Add .pre-commit-config.yaml

* Add .pre-commit-config.yaml
* Fix some ruff issues
* Add some ruff ignores -- to be fixed later

Author: dweindl

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.24.1
+    hooks:
+      - id: validate-pyproject
+        # Optional extra validations from SchemaStore:
+        additional_dependencies: [ "validate-pyproject-schema-store[all]" ]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.1
+    hooks:
+      - id: ruff-check
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      - id: ruff-format
+        types_or: [ python, pyi ]

pyproject.toml

@@ -92,12 +92,26 @@ lint.ignore = [
     "D100",  # Ignore missing docstring in public modules
     "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
+    "RET504",  # Unnecessary assignment before `return`
+    "T201",  # `print` found"
+    "SIM105",  # Use `contextlib.suppress`
+    "S110",  # `try`-`except`-`pass` detected, consider logging the exception
+    "A002",  # Function argument shadowing a Python builtin
+    "E701",  # Multiple statements on one line (colon)
+    "E741",  # Ambiguous variable name
 ]
 [tool.ruff.lint.per-file-ignores]
 "*/__init__.py" = [
     "F401",
     "D400",
     "D205",
 ]
+"docs/source/conf.py" = [
+    "A001", # Variable `copyright` is shadowing a Python builtin
+
+]
 [tool.ruff.lint.pydocstyle]
 convention = "pep257"

src/petab_gui/controllers/sbml_controller.py

@@ -151,12 +151,10 @@ def _overwrite_sbml_with_model(self, sbml_model: SbmlModel):
             "SBML model successfully overwritten.", color="green"
         )
 
-
     def clear_model(self):
-        """Clear the model in case the user wants to start a new problem"""
+        """Clear the model in case the user wants to start a new problem."""
         self.model.antimony_text = DEFAULT_ANTIMONY_TEXT
         self.model.convert_antimony_to_sbml()
         self.view.sbml_text_edit.setPlainText(self.model.sbml_text)
         self.view.antimony_text_edit.setPlainText(self.model.antimony_text)
         self.overwritten_model.emit()
-

src/petab_gui/models/sbml_model.py

@@ -33,7 +33,7 @@ def __init__(self, sbml_model: petab.models.Model, parent=None):
             self.antimony_text = sbmlToAntimony(self.sbml_text)
         else:
             self.antimony_text = DEFAULT_ANTIMONY_TEXT
-            with QSignalBlocker(self) as blocker:
+            with QSignalBlocker(self):
                 self.convert_antimony_to_sbml()
         self.model_id = self._get_model_id()
 
@@ -67,7 +67,7 @@ def get_current_sbml_model(self):
 
     def _get_model_id(self):
         """Extract the model ID from the SBML text."""
-        document =  libsbml.readSBMLFromString(self.sbml_text)
+        document = libsbml.readSBMLFromString(self.sbml_text)
         model = document.getModel()
         model_id = model.getIdAttribute() or "New_File"
         return model_id

src/petab_gui/views/simple_plot_view.py

@@ -390,7 +390,7 @@ class ToolbarOptionManager(QObject):
 
     def __new__(cls):
         if cls._instance is None:
-            cls._instance = super(ToolbarOptionManager, cls).__new__(cls)
+            cls._instance = super().__new__(cls)
         return cls._instance
 
     def __init__(self):