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Add package and model versioning - #42

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rogerwwww merged 3 commits into
coleygroup:mainfrom
computational-metabolomics:version-metadata
Sep 16, 2026
Merged

rogerwwww merged 3 commits into
coleygroup:mainfrom
computational-metabolomics:version-metadata

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@RJMW

@RJMW RJMW commented Sep 15, 2026

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Following our email discussion, this PR puts in place the versioning we suggested, so you can see how it would work in practice. We've filled in the versions where the repository already documents them and made a suggestion for the rest. Please change any of the numbers or names as you see fit.

Package version
The distribution is called ms_pred again, matching the repository and the import name (it was ms_pred at v1.0.0). The version is set once in ms_pred/init.py and pyproject.toml reads it from there.

We've suggested 1.1.0 as the next release after the existing v1.0.0 tag. Some modules have been renamed since then, such as dag_pred becoming iceberg, so under strict semantic versioning 2.0.0 would be another good option. Either way, the changelog notes that earlier changes weren't recorded, and semantic versioning could apply from this release onwards.

Model versions
ms_pred.model_registry records each model's version separately from the package version:

  • ICEBERG 2.1, as in the README. Versions 1.0 and 2.0 are listed with their branches (iceberg_1.0 and iceberg_2.0) and papers.
  • SCARF 1.0, released with the v1.0.0 tag.
  • MARASON 1.0 and GLACIER 1.0. Neither has a version in the repository yet, so 1.0 is our suggestion for their first published versions.

python -m ms_pred --version prints the package version and the model versions, and CHANGELOG.md starts a 1.1.0 section for these changes.

We checked that setuptools picks up the new name and version, and that python -m ms_pred --version lists everything above. Nothing else in the package changes.

@rogerwwww
rogerwwww merged commit e0f7b40 into coleygroup:main Sep 16, 2026
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