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#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2009-2010 Craig J. Anderson
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the... | arunkgupta/gramps | gramps/plugins/drawreport/descendtree.py | Python | gpl-2.0 | 66,162 | [
"Brian"
] | 45a91e231561258647ccfc0ba7ca4e441de30662548c054e1898b186f8417267 |
"""
End-to-end tests for the LMS.
"""
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.course_home import CourseHomePage
from common.test.acceptance.pages.lms.course_wiki import (
CourseWik... | eduNEXT/edunext-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 3,832 | [
"VisIt"
] | eee81a947717177243ee5da45af33593fee53e8d9f60d88b7174de6201d018e5 |
from sqlalchemy import *
from sqlalchemy.sql import table, column, ClauseElement, operators
from sqlalchemy.sql.expression import _clone, _from_objects
from sqlalchemy.testing import fixtures, AssertsExecutionResults, \
AssertsCompiledSQL
from sqlalchemy import testing
from sqlalchemy.sql.visitors import ClauseVis... | rclmenezes/sqlalchemy | test/sql/test_generative.py | Python | mit | 57,284 | [
"ADF",
"VisIt"
] | d886e7b9ffe4c1def322e4928484998fdafc7db515e61359ee57a490592545f3 |
'''
FromScratchGauss.py
Initialize params of a mixture model with gaussian observations from scratch.
'''
import numpy as np
from bnpy.util import discrete_single_draw
from bnpy.data import XData
def init_global_params(hmodel, Data, initname='randexamples', seed=0, K=0, **kwargs):
PRNG = np.random.RandomState(seed)... | daeilkim/refinery | refinery/bnpy/bnpy-dev/bnpy/init/FromScratchGauss.py | Python | mit | 2,016 | [
"Gaussian"
] | 0bbe84f0a4ee516bef29271d182e62ff4a21c48601b8834239adb4dfde7dcd70 |
#!/usr/bin/env python
"""aug2cmds converts an Augeas tree into a set of Augeas commands
Designed for use with augtool and Puppet.
"""
import __init__ as aug2cmds
import outputs
import argparse
def main():
"""Runs aug2cmds as an interactive tool"""
parser = argparse.ArgumentParser(
description="Conve... | domcleal/aug2cmds | aug2cmds/__main__.py | Python | bsd-3-clause | 1,377 | [
"VisIt"
] | 3327c84f3bc5af99d1ffefcc086a13c5a855b1ae9f9dc99af8aa87491e6fff2c |
import logging
import numpy as np
import os
import pkg_resources
from pprint import pformat
import scipy
from scipy.ndimage.morphology import generate_binary_structure, iterate_structure
import caiman.utils.utils
from ...paths import caiman_datadir
from .utilities import dict_compare, get_file_size
class CNMFParams(... | simonsfoundation/CaImAn | caiman/source_extraction/cnmf/params.py | Python | gpl-2.0 | 50,491 | [
"Gaussian",
"NEURON"
] | d51e289f10fc66b911f8c46cae58debb2d5ff03daeac62a312a8ef35e3156612 |
"""
Pairwise distance functions between time series in the input space
==================================================================
They all have the following prototype:
function(bcsc1, bcsc2, **kwargs)
"""
import numpy as np
from numpy.linalg import slogdet
from scipy.linalg import solve, eigh
fro... | daien/daco | distances_linear.py | Python | mit | 14,811 | [
"Gaussian"
] | 735660e1583f08442b0040156c977b2db21b81df8f9206a7a00312fd87af8dae |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licens... | tuffy/python-audio-tools | audiotools/toc/yaccrules.py | Python | gpl-2.0 | 7,986 | [
"Brian"
] | 4aec5af637c6704048e3ae3d19c751d6d3408b517d2337609e7308fd181d94c6 |
import operator
import numpy as np
from time import time
from abc import ABCMeta, abstractmethod
import logging
from dipy.segment.metric import Metric
from dipy.segment.metric import ResampleFeature
from dipy.segment.metric import AveragePointwiseEuclideanMetric
from dipy.segment.metric import MinimumAverageDirectFlip... | FrancoisRheaultUS/dipy | dipy/segment/clustering.py | Python | bsd-3-clause | 25,605 | [
"VisIt"
] | ee67874781b527946e4bd8a27caf583847f5a666e4165ecf53b00affd9d82711 |
# Copyright 2001-2009 Brad Chapman.
# Revisions copyright 2009-2016 by Peter Cock.
# Revisions copyright 2009 by David Winter.
# Revisions copyright 2009-2010 by Leighton Pritchard.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that ... | zjuchenyuan/BioWeb | Lib/Bio/Emboss/Applications.py | Python | mit | 55,897 | [
"Biopython"
] | 9da6f037dee1f5eabd293cd6377a0f29bcd56f923c801599000b362a00d8dfc1 |
# -*- coding: utf-8 -*-
from __future__ import print_function
from util import *
from pattern import graph
from pattern.graph import commonsense
#-------------------------------------------------------------------------
class TestUtilityFunctions(unittest.TestCase):
def setUp(self):
pass
def tes... | hayd/pattern | test/test_graph.py | Python | bsd-3-clause | 26,561 | [
"VisIt"
] | 48f2a3f099b31f79f5ffb2ae4ba5f243d6c3d0fb1379f9f0005422bd3216e922 |
# Copyright 2003 by Sebastian Bassi. sbassi@genesdigitales.com
# All rights reserved. This code is part of the Biopython
# distribution and governed by its license.
# Please see the LICENSE file that should have been included as part
# of this package.
import warnings
warnings.warn("Bio.lcc is deprecated; it has bee... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/lcc.py | Python | apache-2.0 | 4,885 | [
"Biopython"
] | f896f414459740f07387e8ca2a2a5e6927e0596f876c9b5fb9e0bd0f68a30447 |
"""
Main module.
