Update .pre-commit-config.yaml template to best practices from acro…

…ss SciTools repos (#26)

* Readability improvements.

* Updates from SciTools/iris#5937 .

* Updates from SciTools/workflows#50 .

* Updates from SciTools/mo_pack#34 .

* Updates from SciTools/iris-grib#464 .

* Other updates.

.github/workflows/template-sync.yml

@@ -27,4 +27,4 @@ jobs:
  Bot
  Type: Infrastructure
  COMMIT_PREFIX: "👁 TEMPLATE DEVIATIONS:"
- PR_BODY: "## Please read: https://github.com/SciTools/.github/tree/main/templates"
+ PR_BODY: "# [Click for `README`](https://github.com/SciTools/.github/tree/main/templates)"

README.md

@@ -9,11 +9,12 @@ Organisational level things such as the SciTools README and organisation workflo
 - [`./peloton`](./peloton) - contains the scripts for automating population of the 
 [SciTools Peloton project](https://github.com/orgs/SciTools/projects/13?pane=info).
  See also [`.github/workflows/peloton.yml`](.github/workflows/peloton.yml).
+- [`./templates`](./templates) - tooling for standardising files across
+SciTools repos. See also 
+[`.github/workflows/template-sync.yml`](.github/workflows/template-sync.yml).
 
-## Possible uses
+## Possible future uses
 
 - [An organizational README](https://docs.github.com/en/organizations/collaborating-with-groups-in-organizations/customizing-your-organizations-profile#adding-a-public-organization-profile-readme)
 - Workflows for managing organization-level projects
  E.g. [Peloton](./peloton)
-- Automation for comparing SciTools repos
- E.g. linting config, benchmark setup etc.

templates/.pre-commit-config.yaml

@@ -1,34 +1,57 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+# See https://pre-commit.ci/#configuration
+# See https://github.com/scientific-python/cookie#sp-repo-review
 
+ci:
+ autofix_prs: false
+ autoupdate_commit_msg: "chore: update pre-commit hooks"
+
+
+# Alphabetised, for lack of a better order.
 files: |
  (?x)(
+ benchmarks\/.+\.py|
+ docs\/.+\.py|
+ lib\/.+\.py|
  noxfile\.py|
+ pyproject\.toml|
  setup\.py|
- docs\/.+\.py|
- benchmarks\/.+\.py|
+ src\/.+\.py
  )
 minimum_pre_commit_version: 1.21.0
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.5.0
+ rev: v4.6.0
  hooks:
  # Prevent giant files from being committed.
  - id: check-added-large-files
  # Check whether files parse as valid Python.
  - id: check-ast
- # Check for file name conflicts on case-insensitive filesytems.
+ # Check for file name conflicts on case-insensitive filesystems.
  - id: check-case-conflict
  # Check for files that contain merge conflict strings.
  - id: check-merge-conflict
  # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
  - id: debug-statements
+ # Check TOML file syntax.
+ - id: check-toml
+ # Check YAML file syntax.
+ - id: check-yaml
+ # Makes sure files end in a newline and only a newline.
+ # Duplicates Ruff W292 but also works on non-Python files.
+ - id: end-of-file-fixer
+ # Replaces or checks mixed line ending.
+ - id: mixed-line-ending
  # Don't commit to main branch.
  - id: no-commit-to-branch
+ # Trims trailing whitespace.
+ # Duplicates Ruff W291 but also works on non-Python files.
+ - id: trailing-whitespace
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
- rev: "v0.3.4"
+ rev: "v0.4.4"
  hooks:
  - id: ruff
  types: [file, python]
@@ -43,13 +66,7 @@ repos:
  types_or: [asciidoc, python, markdown, rst]
  additional_dependencies: [tomli]
 
-- repo: https://github.com/PyCQA/flake8
- rev: 7.0.0
- hooks:
- - id: flake8
- types: [file, python]
-
-- repo: https://github.com/asottile/blacken-docs
+- repo: https://github.com/adamchainz/blacken-docs
  rev: 1.16.0
  hooks:
  - id: blacken-docs
@@ -61,6 +78,25 @@ repos:
  - id: sort-all
  types: [file, python]
 
+- repo: https://github.com/pre-commit/mirrors-mypy
+ rev: 'v1.10.0'
+ hooks:
+ - id: mypy
+ exclude: 'noxfile\.py|docs/conf\.py'
+
+- repo: https://github.com/abravalheri/validate-pyproject
+ # More exhaustive than Ruff RUF200.
+ rev: "v0.18"
+ hooks:
+ - id: validate-pyproject
+
+- repo: https://github.com/scientific-python/cookie
+ rev: 2024.04.23
+ hooks:
+ - id: sp-repo-review
+ additional_dependencies: ["repo-review[cli]"]
+ args: ["--show=errskip"]
+
 - repo: https://github.com/numpy/numpydoc
  rev: v1.7.0
  hooks: