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#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-recommender | scripts/fixup_recommender_v1_keywords.py | Python | apache-2.0 | 6,452 | [
"VisIt"
] | d2e15d4d08fb5d7f915dfa314de527bccd7f53fde4b05aa4b24f613211f2a1bd |
#!/usr/bin/env python
#
# $File: samplingSeparateVSPs.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can re... | BoPeng/simuPOP | docs/samplingSeparateVSPs.py | Python | gpl-2.0 | 2,041 | [
"VisIt"
] | 96207f9fa2b2b3153d288d770337493f39cb017f49f9f6ef18116130fb1cd38b |
import unittest
from unittest.mock import patch
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
from meerkat_abacus.config import config
from meerkat_abacus import model
from meerkat_abacus.pipeline_worker.process_steps import add_links
from meerkat_abacus.consumer.database_setup import cr... | who-emro/meerkat_abacus | meerkat_abacus/pipeline_worker/tests/test_add_links.py | Python | mit | 7,798 | [
"VisIt"
] | c3ea7f7bab6a61a10430c9dba7279c48743a948e8e19cc74d96367ab3cd1316a |
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{last_name}}",
"{{first_name}} {{la... | joke2k/faker | faker/providers/person/de_CH/__init__.py | Python | mit | 41,031 | [
"Brian"
] | f1d5620d20ad316d9e8ae6298877be4a8e99529c3f4aa3c83ecbf44fbc67c138 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/pmda | pmda/test/test_hydrogenbonds_analysis.py | Python | gpl-2.0 | 9,140 | [
"MDAnalysis"
] | 2ff63901619194eefa7d1a471724355c43f237b34dda5bbab606b447ab964a37 |
##
# Copyright 2009-2012 Ghent University
# Copyright 2009-2012 Stijn De Weirdt
# Copyright 2010 Dries Verdegem
# Copyright 2010-2012 Kenneth Hoste
# Copyright 2011 Pieter De Baets
# Copyright 2011-2012 Jens Timmerman
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://u... | JensTimmerman/easybuild-easyblocks | easybuild/easyblocks/n/ncl.py | Python | gpl-2.0 | 6,733 | [
"NetCDF"
] | 423672ec83af27928b6ed53ac62dcfa42636df1e3dcf25e639bf794ea8bbc61a |
# Copyright (C) 2004-2008 Paul Cochrane
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distribut... | paultcochrane/pyvisi | examples/meshPlot.py | Python | gpl-2.0 | 2,578 | [
"VTK"
] | 892eb107f0d856c7dd8eb4cc6b21a46ece0252683488fbdfc8c507278d7c73f8 |
#!/usr/bin/python
from avocado import Test
from avocado.utils import process
import os, re, vagrant, platform
class VagrantSshfs(Test):
def setUp(self):
self.vagrant_VAGRANTFILE_DIR = self.params.get('vagrant_VAGRANTFILE_DIR')
self.vagrant_PROVIDER = self.params.get('vagrant_PROVIDER', default='')... | projectatomic/adb-tests | cdk-testsuite/tests/vagrant_sshfs.py | Python | gpl-2.0 | 5,438 | [
"CDK"
] | 7eb86f9bf370884bc83277a29452a7cd5e56beb806e30dae34f4621eff6702a9 |
# This file is part of the pyGTM module.
#
# 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 distribut... | JohnKendrick/PDielec | PDielec/test_gtm.py | Python | mit | 3,751 | [
"CRYSTAL"
] | 0e23da7bc09e4435ab200331243736fe61c8b63fee9ff931497c0c4aef4ccdbb |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | ashutoshvt/psi4 | psi4/driver/qcdb/qcformat.py | Python | lgpl-3.0 | 4,080 | [
"Psi4"
] | 3fac9222a62f3d9724b5518c1192af54bd896a5a2acfb6373662e8e19aa1c285 |
import sys
import gzip
from glob import glob
from io import BytesIO
from .. import backends, conventions
from ..core.alignment import auto_combine
from ..core.utils import close_on_error, is_remote_uri
from ..core.pycompat import basestring, OrderedDict, range
def _get_default_engine(path, allow_remote=False):
i... | clarkfitzg/xray | xray/backends/api.py | Python | apache-2.0 | 10,589 | [
"NetCDF"
] | 801533c86164ee61f169b3a0c8a1697f45767817146b95bb5be0800e6e785c07 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module define the various drones used to assimilate data.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
... | xhqu1981/pymatgen | pymatgen/apps/borg/hive.py | Python | mit | 17,218 | [
"Gaussian",
"VASP",
"pymatgen"
] | 97a9babd78f286f5801ee1a946794112df2190b0d237e55531fc6dc239c48910 |
#!/usr/bin/env python2
from sepath_core import *
from itertools import chain
import re
import optparse
import sys
import pysam
import HTSeq
def count(cargo, seb, split):
cargo[seb][split] += 1
def write_bed(se_ga, fn):
with open(fn, "wb") as fh:
for iv, ses in se_ga.steps():
for gene_id, i... | mcieslik-mctp/sepath | sepath_count.py | Python | gpl-2.0 | 6,900 | [
"HTSeq",
"pysam"
] | 5b40eb268f214a151ea90b1ddb5f765cacac4be052f7cc68386e76dc1699c7db |
import pybullet as p
from time import sleep
import pybullet_data
physicsClient = p.connect(p.GUI)
p.setAdditionalSearchPath(pybullet_data.getDataPath())
p.resetSimulation(p.RESET_USE_DEFORMABLE_WORLD)
p.resetDebugVisualizerCamera(3,-420,-30,[0.3,0.9,-2])
p.setGravity(0, 0, -10)
tex = p.loadTexture("uvmap.png")
plan... | nrz/ylikuutio | external/bullet3/examples/pybullet/gym/pybullet_examples/deformable_torus.py | Python | agpl-3.0 | 1,136 | [
"VTK"
] | d387c83f5462da0162fd9685853a48aae6f383e89ce13aa127efa43f5b173154 |
from octopus.modules.es import dao
from datetime import datetime
from octopus.modules.account.exceptions import NonUniqueAccountException
def query_filter(q):
"""Function used by the query endpoint to ensure only the relevant account data is returned"""
# q is an esprit.models.Query object
# this limits t... | JiscPER/magnificent-octopus | octopus/modules/account/dao.py | Python | apache-2.0 | 2,831 | [
"Octopus"
] | 9b567bd638fa7c5f9979a464860747ce41bbe125887315b22b4ee4b25dd6abc1 |
import numpy as np
from ase import Atoms
from ase.units import Bohr
from gpaw.density import RealSpaceDensity
from gpaw.lfc import BasisFunctions
from gpaw.mixer import Mixer
from gpaw.setup import Setups
from gpaw.xc import XC
from gpaw.utilities.tools import coordinates
from gpaw.mpi import rank
class HirshfeldDen... | ajylee/gpaw-rtxs | gpaw/analyse/hirshfeld.py | Python | gpl-3.0 | 5,296 | [
"ASE",
"GPAW"
] | 41846b76c058a276518fa61e315853b2af507c08e452710460448bd773e70efb |
""" A set of tokens and convienence functions for input/output files.