Implement the central Checker class.
Also, it models the Bindings and Scopes.
"""
import __future__
import ast
import bisect
import collections
import contextlib
import doctest
import functools
import os
import re
import string
import sys
import tokenize
from pyflakes import messages
PY2 = sys.versi... | PyCQA/pyflakes | pyflakes/checker.py | Python | mit | 84,839 | [
"VisIt"
] | eb09eac9cd06878b7b7c14feca87ec6b10f6888e8e6ea1d2b5ea7cb0e8bec217 |
#! /usr/bin/python
# Python 2.7.5, requires Biopython.
'''
Created on 07/06/2014
@author: Adam_Taranto
'''
import argparse;
import getopt;
import sys;
import re;
from Bio import SeqIO;
from Bio.Seq import Seq;
#from Bio.Seq import MutableSeq;
from Bio.SeqRecord import SeqRecord;
#from Bio.Alphabet import IUPAC;
de... | Adamtaranto/methFreq | methFreq.py | Python | mit | 9,191 | [
"Biopython"
] | 7e486df9823e7c083f24f69befecd53cb2dc18271cb8c0cabccf72ac5af4be66 |
"""TransformationCleaningAgent cleans up finalised transformations.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN TransformationCleaningAgent
:end-before: ##END
:dedent: 2
:caption: TransformationCleaningAgent options
"""
__RCSID__ = "$Id$"
# # imports
import re
import ast
import os.path
f... | arrabito/DIRAC | TransformationSystem/Agent/TransformationCleaningAgent.py | Python | gpl-3.0 | 27,459 | [
"DIRAC"
] | 6f34db20ef2f361bc06388c8a3f51e58f3fae6c2e9958191dde94ff91e5e22c2 |
#!/usr/bin/env python
import argparse
import logging
import sys
from BCBio import GFF
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqFeature import (
FeatureLocation,
SeqFeature
)
from Bio.SeqRecord import SeqRecord
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)
def par... | Delphine-L/tools-iuc | tools/progressivemauve/xmfa2gff3.py | Python | mit | 5,800 | [
"Biopython"
] | 33ca01db92a1d942f1b9a488b55505cb53fec4ce849fd1e17fc16e2ad17e5b31 |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2016, MIT Probabilistic Computing Project
#
# 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/LICENS... | probcomp/bayeslite | tests/test_kl.py | Python | apache-2.0 | 3,744 | [
"Gaussian"
] | 227df0b06e77de219806d9583a717dda6447756e902e1c7a90bb0db49ab8ce12 |
# 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 | samples/rigid_body.py | Python | gpl-3.0 | 4,204 | [
"ESPResSo"
] | 628c65fa5ca8c90c8b999f00941a69225d2eef6970e082b15c45fd781cb8d8f2 |
from DIRAC.Core.Base.Script import Script
from DIRAC.Core.Utilities.Decorators import deprecated
# TODO: remove it in 8.1
@deprecated("DIRACScript is deprecated, use 'from DIRAC.Core.Base.Script import Script' instead.")
class DIRACScript(Script):
pass
| DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/DIRACScript.py | Python | gpl-3.0 | 258 | [
"DIRAC"
] | 79efe7c09a0772ba59266c486ed8210deea1db04142e8023e7871be1b6f26cdd |
usage = """ compute pixels that should be colored for contours """
import healpy as hp
import numpy as np
#=================================================
def contour_pix(map, vals, all_neighbours=True):
"""
given a healpix map (map) and a set of values, we find and return lists of pixels that constitute the boar... | reedessick/bayesburst | contours.py | Python | gpl-2.0 | 5,435 | [
"VisIt"
] | aaecca98b35654d828f2e4d65239cd285bdb8c9de2e7b4604141824e7603388e |
""" Test functions for stats module
"""
from __future__ import division, print_function, absolute_import
import warnings
import re
import sys
from numpy.testing import (TestCase, run_module_suite, assert_equal,
assert_array_equal, assert_almost_equal, assert_array_almost_equal,
assert_allclose, assert_, asse... | petebachant/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 87,809 | [
"Gaussian"
] | 5854e94c676e2395aa18e0ebc02ca0e108850690b17a0e6199b16eb52925f759 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/procedures/proc.py | Python | gpl-2.0 | 149,058 | [
"Psi4"
] | ab7123b07ef5de3de9eb59d1a61f3555d65836b47a38c4300e868a994187fc8d |
"""-*-python-*-
suggested use:
place a dotted symlink to this
file in your home directory
ln -s /.../pythonrc ~/.pythonrc
and set the environment variable
PYTHONSTARTUP
to the symlink
export PYTHONSTARTUP="${HOME}/.pythonrc"
see also:
https://docs.python.org/3/using/cmdline.html#envvar-PYTHONSTARTUP
### todo
* conn ... | ransomw/dotfiles | pythonrc.py | Python | apache-2.0 | 24,236 | [
"PyMOL"
] | 3018d4c952d1968c39dd0e5b433ffd4b69d49ff823bad61f8b79cd48f3dc1b36 |
#!/usr/bin/env python
# Copyright 2014-2020 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... | sunqm/pyscf | pyscf/gto/basis/parse_nwchem.py | Python | apache-2.0 | 13,409 | [
"NWChem",
"PySCF"
] | 3ef7f56b8c9a0ad0f034ec073ec54e18a3bcada9b68e88975d02e978110eb578 |
########################################################################
# $HeadURL$
########################################################################
""" NotificationDB class is a front-end to the Notifications database
"""
__RCSID__ = "$Id$"
import time
import types
from DIRAC import gConfig, gLogger, S_OK,... | miloszz/DIRAC | FrameworkSystem/DB/NotificationDB.py | Python | gpl-3.0 | 34,669 | [
"DIRAC"
] | 007a0e3bbb146a26f367aaa32ac0202ccb20c5ac0dc2ab96a74a282cf10ea663 |
# dagutil.py - dag utilities for mercurial
#
# Copyright 2010 Benoit Boissinot <bboissin@gmail.com>
# and Peter Arrenbrecht <peter@arrenbrecht.ch>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from node import nullrev
from i18n ... | hekra01/mercurial | mercurial/dagutil.py | Python | gpl-2.0 | 8,316 | [
"VisIt"
] | 94877410d9327a74dd16a9ec3680524f5114d96ccdf55683715c2aee20607004 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
