Merge pull request #355 from StochSS/system-testing

System testing

.github/workflows/run_system_tests.yaml

@@ -0,0 +1,30 @@
+name: Run SpatialPy System Tests
+
+on:
+  push:
+    branches: [staging, develop]
+
+jobs:
+  run-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ]
+
+    steps:
+    - name: Initialize environment
+      uses: actions/checkout@v2
+
+    - name: Install Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+
+    - name: Install Python dependencies
+      run: | 
+        python3 -m pip install --upgrade pip
+        python3 -m pip install -r requirements.txt
+        python3 -m pip install coverage
+        
+    - name: Run tests
+      run: coverage run --source=spatialpy test/run_system_tests.py

run_coverage.sh

@@ -4,4 +4,5 @@
 
 coverage run --source=spatialpy test/run_unit_tests.py -m develop
 coverage run --source=spatialpy test/run_integration_tests.py -m develop
+coverage run --source=spatialpy test/run_system_tests.py -m develop
 coverage html

test/test_solver.py → test/integration_tests/test_solver.py

@@ -204,7 +204,7 @@ def test_solver_expressions(self):
         Ensure that expression conversions to C++ result in (roughly) equivalent values as Python.
         """
         tmpdir = tempfile.mkdtemp()
-        src_path = os.path.join(os.path.dirname(__file__), "assets", "evaluate.c")
+        src_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), "assets", "evaluate.c")
         exe_path = os.path.join(tmpdir, "test")
 
         def build(expr_args: "list[str]", expr_str: "str", use_bool=False):

test/models/birth_death.py

@@ -0,0 +1,50 @@
+# SpatialPy is a Python 3 package for simulation of
+# spatial deterministic/stochastic reaction-diffusion-advection problems
+# Copyright (C) 2019 - 2023 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/>.
+''' spatialpy model file for the spatial birth death example. '''
+import spatialpy
+
+def create_birth_death():
+    ''' Create the spatial birth death model. '''
+    model = spatialpy.Model(name='Spatial Birth-Death')
+
+    model.HABITAT = "Habitat"
+
+    domain = spatialpy.Domain.create_2D_domain(
+        xlim=(0, 1), ylim=(0, 1), numx=10, numy=10, type_id=model.HABITAT, fixed=True
+    )
+    model.add_domain(domain)
+
+    rabbits = spatialpy.Species(name='Rabbits', diffusion_coefficient=0.1)
+    model.add_species(rabbits)
+
+    init_rabbit_pop = spatialpy.ScatterInitialCondition(species='Rabbits', count=100)
+    model.add_initial_condition(init_rabbit_pop)
+
+    k_birth = spatialpy.Parameter(name='k_birth', expression=10)
+    k_death = spatialpy.Parameter(name='k_death', expression=0.1)
+    model.add_parameter([k_birth, k_death])
+
+    birth = spatialpy.Reaction(
+        name='birth', reactants={}, products={"Rabbits":1}, rate="k_birth"
+    )
+    death = spatialpy.Reaction(
+        name='death', reactants={"Rabbits":1}, products={}, rate="k_death"
+    )
+    model.add_reaction([birth, death])
+
+    tspan = spatialpy.TimeSpan.linspace(t=10, num_points=11, timestep_size=1)
+    model.timespan(tspan)
+    return model

test/run_integration_tests.py

@@ -14,8 +14,10 @@
 
 # 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, sys, os
+''' Testing suite for integration tests. '''
+import os
+import sys
+import unittest
 import argparse
 
 parser = argparse.ArgumentParser()
@@ -28,9 +30,9 @@
         print('Running tests in develop mode. Appending repository directory to system path.')
         sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
 
-    import test_model
-    import test_solver
-    #import test_mincde
+    from test.integration_tests import test_model
+    from test.integration_tests import test_solver
+    #from test.integration_tests import test_mincde
 
     modules = [
         test_model,
@@ -42,7 +44,7 @@
         suite = unittest.TestLoader().loadTestsFromModule(module)
         runner = unittest.TextTestRunner(failfast=args.mode == 'develop')
 
-        print("Executing: {}".format(module))
+        print(f"Executing: {module}")
         result = runner.run(suite)
         print('=' * 70)
         if not result.wasSuccessful():

test/run_system_tests.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+# SpatialPy is a Python 3 package for simulation of
+# spatial deterministic/stochastic reaction-diffusion-advection problems
+# Copyright (C) 2019 - 2023 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/>.
+''' Testing suite for system tests. '''
+import os
+import sys
+import unittest
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-m', '--mode', default='develop', choices=['develop', 'release'],
+                    help='Run system tests in develop mode or release mode.')
+
+if __name__ == '__main__':
+    args = parser.parse_args()
+    if args.mode == 'develop':
+        print('Running system tests in develop mode. Appending repository directory to system path.')
+        sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+
+    from test.system_tests import test_compiler
+
+    modules = [
+        test_compiler
+    ]
+
+    for module in modules:
+        suite = unittest.TestLoader().loadTestsFromModule(module)
+        runner = unittest.TextTestRunner(failfast=args.mode == 'develop')
+
+        print(f"Executing: {module}")
+        result = runner.run(suite)
+        print('=' * 70)
+        if not result.wasSuccessful():
+            sys.exit(not result.wasSuccessful())

test/system_tests/test_compiler.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+# SpatialPy is a Python 3 package for simulation of
+# spatial deterministic/stochastic reaction-diffusion-advection problems
+# Copyright (C) 2019 - 2023 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/>.
+''' Tests from the compiler. '''
+import os
+import sys
+import unittest
+
+sys.path.insert(1, os.path.abspath(os.getcwd()))
+from test.models.birth_death import create_birth_death # pylint: disable=wrong-import-position
+
+class TestCompiler(unittest.TestCase):
+    '''
+    ################################################################################################
+    System test for compiler.
+    ################################################################################################
+    '''
+    def setUp(self):
+        self.model = create_birth_death()
+
+    def test_constructor(self):
+        """ Test the compiler. """
+        _ = self.model.run()
+
+if __name__ == '__main__':
+    unittest.main()