author: Brian Schrader
since: 2015-12-28
"""
from __future__ import print_function
from collections import namedtuple
import glob, re
file_pattern = 'mp.{}.output{}'
alias_pattern = '{command}-{output_number}'
class PathToken(object):
""" A... | TorkamaniLab/metapipe | metapipe/models/tokens.py | Python | mit | 6,534 | [
"Brian"
] | 158172b84c46c426d998a1b24b20ccd4756ef4a3da4fd09aa3d2e6a0b3214ebb |
#!/usr/bin/env python
# Copyright 2017-2021 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/pbc/cc/eom_kccsd_rhf.py | Python | apache-2.0 | 68,153 | [
"PySCF"
] | 6b49294c039389fe047619d6ece8e067825b47ca87a6ccec76122b0106fb3322 |
from galaxy_analysis.plot.plot_styles import *
import numpy as np
import matplotlib.pyplot as plt
import deepdish as dd
import h5py, glob, sys
from galaxy_analysis.utilities import utilities
from galaxy_analysis.analysis import Galaxy
from mpl_toolkits.axes_grid1 import make_axes_locatable
from scipy.stats import bi... | aemerick/galaxy_analysis | paperII/abundace_evolution.py | Python | mit | 19,582 | [
"Galaxy"
] | e50036dd2b9f4a5a2dea0c8dcefcf04980e834b4c6aafc76169f1d45aa14928f |
# -*- coding: utf-8 -*-
import math
import os
import tensorflow as tf
import numpy as np
import pandas as pd
import pickle
import pickle as pkl
import cv2
import skimage
import random
import tensorflow.python.platform
from tensorflow.python.ops import rnn
from keras.preprocessing import sequence
from collections import... | dricciardelli/vae2vec | capt_gen_o2e_aux_ms.py | Python | mit | 39,724 | [
"Gaussian"
] | 85721496c1929961a68dbaf177888e5eae24b3774d6c1c87a4d52879076701b7 |
"""This module defines an ASE interface to Turbomole
http://www.turbomole.com/
"""
import os
import sys
import numpy as np
from ase.units import Hartree, Bohr
from ase.io.turbomole import read_turbomole,write_turbomole
from ase.calculators.general import Calculator
class Turbomole(Calculator):
def __init__(sel... | askhl/ase | ase/calculators/turbomole.py | Python | gpl-2.0 | 5,333 | [
"ASE",
"TURBOMOLE"
] | 5928a6fb7321db1772d5cf85f54edcd4c0373f12adf793d89475f663d506317c |
# vim:fileencoding=utf-8:noet
from __future__ import (unicode_literals, division, absolute_import, print_function)
import sys
import os
from functools import partial
from collections import namedtuple
from time import sleep
from platform import python_implementation
from powerline.segments import shell, tmux, pdb, i... | S0lll0s/powerline | tests/test_segments.py | Python | mit | 84,994 | [
"FEFF"
] | 30a01426d6334af081df527cde440036a950bcf4e3bb9c7faa2d94f6c0faac2a |
#!/usr/bin/python
"""
Copyright 2010 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | clreinki/GalaxyHarvester | udUserOther.py | Python | agpl-3.0 | 2,904 | [
"Galaxy"
] | 61e987eb7bc59fb6fcbde0a1a37851ade04c449b4d5e8653966692a68851e242 |
import logging
import os
import pandas
import pysam
import cStringIO as StringIO
import sys
from grocsvs import utilities
from grocsvs.utilities import get_key
class Dataset(object):
def serialize(self):
d = self.__dict__.copy()
d["type"] = self.__class__.__name__
del d["sample"]
r... | grocsvs/grocsvs | src/grocsvs/datasets.py | Python | mit | 4,607 | [
"pysam"
] | c2ec6fa13ab400c6e4f0872be78f1a08fe9fcc97630019096f917ca11870021b |
# Copyright 2013-2020 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 PyUnicycler(PythonPackage):
"""Unicycler is an assembly pipeline for bacterial genomes. It... | iulian787/spack | var/spack/repos/builtin/packages/py-unicycler/package.py | Python | lgpl-2.1 | 1,554 | [
"BLAST"
] | 8ffc41c1195074f8c0a56d8d58a0e61a865db2a361e13009311946b6d7d24d20 |
import logging
import numpy as np
import networkx as nx
from pgmpy.models import BayesianNetwork
from pgmpy.factors.continuous import LinearGaussianCPD
from pgmpy.factors.distributions import GaussianDistribution
class LinearGaussianBayesianNetwork(BayesianNetwork):
"""
A Linear Gaussian Bayesian Network is... | pgmpy/pgmpy | pgmpy/models/LinearGaussianBayesianNetwork.py | Python | mit | 9,688 | [
"Gaussian"
] | adfc61e4f97d4f33ea5fc46a29efce08ad152e8a23e19aa399b3c26bee1f527f |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-production-job-get-input
# Author : Stuart Paterson
########################################################################
"""
Retrieve input sandbox for DIRAC Job
"""
from __future__ import... | petricm/DIRAC | Interfaces/scripts/dirac-wms-job-get-input.py | Python | gpl-3.0 | 1,578 | [
"DIRAC"
] | 21b641c2d164a683f6973e984d42e6c5d3a959ccbb06ac4f4444a12329f0ffc7 |
import copy
import random
import numpy as np
from Hypothesis import Hypothesis
from LOTlib.Miscellaneous import self_update
class VectorHypothesis(Hypothesis):
"""Store n-dimensional vectors (defaultly with Gaussian proposals)."""