########################################################################
# Solves problem 45 from projectEuler.net.
# Finds the second number which is triangular, pentagonal and hexagonal
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software:... | salessandri/programming-contests | project-euler/problem045.py | Python | gpl-3.0 | 1,538 | [
"VisIt"
] | 18b9d1986fdcae0cdef741dbd3b700f2e4ba4466c2984e71f1b08312e3809eaa |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/orca/data/tf/data.py | Python | apache-2.0 | 8,821 | [
"ORCA"
] | 4ccd248479f8c2e0f511fb12e9fc238ff327f3c710ca8319f52e1cd4da9b7cbc |
""" FileManager for ... ?
"""
__RCSID__ = "$Id$"
import os
import datetime
from DIRAC import S_OK, S_ERROR
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.FileManagerBase import FileManagerBase
from DIRAC.Core.Utilities.List import stringListToString, \
intListToString, \
breakListIntoChunks
# Th... | chaen/DIRAC | DataManagementSystem/DB/FileCatalogComponents/WithFkAndPs/FileManagerPs.py | Python | gpl-3.0 | 30,871 | [
"DIRAC"
] | 0bab1d0f12a1fed1f302a46b5f0247bb2bfbc1ac565443524c75e356cba8e431 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Apr 17, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Apr 17, 2012"
import unittest
impo... | yanikou19/pymatgen | pymatgen/io/tests/test_gaussianio.py | Python | mit | 5,056 | [
"pymatgen"
] | acaf40c32dedc7871f92e53b503bf6bd7ceb3cd4fec9f2461c99ca3491432b36 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2017-10-25
# @Filename: base.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: Brian Cherinka
# @Last modified time: 2018-07-25 18:32:35
from ... | sdss/marvin | python/marvin/utils/datamodel/drp/base.py | Python | bsd-3-clause | 24,506 | [
"Brian"
] | e6b7a909f08c124920a1fe3ec1206fef6de5191d2e7aa0114628a1bc1f7cb1be |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from decimal import Decimal
import pytz
import logging
import smtplib
from boto.exception import BotoServerError # this is a super-class of SESError and catches connection errors
from dja... | hkawasaki/kawasaki-aio8-1 | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 27,423 | [
"VisIt"
] | 5ed7383db9f1eed6c98e1fbab6fac87a69fb13d7e67e93e6c6311ee86ac15455 |
"""
Module for validating tests
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
from builtins import object
from .tests import *
import netpy... | Neurosim-lab/netpyne | netpyne/tests/validate_tests.py | Python | mit | 147,030 | [
"NEURON"
] | 574439bb0f2fcd159ce0af37701736500f851241759e2e33070a844fc2248916 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import sys
import pcraster as pcr
import netCDF4 as nc
import virtualOS as vos
# obtaining system arguments containing: clone_map, input_netcdf_filename, output_pcraster_filename, variable_name, date_yyyy_mm_dd
system_argument = sys.argv
#~ # TODO: help/hint about the syst... | edwinkost/edwin_simple_tools | netcdf_to_pcraster/netcdf_to_pcraster.py | Python | gpl-2.0 | 2,042 | [
"NetCDF"
] | d66a02ac6444469014717aed2084d9fed4c5ee0f24b702742141f31818469776 |
"""
Runs Palmapper on single-end or paired-end data.
