text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""@file hs_galaxy_image.py
Utilities to deal with galaxy image in JPEG or PNG format.
Including functions to scale, rotate, transform, and filter galaxy images to
study their morphology
"""
import numpy as np
import subprocess as sub
from os import path
def find_image_center(xsize,ysize):
"""
Find the pixel ... | dr-guangtou/hs_galphot | figure/hsGalaxyJpeg.py | Python | bsd-3-clause | 3,570 | [
"Galaxy"
] | 9760db429f0809dbab31acd94ecb920aa1a8ff86c579730d55b3de9f00989004 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0060_auto_20150816_0023'),
]
operations = [
migrations.AddField(
model_name='visit',
name='... | koebbe/homeworks | visit/migrations/0061_visit_insights.py | Python | mit | 396 | [
"VisIt"
] | 778314db483fcb4fd965bec9dc2a643271c95bf086cdd96b566c482d1172f9c8 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | y12uc231/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 23,969 | [
"VisIt"
] | 75a1e16d860f9727629678a990bf4a6343bfd9230469e1dae6b6db7bc7850737 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# All Rights Reserved.
#
# Androguard is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either versi... | JulianSchuette/android-instrumentation | injector/androguard/decompiler/dad/graph.py | Python | apache-2.0 | 13,100 | [
"VisIt"
] | 70b50110ea566e5d3a840f22e6770b82fe9574096c5bb688bbafd2934693ed81 |
# sybase/base.py
# Copyright (C) 2010-2016 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | sandan/sqlalchemy | lib/sqlalchemy/dialects/sybase/base.py | Python | mit | 28,696 | [
"ASE"
] | 401860d8ea2bae0625bc93be96c1702235e4730d1177486e4c86c2869203954e |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
#
# Copyright (c) 2013 ASMlover. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyrig... | ASMlover/study | python/mini-stl/vector.py | Python | bsd-2-clause | 2,507 | [
"VisIt"
] | eb3e1d4969cfd6e368a93d154b6cfadd3bda36ddcbd4deeee8d44fea98ad5c2b |
"""
Test for the various mlab source functions.
These tests are higher level than the tests testing directly the
MlabSource subclasses. They are meant to capture errors in the formatting
of the input arguments.
"""
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# Copyright (c) 2008, Enthought, Inc... | dmsurti/mayavi | mayavi/tests/test_mlab_source_integration.py | Python | bsd-3-clause | 16,653 | [
"Mayavi"
] | 3f5d1f56fe86004a7bd3938205772447afdcba64ea43fb5a44ea9274ffc754ce |
import tensorflow as tf
import numpy as np
class VariationalAutoencoder(object):
def __init__(self, n_input, n_hidden, optimizer = tf.train.AdamOptimizer()):
self.n_input = n_input
self.n_hidden = n_hidden
network_weights = self._initialize_weights()
self.weights = network_weights... | wujinjun/TFbook | chapter5/models-master/autoencoder/autoencoder_models/VariationalAutoencoder.py | Python | gpl-3.0 | 3,082 | [
"Gaussian"
] | b4f72f771df9bf95d4f36f27a722311d69ecceeed3f1d75f983f8be922ea5430 |
#!/usr/bin/env python3
#
# Copyright (C) 2018 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is... | geraldinepascal/FROGS | tools/affiliation_OTU/affiliation_OTU.py | Python | gpl-3.0 | 34,987 | [
"BLAST"
] | a9a09cdf0a286c95c42b7c71b1cf7719655b291f00f2761f22b40e211a1a9119 |
from rdkit import Chem
from rdkit import rdBase
from rdkit import RDConfig
import os
from rdkit.Chem import rdMolDescriptors as rdMD
from rdkit.Chem import AllChem
import time
def get3D(m,is3d):
if not is3d:
m = Chem.AddHs(m)
# define the new code from RDKit Molecule 3D ETKDG.
ps = AllChe... | rdkit/rdkit | Code/GraphMol/Descriptors/test3D.py | Python | bsd-3-clause | 1,388 | [
"RDKit"
] | 14e87064deb44f78b7650f8725ed52d982a266a7548716a0a158ac2c9853b6fd |
#!/usr/bin/env python
# coding: utf-8
"""
This script analyzes the Abinit source tree and generates the dependency graph
"""
from __future__ import print_function, division, unicode_literals, absolute_import
import sys
import os
import argparse
from fkiss import termcolor
from fkiss.tools import print_dataframe
from ... | abinit/abinit | abisrc.py | Python | gpl-3.0 | 17,717 | [
"ABINIT"
] | 283b6ac5d20ae1091642705eecc2b924fcb8434bc495ca03f3293b3d8f150dc9 |
#
# Adapted from the PyEVtk library, https://bitbucket.org/pauloh/pyevtk
#
# Copyright of the original code is replicated below.
#
# ***********************************************************************************
# * Copyright 2010 Paulo A. Herrera. All rights reserved. *
# * ... | MicroMagnum/MicroMagnum | src/magnum/micromagnetics/io/vtk/vtk.py | Python | gpl-3.0 | 14,403 | [
"VTK"
] | 0df5d2291351c7876ca753634aea6c21856e794a6645addf6bd521cf0c6b0c1e |
import ternary
import numpy as np
import pandas as pd
from functions import *
import sys
from functools import reduce
from sklearn.manifold import *
from sklearn.cluster import *
from pylab import *
import _pickle as cPickle
from skimage.filters import gaussian
#########################################################... | gviejo/ThalamusPhysio | python/main_test_mutual_information_shank_shuf_noSWS.py | Python | gpl-3.0 | 4,896 | [
"Gaussian"
] | 95bfe9283ec854c12288f20914074f08fb105c35463b678b87c084fe9cd01429 |
#!/usr/bin/env python
#JSON {"lot": "RHF/cc-pVDZ",
#JSON "scf": "PlainSCFSolver",
#JSON "linalg": "CholeskyLinalgFactory",
#JSON "difficulty": 2,
#JSON "description": "Basic RHF example with Cholesky decomposition of the ERI"}
from horton import *
# Load the coordinates from file.
# Use the XYZ file from HORTON's... | eustislab/horton | data/examples/hf_dft/rhf_water_cholesky.py | Python | gpl-3.0 | 1,765 | [
"Gaussian"
] | 3a5b5d603937cd762077301e8843d548b0ab729942bedfa8b6755a6e4fe35677 |
"""Actions to start the CitcomS filter.