def __init__(self, value=None, n=1, proposal=None, propose_scale=1.0, propose_... | joshrule/LOTlib | LOTlib/Hypotheses/VectorHypothesis.py | Python | gpl-3.0 | 3,324 | [
"Gaussian"
] | a5f6c9697603a79e1be17c3df13f5b6981d7134508d4fbd3a13260793d590d68 |
import unittest
import pysal
import numpy as np
from pysal.spreg import probit as PB
from pysal.common import RTOL
class TestBaseProbit(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("CRIME"))
y = np.reshape(y, (49,1))
... | lanselin/pysal | pysal/spreg/tests/test_probit.py | Python | bsd-3-clause | 5,150 | [
"COLUMBUS"
] | 3fa6f90372e4751f56aad77fda6b0b7ebdc22c18e867b3c80a142c250504df94 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# validstring - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms ... | heromod/migrid | mig/shared/validstring.py | Python | gpl-2.0 | 5,156 | [
"Brian"
] | b4ebd18f2ed6c79c396f2267336a5c137c94fc4604298a958ae22188e0101da8 |
"""
LAMMPS (sci-physics/lammps) project within gentoo chroot.
"""
from os import path
from glob import glob
from benchbuild.utils.wrapping import wrap_in_uchroot as wrap, strip_path_prefix
from benchbuild.projects.gentoo.gentoo import GentooGroup
from benchbuild.utils.downloader import Wget
from benchbuild.utils.run im... | simbuerg/benchbuild | benchbuild/projects/gentoo/lammps.py | Python | mit | 1,483 | [
"LAMMPS"
] | 7208c74395da8ea676210d9cb9473afbb6b8a5cd2c1f18b8d3360402904d3588 |
from __future__ import absolute_import
input_name = '../examples/linear_elasticity/material_nonlinearity.py'
output_name = 'test_material_nonlinearity.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| rc/sfepy | tests/test_input_material_nonlinearity.py | Python | bsd-3-clause | 223 | [
"VTK"
] | d28e1fed88a2bbf6d4a092e85275bf606ae6d5552f21331f61d81d8afdcfa992 |
from math import pi, sqrt, fabs
import numpy as np
from numpy import exp
from gpaw.poisson import PoissonSolver
from gpaw.utilities import cerf, erf
from gpaw.utilities.gauss import Gaussian
from gpaw.fd_operators import FDOperator, laplace
from gpaw.transformers import Transformer
class HelmholtzGaussian(Gaussian):... | robwarm/gpaw-symm | gpaw/helmholtz.py | Python | gpl-3.0 | 6,261 | [
"GPAW",
"Gaussian"
] | cf0cea195c8c781e266243b8842130671f56910bfd6432dd994e2524f753da6e |
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING #
# Under development #
# pylint: skip-file
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING#... | Andrew-McNab-UK/DIRAC | Workflow/Modules/UploadOutputs.py | Python | gpl-3.0 | 3,477 | [
"DIRAC"
] | 873165088a13ee059158aee4aa3177bb80bb1ebf300a1c764e818f3acdf3928f |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/r-xvector/package.py | Python | lgpl-2.1 | 1,905 | [
"Bioconductor"
] | 797eed5c57a151612bd77b5de5a7a94d2cfdcfd72591c87df055fc1d1dd6f3cb |
# Copyright (c) 2016 Paulo Eduardo Rauber
# 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, publish,... | HanKruiger/tsnetwork | src/modules/thesne.py | Python | mit | 14,623 | [
"Gaussian"
] | 9e7c7d2342f654c67b4e21cea84fdbe85ab7f1f99300340bfee4ea59bba70919 |
rows = [
{'fname': 'Brian', 'lname': 'Jones', 'uid': 1003},
{'fname': 'David', 'lname': 'Beazley', 'uid': 1002},
{'fname': 'John', 'lname': 'Cleese', 'uid': 1001},
{'fname': 'Big', 'lname': 'Jones', 'uid': 1004}
]
from operator import itemgetter
rows_by_fname = sorted(rows,key=itemgetter('fname'))
rows... | giftman/Gifts | Python/moveit/cookbook/p13_sort_list_of_dicts_by_key.py | Python | apache-2.0 | 524 | [
"Brian"
] | 07608b50f676f6ee76c8ceebec48c553307040d58590100a6436b764a73b113e |
"""
Demo if adaptive adversary works against feature squeezing.
Embed the diffrentiable filter layers in a model.
Pass in the (average) gradient (part of loss) to an attack algorithm.
Implement the gaussian-noise-iterative method for non-diffrentiable filter layers (bit depth reduction.)
