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Roadmap

Status as of 2026-09-17. Reflects actual repository state — completed sections are claims you can verify in docs/compliance/, not aspirations.

Done (engineering series, 2026-09)

  • Advanced zero handling and the glmGamPoi dispersion port (issue #21): multiplicative and Bayesian multiplicative replacement with their refusals, provenance and Agda-checked laws; the pure-Julia dispersion pipeline with the un-ported spline refused by name; config/Nickel/JSON/frontend surface; tests, fixtures and the 100/1000/10000-taxa bench. Documentation: docs/statistics/zero-handling.md, docs/statistics/method-conditions/dispersion-glmGamPoi.md.
  • KYAML pilot (owner ruling 2026-09-26): just use-kyaml / just use-yaml / just check-kyaml, the drift list, docs/pilots/kyaml-pilot.md, and the standalone deployment of the toolchain and proof lane (stapeln.toml, Containerfile).
  • Bun toolchain migration (1.3.10 pinned; lockfile text format)
  • Strict TypeScript foundation (165 → 0 errors, zero suppressions)
  • Test & benchmark infrastructure (proven-tests-and-benchmarks patterns)
  • Domain type system (src/types/*; 20+ type-level assertions)
  • Type-driven behavioural tests (67 pass / 5 e2e-lane todos)
  • RSR template & standards alignment (this tree)

Near term (decision points, not started)

  • Finish the KYAML migration. The tool, gate and ruling are in; just use-kyaml has not been run, because it must be run where Julia is (the gate compares bytes against the Julia emitter, and the authoring sandbox had no Julia). One command plus the CI step that holds the result — see docs/pilots/kyaml-pilot.md §8.

  • Enable the proofs lane in CI. proofs job is written and gated on vars.STAPELN_AGDA_IMAGE; the image (stapeln.toml, Containerfile) has not been built yet. Build it, then set the variable.

  • DOM test lane. Plotly-chain modules (PlotlyChart, ChartCustomiser, ChartEditorInner, AnnotationPanel, RunView) are import-blocked under the DOM-less bun lane. Decision queued for the e2e lane: playwright (lane exists, opt-in) vs a DOM harness. Tracked as TODO(tests/e2e-lane) in frontend/tests/unit/plotly-chain.todo.test.ts.

  • Coverage gate. Metrics are reported in CI artefacts (lcov) but not gated — deliberate; a gate lands with CI maturity, against a recorded baseline, not an arbitrary number. Baseline: docs/testing/coverage.md.

  • alphaFig narrowing. useAnalysis.alphaFig is unknown; narrowing to PlotFigure threads the chart response type through analysis state. Listed in docs/types/architecture.md § Known gaps.

  • skipLibCheck exception. Documented exception for react-router 6.30.x (7 upstream .d.ts errors). Retry on react-router@7 upgrade. Tracked in docs/type-system/ and docs/compliance/fixme-index.md.

Medium term

  • Upstream PR cadence. This fork's engineering series is delivered as patch series; the upstream-review/PR flow is an owner decision (base must always be hyperpolymath, never direct push to joshuajewell).
  • e2e smoke set. frontend/tests/e2e/app.e2e.ts exists; grow only after the DOM-lane decision above lands.
  • Benchmark stability window. Informational bench comparison already prints deltas vs bench/baseline.json; promotion to a regression alert (still non-gating) waits for baseline data across several weeks.

Out of scope here (by portfolio rules)

  • Storage/journal/provenance internals — owned by Lithoglyph/GNPL repos.
  • Bioinformatics pipeline semantics — upstream joshuajewell domain; this fork tracks application changes, it does not fork the science.