"""
#Author: Martin Weier
#Copyright (C) 2006 California Institute of Technology
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2 of the L... | geodynamics/citcoms | visual/Mayavi2/original_plugins/plugins/filter/CitcomSFilterActions.py | Python | gpl-2.0 | 1,883 | [
"Mayavi"
] | af153f83d4e98e553cba17cb02cb2b2395d58538955e55b146d93709ee1dbb1d |
import copy
import textwrap
import pytest
from paleomix.common.makefile import MakefileError
from paleomix.pipelines.bam.makefile import read_makefiles
from paleomix.resources import template
def _read_makefile(filepath):
(result,) = read_makefiles([filepath])
return result
##############################... | MikkelSchubert/paleomix | tests/pipelines/bam/makefile_test.py | Python | mit | 20,123 | [
"BWA"
] | 2402f5361e7177382174a03a03e2ade83f0a4fe14462cf2f6f837ec6c6c6b708 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('search_tools')
@click.argument("q", type=str)
@click.option(
"--page",
help="page requested",
default="1",
show_default=True,
type=int
)
@click.option(
"--pa... | galaxy-iuc/parsec | parsec/commands/toolshed_tools/search_tools.py | Python | apache-2.0 | 1,744 | [
"Galaxy"
] | aeaf707c21cc6a55d7167c05d831196acfc652024e971be1ae4a05ea57c45141 |
"""
Filename: gaussian_contours.py
Authors: John Stachurski and Thomas Sargent
Plots of bivariate Gaussians to illustrate the Kalman filter.
"""
from scipy import linalg
import numpy as np
import matplotlib.cm as cm
from matplotlib.mlab import bivariate_normal
import matplotlib.pyplot as plt
# == Set up the Gaussi... | 28ideas/quant-econ | examples/gaussian_contours.py | Python | bsd-3-clause | 3,179 | [
"Gaussian"
] | da2ade5bd241f69cef00a623428115860d2fa81a1792e6a20eef3f49c2dc02dc |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; you can redistribute it an... | ellonweb/merlin | Arthur/views/exiles/exiles.py | Python | gpl-2.0 | 3,389 | [
"Galaxy"
] | 025f00e70173b94bcdca525089e26940e465cff505616a0207f2c529f8dc29fc |
# Open epwmap
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Ladybug is free software; you can redistribute it and/or modify
# it under the ... | samuto/ladybug | src/Ladybug_download EPW Weather File.py | Python | gpl-3.0 | 1,836 | [
"EPW"
] | 189dcc6f62bc7645715af646491de6beddf2a2b7b8ebd90802f89855b31e759f |
#Copyright ReportLab Europe Ltd. 2000-2004
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/pdfbase/cidfonts.py
#$Header $
__version__=''' $Id$ '''
__doc__="""CID (Asian multi-byte) font support.
This defines classes to represent CID fonts. ... | BackupTheBerlios/pixies-svn | pixies/reportlab/pdfbase/cidfonts.py | Python | gpl-2.0 | 14,963 | [
"Brian"
] | 56fa78a344a77045d09c4d7b5b40e076f65d704d83cc59d97bb1e2947243c72b |
""" Test TorsionScanSet """
from torsionfit.tests.utils import get_fun
import torsionfit.TorsionScanSet as torsionset
from cclib.parser import Gaussian
from cclib.parser.utils import convertor
from numpy.testing import assert_almost_equal, assert_array_equal
from parmed.charmm import CharmmParameterSet
import unittest... | jchodera/Torsions | torsionfit/tests/test_torsionScanSet.py | Python | gpl-2.0 | 2,242 | [
"CHARMM",
"Gaussian",
"OpenMM",
"cclib"
] | 30178efce4f9ec153aeac7ba96ee357de3a5887e85c5f67b3a91ed43fbdc9bdc |
#!/usr/bin/env python
"""
Data processing script for LBM binary data files.
Call this script from the same directory where the LBM input file
resides as well as all of the *.b_dat files from the simulation.
No arguments are needed.
Usage:
>>python ./process_lbm_data.py
When done, you should have a set of *.vtk fil... | stu314159/pyNFC | process_lbm_data_mpi.py | Python | mit | 3,269 | [
"VTK"
] | 22a29547a5fef169e16a0fe97ba241d5bade8f83bb0c3c921c90b45427e128ce |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/core/manager.py | Python | lgpl-3.0 | 4,578 | [
"VisIt"
] | 8e309966355f402e1a271b9b5b1d3aa932f74a477d471abe6350c57985a1509c |
# -*- coding: utf-8 -*-
"""
End-to-end tests for contract operation of biz a limited bulk operation feature
"""
from nose.plugins.attrib import attr
from unittest import skip
from .test_ga_contract_operation import BizPersonalinfoMaskTestBase, BizStudentUnregisterTestBase
class BizStudentBulkManagementMixin(obj... | nttks/edx-platform | common/test/acceptance/tests/biz/test_ga_contract_operation_bulk.py | Python | agpl-3.0 | 4,591 | [
"VisIt"
] | 3b0d294f3917061a4305d321f41d44cc8f3c1a2eb0c59cebc93b930ad53e57e9 |
""" DIPStorage class is the client of the DIRAC Storage Element.