Introduce ... | mzweilin/EvadeML-Zoo | attacks/adaptive/adaptive_adversary.py | Python | mit | 13,504 | [
"Gaussian"
] | 91cb7621f8ce05eb72eea888d2340b47af5268c94b560e626730451678dc0a54 |
"""
Create and put Requests to archive files.
**List of operations**
#. Optionally replicate files to SourceSE
#. ArchiveFiles: Create a tarball from input files, upload tarball to TarballSE
#. ReplicateAndRegister Tarball to TargetSE
#. Optionally: Add LFNs to an ArchiveSE
#. Optionally: Check for Tarball Migration... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_create_archive_request.py | Python | gpl-3.0 | 22,616 | [
"DIRAC"
] | b82530ad99bd8120dc7d5b0dd8d70c9786221a464018a695bd23dafbb95730e1 |
"""
Hidden Markov model representation.
"""
import numpy as np
from bhmm.util.logger import logger
__author__ = "John D. Chodera, Frank Noe"
__copyright__ = "Copyright 2015, John D. Chodera and Frank Noe"
__credits__ = ["John D. Chodera", "Frank Noe"]
__license__ = "LGPL"
__maintainer__ = "John D. Chodera"
__email__... | marscher/bhmm | bhmm/hmm/generic_hmm.py | Python | lgpl-3.0 | 20,937 | [
"Gaussian"
] | f17d44325894695eb3dd70c15b207d67574c046f9788e4865148f865b6ec04aa |
from __future__ import unicode_literals, division, absolute_import
import logging
import re
import time
from datetime import datetime, timedelta
from dateutil.parser import parse as dateutil_parse
from sqlalchemy import Table, Column, Integer, String, Unicode, Date, DateTime, Time, or_, func
from sqlalchemy.orm import... | antivirtel/Flexget | flexget/plugins/api_trakt.py | Python | mit | 43,235 | [
"VisIt"
] | bba9c662fbc41560969c574b84c748ccde1895cd4d3cda9c84daf8d1ed9b14d1 |
from __future__ import print_function, division
import os
from os.path import join
import tempfile
import shutil
import io
from io import BytesIO
try:
from subprocess import STDOUT, CalledProcessError, check_output
except ImportError:
pass
from sympy.core.compatibility import unicode, u_decode
from sympy.ut... | wxgeo/geophar | wxgeometrie/sympy/printing/preview.py | Python | gpl-2.0 | 13,192 | [
"VisIt"
] | d6861cbe6a7850a76928086a76284abd722df3974608a87b2ea69c1d61870e94 |
# csv2json.py
#
# Copyright 2009 Brian Gershon -- briang at webcollective.coop
#
# 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 re... | rg3915/django-example | myproject/fixtures/csv2json.py | Python | mit | 2,352 | [
"Brian"
] | 210023c4da00126358a10b0fd1b7cd1a0b90e53c0686bc53cfad82bcda4608b9 |
from __future__ import print_function
import sys
import os
import numpy as np
import pylab as plt
import fitsio
from astrometry.util.fits import fits_table, merge_tables
from astrometry.util.plotutils import PlotSequence, plothist, loghist
from astrometry.util.util import Tan
from legacypipe.survey import LegacySurveyD... | legacysurvey/pipeline | py/legacyanalysis/forced-phot-proper-motion.py | Python | gpl-2.0 | 4,407 | [
"Gaussian"
] | d8d8d1521feeb58e0bd134950b9ac4c434812ac8a78c26cb81392d85f3a17006 |
#!/usr/bin/env python3
from LoLIM.stationTimings.autoCorrelator3_plotPulse import processed_data_dir, plot_stations, plot_one_station, plot_one_station_allData, plot_stations_AllData
## these lines are anachronistic and should be fixed at some point
from LoLIM import utilities
utilities.default_raw_data_loc = "/exp_... | Bhare8972/LOFAR-LIM | LIM_scripts/stationTimings/examples/run_plotPulse.py | Python | mit | 7,557 | [
"Brian"
] | d65753455e9012c7b372e43368194a76d1dc338cf5145945dfd611e91f44b72c |
### All lines that are commented out (and some that aren't) are optional ###
DB_ENGINE = 'sqlite:///db.sqlite'
#DB_ENGINE = 'mysql://user:pass@localhost/monocle'
#DB_ENGINE = 'postgresql://user:pass@localhost/monocle
AREA_NAME = 'SLC' # the city or region you are scanning
LANGUAGE = 'EN' # ISO 639-1 ... | FreddyPoGo/Monocle | config.example.py | Python | mit | 17,810 | [
"VisIt"
] | 9361d6e4837b84fe9cf85157841da1f616ff3aba58a9d4f629d22c63a07f2f2c |
import os
import sys
import re
import bdsf as bdsm # bdsm it is and bdsm it shall remain
import numpy
import Tigger
import tempfile
import astropy.io.fits as pyfits
import yaml
import shlex
import shutil
import glob
import subprocess
from astLib.astWCS import WCS
from Tigger.Models import SkyModel, ModelClasses
CONF... | SpheMakh/Stimela | stimela/cargo/cab/pybdsm/src/run.py | Python | gpl-2.0 | 5,616 | [
"Gaussian"
] | 4b2f1ff5720b3c0258e98731e272a934f5f55178f46ef4b02ae94bcb2882f774 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Configuration file for CV Repository."""
try:
import sphinx_rtd_theme
except ImportError:
sphinx_rtd_theme = None
try:
from sphinxcontrib import spelling
except ImportError:
spelling = None
# If extensions (or modules to document with autodoc) are in ... | kallimachos/cv | doc/conf.py | Python | gpl-3.0 | 6,294 | [
"Brian"
] | 9ea327a93267a96e182caa746ed639bdbd5e9fb8e2a774f6a5370f7d5c383cc3 |
# Copyright 2017 Bateared Collie
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
... | batearedcollie/seisTK | stk/mdExt/hyperCube.py | Python | bsd-3-clause | 4,492 | [
"VTK"
] | 0ce11d39b742c76d694426b637a11893860a1f9d8db43e13c20ca703568167a1 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/forms/__init__.py | Python | gpl-2.0 | 3,653 | [
"Brian"
] | e9a9cd8dd6967fc0ea957b922b7fd7491ba1f7118afd52679e049911ad25f17c |
# -*- coding: utf-8 -*-
#
# evaluate_tsodyks2_synapse.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 t... | terhorstd/nest-simulator | pynest/examples/evaluate_tsodyks2_synapse.py | Python | gpl-2.0 | 5,079 | [
"NEURON"
] | 7b760788cdb26189e241fbc2330a0e8a7a405fa9d219ee043b6a0771e8875803 |
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library ... | FedoraScientific/salome-hexablock | doc/pyplots/test_make_spher_grid.py | Python | lgpl-2.1 | 1,410 | [
"VTK"
] | 9d915edbf843975a82ad57bd7561364514c978d4f3d76bd0fd7c200461d1295b |
#!/usr/bin/python
# -- Content-Encoding: UTF-8 --
"""
Python modules repository
:author: Thomas Calmant
:license: Apache Software License 2.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
... | isandlaTech/cohorte-runtime | python/cohorte/repositories/python/modules.py | Python | apache-2.0 | 21,352 | [
"VisIt"
] | 98387aaea4bed52908fd8eeef250525cb46ad445723f1d4e883568877a98e66f |
"""
Courseware views functions
"""
import logging
import urllib
import json
from collections import defaultdict
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlr... | xiandiancloud/ji | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 38,121 | [
"VisIt"
] | 907af29ec3f8844e010cc00da10e48fe56a0c03bbf41f898042f6d72940ee6c9 |
import numpy as np
from mpl_toolkits.basemap import pyproj
from datetime import datetime
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
def make_remap_grid_file(Cgrd, Cpos='t'):
#create remap file
remap_filename = 'remap_grid_' + Cgrd.name + '_' + Cpos + '.nc'
nc = netCD... | kshedstrom/pyroms | pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/make_remap_grid_file.py | Python | bsd-3-clause | 3,218 | [
"NetCDF"
] | 65e227dba5bd7413dfab7e499bc0830964ff2d0c3a828d48622ab76ef0496cb2 |
"""
NH3 fitter wrapper
==================
Wrapper to fit ammonia spectra. Generates a reasonable guess at the position
and velocity using a gaussian fit
Example use:
.. code:: python
import pyspeckit
sp11 = pyspeckit.Spectrum('spec.nh3_11.dat', errorcol=999)
sp22 = pyspeckit.Spectrum('spec.nh3_22.dat',... | low-sky/pyspeckit | pyspeckit/wrappers/fitnh3.py | Python | mit | 16,036 | [
"Gaussian"
] | c32e6a45a5a9e22706cab7674f5ed12ba8c56c8b3fff1f8c80b015722333521c |
# ======================================================================
# Atomistica - Interatomic potential library and molecular dynamics code
# https://github.com/Atomistica/atomistica
#
# Copyright (2005-2020) Lars Pastewka <lars.pastewka@imtek.uni-freiburg.de>
# and others. See the AUTHORS file in the top-level A... | Atomistica/atomistica | src/python/atomistica/tests.py | Python | gpl-2.0 | 21,869 | [
"ASE"
] | 93d6c1c93870f01bb1a3464f1d388d18c5de7a45a610d7662d178ef9081f0cb1 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Geometry/Testing/Python/rectGrid.py | Python | gpl-3.0 | 3,929 | [
"VTK"
] | 1c744847b66a88547395848a2c5087b37d908ff11c7cee77a463dd0dd433e17a |
# -*- coding: utf-8 -*-
#
# pynag - Python Nagios plug-in and configuration environment
# Copyright (C) 2010 Drew Stinnet
#
# 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 th... | kaji-project/pynag | pynag/Parsers/__init__.py | Python | gpl-2.0 | 129,457 | [
"MOE"
] | e0e83b458adaf955e75500676e9fb105153e7ed1841f450a7b132a492ce74548 |
"""
Script to verify all examples in the readme.
Run from the project directory (i.e. parent) with
python -m tests/test_readme_examples
"""
from __future__ import print_function, division
import numpy as np
from scipy import misc
def main():
example_standard_situation()
example_heavy_augmentations()
ex... | infilect/ml-course1 | week2/deconvolution_segmentation/imgaug/tests/test_readme_examples.py | Python | mit | 13,325 | [
"Gaussian"
] | 3ef2af145d50af69b6b5e63c9dc2dd393b563b940e0fc233d3b905ae527259e7 |
"""Setup script for Bokeh."""
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2014, Continuum Analytics, Inc. All rights reserved.
#
# Powered by the Bokeh Development Team.
#
# The full license is in the file LICENCE.txt, distributed with this software.
#---------... | matbra/bokeh | setup.py | Python | bsd-3-clause | 19,776 | [
"GULP"
] | 60aeb8fb767132303f65b85c8f0c1a43b1083fdb6f9b3fb31d1c1798708bd57c |
"""
Django settings for emw_output project.
Generated by 'django-admin startproject' using Django 1.9.7.