"""
import optparse, os, sys, tempfile, shutil, time, re
def stop_err( msg ):
sys.stderr.write( "%s\n" % msg )
sys.exit()
def __main__():
#os.environ['PATH']=os.environ['PATH']+":/home/galaxy/software/samtools.svn"+":/home/galaxy/software/palmapper-t... | ratschlab/palmapper | galaxy/palmapper_wrapper.py | Python | gpl-3.0 | 18,261 | [
"BWA",
"Galaxy"
] | 67f7b87a66ad4badfe1ad7b97995587cfa96105f67aee1216bb26cc97d04fe5a |
from pyjade import Compiler as _Compiler
from pyjade.runtime import attrs, escape, iteration
import tornado.template
from pyjade.utils import process
from pyjade.exceptions import CurrentlyNotSupported
ATTRS_FUNC = '__pyjade_attrs'
ESCAPE_FUNC = '__pyjade_escape'
ITER_FUNC = '__pyjade_iter'
class Compiler(_Compiler):... | syrusakbary/pyjade | pyjade/ext/tornado/__init__.py | Python | mit | 3,489 | [
"VisIt"
] | e65edff989f6eb71e94dc050da778a0fe249c8bde528e98af59436f6fc35e239 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-service-ports
# Author : Stuart Paterson
########################################################################
"""
Print the service ports for the specified setup
Example:
$ dirac-admin-service-... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_service_ports.py | Python | gpl-3.0 | 1,318 | [
"DIRAC"
] | ed3c4b5437db3d8792c608d2933365362a2a0cd5334a3760177242728099d4f1 |
from __future__ import print_function, absolute_import
import math
from numba import cuda, float32, float64, uint32, int64, uint64, from_dtype,\
jit
import numpy as np
# This implementation is based upon the xoroshiro128+ and splitmix64 algorithms
# described at:
#
# http://xoroshiro.di.unimi.i... | jriehl/numba | numba/cuda/random.py | Python | bsd-2-clause | 9,232 | [
"Gaussian"
] | 55d024248cfa14d5b2fef812e2efd0488667e36a3d397dae4bccfed8b73de121 |
import os
import glob
import sys
import shutil
import pysam
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
from bcbio.utils import (safe_makedir, file_exists)
from bcbio.provenance import do
from bcbio import utils
from bcbio.log import logger
from bcbio.p... | lbeltrame/bcbio-nextgen | bcbio/ngsalign/bismark.py | Python | mit | 7,269 | [
"Bowtie",
"pysam"
] | 1fef7324dac8fca2f0ec0c5db4eabc0eb0719439202a065064bb5ae3dd6e3088 |
import threading
import glob
import gzip
try:
from StringIO import StringIO # Python 2.7
except:
from io import StringIO # Python 3.3+
import uuid
import json
import base64
import re
import os
import sys
import pandas as pd
from prettytable import PrettyTable
import pybars
from .queries import mysql as mys... | LeMeteore/db.py | db/db.py | Python | bsd-2-clause | 60,629 | [
"Brian"
] | 64d7c97c87e47f3983df5b75effad84a3d3e77730b080c261ac3cc920861c158 |
import sys
import textwrap
import pytest
from _pytest import fixtures
from _pytest.config import ExitCode
from _pytest.fixtures import FixtureRequest
from _pytest.pathlib import Path
from _pytest.pytester import get_public_names
def test_getfuncargnames_functions():
"""Test getfuncargnames for normal functions""... | markshao/pytest | testing/python/fixtures.py | Python | mit | 130,347 | [
"VisIt"
] | f11ad568202bbf9705b8fa897d734eed6de298119a6a61bbe171a76f16d77766 |
"""
Handling the download of the shifter Proxy
"""
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
fro... | andresailer/DIRAC | Core/Utilities/Shifter.py | Python | gpl-3.0 | 2,800 | [
"DIRAC"
] | 18de2e90628f6669d80a82142f0dce74cf650c7fa8b112b881638732d9553eb0 |
"""KNRM model."""
import keras
import tensorflow as tf
from matchzoo.engine.base_model import BaseModel
from matchzoo.engine.param import Param
from matchzoo.engine import hyper_spaces
class KNRM(BaseModel):
"""
KNRM model.
Examples:
>>> model = KNRM()
>>> model.params['embedding_input_d... | faneshion/MatchZoo | matchzoo/models/knrm.py | Python | apache-2.0 | 3,057 | [
"Gaussian"
] | da69b6d277da79ff48ba92374c3d1148ef00b090f75790b0993ab50d203f4d21 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/ajax/multiepg.py | Python | gpl-2.0 | 12,887 | [
"VisIt"
] | cbb05c6ccc3f655b10621e1c9bafe1c6ed0b47596ab1076c735eddf3f6ddee8d |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, absolute_import
# Standard module
import math
import operator
# Third-party modules
import numpy
# =============================================================================
# Classes
# ========================================... | jbarnoud/PBxplore | pbxplore/structure/structure.py | Python | mit | 11,538 | [
"MDAnalysis"
] | de91ed771397a8374a32efec72ce0fd9d3e16ffb0439b7b89adcf6e076db190b |
__author__ = 'Harsh Daftary'
try:
import requests
import json
except ImportError:
print("requests and json libraries are required, but not found.")
exit(1)
from functools import wraps
class ApiError(Exception):
pass
class GoDebianApi(object):
def __init__(self, host="http://go.debian.net/... | ninjatrench/GoDebian_api | GoDebian/api.py | Python | mit | 3,025 | [
"VisIt"
] | ce3b1f3d3c66a93a57024166a9244227c45b48a181648da83b071eace82396bb |
#-------------------------------------------------------------------------------
# Copyright (c) 2012 Gael Honorez.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available at
# htt... | IDragonfire/modular-client | src/client/_clientwindow.py | Python | gpl-3.0 | 80,212 | [
"VisIt"
] | 136abe5d136caa6fa95b942a758ce92f51a5e516899e2d93bd6f895c6d0dca17 |
import numpy as np
# -- ANN Ordering -------------------------------------------------------- -- #
def getNodeOrder(nodeG,connG):
"""Builds connection matrix from genome through topological sorting.
Args:
nodeG - (np_array) - node genes
[3 X nUniqueGenes]
[0,:] == Node Id
... | google/brain-tokyo-workshop | WANNRelease/prettyNeatWann/neat_src/ann.py | Python | apache-2.0 | 9,221 | [
"Gaussian"
] | bb0998a73f87e7bdeac4c850cbf1a0e65f93f3a63a027f7ff676b891116232d8 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/normal_chr15.py | Python | mit | 25,844 | [
"MCell"
] | 9ae7cfa7ac0181a9fc0f43caa025b8ff0fc5a63253953cd297e62919f5c5858c |
"""
Signal
======
The signal module constains all kinds of signal processing related functions.
