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"""Test Axis device."""
from copy import deepcopy
from unittest import mock
import axis as axislib
from axis.api_discovery import URL as API_DISCOVERY_URL
from axis.applications import URL_LIST as APPLICATIONS_URL
from axis.applications.vmd4 import URL as VMD4_URL
from axis.basic_device_info import URL as BASIC_DEVICE... | tboyce021/home-assistant | tests/components/axis/test_device.py | Python | apache-2.0 | 14,005 | [
"VMD"
] | d8fefe279d98fd56c471f0fd4df8d21e68c3f45ee7d7c2a0c5b94d56732ae14b |
#########
# ps_drone.py
# (w)+(c) J. Philipp de Graaff, www.playsheep.de, drone@playsheep.de, 2012-2014
# Project homepage: www.playsheep.de/drone and https://sourceforge.net/projects/ps-drone/
# Dependencies: a POSIX OS, openCV2 for video-support.
# Base-program of the PS-Drone API: "An open and enhanced API for unive... | PatrickChrist/CDTM-Deep-Learning-Drones | ps_drone.py | Python | mit | 95,509 | [
"VisIt"
] | 88b0e8cc0b44a357ca5691e6a370854b17701c2c6eff6ce40f94261d33b3c643 |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# Denis A. Engemann <denis-alexander.engemann@inria.fr>
# Michael Eickenberg <michael.eickenberg@inria.fr>... | bnaul/scikit-learn | sklearn/decomposition/_pca.py | Python | bsd-3-clause | 23,545 | [
"Gaussian"
] | 3b4206e0952dac0f4fd4ba7c5f11921fe8857f51e9481c69e6cf9eee50dedea7 |
"""
unittest_motifs.py
Jose Guzman, sjm.guzman@gmail.com
Claudia Espinoza, claudia.espinoza@ist.ac.at
Created: Wed Aug 9 17:49:33 CEST 2017
Unittest environment to test the counting of motifs
"""
import unittest
import numpy as np
from motifs import iicounter, eicounter, iecounter, eecounter
class TestIIMotifCo... | ClaudiaEsp/inet | inet/unittest_motifs.py | Python | gpl-2.0 | 13,861 | [
"NEURON"
] | c6c8069f7344baae8422d4d486836dff2731a40ff0a1249361c9bcc502064df7 |
# Orca
#
# Copyright 2005-2009 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... | h4ck3rm1k3/orca-sonar | src/orca/orca_gui_prefs.py | Python | lgpl-2.1 | 128,646 | [
"ORCA"
] | 64b9d8255fb74c9a7d5ece1a32caf53c9bc2f71f8e5c59f2b94e31d402a8d663 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | mheap/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 11,033 | [
"Galaxy"
] | e2166a22b4d6eda3ab02a6e9265ee1f37ef566d1caeb67cf8d600b0ee86af1c8 |
from openzwave.network import ZWaveNode
from Firefly import logging, scheduler
from Firefly.helpers.device import *
from Firefly.helpers.device.device import Device
from Firefly.helpers.metadata.metadata import action_battery
from Firefly.util.zwave_command_class import COMMAND_CLASS_BATTERY, COMMAND_CLASS_DESC
clas... | Firefly-Automation/Firefly | Firefly/components/zwave/zwave_device.py | Python | apache-2.0 | 7,575 | [
"Firefly"
] | da231a5d6a10cd73001c93385b7e06360d3f592d8affaa116728da93a496acf2 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/logentry.py | Python | lgpl-2.1 | 2,269 | [
"MDTraj"
] | f2dbec87a79599335ef525d485f6bda0c1396d1f37ed2bb7a14a1e1caadc1226 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2016-2018 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser 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 S... | airodactyl/qutebrowser | qutebrowser/browser/browsertab.py | Python | gpl-3.0 | 31,342 | [
"VisIt"
] | 0057a8d9709f8586a7112dde499db1adb7b304dd627f81b81c1a32d668753656 |
#!/usr/bin/env python
"""
@author Luke Campbell <LCampbell@ASAScience.com>
@file ion/services/dm/inventory/dataset_management_service.py
@date Tue Jul 24 08:59:29 EDT 2012
@brief Dataset Management Service implementation
"""
from pyon.public import PRED, RT
from pyon.core.exception import BadRequest, NotFound, Conflict... | ooici/coi-services | ion/services/dm/inventory/dataset_management_service.py | Python | bsd-2-clause | 35,734 | [
"NetCDF"
] | 5bc2627a26d8f61033b8d75cac673121c5fd7f47152c9ef75bd087e9602e4b44 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | grimmjow8/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,066 | [
"Brian",
"Galaxy"
] | 172ee6ac8f642c2bb761f32f51e5ca1267441fc9eed596caef9909bd96c61994 |
# import necessary python packages
import numpy as np
import datetime
import os,sys
import urllib
import cStringIO
import json
from scipy.ndimage.filters import maximum_filter
from scipy.ndimage.morphology import generate_binary_structure, binary_erosion
import dateutil.parser
from matplotlib import pyplot as plt
from... | willettk/rgz-analysis | python/expert_all.py | Python | mit | 37,623 | [
"Galaxy",
"Gaussian"
] | abf970a430821831a8770b180182163a5fd9dbce665ef0bb03b09c120d94d186 |
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 04 07:08:30 2015
@author: Scott
"""
import numpy as np
from neurosrc.spectral.pac import pacfn
from NeuroTools import stgen
import matplotlib.pyplot as plt
# Network parameters
finame = 'pac_mc.hdf5'
Nneu = 100 # Number of neurons
spikeHz_baseline1 = np.arange(20) # Fir... | parenthetical-e/neurosrc | spectral/sim_PACoutput.py | Python | mit | 3,746 | [
"NEURON"
] | 5732e30850c1da9307b53943cb17de4446475908fb7f5d5aa2e6d124c3610632 |
"""
merged implementation of the cache provider
the name cache was not chosen to ensure pluggy automatically
ignores the external pytest-cache
"""
from __future__ import absolute_import, division, print_function
import py
import pytest
import json
import os
from os.path import sep as _sep, altsep as _altsep
class Ca... | tareqalayan/pytest | _pytest/cacheprovider.py | Python | mit | 9,653 | [
"VisIt"
] | ab141ea2169c1b8c6f7bf0475df184f677d79a16d6061b312602ae67d84a7253 |
from brian import *
import time
if __name__=='__main__':
input_freqs = arange(200,450,0.5)
n_inputs = 50
numsims = len(input_freqs)
duration = 2000*ms
v_reset = '''
v = 13.65*mV
v_th = 15*mV
'''
v_rest = 0*mV
tau_mem = 10*ms
refr = 2*ms
eqs = Equations('''
dv/dt = (-... | achilleas-k/brian-scripts | lif_transfer.py | Python | apache-2.0 | 2,425 | [
"Brian"