For more information on this file, see
https://docs.djangoproject.com/en/1.9/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.9/ref/settings/
"""
import os... | anhelus/emw-museum-output | emw_output/settings.py | Python | gpl-3.0 | 3,218 | [
"VisIt"
] | 147027eaf86b176c8046148f8d8679bac256d109beea5301d522455696aefade |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | javierwilson/cuentas | config/urls.py | Python | bsd-3-clause | 1,229 | [
"VisIt"
] | d5f9f9e24a93c397f560bccc3b1fef15f6176e3683d74fe49b659327df53959c |
import sys
import os
import numpy as np
import h5py
import multiprocessing
import cPickle
import matplotlib.pyplot as plt
import itertools
from scipy.stats import sigmaclip
from sklearn.gaussian_process import GaussianProcess
notes = """
In this case, we do a 3-d gaussian interpolation. The elevations are read from
... | acbecker/solar | gp3/gp3.py | Python | mit | 8,986 | [
"Gaussian"
] | b723123e4b209ccf21eb44d9df67470625bb42171808b71d414d88ca46d5d38b |
''' A plot of the Normal (Gaussian) distribution. This example demonstrates the
use of mathtext on axes and in ``Div`` objects.
.. bokeh-example-metadata::
:apis: bokeh.plotting.figure.line, bokeh.plotting.figure.quad, bokeh.models.Div, bokeh.models.TeX
:refs: :ref:`userguide_styling` > :ref:`userguide_styling... | bokeh/bokeh | examples/plotting/file/latex_normal_distribution.py | Python | bsd-3-clause | 2,248 | [
"Gaussian"
] | 482023903bf54951d7bde8ba3e224e47ee39753d8940190fe7eab8cc606b4343 |
# Copyright (c) 2018 PaddlePaddle 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 app... | reyoung/Paddle | python/paddle/fluid/initializer.py | Python | apache-2.0 | 20,383 | [
"Gaussian"
] | b11d70c51399a355a2e5a6786ef8a38e78ddf48e4640f6ed92c9b6c688afdf4f |
#!/usr/bin/env python
'''Description'''
import sys
from Bio.Blast import NCBIXML
def find_match(xmlfile):
aligned_bases = 0
records = NCBIXML.parse(open(xmlfile))
op = open(xmlfile+'.out', 'w')
for record in records:
if record.alignments: # if matched,
alm = record.alignments[0]
... | likit/gimme_protocols | find_match.py | Python | bsd-3-clause | 740 | [
"BLAST"
] | cc47219f5d8b3f3d2a833bdbd3c025ee97bfbd2a9e230f11d72441f17dfff618 |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinitio.tasks import *
from pymatgen.io.abinitio.tasks import TaskPolicy
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..", 'test_files... | yanikou19/pymatgen | pymatgen/io/abinitio/tests/test_tasks.py | Python | mit | 4,854 | [
"pymatgen"
] | c8ecb14bb70d65bcfae9ad811a26888ed031bf76cfdc0531a8c4807c188d7f60 |
#!/usr/bin/env python
"""
Renames a dataset file by appending _purged to the file name so that it can later be removed from disk.
Usage: python rename_purged_datasets.py purge.log
"""
import sys, os
assert sys.version_info[:2] >= ( 2, 4 )
def main():
infile = sys.argv[1]
outfile = infile + ".renamed.log"
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/cleanup_datasets/rename_purged_datasets.py | Python | gpl-3.0 | 1,066 | [
"Galaxy"
] | 5ca4d5272a21ab6d1a0936a9bc5efc7e5300c8da265410d96fa746acaab5b46f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | pmghalvorsen/gramps_branch | gramps/gen/plug/menu/_placelist.py | Python | gpl-2.0 | 1,794 | [
"Brian"
] | f4c5d59bf924e419c7db62482808fdfd16d8e2d170f49f3c67c9122f9417f8b8 |
# -*- coding: utf-8 -*-
## This file is part of Invenio.
## Copyright (C) 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014 CERN.
##
## Invenio 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 versi... | lnielsen/invenio | invenio/legacy/websearch/webcoll.py | Python | gpl-2.0 | 55,782 | [
"VisIt"
] | 53b85abb61f0dc522b9d00307f8f4261aa57c6a6c5264222d03b5a9ac14c057d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
An interface to the excellent spglib library by Atsushi Togo
(http://spglib.sourceforge.net/) for pymatgen.
v1.0 - Now works with both ordered and disordered structure.
v2.0 - Updated for spglib 1.6.
v3.0 ... | richardtran415/pymatgen | pymatgen/symmetry/analyzer.py | Python | mit | 62,326 | [
"CRYSTAL",
"pymatgen"
] | 69db722ab297c9bae72a321edbc3f8e8cf30118bdb9e580d7bd4ba73831bf60f |
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
zeros, arange, sort, amin, amax, any, atleast_1d,
sqrt, ceil, floor, array, compress,
pi, exp, ravel, count_nonzero, ... | aeklant/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 115,276 | [
"Gaussian"
] | a64d041de8fe916fb77f46c711dba8e6837b68c328a54c3f77c97bd7d3207635 |
# coding: utf-8
from scipy import signal
import pandas as pd
import numpy as np
# TODO: Add Gaussian filter
# TODO: Add B-spline
# TODO: Move detrend
def lp_filter(data_in, filter_len=100, fs=1):
fc = 1 / filter_len
nyq = fs / 2
wn = fc / nyq
n = int(2 * filter_len * fs)
taps = signal.firwin(n, ... | DynamicGravitySystems/DGP | dgp/lib/transform/filters.py | Python | apache-2.0 | 1,094 | [
"Gaussian"
] | 048c8a4d75b3d4f1d72b6ed65bfa8a50d68be87852129e090506faeb0a6bab0c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Provides a class for interacting with KPath classes to
generate high-symmetry k-paths using different conventions.
"""
from __future__ import division, unicode_literals
import itertools
import numpy as np
... | gVallverdu/pymatgen | pymatgen/symmetry/bandstructure.py | Python | mit | 12,242 | [
"pymatgen"
] | a42b618421e201c11070b461a6332d4ad62b2a0d376135d8e099d0ff5c5fdb44 |
#!/usr/bin/env python
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the term... | jeremiahyan/lammps | examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py | Python | gpl-2.0 | 26,819 | [
"LAMMPS"
] | b61244ce4cbe147fb0db554e01868dd84e447c23cbaf5cf070c50b36c629858d |
'''
This migration script fixes the data corruption caused in the form_values
table (content json field) by migrate script 65.
