PEP8 Standard E501 (#251)

* Just removed from lint.ignore. Testing new workflows. Refs #242

* adopted line length

* adopted line length in tests as well

Author: PaulJonasJost

pyproject.toml

@@ -88,7 +88,6 @@ lint.ignore = [
     "D101",  # Ignore missing docstring in public classes
     "F401",
     # FIXME: those are ignored for now, should be fixed eventually
-    "E501",  # Ignore line too long
     "ERA001", # Found commented-out code
     "T201",  # `print` found"
     "SIM105",  # Use `contextlib.suppress`

src/petab_gui/commands.py

@@ -12,8 +12,8 @@ def _convert_dtype_with_nullable_int(series, dtype):
     """Convert a series to the specified dtype, handling nullable integers.
 
     When converting to integer types and the series contains NaN values,
-    this function automatically uses pandas nullable integer types (Int64, Int32, etc.)
-    instead of numpy integer types which don't support NaN.
+    this function automatically uses pandas nullable integer types (Int64,
+    Int32, etc.) instead of numpy integer types which don't support NaN.
 
     Args:
         series: The pandas Series to convert

src/petab_gui/controllers/file_io_controller.py

@@ -1,7 +1,7 @@
 """File I/O Controller for PEtab GUI.
 
-This module contains the FileIOController class, which handles all file input/output
-operations for PEtab models, including:
+This module contains the FileIOController class, which handles all
+file input/output operations for PEtab models, including:
 - Opening and saving PEtab YAML files
 - Opening and saving COMBINE archives (OMEX)
 - Opening and saving individual tables
@@ -35,7 +35,8 @@ class FileIOController:
     Attributes
     ----------
     main : MainController
-        Reference to the main controller for access to models, views, and other controllers.
+        Reference to the main controller for access to models, views, and
+        other controllers.
     model : PEtabModel
         The PEtab model being managed.
     view : MainWindow
@@ -60,8 +61,9 @@ def __init__(self, main_controller):
     def save_model(self):
         """Save the entire PEtab model.
 
-        Opens a dialog to select the save format and location, then saves the model
-        as either a COMBINE archive (OMEX), ZIP file, or folder structure.
+        Opens a dialog to select the save format and location, then saves
+        the model as either a COMBINE archive (OMEX), ZIP file, or folder
+        structure.
 
         Returns
         -------
@@ -129,7 +131,8 @@ def save_single_table(self):
         Returns
         -------
         bool or None
-            True if saved successfully, False if cancelled, None if no active table.
+            True if saved successfully, False if cancelled, None if no
+            active table.
         """
         active_controller = self.main.active_controller()
         if not active_controller:
@@ -253,8 +256,9 @@ def _open_file(self, actionable, file_path, sep, mode):
         Parameters
         ----------
         actionable : str
-            Type of file: "yaml", "omex", "sbml", "measurement", "observable",
-            "parameter", "condition", "visualization", "simulation", "data_matrix".
+            Type of file: "yaml", "omex", "sbml", "measurement",
+            "observable", "parameter", "condition", "visualization",
+            "simulation", "data_matrix".
         file_path : str
             Path to the file.
         sep : str
@@ -412,7 +416,8 @@ def _load_file_list(self, controller, file_list, file_type, yaml_dir):
             file_mode = "overwrite" if i == 0 else "append"
             controller.open_table(yaml_dir / file_name, mode=file_mode)
             self.logger.log_message(
-                f"Loaded {file_type} file ({i + 1}/{len(file_list)}): {file_name}",
+                f"Loaded {file_type} file ({i + 1}/{len(file_list)}): "
+                f"{file_name}",
                 color="blue",
             )
 