.. inheritance-diagram:: acoustics.signal
Filtering
*********
.. autoclass:: Filterbank
.. autofunction:: bandpass_filter
.. autofunction:: octave_filter
.. autofunction:: bandpass
.. autofunction:: lowpass
.. autofunct... | FRidh/python-acoustics | acoustics/signal.py | Python | bsd-3-clause | 41,843 | [
"Gaussian"
] | 625996ce54d8384791840bb21309f0b456c0dd32d41bf2f72e661a4e044d8c5f |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_region_url_maps.py | Python | apache-2.0 | 172,085 | [
"Octopus"
] | 05892f2cbbeae724fcb4c5500a05e7474e0e4662a03485b18fe478fe21c251f7 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import time
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms.courseware import CoursewarePage
from ...pages.lms.problem import ProblemPage
from... | olexiim/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 3,652 | [
"VisIt"
] | aa48ccbd453221949ffb3f6d368424c460c369a91df980fb49fcb30746c15b04 |
from __future__ import division, print_function, absolute_import
import numpy as np
import warnings
from dipy.utils.six.moves import xrange
from dipy.core.geometry import cart2sphere, sphere2cart, vector_norm
from dipy.core.onetime import auto_attr
from dipy.reconst.recspeed import remove_similar_vertices
__all__ =... | StongeEtienne/dipy | dipy/core/sphere.py | Python | bsd-3-clause | 20,288 | [
"Gaussian"
] | bbb30f81530144b80b174ae9a3b345118e130a52860b6bce869586db1b8393b9 |
# Copyright (C) 2012,2013,2015(H),2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the t... | fedepad/espressopp | src/interaction/DihedralHarmonic.py | Python | gpl-3.0 | 5,374 | [
"ESPResSo",
"Gromacs"
] | 72727b06d8acab67e08eec717368b9c47d3b9864206706d02ccb4b266ffe4de2 |
# BioLite - Tools for processing gene sequence data and automating workflows
# Copyright (c) 2012-2014 Brown University. All rights reserved.
#
# This file is part of BioLite.
#
# BioLite is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the... | cypridina/gloTK | gloTK/wrappers_biolite.py | Python | gpl-3.0 | 32,239 | [
"BLAST",
"Bowtie"
] | a3b42fc286bb7ce97005f7a97dd222334ed73f88b01ad5d0400e838746ea9faa |
"""AMBER force-field parameters"""
atoms_per_residue = {
'GLH': ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'CG', 'HG2', 'HG3', 'CD', 'OE1', 'OE2', 'HE2', 'C', 'O'],
'ILE': ['N', 'H', 'CA', 'HA', 'CB', 'HB', 'CG2', 'HG21', 'HG22', 'HG23', 'CG1', 'HG12', 'HG13', 'CD1', 'HD11',
'HD12',
'HD... | brianjimenez/lightdock | lightdock/scoring/sd/data/amber.py | Python | gpl-3.0 | 125,069 | [
"Amber"
] | 0d248d72b4f52ce2b07503e25b6aea1f5a3aaf8a4430ef68a9e8efe78b59a130 |
import os
import numpy as np
import sklearn.metrics as metrics
import sklearn.decomposition as decomp
import pdb
import matplotlib.pyplot as plt
from . import sc3_clustering_impl as sc
def load_dataset_tsv(fname, fgenes=None, flabels=None):
# check data filename
if not os.path.exists(fname):
raise Ex... | nicococo/scRNA | scRNA/utils.py | Python | mit | 11,107 | [
"Gaussian"
] | 3acc461e9d416b73d08ac82c704d04da6898f226de870e72c18c84a09e661094 |
"""
Tests for geography support in PostGIS
"""
from __future__ import unicode_literals
import os
from unittest import skipUnless
from django.contrib.gis.db.models.functions import Area, Distance
from django.contrib.gis.gdal import HAS_GDAL
from django.contrib.gis.measure import D
from django.test import TestCase, ign... | DONIKAN/django | tests/gis_tests/geogapp/tests.py | Python | bsd-3-clause | 5,944 | [
"VisIt"
] | a6b01a7c3c07d0a850236a5020755003cda4a29ee7809e92ec74698d74105377 |
"""Monte Carlo Tree Search, as described in Silver et al 2015.
This is a "pure" implementation of the AlphaGo MCTS algorithm in that it is not specific to the
game of Go; everything in this file is implemented generically with respect to some state, actions,
policy function, and value function.
"""
import numpy as np
... | Rochester-NRT/RocAlphaGo | AlphaGo/mcts.py | Python | mit | 9,222 | [
"VisIt"
] | 445d038ca24b42d5f2853214800de05c78261b849a312862c0874ccc5b707a27 |
#
# 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... | charlesccychen/beam | sdks/python/apache_beam/runners/direct/direct_runner.py | Python | apache-2.0 | 18,219 | [
"VisIt"
] | e1bafa31c952cc8da7ac5a1f01e2dd02b44f7715fb9f090e696c8c7c7518555c |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | test/testCC.py | Python | lgpl-2.1 | 2,406 | [
"GAMESS",
"Gaussian",
"Molpro",
"cclib"
] | 9a126efad048f7e2ae2a51f71c5ffe06c7b590fa67f48c3f8d13487bb1f21892 |
#!/usr/bin/python
#
# CCLib_proxy Utilities - BlueGiga Specific
# Copyright (c) 2014 Ioannis Charalampidis
#
# 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
#... | wavesoft/CCLib | Python/ble_write_flash.py | Python | gpl-3.0 | 5,198 | [
"cclib"
] | 1daffac84d22243c66997f9a15c90e486b29be385e70206a5c908657b97876d3 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/__init__.py | Python | apache-2.0 | 4,319 | [
"PySCF",
"SIESTA"
] | f5f42d17ff6e1f101f59b7c65272b24b661cda9d52c4721f0ee15c35fe41afa4 |
from builtins import object
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# 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 Softw... | mdiener/grace | grace/py27/slimit/visitors/minvisitor.py | Python | gpl-3.0 | 14,207 | [
"VisIt"
] | 26f413206cd0b5dd8b92e95dd7aab93efdcd03a1f62e0cfc824ca15f4a1d360c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
logger = logging.getLogger(__name__)
def upgradeCheck(url):
# upgrade check:
# -------------
# On each startup OMERO.web checks for possible server upgrades
# and logs the upgrade url at the WARNING level. If you would
# like to disable... | knabar/openmicroscopy | components/tools/OmeroWeb/omeroweb/webadmin/webadmin_utils.py | Python | gpl-2.0 | 1,019 | [
"VisIt"
] | 3741c614cdb4f4678125a2650af30706f69d46a1b762ae035488467b8d861060 |
import mdtraj as md
import numpy as np
from . import Featurizer, TrajFeatureUnion
class BaseSubsetFeaturizer(Featurizer):
"""Base class for featurizers that have a subset of active features.