] | c3438cd962fc7b3caadb809df872426f1cad76f2850470761ed2786c084b5a35 |
# -*- coding: utf-8 -*-
#------------------------------------------------------------------------------
# file: $Id$
# auth: Philip J Grabner <phil@canary.md>
# date: 2014/12/03
# copy: (C) Copyright 2014-EOT Canary Health, Inc., All Rights Reserved.
#--------------------------------------------------------------------... | canaryhealth/canarymd-python | canarymd/client.py | Python | mit | 10,597 | [
"VisIt"
] | 2c06dafb5756f36d77d2478505c4f92f77e3528868474bfb3d02a8fafe6ba85e |
from classylss.binding import ClassEngine, Background, Spectra, Perturbs, Primordial, Thermo
from classylss.astropy_compat import AstropyCompat
import numpy
from six import string_types
import os
import functools
def store_user_kwargs():
"""
Decorator that adds the ``_user_kwargs`` attribute to the class to t... | nickhand/nbodykit | nbodykit/cosmology/cosmology.py | Python | gpl-3.0 | 25,992 | [
"VTK"
] | e9fc5b3b5188bf1cfae2ba2307d9dea267ba05ca4e14d8c0bca65032fc9021ca |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/articles/templatetags/articles.py | Python | gpl-3.0 | 1,076 | [
"Brian"
] | 9f754b15d08aaf7dfeac18810a48bc705093db4b432a89597ce9b40844634992 |
from config import config
if config.IMPORT_PYSAM_PRIMER3:
import pysam
# VCF query
def vcf_query(chrom=None, pos=None, ref=None, alt=None, variant_str=None, individual=None, verbose=False, limit=100, release='mainset_July2016'):
if variant_str:
variant_str=str(variant_str).strip().replace('_','-')
... | logust79/phenopolis | vcf/__init__.py | Python | mit | 12,599 | [
"pysam"
] | 2df7e74340a1481d1c419fcdb92df344a42b6945204e2e3974c639a17302f712 |
import requests
#print requests ## DEBUG
TARGET_URL = "https://dirac3.ba.infn.it:5010/DIRAC/"
#r = requests.get(TARGET_URL,verify=False)
#print r ## DEBUG
#print dir(r) ## DEBUG
#print r.text
#r = requests.get(TARGET_URL+"galaxy",verify=False)
#print r.text
LOGIN = "user_servizio"
PASSWORD = "OO31S3r2tRGEoEiUoqv4O... | SuperDIRAC/TESTDIRAC | WebServerSystem/tmpdir/xalfonso/ora-test.py | Python | gpl-3.0 | 491 | [
"DIRAC",
"Galaxy"
] | 9d03e998ff9abd6f8f38e11656d20018c5f3df975144cd776977358426e57d91 |
#!/usr/bin/python
# 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.
#
# Ansible is distributed... | 0x46616c6b/ansible-modules-core | cloud/ec2_elb_lb.py | Python | gpl-3.0 | 26,567 | [
"Dalton"
] | 916d36d920953f5152393d312d85e39871613580147ab51bdda0ee0d1ab13964 |
# -*- coding: utf-8 -*-
#
# test_parrot_neuron.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 Lice... | zifeo/nest-simulator | pynest/nest/tests/test_parrot_neuron.py | Python | gpl-2.0 | 9,793 | [
"NEURON"
] | e2f6ad739b88f2f384dc49e0ac4ab0c3b6012e3b73df94e5941798be1e7f34f8 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | dezinezync/DZDynamicType | build.py | Python | mit | 6,816 | [
"VisIt"
] | 033dc201cb2f1dc0ee17eff56e7a4023ec4a4712f030f50067d45cb61b23cd3b |
r"""
Incompressible Stokes flow with Navier (slip) boundary conditions, flow driven
by a moving wall and a small diffusion for stabilization.
This example demonstrates the use of `no-penetration` boundary conditions as
well as `edge direction` boundary conditions together with Navier or slip
boundary conditions.
Find... | lokik/sfepy | examples/navier_stokes/stokes_slip_bc.py | Python | bsd-3-clause | 4,819 | [
"VTK"
] | 7a12e74a9bff3bd437f11bc25253f44d84d18bec633da49cb1694387d9d5157c |
"""
@name: Modules/House/Family/insteon/insteon_constants.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Apr 19, 2013
@summary: This module is for communicating with Insteon controllers.