'''
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from sqlalchemy.exc import *
import binascii
from galaxy.util.json import loads,... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py | Python | gpl-3.0 | 4,588 | [
"Galaxy"
] | 0dc14d8ea5cc5bfd3576a74d34eb749470a16e3426afd8657136ba37f359952d |
#!/usr/bin/env python
from __future__ import division
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this soft... | wasade/qiita | qiita_ware/test/test_util.py | Python | bsd-3-clause | 21,675 | [
"scikit-bio"
] | 75c32acefad4ec03dcf3eb2b65abcc0e59e0cc1ddd495511abbd5b3613db3bbc |
# coding: utf-8
from __future__ import unicode_literals
import re
import itertools
from .common import InfoExtractor
from ..utils import (
clean_html,
dict_get,
ExtractorError,
float_or_none,
get_element_by_class,
int_or_none,
parse_duration,
parse_iso8601,
try_get,
unescapeHTM... | Dino0631/RedRain-Bot | lib/youtube_dl/extractor/bbc.py | Python | gpl-3.0 | 53,625 | [
"VisIt"
] | 00b2f88f315610bd6bd3d7102f67e7aad13c42c7e117932c582a90be21b54742 |
LVR = '''10 223_0 0.002695616 1 0.00
10 223_100000 0 2 0.00
10 223_200000 0.007806037 3 0.00
10 223_300000 0.00293115 4 0.01
10 324_0 0.009263053 5 0.01
10 324_100000 0 6 0.02
10 4a_100000 0 7 0.02
10 4a_0 0.015445527 8 0.02
10 445_0 0.002410607 9 0.04
10 749_0 0.003562352 10 0.04
10 48a_800000 0.005094611 11 0.04
10 4... | flag0010/mim.genet.alg | draw.any.map.py | Python | mit | 354,192 | [
"Biopython"
] | b003771c67565ec6d065cab8bd17658debf95a91bf9e95fede112cbe166ad345 |
#!/usr/bin/python
"""Test of line navigation."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
# Work around some new quirk in Gecko that causes this test to fail if
# run via the test harness rather than manually.
sequ... | GNOME/orca | test/keystrokes/firefox/line_nav_wiki_down.py | Python | lgpl-2.1 | 43,500 | [
"ORCA"
] | 5415301dab454c9efaa88017ca7e24e3a5907a753b290fe7587769322d6a14d8 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | maurofaccenda/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 30,696 | [
"Galaxy",
"MOOSE"
] | 1214d45b86744ddf0c04b7085e88df0c110c55edbb84f72e96b23e34ac88d0cc |
#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkparameter.py,v $
## Language: Python
## Date: $Date: 2016/07/19 09:49:59 $
## Version: $Revision: 1.6 $
## Copyright (c) Jingfeng Jiang, Yu Wang. All rights reserved.
## See LICENCE file for details.
## This software is distr... | jjiang-mtu/virtual-breast-project | quasi-static_UE/extract_array/vmtkparameter.py | Python | gpl-2.0 | 1,822 | [
"VTK"
] | 33cc9bcf0e6523352a576d2a89ebe3f1c9f1b00376464f3a42d2056702d7f6e6 |
"""
flowfilter.update
-----------------
Module containing Python implementationso of the filter
image model and update methods.
:copyright: 2015, Juan David Adarve, ANU. See AUTHORS for more details
:license: 3-clause BSD, see LICENSE for more details
"""
import math
import numpy as np
impor... | jadarve/optical-flow-filter | python/flowfilter/update.py | Python | bsd-3-clause | 5,061 | [
"Gaussian"
] | 1cbc009804cfe34de6d02e80f5885a988b94ade3908f2602495ea44efc5691e6 |
"""Settings for content moderation and spam control"""
from django.utils.translation import ugettext_lazy as _
from askbot import const
from askbot.deps import livesettings
from askbot.conf.settings_wrapper import settings
from askbot.conf.super_groups import EXTERNAL_SERVICES
SPAM_AND_MODERATION = livesettings.Config... | stianrh/askbot-nordic | askbot/conf/spam_and_moderation.py | Python | gpl-3.0 | 1,128 | [
"VisIt"
] | 9c844d0d19819113bb9e2a689fca6a24cd67e74663ee633a8699f3c06eaed456 |
#-------------------------------------------------------------------------------
# . File : QMCallerQChem.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#-----------------------------------------------... | mfx9/molaris-tools | MolarisTools/QMMM/QMCallerQChem.py | Python | gpl-3.0 | 6,699 | [
"Q-Chem"
] | 0867b52802d6cf6148e26f5697087d8943175b1364541dcd8589f8611159ed2e |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | burzillibus/RobHome | venv/lib/python2.7/site-packages/SOAPpy/Server.py | Python | mit | 27,044 | [
"Brian"
] | 842afcb9b41859dddf5c15fcec082f85d87e23bbddd380b858c9a7295a6bf2b6 |
# -*- coding: utf-8 -*-
"""
sphinx.quickstart
~~~~~~~~~~~~~~~~~
Quickly setup documentation source to work with Sphinx.
:copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from __future__ import print_function
import re
import os
import sys... | WhySoGeeky/DroidPot | venv/lib/python2.7/site-packages/sphinx/quickstart.py | Python | mit | 51,722 | [
"VisIt"
] | 11ba17cf1146bc85015be635acd3c3fe7b12b283d690e225049f6e6988412096 |
# Copyright (C) 2012,2013
# 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 terms of t... | capoe/espressopp.soap | src/interaction/Morse.py | Python | gpl-3.0 | 9,678 | [
"ESPResSo"
] | 9dfbf0423bcda5927f1ac7f496dcd24cc8982a7ce0f6b5d99d441dd935420de2 |
#!/usr/bin/env python
"""
dirac-rss-query-dtcache
Select/Add/Delete a new DownTime entry for a given Site or Service.