n_features refers to the number of active features. n_max refers to the
number of possible features.
Paramet... | stephenliu1989/msmbuilder | msmbuilder/featurizer/subset.py | Python | lgpl-2.1 | 6,212 | [
"MDTraj"
] | a22700b487d8b6c0eb9adf1e7ddfe5add8854f34ada8fda790b03394dd82498e |
#!/usr/bin/env python
# Copyright 2014-2020 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... | sunqm/pyscf | pyscf/lib/misc.py | Python | apache-2.0 | 37,333 | [
"PySCF"
] | b98dea30737ac788d1d0f76068c4dbc812d100b8f0ecae47541ddc0f10aa458e |
from .unit_definitions import (
percent, percents,
permille,
rad, radian, radians,
deg, degree, degrees,
sr, steradian, steradians,
mil, angular_mil, angular_mils,
m, meter, meters,
kg, kilogram, kilograms,
s, second, seconds,
A, ampere, amperes,
K, kelvin, kelvins,
mol, ... | kaushik94/sympy | sympy/physics/units/definitions/__init__.py | Python | bsd-3-clause | 7,194 | [
"Avogadro"
] | 9464395281db87a76236d021418c8c95618dbc0923654cf9492984f870f74a94 |
from json import dumps
from typing import Optional
from pytest import raises
from graphql.error import GraphQLSyntaxError
from graphql.language import Lexer, Source, TokenKind, parse
from graphql.utilities import strip_ignored_characters
from ..fixtures import kitchen_sink_query, kitchen_sink_sdl # noqa: F401
from ... | graphql-python/graphql-core | tests/utilities/test_strip_ignored_characters.py | Python | mit | 14,139 | [
"FEFF"
] | 88b6344b317f0c80dcdabbf7a14bbb63334d195ec8e5f05f63bcba560b59b61d |
import requests, re, random
from bs4 import BeautifulSoup
COMEDIAN_NAMES = {'Seth': 'Seth Meyers',
'Letterman': 'David Letterman',
'Kimmel': 'Jimmy Kimmel',
'Conan': 'Conan O\'Brian',
'Fallon': 'Jimmy Fallon',
'Ferguson': "Craig... | mmisiewicz/slask | limbo/plugins/monologue.py | Python | mit | 1,791 | [
"Brian"
] | 12d64c772a5e5e21cd89400d4bccf2529e297df0b351c0169dc9efdb6e1c553e |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Iris' data model representation of CF UGrid's Mesh and its constituent parts.
Eventual destination: dedicated module in :... | SciTools/iris | lib/iris/experimental/ugrid/mesh.py | Python | lgpl-3.0 | 108,372 | [
"NetCDF"
] | 8dc532465a7ffc88e466d2121c8e53cc3e11b5cf984e3a77b26dbd26234d09a5 |
#!/usr/bin/python
# python parser module for lattice preparation from bowtie 23/6/2012
# version 3 16-4-2014
# Usage mirlattice_preparator.py <bowtie_out> <output file> <norm_factor> <bowtie index> <option tag>
import sys, subprocess
from collections import defaultdict
from smRtools import *
from numpy import mean, m... | JuPeg/tools-artbio | unstable/local_tools/mirlattice_preparator.py | Python | mit | 3,181 | [
"Bowtie"
] | 9d758340a0e34bb6508bf76a6ddb79e8c5ede1ab6a72f32c39f86790c59fce3b |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import datetime
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from mock import patch
from zerver.lib.test_helpers import MockLDAP
from confirmation.models import Confirmation
from zilencer.models i... | AZtheAsian/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 50,381 | [
"VisIt"
] | daa4495145663fb880f94591a5f3c183c8c44a3771c690b792ed6b8dd0dc0607 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Lee-Ping Wang
# Contributors: Robert McGibbon and Jason Swails... | leeping/mdtraj | mdtraj/formats/arc.py | Python | lgpl-2.1 | 13,725 | [
"MDTraj",
"TINKER"
] | aae4c6e78c03193f60a5553dee93103d95c48abfe61b97cbc0e882995e84c0fd |
# Copyright (c) 2015-2017 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | kireledan/molecule | molecule/config.py | Python | mit | 12,826 | [
"Galaxy"
] | 86e4e4b4c7d195dc72917d10dea333d8666d0c418f5fec5eb8d6539f543f5c7a |
#!/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/symm/geom.py | Python | apache-2.0 | 31,112 | [
"PySCF"
] | bc1ec687c169bbbd3593f5bd00f479b7dc0d0c8e69103766633cbbdb6fd9782b |
from __future__ import unicode_literals
from __future__ import absolute_import
import logging
from functools import reduce
from docker.errors import APIError
from .config import get_service_name_from_net, ConfigurationError
from .const import LABEL_PROJECT, LABEL_SERVICE, LABEL_ONE_OFF, DEFAULT_TIMEOUT
from .service ... | rstacruz/compose | compose/project.py | Python | apache-2.0 | 11,752 | [
"VisIt"
] | fc2f551b5c2c054d94ebbb6106da837957bbc515d897ea9de72747fd41b8f9c1 |
"""
Acceptance tests for the teams feature.
