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|---|---|---|---|---|---|---|---|
from neuron import Neuron
import math
import random
sigm = lambda x: (1.0/(1+pow(math.e, x)))
sigmp = lambda x: sigm(x)*(1.0-sigm(x))
error = lambda x, y: 0.5*pow(x-y, 2)
def first_last_errors(errors):
sq = int(math.sqrt(len(errors)))
first_errors = sum(errors[:sq])/sq
last_errors = sum(errors[-sq:])/sq
... | rylans/nn-from-scratch | neuron_test.py | Python | apache-2.0 | 2,816 | [
"NEURON"
] | 008b49e3a16230ffd62aff811949b9b5c477a53a4eab1b63454b3e73bbff1b38 |
from mdtraj.testing import get_fn, eq
from mdtraj import element
import mdtraj as md
def test_element_0():
t = md.load(get_fn('bpti.pdb'))
a = t.top.atom(15)
H = element.Element.getBySymbol('H')
eq(a.element, element.hydrogen)
| casawa/mdtraj | mdtraj/formats/pdb/tests/test_element.py | Python | lgpl-2.1 | 247 | [
"MDTraj"
] | bf16db87613200030c4800096879f58a0e3f2958b29f0066d740338b06992909 |
#
# Copyright (c) 2017, 2017, 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... | akunft/fastr | mx.fastr/mx_fastr_edinclude.py | Python | gpl-2.0 | 6,178 | [
"VisIt"
] | 0577b2d4fea81c5be814b580fc5a763090076dc0f749932552faf0bc035c2b01 |
#!/usr/bin/python
#=============================================================================================
# example files for reading in MD simulation files and performing
# statistical analyses according to manuscript "Simple tests for
# validity when sampling from thermodynamic ensembles", Michael
# R. Shirts... | shirtsgroup/checkensemble | checkensemble/readmdfiles.py | Python | gpl-2.0 | 12,189 | [
"Desmond"
] | 4b180f6f83252b029641b1b96e71684bfac3e5cb45055e3b4318aa517f5ec446 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module implements equivalents of the basic ComputedEntry objects, which
is the basic entity that can be used to perform many analyses. ComputedEntries
contain c... | sonium0/pymatgen | pymatgen/entries/computed_entries.py | Python | mit | 7,343 | [
"VASP",
"pymatgen"
] | 8148ad0780cca96993562489ee0541310254e3f3fa41f2af58f7a5d3f6b765a5 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'EphysPropSummary'
db.create_table('neuroelectro_ephyspropsummary', (
... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0029_auto__add_ephyspropsummary__add_neuronsummary__add_articlesummary.py | Python | gpl-2.0 | 21,123 | [
"NEURON"
] | 2ea19aef9386a528218807decd0e2503f66becc2f132d0deed4a9a76008e6fce |
#!/usr/bin/env python
from __future__ import print_function
from jinja2 import Environment, FileSystemLoader
import argparse
import urllib2
import csv
import os
import shutil
import sys
import os.path
import subprocess
UBUNTU_RELEASE_URL = 'http://cloud-images.ubuntu.com/query/trusty/server/released.current.txt' #... | azavea/docker-deep-learning | deployment/driver.py | Python | apache-2.0 | 3,798 | [
"Galaxy"
] | 3afaefb6f039b94de2807f54934e75d01ebb3d288a5d298b42e16531cbce960a |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'DataDomainIndex.groups'
db.delete_column(u'profiles_datadomainindex', 'groups_id')
... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0069_auto__del_field_datadomainindex_groups__add_field_datadomainindex_grou.py | Python | mit | 23,239 | [
"MOE"
] | 74428156524dcd3e5073701e2044fd6bccf8ec3e78a6b41bd69e64e4aa2e64ed |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | samples/electrophoresis.py | Python | gpl-3.0 | 8,819 | [
"ESPResSo"
] | d2926a33cc5551ced3eadcda31a51491cbdf016999fa4a1e6409a2b590cca783 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | rmatsuda/invesalius3 | invesalius/reader/others_reader.py | Python | gpl-2.0 | 2,046 | [
"VTK"
] | 9a5c5171a34050b97d038198b7b0e7962bb9b885c843efe8aa3875c8a3df557b |
"""
This file provides the categories and sizes for different ships in the EVE
Online MMORPG by CCP games. Data from EVE University.
"""
CATEGORIES = {
'Abaddon': 'Battleship',
'Absolution': 'Command Ship',
'Aeon': 'Carrier',
'Algos': 'Destroyer',
'Anathema': 'Covert Ops',
'Anshar': 'Jump Freig... | StephenSwat/EVE-Fleetboss | fleetboss/ships.py | Python | gpl-3.0 | 9,057 | [
"Jaguar",
"ORCA"
] | 46e4c9e2eaa88e98a87adaa30502c81c32bd3442f0904d278ea4132e4a2298e0 |
"""Mass-balance models"""
# Built ins
import logging
# External libs
import cftime
import numpy as np
import pandas as pd
import netCDF4
from scipy.interpolate import interp1d
from scipy import optimize as optimization
# Locals
import oggm.cfg as cfg
from oggm.cfg import SEC_IN_YEAR, SEC_IN_MONTH
from oggm.utils import... | TimoRoth/oggm | oggm/core/massbalance.py | Python | bsd-3-clause | 57,645 | [
"Gaussian"
] | 7412be97c5fce2c28c83f125dc484b571c9a958854a3e00228bb105116c80efa |
#import stuff
import os
import random
import math
from scipy import stats as scstats
from matplotlib import pyplot as plt
from tabulate import tabulate as tabulate
import matplotlib.cm as cm
import sys
import numpy as np
import scipy.stats as stats
#### data preprocessing ####
class Enri():
def __init__(self):
... | fibonaccirabbits/enri | enri.py | Python | mit | 69,117 | [
"Gaussian"
] | b9395e4fc2e2c8ca1f07928b4ec8287726d3b71a18e0f5db21dc32bc076491b0 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division
# 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 2.1
# S... | BhallaLab/moose-core | tests/core/test_steady_state_solver.py | Python | gpl-3.0 | 5,039 | [
"MOOSE"
] | c11ffb7cfc7df1979ea9f1d6572d2dfa5f81b1450685c2aeef918a9b23398e47 |
#
# @file TestCVTerms_newSetters.py
# @brief CVTerms unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id: TestCVTerms_newSetters.py 11441 2010-07-09 02:22:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/python/test/annotation... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/annotation/TestCVTerms_newSetters.py | Python | gpl-3.0 | 6,280 | [
"VisIt"
] | 669cf1b241c29c9b35e6bd0d5a218fddd793d736d389aafe71343593d94ed821 |
'''
'''
from __future__ import print_function
import shutil
from os.path import dirname, exists, join, realpath, relpath
import os, re, subprocess, sys, time
import versioneer
# provide fallbacks for highlights in case colorama is not installed
try:
import colorama
from colorama import Fore, Style
def ... | draperjames/bokeh | _setup_support.py | Python | bsd-3-clause | 15,550 | [
"GULP"
] | 1597a421404f6386db9b2adfaa985032876294da2c8b3d8cac4ed49fe145fb8f |
# Copyright 2010 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# 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 L... | sebrandon1/nova | nova/tests/unit/matchers.py | Python | apache-2.0 | 20,022 | [
"VisIt"
] | 7f7b68e9db7e9e4baeafff0077f8e4b133842de53f1fadc221d11dd4fa8b315f |
#!/usr/bin/env python2
import sys
#sys.path.append('/data/antares/aux')
#sys.path.append('/mnt/data/antares/aux/sne.space/')
#sys.path.append('/home/antares/nfs_share/tzaidi/HonorsThesisTZ/ThesisCode/classification/')
sys.path.append('../classification')
import os
import glob
import json
import numpy as np
import matpl... | tayebzaidi/HonorsThesisTZ | ThesisCode/gen_lightcurves/parse_sne_spaceMod.py | Python | gpl-3.0 | 16,874 | [
"Gaussian"
] | 138d331ad9f84df84e1c33ef8bc470d856dec2e1a1d03b8987a12a807c363170 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_salequoteitemeditor.py | Python | gpl-2.0 | 10,137 | [
"VisIt"
] | 5db4a7a5dca8bae25a71c78d20e953c6fbefe4dd2e0c3e2e90943472218b9d02 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | ssaeger/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 67,255 | [
"Gaussian"
] | b0792d34ed3dc62f992c418a6b8fed88d7883ff7fb36a6a030918e3d2e59a021 |
########################################################################
# $HeadURL$
########################################################################
""" ProfileManager manages web user profiles
in the DISET framework
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import types
from DIRAC.Co... | petricm/DIRAC | FrameworkSystem/Service/UserProfileManagerHandler.py | Python | gpl-3.0 | 6,219 | [
"DIRAC"
] | ff091651c93c6feebb8fef90b4c36b989112b72b9049e7a272fdc194d293b911 |
"""
Align direct images & make mosaics
"""
import os
import inspect
from collections import OrderedDict
import glob
import traceback
import numpy as np
import matplotlib.pyplot as plt
# conda install shapely
# from shapely.geometry.polygon import Polygon
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
... | gbrammer/grizli | grizli/prep.py | Python | mit | 197,852 | [
"Gaussian",
"VisIt"
] | 5f608bf38bac710f7006370f509d1ebbad0379b208c59123d00b60e717511980 |
import os
import unittest
from os.path import join
from pymatgen.core.structure import Molecule
from pymatgen.io.adf import AdfInput, AdfKey, AdfOutput, AdfTask
from pymatgen.util.testing import PymatgenTest
__author__ = "Xin Chen, chenxin13@mails.tsinghua.edu.cn"
test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR,... | gmatteo/pymatgen | pymatgen/io/tests/test_adf.py | Python | mit | 9,858 | [
"ADF",
"pymatgen"
] | 632820d1d5b8382dac967f1792ed256b7085fbb21a4580ef1d718c91f21d536e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division, print_function, absolute_import, unicode_literals
import ast
import codecs
import os
import shutil
from collections import OrderedDict
from six import string_types
from sphinx_explorer.plugin import extension
from sphinx_explorer.plugin.ex... | pashango2/sphinx-explorer | sphinx_explorer/util/conf_py_parser.py | Python | mit | 5,427 | [
"VisIt"
] | f471efeb1042f4292d8370766e42017901eb58bec7ceaab2b99336e56e255f1c |
import numpy
import pdb
import numpy as Math
class DataGenerator(object):
def __init__(self, batch_size):
self.batch_size = batch_size
def fit(self, inputs, targets):
self.start = 0
self.inputs = inputs
self.targets = targets
def __next__(self):
return self.next... | MdAsifKhan/DNGR-Keras | utils.py | Python | mit | 5,301 | [
"Gaussian"
] | a3aad97c97c3193dab0edaead9be5e8ee70a52dcd307b15eb1fcaee65da83817 |
#
# Copyright (C) 2017-2019 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/accumulator_mean_variance.py | Python | gpl-3.0 | 2,616 | [
"ESPResSo"
] | fdb10e87abc6b7d39f4609d5bb3eb9c106f7f124834502c79d7cdad582b624d1 |
# -*- coding: utf-8 -*-
#
# gif_population.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,... | alberto-antonietti/nest-simulator | pynest/examples/gif_population.py | Python | gpl-2.0 | 5,063 | [
"NEURON"
] | bd99932e444dda7c7611a718c318fc123422ed142cc142fc5b46b4dda5cce390 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2017 Malcolm Ramsay <malramsay64@gmail.com>
#
# Distributed under terms of the MIT license.
"""Module for testing the initialisation."""