Usage:
dirac-rss-query-dtcache [option] <query>
Queries:
[select|add|delete]
Options:
--downtimeID= The ID of the downtime
--element= ... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/scripts/dirac-rss-query-dtcache.py | Python | gpl-3.0 | 12,464 | [
"DIRAC"
] | ad52d668763403a7423610de9cfb8864007af87ef3c8e88cbe5b21b0bd8d876d |
# -*- coding: utf-8 -*-
"""
Insert temporary allocations and deallocations into the IR.
"""
from __future__ import absolute_import, division, print_function
from pykit.ir import interp, visit, transform, Op, Builder, ops
from pykit import types
def insert_allocations(func, env):
b = Builder(func)
# IR posi... | XinSong/blaze | blaze/compute/air/frontend/allocation.py | Python | bsd-3-clause | 1,323 | [
"VisIt"
] | 4640c7895e547a5cf77f11b731532d746677f994074e47426ec289c4d3b1fda2 |
#!/usr/bin/env python
# A python script to parse log file to generate cross-reference information
# and print out the cross-reference information based on the input.
# To run the script, please do
# python CrossReferenceConsole.py -l <logFileDir> -r <VistA-Repository-Dir> -d <Dox-Repository-Dir>
# enter quit to exit
#... | JimDeanSpivey/ATF-for-Vista-FOIA | Dox/PythonScripts/CrossReferenceConsole.py | Python | apache-2.0 | 15,774 | [
"VisIt"
] | c6b56707d50d6e5fab1e7bbc0daaab0566e425eb3fe73d7e5e924f90c1bd2000 |
# $Id$
__revision__ = '$Rev$'
import sys
from itcc.molecule import read
from itcc.tinker import parameter, analyze, tinker, molparam
from itcc.torsionfit import tools, parmfit
def printefit(datfname, idxfname, param):
'''Only print E_fit'''
import csv
fnames, enes, weights = tools.readdat(datfname)
i... | lidaobing/itcc | itcc/torsionfit/printefit.py | Python | gpl-3.0 | 1,167 | [
"TINKER"
] | 08295163fd7e12eaf93b319a438cd342d2a279ca146cb50e38503a4809aa3927 |
'''
Hodgkin-Huxley equations (1952).
Spikes are recorded along the axon, and then velocity is calculated.
'''
import os
import matplotlib
matplotlib.use('Agg')
from brian2 import *
import brian2cuda # cuda_standalone device
from scipy import stats
name = os.path.basename(__file__).replace('.py', '')
codefolder = os.p... | brian-team/brian2cuda | examples/compartmental/hh_with_spikes_cuda.py | Python | gpl-2.0 | 3,151 | [
"NEURON"
] | 57004620860fda252012e1ada8bc4c717f41cd38171bdfcf36a5f3a9d2ada87e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/inftauinterpolated/neuron.py | Python | bsd-2-clause | 6,808 | [
"NEURON"
] | ffa32d9d10693a4481cb6e71c32a1349cbaadba13ca57d33a29c8fce1b21e8b1 |
"""Linear Predictive Coding analysis and resynthesis for audio."""
import numpy as np
import scipy.signal
def lpcfit(x, p=12, h=128, w=None, overlaps=True):
"""Perform LPC analysis of short-time windows of a waveform.
Args:
x: 1D np.array containing input audio waveform.
p: int, order of LP models to fit... | dpwe/elene4896 | L06/lpc.py | Python | mit | 6,369 | [
"Gaussian"
] | 45fed0d62cc605bbb1a28d3039ff47d73115e5466802ccfe34f97b99f30234d8 |
from .. import Provider as LoremProvider
class Provider(LoremProvider):
"""Implement lorem provider for ``en_US`` locale.
Word list is based on the source(s) below, and some words have been removed
to make the word list appropriate for public testing.
Sources:
- http://www.ef.edu/english-resour... | joke2k/faker | faker/providers/lorem/en_US/__init__.py | Python | mit | 17,423 | [
"VisIt"
] | 2784b7e5b3a9e40f873588a6939dc714d5f25aaa831c81c5f543535f179b7b68 |
from __future__ import print_function, absolute_import, division
import _pygaussian
import f90wrap.runtime
import logging
class Gaussianstuff(f90wrap.runtime.FortranModule):
"""
Module gaussianstuff
Defined at gaussian.F90 lines 4-789
"""
@f90wrap.runtime.register_class("gaussian")
... | FPAL-Stanford-University/FloATPy | floatpy/filters/pygaussian.py | Python | lgpl-3.0 | 3,387 | [
"Gaussian"
] | 42e0182f091e1b0a19434ac8f760528f65f795fc2273b6faa1e82c038a88cca6 |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['Aperture', 'Aperture_Watchpoint', 'Watchpoint']
for el_name in names:
if ... | mrakitin/sirepo | tests/template/srw_generate_data/tabulated-undulator-example.py | Python | apache-2.0 | 21,771 | [
"Gaussian"
] | d9afb4489f2d5f13179800ddc7cb6b3fa9cef64d3a90c236d7a79408d8430995 |
"""
Tests the ComponentMonitoring DB and Service by creating, checking,
updating and removing several instances of each table in the DB
This program assumes that the service Framework/ComponentMonitoring is running
"""
# pylint: disable=invalid-name,wrong-import-position
import unittest
import datetime
from DIRAC.Co... | arrabito/DIRAC | tests/Integration/Framework/Test_InstalledComponentsDB.py | Python | gpl-3.0 | 16,132 | [
"DIRAC"
] | 4fe3347e5847dc4df5e0163569159a1c17cbcd4e63d92ec0bb92bbe392c4377b |
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