Note! This is... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/insteon_constants.py | Python | mit | 4,802 | [
"Brian"
] | 28e15d033f920d25fce90b06551d125bd7795e66109c081dd59ed3aef60afb61 |
# An implementation of the Scaler interface using CCP4 programs and Aimless.
from __future__ import annotations
import copy
import logging
import math
import os
import re
from xia2.Handlers.CIF import CIF, mmCIF
from xia2.Handlers.Citations import Citations
from xia2.Handlers.Files import FileHandler
from xia2.Hand... | xia2/xia2 | src/xia2/Modules/Scaler/CCP4ScalerA.py | Python | bsd-3-clause | 45,928 | [
"CRYSTAL"
] | 3da192c102ba91391fa308eea8b510fc5badc15e0b022c0385bcd1ff74baf4b8 |
#!/usr/bin/env python
"""script to concatenate the dirac.cfg file's Systems sections with the content of the ConfigTemplate.cfg files."""
import sys
from diracdoctools.cmd.concatcfg import run
from diracdoctools.Config import CLParser
sys.exit(run(**(CLParser().optionDict())))
| fstagni/DIRAC | docs/diracdoctools/scripts/dirac-docs-concatenate-diraccfg.py | Python | gpl-3.0 | 279 | [
"DIRAC"
] | 04a0cb20d7df79ac13749191a58ebbf898430fdcc2eb4245572b3be5dca3168f |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-adsplit/package.py | Python | lgpl-2.1 | 2,170 | [
"Bioconductor"
] | 75d40917b18fc885833e816130b4b7a0b8b964605fc572c5213d17d17a570860 |
#! /usr/bin/python
######
# Copyright 2007-2009 Sun Microsystems, Inc. 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 b... | SunLabsAST/AURA | Bridge/pyaura/var/dump_artists.py | Python | gpl-2.0 | 1,933 | [
"VisIt"
] | 3f1c35ee271495b06c22d67f710df1019880d99f52ca34ebee359d9bfecf8145 |
"""Metrics to assess performance on classification task given class prediction.
Functions named as ``*_score`` return a scalar value to maximize: the higher
the better.
Function named as ``*_error`` or ``*_loss`` return a scalar value to minimize:
the lower the better.
"""
# Authors: Alexandre Gramfort <alexandre.gr... | huzq/scikit-learn | sklearn/metrics/_classification.py | Python | bsd-3-clause | 96,977 | [
"Brian"
] | 2b47f5a77f1d817df855ea841ec46695d61c47c8e6d075851d1d856ebc13b6f5 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Jason Swails
# Contributors: Robert McGibbon
#
# MDTraj is fre... | kyleabeauchamp/mdtraj | mdtraj/tests/test_psf.py | Python | lgpl-2.1 | 4,591 | [
"CHARMM",
"MDTraj",
"VMD"
] | 455335f18b7a0112a25fc8e476c35509465d152e504a7a1f39de766242c5075a |
#!@PYTHON_EXECUTABLE@
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
#... | kannon92/psi4 | psi4/run_psi4.py | Python | gpl-2.0 | 9,299 | [
"Psi4"
] | 8ef3d1405816bc2d9dc3b7139ee0079e1910ec9db054525a1f101fa772c02fd8 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## 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 Softwar... | ostrokach/biskit | scripts/Biskit/amber2traj.py | Python | gpl-3.0 | 2,421 | [
"Amber"
] | 00483b65d4f568bc75001a1d08b582ce795fc348fd0ca00cfb80c8e68ecb6159 |
from __future__ import print_function
__author__ = 'Tom Schaul, tom@idsia.ch; Justin Bayer, bayerj@in.tum.de'
import gc
import pickle
import logging
import threading
import os
import operator
from itertools import count
from math import sqrt
from random import random, choice
from scipy import where, array, exp, zer... | comepradz/pybrain | pybrain/utilities.py | Python | bsd-3-clause | 24,382 | [
"NetCDF"
] | 872975aef280a71fbd4df825f1c71316b52e09bbee2d712f21d3179e0d95ed08 |
# (C) British Crown Copyright 2010 - 2018, 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... | dkillick/iris | lib/iris/cube.py | Python | lgpl-3.0 | 154,273 | [
"NetCDF"
] | ba10d3fcff747ae696bee7b0fafb661182426f636e97d97e8f663537cc66cb38 |
from setuptools import setup
from pip.req import parse_requirements
from pip.download import PipSession
links = []
requires = []
requirements = parse_requirements('requirements.txt', session=PipSession())
for item in requirements:
# we want to handle package names and also repo urls
if getattr(item, 'url', N... | bewestphal/SeleniumAI | setup.py | Python | mit | 1,357 | [
"Brian"
] | 414416bf6807e81623134565bfc00c614a5754e0bf438284ec3e73f3ce80e21b |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Unit tests for the engine.activate() call within the
`iris.fileformats.netcdf._load_cube` function.
