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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
restart_particles - create a spawning file for particle tracking based on the
end position on a particle tracking run
restart_particles -i Input_file -o Output_file Date Time
Input_file - name of the netcdf fi... | tiagoams/python_tools | restart_particles.py | Python | gpl-3.0 | 3,599 | [
"NetCDF"
] | 637047698ae77b85a7d8b07bca35be18295eefca18e049c1f1f7e9c2fa0e5f83 |
#!/usr/bin/env python
"""
Create generic LPU and simple pulse input signal.
"""
from itertools import product
import sys
import numpy as np
import h5py
import networkx as nx
def create_lpu(file_name, lpu_name, N_sensory, N_local, N_proj):
"""
Create a generic LPU.
Creates a GEXF file containing the neu... | cerrno/neurokernel | examples/generic/data/gen_generic_lpu.py | Python | bsd-3-clause | 9,588 | [
"NEURON"
] | 7b7700b9eae6facf737112ea46c482aa142b4d56502140fd5b7d709136438ce1 |
"""
This is used to test the MySQLDB module.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import sys
import time
import pytest
import DIRAC
from DIRAC import gLogger, gConfig
from DIRAC.Core.Utilities import Time
from DIRAC.Core.Utilities.M... | yujikato/DIRAC | tests/Integration/Core/Test_MySQLDB.py | Python | gpl-3.0 | 9,133 | [
"DIRAC"
] | c5957930c1f3208df1390ffb10c2fb5412116fb422c826b3f6c651c4fdf83e0e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
import os
from rmgpy import getPath
from rmgpy.qm.main import QMSettings, QMCalculator
from rmgpy.molecule import Molecule
import qmdata
class TestQMSettings(unittest.TestCase):
"""
Contains unit tests for the QMSettings class.
"""
def setUp(self):
"... | faribas/RMG-Py | rmgpy/qm/mainTest.py | Python | mit | 10,829 | [
"Gaussian",
"MOPAC",
"Molpro"
] | 7c4821d5676170e7ac12d2a585c710c3cf192f5fbe638fe4420e2f41ee2be431 |
#!/usr/bin/env python
"""
Blast XML parser that extracts the best hits for each query sequence
and presents the results in order by e-value in
tab-separated format
Author: Mauricio Barrientos-Somarribas
Email: mauricio.barrientos@ki.se
Copyright 2014 Mauricio Barrientos-Somarribas
Licensed under the Apache License,... | maubarsom/biotico-tools | python/blastxml_hitsort.py | Python | apache-2.0 | 5,419 | [
"BLAST"
] | 919e06be687d13240cd850c43300c55dc1b4d8d21cd9843cbe3bd3c1f52266cd |
import numpy as np
import tomviz.utils
from vtk import vtkImageData
_installed = False
try:
from databroker import catalog
from databroker.queries import TimeRange
_installed = True
except ImportError:
pass
def installed():
return _installed
def catalogs():
cats = []
for name, cat in ... | OpenChemistry/tomviz | tomviz/python/tomviz/io/_databroker.py | Python | bsd-3-clause | 2,539 | [
"VTK"
] | fc986deafb7a792c3f777ee349fb91f8ad8d60d250b6d25c0cfcab4d19de7b51 |
#!/usr/bin/python
import urllib2
import json
import cgi
import cgitb
#cgitb.enable()
class City :
def __init__(self,Name,Tags,Weather,Picture,Points) :
self.Points = Points
self.Name = Name
self.Weather = Weather
self.Tags = Tags
class Result :
def __init__(self,Name,Price,O... | arunrawlani/wutodo | Python-scripts/Main.py | Python | apache-2.0 | 6,951 | [
"VisIt"
] | 67dbc00189f2059ca8d9b9541c6b757c36d9cf1987c619add4bb884d05e9f28d |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO parser for Exonerate vulgar output format."""
import re
from Bio._py3k i... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py | Python | gpl-2.0 | 8,131 | [
"Biopython"
] | 580fcaec3638147b53d3849aa7306d4811892665cecad6b28fd123712384ed6e |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | tlksio/tlksio | env/lib/python3.4/site-packages/pylint/lint.py | Python | mit | 45,233 | [
"VisIt"
] | 5970584b18436927c7c487bb9e3a1ff3424ae7940706e47ffe8dc56050382b93 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/util/tests/test_misc.py | Python | bsd-3-clause | 8,027 | [
"scikit-bio"
] | 9d024840a67f65ba922a1420e93f5b0d447382d327b625388dd0600082d96356 |
# -*- coding: utf-8 -*-
# MLC (Machine Learning Control): A genetic algorithm library to solve chaotic problems
# Copyright (C) 2015-2017, Thomas Duriez (thomas.duriez@gmail.com)
# Copyright (C) 2015, Adrian Durán (adrianmdu@gmail.com)
# Copyright (C) 2015-2017, Ezequiel Torres Feyuk (ezequiel.torresfeyuk@gmail.com)
# ... | MachineLearningControl/OpenMLC-Python | MLC/Population/Creation/MixedRampedGauss.py | Python | gpl-3.0 | 3,192 | [
"Gaussian"
] | 99eb74cf70a64bc897daf32d90336f3bc591398cf3df27bec3180afdb0d0586a |
"""Fonction qui peuvent etre appelees a l'interieur
d'un programmable filter ou programmable source
remplacement de UPDATE_TIME_STEPS par UPDATE_TIME_STEP
dans la version 3.4
"""
try: from paraview import vtk
except: import vtk
#_________________________________________________________________________________... | aurmarsan/pyturbo | fonctions_gestion_temps_paraview.py | Python | mit | 4,058 | [
"ParaView",
"VTK"
] | 458bb8a56bc10fd79e0156df416559f4b0ea5536bdba88707ba81e76c7ceb0bc |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose | moose-examples/snippets/reacDiffBranchingNeuron.py | Python | gpl-3.0 | 8,284 | [
"MOOSE",
"NEURON"
] | 865c94cc3f2968c6df056b9fd634b7bb6ff6fb7b566beefb85308f03558efa4e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Views tests for the OSF."""
