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chore(release): relicense to MIT and bump to 0.1.0a1 (#15)
* LICENSE: replace GPL-3.0-or-later with the MIT License. * pyproject.toml: version 0.0.1 -> 0.1.0a1; license -> MIT; Development Status classifier 2 (Pre-Alpha) -> 3 (Alpha); License classifier -> MIT. * README: relicense statement (independent reimplementation under MIT, RAVEN citation retained); License section -> MIT; Documentation section no longer promises a hosted ReadTheDocs site (not yet published). * CHANGELOG: add the 0.1.0a1 release entry. Prepares the first alpha release.
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CHANGELOG.md

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@@ -4,6 +4,23 @@ Milestones in the raven-python port. For function-level status see
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[docs/raven_migration.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/migration.md); for open work see
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[docs/todo.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/todo.md).
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## 0.1.0a1 — 2026-05-30
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First alpha release. Covers the functional scope of RAVEN built on cobrapy:
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de-novo reconstruction (KEGG / homology), context-specific modeling (tINIT / ftINIT),
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metabolic-task validation, connectivity gap-filling, HPA omics ingestion, sub-cellular
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localisation, N-model comparison, reporter metabolites, FSEOF, flux sampling, and the
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RAVEN-style I/O formats (YAML / SIF / Excel). Validated against MATLAB RAVEN on Human-GEM
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(Jaccard 0.975–0.980).
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* **Licensing:** released under the **MIT** license (previously GPL-3.0-or-later).
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* **Docs:** Sphinx + MyST documentation site (sources under `docs/`).
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* Not yet implemented: visualization (`plotting/`), metabolomics-based (f)tINIT scoring,
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and published binary / KEGG-artefact release bundles. See the README and
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[docs/todo.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/todo.md).
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The milestone sections below record the incremental development history leading to this release.
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## Infrastructure
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* **GitHub Actions CI** ([.github/workflows/ci.yml](https://github.com/SysBioChalmers/raven-python/blob/develop/.github/workflows/ci.yml)) —

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