Test rules activation ... | rcomer/iris | lib/iris/tests/unit/fileformats/nc_load_rules/actions/test__hybrid_formulae.py | Python | lgpl-3.0 | 10,925 | [
"NetCDF"
] | 7c18ce74fb2abcdaa21b086b95a3c04c7b119fd279de3a965aa4d5d73cd56832 |
import abc
import numpy as np
import six
from ..fit.io.file import FileIOMixin
__all__ = ['ParameterConstraintException', 'ParameterConstraint', 'GaussianSimpleParameterConstraint',
'GaussianMatrixParameterConstraint']
class ParameterConstraintException(Exception):
pass
@six.add_metaclass(abc.ABCMe... | dsavoiu/kafe2 | kafe2/core/constraint.py | Python | gpl-3.0 | 12,225 | [
"Gaussian"
] | ad98d746ad47acb5f9359ecc4cb4aa834feba129524de5e162d2d16b1c5465fb |
# -*- coding: utf-8 -*-
"""Testing functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
from contextlib import contextmanager
from distutils.version import LooseVersion
from functools import partial, wraps
import os
import inspect
from io import StringIO
from shutil impor... | bloyl/mne-python | mne/utils/_testing.py | Python | bsd-3-clause | 17,583 | [
"Mayavi",
"VTK"
] | 28e9a3674c164dfe6a76068f03da28a5a7e195d4d84dd3374a3a420ddb90568b |
import operator as op
from functools import partial
from itertools import permutations, combinations
import logging
import lib.const as C
import lib.visit as v
from ... import add_artifacts
from ... import util
from ... import sample
from ...encoder import add_ty_map
from ...meta import class_lookup
from ...meta.temp... | plum-umd/pasket | pasket/rewrite/android/observer.py | Python | mit | 29,595 | [
"VisIt"
] | 89dd6204fb174488d7804bd7c4d06503e173fba1370206b6ad53e2dffae7ba30 |
#* 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
from subpro... | nuclear-wizard/moose | modules/navier_stokes/test/tests/scalar_adr/supg/run_cases.py | Python | lgpl-2.1 | 1,565 | [
"MOOSE"
] | 9c648df295cd06ef79ecbbe453d69e4bd46f4fe8341b7d23017f8fd1349c529d |
class InputSection(object):
"""Base class for all the automatically created classes that represents
sections in the CP2K input structure.
"""
def __init__(self):
self._name = None
self._keywords = {}
self._repeated_keywords = {}
self._default_keywords = {}
self._r... | SINGROUP/pycp2k | pycp2k/inputsection.py | Python | lgpl-3.0 | 8,058 | [
"CP2K"
] | 5fb4b8005ce0833be49839afe663c398d1cfca2497829c2f388c5a6f41f67e10 |
import os, sys, inspect
import h5py
import numpy as np
import random
import math
import multiprocessing
from Crypto.Random.random import randint
import gc
import resource
# Visualization
import matplotlib
import matplotlib.pyplot as plt
from PIL import Image
# from mayavi import mlab
# from mayavi.core.ui.mayavi_scene... | srinituraga/caffe_neural_models | dataset_06/greentea_brew_tool.py | Python | bsd-2-clause | 14,490 | [
"Mayavi"
] | e71aa22a36e7f315cfe53dcfee57f1010ce3abf29ddb8cf4138f405e4fb3f7fb |
# -*- coding: utf-8 -*-
#
# ABOUT
# Artisan PID Controllers (Fuji, DTA, Arduino TC4)
# LICENSEsvLen
# This program or module is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as published
# by the Free Software Foundation, either version 2 of the License, or... | artisan-roaster-scope/artisan | src/artisanlib/pid_control.py | Python | gpl-3.0 | 97,075 | [
"ESPResSo"
] | c811a75973b406b7f02ada56a3fab4286db81fa805b393ccecc415d1db39861c |
import numpy as np
from collections import deque
from astropy.table import Table
from scipy.optimize import fmin_bfgs,check_grad,approx_fprime
#from scipy.optimize.linesearch import (line_search_BFGS, line_search_wolfe1, line_search_wolfe2, line_search_wolfe2 as line_search)
#from optimize import fmin_bfgs
import cop... | ChileanVirtualObservatory/acalib | acalib/algorithms/attic/gaussClumps.py | Python | gpl-3.0 | 39,243 | [
"Gaussian"
] | 4165105e2ee6b9933e6ba45175ef6e2d300fe71ec97a5602e95a4c92c40b1f67 |
"""
====================================================================
K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
====================================================================
Provides routines for k-means clustering, generating code books
from k-means models, and quantizing vectors ... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/scipy/cluster/vq.py | Python | mit | 28,214 | [
"Gaussian"
] | da604791e6a0e5011fee94e52fe46dc1788ac60cdfd8f5b737492e6f4285fee7 |
# -*- coding: utf-8 -*-
#----------------------------------------------------------------------------
# A turn by turn navigation module.
#----------------------------------------------------------------------------
# Copyright 2007, Oliver White
#
# This program is free software: you can redistribute it and/or modify
... | ryfx/modrana | modules/mod_turnByTurn/mod_turnByTurn.py | Python | gpl-3.0 | 39,661 | [
"VisIt"
] | 29c7ac34ab7c6876d583c62672f9be6aeff963427beed1795c13308f48eb0e3b |
# -*- coding: utf-8 -*-
###############################################################################
#
# PyLint tests that will never be applied for this file.
#
# Unused variables, these functions are organized so that they can be called
# from a string at runtime, from it's name being stored
# ... | Equitable/trump | trump/aggregation/symbol_aggs.py | Python | bsd-3-clause | 8,856 | [
"ADF"
] | 6bf50f47bcc3cd58ef416d43ccaded47ba02a73287f6e2f78a636a180bf2c235 |
"""
API operations related to tagging items.