from __future__ import absolute_import
import datetime as dt
import httplib as http
import json
import time
import pytz
import unittest
from flask import request
import mock
import pytest
from nose.tools import * # noqa PEP8 asserts
from d... | Nesiehr/osf.io | tests/test_views.py | Python | apache-2.0 | 206,502 | [
"Brian",
"VisIt"
] | aa3efbf375469c9c0f4c9601138bbc40f20a41060860064e7e24df2e027242ea |
#config.py - pyMCS configuration file
###################
### FITS FILE: ####
###################
#Name of the image (use * for multiple images):
FILENAME = 'in.fits'
#number of files (will disappear soon):
FILE_NB = 1
##########################
### General parameters ###
##########################
#True for showing... | COSMOGRAIL/COSMOULINE | sampleconfig/template_pyMCS_psf_config.py | Python | gpl-3.0 | 4,717 | [
"Gaussian"
] | 040ad28f8c3fe691da2616329ccd4f7851735c79d17132769da51ffc4f98d570 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/ci/__init__.py | Python | apache-2.0 | 1,298 | [
"PySCF"
] | c9e630b701b8c006f3c1b338d4846b53116c277c26db3b98529269965a6f992a |
# -*- coding: utf-8 -*-
"""
=====================
Cython related magics
=====================
Magic command interface for interactive work with Cython
.. note::
The ``Cython`` package needs to be installed separately. It
can be obtained using ``easy_install`` or ``pip``.
Usage
=====
To enable the magics below,... | thedrow/cython | Cython/Build/IpythonMagic.py | Python | apache-2.0 | 12,030 | [
"Brian"
] | e4239940ba25853f07e286d6d39a46c65bc33e9944fe090d13e93f7e93b89aed |
# coding: utf-8
"""
=======
Presets
=======
This notebook demonstrates how to use the `presets` package to change the
default parameters for librosa.
"""
# Code source: Brian McFee
# License: ISC
##################################################
# We'll need numpy and matplotlib for this example
from __future__ imp... | r9y9/librosa | docs/examples/plot_presets.py | Python | isc | 3,179 | [
"Brian"
] | 43e09d08d7a451a94dc379ca06879c015242c3c8466949fb56df03a2c92d32b9 |
d=dump("post/dump.movingMesh")
v=vtk(d)
v.manyGran("post/vtk_out")
| tm1249wk/WASHLIGGGHTS-2.3.7 | examples/LIGGGHTS/Tutorials_public/movingMeshGran/post.py | Python | gpl-2.0 | 67 | [
"VTK"
] | 2ae3a7f4a24b1a52e856ba2e013b52a3d26c24e5e6e13fffd5f948b75e3ad1c3 |
########################################################################
# $HeadURL$
########################################################################
""" GraphData encapsulates input data for the DIRAC Graphs plots
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/... | Sbalbp/DIRAC | Core/Utilities/Graphs/GraphData.py | Python | gpl-3.0 | 17,307 | [
"DIRAC"
] | 4443168cd6a0f605142fad857497346e623a057da27c8d3a2a978bb3660de407 |
# coding: utf-8
# Copywrite (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
"""
Utility script to find if endpoint slabs are matching with substrate
Usage: Provide inputs <path to poscar substrate>, <path to poscar 2D> and
ma... | henniggroup/MPInterfaces | mpinterfaces/tests/eg_lma.py | Python | mit | 1,874 | [
"pymatgen"
] | c92bca6f07b0f49049afcfa3a745381dbf49f886b4d6db9dc0975bf27c8b4039 |
"""Next gen sequence alignments with Bowtie2.
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
"""
import os
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance import do
from bcbio import bam, utils
from bcbio.pipeline import datadict as dd
fr... | lbeltrame/bcbio-nextgen | bcbio/ngsalign/bowtie2.py | Python | mit | 6,947 | [
"Bowtie",
"Galaxy"
] | 588b93414b3979833778ce17a92cb6fa9858cc58d0f9004b3e4b4d37b7b0e370 |
import datetime
from glob import glob
import os
from shutil import rmtree
from extractnested import AppropriateFolderName, ExtractNested
"""
This section adapted from https://github.com/keepitsimple/pyFTPclient
"""
import threading
import ftplib
import socket
import time
def setInterval(interval, time... | CI-WATER/erfp_era_interim_process | imports/ftp_ecmwf_download.py | Python | mit | 6,844 | [
"NetCDF"
] | 8272a7c2151ef23e8f125eaa4aac6820b93b1bd33951f5f4eca6643223b2a6a0 |
"""
The B{0install add} command-line interface.