"""
from __future__ import absolute_import
import json
import random
import time
from uuid import uuid4
import ddt
from dateutil.parser import parse
from selenium.common.exceptions import TimeoutException
from six.moves import map, range
from common.test.acceptance.fixture... | ESOedX/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 84,355 | [
"VisIt"
] | d4f2739b4891409d86282af2eefe764705a6a184888a5de953fc723ad908b09a |
import os
import sys
import re
import roblib
import gzip
'''Combine .gbff and .fna files to get just the coding sequences. We need to get the data from RefSeq and they have
split DNA sequences out of GenBank files so it is not clear that biopython etc will work.
This is just a quick parser and then we get the string... | linsalrob/EdwardsLab | ncbi/combine_gbff_fna.py | Python | mit | 2,943 | [
"Biopython"
] | 3a1266f7a43029e63a2e429406d60df7b9fd26fd87264eed9e5c787d208b7ab2 |
import pytest
from cplpy import run_test, prepare_config
import subprocess as sp
import os
import glob
import numpy as np
class cd:
"""Context manager for changing the current working directory"""
def __init__(self, newPath):
self.newPath = os.path.expanduser(newPath)
def __enter__(self):
... | Crompulence/cpl-library | test/lammps/single/no_wall/constant_force/test_falling.py | Python | gpl-3.0 | 2,107 | [
"LAMMPS"
] | edc27aebfba7f02a4a9cbd62ebafd8fd7b0ba655928481f347423f3dd16e8ba2 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | vthorsteinsson/tensor2tensor | tensor2tensor/models/image_transformer.py | Python | apache-2.0 | 37,784 | [
"MOE"
] | 9b702689ad62e7719ecea06d4efa0098da2ca1d97b6043068cdd80fd173d353a |
# -*- coding: utf-8 -*-
"""
molvs.metal
~~~~~~~~~~~
This module contains tools for disconnecting metal atoms that are defined as covalently bonded to non-metals.
:copyright: Copyright 2016 by Matt Swain.
:license: MIT, see LICENSE file for more details.
"""
import logging
from rdkit import Chem
log = logging.get... | bp-kelley/rdkit | rdkit/Chem/MolStandardize/metal.py | Python | bsd-3-clause | 3,082 | [
"RDKit"
] | 9ef764f55473933a06109f990d9a8ee1946aaf930e64cbd56a9a1ab3d52ceb76 |
# pylint: disable=bad-continuation
"""
Certificate HTML webview.
"""
import logging
import urllib
from datetime import datetime
from uuid import uuid4
import pytz
from django.conf import settings
from django.contrib.auth.models import User
from django.http import Http404, HttpResponse
from django.template import Reque... | proversity-org/edx-platform | lms/djangoapps/certificates/views/webview.py | Python | agpl-3.0 | 31,811 | [
"VisIt"
] | 2a77213e37290b96261f9694438e60f4d220c6d7027584b3fb9d6050bf5675bd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Extract sequences from a fasta file and group them in output files.
Groups of 'number' sequences are formed.
Output file names will begin by 'stub'.
Usage:
%program <input_file> <number> <stub>"""
import sys
import re
try:
from Bio import SeqIO
except:
p... | enormandeau/Scripts | fasta_extract_group.py | Python | gpl-3.0 | 1,332 | [
"Biopython"
] | dfb2697987404134a2a3762fc4f0567bf04a42554893dabd3c038a65bffb771b |
from setuptools import setup
setup(
name = 'tracermppt',
py_modules = ['tracermppt'],
version = '0.3',
description = 'Interface for controlling and interrogating the '
'Tracer-2210RN and similar charge cotnrollers via the remote '
'monitoring port',
author = 'Brian Mayton',
auth... | bmayton/tracermppt | setup.py | Python | mit | 612 | [
"Brian"
] | a68eb2554c7e8e47fe6a8610fdca6789c8f1a3f1fca8d3439ec02861be21c202 |
"""A notebook manager that uses the local file system for storage.
Authors:
* Brian Granger
* Zach Sailer
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/IPython/html/services/notebooks/filenbmanager.py | Python | gpl-3.0 | 18,871 | [
"Brian"
] | 626e570c0dff914437e1c940ad811cf18d9702fc0f11dc32b3510ae82188942c |
import os
import os.path
try:
from ase.units import AUT # requires rev1839 or later
except ImportError:
from ase.units import second, alpha, _hbar, _me, _c
AUT = second * _hbar / (alpha**2 * _me * _c**2)
del second, alpha, _hbar, _me, _c
from ase.units import Bohr, Hartree
from ase.data import atomic_... | qsnake/gpaw | gpaw/io/__init__.py | Python | gpl-3.0 | 26,399 | [
"ASE",
"GPAW",
"NetCDF"
] | 74a822d364273f32b1ce0ee81594b0a7716ae1ee2cfb6a8d22c891c1d3ed7470 |
# -*- coding: utf-8 -*-
"""
Tests the "preview" selector in the LMS that allows changing between Staff, Student, and Content Groups.
