmptrapprofile.py | Python | bsd-3-clause | 3,396 | [
"VisIt"
] | f9c5c18221027d7ec8972891dd35ddd34e08b515ae451ce897cab35aecbd45ca |
"""These classes are here to alter simulation products or other sequences"""
import math
from seqtools.sequence import rc, Sequence
from seqtools.simulation.randomsource import RandomSource
from seqtools.format.fastq import FASTQ
class ErrorMakerGeneric(object):
"""Add errors to sequences"""
def __init__(self,ra... | jason-weirather/py-seq-tools | seqtools/simulation/permute.py | Python | apache-2.0 | 9,854 | [
"Gaussian"
] | d5bf3907ea1d93669f780ee79d5f60a867535abbc7273f7d283d04b5e0c32a7e |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 19 16:06:40 2019
@author: raf
"""
# IMPORT STUFF
from pdb import set_trace as stop
from collections import OrderedDict
import os
import copy
import numpy as np
import os
from astropy import table
import glob
import gc
import string as st
import pan... | ruymanengithub/vison | vison/metatests/metacal.py | Python | gpl-3.0 | 22,778 | [
"DIRAC"
] | ed3e65036a04f5c91500c4b08e7a140f05543d5760b2664eedd6a596c56acda7 |
"""User preferences for KlustaViewa."""
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
import logging
import numpy as np
# -----------------------------------------------------------------------... | klusta-team/kwiklib | kwiklib/utils/preferences_default.py | Python | bsd-3-clause | 3,308 | [
"Gaussian"
] | dd26b697daa0167c4040fb1e4cd768ecd788b9808c1121a82333bc78c87f5977 |
"""
functions to access the data dictionary in a clearer way
"""
import os
import toolz as tz
from bcbio.utils import file_exists
from bcbio.log import logger
import sys
LOOKUPS = {
"config": {"keys": ['config']},
"num_cores": {"keys": ['config', 'algorithm', 'num_cores'],
"default": 1},
... | elkingtonmcb/bcbio-nextgen | bcbio/pipeline/datadict.py | Python | mit | 8,324 | [
"Galaxy"
] | 1b5465b0a594cc9bfbe193db4ea17f4fc92119f19db9ce93f4d4d2bbad0a153b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; ... | Fedik/gramps | gramps/plugins/quickview/filterbyname.py | Python | gpl-2.0 | 18,863 | [
"Brian"
] | b82fb92a1d767c5ce3afc03f4779ec38e0e37289fb31698203545f5ed4fceb87 |
# Copyright 2016 Brian Innes
#
# 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 in writing, ... | brianinnes/vPiP | python/vPiP/config.py | Python | apache-2.0 | 12,670 | [
"Brian"
] | 694aace60f5cdae85a4247b73451a86b3588176fc41a1ea036e688b0b34879b1 |
#
# 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... | axbaretto/beam | sdks/python/apache_beam/pipeline.py | Python | apache-2.0 | 58,770 | [
"VisIt"
] | a8d02f32367ffd999d8b6e5b4646e1e307f030786b4b84a1a9d0624e631eb9e5 |
#!/usr/bin/env python
#===============================================================================
# Copyright 2017 Geoscience Australia
#
# 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... | alex-ip/geophys_utils | geophys_utils/test/test_crs_utils.py | Python | apache-2.0 | 6,019 | [
"NetCDF"
] | b2f15e7726cd21b605ff29ea11799a3349d9e325091210f8d933add369813194 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# All Rights Reserved.
#
# Androguard is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either versi... | JulianSchuette/android-instrumentation | injector/androguard/decompiler/dad/writer.py | Python | apache-2.0 | 15,928 | [
"VisIt"
] | 7e4ba378e7b3af5d088fa090efb898ff1bee44523bdcbc984a0660a6d9e412f1 |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from nose.tools import assert_true, assert_in, assert_false # pylint: disable=E0611
from auth.authz import get_user_by_email, get_course_groupname_for_role
from django.conf import settings
from selenium.webdriver.common.keys import Keys... | morpheby/levelup-by | cms/djangoapps/contentstore/features/common.py | Python | agpl-3.0 | 9,621 | [
"VisIt"
] | 9752d187a2d9b4f5916bb6d229b9a31c36199079302cbe94bc80ce34564c39bf |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# 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
#
# ... | dongjoon-hyun/neon | examples/mnist_mlp.py | Python | apache-2.0 | 3,458 | [
"Gaussian"
] | b680cb687860f8dbd249351c8034ed76c9007b1748977f2959321bcca108bd59 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module is used for analysis of materials with potential application as
intercalation batteries.
