Docs refresh + fix red CI (commit bundled fixture) - #30
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CI's `rust` job (and the release bundle step, and `frontdoor_demo`) assumed
examples/data/illumina_toy/{reference.fa,alignments.bam} existed, but that dir
was gitignored ("Generated demo datasets") — so on a clean checkout the
frontdoor_demo integration test failed (exit 101) and the whole CI `rust` job
went red, every run this session. Fix: commit a SMALL bundled fixture
(reference.fa 4 KB + alignments.bam 15 KB, generate_toy_data.py --length 4000)
and narrow the ignore to keep just those two files (the large reads/SAM/VCF stay
generated). This also makes the README's "bundled data" promise true on a fresh
clone and unblocks the release.yml bundle step + install.sh demo. Also removes a
pasted LICENSE block that had corrupted .gitignore, and drops an unnecessary
`mut` on a closure in tests/germline_accuracy.rs (the one CI build warning).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- Add the `rosalind features` ML feature substrate and `eval-germline` to the capability list and the subcommand reference. - New "Accuracy" section with the measured detection precision/recall (1.00/1.00 clean, 0.90/0.68 stress) and the honest scope; soften the E. coli proof's "memory not accuracy" line to point at it. - Rewrite the Python section to lead with the real python/rosalind.py feature boundary (the dead-end PyO3 stub is demoted to "legacy"). - Refresh the Roadmap: Phase C is done (not "in review") + a "Hardening & reach (done)" entry covering the unbiased cap, CI memory gate, measured accuracy, the feature substrate, and the adoption on-ramp + GitHub Action. - Note numpy for the feature boundary in prerequisites. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
Two things: refresh the docs to the current state of the system, and fix CI — which has been red on every run this session because of an uncommitted test fixture (masked because I verified locally and merged without watching GitHub).
CI / release fix
examples/data/illumina_toy/was gitignored ("Generated demo datasets"), butfrontdoor_demo, therelease.ymlbundle step, andinstall.sh's demo all assume it exists. On a clean checkout thefrontdoor_demointegration test failed (exit 101) → the wholerustCI job went red. Fix:reference.fa4 KB +alignments.bam15 KB) and narrow the ignore to keep just those two files (large reads/SAM/VCF stay generated). Makes "bundled data" true on a fresh clone; unblocks the release bundle + install demo..gitignore.mutingermline_accuracy.rs).Docs refresh (README)
rosalind featuressubstrate +eval-germlineto the capability list + subcommand reference.python/rosalind.pyboundary (demote the dead-end PyO3 stub to "legacy").Test plan
cargo testgreen;cargo fmt --checkclean; 0 warnings (incl. test build)frontdoor_demopasses against the committed small fixture🤖 Generated with Claude Code