@@ -478,8 +483,8 @@ def open_yaml_and_load_files(self, yaml_path=None, mode="overwrite"):
             )
             if not all_exist:
                 error_msg = (
-                    "The following files referenced in the YAML are missing:\n  - "
-                    + "\n  - ".join(missing_files)
+                    "The following files referenced in the YAML are "
+                    "missing:\n  - " + "\n  - ".join(missing_files)
                 )
                 self.logger.log_message(error_msg, color="red")
                 QMessageBox.critical(self.view, "Missing Files", error_msg)
@@ -565,7 +570,10 @@ def open_yaml_and_load_files(self, yaml_path=None, mode="overwrite"):
             self.main.unsaved_changes_change(False)
 
         except FileNotFoundError as e:
-            error_msg = f"File not found: {e.filename if hasattr(e, 'filename') else str(e)}"
+            error_msg = (
+                f"File not found: "
+                f"{e.filename if hasattr(e, 'filename') else str(e)}"
+            )
             self.logger.log_message(error_msg, color="red")
             QMessageBox.warning(self.view, "File Not Found", error_msg)
         except KeyError as e:
@@ -659,12 +667,14 @@ def load_example(self, example_name):
         Parameters
         ----------
         example_name : str
-            Name of the example subdirectory (e.g., "Boehm", "Simple_Conversion").
+            Name of the example subdirectory (e.g., "Boehm",
+            "Simple_Conversion").
 
         Notes
         -----
         Finds and loads the example dataset from the package directory.
-        No internet connection required - the example is bundled with the package.
+        No internet connection required - the example is bundled with the
+        package.
         """
         try:
             # Use importlib.resources to access packaged example files
@@ -687,7 +697,10 @@ def load_example(self, example_name):
 
             with as_file(yaml_file) as yaml_path:
                 if not yaml_path.exists():
-                    error_msg = f"Example '{example_name}' not found or problem.yaml file is missing."
+                    error_msg = (
+                        f"Example '{example_name}' not found or "
+                        f"problem.yaml file is missing."
+                    )
                     self.logger.log_message(error_msg, color="red")
                     QMessageBox.warning(
                         self.view, "Example Invalid", error_msg

src/petab_gui/controllers/mother_controller.py

@@ -728,7 +728,8 @@ def replace(self):
         self.view.toggle_replace()
 
     def _toggle_whats_this_mode(self, on: bool):
-        """Enable/disable click-to-help mode by installing/removing the global filter.
+        """
+        Enable/disable click-to-help mode.
 
         On enter: show a short instruction bubble.
         """
@@ -754,7 +755,7 @@ def _toggle_whats_this_mode(self, on: bool):
         self._show_help_welcome()
 
     def _show_help_welcome(self):
-        """Centered welcome with a 'Don't show again' option persisted in QSettings."""
+        """Welcome with a 'Don't show again' option persisted in QSettings."""
         settings = settings_manager.settings
         if settings.value("help_mode/welcome_disabled", False, type=bool):
             return
@@ -765,9 +766,12 @@ def _show_help_welcome(self):
         msg.setText(
             "<b>Welcome to help mode</b><br>"
             "<ul>"
-            "<li>Click any widget, tab, or column header to see its help.</li>"
-            "<li>Click the same item again or press <b>Esc</b> to close the bubble.</li>"
-            "<li>Press <b>Esc</b> with no bubble, or toggle the <i>?</i> button, to exit.</li>"
+            "<li>Click any widget, tab, or column header to see its "
+            "help.</li>"
+            "<li>Click the same item again or press <b>Esc</b> to close "
+            "the bubble.</li>"
+            "<li>Press <b>Esc</b> with no bubble, or toggle the <i>?</i> "
+            "button, to exit.</li>"
             "</ul>"
         )
         dont = QCheckBox("Don't show again")
@@ -795,7 +799,7 @@ def about(self):
         )
 
     def _show_next_steps_panel(self):
-        """Show the next steps panel (ignores 'don't show again' preference)."""
+        """Show the next steps panel."""
         # Sync checkbox state with current settings
         dont_show = settings_manager.get_value(
             "next_steps/dont_show_again", False, bool

