docs: the published package list pointed users at archived repositories

[belkassaby]

The problem

docs/reference/available-packages.md is published on the docs site (mkdocs nav, "Reference → Available Packages") and told readers:

Each package has its own documentation and code repository, which can be found in the links above.

That is no longer true. Checked each repo with gh:

Repo	Archived	Last push
geneweaver-core	no	2025-04-30
geneweaver-db	yes	2026-03-20
geneweaver-client	yes	2024-12-11
geneweaver-tools	yes	2025-01-15
geneweaver-testing	yes	2024-03-18
geneweaver-boolean-algebra	yes	2025-01-15

Core, db, client and tools are developed here under packages/; five of the six standalone repos are archived.

Why geneweaver-tools is the sharpest case

The page describes it as "a framework for creating analysis tools" and links to PyPI. The archived repo at 0.0.5 contains only src/geneweaver/tools/framework/ — abstract.py, enum.py, schema.py — and no tool implementations at all.

The nine ported analysis tools (BooleanAlgebra, Combine, DBSCAN, HyperGeometric, JaccardClustering, JaccardSimilarity, MSET, PhenomeMap, UpSet) live in this monorepo at packages/tools (0.20.0a0) and are unpublished. A reader following that link expecting to run GeneWeaver's analysis tools finds none of them.

The change

One admonition after the package list. Deliberately conservative:

• PyPI links stay. They are still valid install targets, and pip install geneweaver-client is the recommended path for researchers further down the same page.
• Names which repos are archived, rather than implying all are — geneweaver-core's is not.
• Calls out the tools gap explicitly, since that is the one that would actually mislead someone into a dead end.
• Replaces the "each package has its own … code repository" sentence.

Left alone: the two mermaid diagrams. The relationship graph is arguably stale too (it shows geneweaver-boolean-algebra feeding the application, whereas it is now a plugin dependency of the AsyncTask service), but redrawing it is an editorial call rather than a factual fix, and I did not want to bundle it.

Verification

mkdocs build --strict exits 0 with zero warnings.

Related

Separate from #32 (AsyncTask plugin registration), which touches docs/tools/TOOLS_MIGRATION.md but not this page. Two findings worth flagging that are not addressed here:

1. geneweaver-testing is archived, yet it is still a live dev dependency of this repo ([dependency-groups] dev = ["geneweaver-testing>=0.1.2"], resolved from PyPI, not the workspace).
2. geneweaver-boolean-algebra is archived, yet the AsyncTask service still depends on 0.3.0a23. That is useful input to the open question of whether it or packages/tools' BooleanAlgebra is authoritative.