- add test for constraints

copasi · Oct 18, 2024 · 19a3128 · 19a3128
1 parent 5b4ee8f
commit 19a3128
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 2 deletions.
diff --git a/basico/task_optimization.py b/basico/task_optimization.py
@@ -191,7 +191,7 @@ def set_opt_parameters(opt_parameters, model=None):
             logger.warning('object {0} not found'.format(name))
             continue
 
-        opt_item = problem.addOptItem(cn)
+        opt_item = problem.addOptItem(COPASI.CRegisteredCommonName(cn))
         assert (isinstance(opt_item, COPASI.COptItem))
         if 'lower' in item:
             opt_item.setLowerBound(COPASI.CRegisteredCommonName(str(item['lower'])))
@@ -249,7 +249,7 @@ def set_opt_constraints(opt_constraints, model=None):
             logger.warning('object {0} not found'.format(name))
             continue
 
-        opt_item = problem.addOptConstraint(cn)
+        opt_item = problem.addOptConstraint(COPASI.CRegisteredCommonName(cn))
         assert (isinstance(opt_item, COPASI.COptItem))
         if 'lower' in item:
             opt_item.setLowerBound(COPASI.CRegisteredCommonName(str(item['lower'])))

diff --git a/tests/test_optimization.py b/tests/test_optimization.py
@@ -23,6 +23,10 @@ def test_optitems(self):
         items = basico.get_opt_parameters()
         self.assertIsNotNone(items)
 
+        basico.set_opt_constraints(items)
+        items = basico.get_opt_constraints()
+        self.assertIsNotNone(items)
+
     def test_settings(self):
         settings = basico.get_opt_settings()
         self.assertIsNotNone(settings)

diff --git a/tests/test_timecourse.py b/tests/test_timecourse.py
@@ -14,6 +14,14 @@ def test_custom_output(self):
         self.assertIsNotNone(tc)
         self.assertListEqual(tc.columns.to_list(), ['Time', '[S1]', '[S2]', 'Values[k1]'])
 
+    def test_values(self):
+        tc = basico.run_time_course(values=[10, 20, 30])
+        tc2 = basico.run_time_course(values=[10, 20, 30], start_time=10)
+        self.assertIsNotNone(tc)
+        self.assertEqual(tc.shape, (4, 1))
+        self.assertEqual(tc2.shape, (3, 1))
+
+
     def test_stochastic(self):
         basico.new_model(name='Simple Model')
         basico.add_reaction('R1', 'A ->')