#49 fix an issue when using pandas dataframes for setting compartment…

… sizes
copasi · Apr 18, 2024 · 92e2ee5 · 92e2ee5
1 parent 4f77af6
commit 92e2ee5
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Showing 2 changed files with 42 additions and 1 deletion.
diff --git a/basico/model_info.py b/basico/model_info.py
@@ -2897,7 +2897,7 @@ def _set_compartment(compartment, c_model, **kwargs):
         _set_expression(compartment, kwargs['expression'], model=c_model.getObjectDataModel())
         c_model.setCompileFlag(True)
     if 'dimensionality' in kwargs:
-        compartment.setDimensionality(kwargs['dimensionality'])
+        compartment.setDimensionality(int(kwargs['dimensionality']))
     if 'notes' in kwargs:
         compartment.setNotes(kwargs['notes'])
     if 'sbml_id' in kwargs:

diff --git a/tests/test_basico_info.py b/tests/test_basico_info.py
@@ -350,9 +350,26 @@ def test_compartment(self):
         self.assertEqual(v['type'], 'assignment')
         self.assertEqual(v['expression'], 'Time')
         self.assertEqual(v['initial_expression'], '')
+        self.assertEqual(v['dimensionality'], 3)
+
+
+        # change dimensions to two
+        basico.set_compartment('v', exact=True, dimensionality=2)
+        v_df = basico.get_compartments('v')
+        v = basico.as_dict(v_df)
+        self.assertEqual(v['dimensionality'], 2)
+
+        basico.set_compartment('v', exact=True, dimensionality=v['dimensionality'])
+        basico.set_compartment('v', exact=True, dimensionality=v_df.iloc[0]['dimensionality'])
+
+        # apply all recorded changes
+        basico.set_compartment(exact=True, **v)
+
+
         basico.remove_compartment('v')
         self.assertIsNone(basico.get_compartments('v', exact=True))
 
+
     def test_global_parameters(self):
         basico.add_parameter('p', initial_value=3)
         v = basico.get_parameters('p', exact=True)
@@ -532,5 +549,29 @@ def test_retrieval_from_multiple_models(self):
         basico.remove_datamodel(dm1)
         basico.remove_datamodel(dm2)
 
+    def test_expresssions(self):
+        dm = basico.new_model(name='Test Model');
+        basico.add_species('X');
+        basico.add_species('Y');
+        basico.add_parameter('a', initial_value=1);
+
+        basico.add_parameter('b', initial_value=1);
+        basico.set_parameters('b', exact=True, expression='{Values[a].InitialValue}/2', status='assignment')
+        params1 = basico.as_dict(basico.get_parameters(type='assignment'))
+        basico.set_parameters('b', exact=True, expression='Values[a].InitialValue/2', status='assignment')
+        params2 = basico.as_dict(basico.get_parameters(type='assignment'))
+
+        basico.add_parameter('c', initial_value=1);
+        basico.set_parameters('c', exact=True, expression='{[X]}+{[Y]}', status='assignment')
+        params31 = basico.as_dict(basico.get_parameters(type='assignment'))
+        basico.set_parameters('c', exact=True, expression=' {[X]} + {[Y]}', status='assignment')
+        params3 = basico.as_dict(basico.get_parameters(type='assignment'))
+        basico.set_parameters('c', exact=True, expression=' [X] + [Y]', status='assignment')
+        params4 = basico.as_dict(basico.get_parameters(type='assignment'))
+        params = basico.as_dict(basico.get_parameters(type='assignment'))
+
+
+        basico.remove_datamodel(dm);
+
 if __name__ == "__main__":
     unittest.main()