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# 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 Fpocket(MakefilePackage):
"""fpocket is a very fast open source protein pocket detection a... | LLNL/spack | var/spack/repos/builtin/packages/fpocket/package.py | Python | lgpl-2.1 | 879 | [
"NetCDF"
] | a1365302ac1c04c81e74a6b13aad06a73eb01061d73b600d6dd3f64dc81c1c97 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Vispy Development Team.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
from __future__ import division
import numpy as np
from ..gloo import Texture2D, VertexBuffer
from ..color import get_colormap
from .shaders import Function, FunctionChain
f... | ghisvail/vispy | vispy/visuals/image.py | Python | bsd-3-clause | 15,671 | [
"Gaussian"
] | 392a168c5ac6ee6216a036c80d1285fd007533058002701fe34a04e3417a0efc |
"""Color transformations on 2D image."""
from skimage import data, color
from skimage.filters import gaussian
from skimage.io import imsave
import matplotlib.pyplot as plt
import numpy as np
import compoda.core as coda
from compoda.utils import truncate_range
from matplotlib import rcParams
rcParams['font.family'] = "... | ofgulban/tetrahydra | examples/conversions/2D_example.py | Python | bsd-3-clause | 3,781 | [
"Gaussian"
] | 560cd5cfaba28561be085ccd99812cadecfbaf2c3ae4ca179803651a6c50c29d |
# import aeropy.CST_lib as cst
import aeropy.CST_3D as cst
import aeropy.CST_3D.mesh_tools as meshtools
import panairwrapper
from aeropy.filehandling.vtk import generate_surface
import numpy as np
import matplotlib.pyplot as plt
# wing_points = stl_processing.points_from_stl('./wing_right.stl')
# wing_points = np.ge... | leal26/pyXFOIL | examples/3D/full_aircraft.py | Python | mit | 13,276 | [
"VTK"
] | a09fae9e086d52728069060697c9ce699ac2d1729656ab4f1843a5ecb0e9ccc2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Module contains classes presenting Element and Specie (Element + oxidation state) and PeriodicTable."""
import re
import json
import warnings
from io import open
from pathlib import Path
from enum import En... | mbkumar/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 50,280 | [
"CRYSTAL",
"pymatgen"
] | 4ca255acb4ac4837ce80db92be7895c7c30390a43c8d6fb38788c08a9ee4a620 |
#!/usr/bin/env python
# Author: Jason Buenrostro, Stanford University
# Modifiedi by Aaron Daugherty, Stanford University
##### IMPORT MODULES #####
# import necessary for python
import os
import re
import sys
import gzip
import string
#from Bio import SeqIO
#from Bio import AlignIO
from optparse import ... | brunetlab/CelegansATACseq | Fig1/pyadapter_trim.py | Python | gpl-3.0 | 5,271 | [
"Bowtie"
] | 320efc9884e5add1ac1542949b2b8a059cedc9e137b827db7434b806610b9f08 |
# NOTE that in general, PyMOL API calls should not be made during the
# __call__ method of a callback object. The PYMOL API is not designed
# to be re-entrant, and the callback object's __call__ method may in
# fact be called as far of an API fuction (refresh, ray, etc.).
# There are a few exceptions, which you may ... | gratefulfrog/lib | python/pymol/callback.py | Python | gpl-2.0 | 608 | [
"PyMOL"
] | 671308b272467dc96a5a96e8cb99a526cb6bf88010fa68cbd9b85e307cd34c15 |
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2020 Dave Hocker
#
# 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, version 3 of the... | dhocker/athomepowerlineserver | services/TimerServiceThread.py | Python | gpl-3.0 | 9,400 | [
"xTB"
] | 1bbf7dbe7bc148af86a91d7f6c663051d40b2e231b80857b7b068201732a19b5 |
# ppgplot_numpy_spb.py
# imports ppgplot functions and sets up useful variables
from ppgplot_numpy import *
import numpy as N
import os
from os.path import join as pjoin
import pyfits
from glob import glob
from gaussian import gaussian2d
import sys
#import nr as nr
import rostat as rostat
pgplot_extras_path = '/User... | bamford/astrobamf | ppgplot_numpy_spb.py | Python | mit | 10,133 | [
"Gaussian"
] | 48747c02cc6b75bcd5361f77d6d7d5267db855b78dd6a5c5b90ce356e163c2aa |
# coding=utf-8
# Copyright 2022 The Balloon Learning Environment 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 require... | google/balloon-learning-environment | balloon_learning_environment/env/features.py | Python | apache-2.0 | 22,742 | [
"Gaussian"
] | 4a1321974c33ee1f18cfa8a2939cbab28aef9c59c39a5cbc4be79cb9b996cdaa |
#!/usr/local/bin/python
# -*- coding: iso-8859-1 -*-
# Id
# Copyright (c) 2004, 2008 Kungliga Tekniska Högskolan
# (Royal Institute of Technology, Stockholm, Sweden).
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the follo... | GaloisInc/hacrypto | src/C/NetBSD-7.0/crypto/external/bsd/heimdal/dist/lib/wind/rfc4518.py | Python | bsd-3-clause | 5,601 | [
"FEFF"
] | ec9467653090d5bdf1f882bbc52325a084f7516be52e346ebb7f17d5ca02fb48 |
"""
Basic tool parameters.
"""
import logging, string, sys, os, os.path
from elementtree.ElementTree import XML, Element
from galaxy import config, datatypes, util
from galaxy.web import form_builder
from galaxy.util.bunch import Bunch
import validation, dynamic_options
# For BaseURLToolParameter
from galaxy.web impor... | dbcls/dbcls-galaxy | lib/galaxy/tools/parameters/basic.py | Python | mit | 60,021 | [
"Galaxy"
] | 9d21ec8a21eb1ea2211f64535720edeb64d156ad1e5158c326d6729173aec20e |
"""Provide variant calling with VarScan from TGI at Wash U.
http://varscan.sourceforge.net/
"""
from collections import namedtuple
import contextlib
from distutils.version import LooseVersion
import os
import shutil
from bcbio import broad, utils
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
... | elkingtonmcb/bcbio-nextgen | bcbio/variation/varscan.py | Python | mit | 16,073 | [
"pysam"
] | 0ebb9f2be9a936403ba75480b79d36bf34ecabd87a4e7a5f478e81f16ac0ef72 |
#!/usr/bin/env python
"""
Python wrapper around jnml command.