"""
import logging
from galaxy import web
from galaxy.web.base.controller import BaseAPIController, UsesTagsMixin
from paste.httpexceptions import HTTPBadRequest
log = logging.getLogger( __name__ )
class BaseItemTagsController( BaseAPIController, UsesTagsMixin ):
"""
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/item_tags.py | Python | gpl-3.0 | 2,393 | [
"Galaxy"
] | 1bf4e5cacab0b78be175a8db064d9627cfacbc674094ac1d4611778d8154f1ad |
#
# 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... | fweik/espresso | testsuite/python/langevin_thermostat_stats.py | Python | gpl-3.0 | 9,562 | [
"ESPResSo"
] | aa571051f9b36cb18477a219e099b59d96fbec66feaddfd304652ec1743b9f60 |
#!/usr/bin/env python
""" move base utils
modified from movebasesquare
ren ye 2016-10-19
"""
import rospy
import actionlib
from actionlib_msgs.msg import *
from geometry_msgs.msg import Pose, Point, Quaternion, Twist, Vector3
from sensor_msgs.msg import NavSatFix
from nav_msgs.msg import Odometry
from move_ba... | phamngtuananh/Singaboat_RobotX2016 | robotx_nav/nodes/move_base_util.py | Python | gpl-3.0 | 13,294 | [
"xTB"
] | 1c788c88cff7eaea4fde4d0298c272d1c5515ae3d2db92b18d35b18011ddafe4 |
# uncompyle6 version 2.9.10
# Python bytecode 2.7 (62211)
# Decompiled from: Python 3.6.0b2 (default, Oct 11 2016, 05:27:10)
# [GCC 6.2.0 20161005]
# Embedded file name: mimetypes.py
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=1) -- guess the MIME type and encod... | DarthMaulware/EquationGroupLeaks | Leak #5 - Lost In Translation/windows/Resources/Python/Core/Lib/mimetypes.py | Python | unlicense | 19,263 | [
"NetCDF"
] | 88ada33f3f66f146885825b46d871eb22dc9fdc1f00c8da16e7ba0775ea7ffa4 |
'''
Created on 26/04/2011
@author: jose
'''
import unittest
import os.path, subprocess, sys
from tempfile import NamedTemporaryFile
import franklin
from franklin.utils.misc_utils import TEST_DATA_DIR
from franklin.seq.writers import create_temp_seq_file
from franklin.seq.readers import seqs_in_file
from franklin.seq... | JoseBlanca/franklin | test/scripts/clean_reads_test.py | Python | agpl-3.0 | 22,214 | [
"BLAST"
] | a47e4dbb16bd81f5c914e7d9d81f10000cb1f14fd727c3ce0ea775582a42cd5e |
# -*- coding: utf-8 -*-
#
# GCAC-doc documentation build configuration file, created by
# sphinx-quickstart on Tue Jun 30 10:12:08 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# ... | LynnLab-JNU/GCAC | docs/source/conf.py | Python | gpl-3.0 | 8,589 | [
"Galaxy"
] | 10aa0893bf5e516e71a60a4d9323b95ca72f1bb3515820b401850bde1b8b0f2c |
#!/usr/bin/env python
from sys import argv, stderr, exit
import subprocess
import numpy as np
from argparse import ArgumentParser
try:
from exactP import exactP_list
except:
stderr.write("Please build the exactP module by running 'make exactP'.\n")
exit(1)
try:
from PISMNC import PISMDataset
except:
... | talbrecht/pism_pik07 | test/test_hydrology/runTestP.py | Python | gpl-3.0 | 9,613 | [
"NetCDF"
] | f9f2e410808936840a4d72cc87f8ee3e822d0423a75f44053b7e0ba172e91f2d |
"""The Mayavi UI plugin
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
import logging
# Enthought library imports.
from traits.api import List, on_trait_change
from envisage.api import Plugin
from pyface.wor... | dmsurti/mayavi | mayavi/plugins/mayavi_ui_plugin.py | Python | bsd-3-clause | 8,008 | [
"Mayavi"
] | 77b40462e987935b5533d5f111d541bd5eee8addd3c1e03b8d8b6b472dc3753e |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | liuwenf/moose | python/chigger/tests/edge/edge.py | Python | lgpl-2.1 | 1,599 | [
"MOOSE",
"VTK"
] | ec1b2c8733f0f0f626a2a472910da78939b44c4913781a989de2eff142017ad5 |
import numpy
from PyMca import PyMcaQt as qt
from PyMca import ScanWindow
from PyMca import specfilewrapper as sf
from PyMca import SimpleFitModule as SFM
from PyMca import SpecfitFunctions
from PyMca import Elements
from PyMca import ConfigDict
from PyMca import PyMcaDirs
from PyMca import QSpecFileWidget
from PyMca i... | tonnrueter/pymca_devel | PyMca/PyMcaPlugins/SumRulesPlugin.py | Python | gpl-2.0 | 83,508 | [
"TINKER"
] | 986d3851f1d23f17489095fbfffcc1354ed7941cde2e5fa681c270b4e050488d |
from __future__ import print_function, division
import os
import tempfile
import mdtraj as md
import pandas as pd
import numpy as np
from numpy.testing import assert_approx_equal
from mdtraj.testing import eq
from sklearn.externals.joblib import load, dump
import sklearn.pipeline
from six import PY3
from msmbuilder.u... | rmcgibbo/msmbuilder | msmbuilder/tests/test_msm.py | Python | lgpl-2.1 | 11,980 | [
"Gaussian",
"MDTraj"
] | aa7d110b13ead67ca9f5db4b393083448cf35503b50165822f22c145c087e886 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-get-queue-cpu-time.py
# Author : Federico Stagni
########################################################################
""" Report CPU length of queue, in seconds
This script is used by the dirac-... | andresailer/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-get-queue-cpu-time.py | Python | gpl-3.0 | 1,263 | [
"DIRAC"
] | b435e719c4a20e42eb6be8b1c62d9f50128fec80186d10eeea963c56cb8190f2 |
"""
.. _statsrefmanual:
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. currentmodule:: scipy.stats
This module contains a large number of probability distributions,
summary and frequency statistics, correlation functions and statist... | e-q/scipy | scipy/stats/__init__.py | Python | bsd-3-clause | 12,444 | [
"Gaussian"
] | 97097865763060ca772ab2f1630ea864184b7f7bf8a27da3d8b84bd41a357f24 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
"""
This module has methods for parsing names and versions of packages from URLs.
