chore: improve pyproject.toml from sp-repo-review checks

[henryiii]

This is a quick pass with uvx sp-repo-review[all] . and fixing the low hanging fruit. 3.8 is still supported? It's about time to drop 3.9 (official EoL) or 3.11 (SPEC 0). ;)

I'd recommend the remaining checks be worked on, and maybe move from black to ruff-format, and use SPDX license.

General

• Detected build backend: hatchling.build
• Detected license(s): Apache Software License

?	Name	Description
✅	PY001	Has a pyproject.toml
✅	PY002	Has a README.(md|rst) file
✅	PY003	Has a LICENSE* file
✅	PY004	Has docs folder
✅	PY005	Has tests folder
✅	PY006	Has pre-commit config
✅	PY007	Supports an easy task runner (nox, tox, pixi, etc.)

PyProject

?	Name	Description
✅	PP002	Has a proper build-system table
✅	PP003	Does not list wheel as a build-dep
✅	PP004	Does not upper cap Python requires
⚠️	PP005	Using SPDX project.license should not use deprecated trove classifiers
✅	PP301	Has pytest in pyproject
✅	PP302	Sets a minimum pytest to at least 6
✅	PP303	Sets the test paths
✅	PP304	Sets the log level in pytest
✅	PP305	Specifies xfail_strict
✅	PP306	Specifies strict config
✅	PP307	Specifies strict markers
✅	PP308	Specifies useful pytest summary
✅	PP309	Filter warnings specified

GitHub Actions

?	Name	Description
✅	GH100	Has GitHub Actions config
✅	GH101	Has nice names
✅	GH102	Auto-cancel on repeated PRs
✅	GH103	At least one workflow with manual dispatch trigger
✅	GH104	Use unique names for upload-artifact
✅	GH200	Maintained by Dependabot
✅	GH210	Maintains the GitHub action versions with Dependabot
✅	GH211	Do not pin core actions as major versions
✅	GH212	Require GHA update grouping

Pre-commit

?	Name	Description
✅	PC100	Has pre-commit-hooks
✅	PC110	Uses black or ruff-format
✅	PC111	Uses blacken-docs
✅	PC140	Uses a type checker
✅	PC160	Uses a spell checker
✅	PC170	Uses PyGrep hooks (only needed if rST present)
❌	PC180	Uses a markdown formatter Must have one of https://github.com/hukkin/mdformat, https://github.com/rbubley/mirrors-prettier, https://github.com/rvben/rumdl-pre-commit in .pre-commit-config.yaml
✅	PC190	Uses Ruff
✅	PC191	Ruff show fixes if fixes enabled
✅	PC192	Ruff uses `ruff-check` instead of `ruff` (legacy)
✅	PC901	Custom pre-commit CI message

MyPy

?	Name	Description
✅	MY100	Uses MyPy (pyproject config)
✅	MY101	MyPy strict mode
✅	MY102	MyPy show_error_codes deprecated
✅	MY103	MyPy warn unreachable
✅	MY104	MyPy enables ignore-without-code
✅	MY105	MyPy enables redundant-expr
✅	MY106	MyPy enables truthy-bool

Ruff

?	Name	Description
✅	RF001	Has Ruff config
✅	RF002	Target version must be set
✅	RF003	src directory doesn't need to be specified anymore (0.6+)
❌	RF101	Bugbear must be selected Must select the flake8-bugbear B checks. Recommended: [tool.ruff.lint] extend-select = [ "B", # flake8-bugbear ]
❌	RF102	isort must be selected Must select the isort I checks. Recommended: [tool.ruff.lint] extend-select = [ "I", # isort ]
✅	RF103	pyupgrade must be selected
✅	RF201	Avoid using deprecated config settings
✅	RF202	Use (new) lint config section

Documentation

?	Name	Description
✅	RTD100	Uses ReadTheDocs (pyproject config)
✅	RTD101	You have to set the RTD version number to 2
✅	RTD102	You have to set the RTD build image
✅	RTD103	You have to set the RTD python version
✅	RTD104	You have to specify a build configuration now for readthedocs.

Setuptools Config

?	Name	Description
⚠️	SCFG001	Avoid deprecated setup.cfg names

Validate-PyProject

Checks [build-system], [project], [tool.black], [tool.cibuildwheel], [tool.hatch], [tool.maturin], [tool.mypy], [tool.pdm], [tool.poe], [tool.poetry], [tool.pyright], [tool.pytest], [tool.repo-review], [tool.ruff], [tool.scikit-build], [tool.setuptools_scm], [tool.taskipy], [tool.tombi], [tool.tox], [tool.ty], [tool.uv], [tool.setuptools]

