Merge branch 'develop' into about

Author: dweindl

src/petab_gui/controllers/mother_controller.py

@@ -840,13 +840,15 @@ def new_file(self):
                 continue
             controller.clear_table()
         self.view.plot_dock.plot_it()
+        self.unsaved_changes_change(False)
 
     def check_model(self):
         """Check the consistency of the model. And log the results."""
         capture_handler = CaptureLogHandler()
-        logger = logging.getLogger("petab.v1.lint")  # Target the specific
-        # logger
-        logger.addHandler(capture_handler)
+        logger_lint = logging.getLogger("petab.v1.lint")
+        logger_vis = logging.getLogger("petab.v1.visualize.lint")
+        logger_lint.addHandler(capture_handler)
+        logger_vis.addHandler(capture_handler)
 
         try:
             # Run the consistency check
@@ -865,17 +867,22 @@ def check_model(self):
 
             # Log the consistency check result
             if not failed:
-                self.logger.log_message("Model is consistent.", color="green")
+                self.logger.log_message(
+                    "PEtab problem has no errors.", color="green"
+                )
                 for model in self.model.pandas_models.values():
                     model.reset_invalid_cells()
             else:
-                self.logger.log_message("Model is inconsistent.", color="red")
+                self.logger.log_message(
+                    "PEtab problem has errors.", color="red"
+                )
         except Exception as e:
             msg = f"PEtab linter failed at some point: {filtered_error(e)}"
             self.logger.log_message(msg, color="red")
         finally:
             # Always remove the capture handler
-            logger.removeHandler(capture_handler)
+            logger_lint.removeHandler(capture_handler)
+            logger_vis.removeHandler(capture_handler)
 
     def unsaved_changes_change(self, unsaved_changes: bool):
         self.unsaved_changes = unsaved_changes
@@ -1176,3 +1183,7 @@ def about(self):
             f"<small>Settings are stored in "
             f"<a href='file://{config_file}'>{config_file}</a></small>",
         )
+
+    def get_current_problem(self):
+        """Get the current PEtab problem from the model."""
+        return self.model.current_petab_problem

src/petab_gui/controllers/table_controllers.py

@@ -1,5 +1,6 @@
 """Classes for the controllers of the tables in the GUI."""
 
+import logging
 import re
 from collections.abc import Sequence
 from pathlib import Path
@@ -22,7 +23,12 @@
     PandasTableModel,
 )
 from ..settings_manager import settings_manager
-from ..utils import ConditionInputDialog, get_selected, process_file
+from ..utils import (
+    CaptureLogHandler,
+    ConditionInputDialog,
+    get_selected,
+    process_file,
+)
 from ..views.other_views import DoseTimeDialog
 from ..views.table_view import (
     ColumnSuggestionDelegate,
@@ -1278,19 +1284,27 @@ def check_petab_lint(
         col_name: str = None,
     ):
         """Check a number of rows of the model with petablint."""
+        # Validate full parameter table
         if row_data is None:
             row_data = self.model.get_df()
-        observable_df = self.mother_controller.model.observable.get_df()
-        measurement_df = self.mother_controller.model.measurement.get_df()
-        condition_df = self.mother_controller.model.condition.get_df()
-        sbml_model = self.mother_controller.model.sbml.get_current_sbml_model()
-        return petab.check_parameter_df(
-            row_data,
-            observable_df=observable_df,
-            measurement_df=measurement_df,
-            condition_df=condition_df,
-            model=sbml_model,
-        )
+            observable_df = self.mother_controller.model.observable.get_df()
+            measurement_df = self.mother_controller.model.measurement.get_df()
+            condition_df = self.mother_controller.model.condition.get_df()
+            sbml_model = (
+                self.mother_controller.model.sbml.get_current_sbml_model()
+            )
+            return petab.check_parameter_df(
+                row_data,
+                observable_df=observable_df,
+                measurement_df=measurement_df,
+                condition_df=condition_df,
+                model=sbml_model,
+            )
+
+        # Validate a single parameter row
+        # In this case, we don't pass any other dataframes/models to avoid
+        # false positives due to the incomplete parameter table.
+        return petab.check_parameter_df(row_data)
 