The idea is to allow package creators to... | rspavel/spack | lib/spack/spack/url.py | Python | lgpl-2.1 | 31,271 | [
"BLAST",
"HOOMD-blue",
"VTK"
] | b4954db5173718405ad7051c7f7275a43acea2db13b43bed09edc1cf48bc0aac |
#!/usr/bin/env python
# This shows how to probe a dataset with a plane. The probed data is
# then contoured.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Read data.
pl3d = vtk.vtkPLOT3DReader()
pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
pl3d.SetQFileName(VTK_DA... | CMUSV-VisTrails/WorkflowRecommendation | examples/vtk_examples/VisualizationAlgorithms/probeComb.py | Python | bsd-3-clause | 4,014 | [
"VTK"
] | b0a73daffe9f74c229e89ee6097679d114af8a0571a01af2bd4a6d2e26d8c430 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/mediaitem.py | Python | gpl-2.0 | 36,369 | [
"VisIt"
] | e542bce3d0290c01f71f27d79ac017935a01bfdddd6306f6502b4b0ec64fe595 |
#!/usr/bin/env python
#author: Peter Thorpe September 2016. The James Hutton Insitute,Dundee,UK.
#Title:
#script perform stats on the coverage files already generated"
#imports
import os
import sys
import numpy
from sys import stdin,argv
import sys
import datetime
from optparse import OptionParser
#################... | widdowquinn/THAPBI | ITS_region_genomic_coverage/summary_stats.py | Python | mit | 6,353 | [
"BLAST"
] | cd63f1a6bcba223dce8163f00bffba55f16c4ed8e39bae710012ed4ef46d74f2 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/bowtie2/package.py | Python | lgpl-2.1 | 2,575 | [
"Bowtie"
] | 2ab8d26c4088d792d08505b6ca57de8d4790f8816d95d74b574e363e602b995a |
#! /usr/bin/env python2
import sys
import vtk
import vtkDICOMPython
# put everything into the vtk namespace
for a in dir(vtkDICOMPython):
if a[0] != '_':
setattr(vtk, a, getattr(vtkDICOMPython, a))
m = vtk.vtkDICOMMetaData()
if vtk.vtkVersion.GetVTKMajorVersion() < 6:
sys.stderr.write("This test req... | hendradarwin/vtk-dicom | Testing/TestDICOMPython.py | Python | bsd-3-clause | 540 | [
"VTK"
] | ca1ddbc722b746c21bc14760b14974d1b2b74f47504a6931db3d41c28e7887bf |
"""
Copyright 2015 Google, 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
Unless required by applicable law or agreed to in writing, software
di... | openconfig/oc-pyang | openconfig_pyang/plugins/yangdoc.py | Python | apache-2.0 | 14,380 | [
"VisIt"
] | 410253d02a74ebdf070341b385422602e2d0fbe3dbdeeeda9687cfdba13b6f8d |
'''
Random field generation using rft1d.random.Generator1D
Notes:
-- Using Generator1D is faster than rft1d.randn1d for iterative
generation.
-- When FWHM gets large (2FWHM>nNodes), the data should be
padded using the *pad* keyword.
'''
import numpy as np
from matplotlib import pyplot
import rft1d
#(0) Set param... | 0todd0000/rft1d | rft1d/examples/random_fields_2.py | Python | gpl-3.0 | 898 | [
"Gaussian"
] | 53ea50141a275a8d5a72fd7a364d4b3ebad6605ad9ad35402aba061cc6d1cc3b |
#
# Copyright 2008, 2009, 2010 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (at your option)
# any later ... | n4hy/gnuradio | gr-wxgui/src/python/plotter/waterfall_plotter.py | Python | gpl-3.0 | 9,471 | [
"VMD"
] | 9c10aaf319c5cc986511e60e64e085e1748e8af5975620d82e7416cb1eebaf71 |
###########################################################################
# Mean prediction from Gaussian Processes based on
# classifier_libsvm_minimal_modular.py
# plotting functions have been adapted from the pyGP library
# https://github.com/jameshensman/pyGP
######################################################... | sanuj/shogun | examples/undocumented/python_modular/graphical/regression_gaussian_process_demo.py | Python | gpl-3.0 | 9,249 | [
"Gaussian"
] | 0c9e3a88ed78662130a3620157efa7978c13745251418fb754310396aa148628 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | fweik/espresso | testsuite/scripts/tutorials/test_constant_pH__ideal.py | Python | gpl-3.0 | 1,723 | [
"ESPResSo"
] | 9f3f15b38d3578b4444744c5c3f350e25de25bc7a6bb6f0509af7aef6ff5f83f |
# coding: utf8
""" Implementation of full and banded matrix models for :math:`\beta`-Ensemble:
- Hermite Ensemble (full + tridiagonal)
- Laguerre Ensemble (full + tridiagonal)
- Jacobi Ensemble (full + tridiagonal)
- Circular Ensemble (full + quindiagonal)
- Ginibre Ensemble (full)
.. seealso:
`Documentation on ... | guilgautier/DPPy | dppy/random_matrices.py | Python | mit | 10,337 | [
"Gaussian"