"""
__author__ = "Anubhav Jain, Shyue Ping Ong"
__co... | migueldiascosta/pymatgen | pymatgen/apps/battery/insertion_battery.py | Python | mit | 20,676 | [
"pymatgen"
] | f43c3716cc4d7f65e9560869d8a261a9fd2f935aafe74f5d300101af6365ee85 |
# 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 NetcdfCxx(AutotoolsPackage):
"""Deprecated C++ compatibility bindings for NetCDF.
Thes... | LLNL/spack | var/spack/repos/builtin/packages/netcdf-cxx/package.py | Python | lgpl-2.1 | 1,592 | [
"NetCDF"
] | f8a6cb965b47cf0406acfcbcf05cb4acae1f66fa26ce959619b2b2e9b2e581e8 |
# Author: Robert McGibbon <rmcgibbo@gmail.com>
# Contributors:
# Copyright (c) 2014, Stanford University and the Authors
# All rights reserved.
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
from ... | stephenliu1989/msmbuilder | msmbuilder/example_datasets/alanine_dipeptide.py | Python | lgpl-2.1 | 2,853 | [
"MDTraj",
"OpenMM"
] | aa6e69950f89e8904e78982e445eea46a40c8a87238177e6a4a10ccb2709bffe |
from setuptools import setup
setup(
name="public-drive-urls",
version='1.0.0',
author="Brian Peterson",
author_email="bepetersn@gmail.com",
description="Find Google Drive download URLs from a file's sharing URL",
license="MIT",
url='https://github.com/bepetersn/public-drive-urls/',
py_... | bepetersn/public-drive-urls | setup.py | Python | mit | 504 | [
"Brian"
] | d3290a388cbaaa73b9c51cf22b7135eb326a0db35b21c897215ea836f686ecc1 |
from skimage.filters import gabor_kernel
from scipy.ndimage.filters import convolve as convolveim
import numpy as np
import time
class GaborFilter:
real_time = 0
real_cont = 0
imag_time = 0
imag_cont = 0
magnitude_time = 0
magnitude_cont = 0
def __init__(self, frequency, theta, sigma_x... | benitesf/Skin-Lesion-Analysis-Towards-Melanoma-Detection | features_extraction/methods/gabor_filter_banks.py | Python | mit | 4,150 | [
"Gaussian"
] | fe05eab3e1b2618d51b10f105166f97f4785da746d22030da55f464befa5beff |
"""
==================================================
Automatic Relevance Determination Regression (ARD)
==================================================
Fit regression model with Bayesian Ridge Regression.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary l... | manhhomienbienthuy/scikit-learn | examples/linear_model/plot_ard.py | Python | bsd-3-clause | 3,655 | [
"Gaussian"
] | 71f30d2d3e2e1f0993568b62fc685e12e205f7ce4741051b77f5b9811fd84c13 |
from lan.lan_ast import *
import copy
class AddToId(NodeVisitor):
""" Finds the Id and replaces it with a binop that
adds another variable to the id.
"""
def __init__(self, id, variable):
self.id = id
self.variable = variable
def changeIdNode(self, node):
if isinstance(no... | dikujepsen/OpenTran | v2.0/framework/unused/transf_visitor_unused.py | Python | mit | 13,670 | [
"VisIt"
] | e912b3111e0efd15975712c3fc27cf52798866170ca9b21e971ee5032d9c8e69 |
# DIALS_ENABLE_COMMAND_LINE_COMPLETION
from __future__ import annotations
import copy
import os
import sys
import iotbx.phil
from cctbx import sgtbx
from rstbx.symmetry.constraints import parameter_reduction
import dials.util
from dials.algorithms.indexing.assign_indices import AssignIndicesGlobal
from dials.algor... | dials/dials | command_line/reindex.py | Python | bsd-3-clause | 14,144 | [
"CRYSTAL"
] | 24fe7a2c8053fc2af61445fc545a907c90633885a861fe433e2008eec5aec958 |
# ######################################################################
# Original code: #
# @author: Robert B. Von Dreele and Brian Toby #
# General Structure Analysis System - II (GSAS-II) #
# https://subversion.xor.aps... | yugangzhang/scikit-beam | skbeam/io/gsas_file_reader.py | Python | bsd-3-clause | 8,616 | [
"Brian"
] | 5c6b0570bc54aaaa0eb531019bae610968a7cb5c0e9f7af56bb6dda0dcc92ff5 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/motion_only/hmm_crossvalidation_motion_10_states.py | Python | mit | 16,433 | [
"Gaussian",
"Mayavi"
] | 37bf8eae31722a34d568974b0e5a2420bd788b9765fc68b301e377592f5793b4 |
"""Test the Elk-M1 Control config flow."""
from unittest.mock import MagicMock, patch
from homeassistant import config_entries, setup
from homeassistant.components.elkm1.const import DOMAIN
def mock_elk(invalid_auth=None, sync_complete=None):
"""Mock m1lib Elk."""
def handler_callbacks(type_, callback):
... | sander76/home-assistant | tests/components/elkm1/test_config_flow.py | Python | apache-2.0 | 10,094 | [
"Elk"
] | cc5ce977376b861f396bf9880e98253464e1646b86b74717ab902882eb6ad77c |
"""SCons.Util
Various utility functions go here.
"""
#
# Copyright (c) 2001 - 2016 The SCons Foundation
#
# 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
# wit... | EmanueleCannizzaro/scons | src/engine/SCons/Util.py | Python | mit | 50,268 | [
"VisIt"
] | c62b7eb380bed5b58a0cb8f9444babd1175f56db45639e9785f705746837f88c |
# 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... | hmenke/espresso | testsuite/python/analyze_gyration_tensor.py | Python | gpl-3.0 | 3,913 | [
"ESPResSo"
] | fe02939123a801c64215b7945a0ade0e093c8a0f15206cf82bc6720188db33fe |
# Demo program using ManGrating.
#
# Copyright (C) 2010-2011 Huang Xin
#
# See LICENSE.TXT that came with this file.
"""
USAGE:
Move the mouse cursor to change the position of the grating.
Scroll the mouse wheel to change the orientation.
Press right arrow to increase the spatial frequency.
... | chrox/RealTimeElectrophy | StimControl/LightStim/demo/mangrating.py | Python | bsd-2-clause | 2,020 | [
"Gaussian"
] | fbe9c75bd6dd0b893317f15ecfd10361ac2307e9324b97d2950335d71e8eb3b6 |
"""
XML format classes
"""
import data
import logging
from galaxy.datatypes.sniff import *
log = logging.getLogger(__name__)
class BlastXml( data.Text ):
"""NCBI Blast XML Output data"""
file_ext = "blastxml"
def set_peek( self, dataset, is_multi_byte=False ):
"""Set the peek and blurb text"""
... | volpino/Yeps-EURAC | lib/galaxy/datatypes/xml.py | Python | mit | 1,456 | [
"BLAST",
"Galaxy"
] | 9137ab4761e7d5e7ba50ae77f68de6ca1fe65b3eccf230b637132547d2feacf0 |
# -*- coding: utf-8 -*-
import unittest
import logging
import datetime
import cmath as math
from sea_object import *
from util.util import feet_to_meters, knots_to_meters
from sound import sound
logger = logging.getLogger("subsim")
"""
A novice asked the Master: “Here is a programmer that never designs,
documents o... | ftfarias/PySubsim | old/sea.py | Python | gpl-3.0 | 21,237 | [
"Gaussian"
] | 0b4ecd84e0f9c8e64ed97cfd3b570e6fead05c13406018a772e4c8784c19c0a6 |
"""
The following tools have been eliminated from the distribution:
1: BAM-to-SAM converts BAM format to SAM format
2: Categorize Elements satisfying criteria
3: Compute Motif Frequencies For All Motifs motif by motif
4: Compute Motif Frequencies in indel flanking regions
5: CTD analysis of chemicals, diseases, o... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py | Python | gpl-3.0 | 3,304 | [
"Galaxy"
] | fae4a74d1211df9d8868c1e41ab8ef8ffb927492bc318a5d6125d4466c10a5f7 |
# 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(dat... | wmvanvliet/mne-python | mne/preprocessing/infomax_.py | Python | bsd-3-clause | 11,848 | [
"Gaussian"
] | 36cd3fc75d6ec1b044851b0a7fb6f9752b210ae6ce339873f0d9d8b650c7718c |
import unittest
from ladygeek.graph.client import get_graph_url
from ladygeek.graph.entities import User
from py2neo import Graph
class TestUser(unittest.TestCase):
USER_DATA = {'contributors_enabled': False,
'created_at': 'Fri Jun 12 11:13:21 +0000 2009',
'default_profile': Fal... | salimfadhley/neowrapper | test/test_neowrapper/test_user.py | Python | mit | 7,113 | [
"VisIt"
] | ed782c0a39ce5b4508d265671c435b12378ab1f1572faa4964a8777aae9023ee |
#!/usr/bin/env python3
# Version 1.1
# Author Alexis Blanchet-Cohen
# Date: 09/06/2014
import argparse
import glob
import os
import os.path
import pandas
import subprocess
import util
# Read the command line arguments.
parser = argparse.ArgumentParser(description="Generates bedtools coverage scripts.")
parser.add_ar... | blancha/abcngspipelines | utils/bedtools_coverage.py | Python | gpl-3.0 | 3,688 | [
"BWA"
] | cffb68fe4140724ec3014747526704b7cca668174fe09f33b34ba5973404a1ee |
from django.conf.urls import patterns, url
urlpatterns = patterns('',
(r'^(?P<project_id>\d+)/multiple-presynaptic-terminals$', 'vncbrowser.views.multiple_presynaptic_terminals'),
(r'^(?P<project_id>\d+)/go-to/connector/(?P<connector_id>\d+)/stack/(?P<stack_id>\d+)$', 'vncbrowser.views.goto_connector'),
(... | htem/CATMAID | django/applications/vncbrowser/urls.py | Python | agpl-3.0 | 1,208 | [
"NEURON"
] | 03f7840c51746f455094ea7e3713508aa794c6fb32f371359c34f011d26b9984 |
"""
CP decomposition by classic alternating least squares (ALS).
Author: N. Benjamin Erichson <erichson@uw.edu> and Alex H. Williams
"""
import numpy as np
from scipy import linalg
from tensortools.operations import unfold, khatri_rao
from tensortools.tensors import KTensor
from tensortools.optimize import FitResult... | ahwillia/tensortools | tensortools/optimize/mcp_als.py | Python | mit | 4,810 | [
"Gaussian"
] | 81ea3d9465957a1a4617219a814cdf02e14caf004533bbd142ba65cae1db6a8c |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/topology/TPRParser.py | Python | gpl-2.0 | 9,416 | [
"Gromacs",
"MDAnalysis"
] | d4ed30e196c2b4db1f189333be3fb601f67f7f3ed6b3b52cbf196be988966149 |
# 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... | seanli9jan/tensorflow | tensorflow/python/autograph/converters/side_effect_guards.py | Python | apache-2.0 | 6,845 | [
"VisIt"
] | 3067c9d00c2fefa3c49755f2ea78d2f38862c60197c5e0a26042680959806aae |
'''
THIS MODULE HAS BEEN REPLACED BY `gproc.py` AND IT REMAINS HERE FOR LEGACY
PURPOSES
This module defines a class, `GaussianProcess`, which is an
abstraction that allows one to easily work with Gaussian processes.
One main use for the `GaussianProcess` class is Gaussian process
regression (GPR). GPR is also known as... | treverhines/RBF | rbf/gauss.py | Python | mit | 67,258 | [
"Gaussian"
] | 20507e75fa47c2b1a2ebdef8366d9620e388fa6eafa8534be830559ebb40ab85 |
"""@package gen_tex_tables
Generate tables in LaTeX format for insertion into writeup
"""
import os
import numpy as np
class filterdat():
def __init__(self,name,notes = None):
## identifying name
self.name = name
## 3 x 4 array of data; each coumn is MSE1, MSE2, percentage conservative, percent overconfident
... | fatadama/estimation | challenge_problem/processing/gen_tex_tables.py | Python | gpl-2.0 | 6,577 | [
"Gaussian"
] | fcf5ce041e2452e27ac1cb12cacc287d421260d8216b2421ccca8cb41ac61db9 |
# Copyright (C) 2015 Hydriz Scholz
#
# 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 ... | Hydriz/DBReports | reports/mostinvokes.py | Python | gpl-3.0 | 1,989 | [
"VisIt"
] | cffd61e0634065bf71da779b622b8341e077c2f0c4b82519926fb53d47da4d1f |
import vtk
import random
class ParametricObjects():
def ParametricObjects(self):
parametricObjects = list()
parametricObjects.append(vtk.vtkParametricBoy())
parametricObjects.append(vtk.vtkParametricConicSpiral())
parametricObjects.append(vtk.vtkParametricCrossCap())
param... | bond-anton/Space_visualization | demo/10_pure_vtk.py | Python | apache-2.0 | 5,212 | [
"VTK"
] | a9e4b88741487d43894f89f47f7789ed5793de5058993383bbce0b9d0c305455 |
# -*- coding: utf-8 -*-
__author__ = "HarshaRani"
__credits__ = ["Upi Lab"]
__license__ = "GPL3"
__version__ = "1.0.0"
__maintainer__ = "HarshaRani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
__updated__ = "Sep 03 2018"
'''
mooseAddChemSolver and mooseD... | dilawar/moose-core | python/moose/chemUtil/add_Delete_ChemicalSolver.py | Python | gpl-3.0 | 5,578 | [
"MOOSE"
] | 0560c1d18193d73d0c396d9beff99798359e34ef30932ee19fdd768b7b00cf94 |
"""\
This program inputs a GAMESS basis, e.g. from the EMSL basis set order
form, and formats it into PyQuante format
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
license. Please see the file LICENSE that is part of this
distribution.
"... | berquist/PyQuante | PyQuante/Basis/Tools.py | Python | bsd-3-clause | 4,058 | [
"GAMESS"
] | ee5ccd720a7bed3897d6a04daedf482e6fa3b8e26bbd252d8203712e5290e382 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Change directory to p... | rameshvs/nipype | nipype/interfaces/fsl/model.py | Python | bsd-3-clause | 82,958 | [
"Gaussian"
] | 7dd1194c8fec5f51bb10074e567dc9f1d8036067ad7522fb3ae05bc1ca894701 |
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