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import sys
from zeroinstall.cmd import UsageError, select
from zeroinstall.injector import model, requirements
syntax = "PE... | dsqmoore/0install | zeroinstall/cmd/add.py | Python | lgpl-2.1 | 976 | [
"VisIt"
] | 6ca237449ede56d860f6989fca65b5c2a2e52b558250cb00d7b83fe8b9567237 |
#!/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/morphforge/management/__init__.py | Python | bsd-2-clause | 11,015 | [
"NEURON"
] | 9a68d9915ea8989b04055d29597b61ee5503c330c42cdbfa5bc653aab3c2f281 |
#! /usr/bin/env python
import quantities as pq
import gdfio
import neo
import os
from active_worker.task import task
from task_types import TaskTypes as tt
@task
def gdf2NeoH5_task(gdf_file, t_start, t_stop, gdf_id_list):
"""
Task Manifest Version: 1
Full Name: gdf2NeoH5_task
Caption: gdf2... | jakobj/UP-Tasks | Elephant/gdf2NeoH5_task/gdf2NeoH5_task.py | Python | gpl-2.0 | 2,401 | [
"NEURON"
] | b960b1bd6d3421e91d99c2022f6f988b039e7242025c4051eea0e90359d786f4 |
# -*- coding: utf-8 -*-
#
#
# Building Module
#
#
#
r"""
.. currentmodule: building
.. autosummary::
"""
from __future__ import print_function
try:
from tvtk.api import tvtk
from mayavi import mlab
except:
print('Layout:Mayavi is not installed')
import pdb
import sys
import os
import logging
impo... | pylayers/pylayers | pylayers/gis/building.py | Python | mit | 3,037 | [
"Mayavi"
] | 5f73c82736981afa355201e890101698e64f2bcdf1089586a4d95193b4fcf340 |
"""
DIRAC Wrapper to execute python and system commands with a wrapper, that might
set a timeout.
3 FUNCTIONS are provided:
- shellCall( iTimeOut, cmdSeq, callbackFunction = None, env = None ):
it uses subprocess.Popen class with "shell = True".
If cmdSeq is a string, it specifies the command string... | Andrew-McNab-UK/DIRAC | Core/Utilities/Subprocess.py | Python | gpl-3.0 | 21,344 | [
"DIRAC"
] | 555d1cee3ad172f8f41906d0c4c7575329e8bff1d81e6a76b9af862e7ab71d86 |
from ase.io import read
from gpaw import GPAW
atoms = read('tio2v2o5.out')
atoms.calc = GPAW(h=0.20,
kpts=(2,2,1),
xc='RPBE')
ncpus = 8
| robwarm/gpaw-symm | gpaw/test/big/scf/trouble/tio2v2o5.py | Python | gpl-3.0 | 172 | [
"ASE",
"GPAW"
] | b7bea8ab3c63892410102a34bcf154f3445347cae78b119441f21446255215dd |
# Copyright (C) 2011-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/ek_eof_one_species_base.py | Python | gpl-3.0 | 13,486 | [
"ESPResSo"
] | 37529132a046eda67e3494d54902ac6af819d5eaf8fdc922cbbc9a9b2cd4ae10 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... | usc-isi/horizon-old | horizon/horizon/base.py | Python | apache-2.0 | 21,915 | [
"VisIt"
] | 1366b63d589351e1a35b465e2320606dc0f2454a156755e88853560dc8a51395 |
''' Blurs all weights in the selected vertex group.
This is still one of my first blender addons, so please keep in mind I may be
implementing various operations badly or just plain wrong.'''
'''
*******************************************************************************
License and Copyright
Copyright 2012 Jor... | assumptionsoup/Blur-Weights | blur_weights.py | Python | gpl-3.0 | 10,843 | [
"Gaussian"
] | e64ffff152b009c23d4422439d68c1d7903040352584c948d5db34ba414a2dad |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import urllib
from datetime import datetime, timedelta
from textwrap import dedent
import pytz
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, CourseUpdateDesc, XBlockFixtureDesc
from common.test.accep... | hastexo/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 53,097 | [
"VisIt"
] | 28b1cb4c809d90125a0eb01459b9218fa84b61acf8af1dcd0155db66e47980ec |
# -*- coding: utf-8 -*-
#
# sensitivity_to_perturbation.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... | hakonsbm/nest-simulator | pynest/examples/sensitivity_to_perturbation.py | Python | gpl-2.0 | 8,864 | [
"NEURON"
] | 447918743e76f2374636901c8349987f4296e7563ac5ab79dd596fee56aa9bb6 |
import subsampling
import Blur
import cv2
import numpy as np
from os import listdir
import csv
class Muestreo:
contador = 0
n = 1
numero = 1
archivoCSV = open("train.csv","w")
def leerDirectorio(self, directorio, columna, fila, id):
for archivo in listdir(directorio):
image = ... | DroneSimon/inteligencia_visual | entrenamiento.py | Python | mit | 1,517 | [
"Gaussian"
] | 7774313544d0bd4b1c7e49b32c84326b00875c766fab1ac3949f6a3bba1ceff2 |
""" RocciEndpoint class is the implementation of the rocci interface to
a cloud endpoint via rOCCI-cli
"""
import os
import json
import subprocess
import tempfile
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.File import makeGuid
from VMDIRAC.Resources.Cloud.Endpoint import Endpoint
__RCSID... | xianghuzhao/VMDIRAC | VMDIRAC/Resources/Cloud/RocciEndpoint.py | Python | gpl-3.0 | 7,205 | [
"DIRAC"
] | 325757934d88ce5ce0a9d9e14572a0ae7d556edf75f6903b3d2343e0eb2056e8 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/images/lib/mediaitem.py | Python | gpl-2.0 | 34,484 | [
"Brian"
] | 3d8a61ccfcb3c4f805be093f2de4bf9734f1a78b8148b86c90fafcb1f9914262 |
##############################################################################
# Copyright (c) 2013-2018, 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... | mfherbst/spack | var/spack/repos/builtin/packages/r-biocstyle/package.py | Python | lgpl-2.1 | 1,898 | [
"Bioconductor"
] | 81f290d2a21a58b0113597ae4e0bbf1affe490866918b1f85674bee24e937cee |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py | Python | lgpl-3.0 | 9,397 | [
"NetCDF"
] | 6ffdf418af5cc6c0c7e362433dd9e3a04bf6c075c7542983074b0eb332ea668e |
#! /usr/bin/env python
"""
Takes m8 blast files and generates a table of taxon hit counts for the
given rank. Columns are input files and rows are taxa. If multiple ranks
given (the default), multiple output files are produced, each with the
rank name appended to the output file name.
