#61: automatically adjust output start time when values are used

copasi · Nov 11, 2024 · ec5af2b · ec5af2b
1 parent 600b49c
commit ec5af2b
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Showing 3 changed files with 38 additions and 6 deletions.
diff --git a/basico/model_info.py b/basico/model_info.py
@@ -4901,10 +4901,10 @@ def _set_group_from_dict(group, values, dm=None):
         try:
             if param_type == COPASI.CCopasiParameter.Type_STRING:
                 current_value = values[key]
-                # convert list of strings to comma separated string
+                # convert list of strings to space separated string
                 # converting other data types to string
                 if isinstance(current_value, list):                    
-                    current_value = ', '.join(map(str, current_value))
+                    current_value = ' '.join(map(str, current_value))
                 else:
                     current_value = str(current_value)
                 param.setStringValue(current_value)
@@ -5070,6 +5070,12 @@ def set_task_settings(task, settings, **kwargs):
                 problem.setStepNumber(int(settings['problem']['intervals']))
             if 'StepNumber' in settings['problem']:
                 problem.setStepNumber(int(settings['problem']['StepNumber']))
+            if 'Values' in settings['problem'] and 'Use Values' in settings['problem'] and settings['problem']['Use Values']:
+                desired_values = problem.getValueString().split()
+                first_value = desired_values[0] if desired_values else None
+                if first_value:
+                    # correct start time if needed
+                    problem.setOutputStartTime(float(first_value))                
 
     if 'method' in settings:
         method = task.getMethod()

diff --git a/basico/task_timecourse.py b/basico/task_timecourse.py
@@ -414,6 +414,12 @@ def _setup_timecourse(args, kwargs):
             for val in vals:
                 new_vals += ' ' + str(val)
             vals = new_vals.strip()
+
+        # ensure that the output start time is correct adjusted: 
+        first_value = vals.split(' ')[0] if vals else None
+        if first_value:
+            problem.setOutputStartTime(float(first_value))
+
         problem.setValues(vals)
         problem.setUseValues(True)
     if 'use_values' in kwargs:

diff --git a/tests/test_timecourse.py b/tests/test_timecourse.py
@@ -18,7 +18,9 @@ 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))
+        # we decided that both should have the same shape
+        # see issue #61
+        self.assertEqual(tc.shape, (3, 1))
         self.assertEqual(tc2.shape, (3, 1))
 
 
@@ -94,9 +96,9 @@ def test_issue_61(self):
                         16, 16.5, 17, 17.5, 18, 18.5, 19, 19.5, 20]
 
         problem = {
-                        "AutomaticStepSize": False,
-                        "Duration": 20.0,
-                        "OutputStartTime": 10.0,
+                        "AutomaticStepSize": True,   # should be ignored
+                        "Duration": 200.0,           # should be ignored
+                        "OutputStartTime": 100.0,    # should be ignored
                         "Use Values": True,
                         "Values": desired_values
                     }
@@ -122,6 +124,24 @@ def test_issue_61(self):
         dm.removeInterface(dh)
         self.assertListEqual(data['Time'].to_list(), desired_values)
         self.assertListEqual(df2['Time'].to_list(), desired_values)
+
+
+        # run some more tests white different values for duration and output start time
+        # ensuring that the requested values are still returned
+        desired_values = [ 0, 10, 15, 20]
+        df1 = basico.run_time_course_with_output(output_elements, values=desired_values, model=dm)
+        self.assertListEqual(df1['Time'].to_list(), desired_values)
+        df2 = basico.run_time_course(**{"use_inital_values": True}).reset_index()
+        self.assertListEqual(df2['Time'].to_list(), desired_values)
+
+        desired_values = [ 15, 20 ]
+        df1 = basico.run_time_course_with_output(output_elements, values=desired_values, model=dm)
+        self.assertListEqual(df1['Time'].to_list(), desired_values)
+        df2 = basico.run_time_course(**{"use_inital_values": True, "values":desired_values}).reset_index()
+        self.assertListEqual(df2['Time'].to_list(), desired_values)
+
+
+
         basico.remove_datamodel(dm)