 
 class VisualizationController(TableController):
@@ -1315,3 +1329,81 @@ def __init__(
             undo_stack=undo_stack,
             mother_controller=mother_controller,
         )
+
+    @linter_wrapper(additional_error_check=True)
+    def check_petab_lint(
+        self,
+        row_data: pd.DataFrame = None,
+        row_name: str = None,
+        col_name: str = None,
+    ):
+        """Check a number of rows of the model with petablint."""
+        problem = self.mother_controller.get_current_problem()
+        capture_handler = CaptureLogHandler()
+        logger_vis = logging.getLogger("petab.v1.visualize.lint")
+        logger_vis.addHandler(capture_handler)
+        errors = petab.visualize.lint.validate_visualization_df(problem)
+        if not errors:
+            return not errors
+        captured_output = "<br>&nbsp;&nbsp;&nbsp;&nbsp;".join(
+            capture_handler.get_formatted_messages()
+        )
+        raise ValueError(captured_output)
+
+    def setup_completers(self):
+        """Set completers for the visualization table."""
+        table_view = self.view.table_view
+        # plotTypeSimulation
+        index = self.model.return_column_index("plotTypeSimulation")
+        if index and index > -1:
+            self.completers["plotTypeSimulation"] = ComboBoxDelegate(
+                ["LinePlot", "BarPlot", "ScatterPlot"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["plotTypeSimulation"]
+            )
+        # plotTypeData
+        index = self.model.return_column_index("plotTypeData")
+        if index and index > -1:
+            self.completers["plotTypeData"] = ComboBoxDelegate(
+                ["MeanAndSD", "MeanAndSEM", "replicate", "provided"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["plotTypeData"]
+            )
+        # datasetId
+        index = self.model.return_column_index("datasetId")
+        if index and index > -1:
+            self.completers["datasetId"] = ColumnSuggestionDelegate(
+                self.mother_controller.model.measurement, "datasetId"
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["datasetId"]
+            )
+        # yValues
+        index = self.model.return_column_index("yValues")
+        if index and index > -1:
+            self.completers["yValues"] = ColumnSuggestionDelegate(
+                self.mother_controller.model.observable, "observableId"
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["yValues"]
+            )
+        # xScale
+        index = self.model.return_column_index("xScale")
+        if index and index > -1:
+            self.completers["xScale"] = ComboBoxDelegate(
+                ["lin", "log", "log10", "order"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["xScale"]
+            )
+        # yScale
+        index = self.model.return_column_index("yScale")
+        if index and index > -1:
+            self.completers["yScale"] = ComboBoxDelegate(
+                ["lin", "log", "log10", "order"]
+            )
+            table_view.setItemDelegateForColumn(
+                index, self.completers["yScale"]
+            )

src/petab_gui/models/pandas_table_model.py

@@ -377,7 +377,7 @@ def _set_data_single(self, index, value):
             if error:
                 self.new_log_message.emit(
                     f"Column '{column_name}' expects a value of type "
-                    f"{expected_type}, but got '{value}'",
+                    f"{expected_type.__name__}, but got '{value}'",
                     "red",
                 )
                 return False
@@ -670,7 +670,9 @@ def return_column_index(self, column_name):
         Returns:
             int: The view column index for the given column name, or -1
         """
-        pass
+        if column_name in self._data_frame.columns:
+            return self._data_frame.columns.get_loc(column_name)
+        return -1
 
     def unique_values(self, column_name):
         """Return a list of unique values in a specified column.
@@ -1115,12 +1117,6 @@ def get_default_values(self, index, changed: dict | None = None):
         else:
             command.redo()
 
-    def return_column_index(self, column_name):
-        """Return the index of a column."""
-        if column_name in self._data_frame.columns:
-            return self._data_frame.columns.get_loc(column_name)
-        return -1
-
 
 class ObservableModel(IndexedPandasTableModel):
     """Table model for the observable data."""

src/petab_gui/views/find_replace_bar.py

@@ -25,6 +25,8 @@ def __init__(self, controller, parent=None):
             "Condition Table": self.controller.condition_controller,
             "Parameter Table": self.controller.parameter_controller,
             "Measurement Table": self.controller.measurement_controller,
+            "Visualization Table": self.controller.visualization_controller,
+            "Simulation Table": self.controller.simulation_controller,
         }
         self.selected_controllers = self.controller_map.values()
         self.only_search = False