The following methods are available in the Service interface
getMetadata()
get()
getDir()
put()
putDir()
remove()
"""
__RCSID__ = "$Id$"
import os
import random
from DIRAC import g... | Andrew-McNab-UK/DIRAC | Resources/Storage/DIPStorage.py | Python | gpl-3.0 | 17,735 | [
"DIRAC"
] | abf96da5614af75cbc3c31033272b3f9dde4e40b67bfb3eb3f89178dcda4471a |
from __future__ import absolute_import
from __future__ import print_function
from builtins import range
import numpy as np
import re
from glob import glob
from os import path
from pyproj import Proj
from pyproj import transform
from shyft import api
from .. import interfaces
from netCDF4 import Dataset
from shyft.repo... | felixmatt/shyft | shyft/repository/netcdf/ec_data_repository.py | Python | lgpl-3.0 | 25,964 | [
"NetCDF"
] | 5a8814328d56562fcad544fbf3e90315586fd3183346a3f61cc5bb5106586395 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Linear Regression
=================
This example demonstrates the use of classes :func:`.interp.lstabsdev` and... | bwohlberg/sporco | examples/scripts/misc/regression.py | Python | bsd-3-clause | 3,198 | [
"Gaussian"
] | a973233dce459903b557cf6721ef39be163c68e95972ecd42a0b129e8de92f08 |
#
# 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... | espressomd/espresso | testsuite/python/coulomb_tuning.py | Python | gpl-3.0 | 2,765 | [
"ESPResSo"
] | 88d36a326abb314b2846c5be28fc4910db708e31f534826484d3921a9ef7ede7 |
from . import empty
import aggregators
from serializers import groups
def create():
obj = groups.Group(RecursiveHeader(), RecursiveDescription(), RecursiveData())
return groups.Recursive(obj)
class RecursiveHeader(empty.StageVisitor):
def row_for(self, stage_class):
return stage_class.visit_clas... | alepulver/my-thesis | results-tables/serializers/stage/events.py | Python | mit | 3,229 | [
"VisIt"
] | 6557879b06c7e01cead797347fa673b6fad37a064076be6f44c06accd42fe866 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read a MAF from standard input and print average GC content of each alignment
usage: %prog < maf > out
"""
from __future__ import division
import sys
from bx.align import maf
def __main__():
maf_reader = maf.Reader( sys.stdin )
for m in maf_reader:
... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_gc_content.py | Python | bsd-3-clause | 647 | [
"Galaxy"
] | 2528e5d2d62f1081c1adffa82d0c19f302fbd00f767a40d060d9fffb33c5d2be |
import cairo, math, sys
import cairoplot
from .series import Series
# non-random data for needs of visual comparison of changes
if '--non-random' in sys.argv:
random = lambda : 1.0
print('Plotting nonrandom data')
else:
import random
random = random.random
# Line plotting
test_scatter_plot = 1
test_d... | walterbender/dimensions | cairoplot/seriestests.py | Python | gpl-3.0 | 15,372 | [
"Gaussian"
] | 2cb68a0120b86b115e9d6295c7c63928ffe7abc0d55b3a46feddb51a53be806f |
import unittest
from nose.tools import (assert_true, assert_in, assert_raises, assert_equal)
import io
import numpy
import logging
import sknn
from sknn.mlp import Regressor as MLPR
from sknn.mlp import Layer as L
class LoggingTestCase(unittest.TestCase):
def setUp(self):
self.buf = io.StringIO()
... | gticket/scikit-neuralnetwork | sknn/tests/test_rules.py | Python | bsd-3-clause | 5,006 | [
"Gaussian"
] | 702e59e779b4607d995e4dd26103a6cce27a578342b6b792b2cfa13f794232c2 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2019 The Chromium OS Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Module to detect flashing infrastructure and flash ap firmware.
This script automatically detects the f... | endlessm/chromium-browser | third_party/chromite/lib/firmware/flash_ap.py | Python | bsd-3-clause | 14,696 | [
"Octopus"
] | 8da838055e9fe1b0e9463151451dfcadb507bf99372841e7a9b3a273d56ef066 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/alignment/tests/test_ssw.py | Python | bsd-3-clause | 32,539 | [
"scikit-bio"
] | 28d445a72657dfec24cd750e10edabf5518caa8dad21762824f5f3bf7866c882 |
#!/usr/bin/env python
# CREATED:2013-03-11 18:14:30 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.beat
from __future__ import print_function
from nose.tools import nottest, raises, eq_
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import matplotlib
matplotl... | decebel/librosa | tests/test_beat.py | Python | isc | 5,052 | [
"Brian"
] | e49128162c7d7df1ed41b5c570fde930fa8fbbef50b140ef09067c0e10191f32 |
#!/usr/bin/env python2.7
###
# File : bayesian.js
# Authors : Bjorn Barrefors
# Project : CMS-DDM -> https://github.com/bbarrefors/CMS-DDM
# Description : Popularity prediction using Bayesian Ridge Regression with a Gaussian Naive Bayes distribution
#
# TODO : Follow coding conventions
# DOCS : Document... | bbarrefors/CUADRnT | src/python/cuadrnt/data_analysis/rankings/bayesian.py | Python | mit | 1,693 | [
"Gaussian"
] | 52d35225647a0e868ec2ecedced4fc1fa0397d6f37cc51c50ca93a27f6da2337 |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | ghislainp/iris | lib/iris/io/__init__.py | Python | gpl-3.0 | 13,548 | [
"NetCDF"
] | b9790edb869bca694a6acce7798bb012913213a2b9e1be32ded2a23ad57e3c74 |
#!/usr/bin/python3
import sys
from parser import Parser
from visitor import SymVisitor, TGenerator
def main(filename):
try:
try:
f_tree = open('tree.txt', 'w')
f_table = open('table.txt', 'w')
f_tree2 = open('tree2.txt', 'w')
f_code = open('out.T', 'w')
... | Paradyx/mcc | mcc/mcc.py | Python | gpl-3.0 | 1,306 | [
"VisIt"
] | c42d603cd357a864f7c1725e0dc3b57e4e1bcd42f08fd925cd8357e6fcda671a |
"""Handles polygons drawn interactively by a human."""
