feat: Migrate project metadata to pyproject.toml #201

matthewfeickert · 2025-12-07T07:40:48Z

Migrate pyproject information from setup.cfg to pyproject.toml.
Add maintainers group.
Remove setup.cfg file.
Remove asottile/setup-cfg-fmt pre-commit hook.

Note: This PR should become v0.6.0, as v0.5.9 got yanked and a new release can't be created from the same commit where there is already a tag given the current release CI system.

codecov · 2025-12-07T07:48:00Z

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Copilot

Pull request overview

This PR migrates the project configuration from the deprecated setup.cfg format to the modern pyproject.toml standard (PEP 621), consolidating all project metadata into a single configuration file. The migration includes moving package metadata, dependencies, entry points, and tool configurations (pytest, mypy) to their respective sections in pyproject.toml.

Key changes:

Consolidated project metadata (name, version, dependencies, scripts) in [project] section of pyproject.toml
Migrated pytest and mypy configurations from setup.cfg to pyproject.toml using TOML format
Removed obsolete setup-cfg-fmt pre-commit hook that formatted the now-deleted setup.cfg

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
pyproject.toml	Added `[project]` metadata section with package information, dependencies, scripts; added `[tool.pytest.ini_options]` and `[tool.mypy]` configurations migrated from setup.cfg
setup.cfg	Removed entire file as all configuration has been migrated to pyproject.toml
.pre-commit-config.yaml	Removed `asottile/setup-cfg-fmt` hook which is no longer needed without setup.cfg

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pyproject.toml

Copilot · 2025-12-07T07:55:53Z

pyproject.toml

+
 [tool.setuptools_scm]
 write_to = "src/skhep_testdata/version.py"



Missing setuptools package discovery configuration. The original setup.cfg specified packages = find: with where = src to find packages in the src-layout directory. Add the following configuration after this line:

[tool.setuptools.packages.find] where = ["src"]

Without this, setuptools may fail to find and include the package in the distribution.

Suggested change

[tool.setuptools.packages.find]

where = ["src"]

pyproject.toml

eduardo-rodrigues

Thanks for this @matthewfeickert. The upgrade was due :).

I approve but let me make 2 little suggestions:

At this point it would make sense to add @henryiii as a co-author since he did work on a fair bit of modernisation, IIRC.
I am now noticing that we only officially support 3.10+-. This is a rather easy and useful package leverage in many places. We should not IMO be too harsh with the lower bound on the Python versions supported. For sure there are Scikit-HEP packages supporting 3.9, if not 3.8 (OK, this latter may be a bit pushy at this stage, but let's not forget the timeline of PhD theses, etc., so it does make sense to be kind), and if they need this package for testing ... You get my point. Let's keep this in mind wen we require 3.11+.

matthewfeickert · 2025-12-08T10:28:19Z

At this point it would make sense to add @henryiii as a co-author since he did work on a fair bit of modernisation, IIRC.

Done in rebase. 👍

I am now noticing that we only officially support 3.10+-. This is a rather easy and useful package leverage in many places. We should not IMO be too harsh with the lower bound on the Python versions supported. For sure there are Scikit-HEP packages supporting 3.9, if not 3.8 (OK, this latter may be a bit pushy at this stage, but let's not forget the timeline of PhD theses, etc., so it does make sense to be kind), and if they need this package for testing ... You get my point. Let's keep this in mind wen we require 3.11+.

@eduardo-rodrigues Yeah, I only noticed recently that this happened in PR #193 by a pre-commit hook autofix: 4d5b90d

So maybe this wasn't intended?

I am happy to support an EOL Python for a bit longer than normal

$ pixi exec norwegianblue python
┌───────┬────────────┬─────────┬────────────────┬────────────┬────────────┬──────────┐
│ cycle │  release   │ latest  │ latest release │  support   │    eol     │   pep    │
├───────┼────────────┼─────────┼────────────────┼────────────┼────────────┼──────────┤
│ 3.14  │ 2025-10-07 │ 3.14.2  │   2025-12-05   │ 2027-10-01 │ 2030-10-31 │ PEP-0745 │
│ 3.13  │ 2024-10-07 │ 3.13.11 │   2025-12-05   │ 2026-10-01 │ 2029-10-31 │ PEP-0719 │
│ 3.12  │ 2023-10-02 │ 3.12.12 │   2025-10-09   │ 2025-04-02 │ 2028-10-31 │ PEP-0693 │
│ 3.11  │ 2022-10-24 │ 3.11.14 │   2025-10-09   │ 2024-04-01 │ 2027-10-31 │ PEP-0664 │
│ 3.10  │ 2021-10-04 │ 3.10.19 │   2025-10-09   │ 2023-04-05 │ 2026-10-31 │ PEP-0619 │
│ 3.9   │ 2020-10-05 │ 3.9.25  │   2025-10-31   │ 2022-05-17 │ 2025-10-31 │ PEP-0596 │
│ 3.8   │ 2019-10-14 │ 3.8.20  │   2024-09-06   │ 2021-05-03 │ 2024-10-07 │ PEP-0569 │
│ 3.7   │ 2018-06-27 │ 3.7.17  │   2023-06-05   │ 2020-06-27 │ 2023-06-27 │ PEP-0537 │
│ 3.6   │ 2016-12-23 │ 3.6.15  │   2021-09-03   │ 2018-12-24 │ 2021-12-23 │ PEP-0494 │
│ 3.5   │ 2015-09-13 │ 3.5.10  │   2020-09-05   │   False    │ 2020-09-30 │ PEP-0478 │
│ 3.4   │ 2014-03-16 │ 3.4.10  │   2019-03-18   │   False    │ 2019-03-18 │ PEP-0429 │
│ 3.3   │ 2012-09-29 │ 3.3.7   │   2017-09-19   │   False    │ 2017-09-29 │ PEP-0398 │
│ 3.2   │ 2011-02-20 │ 3.2.6   │   2014-10-12   │   False    │ 2016-02-20 │ PEP-0392 │
│ 2.7   │ 2010-07-03 │ 2.7.18  │   2020-04-19   │   False    │ 2020-01-01 │ PEP-0373 │
│ 3.1   │ 2009-06-27 │ 3.1.5   │   2012-04-06   │   False    │ 2012-04-09 │ PEP-0375 │
│ 3.0   │ 2008-12-03 │ 3.0.1   │   2009-02-12   │   False    │ 2009-06-27 │ PEP-0361 │
│ 2.6   │ 2008-10-01 │ 2.6.9   │   2013-10-29   │   False    │ 2013-10-29 │ PEP-0361 │
└───────┴────────────┴─────────┴────────────────┴────────────┴────────────┴──────────┘

But I would suggest that as Python 3.10 has already been updated in this library that we don't backtrack and that we release a new minor version (v0.6.0) to signal this drop in Python version. I'm fine with keeping Python 3.10 around a bit longer though as we only use this library for testing and not for end-user use.

eduardo-rodrigues · 2025-12-08T10:34:33Z

Agreed, sounds good (I see I should have noticed the change in the pre-commit PR, but didn't - shame on me).

Thanks.

matthewfeickert · 2025-12-08T15:56:44Z

It is easy to miss, and not something I would have expected to come from an autofix. So no worries there.

ariostas

Thank you @matthewfeickert, this looks great! Looking at the repo review here, it seems like the only issue is the Python version not being a string (which Copilot already pointed out). There are other suggestions for things in the pyproject.toml, but maybe it makes more sense to have a separate PR to address all the relevant suggestions.

matthewfeickert · 2025-12-08T16:57:42Z

@ariostas I'm currently on a flight, so I might be missing something, but I see the lack of strings only getting flagged by repo review for tools like mypy, not the project table.

I'm happy to get any project table things fixed up in this PR, and then I agree that we should open up an Issue and a follow up PR to knock as more repo-review fixes. 👍

ariostas · 2025-12-08T17:04:10Z

Yeah, it's only not a string in the mypy table. Since that was also moved over to pyproject.toml in this PR, I think we might as well fix it here. But a follow-up PR with all fixes is fine as well.

* Migrate pyproject information from setup.cfg to pyproject.toml. * Add maintainers group. * Remove setup.cfg file. * Remove asottile/setup-cfg-fmt pre-commit hook. * Add Henry Schreiner as author.

* Use prune in MANIFEST.in to remove everything from the sdist and then add all the contents of src/ and tests/ with graft. This approach is more explicit about the intent of the sdist.

matthewfeickert · 2025-12-09T18:49:49Z

MANIFEST.in

As we're migrating the project files, I've made the sdist definition more explicit.

This now produces

$ rm -rf ./dist && uvx --from build pyproject-build --installer uv . $ python -m tarfile --list ./dist/*.tar.gz scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/ scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/CITATION.cff scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/LICENSE scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/MANIFEST.in scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/PKG-INFO scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/README.md scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/pyproject.toml scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/setup.cfg scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/setup.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/ scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/scikit_hep_testdata.egg-info/ scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/scikit_hep_testdata.egg-info/PKG-INFO scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/scikit_hep_testdata.egg-info/SOURCES.txt scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/scikit_hep_testdata.egg-info/dependency_links.txt scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/scikit_hep_testdata.egg-info/entry_points.txt scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/scikit_hep_testdata.egg-info/requires.txt scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/scikit_hep_testdata.egg-info/top_level.txt scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/ scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/__init__.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/__main__.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/ scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/__init__.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/file_list.txt scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/pyhf-ins1748602-probability-models.doi scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/pylhe-testfile-madgraph-2.0.0-wbj.lhe.readme scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/pylhe-testfile-madgraph-2.2.1-Z-ckkwl.lhe.gz.readme scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/pylhe-testfile-madgraph-2.2.1-Z-fxfx.lhe.gz.readme scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/pylhe-testfile-madgraph-2.2.1-Z-mlm.lhe.gz.readme scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/data/pylhe-testfile-pythia-6.413-ttbar.lhe.readme scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/local_files.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/py.typed scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/remote_datasets.yml scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/remote_files.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/src/skhep_testdata/version.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/tests/ scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/tests/__init__.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/tests/test_local_files.py scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/tests/test_remote_datasets.yml scikit_hep_testdata-0.5.10.dev4+gcddd5bb0a/tests/test_remote_files.py

compared to

$ curl -sLO https://files.pythonhosted.org/packages/75/1f/7e0acd189f16cdee82ae3dc0bf6979b7506af7a84ee8907a978dc1a83b6f/scikit_hep_testdata-0.5.8.tar.gz $ python -m tarfile --list ./scikit_hep_testdata-0.5.8.tar.gz scikit_hep_testdata-0.5.8/ scikit_hep_testdata-0.5.8/.all-contributorsrc scikit_hep_testdata-0.5.8/.github/ scikit_hep_testdata-0.5.8/.github/dependabot.yml scikit_hep_testdata-0.5.8/.github/workflows/ scikit_hep_testdata-0.5.8/.github/workflows/ci.yml scikit_hep_testdata-0.5.8/.gitignore scikit_hep_testdata-0.5.8/.pre-commit-config.yaml scikit_hep_testdata-0.5.8/CITATION.cff scikit_hep_testdata-0.5.8/LICENSE scikit_hep_testdata-0.5.8/MANIFEST.in scikit_hep_testdata-0.5.8/PKG-INFO scikit_hep_testdata-0.5.8/README.md scikit_hep_testdata-0.5.8/dev/ scikit_hep_testdata-0.5.8/dev/make-root/ scikit_hep_testdata-0.5.8/dev/make-root/double32_float16.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_1jag_int_float.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_Run2012BC_DoubleMuParked_Muons_1000evts.md scikit_hep_testdata-0.5.8/dev/make-root/rntuple_atomic_bitset.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_bit.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_emptystruct_invalidvar.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_extension_columns.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_float_types.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_imported_NanoAOD.md scikit_hep_testdata-0.5.8/dev/make-root/rntuple_index_multicluster.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_int_5e4.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_int_float.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_int_multicluster.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_int_vfloat_tlv_vtlv.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_multiple_cluster_groups.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_multiple_representations.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_nested_structs.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_split_3e4.C scikit_hep_testdata-0.5.8/dev/make-root/rntuple_stl_containers.C scikit_hep_testdata-0.5.8/dev/make-root/sample4version.C scikit_hep_testdata-0.5.8/dev/make-root/stl_containers.C scikit_hep_testdata-0.5.8/dev/make-root/uproot-issue-1043.C scikit_hep_testdata-0.5.8/dev/make-root/uproot-issue38c.py scikit_hep_testdata-0.5.8/dev/make-root/uproot_issue_1229.C scikit_hep_testdata-0.5.8/dev/make-root/uproot_issue_407.C scikit_hep_testdata-0.5.8/pyproject.toml scikit_hep_testdata-0.5.8/setup.cfg scikit_hep_testdata-0.5.8/setup.py scikit_hep_testdata-0.5.8/src/ scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/ scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/PKG-INFO scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/SOURCES.txt scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/dependency_links.txt scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/entry_points.txt scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/requires.txt scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/top_level.txt scikit_hep_testdata-0.5.8/src/scikit_hep_testdata.egg-info/zip-safe scikit_hep_testdata-0.5.8/src/skhep_testdata/ scikit_hep_testdata-0.5.8/src/skhep_testdata/__init__.py scikit_hep_testdata-0.5.8/src/skhep_testdata/__main__.py scikit_hep_testdata-0.5.8/src/skhep_testdata/data/ scikit_hep_testdata-0.5.8/src/skhep_testdata/data/__init__.py scikit_hep_testdata-0.5.8/src/skhep_testdata/data/file_list.txt scikit_hep_testdata-0.5.8/src/skhep_testdata/data/pyhf-ins1748602-probability-models.doi scikit_hep_testdata-0.5.8/src/skhep_testdata/data/pylhe-testfile-madgraph-2.0.0-wbj.lhe.readme scikit_hep_testdata-0.5.8/src/skhep_testdata/data/pylhe-testfile-madgraph-2.2.1-Z-ckkwl.lhe.gz.readme scikit_hep_testdata-0.5.8/src/skhep_testdata/data/pylhe-testfile-madgraph-2.2.1-Z-fxfx.lhe.gz.readme scikit_hep_testdata-0.5.8/src/skhep_testdata/data/pylhe-testfile-madgraph-2.2.1-Z-mlm.lhe.gz.readme scikit_hep_testdata-0.5.8/src/skhep_testdata/data/pylhe-testfile-pythia-6.413-ttbar.lhe.readme scikit_hep_testdata-0.5.8/src/skhep_testdata/local_files.py scikit_hep_testdata-0.5.8/src/skhep_testdata/py.typed scikit_hep_testdata-0.5.8/src/skhep_testdata/remote_datasets.yml scikit_hep_testdata-0.5.8/src/skhep_testdata/remote_files.py scikit_hep_testdata-0.5.8/src/skhep_testdata/version.py scikit_hep_testdata-0.5.8/tests/ scikit_hep_testdata-0.5.8/tests/__init__.py scikit_hep_testdata-0.5.8/tests/test_local_files.py scikit_hep_testdata-0.5.8/tests/test_remote_datasets.yml scikit_hep_testdata-0.5.8/tests/test_remote_files.py

which distributes files it doesn't need to.

Oh yeah, that's much better

henryiii

I'd be curious to see a hatchling conversion as a followup (or uv_backend or flit-core). It probably would be faster and simpler. check-sdist might be useful.

matthewfeickert · 2025-12-09T20:32:12Z

I'd be curious to see a hatchling conversion as a followup (or uv_backend or flit-core). It probably would be faster and simpler. check-sdist might be useful.

I also would like to switch to hatchling (or anything other than setuptools), and while I know it is possible to run custom logic like what exists in setup.py, I haven't done that before, so I figured I would keep this scoped to just pyproject.toml for v0.6.0.

matthewfeickert self-assigned this Dec 7, 2025

matthewfeickert added the enhancement New feature or request label Dec 7, 2025

matthewfeickert force-pushed the feat/migrate-to-pyproject branch from bec6337 to 59c5cb6 Compare December 7, 2025 07:47

matthewfeickert force-pushed the feat/migrate-to-pyproject branch from 59c5cb6 to 685099b Compare December 7, 2025 07:49

matthewfeickert marked this pull request as ready for review December 7, 2025 07:51

matthewfeickert requested review from APN-Pucky, ariostas, Copilot, eduardo-rodrigues, henryiii and kratsg December 7, 2025 07:52

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matthewfeickert force-pushed the feat/migrate-to-pyproject branch from 685099b to a9beaef Compare December 8, 2025 10:20

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feat: Migrate project metadata to pyproject.toml

3726fcf

* Migrate pyproject information from setup.cfg to pyproject.toml. * Add maintainers group. * Remove setup.cfg file. * Remove asottile/setup-cfg-fmt pre-commit hook. * Add Henry Schreiner as author.

matthewfeickert force-pushed the feat/migrate-to-pyproject branch from 0a34af3 to 3726fcf Compare December 9, 2025 02:38

matthewfeickert mentioned this pull request Dec 9, 2025

chore: Add sp-repo-review recommendations for pytest #203

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matthewfeickert added 2 commits December 8, 2025 21:04

Restrict packe file search to src

62440a7

build: Explicitly add src and tests to sdist

cddd5bb

* Use prune in MANIFEST.in to remove everything from the sdist and then add all the contents of src/ and tests/ with graft. This approach is more explicit about the intent of the sdist.

matthewfeickert commented Dec 9, 2025

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matthewfeickert requested a review from ariostas December 9, 2025 18:50

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henryiii approved these changes Dec 9, 2025

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matthewfeickert mentioned this pull request Dec 9, 2025

Migrate build system to hatchling (or another non-setuptools option) #204

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matthewfeickert merged commit df87d17 into scikit-hep:main Dec 9, 2025
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matthewfeickert deleted the feat/migrate-to-pyproject branch December 9, 2025 20:34


		[tool.setuptools_scm]
		write_to = "src/skhep_testdata/version.py"

feat: Migrate project metadata to pyproject.toml #201

feat: Migrate project metadata to pyproject.toml #201

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matthewfeickert commented Dec 7, 2025 •

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