Maintenance rework (#35)

Major change to the pre-commit fixes & checks to align with the current state of https://learn.scientific-python.org/development/guides/style/

The main thing: Switching to ruff, motivated by problems updating the pre-commit tools (black made changes that flake8 then complained about). Using ruff replaces using black and flake8 directly. It has a long list of rules that can be configured. A lot of style changes were made automatically, and I've temporarily(?) disabled rules that caused a problem needing manual changes.

Some minor fixes to CI, including switching from the deprecated pre-commit action to the pre-commit.ci application

Author: smithara

.flake8

@@ -4,25 +4,18 @@ on:
   workflow_dispatch:
   pull_request:
     branches: [ main, staging ]
+  schedule:
+    # Weekly on Sunday
+    - cron: "0 1 * * 0"
 
 jobs:
-  pre-commit:
-    name: Format
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - uses: actions/setup-python@v2
-    - uses: pre-commit/[email protected]
-      with:
-        extra_args: --hook-stage manual --all-files
-
   checks:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
     runs-on: ${{ matrix.runs-on }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
         # include:
@@ -36,9 +29,9 @@ jobs:
       run: brew reinstall gfortran
       shell: bash
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/ci.yml

@@ -141,4 +141,8 @@ cython_debug/
 src/*/_version.py
 
 # VSCode
-.vscode/*
+.vscode
+
+# Other dev tool junk
+.ruff_cache
+node_modules

.gitignore

@@ -1,97 +1,91 @@
 exclude: ^(.*/data/.*)
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.1.0
-  hooks:
-  - id: black-jupyter
+  # Strip outputs from notebooks
+  - repo: https://github.com/kynan/nbstripout
+    rev: "0.7.1"
+    hooks:
+      - id: nbstripout
+        args:
+          ["--extra-keys", "metadata.kernelspec metadata.language_info.version"]
 
-- repo: https://github.com/kynan/nbstripout
-  rev: "0.6.1"
-  hooks:
-    - id: nbstripout
-      args: ["--extra-keys", "metadata.kernelspec metadata.language_info.version"]
+  # The rest of the checks are from:
+  # https://github.com/scientific-python/cookie/blob/main/%7B%7Bcookiecutter.project_name%7D%7D/.pre-commit-config.yaml
 
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  hooks:
-  - id: check-added-large-files
-  - id: check-case-conflict
-  - id: check-merge-conflict
-  - id: check-symlinks
-  - id: check-yaml
-  - id: debug-statements
-  - id: end-of-file-fixer
-  - id: mixed-line-ending
-  - id: requirements-txt-fixer
-  - id: trailing-whitespace
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
 
-- repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.10.0
-  hooks:
-  - id: python-check-blanket-noqa
-  # - id: python-check-blanket-type-ignore
-  - id: python-no-eval
-  - id: python-use-type-annotations
-  - id: rst-backticks
-  - id: rst-directive-colons
-  - id: rst-inline-touching-normal
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
 
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    # args: ["-a", "from __future__ import annotations"]  # Python 3.7+
+  # - repo: https://github.com/pre-commit/mirrors-prettier
+  #   rev: "v4.0.0-alpha.8"
+  #   hooks:
+  #     - id: prettier
+  #       types_or: [yaml, markdown, html, css, scss, javascript, json]
+  #       args: [--prose-wrap=always]
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
-  hooks:
-  - id: pyupgrade
-    args: ["--py37-plus"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.2.1"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
 
-# - repo: https://github.com/hadialqattan/pycln
-#   rev: v1.1.0
-#   hooks:
-#   - id: pycln
-#     args: [--config=pyproject.toml]
+  # TODO: Enable type checking
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: "v1.8.0"
+  #   hooks:
+  #     - id: mypy
+  #       files: src|tests
+  #       args: []
+  #       additional_dependencies:
+  #         - pytest
 
-- repo: https://github.com/asottile/yesqa
-  rev: v1.4.0
-  hooks:
-  - id: yesqa
-    exclude: docs/conf.py
-    additional_dependencies: &flake8_dependencies
-      - flake8-bugbear
-      - flake8-print
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.6"
+    hooks:
+      - id: codespell
 
-- repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
-    exclude: docs/conf.py
-    additional_dependencies: *flake8_dependencies
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.9.0.6"
+    hooks:
+      - id: shellcheck
 
-# - repo: https://github.com/pre-commit/mirrors-mypy
-#   rev: v0.930
-#   hooks:
-#   - id: mypy
-#     files: src
-#     args: [--show-error-codes]
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
 
-- repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
-  hooks:
-  - id: codespell
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.16"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
-- repo: https://github.com/shellcheck-py/shellcheck-py
-  rev: v0.9.0.2
-  hooks:
-  - id: shellcheck
-
-- repo: local
-  hooks:
-  - id: disallow-caps
-    name: Disallow improper capitalization
-    language: pygrep
-    entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
-    exclude: .pre-commit-config.yaml
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.28.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs

.pre-commit-config.yaml

@@ -13,14 +13,14 @@ sphinx:
 formats: []
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.11"
 
 python:
   install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - docs
-    - dsecs_cp38_manylinux
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - dsecs_cp311_manylinux

.readthedocs.yml

@@ -9,8 +9,8 @@
 [![GitHub Discussion][github-discussions-badge]][github-discussions-link]
 
 [![Actions Status][actions-badge]][actions-link]
-[![Code style: black][black-badge]][black-link]
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/format.json)](https://github.com/astral-sh/ruff)
 
 ---
 
@@ -30,7 +30,7 @@
 [rtd-badge]:                https://img.shields.io/badge/docs-online-success
 [rtd-link]:                 https://swarmpal.readthedocs.io/
 
-![SwarmPAL diagram](https://swarmpal-benchmarks.netlify.app/swarmpal-diagram.png)
+![SwarmPAL diagram](https://swarmdisc.org/wp-content/uploads/2024/02/SwarmPAL-diagrams-overview.png)
 
 For more information see:
 - <https://swarmdisc.org/lab/>