test_notebooks.py

'''
SpatialPy is a Python 3 package for simulation of
spatial deterministic/stochastic reaction-diffusion-advection problems
Copyright (C) 2021 SpatialPy developers.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as
published by the Free Software Foundation.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU GENERAL PUBLIC LICENSE Version 3 for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
'''

import unittest
import os
import nbformat
from nbconvert.preprocessors import ExecutePreprocessor


class TestNotebooks(unittest.TestCase):
    
    def test_notebooks(self):
        FULL, MINIMAL = 0, 1
        test_set = MINIMAL
        notebooks = {}
        errors = {}
        ep = ExecutePreprocessor(timeout=600, kernel_name='python3', allow_errors=True)

        if test_set == FULL:
            for root, dirs, files in os.walk("../examples/"):
                for file in files:
                    if file.endswith(".ipynb"):
                         with open(os.path.join(root, file)) as f:
                            print('Reading {}...'.format(file))
                            notebooks[file] = nbformat.read(f, as_version=nbformat.NO_CONVERT)

        elif test_set == MINIMAL:
            files = [os.path.join('cylinderDemo', 'SpatialPy_cylinderDemo3D.ipynb'), 
                    os.path.join('tests', 'Diffusion_validation.ipynb'),
                    os.path.join('tests', 'Spatial_Birth_Death.ipynb')]
            root = os.path.join('SpatialPy', 'examples') 
            for file in files:
                with open(os.path.join(root, file)) as f:
                    print('Reading {}...'.format(file))
                    notebooks[file] = nbformat.read(f, as_version=nbformat.NO_CONVERT)

        for file, nb in notebooks.items():
            with self.subTest(msg=file):
                try:
                    print('Executing {}...'.format(file))
                    ep.preprocess(nb, {'metadata': {'path': root}})
                except Exception as err:
                    print('Error executing the notebook "{}".\n\n'.format(file))
                    errors[file] = err

        for fname, err in errors.items():
            if len(err.__str__()) > 500:
                print('{}:\n{}\n...\n{}'.format(fname, err.__str__()[:251], err.__str__()[-251:]))
            else:
                print('{}:\n{}'.format(fname, err))
        self.assertFalse(bool(errors))

        
if __name__ == '__main__':
    unittest.main()