import tempfile
from pathlib import Path
import hoomd
import numpy as np
import pytest
from hypothes... | malramsay64/MD-Molecules-Hoomd | test/initialise_test.py | Python | mit | 5,775 | [
"CRYSTAL"
] | 7976397ebf2f1cefad955abd0493fdd06377978a2457a943a466d44fd71522db |
# trbchan.py ---
#
# Filename: trbchan.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri May 4 14:55:52 2012 (+0530)
# Version:
# Last-Updated: Sun Jun 25 10:08:35 2017 (-0400)
# By: subha
# Update #: 347
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Base clas... | BhallaLab/moose | moose-examples/traub_2005/py/channelbase.py | Python | gpl-3.0 | 5,926 | [
"MOOSE"
] | bc41dd62439ad3ffd6f0ab9364dc0c360613fc0225f92207aba94ec661e2cc94 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/peacock/tests/peacock_app/results_output/test_results_output.py | Python | lgpl-2.1 | 3,607 | [
"MOOSE"
] | 5c1a941d6f1b4e9de1fa13a7bea2c93c7a30260ef9afe81ee7d17b5b121009f8 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authenticate, login
from django.cont... | zofuthan/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 91,744 | [
"VisIt"
] | 6c5442cb02d86748724905643ba94b639319376a766662abcbc9dea256cddcde |
# encoding: utf-8
'''
Various vertical coordinates
Presently, only ocean s-coordinates are supported. Future plans will be to
include all of the vertical coordinate systems defined by the CF conventions.
'''
__docformat__ = "restructuredtext en"
import numpy as np
import warnings
class s_coordinate(object):
""... | kshedstrom/pyroms | pyroms/pyroms/vgrid.py | Python | bsd-3-clause | 14,274 | [
"Brian"
] | 92e0995cd90a2929a7c80f3588bf66eb134f22945cccf5b5feb411fc90a0f176 |
# -*- coding: utf-8 -*-
# ****************************************************************************
# Original work Copyright (C) 2013-2015 SUNCAT
# Modified work Copyright 2015-2017 Lukasz Mentel
#
# This file is distributed under the terms of the
# GNU General Public License. See the file 'COPYING'
# in the root ... | lmmentel/ase-espresso | espresso/utils.py | Python | gpl-3.0 | 4,693 | [
"ASE",
"ESPResSo"
] | 7835e11c799ecc428540ad689614a7340864a466deb0110217e5347b0ab6993b |
import pyspeckit
# Read in J000002.09+155254.1 spectrum, a nice emission-line galaxy
sp = pyspeckit.Spectrum('SIIdoublet.fits')
# Read in rest wavelengths of SII lines. If you didn't know the names already,
# you could do sp.speclines.optical.lines.keys() to see what is available.
SIIa = sp.speclines.optical.lines[... | bsipocz/pyspeckit | examples/doublet_example.py | Python | mit | 1,642 | [
"Galaxy"
] | 6339f27bb0206c16c12ed2433f761176c44f6fe65f05aa33a8eff651ee51bc03 |
import argparse
import em.tools.input_output as IO
def register_parser(subparsers):
parser = subparsers.add_parser('align', usage=usage(), description=description())
add_arguments(parser)
def add_arguments(parser):
parser.add_argument("--input", metavar="FILE", help="Input File or Reference Structure."... | noelcjr/EntropyMaxima | em/subscripts/align.py | Python | gpl-3.0 | 3,061 | [
"CRYSTAL"
] | c32908c2de8f13849f1e973fc1c1d6bbc31aa23613f472d0568a58ef35cbb418 |
try:
from safe_pylab import *
from matplotlib.collections import *
import plot_wkb
except:
pass
from numpy import *
import sys,time
# qgis clashes with the Rtree library (because it includes its own local copy).
# fall back to a wrapper around the qgis spatial index if it looks like we're running
# u... | rustychris/stomel | src/trigrid.py | Python | gpl-2.0 | 113,063 | [
"Bowtie",
"VisIt"
] | 6a3b442a32af4bdd3d01fa5eeadde3e7ffc24c6dccc226f2115399f2497ee879 |
#!/usr/bin/env python3
# Convenience tool to get the JIRA tokens in place.
# This helps with the initial setup when connecting the bot for the first time.
# This is example code from Atlassian - https://bitbucket.org/atlassianlabs/atlassian-oauth-examples/
# The modified version for Python requests was copied from th... | qtproject/qtqa | scripts/jira/jira-bug-closer/oauth_dance.py | Python | gpl-3.0 | 2,820 | [
"VisIt"
] | b4cb0b163e6ab07fb1d9f5759988e1e0ca620eb48c2905903ccc36b7d4514190 |
# -*- coding: utf-8 -*-
r"""
==========================================================
Create a new coordinate class (for the Sagittarius stream)
==========================================================
This document describes in detail how to subclass and define a custom spherical
coordinate frame, as discussed in... | saimn/astropy | examples/coordinates/plot_sgr-coordinate-frame.py | Python | bsd-3-clause | 10,586 | [
"Galaxy"
] | 547790e0143fe9a8b1996e4cecd461eb313bd82630ddb4630845753fd1343eef |
# -*- coding: utf-8 -*-
'''
Provide authentication using YubiKey.
.. versionadded:: 2015.5.0
:depends: yubico-client Python module
To get your YubiKey API key you will need to visit the website below.
https://upgrade.yubico.com/getapikey/
The resulting page will show the generated Client ID (aka AuthID or API ID)... | smallyear/linuxLearn | salt/salt/auth/yubico.py | Python | apache-2.0 | 2,095 | [
"VisIt"
] | ed3319c970e8dfc6c52cf51d0f5fde1dec813466641df6fd51e07c2f659879e2 |
from ase import *
from ase.calculators import TestPotential
np.seterr(all='raise')
a = Atoms('4N',
positions=[(0, 0, 0),
(1, 0, 0),
(0, 1, 0),
(0.1, 0.2, 0.7)],
calculator=TestPotential())
print a.get_forces()
md = VelocityVerlet(a, dt=... | freephys/python_ase | ase/test/verlet.py | Python | gpl-3.0 | 571 | [
"ASE"
] | 2b1ca9d336577c85b0d2003ddb50af387397079bf666d993e9601dca2936bb47 |
import logging
import os
import re
import socket
import sys
import time
from optparse import make_option
import django
from django.conf import settings
from django.core.management.base import BaseCommand, CommandError
from django.db import connections, DEFAULT_DB_ALIAS
from django.core.exceptions import ImproperlyConf... | dpetzold/django-extensions | django_extensions/management/commands/runserver_plus.py | Python | mit | 21,800 | [
"VisIt"
] | 23dfcae84d70060fd9cea56ec650ad32c12c19a8568b6a85350830686297d66f |
# This file is part of wger Workout Manager.
#
# wger Workout Manager is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wger W... | DeveloperMal/wger | wger/exercises/tests/test_equipment.py | Python | agpl-3.0 | 6,236 | [
"VisIt"
] | f2c6514281ec2802857fd04b661368659173297736759841049d4303ac978c90 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
MP2 analytical nuclear gradients.
'''
from pyscf import gto, scf, mp
mol = gto.M(
atom = [
['O' , 0. , 0. , 0],
['H' , 0. , -0.757 , 0.587],
['H' , 0. , 0.757 , 0.587]],
basis = 'ccpvdz')
mf = scf.RHF(mol)... | gkc1000/pyscf | examples/grad/03-mp2_grad.py | Python | apache-2.0 | 676 | [
"PySCF"
] | ada5c5aaf0e2036a2503e50651359b6617b11881c4ac55aa0bf63fad25081b95 |
'''
MFEM example 23
See c++ version in the MFEM library for more detail
'''
import os
import io
import mfem.ser as mfem
from mfem.ser import intArray
from os.path import expanduser, join, dirname
import numpy as np
from numpy import sin, cos, exp, sqrt, pi, abs, array, floor, log, sum
def run(mesh_file="",
... | mfem/PyMFEM | examples/ex23.py | Python | bsd-3-clause | 10,605 | [
"VisIt"
] | e09c3a55ccf0f57003fba87bc2593a3ea84600479a864a03cb1073c7329c38f1 |
"""
KeepNote
Notebook indexing
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@mit.edu>
#
# 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;... | reshadh/Keepnote-LaTeX | keepnote/notebook/connection/fs/index.py | Python | gpl-2.0 | 23,492 | [
"VisIt"
] | 6e9f8432a585ba48483390bf3187c46978a69678d67c3b5a5442393abc365cd9 |
"""
===========================
Formaldehyde mm-line fitter
===========================
This is a formaldehyde 3_03-2_02 / 3_22-221 and 3_03-2_02/3_21-2_20 fitter.
It is based entirely on RADEX models.
"""
from __future__ import print_function
import numpy as np
from . import hyperfine
from . import fitter,model#,mo... | vlas-sokolov/pyspeckit | pyspeckit/spectrum/models/formaldehyde_mm.py | Python | mit | 18,938 | [
"Gaussian"
] | c54f9a109b285d3988798c22dcd7ae7e340de253a4bd30d8e3fec4a73e705d77 |
# 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 ... | ram8647/gcb-mobilecsp | modules/data_removal/data_removal_tests.py | Python | apache-2.0 | 34,158 | [
"VisIt"
] | bee44c890d9e597bf7726acc483a6e519999e6017aff96beeffe81acab9ae0d7 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTIFFReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkTIFFReader.py | Python | bsd-3-clause | 468 | [
"VTK"
] | c965c1b094242d229b47b0e17308b5186061a7334a05421c16f974468f979783 |
# encoding: utf-8
from __future__ import unicode_literals
import json
import mock
import datetime
import pytest
import responses
from nose.tools import * # noqa
from dateutil.parser import parse as parse_datetime
from website import settings
from addons.osfstorage.models import OsfStorageFileNode, OsfStorageFolder
... | erinspace/osf.io | addons/osfstorage/tests/test_views.py | Python | apache-2.0 | 42,315 | [
"Galaxy"
] | 6e6e97ea18526e98265ebff15aa26bed49818753ff6312f5e0a43f0a2c505ef4 |
# -*- coding: utf-8 -*-
# General Django settings for mysite project.
import os
import sys
import django.conf.global_settings as DEFAULT_SETTINGS
import logging
import mysite.pipelinefiles as pipelinefiles
import mysite.utils as utils
from celery.schedules import crontab
try:
import psycopg2
except ImportError:
... | tomka/CATMAID | django/projects/mysite/settings_base.py | Python | gpl-3.0 | 16,810 | [
"NEURON"
] | 797da6467c35af71520e7d5061c41a33b176cab41003c74e05550287fc6153c2 |
# 130. Surrounded Regions QuestionEditorial Solution My Submissions # Total Accepted: 66921
# Total Submissions: 390322
# Difficulty: Medium
# Contributors: Admin
# Given a 2D board containing 'X' and 'O' (the letter O), capture all regions surrounded by 'X'.
#
# A region is captured by flipping all 'O's into 'X's ... | shawncaojob/LC | PY/130_surrounded_regions.py | Python | gpl-3.0 | 9,719 | [
"VisIt"
] | a44de840ff926e0009962ff08928e14722286862a290824059a1db24b7cfb0c1 |
## ENVISIoN
##
## Copyright (c) 2021 Gabriel Anderberg, Didrik Axén, Adam Engman,
## Kristoffer Gubberud Maras, Joakim Stenborg
## All rights reserved.
##
## Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions are met:
##
## 1.... | rartino/ENVISIoN | unit_testing/test_moldyn_parsing.py | Python | bsd-2-clause | 2,654 | [
"VASP"
] | f110d7ec52c3f18ecc93ae7b458431147adf63730f1bc8c1dec8f175dcbae7a6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to represent the phonon density of states, etc.