"""
import sys
import argparse
imp... | jmeppley/py-metagenomics | count_taxa.py | Python | mit | 17,878 | [
"BLAST",
"Galaxy"
] | 13107c59085ab5ffbc97bf57ed7a412d81d2d98411f74b61add26342bfd459d4 |
import sys, os, time,pysam
import argparse
import tempfile,shutil
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument('-t', '--threads', type=int, action='store',
help='''Threads to use''', required=False, default = 1)
parser.add_argument('-b', '--bamfile', type=str, ac... | namphuon/ViFi | scripts/run_hmms.py | Python | gpl-3.0 | 3,766 | [
"pysam"
] | 20ff88defa9f56bc526c84f6232e991afc1470acc92ae6e30a62aeff87399c2a |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
im... | harterj/moose | python/MooseDocs/extensions/listing.py | Python | lgpl-2.1 | 9,682 | [
"MOOSE"
] | eb8e1e2670821f192281aa897cb0f0a53ac9710e742ef2d51937291d0a635fa1 |
# Copyright 2015 Google Inc. 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 applicable law or ag... | KaranToor/MA450 | google-cloud-sdk/lib/surface/feedback.py | Python | apache-2.0 | 5,409 | [
"VisIt"
] | f44e2586e46a0e3312c121bb94c93aea9c3990c5f7daa3fa2bf74b001823a4cf |
#
# QAPI visitor generator
#
# Copyright IBM, Corp. 2011
# Copyright (C) 2014-2016 Red Hat, Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the CO... | shannonz88/qemu | scripts/qapi-visit.py | Python | gpl-2.0 | 10,548 | [
"VisIt"
] | 2e8df82b35c1c80fdb31ceaf96816c1b7eb170753ce0ffc1e2f06c23a7f7cc58 |
""" X509Chain is a class for managing X509 chains with their Pkeys
Link to the RFC 3820: https://tools.ietf.org/html/rfc3820
In particular, limited proxy: https://tools.ietf.org/html/rfc3820#section-3.8
There are also details available about Per-User Sub-Proxies (PUSP)
here: https://wiki.egi.eu/wiki/Usage_of_the_per_... | ic-hep/DIRAC | src/DIRAC/Core/Security/m2crypto/X509Chain.py | Python | gpl-3.0 | 38,633 | [
"DIRAC"
] | a611344ec25e17521780ee81aaed8209555d51569aa82858af8ddcec049e4897 |
from ase import Atoms
from gpaw import GPAW, PW
from gpaw.mpi import rank, size, serial_comm
from gpaw.xc.hybridg import HybridXC
a = 2.0
li = Atoms('Li', cell=(a, a, a), pbc=1)
for spinpol in [False, True]:
for usesymm in [True, False, None]:
if size == 8 and not spinpol and usesymm:
continue
... | robwarm/gpaw-symm | gpaw/test/pw/hyb.py | Python | gpl-3.0 | 1,880 | [
"ASE",
"GPAW"
] | 9fe4001b440aca0dfa710acfb025721f0b0460a116387287be5e2a2cbf0743b2 |
# -*- coding: utf-8 -*-
# @Author: Zachary Priddy
# @Date: 2016-10-13 19:02:52
# @Last Modified by: Zachary Priddy
# @Last Modified time: 2016-10-13 22:18:43
'''
IFTTT API
This API uses the IFTTT Maker channel to send commands to firefly
The URL will be the public facing address of your Serenity web interface:
h... | zpriddy/Firefly | Firefly/core/api/ifttt.py | Python | apache-2.0 | 1,958 | [
"Firefly"
] | 8c5e2837e773bc330aedc1a78d38a4ce106bc6a7cc57a7e8cab4b1fd50422208 |
# $Id$
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" command line utili... | rdkit/rdkit-orig | rdkit/ML/ScreenComposite.py | Python | bsd-3-clause | 54,939 | [
"RDKit"
] | 360faffa4bbb1e58de2a6599e77979b004171387a72217da7c419ddc11c92ec3 |
import rdflib
from rdflib import Namespace
class GOXRef:
@classmethod
def AGI_LocusCode(cls):
"""Returns the link-out URI for objects of "Arabidopsis Genome Initiative".
