- progress making cns compatible with 4.43

basico/model_info.py

@@ -4943,6 +4943,10 @@ def set_task_settings(task, settings, **kwargs):
                 if r_def is not None:
                     report.setReportDefinition(r_def)
 
+def _get_cn_string(cn):
+    if isinstance(cn, COPASI.CCommonName):
+        return cn.getString()
+    return str(cn)
 
 def _collect_data(names=None, cns=None, **kwargs):
     """Collects data from the model, returning it as dataframe

basico/task_parameterestimation.py

@@ -19,6 +19,7 @@
 
 """
 import shutil
+import sys
 
 import pandas
 import COPASI
@@ -30,6 +31,8 @@
 import yaml
 
 import basico
+
+from . import model_info
 from basico.callbacks import get_default_handler
 
 logger = logging.getLogger(__name__)
@@ -631,7 +634,6 @@ def get_fit_item_template(include_local=False, include_global=False, default_lb=
 
     return result
 
-
 def get_fit_parameters(model=None):
     """Returns a data frame with all fit parameters
 
@@ -666,11 +668,11 @@ def get_fit_parameters(model=None):
         name = obj.getObjectDisplayName()
         data.append({
             'name': name,
-            'lower': item.getLowerBound(),
-            'upper': item.getUpperBound(),
+            'lower': model_info._get_cn_string(item.getLowerBound()),
+            'upper': model_info._get_cn_string(item.getUpperBound()),
             'start': item.getStartValue(),
             'affected': _get_affected_experiments(item),
-            'cn': item.getObjectCN(),
+            'cn': model_info._get_cn_string(item.getObjectCN()),
         })
 
     if not data:
@@ -712,11 +714,11 @@ def get_fit_constraints(model=None):
         name = obj.getObjectDisplayName()
         data.append({
             'name': name,
-            'lower': item.getLowerBound(),
-            'upper': item.getUpperBound(),
+            'lower': model_info._get_cn_string(item.getLowerBound()),
+            'upper': model_info._get_cn_string(item.getUpperBound()),
             'start': item.getStartValue(),
             'affected': _get_affected_experiments(item),
-            'cn': item.getObjectCN(),
+            'cn': model_info._get_cn_string(item.getObjectCN()),
         })
 
     if not data:
@@ -767,9 +769,15 @@ def set_fit_parameters(fit_parameters, model=None):
         name = None
 
         if 'cn' in item:
-            cn = COPASI.CCommonName(item.cn)
+            if isinstance(item.cn, COPASI.CRegisteredCommonName):
+                cn_string = item.cn.getString()
+            else:
+                cn_string = str(item.cn)
 
-        elif 'name' in item:
+            if cn_string:
+                cn = COPASI.CRegisteredCommonName(cn_string)
+
+        if 'name' in item and cn is None:
             name = item['name']
             if not cn:
                 obj = basico.model_info._get_object(name, initial=True, model=model)
@@ -940,8 +948,8 @@ def get_parameters_solution(model=None):
         name = obj.getObjectDisplayName()
         data.append({
             'name': name,
-            'lower': item.getLowerBound(),
-            'upper': item.getUpperBound(),
+            'lower': model_info._get_cn_string(item.getLowerBound()),
+            'upper': model_info._get_cn_string(item.getUpperBound()),
             'sol': sol,
             'affected': _get_affected_experiments(item),
         })
@@ -1065,7 +1073,7 @@ def add_experiment(name, data, **kwargs):
                 except AttributeError:
                     logger.error("Cannot map the element {0}".format(current))
             role = _get_role_for_reference(obj.getObjectName())
-            if not obj_map.setObjectCN(i, str(obj.getCN())):
+            if not obj_map.setObjectCN(i, obj.getCN()):
                 logger.error("Error while mapping data for for {0}".format(current))
         obj_map.setRole(i, role)
 
@@ -1363,7 +1371,12 @@ def _get_value_from_bound(bound):
     :rtype: float
     """
     try:
-        value = float(bound)
+        if isinstance(bound, COPASI.CRegisteredCommonName):
+            value = basico.get_value(bound)
+            if value is None: 
+                value = bound.getString()
+        else:
+            value = float(bound)
     except ValueError:
         value = basico.get_value(bound)
     return value

basico/task_profile_likelihood.py

@@ -429,7 +429,7 @@ def _generate_scan_for_item(item, index, data_dir, update_model=False, lower=Fal
     problem2.clearScanItems()
     problem2.addScanItem(1, Arguments["scan_interval"])
     scan_item = problem2.getScanItem(0)
-    scan_item.getParameter("Object").setCNValue(COPASI.CCommonName(item["cn"]))
+    scan_item.getParameter("Object").setCNValue(COPASI.CRegisteredCommonName(item["cn"]))
 
     start_value = item["start_value"]
     param_sd = kwargs.get('param_sds', {}).get(item["name"], None)
@@ -462,7 +462,8 @@ def _generate_scan_for_item(item, index, data_dir, update_model=False, lower=Fal
     report.setConfirmOverwrite(False)
     logger.debug("... Generate Plot")
     plot = COPASI.COutputAssistant.createDefaultOutput(251, scan_task, _DataModel)
-    plot.setObjectName('{0} = {1}'.format('opt', start_value))
+    if plot is not None: 
+        plot.setObjectName('{0} = {1}'.format('opt', start_value))
     out_file = os.path.abspath("{0}/{1}_{2:05d}_{3}.cps".format(data_dir, Arguments['prefix'], index, middle))
     logger.debug(f"Writing '{out_file}'.")
     _DataModel.saveModel(out_file, True)

basico/task_scan.py

@@ -137,6 +137,7 @@ def _scan_item_to_dict(item, model=None):
     int_type = item.getParameter('Type').getIntValue()
     type_name = _scan_type_to_name(int_type)
     cn = item.getParameter('Object').getCNValue().getString() if item.getParameter('Object') else None
+    cn = model_info._get_cn_string(cn)
     num_steps = item.getParameter('Number of steps').getIntValue() if item.getParameter('Number of steps') else None
     min_val = item.getParameter('Minimum').getDblValue() if item.getParameter('Minimum') else None
     max_val = item.getParameter('Maximum').getDblValue() if item.getParameter('Maximum') else None
@@ -176,9 +177,11 @@ def _scan_item_to_dict(item, model=None):
         assert (isinstance(cn_group, COPASI.CCopasiParameterGroup))
         parameter_sets = []
         for i in range(cn_group.size()):
-            cn = cn_group.getParameter(i).getCNValue()
+            _cn = model_info._get_cn_string(cn_group.getParameter(i).getCNValue())
+            if not _cn:
+                continue
             # resolve cn to name
-            obj = model.getObject(cn)
+            obj = model.getObject(COPASI.CCommonName(_cn))
             if obj:
                 parameter_sets.append(obj.getObjectName())
         current['parameter_sets'] = parameter_sets

tests/test_optimization.py

@@ -13,6 +13,9 @@ def setUp(self):
         basico.add_parameter('f', type='assignment',
                              expression='({Values[x].InitialValue}^2+{Values[y].InitialValue}-11)^2+({Values[x].InitialValue}+{Values[y].InitialValue}^2-7)^2')
 
+    def tearDown(self):
+        basico.remove_datamodel(self.dm)
+
     def test_optitems(self):
         self.assertIsNone(basico.get_opt_parameters())
         template = basico.get_opt_item_template(include_global=True)