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: