Ruff Format (#90)

* First ruff checks

* Second ruff checks

* ruff format

* ruff format Error F

* ruff format Error D (some)

* ruff format Error D (some more)

* intermediate ruff

* intermediate ruff by julie

* intermediate stuff by julie

* Docstring by julie

* Final things with julie

* Update src/petab_gui/views/find_replace_bar.py

Co-authored-by: Copilot <[email protected]>

---------

Co-authored-by: Copilot <[email protected]>

Author: PaulJonasJost

pyproject.toml

@@ -56,3 +56,21 @@ include-package-data = true
 
 [tool.setuptools.package-data]
 "petab_gui.assets" = ["PEtab.png"]
+
+[tool.ruff]
+line-length = 79
+lint.select = [
+    "F",  # Pyflakes
+    "I",  # isort
+    "D",  # pydocstyle (PEP 257)
+    "S",  # flake8-bandit
+    "B",  # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "T20",  # flake8-print
+    "W",  # pycodestyle Warnings
+    "E",  # pycodestyle Errors
+    "UP",  # pyupgrade
+    # "ANN",  # flakes-annotations TODO: currently produces ~1500 errors to manual fix
+]
+[tool.ruff.lint.pydocstyle]
+convention = "pep257"

setup.py

@@ -2,6 +2,5 @@
 """Setup script for petab-gui."""
 from setuptools import setup  # type: ignore
 
-
 if __name__ == "__main__":
-    setup(version="0.0.1")
+    setup(version="0.0.1")

src/petab_gui/C.py

@@ -1,4 +1,5 @@
 """Constants for the PEtab edit GUI."""
+
 import numpy as np
 
 COLUMNS = {
@@ -30,36 +31,39 @@
         "nominalValue": {"type": np.float64, "optional": False},
         "estimate": {"type": np.object_, "optional": False},
         "initializationPriorType": {"type": np.object_, "optional": True},
-        "initializationPriorParameters": {"type": np.object_, "optional": True},
+        "initializationPriorParameters": {
+            "type": np.object_,
+            "optional": True,
+        },
         "objectivePriorType": {"type": np.object_, "optional": True},
         "objectivePriorParameters": {"type": np.object_, "optional": True},
     },
     "condition": {
         "conditionId": {"type": np.object_, "optional": False},
         "conditionName": {"type": np.object_, "optional": False},
-    }
+    },
 }
 
 CONFIG = {
-    'window_title': 'My Application',
-    'window_size': (800, 600),
-    'table_titles': {
-        'data': 'Data',
-        'parameters': 'Parameters',
-        'observables': 'Observables',
-        'conditions': 'Conditions'
+    "window_title": "My Application",
+    "window_size": (800, 600),
+    "table_titles": {
+        "data": "Data",
+        "parameters": "Parameters",
+        "observables": "Observables",
+        "conditions": "Conditions",
+    },
+    "summary_title": "Summary",
+    "buttons": {
+        "test_consistency": "Test Consistency",
+        "proceed_optimization": "Proceed to Optimization",
     },
-    'summary_title': 'Summary',
-    'buttons': {
-        'test_consistency': 'Test Consistency',
-        'proceed_optimization': 'Proceed to Optimization'
-    }
 }
 
 # String constants
-ROW = 'row'
-COLUMN = 'column'
-INDEX = 'index'
+ROW = "row"
+COLUMN = "column"
+INDEX = "index"
 
 COPY_FROM = "copy from"
 USE_DEFAULT = "use default"
@@ -120,66 +124,47 @@
     "observable": ALLOWED_STRATEGIES_OBS,
     "parameter": ALLOWED_STRATEGIES_PAR,
     "condition": ALLOWED_STRATEGIES_COND,
-    "measurement": ALLOWED_STRATEGIES_MEAS
+    "measurement": ALLOWED_STRATEGIES_MEAS,
 }
 DEFAULT_OBS_CONFIG = {
     "observableId": {
-        "strategy": COPY_FROM, SOURCE_COLUMN: "observableFormula",
-        DEFAULT_VALUE: "new_observable"
-    },
-    "observableName": {
-        "strategy": COPY_FROM, SOURCE_COLUMN: "observableId"
-    },
-    "noiseFormula": {
-        "strategy": USE_DEFAULT, DEFAULT_VALUE: 1
+        "strategy": COPY_FROM,
+        SOURCE_COLUMN: "observableFormula",
+        DEFAULT_VALUE: "new_observable",
     },
+    "observableName": {"strategy": COPY_FROM, SOURCE_COLUMN: "observableId"},
+    "noiseFormula": {"strategy": USE_DEFAULT, DEFAULT_VALUE: 1},
     "observableTransformation": {
         "strategy": USE_DEFAULT,
-        DEFAULT_VALUE: "lin"
+        DEFAULT_VALUE: "lin",
     },
-    "noiseDistribution": {
-        "strategy": USE_DEFAULT,
-        DEFAULT_VALUE: "normal"
-    }
+    "noiseDistribution": {"strategy": USE_DEFAULT, DEFAULT_VALUE: "normal"},
 }
 DEFAULT_PAR_CONFIG = {
     "parameterName": {
-        "strategy": COPY_FROM, SOURCE_COLUMN: "parameterId",
-        DEFAULT_VALUE: "new_parameter"
-    },
-    "parameterScale": {
-        "strategy": USE_DEFAULT, DEFAULT_VALUE: "log10"
-    },
-    "lowerBound": {
-        "strategy": MIN_COLUMN
-    },
-    "upperBound": {
-        "strategy": MAX_COLUMN
-    },
-    "estimate": {
-        "strategy": USE_DEFAULT, DEFAULT_VALUE: 1
-    },
-    "nominalValue": {
-        "strategy": SBML_LOOK
+        "strategy": COPY_FROM,
+        SOURCE_COLUMN: "parameterId",
+        DEFAULT_VALUE: "new_parameter",
     },
+    "parameterScale": {"strategy": USE_DEFAULT, DEFAULT_VALUE: "log10"},
+    "lowerBound": {"strategy": MIN_COLUMN},
+    "upperBound": {"strategy": MAX_COLUMN},
+    "estimate": {"strategy": USE_DEFAULT, DEFAULT_VALUE: 1},
+    "nominalValue": {"strategy": SBML_LOOK},
 }
 DEFAULT_COND_CONFIG = {
-    "conditionId": {
-        "strategy": USE_DEFAULT, DEFAULT_VALUE: "new_condition"
-    },
-    "conditionName": {
-        "strategy": COPY_FROM, SOURCE_COLUMN: "conditionId"
-    }
+    "conditionId": {"strategy": USE_DEFAULT, DEFAULT_VALUE: "new_condition"},
+    "conditionName": {"strategy": COPY_FROM, SOURCE_COLUMN: "conditionId"},
 }
 DEFAULT_MEAS_CONFIG = {}
 DEFAULT_CONFIGS = {
     "observable": DEFAULT_OBS_CONFIG,
     "parameter": DEFAULT_PAR_CONFIG,
     "condition": DEFAULT_COND_CONFIG,
-    "measurement": DEFAULT_MEAS_CONFIG
+    "measurement": DEFAULT_MEAS_CONFIG,
 }
 
 COMMON_ERRORS = {
     r"Error parsing '': Syntax error at \d+:\d+: mismatched input '<EOF>' "
-    r"expecting \{[^}]+\}" : "Invalid empty cell!"
+    r"expecting \{[^}]+\}": "Invalid empty cell!"
 }

src/petab_gui/__init__.py

@@ -1 +1,3 @@
-from .app import main
+"""Package for the PETAB GUI."""
+
+from .app import main

src/petab_gui/__main__.py

@@ -1,8 +1,9 @@
-import sys
 from petab_gui import app
 
+
 def main():
     app.main()
 
+
 if __name__ == "__main__":
-    main()
+    main()

src/petab_gui/app.py

@@ -1,49 +1,66 @@
-from PySide6.QtWidgets import QApplication
-from PySide6.QtGui import QFileOpenEvent, QIcon
-from PySide6.QtCore import QEvent
-from importlib.resources import files
-import sys
 import os
-import petab.v1 as petab
+import sys
+from importlib.resources import files
+from pathlib import Path
+
+from PySide6.QtCore import QEvent
+from PySide6.QtGui import QFileOpenEvent, QIcon
+from PySide6.QtWidgets import QApplication
 
-from .views import MainWindow
 from .controllers import MainController
 from .models import PEtabModel
-
-from pathlib import Path
+from .views import MainWindow
 
 
 def find_example(path: Path) -> Path:
+    """Find the example directory by traversing up from the given path.
+
+    Args:
+        path: The starting path to search from
+
+    Returns:
+        Path: The path to the example directory
+
+    Raises:
+        FileNotFoundError: If the example directory cannot be found
+    """
     while path.parent != path:
         if (path / "example").is_dir():
             return path / "example"
         path = path.parent
-        
+
     raise FileNotFoundError("Could not find examples directory")
 
 
 def get_icon() -> QIcon:
-    """Get the Icon for the Window"""
+    """Get the Icon for the Window."""
     icon_path = files("petab_gui.assets").joinpath("PEtab.png")
     if not icon_path.is_file():
         raise FileNotFoundError(f"Icon file not found: {icon_path}")
-    icon = QIcon(str(icon_path))
-    return icon
+    return QIcon(str(icon_path))
 
 
 class PEtabGuiApp(QApplication):
+    """Main application class for PEtab GUI.
+
+    Inherits from QApplication and sets up the MVC components.
+    """
+
     def __init__(self):
+        """Initialize the PEtab GUI application.
+
+        Sets up the model, view, and controller components.
+        Handles command line arguments for opening files.
+        """
         super().__init__(sys.argv)
 
-        # Load the stylesheet
-        # self.apply_stylesheet()
         self.setWindowIcon(get_icon())
         self.model = PEtabModel()
         self.view = MainWindow()
         self.view.setWindowIcon(get_icon())
         self.controller = MainController(self.view, self.model)
 
-        # hack to be discussed
+        # Connect the view to the controller
         self.view.controller = self.controller
 
         if len(sys.argv) > 1 and os.path.isfile(sys.argv[1]):
@@ -52,27 +69,50 @@ def __init__(self):
         self.view.show()
 
     def event(self, event):
+        """Handle application events.
+
+        Args:
+            event: The Qt event to handle
+
+        Returns:
+            bool: Result of the event handling from the parent class
+
+        Notes:
+            Currently handles FileOpen events to open files dropped on
+            the application.
+        """
         if event.type() == QEvent.FileOpen:
-            openEvent = QFileOpenEvent(event)            
+            openEvent = QFileOpenEvent(event)
             self.controller.open_file(openEvent.file(), mode="overwrite")
 
         return super().event(event)
 
     def apply_stylesheet(self):
-        """Load and apply the QSS stylesheet."""
+        """Load and apply the QSS stylesheet to the application.
+
+        Reads the stylesheet.css file from the same directory as this module
+        and applies it to the application. If the file doesn't exist,
+        no stylesheet is applied.
+        """
         stylesheet_path = os.path.join(
             os.path.dirname(__file__), "stylesheet.css"
         )
         if os.path.exists(stylesheet_path):
-            with open(stylesheet_path, "r") as f:
+            with open(stylesheet_path) as f:
                 self.setStyleSheet(f.read())
         else:
-            print(f"Warning: Stylesheet '{stylesheet_path}' not found!")
+            pass
 
 
 def main():
+    """Entry point for the PEtab GUI application.
+
+    Creates the application instance and starts the event loop.
+    The function exits with the return code from the application.
+    """
     app = PEtabGuiApp()
     sys.exit(app.exec())
 
+
 if __name__ == "__main__":
     main()