Merge branch 'main' into fix229

Author: PaulJonasJost

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
 description = "Graphical user interface for the PEtab format"
 dependencies = [
     "pyside6",
-    "pandas",
+    "pandas<3.0.0",
     "antimony",
     "python-libsbml",
     "matplotlib",

src/petab_gui/controllers/mother_controller.py

@@ -1555,6 +1555,49 @@ def simulate(self):
         # obtain petab problem
         petab_problem = self.model.current_petab_problem
 
+        # Check if nominalValue column exists, if not add it from SBML model
+        parameter_df = petab_problem.parameter_df.copy()
+        if (
+            parameter_df is not None
+            and not parameter_df.empty
+            and petab.C.NOMINAL_VALUE not in parameter_df.columns
+        ):
+            self.logger.log_message(
+                "nominalValue column missing in parameter table. "
+                "Extracting nominal values from SBML model...",
+                color="orange",
+            )
+            # Extract parameter values from SBML model
+            sbml_model = self.model.sbml.get_current_sbml_model()
+            if sbml_model is not None:
+                nominal_values = []
+                for param_id in parameter_df.index:
+                    try:
+                        value = sbml_model.get_parameter_value(param_id)
+                        nominal_values.append(value)
+                    except Exception:
+                        # If parameter not found in SBML, use default value of 1
+                        nominal_values.append(1.0)
+
+                # Add nominalValue column to parameter_df
+                parameter_df[petab.C.NOMINAL_VALUE] = nominal_values
+                self.logger.log_message(
+                    f"Successfully extracted {len(nominal_values)} "
+                    f"nominal values from SBML model. Add nominalValue "
+                    f"column to parameter table to set values manually.",
+                    color="green",
+                )
+
+                # Update the petab problem with the modified parameter_df
+                petab_problem = petab.Problem(
+                    condition_df=petab_problem.condition_df,
+                    measurement_df=petab_problem.measurement_df,
+                    observable_df=petab_problem.observable_df,
+                    parameter_df=parameter_df,
+                    visualization_df=petab_problem.visualization_df,
+                    model=petab_problem.model,
+                )
+
         # import petabsimualtor
         import basico
         from basico.petab import PetabSimulator

src/petab_gui/utils.py

@@ -408,6 +408,9 @@ def process_file(filepath, logger):
             )
             return None, None
 
+        # if separator is None:
+        #     separator = "\t"
+
         # Case 3.2: Identify the table type based on header content
         if {petab.C.OBSERVABLE_ID, petab.C.MEASUREMENT, petab.C.TIME}.issubset(
             header
@@ -427,7 +430,7 @@ def process_file(filepath, logger):
             petab.C.CONDITION_ID in header
             or f"\ufeff{petab.C.CONDITION_ID}" in header
         ):
-            return "condition", separator
+            return "condition", separator if separator is not None else "\t"
         if petab.C.PLOT_ID in header:
             return "visualization", separator
         logger.log_message(

src/petab_gui/views/simple_plot_view.py

@@ -180,7 +180,7 @@ def _render_on_main_thread(self, payload):
             meas_df is None
             or meas_df.empty
             or cond_df is None
-            or cond_df.empty
+            or not len(cond_df) > 0
         ):
             self._update_tabs(None)
             return