"""
cls.Namespace("http://arabidopsis.org/servlets/TairObject?type=locus&name=")
@classmethod
def ApiDB_P... | BioInterchange/BioInterchange | supplemental/python/biointerchange/goxref.py | Python | mit | 38,007 | [
"BLAST",
"VMD"
] | 1e608986987478a416921a0f1762f2c61b4ee308d22cbc94e9a36716a4c6670d |
"""
Recurrent layers.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import copy
import theano
import theano.tensor as TT
# Nicer i... | wavelets/GroundHog | groundhog/layers/rec_layers.py | Python | bsd-3-clause | 34,050 | [
"Gaussian"
] | 6ee43cec699de42f1f63dc31a5c0eab54cf94d5e34eb940848f1b53617990808 |
from allensdk.model.biophys_sim.neuron.hoc_utils import HocUtils
import logging
class Utils(HocUtils):
_log = logging.getLogger(__name__)
def __init__(self, description):
super(Utils, self).__init__(description)
self.stim = None
self.stim_curr = None
self.sampling_rate = N... | wvangeit/AllenSDK | doc_template/examples/multicell/utils.py | Python | gpl-3.0 | 4,092 | [
"NEURON"
] | cc02cf6bda51bcde9d0f46d29fbf417ddab408111f4ebbb2fb9a884a4e5f3286 |
import numpy as nm
import sfepy.discrete.fem.periodic as per
from sfepy.discrete.fem.mesh import Mesh
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.homogenization.utils import define_box_regions
import sfepy.homogenization.coefs_base as cb
from sfepy import data_dir
# material function
d... | RexFuzzle/sfepy | examples/homogenization/homogenization_opt.py | Python | bsd-3-clause | 5,067 | [
"VTK"
] | 2e92f77548b9f73658559d68bfc2c44ff8f9e1e8c2027e43a05f21a6625ef90d |
# -*- coding: utf-8 -*-
#
# balancedneuron.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 the License,... | weidel-p/nest-simulator | pynest/examples/balancedneuron.py | Python | gpl-2.0 | 7,350 | [
"NEURON"
] | c600965373fc92ada008f59abc7d808138e4d67ad2537c6f5e8140e3bc1c0299 |
../../../../../../../share/pyshared/orca/scripts/apps/acroread/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/acroread/script.py | Python | gpl-3.0 | 72 | [
"ORCA"
] | eeb37cad664416ff2dd23a90d892a862584cd54167560e90c0a7c81ab09f9d39 |
"""
:mod: ReqClient
.. module: ReqClient
:synopsis: implementation of client for RequestDB using DISET framework
"""
import os
import time
import random
# # from DIRAC
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.Utilities.List import randomize, fromC... | miloszz/DIRAC | RequestManagementSystem/Client/ReqClient.py | Python | gpl-3.0 | 23,244 | [
"DIRAC"
] | b8ff1cf4dea3b6b22a4a3314b0ecd0bb720b99eb7271fc133b5191cfe5c986dd |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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... | mjeanson/jenkins-job-builder | jenkins_jobs/modules/scm.py | Python | apache-2.0 | 53,879 | [
"Octopus"
] | 630803e6722acf26d32776e6ee7e0139a1e04965ddf21c61b00cf95b9806af31 |
# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
Implementation for `pmg query` CLI.
"""
import json
import re
from monty.serialization import dumpfn
from tabulate import tabulate
from pymatgen.ext.matproj import MPRester
def do_query(args):
"""
Perform query t... | vorwerkc/pymatgen | pymatgen/cli/pmg_query.py | Python | mit | 2,062 | [
"pymatgen"
] | fa4e821dc4ed3c0d91ffa5243c36147533c057d278bd51316df42668da89a15f |
UPDATED_SLUGS = {
"2010": "parl.2010-05-06",
"2015": "parl.2015-05-07",
"gb-sp-2016-05-05-c": "sp.c.2016-05-05",
"gb-sp-2016-05-05-r": "sp.r.2016-05-05",
"gla-2016-05-05-a": "gla.a.2016-05-05",
"gla-2016-05-05-c": "gla.c.2016-05-05",
"local.barnet.underhill.2016-05-05": "local.barnet.2016-05... | DemocracyClub/yournextrepresentative | ynr/apps/ynr_refactoring/constants.py | Python | agpl-3.0 | 5,454 | [
"Dalton"
] | ecb4870c0c0e87a933949ce60ad427f3bb144a03c003fc8b4cb6e11ba7f1bba9 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | kbrebanov/ansible | lib/ansible/modules/network/avi/avi_alertscriptconfig.py | Python | gpl-3.0 | 3,488 | [
"VisIt"
] | c9e2804a9e03b087f5d73b4ffad61389d104d652a44026adf882b3ea26ba25c0 |
"""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... | xuewei4d/scikit-learn | sklearn/mixture/_gaussian_mixture.py | Python | bsd-3-clause | 28,270 | [
"Gaussian"
] | 0159fbb2e96df8806497222eb8bf3f4922c00d3dec14e1eeb2e463b8186aaa8e |
# coding=utf-8
"""
InaSAFE Disaster risk assessment tool developed by AusAid -
**IS Utilities implementation.**
Contact : ole.moller.nielsen@gmail.com
.. note:: 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 Fre... | easmetz/inasafe | safe/utilities/utilities.py | Python | gpl-3.0 | 13,149 | [
"VisIt"
] | 9cf5c018f95ddfe2f7e2022bb6f1e4b56b280ea8df8d662c3da888b18f2d3d83 |
'''
DiagGaussObsModel.py
Multivariate, full-mean, diagonal-covariance Gaussian observation model.
See Also
--------
GaussObsModel, for full-covariance Gaussians.
'''
import numpy as np
import scipy.linalg
import os
from ..distr import GaussDistr
from ..distr import GaussGammaDistr
from ..util import LOGTWO, LOGPI, ... | daeilkim/refinery | refinery/bnpy/bnpy-dev/bnpy/obsmodel/DiagGaussObsModel.py | Python | mit | 6,701 | [
"Gaussian"
] | 1711ef6734e528ffe67e42411ed9b9297d48bac504a96f8d755eca310cf16fad |
#!/usr/bin/python3
import sys
import numpy as np
import os
import __main__ as main
import pyProbeParticle as PPU
from pyProbeParticle import basUtils
from pyProbeParticle import elements
import pyProbeParticle.GridUtils as GU
#import pyProbeParticle.core ... | ProkopHapala/ProbeParticleModel | generateElFF.py | Python | mit | 5,012 | [
"Gaussian"
] | 6889cbba576639a930a776b56f6e3cb9cc52705cda3ca7ad0e9cf63f23bfe1e5 |
'''
Random field generation using rft1d.randn1d
Note:
When FWHM gets large (2FWHM>nNodes), the data should be padded
using the *pad* keyword.