"""
import numpy as np
import scipy.constants as const
from monty.functools import lazy_property
from monty.json import MSONable
... | richardtran415/pymatgen | pymatgen/phonon/dos.py | Python | mit | 13,551 | [
"Avogadro",
"Gaussian",
"pymatgen"
] | e38dd8255352084ee95170a6cfdde517c91c0d8fe1d6559cd00defbdd141377d |
"""
A myopic global optimizer class.
Author:
Ilias Bilionis
Date:
5/1/2015
"""
__all__ = ['GlobalOptimizer']
import numpy as np
from collections import Iterable
import math
import sys
import warnings
warnings.simplefilter('ignore')
import GPy
import design
import os
from . import colorAlpha_to_rgb
clas... | PredictiveScienceLab/py-bgo | pybgo/_global_optimizer.py | Python | mit | 25,564 | [
"Gaussian"
] | 188da916fb66f8d288fae0813fd6a8d1738812a637eb08accbcd5f719e3d3f28 |
#pylint: disable=missing-docstring
#* 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/... | harterj/moose | python/chigger/utils/FontOptions.py | Python | lgpl-2.1 | 2,493 | [
"MOOSE",
"VTK"
] | d1faad37fd1a435c44194798a996a4e594b122d690ea6439f125bc1475ab0c6f |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | modules/porous_flow/doc/content/modules/porous_flow/tests/heat_conduction/heat_conduction.py | Python | lgpl-2.1 | 2,591 | [
"MOOSE"
] | ed315e22e412a62f259f331cc423198819ef17f42271382223e06577290844b8 |
#!/usr/bin/env python
from __future__ import print_function
#
# LSST Data Management System
# Copyright 2012, 2015 LSST Corporation.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of... | yalsayyad/obs_decam | tests/getRaw.py | Python | gpl-3.0 | 5,285 | [
"VisIt"
] | 20081e8f958ee2b392db0cab1b60493a45ae6cde94eb1140605d088cab6ba6a4 |
#!/usr/bin/env python
from astropy.io import fits
from astropy.time import Time
import glob
import os
import photutils
import scipy.optimize as sco
import numpy as np
# Gaussian functional form assumed for PSF fits
def psf((xx,yy),s0,s1,x0,y0,w):
elow = -50.
arg = - w * ( (xx-x0)**2 + (yy-y0)**2 ... | keatonb/tsphot | fits_process.py | Python | mit | 8,982 | [
"Gaussian"
] | c558e1d6c82bc4fb61c67def7c01ac971f2c5941b3432fe42e784fc31a0bee32 |
# Copyright 2018 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... | dongjoon-hyun/tensorflow | tensorflow/contrib/eager/python/examples/l2hmc/l2hmc.py | Python | apache-2.0 | 12,269 | [
"Gaussian"
] | 9a82940a89c0e4c22a1eb784906bbcf7a4cbc1f5f62ef54b2b414109e33a6e2a |
# __BROKEN__
# Izhikevich_with_synapse.py ---
#
# Filename: Izhikevich_with_synapse.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Sat Apr 19 10:47:15 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
# Change log:
#
... | BhallaLab/moose-examples | snippets/Izhikevich_with_synapse.py | Python | gpl-2.0 | 5,356 | [
"MOOSE",
"NEURON"
] | de2563a815600bc14c12188b85c1020727e9900495e9c18621f4cabc40c3eec2 |
""" Test for Profiler.py
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import time
from os.path import dirname, join
from subprocess import Popen
import pytest
from flaky import flaky
import DIRAC
from DIRAC.Core.Utilities.Profiler import Profiler
... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/test/Test_Profiler.py | Python | gpl-3.0 | 4,254 | [
"DIRAC"
] | c4a49a494a06453b8f0b9ce1acbc81669f372a801f7631e156cecbd4fe7540c8 |
#!/usr/bin/env python
## \file tools.py
# \brief file i/o functions
# \author T. Lukaczyk, F. Palacios
# \version 3.2.9 "eagle"
#
# SU2 Lead Developers: Dr. Francisco Palacios (Francisco.D.Palacios@boeing.com).
# Dr. Thomas D. Economon (economon@stanford.edu).
#
# SU2 Developers: Prof. Juan J.... | chenbojian/SU2 | SU2_PY/SU2/io/tools.py | Python | lgpl-2.1 | 33,910 | [
"ParaView"
] | 9f1e4b172dfa39adef7f3f9763f050de85c7ccb9be11fb660faf5e71543a16cf |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements an XRD pattern calculator.