Also a number of helper functions for
handling/generating/running LEMS/NeuroML2 files
Thanks to Werner van Geit for an initial version of a python wrapper for jnml.
"""
from __future__ import absolute_import
from __future__ import print_function
from __f... | NeuroML/pyNeuroML | pyneuroml/pynml.py | Python | lgpl-3.0 | 95,099 | [
"Brian",
"MOOSE",
"NEURON"
] | d8637fff51674be3c7621812691971a1622608331712d4434e05fe3c1da42bfa |
from __future__ import division
import numpy as np
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import matplotlib.patches as patches
import matplotlib.path as path
import subprocess
plt.style.use('classic')
# Parameters for animation
aL=4
cH=0.25
lam... | letsgoexploring/signalingAnimation | code/signalingAnimationSeparating.py | Python | mit | 7,459 | [
"Brian"
] | 453072925c0ee53975bdf06910dd17a15fa184331d95d071e4ea54df69a17f56 |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2011, MBARI"
__credits__ = ["Chander Ganesan, Open Technology Group"]
__license__ = "GPL"
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__doc__ = '''
Base module for STOQS loaders
@author: __author__
@status: __status__
@l... | josephmfaulkner/stoqs | stoqs/loaders/__init__.py | Python | gpl-3.0 | 69,082 | [
"NetCDF"
] | 69ea124a9d9aa1282a627c5a5e9fae10ce952650e48d8a1af6f4eff1ae167faa |
import os
import click
from apollo import ApolloInstance
from arrow.cli import pass_context
from arrow import config
from arrow.io import warn, info
CONFIG_TEMPLATE = """## Apollo's Arrow: Global Configuration File.
# Each stanza should contian a single galaxy server to control.
#
# You can set the key __default to ... | erasche/python-apollo | arrow/commands/cmd_init.py | Python | mit | 2,614 | [
"Galaxy"
] | a00b5f705d0e52969156bc8b0ff0b1de5d44aeff830d921050cea0ac19cdb479 |
from bioblend import galaxy
from bioblend.galaxy.tools import ToolClient
from bioblend.galaxy.histories import HistoryClient
from bioblend.galaxy.datasets import DatasetClient
import yaml
import subprocess
import argparse
import os
def _get_conf( config_file = '/import/conf.yaml' ):
with open(config_file, 'rb') as... | bgruening/docker-recipes | ipython-notebook-plus/galaxy.py | Python | mit | 5,482 | [
"Galaxy"
] | f6530afab9a4bc66fdf4f24924ad6990d3b4a5aea66d398823f2443070dcb953 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2012 Prof. Richard H. West (r.west@neu.edu),
# Prof. William H. Green (whgreen@mit.edu)
# ... | chatelak/RMG-Py | rmgpy/qm/main.py | Python | mit | 10,617 | [
"Gaussian",
"MOPAC"
] | 930675bb51e1a75a6b02bc1a712d6eafa3c4088186d31fb12b26124ec4d7f79d |
#------------------------------------------------------------------------------
# pycparser: c_generator.py
#
# C code generator from pycparser AST nodes.
#
# Copyright (C) 2008-2015, Eli Bendersky
# License: BSD
#------------------------------------------------------------------------------
from . import c_ast
class... | ARMmbed/yotta_osx_installer | workspace/lib/python2.7/site-packages/pycparser/c_generator.py | Python | apache-2.0 | 13,570 | [
"VisIt"
] | 8589b0b6c7cdd8fdb0e3950bc16b780d8c5aebf7f1db40fc37e293f7cd77a9f9 |
#!/usr/bin/env python
# Description:
# convert topcons result file to fasta format
# output agreement list
# SeqID maxNumIDT numpredictor RLTY
# method 1:
# output files with different agreed numbers
# compare the topology of topcons to subpredictors,
# can be 0 identical, 1 identical, up to 5
#
import os
import sy... | ElofssonLab/TOPCONS2 | topcons2_webserver/workflow/topcons2_to_fasta.py | Python | gpl-2.0 | 18,168 | [
"Octopus"
] | 433a538554d3b0b3eab8a390b4a6c4bc24e884c813f30259184fe3c57676387e |
# -*- coding: utf-8 -*-
"""
TEST: PSF0X
PSF vs. Fluence, and Wavelength
PSF01 - nominal temperature
PSF02 - alternative temperatures
Tasks:
- Select exposures, get file names, get metadata (commandig, HK).
- Check exposure time pattern matches test design.
- Check quality of data (rough scaling of... | ruymanengithub/vison | vison/point/PSF0X.py | Python | gpl-3.0 | 53,986 | [
"Gaussian"
] | 33dbabe82ade14ac3556a72816018cbf1e0a5e5ac5f97ff66b6fb4c9e50d45bc |
# -*- coding: utf-8 -*-
u"""Shadow execution template.
:copyright: Copyright (c) 2017 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkio
from pykern.pkcollections import PKDict
from... | mkeilman/sirepo | sirepo/template/shadow.py | Python | apache-2.0 | 29,803 | [
"CRYSTAL"
] | 837c521bf43db15767b225fc0c3e44b8dd559772fda15f4457f755aa9ace7452 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either versi... | fabian-paul/PyEMMA | pyemma/coordinates/tests/test_random_access_stride.py | Python | lgpl-3.0 | 21,461 | [
"MDTraj",
"NetCDF"
] | 6c3819ac1c9bf0e0f5eeea7755b0d4e219f423fd42d4636428428637cf30ae7b |
"""
NGS indexes
"""
import os
import logging
from metadata import MetadataElement
from text import Html
log = logging.getLogger(__name__)
class BowtieIndex( Html ):
"""
base class for BowtieIndex
is subclassed by BowtieColorIndex and BowtieBaseIndex
"""
MetadataElement( name="base_name", desc="b... | icaoberg/cellorganizer-galaxy-tools | datatypes/ngsindex.py | Python | gpl-3.0 | 2,783 | [
"Bowtie"
] | ba9227877fd5cbca3b94d729ef0d9e67aa72a2398365c6d64b04161763f59847 |
"""
Tests on the deposit functions
"""
from octopus.modules.es.testindex import ESTestCase
from service import deposit, models
from octopus.modules.jper import client
from octopus.modules.jper import models as jmod
from octopus.modules.store import store
from service.tests import fixtures
from octopus.lib import dates... | JiscPER/jper-sword-out | service/tests/unit/test_deposit.py | Python | apache-2.0 | 22,540 | [
"Octopus"
] | a4148ed4e4b2ddee26da24b479d8d1878442fdf977172b7465fd7f2b31a8fa6d |
#!/usr/bin/env python
# Copyright 2014 the V8 project authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# This script retrieves the history of all V8 branches and
# their corresponding Chromium revisions.
# Requires a chromium checkout ... | sloanyang/raspberrry2v8 | deps/v8/tools/release/releases.py | Python | gpl-2.0 | 18,126 | [
"VisIt"
] | 93c7aa933114a3beb8183f56af2cc7e3c66eb7106bdf63f8a9fa275732920d7b |
# Pavel Polishchuk, 2017
import sys
import re
from collections import defaultdict
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdMMPA
from crem.mol_context import get_canon_context_core, combine_core_env_to_rxn_smarts
from multiprocessing import Pool, cpu_count
import sqlite3
import ran... | DrrDom/crem | crem/crem.py | Python | bsd-3-clause | 42,632 | [
"RDKit"
] | 3d86618346688bd89bd55b9c3dbe28df7787e5202925044fdd76c72468c83786 |
# Portions Copyright (c) Facebook, Inc. and its affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# copies.py - copy detection for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed acco... | facebookexperimental/eden | eden/hg-server/edenscm/mercurial/copies.py | Python | gpl-2.0 | 34,090 | [
"VisIt"
] | cb104c7571112570132c470e3de685b99a4180498baa96197f8be1b42926d95b |
# Copyright (C) 2012,2013,2016
# 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 terms of ... | espressopp/espressopp | src/tools/warmup.py | Python | gpl-3.0 | 2,321 | [
"ESPResSo"
] | 69fdd8f3a2d0397f558b423770abe537d252760c8c82837da7f763e07b4f9e35 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | alexgorban/models | research/object_detection/core/preprocessor.py | Python | apache-2.0 | 165,335 | [
"Gaussian"
] | e1dee1083fce8486d611259b038d279f986529687e5b11cce67bdb564df2d958 |
# coding: utf-8
"""
Collection of low-level tools that faciliate the interface with resource managers.
The preferred way of importing this module is:
import qutils as qu
"""
from __future__ import print_function, division, unicode_literals
from monty.string import is_string
from pymatgen.core.units import Time, ... | Bismarrck/pymatgen | pymatgen/io/abinit/qutils.py | Python | mit | 4,211 | [
"pymatgen"
] | 2af490667976f3ef6d36994655acc03168cb359a34887c494acd44b305c7b317 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-fix-mysql-script
# Author : Ricardo Graciani
########################################################################
"""
Fixes the mysql.server script, it requires a proper /LocalInstallation s... | andresailer/DIRAC | Core/scripts/dirac-fix-mysql-script.py | Python | gpl-3.0 | 1,005 | [
"DIRAC"
] | ae694a161ad97b33c9b7aa7cfa001c9c7c0dcef7ce6a33e22096774edca956fc |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('professionals', '0001_initial'),
('services', '0001_initial'),
('purchases', '0001_initial'),
('products', '0001_init... | dogukantufekci/supersalon | supersalon/purchases/migrations/0002_auto_20151111_2207.py | Python | bsd-3-clause | 2,022 | [
"VisIt"
] | 1998e9c3c9e1d1bd12ac23c3dca5c95dd707b1b5c4e3aba4c97852ca6426583d |
##################################################################
# Copyright 2016 OSGeo Foundation, #
# represented by PyWPS Project Steering Committee, #
# licensed under MIT, Please consult LICENSE.txt for details #
####################################################... | ldesousa/PyWPS | pywps/inout/formats/__init__.py | Python | mit | 6,850 | [
"NetCDF"
] | f3f62a00b7ab3f700d3c16f98344a3ba812621fd754276c1e93a4daf77a6cd2b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import inspect
import numpy as np
import emcee
import george
from george import kernels
import os
import sys
currentframe = inspect.currentframe()
currentdir = os.path.dirname(os.path.abspath(inspect.getfile(currentframe)))
parentdir = os.path.dirname(currentdir)
sys.pa... | mtjvc/gpew | examples/chi2_vs_gp.py | Python | mit | 4,487 | [
"Gaussian"
] | 58e8567632c6499174d983ee8c3f2f4d15d73b7d7b1af775b16ab88172223eed |
"""
API operations on User objects.
"""
import logging
from paste.httpexceptions import HTTPBadRequest, HTTPNotImplemented
from galaxy import util, web, exceptions
from galaxy.security.validate_user_input import validate_email
from galaxy.security.validate_user_input import validate_password
from galaxy.security.valid... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/users.py | Python | gpl-3.0 | 6,221 | [
"Galaxy"
] | 8c2933685391f34a35435c7613a006c4e97d0ae7e75a34425a4859ea54a33b79 |
####################################################################################################
# @file __init__.py
# @package puli.dispatcher.strategies
# @author Olivier Derpierre
# @date 2009/04/28
# @version 0.1
#
# This module exports all the basic dispatch strategies:
# - AsIsStrategy, a strategy that does n... | mikrosimage/OpenRenderManagement | src/octopus/dispatcher/strategies/__init__.py | Python | bsd-3-clause | 5,029 | [
"Octopus"
] | 0c3506476d16e57d7dc9ffa2faaa2cdfa9c1e22a5fd4cf6b48f39dcb30ac7342 |
from syn.types.a import Type, NONE, \
hashable, serialize, deserialize, estr, rstr, visit, find_ne, \
DifferentTypes, primitive_form
from syn.types.a import enumerate as enumerate_
from syn.base_utils import is_hashable
#-------------------------------------------------------------------------------
# None
de... | mbodenhamer/syn | syn/types/a/tests/test_special.py | Python | mit | 1,325 | [
"VisIt"
] | 195582ffc7374aef64b24a7035145fcb4c08ae7e9533591babb0bad95ca7a955 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2016
# Author(s):
# Thomas Leppelt <thomas.leppelt@dwd.de>
# This file is part of sauventory.
# Spatial Autocorrelated Uncertainty of Inventories
# sauventory is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gener... | m4sth0/sauventory | sauventory/inventory.py | Python | gpl-3.0 | 12,416 | [
"Gaussian"
] | cc157ebe9c5926570669172e38b3b8a3f0ac061a9fdec22297eb05428c5b4481 |
"""
loess(formula, data, weights, subset, na.action, model = FALSE,
span = 0.75, enp.target, degree = 2,
parametric = FALSE, drop.square = FALSE, normalize = TRUE,
family = c("gaussian", "symmetric"),
method = c("loess", "model.frame"),
control = loess.control(...), ...)
a formula specify... | hadley/ggplot | ggplot/components/loess.py | Python | bsd-2-clause | 1,493 | [
"Gaussian"
] | 2ee1c6fc6eee7fddd92b41482704899a99753518bdf4360b82b945b628f0be9d |
#
# Copyright (C) 2013-2019 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... | espressomd/espresso | src/python/espressomd/checkpointing.py | Python | gpl-3.0 | 9,755 | [
"ESPResSo"
] | 843b2509e0d8a41d588e7c6ef54d1c4ddeb45b7815a2e91dc7301d76d9c7bc8d |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 7 14:38:46 2011
Plot pca test error vs train error
@author: -
"""
# Computes the gaussian gradients on a boxm_alpha_scene
import os;
import optparse;
import time;
import sys;
import numpy as np
import matplotlib.pyplot as plt
import glob
if __name__=="__main__":
... | mirestrepo/voxels-at-lems | dbrec3d/bof/general/learn_categories/plot_histograms_in_one.py | Python | bsd-2-clause | 3,335 | [
"Gaussian"
] | 2b1650fb274a4a73e128fe51012e57c4a573bd793df493f733a43dba1b56889a |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Xeralux/tensorflow | tensorflow/contrib/py2tf/pyct/compiler.py | Python | apache-2.0 | 2,523 | [
"VisIt"
] | 22586b4f596b6b6c38dfffcd0307d11914382e264cf1b0843faea99762142f07 |
"""Gaussian Mixture Model."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
import numpy as np
from scipy import linalg
from ._base import BaseMixture, _check_shape
from ..utils import check_array
from ..utils.extmath import row_nor... | glemaitre/scikit-learn | sklearn/mixture/_gaussian_mixture.py | Python | bsd-3-clause | 28,380 | [
"Gaussian"
] | eb5536cc8f89dc45f6f6810c7748dad56e4bda25a5f2e11c53b74885a69dd08a |
"""
Handling the download of the shifter Proxy
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.FrameworkSystem.Client.ProxyMana... | yujikato/DIRAC | src/DIRAC/Core/Utilities/Shifter.py | Python | gpl-3.0 | 3,076 | [
"DIRAC"
] | 745498dde25c38cd7099024178b14c06ada2340138510d1a34d10e8e557641b2 |
"""This demo program solves the incompressible Navier-Stokes equations
on an L-shaped domain using Chorin's splitting method."""
# Copyright (C) 2010-2011 Anders Logg
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Publi... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Examples/Catalyst/PythonDolfinExample/simulation.py | Python | gpl-3.0 | 3,763 | [
"ParaView"
] | df810bee9627036af1d4d3a6f83b95d059514b242e4dae84973b76e0f8ab7b14 |
"""
grdtrack - Sample grids at specified (x,y) locations.
"""
import pandas as pd
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
GMTTempFile,
build_arg_string,
data_kind,
fmt_docstring,
kwargs_to_strings,
use_alias,
)
@fmt_docstring
@use... | GenericMappingTools/gmt-python | pygmt/src/grdtrack.py | Python | bsd-3-clause | 14,558 | [
"NetCDF"
] | 61666f1a66a57a4233815164fea2ea35fe9b8f919b1e52523f3d632c01f1b23d |
# -*- coding: utf-8 -*-
"""Node search functions."""