'''
import numpy as np
from matplotlib import pyplot
from spm1d import rft1d
#(0) Set parameters:
np.random.seed(12345)
nResponses = 5
nNodes = 101
FWHM = 20.0
... | 0todd0000/spm1d | spm1d/rft1d/examples/random_fields_1.py | Python | gpl-3.0 | 635 | [
"Gaussian"
] | 0b617c3bf5570edd83ef5a0f2efe888a5913ab55e9ea85f61245c55825f000d6 |
from __future__ import print_function
import unittest
import SimPEG.dask
from SimPEG import (
directives,
maps,
inverse_problem,
optimization,
data_misfit,
inversion,
utils,
regularization,
)
from discretize.utils import meshutils
import shutil
# import SimPEG.PF as PF
from SimPEG.pot... | simpeg/simpeg | tests/dask/test_mag_inversion_linear_Octree.py | Python | mit | 5,816 | [
"Gaussian"
] | 08cc90a3e56e77d9df0a44334aa5ea123b13c076db492102f86f5b0a1332a160 |
"""
More generic ML and DL tools
ML part could contain
- cluster
- decomposition, e.g. SVD, PCA, NMF
- other unmixing (e.g., nonlinear unmixing, tensor factorization, etc.)
- gaussian mixture modelling
Dl part could contain
- cleaning / denoising
- autoencoders
Submodules
----------
.. autosummary::
:toctree: _a... | pycroscopy/pycroscopy | pycroscopy/learn/__init__.py | Python | mit | 532 | [
"Gaussian"
] | ffe1ae402aa21227eaaa964f7aca687121d35cb9617ced4215d6e20981346098 |
#!/usr/bin/env python
## This is call back script which will be executed after created the grib2 files.
##
## Hycom Model Input requires analysis of 06, 09, 12, 15, 18, 21-hours from
## yesterday and 00 & 03-hours from today date. All 3-hourly forecasts from
## today date.
##
## While creating tar ball, all files m... | arulalant/UMRider | bsubScripts/ncum_india_gnc/create_sfc_nc.py | Python | gpl-2.0 | 2,471 | [
"NetCDF"
] | 5c075ecfdc92555420444e4d8c1e1ecd96cf282a55e5eda6bdbf97f3b97e9e71 |
# ----------------------------------------------------------------------------
# pyglet
# Copyright (c) 2006-2008 Alex Holkner
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistribu... | alcemirfernandes/irobotgame | lib/pyglet/graphics/__init__.py | Python | gpl-3.0 | 25,169 | [
"VisIt"
] | eaaebb38409857b7afd82b75dd20adbbecc733833f5083bf23e11a2b5710ca12 |
#
# Copyright (c) 2016, 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 2 only, as
# published by the Free Softwar... | jjfumero/fastr | mx.fastr/mx_fastr_pkgs.py | Python | gpl-2.0 | 17,992 | [
"VisIt"
] | 4487212e0f7d2399f5032d6e8ccfd89263f66e5dc950e05a274f6d333d7720df |
#! /usr/bin/python
# -*- coding: utf8 -*-
import tensorflow as tf
import tensorlayer as tl
import numpy as np
import time
import numbers
import random
import os
import re
import sys
import threading
# import Queue # <-- donot work for py3
is_py2 = sys.version[0] == '2'
if is_py2:
import Queue as queue
else:
... | arcyfelix/ML-DL-AI | Supervised Learning/GANs/dcgan-tensorflayer/tensorlayer/prepro.py | Python | apache-2.0 | 60,321 | [
"Gaussian"
] | 56e39b021af1d40c126d938d6d3965390110f9ef8fd6b2e53ecf3d67fffddc0c |
###########################################################################
#
# 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
#
# https://www.apache.org/l... | google/starthinker | dags/email_to_bigquery_dag.py | Python | apache-2.0 | 5,966 | [
"VisIt"