"""
import json
import os
from math import asin, cos, degrees, pi, radians, sin
import numpy as np
from pymatgen.symmetry.analyzer import SpacegroupAnaly... | gmatteo/pymatgen | pymatgen/analysis/diffraction/xrd.py | Python | mit | 11,153 | [
"CRYSTAL",
"pymatgen"
] | 0a197cffc7acec394433b818b25c569ed97a103e0e197ac872297639158b206d |
# the inputs list tells MCEdit what kind of options to present to the user.
# each item is a (name, value) pair. name is a text string acting
# both as a text label for the input on-screen and a key for the 'options'
# parameter to perform(). value and its type indicate allowable and
# default values for the option:
... | mcedit/mcedit | filters/demo/filterdemo.py | Python | isc | 5,188 | [
"VisIt"
] | 1040e363d9509118f675abdb13c0be1fd36f7836661616ee43e0cf0e02dd7ba3 |
#! /usr/bin/python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Version: 0.8+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
For developers who work from a V... | tvd-dataset/TheBigBangTheory | versioneer.py | Python | mit | 25,132 | [
"Brian"
] | c82471d0f49942515f6ea66aa35117113cd56a9df141a1050ed5ffbd247da5ce |
#
# io - Data input and output
#
from info import __doc__
from numpy import deprecate
# matfile read and write
from matlab import loadmat, savemat
# netCDF file support
from netcdf import netcdf_file, netcdf_variable
from matlab import byteordercodes
from data_store import save_as_module
from mmio import mminfo, ... | scipy/scipy-svn | scipy/io/__init__.py | Python | bsd-3-clause | 470 | [
"NetCDF"
] | f5418f61d838c23120537a12baf6e106f2ec8b45ddd7274c57e390ab9a350082 |
# Downloaded from http://www.logarithmic.net/pfh-files/blog/01208083168/sort.py
"""
Tarjan's algorithm and topological sorting implementation in Python
by Paul Harrison
Public domain, do with it as you will
"""
def strongly_connected_components(graph):
""" Find the strongly connected compon... | joxeankoret/diaphora | others/tarjan_sort.py | Python | agpl-3.0 | 2,807 | [
"VisIt"
] | 3d24ca359cc900d317a7efac392da2b43c407fb3b559fe92c451aaad4ad18e47 |
"""User preferences for KlustaViewa."""
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
import logging
import numpy as np
# --------------------------------------------------------------... | DavidTingley/ephys-processing-pipeline | installation/klustaviewa-0.3.0/kwiklib/utils/preferences_default.py | Python | gpl-3.0 | 3,402 | [
"Gaussian"
] | 4fb6fdf0b9217cf44912a501065f570336f71131bc63d94fb65b6af88e5af2de |
from ase import *
from hotbit import *
from ase.data.molecules import molecule
atoms=molecule('C6H6')
atoms.set_pbc(False)
atoms.center(vacuum=3)
calc=Hotbit(SCC=True, txt='benzene.cal')
atoms.set_calculator(calc)
traj=PickleTrajectory('quench.traj','w',atoms=atoms)
qn=QuasiNewton(atoms)
qn.attach(traj.write)
qn.run(... | pekkosk/hotbit | hotbit/doc/examples/benzene.py | Python | gpl-2.0 | 322 | [
"ASE"
] | 45f3a8a846b7c442b0b1cbf65d09873af278ff9a92f5bb7a72c24e03488b8ff6 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/Community-Zenpacks | ZenPacks.AndreaConsadori.Asterisk16/ZenPacks/AndreaConsadori/Asterisk16/modeler/plugins/AsteriskDeviceMap.py | Python | gpl-2.0 | 1,317 | [
"VisIt"
] | 63fb3711d651a6536272f9c15eb3500f4b375e836081c3032e9d5937791c97b4 |
"""
Fit the mass-ratio using emcee
"""
import os
import numpy as np
import emcee
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib import gridspec
from matplotlib.ticker import FuncFormatter
import pandas as pd
from CombineCCFs import get_rv
sns.set_context('paper', font_scale=2.0)
# Functions... | kgullikson88/Planet-Finder | MassRatio_Fitter.py | Python | mit | 11,022 | [
"Gaussian"
] | ec672c5b873a8af049fb669683a78a1cd73efe1640868775966fb83eb76a3373 |
#-*- encoding: utf-8 -*-
"""
Monopoly odds
In the game, Monopoly, the standard board is set up in the following way:
GO A1 CC1 A2 T1 R1 B1 CH1 B2 B3 JAIL
H2 C1
T2 U1
H1 C2
CH3 ... | zlsun/ProjectEuler | 084.py | Python | mit | 3,189 | [
"VisIt"
] | 9a0754f8779d65ec32329241a4deb0751c93758ddbb26cbf02c6b6cc084c0a33 |
#!/usr/bin/env python3
"""
Reads the uniref100 flat file and creates a SQLite3 database of commonly-accessed attributes
for each entry.
INPUT
When you BLAST against a database like UniRef100 or UniRef90 you'll get accessions like:
UniRef100_A8PWR2 RepID=A8PWR2_MALGO
UniRef100_M9MHS5 RepID=M9MHS5_PSEA3... | zctea/biocode | blast/uniref_to_sqlite3.py | Python | gpl-3.0 | 7,123 | [
"BLAST"
] | 40fd6ff03abb3a807af1164cd8c15b885221c13416d49e5a05378430af5ec610 |
"""
autotune.py - module generate test data for autotune
Usage:
import autotune
autotune.baseline_test()
autotune.rms_spectrum_test(song='tainted', tuning_f0=110.) # RMS power of equal-temperament bins for song 'tainted'
autotune.mixture_test(song='tainted', tuning_f0=110.) # apply autotune algorithm to song/vocal... | bregmanstudio/voxid | autotune.py | Python | apache-2.0 | 14,190 | [
"Gaussian"
] | 6b18ada881948697494b641d98fb43bfd4612b8f07b8027b294e20656d44c7bc |
# -*- coding: utf-8 -*-
import numpy as np
def vectoa(Xg,Yg,X,Y,U,V,corrlenx,corrleny,err,b=0):
'''
(Adapted from Filipe Fernandes function)
Vectoa is a vectorial objective analysis function.
It interpolates a velocity field (U and V, east and north velocity components)
into a streamfunction ... | iuryt/ocean | OceanLab/oa.py | Python | mit | 6,744 | [
"Gaussian"
] | cba782a8a06755b46d3579ab0dc813eb6fdacbe063d32094a2b302ff2ea60ba1 |
""" AlwaysProbingPolicy module """
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
class AlwaysProbingPolicy(PolicyBase):
"""
The AlwaysProbingPolicy is a dummy module that can be used as example, it
always returns Probing status.