import warnings
import numpy
import matplotlib.pyplot as pyplot
import netCDF4
from PIL import Image
import shapely.geometry
from roipoly import MultiRoi
from gewittergefahr.gg_utils import polygons
from gewittergefahr.gg_utils import general_utils
from gewitterge... | thunderhoser/GewitterGefahr | gewittergefahr/gg_utils/human_polygons.py | Python | mit | 44,511 | [
"NetCDF"
] | 184ed4ad420864d89b1624fcf066243101276f295f97c4c00b1137b52969dfec |
"""
Python bindings for the `webkit-server <https://github.com/niklasb/webkit-server/>`_
"""
import sys, os
import subprocess
import re
import socket
import atexit
import json
# path to the `webkit_server` executable
SERVER_EXEC = os.path.abspath(os.path.join(os.path.dirname(__file__),
... | nabilbendafi/plugin.video.rainiertamayo | resources/lib/webkit_server.py | Python | gpl-3.0 | 16,286 | [
"VisIt"
] | f1d1ddab36557cefcea1a6a9fcf4bd4aef50deb45e9f0fb4f59ca71d94ff1267 |
import unittest
import mock
from kalliope.core.NeuronModule import MissingParameterException
from kalliope.neurons.brain.brain import Brain
class TestBrain(unittest.TestCase):
def test_is_parameters_ok(self):
# valid neuron with boolean
synapse_name = "synapse_name"
enabled = True
... | kalliope-project/kalliope | kalliope/neurons/brain/tests/test_brain.py | Python | gpl-3.0 | 2,391 | [
"NEURON"
] | f7cbcd3076ba776d0a672de8be7e94ccd3bff2204032822a0cf88d8ebb3a7d2c |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/planner/script.py | Python | gpl-3.0 | 1,877 | [
"ORCA"
] | b4ff3b138234532a37a7588d80980e776bd469e7e42980cb5e2c2978d6485487 |
""" :mod: RequestTests
=======================
.. module: RequestTests
:synopsis: test cases for Request class
.. moduleauthor:: Krzysztof.Ciba@NOSPAMgmail.com
test cases for Request class
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import divi... | ic-hep/DIRAC | src/DIRAC/RequestManagementSystem/Client/test/Test_Request.py | Python | gpl-3.0 | 14,979 | [
"DIRAC"
] | a299aef24d132eae89a6eba724771987fbe16a8e7a0bf66cdaa09df74ba0e763 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | Forage/Gramps | gramps/gen/filters/rules/media/_hassourcecount.py | Python | gpl-2.0 | 1,807 | [
"Brian"
] | 125ccac345d417a5a68f057b07c00e25211de3cd1df239ab05d7cae8a6fde565 |
"""
.. module::
:platform: Unix
:synopsis: ???
.. moduleauthor: Jan Hajic <hajicj@gmail.com>
"""
import cPickle
import numpy
import safire.utils
import theano
import theano.tensor as TT
from theano.tensor.shared_randomstreams import RandomStreams
from safire.learning.models.autoencoder import Autoencoder
c... | hajicj/safire | safire/learning/models/denoising_autoencoder.py | Python | gpl-3.0 | 8,244 | [
"NEURON"
] | af332b1f913039ccb7543902b302a7f37dcb518fb263b5fee8a883eac893ca67 |
## -*- coding: utf-8 -*-
## Copyright (c) 2015-2020, Exa Analytics Development Team
## Distributed under the terms of the Apache License 2.0
#"""
#Parser for ADF's SCF Section
################################
#Parses the 'S C F' section of an ADF block output.
#"""
#from exa import Parser, Matches, Match
#
#
#class SCF... | exa-analytics/atomic | exatomic/adf/adf/scf.py | Python | apache-2.0 | 793 | [
"ADF"
] | fbd108118e9e1534d53cccac690d1b66524fddee3f313edf74b8a83c112065dd |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | bguenther8113/bg_blog | config/urls.py | Python | bsd-3-clause | 1,277 | [
"VisIt"
] | 906499658efba286930e8a18e47398ff2eb2ce14cd68be418661a61f53076a6f |
# -*- coding: utf-8 -*-
'''This example uses a convolutional stack followed by a recurrent stack
and a CTC logloss function to perform optical character recognition
of generated text images. I have no evidence of whether it actually
learns general shapes of text, or just is able to recognize all
the different fonts thr... | infilect/ml-course1 | keras-scripts/image_ocr.py | Python | mit | 21,310 | [
"Gaussian"
] | 78f94660ad16167c2e9ca593a6c2373212d5a91206c193209af9b01b4d466f96 |
#!/usr/bin/env python
import getopt, getpass, sys, string, time, pham
from phamerator_manage_db import *
from plugins import phamchecker
from plugins.phamchecker import *
import db_conf
def usage():
'''Prints program usage information'''
print """phamBuilder4.py [OPTION] [ARGUMENT]
-h, --help: print th... | byuphamerator/phamerator-dev | phamerator/phamBuilder4.py | Python | gpl-2.0 | 6,753 | [
"BLAST"
] | 216e844c294c89e0c08fe1bfc60998e20f7ec5bafab8870e5120f6d29e2723b0 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | lavalamp/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 38,815 | [
"CDK"
] | db6e2cf46f21e6f2956947baac13b3a481b975543677cf9ee9c978e5be6a4862 |
# Copyright 2018 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 writin... | google/svcca | numpy_pca.py | Python | apache-2.0 | 1,621 | [
"NEURON"