] | 3578cfa1c141e4330ebe1dccc886eae2461e130bd9f82b748be3e27acb90de50 |
# Copyright (C) 2012-2014 by the Free Software Foundation, Inc.
#
# This file is part of GNU Mailman.
#
# GNU Mailman 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 you... | trevor/mailman3 | src/mailman/runners/tests/test_confirm.py | Python | gpl-3.0 | 10,596 | [
"VisIt"
] | 60ef104dd81a5d3f71142d48145d9cca22d2a3bf0af8657f42d1d5cb3e0231e4 |
import ConfigParser
import sys
from decimal import Decimal
#from interval import Interval, IntervalSet
from collections import defaultdict
import Queue
import multiprocessing
import pandas as pd
import matplotlib
import statsmodels.api as sm
import numpy as np
matplotlib.use('Agg')
from IPython import embed
import m... | jeffhsu3/genda | scripts/test_splice_events.py | Python | bsd-3-clause | 14,617 | [
"pysam"
] | 55509b2a2f633ed9e83f54bedcaf1527bcbb423d50d973928f45207e8166b792 |
# Copyright 2020 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... | tombstone/models | research/object_detection/utils/target_assigner_utils.py | Python | apache-2.0 | 16,121 | [
"Gaussian"
] | 0752fc1c490bf1f3a70956aee3adc8c6292c6d191c7a50076060cea4c4bd8930 |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
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 ... | madscatt/zazzie | src_2.7/sassie/simulate/torsion_angle_md/write_tamd_input.py | Python | gpl-3.0 | 43,980 | [
"CHARMM"
] | 3c99cf791d4deb2cf820022ec3a5175a02ef1d5cd557592ea4e103abb0a99267 |
# -*- coding: utf-8 -*-
#growInstitute.py
import random, time, os, datetime
from splinter import Browser
def centerText(entry, linelength):
### center title
length = len(entry)
spacerLen = int((linelength - length)/2)
spacer = ""
for s in range(spacerLen):
spacer = spacer + " "
return spacer+entry
def do... | plummerfernandez/InstituteOf | growInstitute.py | Python | gpl-2.0 | 2,771 | [
"VisIt"
] | da961eabd367074c1e30b4c58b9a7be3285e8fd5dfcc1b3de179692075efc825 |
# Online haptic_map implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
import os
#import hrl_lib.mayavi2_util as mu
i... | tapomayukh/projects_in_python | rapid_categorization/haptic_map/outlier/online_map_outlier.py | Python | mit | 20,152 | [
"Gaussian",
"Mayavi"
] | dc61f467f501234ab4e4d5a5b239e8cd8ddbe3f9a909e384f37788c462f2f1b6 |
### Highboost filtering
def high_boost(img, img_mblur, c, device, debug):
# High-boost filtering is a method used to sharpen images
# This method will sharpen regions of high contrast while keeping blurred regions intact
# See Digital Image Processsing by Gonzalez and Woods
# img = image for filtering
# img_m... | dlebauer/plantcv | lib/plantcv/dev/high_boost.py | Python | gpl-2.0 | 962 | [
"Gaussian"
] | 92ebf7938a1d9908bab047b5b61c89fbb116962b475cce8bb206e71cc9cd6d2b |
"""
Representations which use local bases function (e.g. kernels) distributed
in the statespace according to some scheme (e.g. grid, random, on previous
samples)
"""
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
from __future__ import unicode_literals
from ... | rlpy/rlpy | rlpy/Representations/LocalBases.py | Python | bsd-3-clause | 7,491 | [
"Gaussian"
] | 52e83f81344330e3c6d8804d4247da8fbfc7f8b0277fdadaca01bc96ad3d22db |
'''
synbiochem (c) University of Manchester 2016
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
import sys
from synbiochem.utils.ice_utils import ICEClient
from synbiochem.utils.net_utils import NetworkError
de... | neilswainston/development-py | synbiochemdev/design/ice_analysis.py | Python | mit | 1,502 | [
"VisIt"
] | 9394583296f8e3ffda1d1918b054f4ce0ba4a74af12fcfbb5b38668d0176624a |
import os
import unittest
from ansiblelint import Runner, RulesCollection
class TestDependenciesInMeta(unittest.TestCase):
def setUp(self):
rulesdir = os.path.join('lib', 'ansiblelint', 'rules')
self.rules = RulesCollection.create_from_directory(rulesdir)
def test_bitbucket_in_meta_dependen... | MatrixCrawler/ansible-lint | test/TestDependenciesInMeta.py | Python | mit | 1,326 | [
"Galaxy"
] | 53c6783cface81353e2c7abff2be8ea262c43af9a47ef7cbd3f82ce04c9ad1db |
#!/usr/bin/python
# This script is for cleaning up of all data from system including
# all transactions and masters (excludes default masters).
# Basically after running this file, system will reset to it's
# initial state.
# This script can be executed from lib/wnf.py using
# lib/wnf.py --cleanup-data
from __fut... | gangadhar-kadam/adb-erp | utilities/cleanup_data.py | Python | agpl-3.0 | 6,562 | [
"VisIt"
] | d8f07d7ce90a226920143fd4bab7733885f76c946ab3ceb3147b2ea752d2f2d9 |
#!/usr/bin/python
# pylint: disable=C0111, C0325
# Upload a contrived ihmpdcc test dataset using osdf-python and cutlass.
import argparse
import logging
import pprint
import sys
from cutlass import iHMPSession, mixs, mims, mimarks
## globals
# hard-coded ID of top-level project node
PROJECT_ID = '3fffbefb34d749c629... | ihmpdcc/cutlass | examples/test-upload.py | Python | mit | 8,902 | [
"VisIt"
] | 2990a8b942c5614bc2aebd7c5443cb7eb6edea9bde7ef104a769c91102e0e8e3 |
"""
A script to generate an input file to the RMG-Java QM Data estimator,
to aid comparison.
