Implement pre-commit hooks

Author: SeCuReDmE-main-dev

.github/scripts/run_staged_ruff.py

@@ -0,0 +1,43 @@
+"""Run Ruff against staged Python files for pre-commit hooks."""
+
+from __future__ import annotations
+
+import subprocess
+import sys
+from pathlib import Path
+
+
+def staged_python_files() -> list[str]:
+    result = subprocess.run(
+        ["git", "diff", "--cached", "--name-only", "--diff-filter=ACMR"],
+        check=True,
+        capture_output=True,
+        text=True,
+    )
+    files = []
+    for line in result.stdout.splitlines():
+        path = Path(line)
+        if path.suffix in {".py", ".pyi"} and path.exists():
+            files.append(line)
+    return files
+
+
+def main() -> int:
+    if len(sys.argv) != 2 or sys.argv[1] not in {"check", "format"}:
+        print("Usage: run_staged_ruff.py {check|format}", file=sys.stderr)
+        return 2
+
+    files = staged_python_files()
+    if not files:
+        print("No staged Python files to check.")
+        return 0
+
+    command = ["uv", "run", "ruff", sys.argv[1]]
+    if sys.argv[1] == "check":
+        command.append("--fix")
+    command.extend(files)
+    return subprocess.run(command).returncode
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: local
+    hooks:
+      - id: ruff-staged-check
+        name: ruff check staged Python files
+        entry: python .github/scripts/run_staged_ruff.py check
+        language: system
+        pass_filenames: false
+        types_or: [python, pyi]
+      - id: ruff-staged-format
+        name: ruff format staged Python files
+        entry: python .github/scripts/run_staged_ruff.py format
+        language: system
+        pass_filenames: false
+        types_or: [python, pyi]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-toml
+      - id: check-yaml

README.md

@@ -77,6 +77,17 @@ SeQUeNCe includes a comprehensive test suite, this can be ran with the following
 uv run pytest tests
 ```
 
+#### Pre-commit hooks
+To run lightweight checks before each commit, install the pre-commit hooks:
+```bash
+uv run pre-commit install
+```
+
+The hooks run Ruff against staged Python files and perform basic file checks. They can also be run manually:
+```bash
+uv run pre-commit run --all-files
+```
+
 ## Citation
 Please cite us, thank you!
 ```

pyproject.toml

@@ -67,10 +67,11 @@ dev = [
     "ty>=0.0.16",
     "pandas-stubs~=2.3.3",
     "scipy-stubs~=1.16.3",
+    "pre-commit>=4.6.0",
 ]
 
 [project.urls]
 Homepage = "https://github.com/sequence-toolbox/SeQUeNCe"
 Documentation = "https://sequence-rtd-tutorial.readthedocs.io/"
 Issues = "https://github.com/sequence-toolbox/SeQUeNCe/issues"
-Changelog = "https://github.com/sequence-toolbox/SeQUeNCe/blob/master/CHANGELOG.md"
+Changelog = "https://github.com/sequence-toolbox/SeQUeNCe/blob/master/CHANGELOG.md"