adding test to check all notebooks.

.github/workflows/run-integration-tests.yml

@@ -25,6 +25,8 @@ jobs:
         python3 -m pip install --upgrade pip
         python3 -m pip install -r requirements.txt
         python3 -m pip install coverage
+        python3 -m pip install nbformat
+        python3 -m pip install nbconvert
 
     - name: Run tests
       run: coverage run test/run_integration_tests.py

test/run_integration_tests.py

@@ -32,11 +32,13 @@
 
     import test_model
     import test_solver
+    import test_notebooks
     #import test_mincde
 
     modules = [
         test_model,
         test_solver,
+        test_notebooks
         #test_mincde,
     ]
 

test/test_notebooks.py

@@ -0,0 +1,70 @@
+'''
+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()