from typing import Iterable
from pybel import BELGraph, BaseEntity
from pybel.struct.filters import build_node_name_search, filter_nodes
from pybel.typing import Strings
from ..filters.node_filters import namespace_inclusion_builder
__all__ = [
'search_node_n... | pybel/pybel-tools | src/pybel_tools/selection/search.py | Python | mit | 2,038 | [
"Pybel"
] | fb9632ff6790e90b6d6389dcb5f510ca49294397e512efa1cc6c084b30e2f7b9 |
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__=''' $Id$ '''
__doc__='''The parser used to process markup within paragraphs'''
import string
import re
import sys
im... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/reportlab/platypus/paraparser.py | Python | agpl-3.0 | 45,964 | [
"VisIt"
] | 301a6d1c9ec43e5daca6844a0edb8c30b2d50f5c944a72b63187f51fa710edfc |
"""
Find runs that match crAssphage with a minimum number of runs, a minimum alignment length, and a minimum percent
identity
"""
import os
import sys
import argparse
import pysam
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Find bam files that match crAssphage")
parser.add_argume... | linsalrob/EdwardsLab | crAssphage/runs_that_match.py | Python | mit | 1,631 | [
"pysam"
] | 6b9ac64a47bfe18395c25fddd095cd7a7360c85a3fbdbdcd3aa64c33432da529 |
# sybase/base.py
# Copyright (C) 2010-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | adamwwt/chvac | venv/lib/python2.7/site-packages/sqlalchemy/dialects/sybase/base.py | Python | mit | 28,629 | [
"ASE"
] | cdcb88e472087857d2d65c3b6b9993d64debdd7cbb2f993c174f53e05c73c692 |
""" Bunch is a subclass of dict with attribute-style access.
>>> b = Bunch()
>>> b.hello = 'world'
>>> b.hello
'world'
>>> b['hello'] += "!"
>>> b.hello
'world!'
>>> b.foo = Bunch(lol=True)
>>> b.foo.lol
True
>>> b.foo is b['foo']
True
It is safe to import *... | mwaskom/moss | moss/external/bunch.py | Python | bsd-3-clause | 14,775 | [
"Brian"
] | f6abe0145be7630c3b642445c14ab1c58bf46c09066eb7ac206da85d4707885c |
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of source... | trendelkampschroer/PyEMMA | pyemma/coordinates/tests/test_assign.py | Python | bsd-2-clause | 6,750 | [
"Gaussian"
] | 1abdc396da139472fd7f51704b9c5c46d72735af68c16c3da06251432de8057d |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, or ntpath
- os.name is 'posix', 'nt', 'os2', 'ce' or 'riscos'
- os.curdir is a string representing the current di... | isandlaTech/cohorte-devtools | org.cohorte.eclipse.runner.basic/files/jython/Lib/os.py | Python | apache-2.0 | 25,531 | [
"VisIt"
] | 2a82b6cc5208cd4b1bfe9393fb869353fe87fafe42ecc193f7d7a5d9161820c1 |
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 22 10:15:36 2015
Blosum62
@author: brian
"""
from Bio.SubsMat import MatrixInfo
def score_match(pair, matrix):
if pair not in matrix:
return matrix[(tuple(reversed(pair)))]
else:
return matrix[pair]
def score_pairwise(seq1, seq2, matrix, gap_s, g... | andretadeu/jhu-immuno | code/blosumDistance.py | Python | mit | 1,018 | [
"Brian"
] | 6f4826305399a7188100cf34fd9c963fda172aafdae75a12d754adbc7bb0c110 |
#!/usr/bin/env python
#Adam Bowen - Apr 2016
#This script provisions a vdb or dSource
# Updated by Corey Brune Aug 2016
# --- Create vFiles VDB
#requirements
#pip install docopt delphixpy
#The below doc follows the POSIX compliant standards and allows us to use
#this doc to also define our arguments for the script.
... | mcbrune/delphixpy-automation | v1_7_0/dx_provision_vdb.py | Python | mit | 48,516 | [
"ASE"
] | 7d67205807748fa355ba9a0a5a2e5197c318c5d4dcca20b831107ba10b82e940 |
"""
Module :mod:`pyesgf.logon`
==========================
Manage the client's interaction with ESGF's security system. Using this module requires installing the MyProxyClient_ library.
.. _MyProxyClient: http://pypi.python.org/pypi/MyProxyClient
To obtain ESGF credentials create a :class:`LogonManager` instance an... | sterlingbaldwin/esgf-pyclient | pyesgf/logon.py | Python | bsd-3-clause | 10,018 | [
"NetCDF"
] | 530c9f49f26f88a70b0a8041a608f6185708a57fea93b71195bea702908f7d8f |
from __future__ import print_function, division, absolute_import
import numpy as np
import scipy.linalg
from time import time
import logging
from mdtraj import io
from mdtraj.utils.six.moves import cPickle
from msmbuilder.metrics import Vectorized
from msmbuilder.reduce import AbstractDimReduction
logger = logging.g... | mpharrigan/msmbuilder | MSMBuilder/reduce/tICA.py | Python | gpl-2.0 | 14,202 | [
"MDTraj"
] | 8c02bb3e61c5f40324b2eef807cd354a4d3eaa1be2b15062315f0bc8c0068a44 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# grid_webdavs - secure WebDAV server providing access to MiG user homes
# Copyright (C) 2003-2015 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/server/grid_webdavs.py | Python | gpl-2.0 | 25,823 | [
"Brian"
] | 399138157ac26c5c142fe1a59d3f2bbf2eff2cc1d6ddcddc851143c3f3a22239 |
from __future__ import absolute_import, unicode_literals
type_query = {
'hospital':
{'query': 'node["amenity"="hospital"]({0});way["amenity"="hospital"]({0});relation["amenity"="hospital"]({0});',
'distance': 10000},
u'\\U0001f3e5':
{'query': 'node["amenity"="hospital"]({0});way["amenit... | Xevib/osmbot | bot/overpass_query.py | Python | gpl-3.0 | 54,374 | [
"CASINO"
] | a4f23c1284872bc83e92be39f8ab8ece698f262dd1f04b9ebcfe6e8069ec981a |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Interfaces to assorted Freesurfer utility programs.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> d... | grlee77/nipype | nipype/interfaces/freesurfer/utils.py | Python | bsd-3-clause | 55,883 | [
"Gaussian",
"VTK"
] | cc4db29c994e4dd5797457570859bf2cbf746ac894ee8ed3664b71760ec7a641 |
''' Tests for netcdf '''
from __future__ import division, print_function, absolute_import
import os
from os.path import join as pjoin, dirname
import shutil
import tempfile
from io import BytesIO
from glob import glob
from contextlib import contextmanager
import numpy as np
from numpy.testing import assert_, assert_a... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/scipy/io/tests/test_netcdf.py | Python | agpl-3.0 | 6,738 | [
"NetCDF"
] | 6e8f55bc642dcde080c2945167908d71ed9eb58c14e01828185e4c9076b76e3f |
# -*- coding: utf-8 -*-
"""Read data from 'German National Library'.
Records: 14.1 Million
Size: 2.6 GB (compressed),
Info: http://datendienst.dnb.de/cgi-bin/mabit.pl?userID=opendata&pass=opendata&cmd=login
Data:
http://datendienst.dnb.de/cgi-bin/mabit.pl?cmd=fetch&userID=opendata&pass=opendata&mabheft=DNBTitel.rd... | coblo/isccbench | iscc_bench/readers/dnbrdf.py | Python | bsd-2-clause | 8,144 | [
"VisIt"
] | bf4d34985ba675ed7b52851246ec1d743a0cbf9b05299c103a6c24cd0f00b2f2 |
'''
Created on Jul 19, 2011
@author: sean
'''
from __future__ import print_function
from meta.asttools import Visitor
import sys
import _ast
from warnings import warn
if sys.version_info.major < 3:
from StringIO import StringIO
else:
from io import StringIO
class Indentor(object):
def __init__(self, pr... | enthought/Meta | meta/asttools/visitors/print_visitor.py | Python | bsd-3-clause | 5,048 | [
"VisIt"
] | d540e91b0da1b3237693e99b6c7c56db4a1e79968c064e9f76301076e9da6f08 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/result/executionresult.py | Python | mit | 4,965 | [
"VisIt"
] | 1d9cd4d6a8ce3a27fd2676b73e184e20a5456bb101e2dbcaedf4260c27df1744 |
#!/usr/bin/python
"""
Michael DeHaan <mdehaan@fedoraproject.org>, 2008
This software may be freely redistributed under the terms of the GNU
general public license.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 675 Mass ... | pombredanne/func | pusher.py | Python | gpl-2.0 | 4,025 | [
"VisIt"
] | 4099bacedf5d007e392e5e436eaba67069d1712dcf5c652510685b2c6f8ef5db |
# 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 RComplexheatmap(RPackage):
"""Make Complex Heatmaps
Complex heatmaps are efficient... | LLNL/spack | var/spack/repos/builtin/packages/r-complexheatmap/package.py | Python | lgpl-2.1 | 2,281 | [
"Bioconductor"
] | 9e3a384e5e616eee4fd14e0169f081f9c3411fe2b1e1ad37d010038a63a47ba7 |
# Copyright (c) 2015, Imperial College London
# All rights reserved.
#
# 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 condi... | london-escience/libhpc-cf | libhpc/wrapper/bio/gatk.py | Python | bsd-3-clause | 6,490 | [
"BWA"
] | 15b87f1667961f4cf874e993dbf94a096cf5ac00af403e63ec6d0599d94d7a98 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import re
import time
import xml.etree.ElementTree as etree
from .common import InfoExtractor
from ..compat import compat_urlparse
from ..utils import (
unescapeHTML,
urlencode_postdata,
unified_timestamp,
ExtractorError,
)
MSO_INFO = {... | nickleefly/youtube-dl | youtube_dl/extractor/adobepass.py | Python | unlicense | 34,057 | [
"COLUMBUS",
"Elk"
] | f98f2a9ffd33978f88b73117826a6625f04b2e867eb28ad98ee793b87f1b709e |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# 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... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/toolkits/Gecko/bookmarks.py | Python | gpl-3.0 | 11,798 | [
"ORCA"
] | 4af5e6097ebc879448c7ce736d1f4cf1a7f6adc0d89f74a0611555bc3cd87811 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004 Martin Hawlisch
# Copyright (C) 2004-2006, 2008 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/o... | beernarrd/gramps | gramps/plugins/export/exportgeneweb.py | Python | gpl-2.0 | 19,397 | [
"Brian"
] | 867da6bca80755e6663016846a671336b328c1d80f74f46e18ac6a570da90275 |
#!/usr/bin/env python3
"""Create amplicon variant table."""
import argparse
import json
from collections import defaultdict
import HTSeq
def parse_arguments():
"""Parse command line arguments."""
parser = argparse.ArgumentParser(description="Create amplicon variant table.")
parser.add_argument("master_fi... | genialis/resolwe-bio | resolwe_bio/tools/make_amplicon_table.py | Python | apache-2.0 | 7,008 | [
"HTSeq"
] | 420f37332f6f039fb8a2a1010bf6375a6ba978b4fb9efdb37e69f3629c6edba7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# 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) any later version.
#
... | napkindrawing/ansible | lib/ansible/modules/files/acl.py | Python | gpl-3.0 | 11,720 | [
"Brian"
] | 467a32728e44d995c6b1d869a413f988e8b838823a937f941f4ed4aa02503f1b |
import numpy as np
from datetime import datetime
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
def nc_create_roms_file(filename, grd, ocean_time, lgrid=True):
# create file
nc = netCDF.Dataset(filename, 'w', format='NETCDF3_64BIT')
nc.Description = 'ROMS file'
nc.Author = 'pyroms... | kshedstrom/pyroms | pyroms_toolbox/pyroms_toolbox/nc_create_roms_file.py | Python | bsd-3-clause | 8,491 | [
"NetCDF"