src/petab_gui/controllers/plot_coordinator.py

@@ -23,7 +23,8 @@ class PlotCoordinator:
     Attributes
     ----------
     main : MainController
-        Reference to the main controller for access to models, views, and other controllers.
+        Reference to the main controller for access to models, views, and
+        other controllers.
     model : PEtabModel
         The PEtab model being visualized.
     view : MainWindow
@@ -188,7 +189,8 @@ def _on_plot_point_clicked(self, x, y, label, data_type):
         x : float
             X-coordinate of the clicked point (time).
         y : float
-            Y-coordinate of the clicked point (measurement or simulation value).
+            Y-coordinate of the clicked point (measurement or simulation
+            value).
         label : str
             Label of the clicked point (observable ID).
         data_type : str
@@ -250,7 +252,8 @@ def column_index(name):
                 and self._floats_match(row_y, y)
             ):
                 # Manually update highlight BEFORE selecting row
-                # This ensures the circle appears even though we skip the signal handler
+                # This ensures the circle appears even though we skip
+                # the signal handler
                 if data_type == "measurement":
                     self.plotter.highlight_from_selection([row])
                 else:
@@ -272,7 +275,8 @@ def column_index(name):
         # Provide feedback if no match found
         if not matched:
             self.logger.log_message(
-                f"No matching row found for plot point (obs={obs}, x={x:.4g}, y={y:.4g})",
+                f"No matching row found for plot point "
+                f"(obs={obs}, x={x:.4g}, y={y:.4g})",
                 color="orange",
             )
 

src/petab_gui/controllers/simulation_controller.py

@@ -22,7 +22,8 @@ class SimulationController:
     Attributes
     ----------
     main : MainController
-        Reference to the main controller for access to models, views, and other controllers.
+        Reference to the main controller for access to models, views, and
+        other controllers.
     model : PEtabModel
         The PEtab model being simulated.
     logger : LoggerController
@@ -80,7 +81,7 @@ def simulate(self):
                         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
+                        # If parameter not found in SBML, use default value
                         nominal_values.append(1.0)
 
                 # Add nominalValue column to parameter_df
@@ -108,7 +109,8 @@ def simulate(self):
 
         # report current basico / COPASI version
         self.logger.log_message(
-            f"Simulate with basico: {basico.__version__}, COPASI: {basico.COPASI.__version__}",
+            f"Simulate with basico: {basico.__version__}, "
+            f"COPASI: {basico.COPASI.__version__}",
             color="green",
         )
 

src/petab_gui/controllers/table_controllers.py

@@ -227,8 +227,9 @@ def append_df(self, new_df: pd.DataFrame):
         self.model.beginResetModel()
         current_df = self.model.get_df()
 
-        # For tables without a named index (measurement, visualization, simulation),
-        # ignore the index to avoid removing appended data due to index conflicts
+        # For tables without a named index (measurement, visualization,
+        # simulation), ignore the index to avoid removing appended data due
+        # to index conflicts
         if self.model.table_type in [
             "measurement",
             "visualization",
@@ -238,7 +239,8 @@ def append_df(self, new_df: pd.DataFrame):
                 [current_df, new_df], axis=0, ignore_index=True
             )
         else:
-            # For tables with named indices, concatenate and remove duplicate indices
+            # For tables with named indices, concatenate and remove
+            # duplicate indices
             combined_df = pd.concat([current_df, new_df], axis=0)
             combined_df = combined_df[
                 ~combined_df.index.duplicated(keep="first")
@@ -784,12 +786,14 @@ def _detect_time_column(self, df) -> str | None:
         return None
 
     def _rank_dose_candidates(self, df: pd.DataFrame) -> list[str]:
-        """Rank DataFrame columns by likelihood of containing dose/concentration data.
+        """Rank columns by likelihood of containing dose/concentration data.
 