"""
@staticmethod... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/AlwaysProbingPolicy.py | Python | gpl-3.0 | 599 | [
"DIRAC"
] | 2964c0761ad7cc65d70934ca8f8d7c388a41e60441b53be510ce65457738f7fc |
import gen_utils
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import vtktud
class MyGlyph3D(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, mod... | chrisidefix/devide | modules/user/opticflow/MyGlyph3D.py | Python | bsd-3-clause | 2,484 | [
"VTK"
] | ab2783d3559e939edff7639d96b90c42eddd37b3a70f4cbf89c06f3f49769f35 |
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as sio
from sklearn import svm
## Machine Learning Online Class - Exercise 6: Support Vector Machines
# Instructions
# ------------
#
# This file contains code that helps you get started on the
# linear exercise. You will need to complete the fol... | cameronlai/ml-class-python | solutions/ex6/ex6.py | Python | mit | 6,354 | [
"Gaussian"
] | a5b38baaffb86c39b51c86c023cd4da5e4390296ae538ad71956b407afd2d7ac |
# coding: utf-8
# Adam Petrone
# March 2014
import os
import re
import logging
from pegasus.commands import *
from pegasus.models import (
FileGroup,
FileWriter,
DefaultDict,
Driver,
Path,
ProductType,
VariableContext,
make_paths_relative_to_project)
from pegasus.core import Architecture
from pegasus.util imp... | apetrone/pegasus | drivers/xcode.py | Python | bsd-2-clause | 48,957 | [
"VisIt"
] | ccc0e09358354dbdbd0d425fc1782bd54e2aa3b007a2eebf6c86fddf3edc704b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | dermoth/gramps | gramps/plugins/tool/finddupes.py | Python | gpl-2.0 | 23,285 | [
"Brian"
] | ede533ce8fbe87942d9fd6dc415733fcf025a4efe5675d260c8f985b0a5b9a3f |
#!/usr/bin/python
import httplib
import httplib2
import os
import random
import sys
import time
from apiclient.discovery import build
from apiclient.errors import HttpError
from apiclient.http import MediaFileUpload
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oau... | deathmetalland/IkaLog | upload_video.py | Python | apache-2.0 | 6,729 | [
"VisIt"
] | a7f33c858113e1527a7e5ce9c9828ee5ae7228a86f73cdc8c193f16f9c1e7988 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0070_visit_siblings_under_5_present'),
]
operations = [
migrations.AlterModelOptions(
name=... | koebbe/homeworks | visit/migrations/0071_auto_20150826_2053.py | Python | mit | 1,078 | [
"VisIt"
] | 5d94886c91c2cf49a9308870feb6902bb10062412fa745d655c36a9eee9165e7 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | ueshin/apache-spark | python/pyspark/mllib/util.py | Python | apache-2.0 | 22,859 | [
"Gaussian"
] | 59c2905bfc23972eaab48693b4902ac9060162055f9c315f7be8fcaff8fe1cf1 |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2007-2008 Matthew Perry
Copyright (C) 2008-2010 Borys Jurgiel
/***************************************************************************
* *
* This program is free software; you can redistribute it a... | mola/qgis | python/plugins/plugin_installer/installer_gui.py | Python | gpl-2.0 | 41,380 | [
"VisIt"
] | 443762e2a77c0418a3e5352393934848deb21333cc868b2f394e0f863fa437bb |
#
# The Qubes OS Project, https://www.qubes-os.org/
#
# Copyright (C) 2010-2015 Joanna Rutkowska <joanna@invisiblethingslab.com>
# Copyright (C) 2014-2015 Wojtek Porczyk <woju@invisiblethingslab.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Publi... | kalkin/qubes-core-admin | qubes/dochelpers.py | Python | gpl-2.0 | 15,474 | [
"VisIt"
] | 04facebf3dac7d6cf6165075e6c7ff1e6115e0dec7fe9a5cb2b43a2b95993a1f |
#!/usr/bin/env python3
import math
from numbers import Number
import torch
from torch.distributions import constraints
from torch.nn import Module as TModule
from .prior import Prior
class WishartPrior(Prior):
"""Wishart prior over n x n positive definite matrices
pdf(Sigma) ~ |Sigma|^(nu - n - 1)/2 * exp... | jrg365/gpytorch | gpytorch/priors/wishart_prior.py | Python | mit | 4,266 | [
"Gaussian"
] | 5af755cfc081254a9416c03042c22cf7e484e98eed5157e0c7bec81950fb3722 |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 y... | jat255/hyperspy | hyperspy/_signals/signal1d.py | Python | gpl-3.0 | 64,370 | [
"Gaussian"
] | b166d595fb65d8c96b0bde5117af76eca1e54d3f1f9de58135ba22993a0f170f |
# -*- coding: utf-8 -*-
#
# Copyright © 2009-2010 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""Utilities and wrappers around inspect module"""
from __future__ import print_function
import inspect
import re
# Local imports:
from spyderlib.utils import enco... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/spyderlib/utils/dochelpers.py | Python | gpl-3.0 | 11,439 | [
"VTK"
] | cf93b84ef9489252d6c49d4847c2fc504181eed5648460cec9e86e47109edb15 |
import math
from ecell4.reaction_reader.decorator2 import species_attributes, reaction_rules
from ecell4.reaction_reader.network import generate_reactions
@species_attributes
def attributegen():
gTetR(lac1,lac2) | 1
gCI(tet1,tet2) | 1
gLacI(cI1,cI2) | 1
# gTetR(lac1^1,lac2^2).pLacI(tet^1).pLacI(tet^2... | navoj/ecell4 | python/samples/reaction_reader/Repressilator/Repressilator.py | Python | gpl-2.0 | 7,171 | [
"Avogadro"
] | e08746a0b56b19cbaa7959e0575d4fcd78cd92df2143b46a3d4310c0d4a5389c |
########################################################################
# File : SiteDirector.py
# Author : A.T.
########################################################################
""" The Site Director is a simple agent performing pilot job submission to particular sites.
