Use pre-commit for linting and formatting (#72)

* Remove more files with clean session

* Match workflow files to Landlab

* Use pre-commit hooks for linting

* Remove unused dependencies

* Remove coverage artifacts

* Back to flake8 from ruff

* Rename job and call the lint session

* Add pre-commit hooks

.flake8

@@ -0,0 +1,10 @@
+[flake8]
+exclude = docs, build, .nox
+ignore =
+  E203
+  E501
+  W503
+  W605
+max-line-length = 88
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

.github/workflows/format.yml → .github/workflows/lint.yml

@@ -1,10 +1,10 @@
-name: Format
+name: Lint
 
 on: [push, pull_request]
 
 jobs:
 
-  format:
+  lint:
     name: Check for lint and format code to a standard style
     if:
       github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
@@ -24,4 +24,4 @@ jobs:
         run: pip install nox
 
       - name: Format code
-        run: nox -s format -- --check --verbose --diff
+        run: nox -s lint

.pre-commit-config.yaml

@@ -0,0 +1,98 @@
+repos:
+- repo: local
+  hooks:
+    - id: unnecessary_doctest_directives
+      name: Check for redundant doctest directives
+      description:
+        "Check for inline doctest directives that are specified globally through pyproject.toml"
+      types: [python]
+      entry: >
+        (?x)(
+          \+IGNORE_EXCEPTION_DETAIL|
+          \+NORMALIZE_WHITESPACE
+        )
+      language: pygrep
+
+- repo: https://github.com/psf/black
+  rev: 24.4.0
+  hooks:
+  - id: black
+    name: black
+    description: "Black: The uncompromising Python code formatter"
+    entry: black
+    language: python
+    language_version: python3
+    minimum_pre_commit_version: 2.9.2
+    require_serial: true
+    types_or: [python, pyi]
+  - id: black-jupyter
+    name: black-jupyter
+    description:
+      "Black: The uncompromising Python code formatter (with Jupyter Notebook support)"
+    entry: black
+    language: python
+    minimum_pre_commit_version: 2.9.2
+    require_serial: true
+    types_or: [python, pyi, jupyter]
+    additional_dependencies: [".[jupyter]"]
+
+- repo: https://github.com/keewis/blackdoc
+  rev: v0.3.9
+  hooks:
+  - id: blackdoc
+    description: "Black for doctests"
+    additional_dependencies: ["black==24.4.0"]
+  - id: blackdoc-autoupdate-black
+
+- repo: https://github.com/pycqa/flake8
+  rev: 7.0.0
+  hooks:
+  - id: flake8
+    additional_dependencies:
+    # - flake8-bugbear!=24.4.21
+    # - flake8-comprehensions
+    - flake8-simplify
+
+- repo: https://github.com/nbQA-dev/nbQA
+  rev: 1.8.5
+  hooks:
+    - id: nbqa-pyupgrade
+      args: ["--py310-plus"]
+    # - id: nbqa-isort
+    - id: nbqa-flake8
+      args: ["--extend-ignore=E402"]
+
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.7.1
+  hooks:
+    - id: nbstripout
+      description: Strip output from jupyter notebooks
+      args: [--drop-empty-cells]
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.15.2
+  hooks:
+  - id: pyupgrade
+    args: [--py310-plus]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+    name: isort (python)
+    # args: [--force-single-line-imports]
+    types: [python]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+    - id: check-builtin-literals
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-toml
+    - id: check-yaml
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: forbid-new-submodules
+    - id: mixed-line-ending
+    - id: trailing-whitespace

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - rioxarray
   - bmipy
   - black
-  - ruff
+  - flake8
   - isort
   - nox
   - pytest

noxfile.py

@@ -58,18 +58,10 @@ def test_cli(session: nox.Session) -> None:
 
 
 @nox.session
-def format(session: nox.Session) -> None:
+def lint(session: nox.Session) -> None:
     """Clean lint and assert style."""
-    session.install(".[dev]")
-
-    if session.posargs:
-        black_args = session.posargs
-    else:
-        black_args = []
-
-    session.run("black", *black_args, *PATHS)
-    session.run("isort", *PATHS)
-    session.run("ruff", "check", *PATHS)
+    session.install("pre-commit")
+    session.run("pre-commit", "run", "--all-files")
 
 
 @nox.session(name="prepare-docs")
@@ -148,6 +140,8 @@ def clean(session):
     shutil.rmtree(f"{PACKAGE}.egg-info", ignore_errors=True)
     shutil.rmtree(".pytest_cache", ignore_errors=True)
     shutil.rmtree(".venv", ignore_errors=True)
+    if os.path.exists("coverage.xml"):
+        os.remove("coverage.xml")
     if os.path.exists(".coverage"):
         os.remove(".coverage")
     for p in chain(ROOT.rglob("*.py[co]"), ROOT.rglob("__pycache__")):

pyproject.toml

@@ -56,9 +56,6 @@ Changelog = "https://github.com/csdms/bmi-topography/blob/main/CHANGES.md"
 
 [project.optional-dependencies]
 dev = [
-  "black",
-  "ruff",
-  "isort",
   "nox",
 ]
 build = [
@@ -118,14 +115,6 @@ force_grid_wrap = 0
 combine_as_imports = true
 line_length = 88
 
-[tool.ruff]
-exclude = ["docs"]
-line-length = 88
-ignore = [
-	"E203",
-	"E501",
-]
-
 [tool.coverage.run]
 relative_files = true