Update packaging #137

DimitriPapadopoulos · 2026-01-16T13:06:53Z

Summary by CodeRabbit

Chores
- Added explicit Python support >=3.10, <3.13 (includes 3.12).
- Upgraded packaging/build requirement to flit_core >=3.12.
- Clarified project metadata and consolidated authorship contact.
- Added BSD-3-Clause license declaration and included license file.
- Added official project homepage URL.
- Declared optional dependencies for visualization (Bokeh, Matplotlib, Plotly) and documentation tooling; updated the combined "all" group.

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coderabbitai · 2026-01-16T13:07:08Z

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📝 Walkthrough

Walkthrough

Updated pyproject.toml: bumped build-system flit_core to >=3.12,<4; replaced single author fields with an authors list and added project.urls; removed module, dist-name, and readme-content-type; added license metadata; tightened requires-python; expanded optional dependency groups (bokeh, matplotlib, plotly, docs).

Changes

Cohort / File(s)	Summary
Project metadata & build system `pyproject.toml`	Updated `[build-system].requires` to `flit_core >=3.12,<4`; replaced `author`/`author-email` with `authors` list; removed `module`, `dist-name`, and `readme-content-type`; added `license = "BSD-3-Clause"` and `license-files = ["LICENSE"]`; added `[project.urls]` Homepage; updated `requires-python` to `>=3.10, <3.13`; adjusted classifiers (added Python 3.12; removed BSD license classifier).
Optional dependencies `pyproject.toml`	Added per-feature optional dependency groups: `bokeh = ["bokeh>=3.4.1"]`, `matplotlib = ["matplotlib"]`, `plotly = ["plotly"]`, `docs = [...]`; updated `all` group to include `bokeh`, `plotly`, and `matplotlib`.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐇 I nibbled TOML fields in evening's glow,
Authors rearranged in tidy row,
License tucked and python bounds refined,
Extras added so plots can be combined,
A tiny hop — configuration aligned.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Update packaging' is vague and overly generic. While it relates to the changeset (modifications to pyproject.toml), it does not convey what specific packaging aspect was updated or why.	Consider a more specific title such as 'Update pyproject.toml metadata and dependencies' or 'Update build system and project metadata configuration' to better describe the actual changes.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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Copilot

Pull request overview

This PR modernizes the pyproject.toml configuration to align with current PEP 621 standards. The changes migrate deprecated metadata fields to their modern equivalents and add support for newer Python versions.

Changes:

Updated flit_core minimum version from 3.2 to 3.12.0
Migrated deprecated author fields to modern authors array format
Moved homepage URL to new [project.urls] section
Added Python 3.12 and 3.13 classifiers and updated license specification

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pyproject.toml

Copilot · 2026-01-16T13:08:17Z

pyproject.toml

    "Topic :: Scientific/Engineering :: Chemistry",
 ]
+license = "BSD-3-Clause"
+license-files = ["LICENSE"]


The license-files field is redundant when using the SPDX license identifier format. When license is specified as a string (SPDX identifier), the license-files field is not needed according to PEP 621. Either use license = {text = \"BSD-3-Clause\"} with license-files, or use just license = \"BSD-3-Clause\" without license-files.

Suggested change

license-files = ["LICENSE"]

Where does this come from? It's a bad idea and it's not compliant with PEP 639.

See "Use a default value for license-files if not specified" in Appendix: Rejected Ideas of PEP 639.

coderabbitai

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@pyproject.toml`:
- Around line 7-11: The authors array currently contains two separate entries
(one with {name} and one with {email}) which yields separate authors; update the
authors array so the contact is a single table entry containing both keys (e.g.,
combine into one {name = "...", email = "..."} object) so the metadata has one
author with a contact email; edit the authors block in pyproject.toml to replace
the two entries with a single combined table.

📜 Review details

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 29e0e80 and 8fa9c37.

📒 Files selected for processing (1)

pyproject.toml

🔇 Additional comments (1)

pyproject.toml (1)

2-2: No action needed. The flit_core>=3.12.0 version requirement is correct—flit_core 3.12.0 explicitly added support for PEP 639 SPDX license expressions and the license-files field used in this pyproject.toml (lines 25–26).

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pyproject.toml

Copilot

Pull request overview

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pyproject.toml

Copilot · 2026-01-16T14:57:12Z

pyproject.toml

 readme = "README.md"
-readme-content-type = "text/markdown"
 classifiers = [
    "Intended Audience :: Science/Research",


The 'License :: OSI Approved :: BSD License' classifier was removed but not replaced with a more specific classifier. Consider adding 'License :: OSI Approved :: BSD License' back to the classifiers list to maintain discoverability on PyPI, as classifiers serve a different purpose than the license field.

Suggested change

"Intended Audience :: Science/Research",

"Intended Audience :: Science/Research",

"License :: OSI Approved :: BSD License",

Your suggestion is not compliant with current Python packaging standards and PyPi is perfectly aware of the license field.