?	Name	Description
✅	VPP001	Validate pyproject.toml

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.23%. Comparing base (316bcae) to head (88d2369).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2623   +/-   ##
=======================================
  Coverage   98.23%   98.23%           
=======================================
  Files          65       65           
  Lines        4198     4198           
  Branches      592      592           
=======================================
  Hits         4124     4124           
  Misses         45       45           
  Partials       29       29           

Flag	Coverage Δ
contrib	97.97% <ø> (ø)
doctest	98.09% <ø> (ø)
unittests-3.10	96.28% <ø> (ø)
unittests-3.11	96.28% <ø> (ø)
unittests-3.12	96.28% <ø> (ø)
unittests-3.13	96.28% <ø> (ø)
unittests-3.8	96.28% <ø> (ø)
unittests-3.9	96.33% <ø> (ø)

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[matthewfeickert]

This is a quick pass with uvx sp-repo-review[all] . and fixing the low hanging fruit.

Thanks @henryiii

3.8 is still supported? It's about time to drop 3.9 (official EoL) or 3.11 (SPEC 0). ;)

c.f. PR #2566. We're dropping and going to Python 3.9 for the lower bound for pyhf v0.8.0, but yeah, Python 3.9 EOL is just around the corner

$ pixi exec --with norwegianblue eol python
┌───────┬────────────┬─────────┬────────────────┬────────────┬────────────┐
│ cycle │  release   │ latest  │ latest release │  support   │    eol     │
├───────┼────────────┼─────────┼────────────────┼────────────┼────────────┤
│ 3.14  │ 2025-10-07 │ 3.14.0  │   2025-10-07   │ 2027-10-01 │ 2030-10-31 │
│ 3.13  │ 2024-10-07 │ 3.13.9  │   2025-10-14   │ 2026-10-01 │ 2029-10-31 │
│ 3.12  │ 2023-10-02 │ 3.12.12 │   2025-10-09   │ 2025-04-02 │ 2028-10-31 │
│ 3.11  │ 2022-10-24 │ 3.11.14 │   2025-10-09   │ 2024-04-01 │ 2027-10-31 │
│ 3.10  │ 2021-10-04 │ 3.10.19 │   2025-10-09   │ 2023-04-05 │ 2026-10-31 │
│ 3.9   │ 2020-10-05 │ 3.9.24  │   2025-10-09   │ 2022-05-17 │ 2025-10-31 │
│ 3.8   │ 2019-10-14 │ 3.8.20  │   2024-09-06   │ 2021-05-03 │ 2024-10-07 │
│ 3.7   │ 2018-06-27 │ 3.7.17  │   2023-06-05   │ 2020-06-27 │ 2023-06-27 │
│ 3.6   │ 2016-12-23 │ 3.6.15  │   2021-09-03   │ 2018-12-24 │ 2021-12-23 │
│ 3.5   │ 2015-09-13 │ 3.5.10  │   2020-09-05   │   False    │ 2020-09-30 │
│ 3.4   │ 2014-03-16 │ 3.4.10  │   2019-03-18   │   False    │ 2019-03-18 │
│ 3.3   │ 2012-09-29 │ 3.3.7   │   2017-09-19   │   False    │ 2017-09-29 │
│ 3.2   │ 2011-02-20 │ 3.2.6   │   2014-10-12   │   False    │ 2016-02-20 │
│ 2.7   │ 2010-07-03 │ 2.7.18  │   2020-04-19   │   False    │ 2020-01-01 │
│ 3.1   │ 2009-06-27 │ 3.1.5   │   2012-04-06   │   False    │ 2012-04-09 │
│ 3.0   │ 2008-12-03 │ 3.0.1   │   2009-02-12   │   False    │ 2009-06-27 │
│ 2.6   │ 2008-10-01 │ 2.6.9   │   2013-10-29   │   False    │ 2013-10-29 │
└───────┴────────────┴─────────┴────────────────┴────────────┴────────────┘

I'd recommend the remaining checks be worked on, and maybe move from black to ruff-format

Yeah, Ruff is a TODO item. Also doing a large PR where we apply a lot of the style changes in one go to make it a transition point.

[matthewfeickert]

@henryiii Do you have a GitHub Action setup to run sp-repo-review[all] on PRs?

edit: Yes.

• pre-commit

- repo: https://github.com/scientific-python/repo-review
  rev: <version>
  hooks:
    - id: repo-review
      additional_dependencies: ["repo-review[cli]", "sp-repo-review==<version>"]

• GitHub Actions

- uses: scientific-python/repo-review@<version>
  with:
    plugins: sp-repo-review

[matthewfeickert]

Commit message:

* Update Ruff pre-commit hook to v0.12.0 to use ruff-check.
* Apply revisions to pass more of sp-repo-review.
   - RF003 src directory doesn't need to be specified anymore (0.6+)
   - Use "INFO" to avoid Error: tool.pytest.ini_options.log_cli_level must
     be valid exactly by one definition.
* Remove License trove classifier as using SPDX project license.