Domain plugins for the stringency engine. One
package per subdirectory under plugins/, one uv workspace, one tag for all plugins. A plugin
teaches the engine a domain's vocabulary (object types and extractors, the design schema,
predicates, controlled vocabularies, phrasing); it runs no analysis. Analyses live in method
repositories (stringency-xenium-method, stringency-plasmidsaurusRNAseq-method), which depend
on these plugins.
| plugin | domain | status |
|---|---|---|
plugins/stringency-singlecell |
single-cell and spatial (Xenium) | 0.5.1 (2026-10-14, needs engine 0.2.19; 0.5.0 of 2026-10-08 ran Lyons v2): the object types, extractors, design schema, predicates, vocabularies (punch_qc_verdict@2, batch_route@1, cell_types_mouse@2) and typed operations that stringency-xenium-method's xenium-qc-tma and xenium-upstream pipelines use; see its README |
plugins/stringency-bulkrna |
bulk RNA-seq | not started (engine roadmap Lane B, dormant) |
uv sync
uv run pytest # tests marked institutional skip off the lab workstation, naming the path
uv run ruff check .
uv run mypy plugins/stringency-singlecell/src.github/workflows/ci.yml runs the same on every push and pull request. The engine the tests
run against is the tag tool.uv.sources pins; bump it with the stringency>= floor in the
plugin's pyproject.toml and uv lock when a plugin needs a newer engine.
Every tag from v0.2.0 on was pushed after ruff and the tests passed. The tags v0.1.2,
v0.1.3, v0.1.5 and v0.1.6 (2026-09-18) were pushed before the checks ran and are not
usable; they stay because session notes and project traces cite them.
scripts/install.sh --prefix <prefix> \
--plugin git+https://github.com/santangelo-lab/stringency-plugins@<tag>#subdirectory=plugins/stringency-singlecellRepository layout decided 2026-09-17 (engine spec/archive/roadmap-2026-09.md, Lane D item 2). A CI workflow, a requires check against the engine and a version test are scheduled in the engine's spec/plans/roadmap-2026-10.md (W3).