] | 2a18fe843e87fefd43ff5f5274a0c0a66972fd3c45f0e72b34a0ba8019761a4e |
from vpython import *
# Bruce Sherwood
N = 4 # N by N by N array of atoms
# Surrounding the N**3 atoms is another layer of invisible fixed-position atoms
# that provide stability to the lattice.
k = 1
m = 1
spacing = 1
atom_radius = 0.3*spacing
L0 = spacing-1.8*atom_radius
V0 = pi*(0.5*atom_radius)**2*L0 # initial vo... | mwcraig/vpython-jupyter | Demos_no_notebook/AtomicSolid.py | Python | mit | 4,295 | [
"CRYSTAL"
] | 09bcef291009fb28111a7328ededcf6fa0606780f1986dbad6d444acff62fec7 |
# Copyright 2020 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 agreed to in writing,... | google/qkeras | experimental/lo/dense.py | Python | apache-2.0 | 9,414 | [
"ESPResSo"
] | 4a237d84fdc0231676d37745e2b6d154441c26ef2f15387a95f1e6a445532a9b |
#! /usr/bin/env python
# group the genes according to expression level
# analyze RNAseq data by counting tags for each gene using HTSeq.scripts.count or use bedtools muticov
# it genrates a file (K562_htseq_count.out.clean) with two columns, column 1 are gene names, column 2 are
#counts that mapped to all the exon... | crazyhottommy/some-unorganized-old-scripts | python_scripts/metaPlot_at_TSS.py | Python | mit | 5,698 | [
"Bioconductor",
"HTSeq"
] | 255efcb40bf4377036ebe133066295bb067e0494fb9a512183f72b8032bec34f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/topology/test_dlpoly.py | Python | gpl-2.0 | 3,075 | [
"MDAnalysis"
] | 1da03032061f1da6c1c2db92bc66f5a266a76a1627aa0a06842e7ca9b569efc0 |
#!/usr/bin/env python
# This program is public domain
# Author: Paul Kienzle
"""
Read xpeek stream.
XPeek is a class which captures an xpeek data stream and prepares
it for display. You interact with the class by inheriting from
it and overriding the the newstream and newpoint methods.
See the following for a descri... | scattering/ipeek | siopeek/xpeek.py | Python | unlicense | 31,994 | [
"Gaussian"
] | 09880158cf11b97b4c83be061394e87ad4c18efb0444a2c5edc3fede8c93e26e |
# c: 07.05.2007, r: 08.07.2008
from sfepy import data_dir
filename_mesh = data_dir + '/meshes/2d/special/circle_in_square.mesh'
dim = 2
field_1 = {
'name' : 'a_harmonic_field',
'dtype' : 'real',
'shape' : 'scalar',
'region' : 'Omega',
'approx_order' : 1,
}
variables = {
't': ('unknown field'... | olivierverdier/sfepy | tests/test_msm_symbolic.py | Python | bsd-3-clause | 8,733 | [
"VTK"
] | 7f91e726b2f76fdcf9a78fe5ac3292b5fd6017869ded65a6ad4f63e6b2a5cce2 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
# My Stuff
from Entity import Entity
__doc__="The structure class, representing a macr... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/Structure.py | Python | mit | 1,394 | [
"Biopython"
] | bc8daed5ddf844838f38d3f884de5a57f16d66081627b161633fbc687621acc9 |
"""
this pipeline annotation variant calling results in vcf file and then
use provean to predict the effect
"""
import sys,subprocess,os
sys.path.append('/home/shangzhong/Codes/Pipeline')
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from Modules.f11_snpEff_provean import *
from Modules.p01_File... | shl198/Pipeline | VariantCall/05_snpEff_Provean_Vari_Annotation.py | Python | mit | 7,668 | [
"BLAST"
] | f18925d063cbf6a3b5cca1b6fd30a7d43813854d677b3eb6dec7e840260c1c39 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/procrouting/dft/lda_functionals.py | Python | lgpl-3.0 | 1,349 | [
"Psi4"
] | 6ded45e447665bf22d5dc8d81f73a5900da99430cd44b6112baaf877ee02f10d |
__author__ = "Mark Santcroos, Andre Merzky, Ole Weidner"
__copyright__ = "Copyright 2015, The RADICAL Project"
__license__ = "MIT"
""" TORQUE job adaptor implementation
"""
import threading
import saga.url as surl
import saga.utils.pty_shell as sups
import saga.adaptors.base
import saga.adaptors.c... | telamonian/saga-python | src/saga/adaptors/torque/torquejob.py | Python | mit | 46,103 | [
"Jaguar"
] | 60d416e5a88dc125b9993bf86becc93f805bcd9e9a0d16af87623224b0c42927 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Sof... | andrebellafronte/stoq | stoqlib/net/calendarevents.py | Python | gpl-2.0 | 14,125 | [
"VisIt"
] | 58815065806d9cd4d2bac0aadd09ba04027f9ae0eced10d7c6bf2f543560c5e9 |
#! /usr/bin/env python
from MDAnalysis import *
import numpy
import math
import sys
my_pdb = sys.argv[1]
my_traj = sys.argv[2]
u = Universe(my_pdb,my_traj)
v = Universe(my_pdb)
fout_name = 'pepdist123.dat' + str(my_traj)
# helices
a1 = u.selectAtoms("segid A and resid 28")
a2 = u.selectAtoms("segid A and resid 98"... | demharters/git_scripts | dist_pep123.py | Python | apache-2.0 | 865 | [
"MDAnalysis"
] | 682073f4531ff6b2de71bf27c4fbe0aaaed30e3bd68c36a79617d084fad78625 |
"""
DictCache.
"""
__RCSID__ = "$Id$"
import datetime
# DIRAC
from DIRAC.Core.Utilities.LockRing import LockRing
class DictCache( object ):
"""
.. class:: DictCache
simple dict cache
"""
def __init__( self, deleteFunction = False ):
"""
Initialize the dict cache.
