Merge pull request #2 from alan-turing-institute/update-pre-commit-ci-and-config

Update pre-commit CI and config

Author: sgreenbury

.github/workflows/ci.yaml

@@ -48,6 +48,10 @@ jobs:
         run: |
           uv sync --extra dev
 
+      - name: Run pre-commit
+        run: |
+          uv run pre-commit run --hook-stage manual --all-files
+
       - name: Test with pytest
         run: |
           # stop pytest after 3 failures to save CI time

.pre-commit-config.yaml

@@ -11,11 +11,10 @@ repos:
     - id: ruff-format
       types_or: [ python, pyi ]
 - repo: https://github.com/RobertCraigie/pyright-python
-  rev: v1.1.405
+  rev: v1.1.407
   hooks:
   - id: pyright
-# - repo: https://github.com/kyanan/nbstripout
-#   rev: 0.8.1
-#   hooks:
-#   - id: nbstripout
-#     exclude: ^case_studies/
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.8.1
+  hooks:
+  - id: nbstripout

pyproject.toml

@@ -15,7 +15,7 @@ dev = [
     "pytest>=9.0.1",
     "pytest-cov>=7.0.0",
     "ruff==0.14.4",
-    "pyright==1.1.405",
+    "pyright==1.1.407",
     "pre-commit>=4.4.0",
 ]
 
@@ -25,3 +25,62 @@ auto-x = "auto_x:main"
 [build-system]
 requires = ["uv_build>=0.8.15,<0.9.0"]
 build-backend = "uv_build"
+
+[tool.pyright]
+venvPath = "."
+venv = ".venv"
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
+select = [
+    "D",   # docstring conventions
+    "E",
+    "F",
+    "W",   # flake8
+    "B",   # flake8-bugbear
+    "I",   # isort
+    "ARG", # flake8-unused-arguments
+    "C4",  # flake8-comprehensions
+    "EM",  # flake8-errmsg
+    "ICN", # flake8-import-conventions
+    "ISC", # flake8-implicit-str-concat
+    "G",   # flake8-logging-format
+    "PGH", # pygrep-hooks
+    "PIE", # flake8-pie
+    "PL",  # pylint
+    "PT",  # flake8-pytest-style
+    "RET", # flake8-return
+    "RUF", # Ruff-specific
+    "SIM", # flake8-simplify
+    "UP",  # pyupgrade
+    "YTT", # flake8-2020
+    "EXE", # flake8-executable
+]
+
+ignore = [
+    "PLR2004", # Magic value used in comparison
+    "EM102",   # Exception must not use an f-string literal, assign to variable first
+    "ISC001",  # Conflicts with formatter
+    # "D417",    # Missing trailing new line in docstring
+    "D100",    # Missing docstring in public module
+    "D104",    # Missing docstring in public package
+    "PLR0913", # too many arguments
+]
+
+unfixable = [
+    "F401", # Would remove unused imports
+    "F841", # Would remove unused variables
+]
+flake8-unused-arguments.ignore-variadic-names = true # allow unused *args/**kwargs
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = ["D"]

src/auto_x/__init__.py

@@ -1,2 +1,2 @@
-def main() -> None:
+def main() -> None:  # noqa: D103
     print("Hello from auto-x!")

tests/test_imports.py

@@ -1,2 +1,2 @@
 def test_imports():
-    import auto_x  # noqa: F401
+    import auto_x  # noqa: F401, PLC0415