] | 52054041dc091bef0fd53bd051edcb21aa324df97f01c0685eccbd0f1c764bce |
# Copyright 2005 by Jason A. Hackney. 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.
"""
Parser for dealing with text output from the MEME motif search program
"""
| dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/MEME/__init__.py | Python | apache-2.0 | 308 | [
"Biopython"
] | fe514a2c18d83697d30f1108c2bd21a211fb9ab8f94808c1ea18eb722e388234 |
from setuptools import setup, find_packages
import sys, os
version = '0.1'
setup(name='emmetrop',
version=version,
description="A biological analysis of a schematic eye and natural images",
long_description=""" """,
install_requires=["Sphinx",
"numpy",
... | bps10/emmetrop | setup.py | Python | mit | 982 | [
"Brian"
] | 2b9f3b69a2a674a45b0bf5b1eb18da19b2f064dd2e22ce65e6e60cc65e9a5fa6 |
################################################################################
#
# Copyright 2015-2021 Félix Brezo and Yaiza Rubio
#
# This program is part of OSRFramework. You can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Softwa... | i3visio/osrframework | osrframework/searchfy.py | Python | agpl-3.0 | 9,100 | [
"VisIt"
] | f556c04d470e11aa5c200cea25683eb2a300ec3e4a39f37827a314fa625d8cd9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/cfour.py | Python | lgpl-3.0 | 47,615 | [
"CFOUR",
"Psi4"
] | f472fbe5b010a5368a3170fc31ae7baffa4093fd453f91a1eee196aa9b07f265 |
#!/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_graph(lpu_name, N_sensory, N_local, N_proj):
"""
Create a generic LPU graph.
Creates a graph containing the neuron... | AdamRTomkins/Neurokernel-singularity-container | examples/data/gen_generic_lpu.py | Python | apache-2.0 | 12,988 | [
"NEURON"
] | 660554cd2995f9924cb88d473078f5dd57730f382aa79c1b20744c5741fa15b9 |
"""
=====================================
Blind source separation using FastICA
=====================================
An example of estimating sources from noisy data.
:ref:`ICA` is used to estimate sources given noisy measurements.
Imagine 3 instruments playing simultaneously and 3 microphones
recording the mixed si... | gtrichards/PHYS_T480 | code/plot_ica_blind_source_separation.py | Python | mit | 2,241 | [
"Gaussian"
] | 88f27933a1a1d4a4d2cea8ee1d29b2e7abe6acea85a3da219e79e42558d150a7 |
"""
Tests to try and ensure that important mayavi imports work with no UI.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2009, Enthought, Inc.
# License: BSD Style.
import sys
import unittest
from traits.etsconfig.api import ETSConfig
class TestNoUIToolkit(unittest.TestCase):
"""Te... | dmsurti/mayavi | mayavi/tests/test_no_ui_toolkit.py | Python | bsd-3-clause | 2,082 | [
"Mayavi"
] | b47eee9d50fc07ecad0078c13af110cc46507e5772184e5a2b8842f67e8d0972 |
"""This is a set of tools built up over time for working with Gaussian and
QChem input and output."""
########################################################################
# #
# ... | thompcinnamon/QM-calc-scripts | gautools/__init__.py | Python | apache-2.0 | 1,715 | [
"Gaussian"
] | 20e383d8f2fa772792f5ebe58f50f8a2d514b5bc04915da421c553bd724257ae |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-2009 Tiny SPRL (<http://tiny.be>).
# Copyright (C) 2010-2014 OpenERP s.a. (<http://openerp.com>).
#
# This program is free software: you ca... | charbeljc/OCB | openerp/tools/misc.py | Python | agpl-3.0 | 45,843 | [
"VisIt"
] | fc33add885ffd0e862b90ac685022546c090928f6f54ef0500cbb1dba39d8829 |
'''
First Created 2016/05/06 by Blaise Thompson
Last Edited 2016/08/08 by Blaise Thompson
Contributors: Blaise Thompson
'''
### import ####################################################################
import os
import sys
import importlib
import collections
import WrightTools as wt
### define ##############... | wright-group/WrightData | unpublished Thompson - Automated OPA Tuning/workup.py | Python | cc0-1.0 | 15,119 | [
"Gaussian"
] | 13af9b311dfd3ec6011abb52e9b6a85e547c9d1455df411da9d2f395d9c93e1f |
#
# 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... | KonradBreitsprecher/espresso | samples/minimal-diamond.py | Python | gpl-3.0 | 1,533 | [
"ESPResSo"
] | 7192725d0d83fb55e10797d91e3a72178a133c8c6842c576c2c69e1491932467 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | 7kbird/chrome | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 15,975 | [
"Galaxy"
] | 41166d93284ea75cff236803a04394b668c9d7ced3d704bb3b72446ab8cd16ed |
#!/usr/bin/env python3
"""
Usage:
heatmaps.py [ --term-file=<file> --pickle-file=<file> --ipython --make-csv=<file> --ice ]
heatmaps.py -h | --help
Options:
-t --term-file=<file> newline separate list of terms
-p --pickle-file=<file>
-c --make-csv=<file>
-i --ipython
--ice ... | CheerfulTeapot/heatmaps | heatmaps.py | Python | mit | 38,676 | [
"NEURON"
] | a434135cf19bfabda5886ba0651f99359c352bbd0801605643907261e3fc227a |
from . import numdifftools, numpy as np
import pytest
from pyRSD.rsd.power.gal.derivatives import dPgal_dsigma_c
NMU = 41
@pytest.mark.parametrize("socorr", [True, False])
@pytest.mark.parametrize("fog_model", ['modified_lorentzian', 'lorentzian', 'gaussian'])
def test_partial(driver, socorr, fog_model):
# set t... | nickhand/pyRSD | pyRSD/tests/test_gal_derivatives/test_sigma_c.py | Python | gpl-3.0 | 1,146 | [
"Gaussian"
] | 4483b6d2a226b990f89dd25054b98513d1342388e3b25bb764bb7bba475d83f8 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Copyright 2015 Diamond Light Source <stuart.fisher@diamond.ac.uk>
#
# 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:... | tcspain/SynchWeb | api/formulatrix/uploader/formulatrix_uploader.py | Python | apache-2.0 | 13,823 | [
"VisIt"
