#33 : add missing simulation method

copasi · Jun 9, 2023 · da63f74 · da63f74
1 parent 456b953
commit da63f74
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Showing 2 changed files with 32 additions and 2 deletions.
diff --git a/basico/task_timecourse.py b/basico/task_timecourse.py
@@ -75,6 +75,7 @@ def __method_name_to_type(method_name):
     methods = {
         'deterministic': COPASI.CTaskEnum.Method_deterministic,
         'lsoda': COPASI.CTaskEnum.Method_deterministic,
+        'hybrid': COPASI.CTaskEnum.Method_hybrid,
         'hybridode45': COPASI.CTaskEnum.Method_hybridODE45,
         'hybridlsoda': COPASI.CTaskEnum.Method_hybridLSODA,
         'adaptivesa': COPASI.CTaskEnum.Method_adaptiveSA,
@@ -117,7 +118,7 @@ def run_time_course_with_output(output_selection, *args, **kwargs):
        |   * `deterministic` / `lsoda`: the LSODA implementation
        |   * `stochastic`: the Gibson & Bruck Gillespie implementation
        |   * `directMethod`: Gillespie Direct Method
-       |   * others: `hybridode45`, `hybridlsoda`, `adaptivesa`, `tauleap`, `radau5`, `sde`
+       |   * others: `hybrid`, `hybridode45`, `hybridlsoda`, `adaptivesa`, `tauleap`, `radau5`, `sde`
 
      - `duration` (float): the duration in time units for how long to simulate
 
@@ -273,7 +274,7 @@ def run_time_course(*args, **kwargs):
        |   * `deterministic` / `lsoda`: the LSODA implementation
        |   * `stochastic`: the Gibson & Bruck Gillespie implementation
        |   * `directMethod`: Gillespie Direct Method
-       |   * others: `hybridode45`, `hybridlsoda`, `adaptivesa`, `tauleap`, `radau5`, `sde`
+       |   * others: `hybrid`, `hybridode45`, `hybridlsoda`, `adaptivesa`, `tauleap`, `radau5`, `sde`
 
      - `duration` (float): the duration in time units for how long to simulate
 

diff --git a/tests/test_timecourse.py b/tests/test_timecourse.py
@@ -14,6 +14,35 @@ def test_custom_output(self):
         self.assertIsNotNone(tc)
         self.assertListEqual(tc.columns.to_list(), ['Time', '[S1]', '[S2]', 'Values[k1]'])
 
+    def test_stochastic(self):
+        basico.new_model(name='Simple Model')
+        basico.add_reaction('R1', 'A ->')
+        basico.add_reaction('R2', 'B -> B + C')
+        basico.set_species('A', initial_particle_number=50)
+        basico.set_species('B', initial_particle_number=10)
+        basico.set_species('C', initial_particle_number=0)
+        basico.set_reaction_parameters('(R1).k1', value=1)
+        basico.set_reaction_parameters('(R2).k1', value=1)
+        basico.add_event('E1', 'A <= 10', [('B', '50')])
+        result = basico.run_time_course(duration=10, method='stochastic', use_numbers=True)
+        self.assertIsNotNone(result)
+
+        # test that we can set hybrid methods
+        result = basico.run_time_course(duration=1, method='hybrid', use_numbers=True)
+        self.assertIsNotNone(result)
+        settings = basico.get_task_settings(basico.T.TIME_COURSE)
+        self.assertEqual(settings['method']['name'], 'Hybrid (Runge-Kutta)')
+
+    def test_stoch2(self):
+        basico.new_model(name='Simple Model', substance_unit='1')
+        basico.add_reaction('R1', 'A ->')
+        basico.set_species('A', initial_particle_number=50)
+        basico.set_reaction_parameters('(R1).k1', value=1)
+        basico.add_event('E1', 'A.ParticleNumber <= 1', [('A.ParticleNumber', '50')])
+
+        result = basico.run_time_course(duration=20, method='directMethod', use_numbers=True)
+        self.assertIsNotNone(result)
+
 
 if __name__ == '__main__':
     unittest.main()