] | 2822004971b255e4added86bb24d69756017bfd310b945c0a9fd7d453fe95d3e |
#-------------------------------------------------------------------------
#
# Copyright (c) 2013
# IMB, RWTH Aachen University,
# ISM, Brno University of Technology
# All rights reserved.
#
# This software is provided without warranty under the terms of the BSD
# license included in the AramisCDT top directory "licens... | simvisage/aramis_cdt | aramis_cdt/aramis_ui.py | Python | bsd-3-clause | 8,271 | [
"Mayavi"
] | 5bf6fc2f2b150148f0ba2078db99cfd4464d7eba9220880eaacdde97beb044f4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""\
Eulerian cycle
jill-jênn vie et christoph dürr - 2015-2020
"""
import random
from tryalgo.graph import write_graph
# snip{ eulerian_tour_undirected
def eulerian_tour_undirected(graph):
"""Eulerian tour on an undirected graph
:param graph: directed graph... | jilljenn/tryalgo | tryalgo/eulerian_tour.py | Python | mit | 4,665 | [
"VisIt"
] | 9344baa2dcc196e4b329058861fb9dffc10d557927195a8efd98609e9f1682c0 |
# coding: utf-8
# pylint: disable=C0111
from __future__ import print_function, unicode_literals
from copy import deepcopy
from six import iteritems, itervalues, iterkeys
import numpy as np
from numpy import full, issubdtype
from numpy.linalg import norm
import vtk
from vtk.util.numpy_support import numpy_to_vtk
from ... | saullocastro/pyNastran | pyNastran/gui/qt_files/gui_qt_common.py | Python | lgpl-3.0 | 19,841 | [
"VTK"
] | 639bffc1a36b1fc5a494dbfc26676761f17e09922ef1ad7005fab089d1664ffb |
# $HeadURL: $
""" ResourceStatus
Module use to switch between the CS and the RSS.
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.DIRACSingleton import DIRACSingleton
from DIRAC.ConfigurationSystem.Client.Helpers import Re... | avedaee/DIRAC | ResourceStatusSystem/Client/ResourceStatus.py | Python | gpl-3.0 | 12,721 | [
"DIRAC"
] | c31a18b9950a59511f93a4e13ef3553b27f72e978f069d3277fee85812434018 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rabipanda/tensorflow | tensorflow/contrib/py2tf/pyct/templates.py | Python | apache-2.0 | 4,331 | [
"VisIt"
] | bb471d21a3b725b12efbfb44cd6d6d83d675b4e17df99adfef8b747ba991f149 |
r"""*README shell command doctests for* ``sphobjinv``.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
6 Aug 2018
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
http://www.github.... | bskinn/sphobjinv | tests/test_readme.py | Python | mit | 2,006 | [
"Brian"
] | 6d134a24cce9b318231e0f97926663078732dfcf47378b4e7d8db8339b779362 |
#!/usr/bin/env python
"""
Restart DIRAC component using runsvctrl utility
"""
from __future__ import print_function
__RCSID__ = "$Id$"
#
from DIRAC.Core.Base import Script
Script.disableCS()
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
... | fstagni/DIRAC | FrameworkSystem/scripts/dirac-restart-component.py | Python | gpl-3.0 | 1,217 | [
"DIRAC"
] | 26a16ca72300a6ab61f25ae6c9d66d37cc5fab79dc771c7b2f67051271e7ae3d |
""" VOMS2CSSyncronizer is a helper class containing the logic for synchronization
of the VOMS user data with the DIRAC Registry
"""
__RCSID__ = "$Id$"
from collections import defaultdict
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.Core.Security.VOMSService import VOMSService
from DIRAC.Core.Uti... | petricm/DIRAC | ConfigurationSystem/Client/VOMS2CSSynchronizer.py | Python | gpl-3.0 | 17,967 | [
"DIRAC"
] | 1c29b5cf59f3e148526efe4addd48a82961eb53f1079c77814d6ea97b13270da |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAffycoretools(RPackage):
"""Functions useful for those doing repetitive analyses with Aff... | LLNL/spack | var/spack/repos/builtin/packages/r-affycoretools/package.py | Python | lgpl-2.1 | 2,126 | [
"Bioconductor"
] | 0e1ab049c7342732cffc119bf0577f31d9966e4a37ba075f8c8a651e5c5260a5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Exoline - Exosite IoT Command Line
https://github.com/exosite/exoline
Usage:
exo [--help] [options] <command> [<args> ...]
Commands:
{{ command_list }}
Options:
--host=<host> OneP host. Default is $EXO_HOST or m2.exosite.com
--port=<port> OneP p... | tadpol/exoline | exoline/exo.py | Python | bsd-3-clause | 143,870 | [
"VisIt"
] | ded0e774d3caf6ae8ac459332f853e4c8d2581ef2f9445c64c8fc8a49c589d26 |
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: mojosixbit.py,v 1.4 2002/12/02 19:58:53 myers_carpenter Exp $"
import re, string, types, binascii
... | zooko/egtp_new | egtp/mojosixbit.py | Python | lgpl-2.1 | 5,144 | [
"VisIt"
] | 85ed711f4dd2522c8504cd07c1f1ee6d27ce1a7f559baea85f9e86e2a9bf0516 |
#!/usr/bin/env python
"""
Extract genomic signal label sequences from the genome sequence and annotation file.