And where does "classifiers serve a different purpose than the license field" come from? Please provide links to authoritative documentation.

PyPI moved to license in 2024:
pypi/warehouse#16620 (comment)

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Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

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pyproject.toml

coderabbitai

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@pyproject.toml`:
- Line 2: Update the pyproject.toml requires entry to reflect the true minimum
for PEP 639 support or document the reason for the higher pin: either change the
requires line from "flit_core >=3.12.0,<4" to "flit_core >=3.11.0,<4" if you
want the strict minimum that added PEP 639 support, or keep ">=3.12.0,<4" but
add a brief comment near the requires declaration explaining that 3.12.0 was
chosen for additional SPDX AND/OR and license-file handling improvements rather
than being the minimal PEP 639 requirement.

pyproject.toml

Follow Python Packaging User Guide: https://packaging.python.org/en/latest/guides/writing-pyproject-toml/

Copilot

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

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pyproject.toml

jcharkow

Looks good on my end.

jcharkow · 2026-01-19T17:27:34Z

pyproject.toml

-author = "OpenMS Team"
+authors = [
+    {name = "OpenMS Team", email = "[email protected]"},
+    {name = "Joshua Charkow", email = "[email protected]"},


We can likely remove my name/email and just keep the OpenMS team in this new format

jcharkow · 2026-01-19T17:48:53Z

@singjc do you know why the deploy documentation is failing? It seems to be related to your recent PR changing to personal access token.

singjc · 2026-01-19T18:06:17Z

@singjc do you know why the deploy documentation is failing? It seems to be related to your recent PR changing to personal access token.

I was testing using a different secuirty token, because I was running into permission issues with the deploy documentation action, for PRs made from my fork. Which I didn't get from PRs made from the upstream repo. But it doesn't seem to help, or the token doesn't have the right permissions..

I changed it back to the original GITHUB_TOKEN token

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singjc · 2026-01-19T18:08:38Z

Yeah, it still seems to fail, I was getting this error too

 remote: Permission to OpenMS/pyopenms_viz.git denied to github-actions[bot].
fatal: unable to access 'https://github.com/OpenMS/pyopenms_viz/': The requested URL returned error: 403
Error: Process completed with exit code 128.

The error doesn't occur if you're making a PR from the main repo, only from forks it seems

jcharkow · 2026-01-19T21:59:32Z

Yeah, it still seems to fail, I was getting this error too
 remote: Permission to OpenMS/pyopenms_viz.git denied to github-actions[bot].
fatal: unable to access 'https://github.com/OpenMS/pyopenms_viz/': The requested URL returned error: 403
Error: Process completed with exit code 128.
The error doesn't occur if you're making a PR from the main repo, only from forks it seems

I could not get that far even, I run into an error with personal access tokens.

It seems that it is a permissions thing which is causing it to fail then.

It seems that this PR is good for the most part though so should be good to merge?

jcharkow · 2026-01-19T21:59:32Z

Yeah, it still seems to fail, I was getting this error too
 remote: Permission to OpenMS/pyopenms_viz.git denied to github-actions[bot].
fatal: unable to access 'https://github.com/OpenMS/pyopenms_viz/': The requested URL returned error: 403
Error: Process completed with exit code 128.
The error doesn't occur if you're making a PR from the main repo, only from forks it seems

I could not get that far even, I run into an error with personal access tokens.

It seems that it is a permissions thing which is causing it to fail then.

It seems that this PR is good for the most part though so should be good to merge?

singjc · 2026-01-19T22:46:42Z

Yeah looks good, will merge. Will have to look into the issue with Deploy Documentation in another PR.

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DimitriPapadopoulos force-pushed the PEP639 branch from 0d5c207 to 62ca287 Compare January 17, 2026 18:54

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DimitriPapadopoulos added 5 commits January 17, 2026 21:58

PEP 639 compliance

6c09097

Update pyproject.toml

2718ac4

Follow Python Packaging User Guide: https://packaging.python.org/en/latest/guides/writing-pyproject-toml/

Update Python versions in Trove classifiers

0cadce3

Ooops...

5298303

Fix authors

0739358

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DimitriPapadopoulos force-pushed the PEP639 branch from 323cf26 to c862cdb Compare January 17, 2026 20:58

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Python 3.13 not supported yet

4dbf3ce

DimitriPapadopoulos force-pushed the PEP639 branch from c862cdb to 4dbf3ce Compare January 17, 2026 22:16

jcharkow approved these changes Jan 19, 2026

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Merge branch 'main' into PEP639

390de13

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Keep the OpenMS team as the only author

894a5e0

singjc merged commit 8e6c9a6 into OpenMS:main Jan 19, 2026
8 of 10 checks passed

	"Intended Audience :: Science/Research",
	"Intended Audience :: Science/Research",
	"License :: OSI Approved :: BSD License",

Update packaging #137

Update packaging #137

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