Testing Refactor

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

@@ -0,0 +1,23 @@
+name: Run StochSS Integration Tests
+
+on:
+  push:
+    branches: [main, develop]
+
+jobs:
+  run-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-20.04 ]
+
+    steps:
+    - name: Initialize environment
+      id: checkout
+      uses: actions/checkout@v2
+
+    - name: Run Integration Tests
+      id: run_integration_tests
+      uses: ./
+      with:
+        testin: '/stochss/stochss/tests/run_integration_tests.py'

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

@@ -0,0 +1,21 @@
+name: Run StochSS Unit Tests
+
+on: [push]
+
+jobs:
+  run-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-20.04 ]
+
+    steps:
+    - name: Initialize environment
+      id: checkout
+      uses: actions/checkout@v2
+
+    - name: Run Unit Tests
+      id: run_unit_tests
+      uses: ./
+      with:
+        testin: '/stochss/stochss/tests/run_unit_tests.py'

Makefile

@@ -148,7 +148,7 @@ test: create_working_dir
 		-v $(DOCKER_WORKING_DIR):/home/jovyan/ \
 		-p 8888:8888 \
 		$(DOCKER_STOCHSS_IMAGE):latest \
-		/stochss/stochss/tests/run_tests.py
+		/stochss/stochss/tests/run_all_tests.py
 
 build_and_test: build test
 

stochss/tests/integration_tests/test_gillespy2.py

@@ -0,0 +1,158 @@
+'''
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2023 StochSS developers.
+
+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 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 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 os
+import unittest
+
+import gillespy2
+
+from example_models import (
+    create_vilar_oscillator, create_dimerization, create_trichloroethylene, create_lac_operon, create_schlogl,
+    create_michaelis_menten, create_toggle_switch, create_decay, create_tyson_2_state_oscillator,
+    create_oregonator, create_opioid, create_telegraph_model
+)
+
+os.chdir('/stochss')
+
+# pylint: disable=import-outside-toplevel
+class TestGillesPy2Dependency(unittest.TestCase):
+    '''
+    ####################################################################################################################
+    Unit tests for GillesPy2 dependency.
+    ####################################################################################################################
+    '''
+    def setUp(self):
+        ''' Create a list of common example paths for each test. '''
+        self.test_ode_models = [
+            create_vilar_oscillator, create_dimerization, create_trichloroethylene, create_lac_operon, create_schlogl,
+            create_michaelis_menten, create_toggle_switch, create_decay, create_tyson_2_state_oscillator,
+            create_oregonator, create_opioid, create_telegraph_model
+        ]
+        self.test_ssa_models = [
+            create_vilar_oscillator, create_dimerization, create_trichloroethylene, create_schlogl,
+            create_michaelis_menten, create_toggle_switch, create_decay, create_tyson_2_state_oscillator,
+            create_opioid, create_telegraph_model
+        ]
+        self.test_hybrid_models = [
+            create_dimerization, create_trichloroethylene, create_schlogl, create_michaelis_menten,
+            create_toggle_switch, create_decay, create_opioid, create_telegraph_model
+        ]
+
+    ####################################################################################################################
+    # Unit tests for GillesPy2 dependency check_cpp_support.
+    ####################################################################################################################
+
+    def test_check_cpp_support(self):
+        ''' Check if the check cpp support functions works in StochSS. '''
+        from gillespy2.solvers.utilities.cpp_support_test import check_cpp_support
+
+        self.assertIsInstance(check_cpp_support(), bool)
+
+    ####################################################################################################################
+    # Unit tests for GillesPy2 dependency get_best_solver.
+    ####################################################################################################################
+
+    def test_get_best_solver(self):
+        ''' Check if the get best solver function works in StochSS. '''
+        test_model = self.test_ode_models[0]()
+        test_solver = test_model.get_best_solver()
+        self.assertIsInstance(test_solver(model=test_model), gillespy2.GillesPySolver)
+
+    ####################################################################################################################
+    # Unit tests for GillesPy2 dependency get_best_solver_algo.
+    ####################################################################################################################
+
+    def test_get_best_solver_algo(self):
+        ''' Check if the get best solver algo function works in StochSS. '''
+        test_algos = ["ODE", "SSA", "CLE", "Tau-Leaping", "Tau-Hybrid"]
+        test_model = self.test_ode_models[0]()
+        for test_algo in test_algos:
+            with self.subTest(test_algo=test_algo):
+                test_solver = test_model.get_best_solver_algo(algorithm=test_algo)
+                self.assertIsInstance(test_solver(model=test_model), gillespy2.GillesPySolver)
+
+    ####################################################################################################################
+    # Unit tests for GillesPy2 dependency solvers.
+    ####################################################################################################################
+
+    def test_ode_solver(self):
+        ''' Check if the test_models run with the ODESolver. '''
+        for model in self.test_ode_models:
+            test_model = model()
+            msg = f"Running {test_model.name} using {gillespy2.ODESolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=gillespy2.ODESolver, timeout=30)
+
+    def test_ode_c_solver(self):
+        ''' Check if the test_models run with the ODECSolver. '''
+        for model in self.test_ode_models:
+            test_model = model()
+            test_solver = gillespy2.ODECSolver(model=test_model)
+            msg = f"Running {test_model.name} using {gillespy2.ODECSolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=test_solver, timeout=30)
+
+    def test_numpy_ssa_solver(self):
+        ''' Check if the test_models run with the NumPySSASolver. '''
+        for model in self.test_ssa_models:
+            test_model = model()
+            msg = f"Running {test_model.name} using {gillespy2.NumPySSASolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=gillespy2.NumPySSASolver, timeout=30)
+
+    def test_ssa_c_solver(self):
+        ''' Check if the test_models run with the SSACSolver. '''
+        for model in self.test_ssa_models:
+            test_model = model()
+            test_solver = gillespy2.SSACSolver(model=test_model)
+            msg = f"Running {test_model.name} using {gillespy2.SSACSolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=test_solver, timeout=30)
+
+    def test_tau_leaping_solver(self):
+        ''' Check if the test_models run with the TauLeapingSolver. '''
+        for model in self.test_ssa_models:
+            test_model = model()
+            msg = f"Running {test_model.name} using {gillespy2.TauLeapingSolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=gillespy2.TauLeapingSolver, timeout=30)
+
+    def test_tau_leaping_c_solver(self):
+        ''' Check if the test_models run with the TauLeapingCSolver. '''
+        for model in self.test_ssa_models:
+            test_model = model()
+            test_solver = gillespy2.TauLeapingCSolver(model=test_model)
+            msg = f"Running {test_model.name} using {gillespy2.TauLeapingCSolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=test_solver, timeout=30)
+
+    def test_tau_hybrid_solver(self):
+        ''' Check if the test_models run with the TauHybridSolver. '''
+        for model in self.test_hybrid_models:
+            test_model = model()
+            msg = f"Running {test_model.name} using {gillespy2.TauHybridSolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=gillespy2.TauHybridSolver, timeout=30)
+
+    def test_tau_hybrid_c_solver(self):
+        ''' Check if the test_models run with the TauHybridCSolver. '''
+        for model in self.test_hybrid_models:
+            test_model = model()
+            test_solver = gillespy2.TauHybridCSolver(model=test_model)
+            msg = f"Running {test_model.name} using {gillespy2.TauHybridCSolver.name} failed!"
+            with self.subTest(msg=msg):
+                test_model.run(solver=test_solver, timeout=30)

stochss/tests/run_all_tests.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+
+'''
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2023 StochSS developers.
+
+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 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 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 os
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument(
+    '-m', '--mode', default='staging', choices=['staging', 'release'],
+    help='Run tests in staging mode or release mode.'
+)
+
+if __name__ == "__main__":
+    os.chdir('/stochss')
+    args = parser.parse_args()
+    print(os.path.dirname(__file__))
+
+    from run_unit_tests import run as run_unit
+    from run_integration_tests import run as run_integration
+
+    run_unit(mode=args.mode)
+    run_integration(mode=args.mode)

stochss/tests/run_integration_tests.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python3
+
+'''
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2023 StochSS developers.
+
+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 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 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 os
+import sys
+import unittest
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument(
+    '-m', '--mode', default='staging', choices=['staging', 'release'],
+    help='Run integration tests in staging mode or release mode.'
+)
+
+def run(mode=None):
+    ''' Run the integration tests. '''
+    from integration_tests import test_gillespy2
+
+    modules = [
+        test_gillespy2
+    ]
+
+    for module in modules:
+        suite = unittest.TestLoader().loadTestsFromModule(module)
+        runner = unittest.TextTestRunner(failfast=mode == 'staging', verbosity=1)
+
+        print("Executing: {}".format(module))
+        result = runner.run(suite)
+        print('=' * 70)
+        if not result.wasSuccessful():
+            sys.exit(not result.wasSuccessful())
+
+if __name__ == "__main__":
+    os.chdir('/stochss')
+    args = parser.parse_args()
+    print(os.path.dirname(__file__))
+
+    run(mode=args.mode)

stochss/tests/run_tests.py → stochss/tests/run_unit_tests.py

@@ -17,43 +17,44 @@
 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 sys
 import os
+import sys
+import unittest
 import argparse
 
 parser = argparse.ArgumentParser()
-parser.add_argument('-m', '--mode', default='staging', choices=['staging', 'release'],
-                    help='Run tests in staging mode or release mode.')
-
-if __name__ == "__main__":
-    os.chdir('/stochss')
-    args = parser.parse_args()
-    print(os.path.dirname(__file__))
-
-    import test_model_template
-    import test_settings_template
-    import test_stochss_base
-    import test_stochss_file
-    import test_gillespy2
-
+parser.add_argument(
+    '-m', '--mode', default='staging', choices=['staging', 'release'],
+    help='Run unit tests in staging mode or release mode.'
+)
+
+def run(mode=None):
+    ''' Run the unit tests. '''
+    from unit_tests import test_model_template
+    from unit_tests import test_settings_template
+    from unit_tests import test_stochss_base
+    from unit_tests import test_stochss_file
+
     modules = [
         test_model_template,
         test_settings_template,
-        test_gillespy2,
         test_stochss_base,
         test_stochss_file
     ]
 
     for module in modules:
         suite = unittest.TestLoader().loadTestsFromModule(module)
-        runner = unittest.TextTestRunner(failfast=args.mode == 'staging', verbosity=1)
+        runner = unittest.TextTestRunner(failfast=mode == 'staging', verbosity=1)
 
         print("Executing: {}".format(module))
         result = runner.run(suite)
         print('=' * 70)
         if not result.wasSuccessful():
             sys.exit(not result.wasSuccessful())
+
+if __name__ == "__main__":
+    os.chdir('/stochss')
+    args = parser.parse_args()
+    print(os.path.dirname(__file__))
+
+    run(mode=args.mode)