Transcription Start Site[tss],
Translational Initiation Site[tis],
Splice Sites [don, acc],
Transcription Stop Site[cleave]
Translation Stop Site [cdsstop]
the resulting label sequ... | vipints/genomeutils | signal_labels/generate_genome_seq_labels.py | Python | bsd-3-clause | 59,540 | [
"Biopython"
] | aa6ce760f0cb104a974d12a0e792ffad97933eff8d295f767299515526a11011 |
#!/usr/bin/env python
import random
import math
import pickle
"""
Neural_Netwotk.py
Creates a data structure that models artificial neural network
Authors:
Joseph Fuchs <jjf2614@rit.edu>
Damien Cremilleux <dxc9849@rit.edu>
"""
def sigmoid(t):
'''
The sigmoid function
'''
return 1 / (1 + mat... | damien-cremilleux/RecyclingUsedParts | MLP/Neural_Network.py | Python | gpl-3.0 | 7,610 | [
"NEURON"
] | 9fb79abf05a78388d6cd166a49379dd0cdffbc269cd0bfa74ecbeaa0a22fa3f9 |
"""
===================================================================
EXPERIMENTS
This toolbox contains all the experiments necessary for the paper.
Marta Martinez-Camara, EPFL
===================================================================
"""
from __future__ import division # otherwise we get just an int as ou... | LCAV/linvpy | tests/regularizedtau/toolboxexperiments.py | Python | bsd-2-clause | 46,304 | [
"Gaussian"
] | ff026c8f61e0ce253c56e8c811699ab69647a4c2760d4b82c3bdffebb747f5aa |
# -*- coding: utf-8 -*-
""" Python test discovery, setup and run of test functions. """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import collections
import fnmatch
import inspect
import os
import sys
import warnings
from functools import partial
from t... | cloudera/hue | desktop/core/ext-py/pytest-4.6.11/src/_pytest/python.py | Python | apache-2.0 | 55,254 | [
"VisIt"
] | c30ae40f482c3354e6e1af768463340fb605552af26955f72b6452c979f6bc32 |
#!/usr/bin/env python
import logging
import os
import json
from source import Source
from server import Server
from cbtestlib.memcached.helper.data_helper import MemcachedClientHelper
class MemcachedSource(Source):
META_FILE = "%s/../metadata/stats.json" % os.path.dirname(__file__)
MC_STATS = ["", "allocat... | couchbaselabs/cbtop | libcbtop/mc_source.py | Python | apache-2.0 | 2,581 | [
"VisIt"
] | 31f6f37b12d6665c83ccaeb4ea7c6320f0111b3e88005c35725c57e4e30a7be8 |
#! test QC_JSON Schema for response properties
import psi4
import numpy as np
import json
import os
from distutils import dir_util
# Generate JSON input
json_data = {
"schema_name": "qcschema_input",
"schema_version": 1,
"molecule": {
"geometry": [
0.0, 0.0, -0.1294769411935893, 0.0, ... | jturney/psi4 | samples/json/schema-1-response/input.py | Python | lgpl-3.0 | 4,820 | [
"Psi4"
] | c0c64b3e677b977a63f092ac74708362b7b8e7be0983010837c35fa39ab07a53 |
"""
"""
from cloudbio.galaxy.utils import _chown_galaxy
from fabric.contrib.files import *
from shared import _write_to_file
def install_protvis(env):
""" Installs Andrew Brock's proteomics visualize tool.
https://bitbucket.org/Andrew_Brock/proteomics-visualise/
"""
_setup_protvis_env(env)
prot... | chapmanb/cloudbiolinux | cloudbio/custom/galaxyp.py | Python | mit | 2,287 | [
"Galaxy"
] | 733a2ecefbd3e07605df04ce6a2587d65b50ab23b504aad8e281f49aec54ed20 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Calculation of Bickelhaupt population analysis based on data parsed by cclib."""
import random
import nump... | cclib/cclib | cclib/method/bickelhaupt.py | Python | bsd-3-clause | 5,473 | [
"cclib"
] | f3968be79353bf4e783a92eb33a71da5ae7e80c7fa3d1691a05a4ca794580e68 |
#
# Copyright (C) 2017-2018 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 | testsuite/python/rdf.py | Python | gpl-3.0 | 3,710 | [
"ESPResSo"
] | c4774c8e848e50a2c187409baaff9b76a418ff58729daf59a2b66a66d2169590 |
#!/usr/bin/env python
# coding=utf-8
from termcolor import cprint
import json, requests, os
import google
import argparse
import random
API_URL = "https://www.censys.io/api/v1"
UID = ""
SECRET = ""
pages = float('inf')
page = 1
def arguments():
parser = argparse.ArgumentParser(description = banner())
parser... | mthbernardes/EvilTool | EvilTool.py | Python | gpl-2.0 | 10,545 | [
"VisIt"
] | f1c0a6d7e20f75d61ba4b785e85265ac83130760e38b67ffcbc35a365ccd0526 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import os
import time
import xml.sax
import numpy as np
import ase
from ase.version import version as ase_version
import gpaw
from gpaw.version import version as gpaw_version
try:
#new style cmr io
import cmr
... | ajylee/gpaw-rtxs | gpaw/io/cmr_io.py | Python | gpl-3.0 | 8,736 | [
"ASE",
"GPAW"
] | 6e59549994dad000b5fb89745d44bcd745db474872fbb8da4801316719a5b990 |
"""Stand alone script to convert standard NCEP files to Fall3d-NCEP
The script equips the files with global attributes of the form below -
mostly by deriving them from the data itself.
// global attributes:
:LONMIN = -180.f ;
:LONMAX = 177.5f ;
:LATMIN = -90.f ;
:LATMAX = 90.f ;
:NX = 144 ;
:NY = 73 ;
... | GeoscienceAustralia/PF3D | source/aim/convert_NCEP.py | Python | gpl-3.0 | 2,117 | [
"NetCDF"
] | 215c406a38be0e6b7f747215cffa6c0bdefc7bdef2266a2fd70692f8553c7e36 |
# -*- coding: utf-8 -*-
'''
Copyright 2017 by Tobias Houska, Benjamin Manns
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Benjamin Manns
This module contains a framework to summarize the distance between the model simulations and corresponding observations
by calculating likelihood value... | bees4ever/spotpy | spotpy/likelihoods.py | Python | mit | 45,203 | [
"Gaussian"
] | 1a995bd016514f779c473c322aa5c43b69d5dd99feb0587b1b497d325b26a74f |
# -*- coding: utf-8 -*-
# The MIT License (MIT) - Copyright (c) 2016-2021 Dave Vandenbout.
"""
Handles complete circuits made of parts and nets.
"""
from __future__ import ( # isort:skip
absolute_import,
division,
print_function,
unicode_literals,
)
import functools
import json
import os.path
impor... | xesscorp/skidl | skidl/circuit.py | Python | mit | 42,422 | [
"Elk"
] | 2d0533d9eaee668065299a6b7d1de48321612557be964ee377e4d441e1ab8fd8 |
from rauth.service import OAuth1Service, OAuth1Session
from xml.dom.minidom import parseString
import configparser
class LocalLib_GRAPI():
def get_user_info(self):
ACCESS_TOKEN = self.session.access_token
ACCESS_TOKEN_SECRET = self.session.access_token_secret
username_xml = self.session.get... | anirudhr/LocalLibrary | getinfo.py | Python | gpl-2.0 | 2,116 | [
"VisIt"
] | f2c02e0fc97cf1edd6b07c4ad150c3778ee287ceaf81173fa80e6452ad16acf0 |
from property import *
import nest
import numpy.random as random
# Neuron parameters
iaf_neuronparams = {'E_L': -70., # Resting membrane potential in mV
'V_th': -50., # Spike threshold in mV
'V_reset': -67., # Reset membrane potential after a spike in ... | research-team/NEUCOGAR | NEST/cube/integration/surprise/parameters.py | Python | gpl-2.0 | 4,227 | [
"NEURON"
] | afa8dee693ef8aee414dabfc1b327dd2b1b0debd4af963012887993c265ea0f2 |
#!/usr/bin/env python
#
# @file generate-class-name-list.py
# @brief Generate a list of class names defined in libSBML
# @author Michael Hucka
# @date Created 2013-12-19
#
# This program takes one argument, the root of the libSBML src/sbml
# directory. It walks down the directory tree recursively, looking in .h
#... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/docs/src/utilities/generate-class-name-list.py | Python | bsd-3-clause | 2,398 | [
"VisIt"
] | 3ca849bcac4152ce321074191e00ceb468bccc970d70edea2fc268e3427a09e6 |
# -*- coding: utf-8 -*-
# Copyright (c) 2013-2014 Will Thames <will@thames.id.au>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the righ... | ansible/ansible-lint | test/TestUtils.py | Python | mit | 18,697 | [
"Galaxy"
] | 8bddcc55a50f740adff6e73c0e8a3db4ac46b4d9c0f5f9423764729b2752139d |
from __future__ import division, print_function, absolute_import
import numpy as np
import warnings
from ..utils.six.moves import xrange
from dipy.core.geometry import cart2sphere, sphere2cart, vector_norm
from dipy.core.onetime import auto_attr
from dipy.reconst.recspeed import remove_similar_vertices
__all__ = ['... | sinkpoint/dipy | dipy/core/sphere.py | Python | bsd-3-clause | 20,266 | [
"Gaussian"
] | f04a8dea51f33377c96e9e3ff3038dbce8b4549f531648ef1a2ef68498a8755d |
r"""
The paraview package provides modules used to script ParaView. Generally, users
should import the modules of interest directly e.g.::
from paraview.simple import *
However, one may want to import paraview package before importing any of the
ParaView modules to force backwards compatibility to an older version:... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Wrapping/Python/paraview/__init__.py | Python | gpl-3.0 | 4,737 | [
"ParaView"
] | 0aea97f8c0512e4a44a7e1e7ddc3982428d3fc341020df5ca477a3a940b6a01a |
import re
import requests
from difflib import SequenceMatcher
from coalib.results.Diff import Diff
from coalib.bears.LocalBear import LocalBear
from coalib.bears.requirements.PipRequirement import PipRequirement
from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
from coalib.results.Result import Result
from c... | sounak98/coala-bears | bears/general/InvalidLinkBear.py | Python | agpl-3.0 | 6,956 | [
"VisIt"
] | 829d2f57df92698bb1504a5ec5984794da2495e3556039ad24e772b46b4c0827 |
"""
Copyright (c) 2012-2013 RockStor, Inc. <http://rockstor.com>
This file is part of RockStor.
