Milestones and Acceptance Tests

One milestone per session. Plan → write tests → implement → write docs.

M0 — Scaffold

Cargo workspace (ligase-core, ligase-py), maturin, python/ligase, CI running fmt, clippy, ruff, mypy, cargo test, pytest.

Done when: pip install -e . works and import ligase succeeds in CI.

M1 — Types and dimensions

Done when: - HXB2 FASTA and a sample BAM are loaded with dimensions inferred from headers. - A BAM aligned to a different reference fails check() with a clear DimensionError. - A chr1 vs 1 mismatch raises a distinct error.

M2 — Graph

Done when: the golden example builds a graph without executing anything, and ligase check reports all type errors in one pass.

M3 — Execution and cache

Done when: - The demo runs end to end on 3–4 runs from PRJNA517147. - A second run completes entirely from cache. - Changing min_freq reruns only call and resistance. - Adding one sample processes only that sample.

M4 — Semantic hashing and early cutoff

Done when: rerunning alignment with a different thread count produces the same canonical hash and downstream steps are skipped.

M5 — Provenance

Done when: ligase methods outputs a methods paragraph with tool versions, parameters, reference accession and citations, plus a bundle that reproduces the results on a clean machine.

M6 — Validation

Done when: resistance calls match published results for PRJNA517147 and the Sanger ground truth for PRJNA1218827, with discrepancies explained.

Done. The calls are checked against the published Stanford HIVdb reports for PRJNA1218827: 81 of 81 drug calls agree exactly at the 15% and 5% thresholds, and the nine that differ at 2% each carry a cause. The scoring engine separately reproduces 3,348 published expectations.

PRJNA517147 could not serve as a source of expected answers: its per-sample calls are published only as colour in a heatmap, reverse transcriptase only. It remains the demo'''s default dataset. See validation.