- performance improvements

copasi · Dec 20, 2022 · 63b62aa · 63b62aa
1 parent 7a31e79
commit 63b62aa
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Showing 8 changed files with 250 additions and 167 deletions.
diff --git a/basico/model_info.py b/basico/model_info.py
diff --git a/basico/task_optimization.py b/basico/task_optimization.py
@@ -330,6 +330,8 @@ def run_optimization(expression=None, output=None, settings=None, **kwargs):
     """
     model = model_io.get_model_from_dict_or_default(kwargs)
 
+    model.getModel().compileIfNecessary()
+
     task = model.getTask(basico.T.OPTIMIZATION)
     assert (isinstance(task, COPASI.COptTask))
     problem = task.getProblem()

diff --git a/basico/task_parameterestimation.py b/basico/task_parameterestimation.py
@@ -965,6 +965,8 @@ def run_parameter_estimation(**kwargs):
     model = model_io.get_model_from_dict_or_default(kwargs)
     assert (isinstance(model, COPASI.CDataModel))
 
+    model.getModel().compileIfNecessary()
+
     task = model.getTask(TASK_PARAMETER_ESTIMATION)
     assert (isinstance(task, COPASI.CFitTask))
 

diff --git a/basico/task_scan.py b/basico/task_scan.py
@@ -461,6 +461,8 @@ def run_scan(**kwargs):
     """
     model = model_io.get_model_from_dict_or_default(kwargs)
 
+    model.getModel().compileIfNecessary()
+
     if 'settings' in kwargs:
         set_scan_settings(settings=kwargs['settings'], model=model)
 

diff --git a/basico/task_sensitivities.py b/basico/task_sensitivities.py
@@ -369,6 +369,8 @@ def run_sensitivities(**kwargs):
     model = model_io.get_model_from_dict_or_default(kwargs)
     assert (isinstance(model, COPASI.CDataModel))
 
+    model.getModel().compileIfNecessary()
+
     if 'settings' in kwargs:
         basico.set_sensitivity_settings(kwargs['settings'], model=model)
 

diff --git a/basico/task_steadystate.py b/basico/task_steadystate.py
@@ -54,6 +54,8 @@ def run_steadystate(**kwargs):
     model = model_io.get_model_from_dict_or_default(kwargs)
     assert (isinstance(model, COPASI.CDataModel))
 
+    model.getModel().compileIfNecessary()
+
     task = model.getTask('Steady-State')
     assert (isinstance(task, COPASI.CSteadyStateTask))
 

diff --git a/basico/task_timecourse.py b/basico/task_timecourse.py
@@ -148,6 +148,9 @@ def run_time_course_with_output(output_selection, *args, **kwargs):
 
     """
     model = model_io.get_model_from_dict_or_default(kwargs)
+
+    model.getModel().compileIfNecessary()
+
     dh, columns = create_data_handler(output_selection, model=model)
 
     task, use_initial_values = _setup_timecourse(args, kwargs)
@@ -308,6 +311,8 @@ def run_time_course(*args, **kwargs):
     """
     model = model_io.get_model_from_dict_or_default(kwargs)
 
+    model.getModel().compileIfNecessary()
+
     task, use_initial_values = _setup_timecourse(args, kwargs)
 
     result = task.initializeRaw(COPASI.CCopasiTask.OUTPUT_UI)

diff --git a/tests/test_basico_info.py b/tests/test_basico_info.py
@@ -7,9 +7,9 @@
 class TestBasicoIO_Brus(unittest.TestCase):
 
     def setUp(self):
-        dm = basico.load_example('brusselator')
-        self.assertTrue(dm is not None)
-        self.assertTrue(isinstance(dm, COPASI.CDataModel))
+        self.dm = basico.load_example('brusselator')
+        self.assertTrue(self.dm is not None)
+        self.assertTrue(isinstance(self.dm, COPASI.CDataModel))
         self.assertTrue('The Brusselator' in basico.model_io.overview())
 
     def test_get_species(self):