-        This method implements a lightweight scoring system to identify and rank
-        columns that are most likely to contain dose, concentration, or drug-related
-        data. The ranking is based on multiple heuristics including column naming
-        patterns, data types, value ranges, and statistical properties.
+        This method implements a lightweight scoring system to identify
+        and rank columns that are most likely to contain dose,
+        concentration, or drug-related
+        data. The ranking is based on multiple heuristics including column
+        naming patterns, data types, value ranges, and statistical
+        properties.
 
         Parameters
         ----------
@@ -800,29 +804,32 @@ def _rank_dose_candidates(self, df: pd.DataFrame) -> list[str]:
         Returns
         -------
         list[str]
-            Column names sorted by descending likelihood of containing dose data.
-            Columns with higher scores appear first. In case of tied scores,
-            columns with fewer unique values are ranked higher.
+            Column names sorted by descending likelihood of containing
+            dose data. Columns with higher scores appear first. In case of
+            tied scores, columns with fewer unique values are ranked higher.
 
         Notes
         -----
         The scoring algorithm considers the following criteria:
 
-        - **Name matching** (+2.0 points): Column names containing keywords like
-          'dose', 'conc', 'concentration', 'drug', 'compound', 'stim', 'input',
-          or patterns like 'u<digit>' (case-insensitive).
+        - **Name matching** (+2.0 points): Column names containing keywords
+          like 'dose', 'conc', 'concentration', 'drug', 'compound', 'stim',
+          'input', or patterns like 'u<digit>' (case-insensitive).
 
-        - **Numeric data type** (+1.0 points): Columns with integer or float dtype.
+        - **Numeric data type** (+1.0 points): Columns with integer or float
+          dtype.
 
-        - **Reasonable cardinality** (+0.8 points): Columns with 2-30 unique
-          non-null values, which is typical for dose series.
+        - **Reasonable cardinality** (+0.8 points): Columns with 2-30
+          unique non-null values, which is typical for dose series.
 
-        - **Non-negative values** (+0.3 points): All values are >= 0 when converted
-          to numeric (dose/concentration values are typically non-negative).
+        - **Non-negative values** (+0.3 points): All values are >= 0 when
+          converted to numeric (dose/concentration values are typically
+          non-negative).
 
-        - **Monotonic tendency** (+0.2 points): At least 70% of consecutive numeric
-          differences are non-decreasing, indicating potential dose escalation
-          patterns. Requires at least 5 non-null numeric values.
+        - **Monotonic tendency** (+0.2 points): At least 70% of
+          consecutive numeric differences are non-decreasing, indicating
+          potential dose escalation patterns. Requires at least 5 non-null
+          numeric values.
 
         Raises
         ------

src/petab_gui/controllers/utils.py

@@ -29,9 +29,12 @@ class _WhatsThisClickHelp(QObject):
 
     While the action is checked:
       • Left-click shows a What's This bubble for the target under cursor.
-      • Clicking the SAME target again closes the bubble (stays in help mode).
-      • ESC closes the bubble if one is open; if none is open, exits help mode.
-      • Special cases: QTabBar tabs and QHeaderView sections handled explicitly.
+      • Clicking the SAME target again closes the bubble (stays in help
+        mode).
+      • ESC closes the bubble if one is open; if none is open, exits help
+        mode.
+      • Special cases: QTabBar tabs and QHeaderView sections handled
+        explicitly.
     """
 
     def __init__(self, action):
@@ -81,7 +84,8 @@ def eventFilter(self, _obj, ev):
             if isinstance(w, QScrollBar):
                 return False
 
-            # If click landed outside app widgets (e.g., on the bubble), just close it
+            # If click landed outside app widgets (e.g., on the bubble),
+            # just close it
             if not w:
                 self._has_bubble = False
                 return True

src/petab_gui/controllers/validation_controller.py

@@ -23,7 +23,8 @@ class ValidationController:
     Attributes
     ----------
     main : MainController
-        Reference to the main controller for access to models, views, and other controllers.
+        Reference to the main controller for access to models, views, and
+        other controllers.
     model : PEtabModel
         The PEtab model being validated.
     logger : LoggerController