If a delete function is sp... | miloszz/DIRAC | Core/Utilities/DictCache.py | Python | gpl-3.0 | 4,838 | [
"DIRAC"
] | 0ef30b553bbdb67f80d96f911e0de0af7616137bdf914587df225adf5bc743de |
from __future__ import print_function
def driver(*args):
'''
the first argument is for the spectra stack normalization, and it can be one of these three options: 'Ha', 'Hb', 'UV', 'none'
the second argument shows which line you want to fit a gaussian to: 'Ha', 'Hb', 'oiii', 'oii'
if you want a second ... | IreneShivaei/specline | stack_driver.py | Python | mit | 3,417 | [
"Gaussian"
] | 683c6874a6ae89a52fb321ff29e72a8192fe94bcbc651d33596e7e22818155f7 |
#!/bin/env python
# -*- coding: utf-8 -*-
"""
Created on 31.03.17
Created for pymepps-streaming
@author: Tobias Sebastian Finn, tobias.sebastian.finn@studium.uni-hamburg.de
Copyright (C) {2017} {Tobias Sebastian Finn}
This program is free software: you can redistribute it and/or modify
it under the ter... | maestrotf/pymepps-streaming | tests/stream/test_ncsubset.py | Python | gpl-3.0 | 5,370 | [
"NetCDF"
] | 11186503c1261c2b99bd9f57dbedb4fe6b67d63052b4ccdf91482aaaf80cda88 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Basis Set Support
##########################
Specific functions for NWChem basis set support.
"""
import numpy as np
def cartesian_ordering_function(l):
"""
Generates a... | alexvmarch/atomic | exatomic/nwchem/basis.py | Python | apache-2.0 | 1,208 | [
"NWChem"
] | 7c9befb0a42dc05e3c805fa75a7c3a116c650fbde6d3c71c5054235078ba09a8 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/dialogs/receivingdialog.py | Python | gpl-2.0 | 4,733 | [
"VisIt"
] | 1235f16568356542787491ec2f90bc87d4dd8a1a41493ce59c27c2b1510d342b |
#!/usr/bin/env python
import numpy as np
import h5py
import argparse
import roditore.utils.image_utils as imutils
def remove_short_edges(corrmat, index, dimensions, radius):
neighbourhood = imutils.voxel_neighbourhood(radius, dimensions)
voxelmap = imutils.voxel_map(index)
for i in xrange(0, len(inde... | adliska/roditore | src/roditore/network/remove_short_edges.py | Python | gpl-3.0 | 2,510 | [
"NEURON"
] | 27eae7a473317c1260bce167e88638ac9fa32985f60181d14acbfcc55b0b3e5e |
import os
import vtkAll as vtk
from shallowCopy import shallowCopy
def readPolyData(filename, computeNormals=False):
ext = os.path.splitext(filename)[1].lower()
readers = {
'.vtp' : vtk.vtkXMLPolyDataReader,
'.vtk' : vtk.vtkPolyDataReader,
'.ply' : vtk.vtkPLYReader,
... | edowson/director | src/python/ddapp/ioUtils.py | Python | bsd-3-clause | 2,800 | [
"VTK"
] | 712c466806c87423146c27554c9846b48ffd105dcdc77070dc9c2c9815ae8a5a |
import astropy.io.fits as fits
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as p
import numpy as n
import os
import sys
from scipy.stats import scoreatpercentile as sc
from scipy.interpolate import interp1d
survey = sys.argv[1]
z_min, z_max = 0., 1.6
imfs = ["Chabrier_ELODIE_", "Chabrier_MILES_",... | JohanComparat/pySU | spm/bin_SMF/create_table_snr.py | Python | cc0-1.0 | 8,566 | [
"Firefly",
"Galaxy"
] | 15bcb4d8ca0f7fa8e319071d5f08522c40609612ada058f3fdb7a3214ba08cd2 |
from numpy.testing import TestCase, run_module_suite, assert_,\
assert_raises
from numpy import random
from numpy.compat import asbytes
import numpy as np
class TestMultinomial(TestCase):
def test_basic(self):
random.multinomial(100, [0.2, 0.8])
def test_zero_probability(self):
random... | devs1991/test_edx_docmode | venv/lib/python2.7/site-packages/numpy/random/tests/test_random.py | Python | agpl-3.0 | 19,954 | [
"Gaussian"
] | be4e567f32a38097bd18a6a0a1bc62615ce6daa27958422f26bcf1ff2d268da3 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-14 22:51:01 by Brian McFee <brian.mcfee@nyu.edu>
"""Unit tests for display module"""
# Disable cache
import os
try:
os.environ.pop("LIBROSA_CACHE_DIR")
except KeyError:
pass
from packaging import version
import pytest
matplotlib = pytest.im... | bmcfee/librosa | tests/test_display.py | Python | isc | 25,590 | [
"Brian"
] | ff480c081dcfb88d6319ebe2366fa5227f465b74cd8cf432e617c49951c3edf4 |
# LiuTaoTao github.com/Bookaa/LiuD
from libforgen import *
def GenPython01(mod):
assert isinstance(mod, LiuD_Module)
visit = Visit_Gen01()
mod.walkabout(visit)
grmlst = visit.AllLst()
return grmlst, visit.sample_text
class Visit_Gen02(LiuD_sample_visitor_01):
def __init__(self, cur_syntax, ar... | Bookaa/LiuD | GenPythonSrc.py | Python | mit | 58,880 | [
"BLAST",
"VisIt"
] | 65e4f0b56d0ce629ef7c8a19059f98173f4a4acfff80b516558269c150b471ae |
#!/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/prop/polarizability/uks.py | Python | apache-2.0 | 3,011 | [
"PySCF"
] | c94d4729686017701eb67f4fd2780e661814008e13b32a41c530767d8985e6c4 |
#!/usr/bin/env python
import ast
import os.path
from setuptools import setup, find_packages
class GetVersion(ast.NodeVisitor):
def __init__(self, path):
with open(path) as f:
self.visit(ast.parse(f.read(), path))
def visit_Assign(self, node):
if any(target.id == 'VERSION' for targ... | Elec/django-bitfield | setup.py | Python | apache-2.0 | 1,561 | [
"VisIt"
] | c36228f26116086992767952935878498a97d60c104cdf3c6d6172a8be5ac266 |
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