] | 78cf07f169bd5c9a78e516b4a3ae3d8111e32f2a87ba2a7bde69d3271e70827a |
# -*- coding: utf-8 -*-
#
# Copyright (c), 2015-2016, Quantum Espresso Foundation and SISSA (Scuola
# Internazionale Superiore di Studi Avanzati). All rights reserved.
# This file is distributed under the terms of the MIT License. See the
# file 'LICENSE' in the root directory of the present distribution, or
# http://o... | afonari/q-e_schrodinger | bin/qexsd/qespresso/xsdtypes/etree.py | Python | gpl-2.0 | 7,763 | [
"Quantum ESPRESSO"
] | f0d6d2efea46ca3aaf5e56e0cd5879b39d318fcdd3f1f76c45c086e951a05bf3 |
import copy
import logging
from typing import List, Dict, Iterator, Tuple, Iterable, Optional
from randovania.game_description.game_patches import GamePatches
from randovania.game_description.requirements import Requirement, RequirementAnd
from randovania.game_description.resources.pickup_index import PickupIndex
from... | henriquegemignani/randovania | randovania/game_description/world/world_list.py | Python | gpl-3.0 | 12,975 | [
"BLAST"
] | 900d5ff87b7c3598c1d838c2d7697760eb8b4c754ea8663a24eb3fd60940658e |
from nanopore.mappers.lastz import Lastz
import pysam
import os
from nanopore.analyses.utils import pathToBaseNanoporeDir
class LastzParams(Lastz):
def run(self):
#scoreFile = os.path.join(pathToBaseNanoporeDir(), "nanopore", "mappers", "last_em_575_M13_2D_scores.txt")
#Lastz.run(self, args="--hsp... | mitenjain/nanopore | nanopore/mappers/lastzParams.py | Python | mit | 1,004 | [
"pysam"
] | 75179e2a04c5b6c8bc34e08d3d03358dc29308c620ca959fea2a92253b2c1b24 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '... | shepdelacreme/ansible | lib/ansible/modules/system/svc.py | Python | gpl-3.0 | 9,270 | [
"Brian"
] | dd245a4cf513beb2b3838adb9a82ecb357c051e5da4543bcd2577211755b9988 |
#!/usr/bin/env python
""" update local cfg
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Core.Base import Script
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
... | yujikato/DIRAC | tests/Jenkins/dirac-cfg-update-services.py | Python | gpl-3.0 | 2,642 | [
"DIRAC"
] | 5ab12c536bc4ddb12c0848de645e981ef59655aae80afb9df5e72689ed23e14e |
#===============================================================================
#
# SpecificPopulation.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2013-2016 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: yo... | vitay/ANNarchy | ANNarchy/core/SpecificPopulation.py | Python | gpl-2.0 | 94,487 | [
"Brian",
"Gaussian",
"NEURON"
] | a58245acb473bb6d0861581acb7f6736beaaf1ca1806fcbbc279eeee80a5d158 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright INRIA
# Contributors: Nicolas P. Rougier (Nicolas.Rougier@inria.fr)
#
# DANA is a computing framework for the simulation of distributed,
# asynchronous, numerical and adaptive models... | rougier/dana | dana/functions.py | Python | bsd-3-clause | 21,860 | [
"Gaussian"
] | 91e1038b0f757507c182be0d77c6ba8401ca156078a5bc4ed9903d42aac00080 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | properties/nodes/diffuse_btdf.py | Python | mit | 3,573 | [
"VisIt"
] | 5dee8b6df6885061e70c2391e82da9be12410d5cba758973c45e815ae589252c |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/cutLoop.py | Python | gpl-3.0 | 3,804 | [
"VTK"
] | fab72eb57fe8d6b68ea655659d6a741f9e5cacd8388a8b2c72dc281d45109360 |
#!/usr/bin/env python3
import argparse
import os
import re
from lib.coordreaders import PDBReader, GROReader
from lib.moldatabase import MolDatabase
from lib.atomdatabase import AtomDatabase
from lib.bonddatabase import BondDatabase
class NonMatchingAtomException(Exception):
def __init__(self, num, name1, name2... | jag1g13/pdb2lmp | pdb2lmp.py | Python | mit | 13,610 | [
"LAMMPS"
] | ea8b54ca0fff55f736198d1d466db55a14476729d5d2ee120208a63d411eae0e |
# -*- coding: utf-8 -*-
"""
sphinx.cmdline
~~~~~~~~~~~~~~
sphinx-build command-line handling.
:copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from __future__ import print_function
import sys
import optparse
import traceback
from os impo... | axbaretto/beam | sdks/python/.tox/docs/lib/python2.7/site-packages/sphinx/cmdline.py | Python | apache-2.0 | 11,907 | [
"VisIt"
] | 7a4ca263a91acbe6e0d19deeb6f80a74151f6013bd600fc6dbbb2f01077daa2a |
#!/usr/bin/env python
"""
Install.py tool to build the CSlib library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import fullpath
parser ... | akohlmey/lammps | lib/message/Install.py | Python | gpl-2.0 | 2,521 | [
"LAMMPS"
] | dfb884a050e051b299b018cd5f85096847cdb6d389a1dc7b5e4ab8c64c032240 |
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