RockStor is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published
by the Free Software Foundation; either version 2 of the License,
or (at your option) any la... | kamal-gade/rockstor-core | src/rockstor/storageadmin/views/user.py | Python | gpl-3.0 | 6,668 | [
"EPW"
] | b962e4df35df71ff92a99cde780ca98a55388c181400266d928c954e88732410 |
#!/usr/bin/env python
from __future__ import print_function
import os
import pysam
import random
import logging
import argparse
import itertools
import subprocess
logger = logging.getLogger(__name__)
from uuid import uuid4
import multiprocessing as mp
from collections import defaultdict as dd
from bx.intervals.in... | adamewing/tebreak | scripts/prefetch.py | Python | mit | 18,000 | [
"BWA",
"pysam"
] | fabbb1f694e54294219b8a541fb89e04a1c1aa7a316f6e9843e87266561169d8 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTimePointToString(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkTimePointToString.py | Python | bsd-3-clause | 499 | [
"VTK"
] | 557ebb744360b0f7398898bb8a14d52e14d081a344818b50528aa9d68f0ba0c4 |
from template.test import TestCase, main
class BlockTest(TestCase):
def testBlock(self):
ttcfg = {
'INCLUDE_PATH': [ 'test/lib' ],
'POST_CHOMP': 1,
'BLOCKS': {
'header': '<html><head><title>[% title %]</title></head><body>',
'footer': '</body></html>',
'block_a': lambda ... | gsnedders/Template-Python | t/block_test.py | Python | artistic-2.0 | 2,019 | [
"Galaxy"
] | a2162aa0a71080b41f90f45b6e293ad2cbe380a7d4f806e5ce16116f9941b49d |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham, A. Roitman
# Copyright (C) 2007-2009 B. Malengier
# Copyright (C) 2008 Lukasz Rymarczyk
# Copyright (C) 2008 Raphael Ackermann
# Copyright (C) 2008 Brian G. Matherly
# Copyright... | beernarrd/gramps | gramps/cli/argparser.py | Python | gpl-2.0 | 19,332 | [
"Brian"
] | 0dfd9771ff8fb0925ee59a983488a1415d9549a9a1f3b1e83412a8dc57e2f41c |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import Directive, directives
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.domains.std import Cmdoption
from sphinx.util.console import ... | hasura/docs | _ext/djangodocs.py | Python | mit | 10,823 | [
"VisIt"
] | bad3649e81454bd99223511804a689810c8ccf87bae293e1416c9e553ac68b63 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.conf.urls.i18n import i18n_patterns
admin.au... | dwcaraway/homeschoolring | config/urls.py | Python | bsd-3-clause | 2,398 | [
"VisIt"
] | 5df20b78826c4eef6e097bb44672b998bc101ae79f908b362f8e28f78ede0c3a |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/analysis/PressureTensorLayer.py | Python | gpl-3.0 | 3,581 | [
"ESPResSo"
] | 55d262c7f7ae56ed2d2c25e722b71baea783088282dd592e9fd1a6a1e40cbf48 |
# -*- coding: utf-8 -*-
import moose
print(moose.about())
import numpy as np
import chan_proto
import param_chan
t_stop = 10
dend_diameter = 2.2627398e-6
dend_length = 1.131369936e-6
Cm = 4.021231698e-12
Rm = 1865100032
Em = -0.07100000232
Vm_0 = -0.0705
dt = 50e-6
spines_no = 0
difshell_no = 2
difshell_name = "Ca_sh... | dilawar/moose-core | tests/core/test_difshells.py | Python | gpl-3.0 | 6,569 | [
"MOOSE"
] | 7b64d4266901a37df525a1a54c63bb2e6412438d1f8372e14a8d456fd49b9268 |
# $HeadURL$
from __future__ import print_function
__RCSID__ = "$Id$"
import threading
class Synchronizer:
""" Class encapsulating a lock
allowing it to be used as a synchronizing
decorator making the call thread-safe"""
def __init__( self, lockName = "", recursive = False ):
from DIRAC.Core.Utilities.Loc... | fstagni/DIRAC | Core/Utilities/ThreadSafe.py | Python | gpl-3.0 | 2,662 | [
"DIRAC"
] | 0f7a4d574c4406e22d2d8167c9da9c80982d06d114c4a62d9cbecc835d707e01 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
The transformations package defines various transformations that can be applied
on structures, i.e., converting one structure to another.
"""
| sonium0/pymatgen | pymatgen/transformations/__init__.py | Python | mit | 256 | [
"pymatgen"
] | 83445b62904582ba1b030023ff2e80c2149c5fd4aed37b18df160c974e329de6 |
"""
Command line interface to several manipulations of D-WAQ formatted
hydrodynamic data.
Typical invocation:
python -m stompy.model.delft.waq_hydro_editor -h
(to get help message).
python -m stompy.model.delft.waq_hydro_editor -i path/to/com-foo.hyd -a agg.shp -o output_agg/output
Read existing, serial DWAQ ... | rustychris/stompy | stompy/model/delft/waq_hydro_editor.py | Python | mit | 9,878 | [
"NetCDF"
] | 14e21d94c34892174458001205735d93e4f52d13543536b3d9e89617370c55b4 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/movietags.py | Python | gpl-2.0 | 5,055 | [
"VisIt"
] | 18c96535d71a82ae2c5763ead5b94fbae5f2206b7ff9f12a88cc39eefb970e9e |
__docformat__ = "restructuredtext en"
import mdp
from mdp import ClassifierNode, utils, numx, numx_rand, numx_linalg
# TODO: The GaussianClassifier and NearestMeanClassifier could be parallelized.
class SignumClassifier(ClassifierNode):
"""This classifier node classifies as ``1`` if the sum of the data points
... | ME-ICA/me-ica | meica.libs/mdp/nodes/classifier_nodes.py | Python | lgpl-2.1 | 24,683 | [
"Gaussian"
] | 80726a129cf7b8d8a3a87d6440e17ca2366e79938f1f9009b41447ee12131f94 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | tutorials/ChemicalBistables/mapkFB.py | Python | gpl-2.0 | 3,025 | [
"MOOSE"
] | 9eed50fb92c484b9b55148ff422a61ec2866d6e307bdda0d49be1f3df97416b7 |
import sys,os,subprocess
import random
import argparse
from genomics_tools.file_formats import bam,fasta
from genomics_tools.simulate import genome,contigs,reads
from mapping import align
from genomics_tools.file_formats.various_annotations import to_AGP,to_GFF
def simulate_instance(args):
#print 'Started simulat... | ksahlin/GapEst | scripts/simulate_data.py | Python | lgpl-3.0 | 7,061 | [
"BWA"
] | 09a0de7f5709ad8b02c552d1f261d1d179b3e1de45a81ced6a072a2b7a2a5059 |
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