"""
from rmgpy.molecule import Molecule
from rmgpy.species import *
from rmgpy.thermo import ThermoData
from rmgpy.statmech import *
from rmgpy.quantity import constants
import rmgpy.qm
import rmgpy.qm.main
import re
folder ... | faribas/RMG-Py | testing/qm/processThermoTest.py | Python | mit | 2,884 | [
"MOPAC"
] | 79a812ccafa278d96282c5f20c15bb824d42e446c396d69b52ebe07164a00b5b |
import random
import h5py
import numpy
from rdkit import Chem
from util import data_validation, file_structure, file_util, misc, process_pool, logger, constants, hdf5_util
class Substructure:
@staticmethod
def get_id():
return 'substructure'
@staticmethod
def get_name():
return 'Su... | patrick-winter-knime/mol-struct-nets | molstructnets/steps/targetgeneration/substructure/substructure.py | Python | gpl-3.0 | 5,888 | [
"RDKit"
] | da7b63d67903219fecc71a4e46c62cc4937164e59134c6e9653e49797d19a79f |
# -*- encoding: utf-8 -*-
# Yuuno - IPython + VapourSynth
# Copyright (C) 2017 StuxCrystal (Roland Netzsch <stuxcrystal@encode.moe>)
#
# 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 Foundation, eit... | stuxcrystal/yuuno | yuuno_ipython/ipython/feature.py | Python | lgpl-3.0 | 1,220 | [
"MOE"
] | 997566038273dcc63e2f6dcc95f69e18f482735fd95633790155d3d569fdc856 |
#
# Copyright (C) 2001-2017 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import collections
from rdkit... | rvianello/rdkit | rdkit/Chem/Descriptors.py | Python | bsd-3-clause | 6,855 | [
"RDKit"
] | 29fb2e987ef778abac2499b3f18f21bd96a90a258cb18be5311205e65417e113 |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | richter-t/espresso | doc/tutorials/python/01-lennard_jones/scripts/lj_tutorial.py | Python | gpl-3.0 | 6,372 | [
"ESPResSo"
] | 6fd6e0f438d2e72c889d0c132b59885b9d44a97aebd47671fa942a7a56ffa975 |
#!/usr/bin/env python
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "... | irinabov/debian-qpid-cpp-1.35.0 | src/tests/acl.py | Python | apache-2.0 | 196,145 | [
"MOE"
] | 61b5ae488cda850b60cac895184df8edd85a70cc74114d10d3c130464cf31272 |
import neuroml as nml
import sys
import os
import pprint
import airspeed
from pyneuroml.pynml import print_comment_v
pp = pprint.PrettyPrinter(depth=4)
def check_brackets(line, bracket_depth):
if len(line)>0:
bracket_depth0 = bracket_depth
for c in line:
if c=='{':
... | rgerkin/pyNeuroML | pyneuroml/neuron/mod/parse_mod_file.py | Python | lgpl-3.0 | 3,330 | [
"NEURON"
] | 034f0484636c328ddf9c661c4de74ee72abcfe9d1d126ce6939c856eea30fae7 |
#
# @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
#... | susilehtola/psi4 | psi4/driver/qcdb/libmintscoordentry.py | Python | lgpl-3.0 | 24,474 | [
"CFOUR",
"Psi4"
] | 1101cebac3adcc1019c57f2efe8138f762d473b3169f566b33b879f389d3585a |
"""
========================================================
Gaussian process regression (GPR) on Mauna Loa CO2 data.
========================================================
This example is based on Section 5.4.3 of "Gaussian Processes for Machine
Learning" [RW2006]. It illustrates an example of complex kernel engine... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/gaussian_process/plot_gpr_co2.py | Python | mit | 5,730 | [
"Gaussian"
] | 573b75c636fd3a402d63e1fd83c1d28aef7badbef8f5095cc904443ac3352cbd |
'''
1. all the functions are defined and built consistently.
Data types:
- Use only numpy arrays to ensure consistency across formatting and type
*** x, x0 = parameters vector - 1D numpy array
*** setang1, setang2 = angles for refinement - 1D numpy arrays, 3 elements
*** hkl1, hkl2 = numpy arrays (3 columns) having... | dymkowsk/mantid | scripts/DiamondAttenuationCorrection/FitTrans.py | Python | gpl-3.0 | 47,617 | [
"CRYSTAL",
"Gaussian"
] | 287520cbc9624d60588551df362c996c89828b196b10305e0f8c937281014fba |
# $Id$
#
# Copyright (C) 2003-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | rvianello/rdkit | rdkit/ML/UnitTestBuildComposite.py | Python | bsd-3-clause | 6,697 | [
"RDKit"
] | b75a318e2e8fe360b3454d3d639d2d6c9e874ec834cf3283cbfb13e54d79a372 |
#!/usr/bin/env python
def rev_test(inr, outr, minFrac=0.0, minPV=0, cap=93, minFM=0):
if inr.opt("FM") < minFM:
return 0
# They have the same family size.
for qin, pvin, fain, qout, pvout, faout in zip(inr.query_qualities, inr.opt("PV")[::-1], inr.opt("FA")[::-1],
outr.query_qualities, ... | ARUP-NGS/BMFtools | sample_test/cap_test.py | Python | mit | 2,337 | [
"pysam"
] | 4cf0b171c9c7b2a667de400a90688343cb0523688557b3dd592fc21c51246ac5 |
"""
Module defining Network class and methods
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
from ..specs import ODict
from neuron import h... | Neurosim-lab/netpyne | netpyne/network/network.py | Python | mit | 7,260 | [
"NEURON"
] | 22f0f207c3de5136955c0babccfef75a144ff1e7397b0020f2453c34a0962693 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# rm - [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 of the GN... | heromod/migrid | mig/cgi-bin/rm.py | Python | gpl-2.0 | 1,092 | [
"Brian"
] | 1a175221724032b5c7dc032d2b2d8a97ae8d96d571bc41663a0b13e72c93be68 |
""" DIRAC.TransformationSystem package """
| DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/__init__.py | Python | gpl-3.0 | 43 | [
"DIRAC"
] | 29395068306fa6a4dfd16c706d820e4a9a4d277e166646da4c6d57056101bcdd |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/simulation/nest_utils.py | Python | gpl-3.0 | 18,052 | [
"NEURON"
] | 1b1edbacc376fa74ce4ab980941ac920ceb4bed417a84c29f6dc8e2a0d504220 |
# -*- coding: utf-8 -*-
# h10.CNG.moose.py ---
#
# Filename: h10.CNG.moose.py
# Description:
# Author: subha
# Maintainer:
# Created: Sat Apr 30 02:10:09 2016 (-0400)
# Version:
# Last-Updated: Sat Apr 30 03:12:18 2016 (-0400)
# By: subha
# Update #: 95
# URL:
# Keywords:
# Compatibility:
#
#
# Commentar... | dharmasam9/moose-core | tests/issues/hsolve/h10.CNG.moose.py | Python | gpl-3.0 | 3,090 | [
"MOOSE",
"NEURON"
] | cc97b22f065f78f9f8b7b8be8c1d38c9cbb8c696778d0c0142c3c48cd889c007 |
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