"""
from nose.plugins.attrib import attr
from ..ga_role_helpers import GaccoTestRoleMixin
from ..helpers import UniqueCourseTest, create_user_partition_json
from ...pages.studio.auto_aut... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_user_preview.py | Python | agpl-3.0 | 13,047 | [
"VisIt"
] | f4c0f4b260f32a1fdf2f73a6769a052741e89fd10f67fa5bf3167090ac16be63 |
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from numpy import *
import Avogadro
# always use 'Extension' for class name
class Extension(QObject):
def __init__(self):
QObject.__init__(self)
def name(self):
return "My Extension"
def description(self):
return "Extension for ..."... | rcplane/periodicdisplay | reference/avogadro/libavogadro/examples/python/extensiontemplate.py | Python | gpl-2.0 | 669 | [
"Avogadro"
] | 3137b86654c389e44712be8f1b459531eceb5636271e5d09f039fadc9e5c7133 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.utils.translation import ugettext_lazy as _
from django.conf.urls.i18n import i18n_patterns
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
... | tuticfruti/tuticfruti_blog | config/urls.py | Python | bsd-3-clause | 1,459 | [
"VisIt"
] | 82aadabac29c1031a78ad751c0d6c62ce054a245929904af1a65af78a2662e35 |
try: paraview.simple
except: from paraview.simple import *
Glyph3 = GetActiveSource()
AddAdditionalAttribute1 = AddAdditionalAttribute()
AddAdditionalAttribute1.AttributeName = 'Density'
AddAdditionalAttribute1.AdditionalAttributeFile = '/Users/corbett/Documents/Projects/Work/Viz/pvaddons/testdata/b1.00300.d0-1000.de... | corbett/parastro | ExamplePython/AddAdditionalAttribute.py | Python | lgpl-3.0 | 1,153 | [
"ParaView"
] | e61b6b54b578df7f60d293126ba305a66f0372c6890e2fde758361edddd3c01a |
# 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 OfCatalyst(CMakePackage):
"""Of-catalyst is a library for OpenFOAM that provides a runtime... | LLNL/spack | var/spack/repos/builtin/packages/of-catalyst/package.py | Python | lgpl-2.1 | 1,893 | [
"ParaView"
] | 85e85dae110e15b4c50f96e2f68748d1e286884d4b2e8f0239c611815da83156 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/stats/ordination/tests/test_redundancy_analysis.py | Python | bsd-3-clause | 10,422 | [
"scikit-bio"
] | 13d456d23a1799537d057a9bf500f79cf5fb22bd2de2014101e52cc04c3bc537 |
#! /usr/bin/env python3
"""
retrain_emission.py: take an HDF5 file and segmentations, and output parameters of a mixture model.
"""
# std lib:
import argparse
import os
import sys
import random
from collections import defaultdict
from tqdm import tqdm
# numerics:
import numpy as np
import h5py
from sklearn.mixture impo... | jts/nanopolish | scripts/polya_training/retrain_emission.py | Python | mit | 4,076 | [
"Gaussian"
] | 2aacc36906ebd6e0ff06bfeac99f52a5995c509dfb69f35f06e57c7681d7b111 |
#from opengmcore import _opengmcore.adder as adder
from opengmcore import *
from __version__ import version
from functionhelper import *
from _inf_param import _MetaInfParam , InfParam
from _visu import visualizeGm
from _misc ... | CVML/opengm | src/interfaces/python/opengm/__init__.py | Python | mit | 10,778 | [
"VisIt"
] | a4515fd23686cecde28cbd8cd837daf6d3adef97023673815c73670c67ca94df |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkHierarchicalDataExtractDataSets(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager... | chrisidefix/devide | modules/vtk_basic/vtkHierarchicalDataExtractDataSets.py | Python | bsd-3-clause | 541 | [
"VTK"
] | df6aaaa7cdab94705d83ec89d966db2c835dc55599c17844bfc6c91b98f1a384 |
"""Make sure all the describe features are putting the right features in the
right place
"""
import mdtraj as md
import numpy as np
import pandas as pd
from mdtraj.testing import eq
from scipy.stats import vonmises as vm
from msmbuilder.example_datasets import MinimalFsPeptide
from msmbuilder.feature_selection import ... | dr-nate/msmbuilder | msmbuilder/tests/test_feature_descriptor.py | Python | lgpl-2.1 | 6,930 | [
"MDTraj"
] | b26e0049ffae1d9720dec586ac2b8a441a01397e80bbd4cb5ec0a59bc20dfacf |
# -*- coding utf-8-*-
"""
Created on Tue Nov 23 10:15:35 2018
@author: galad-loth
"""
import mxnet as mx
import logging
import sys
from hash_net import get_ssdh_symbol
from evaluate_metric import MyAccuracy
from data import get_img_class_iter
root_logger = logging.getLogger()
stdout_handler = logging.St... | galad-loth/LearnDescriptor | deephash/train_model.py | Python | apache-2.0 | 2,364 | [
"Gaussian"
] | c8ac29f8f9504e330774d3b2830766aaee02bc9de72f7b9e59516d971bd53682 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
:py:mod:`detrender.py` - De-trending models
-------------------------------------------
This module contains the generic models used to de-trend light curves for
the various supported missions. Most of the functionality is implemented in
:py:class:`Detrender`, and spec... | rodluger/everest | everest/detrender.py | Python | mit | 68,576 | [
"Gaussian"
] | a989af1f8bee67b514837342a20af4d9b2528b6fa69b6919c8fb55f3adbcfa03 |
#!/usr/bin/env python3
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
#
# 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,... | espressopp/espressopp | testsuite/vectorization/test_vectorization.py | Python | gpl-3.0 | 4,635 | [
"ESPResSo"
] | db1ac0536d861e0a2e80949a0858788b9f1f2493c0291979d59d5033509c9c27 |
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