"""
import os
import base64
import... | vmendez/DIRAC | WorkloadManagementSystem/Agent/SiteDirector.py | Python | gpl-3.0 | 48,832 | [
"DIRAC"
] | f00dec9c6547e949bcd4f8130ec9450dc954dac60a118131c47b1ccabc2a09b3 |
'''
GaussianDistr.py
Gaussian probability distribution
Attributes
-------
m : D-dim vector, mean
L : DxD matrix, precision matrix
'''
import numpy as np
import scipy.linalg
from ..util import dotABT, MVgammaln, MVdigamma, gammaln, digamma
from ..util import LOGTWOPI, EPS
from .Distr import Distr
class GaussDistr( D... | daeilkim/refinery | refinery/bnpy/bnpy-dev/bnpy/distr/GaussDistr.py | Python | mit | 3,573 | [
"Gaussian"
] | abdff12fa476066783bc64d516f2002aae5e2fd0d85b5f8932750b0f9f3fdeaf |
import pytest # NOQA
import hashlib
import os
import utilities
import expected
from openwpmtest import OpenWPMTest
from ..automation import TaskManager
from ..automation.utilities.platform_utils import parse_http_stack_trace_str
class TestHTTPInstrument(OpenWPMTest):
NUM_BROWSERS = 1
def get_config(self, da... | tommybananas/OpenWPM | test/test_http_instrumentation.py | Python | gpl-3.0 | 5,457 | [
"VisIt"
] | 1541afa6e78e3f7aad12e2c23b8dfb0d800bf41d6a35eee2db80367282437c7a |
# -*- coding: utf-8 -*-
"""
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join('README.md'... | brianhuey/vissim | setup_v8.py | Python | mit | 4,040 | [
"Brian"
] | df05dc6dbbab96c372edb36216a2849540a687b1533e387ab4dd837461352d7e |
"""
Plot summary statistics as a function of S/N for stars in the training set,
showing us compared to ASPCAP for whatever labels in the model.
"""
import numpy as np
import matplotlib.pyplot as plt
import os
from astropy.io import fits
from astropy.table import Table
from six.moves import cPickle as pickle
import An... | peraktong/AnniesLasso | sandbox-scripts/mudbox_compare_models.py | Python | mit | 5,549 | [
"VisIt"
] | cc68510067dcb86fc3dfd547b7d5b4c990a56ddaa2dec321fb3fe3a925917d4c |
"""
Galaxy control queue and worker. This is used to handle 'app' control like
reloading the toolbox, etc., across multiple processes.
"""
import logging
import threading
import sys
import galaxy.queues
from galaxy import eggs, util
eggs.require('anyjson')
if sys.version_info < (2, 7, 0):
# Kombu requires import... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/queue_worker.py | Python | gpl-3.0 | 4,957 | [
"Galaxy"
] | 144e0b9830e8d5a3c1841d453fd70a64c00551915278e644d6c4ef27d2f94590 |
"""
@created_at 2014-07-17
@author Exequiel Fuentes <efulet@gmail.com>
@author Brian Keith <briankeithn@gmail.com>
"""
# Se recomienda seguir los siguientes estandares:
# 1. Para codificacion: PEP 8 - Style Guide for Python Code (http://legacy.python.org/dev/peps/pep-0008/)
# 2. Para documentacion: PEP 257 - Docst... | efulet/pca | pca/lib/graph_exception.py | Python | mit | 694 | [
"Brian"
] | 13fcf916775ed13953fd60ab3c11186c85da82bda75fec816dbc5ad8105b383b |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_external_vpn_gateways.py | Python | apache-2.0 | 101,376 | [
"Octopus"
] | e6288a53a6063f8b65b56545d4e0a53e4abb49ff1fede4adc3e2937ef5d18f07 |
from __future__ import unicode_literals
import json
import os
from django.contrib.auth import get_user_model
from django.contrib.auth.models import Group, Permission
from django.core.files.base import ContentFile
from django.forms.utils import ErrorDict
from django.test import TestCase, modify_settings
from django.te... | torchbox/wagtailmedia | tests/test_views.py | Python | bsd-3-clause | 41,981 | [
"exciting"
] | 7decdc86432909b0e76a867ec74edfc3750402d2fec776b081b7e945fee3e4c3 |
"""
Test of the classical LM model for language modelling
"""
from groundhog.datasets import LMIterator
from groundhog.trainer.SGD_momentum import SGD as SGD_m
from groundhog.trainer.SGD import SGD
from groundhog.mainLoop import MainLoop
from groundhog.layers import MultiLayer, \
RecurrentMultiLayer, \
Re... | sjtufs/GroundHog | tutorials/DT_RNN_Tut_Ex_Skeleton.py | Python | bsd-3-clause | 15,646 | [
"Gaussian"
] | 51c943820d6a9625594ccbcf4e69cd1234d902b64254a31955d8331f10dc9581 |
"""
====================================================================
Linear and Quadratic Discriminant Analysis with confidence ellipsoid
====================================================================
Plot the confidence ellipsoids of each class and decision boundary
"""
print __doc__
from scipy import lina... | joshbohde/scikit-learn | examples/plot_lda_qda.py | Python | bsd-3-clause | 4,715 | [
"Gaussian"
] | 4dab99f348a2a75f2c30cdaf8b734f1e486c997d1be37b1086e5c5ff86271d96 |
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