feat: add opt-in taxon-filtered fullmaps and InChIKey support

[SkyeAv]

Adds an opt-in top-100 experimental taxon allowlist for fullmap builds and preserves InChIKey terms during ingestion. Default fullmap builds and existing Python callers remain unchanged.

Taxon-filtered fullmaps

• Checked-in allowlist: Adds src/tablassert/data/experimental_taxa.yaml containing 100 deterministic NCBI taxon IDs ranked from observed frequencies across the MultiomicsNext and MultiomicsHarness corpora.
• Rust filtering: Adds optional taxon_allowlist support to rust/src/fullmap.rs, filtering non-OrganismTaxon rows before interning.
• Retention semantics: Retains taxonless rows, including NCBITaxon:0 and malformed taxon values; retains rows with any allowlisted taxon; retains all rows whose categories include OrganismTaxon.
• Build identity: Records a deterministic META.taxon_allowlist identity for filtered databases.
• CLI behavior: Adds --taxon-allowlist to tablassert build-fullmap. This mode always builds from BABEL sources and never reuses an unfiltered prebuilt database.

InChIKey support

• Token QC: Removes the inchikey rejection from Rust fullmap token validation while preserving newline, tab, hypothetical, uncharacterized, and dead-token filtering.
• Normalization: Verifies both raw normalized terms such as abc-def and CURIE-form terms such as inchikey:abc-def.

Tests and documentation

• Coverage: Adds Python and Rust coverage for allowlist filtering, taxonless sentinels, malformed taxa, multi-taxon rows, multi-category OrganismTaxon rows, deterministic metadata, CLI prebuilt bypass behavior, and InChIKey lookup.
• Documentation: Updates docs/cli.md and docs/fullmap.md with the allowlist workflow, retention semantics, and metadata behavior.
• Packaging: Explicitly includes the allowlist data file in the maturin package.
• Compatibility: Updates src/tablassert/rs.pyi and existing Rust call sites while preserving the default unfiltered build path.

Testing

• uv run pytest -q → 1327 passed, 43 skipped
• uv run pytest -n 0 tests/test_cover_fullmap.py tests/test_cover_cli.py tests/test_docs_source_of_truth.py tests/test_docs_cli_coverage.py -q → 198 passed
• cargo test --manifest-path rust/Cargo.toml --no-fail-fast → passed
• cargo check --manifest-path rust/Cargo.toml → passed
• cargo fmt --manifest-path rust/Cargo.toml --check → passed
• uv run ruff check . → passed
• uv run ruff format --check . → passed
• uv build --wheel --out-dir /tmp/taxon-wheel-final → passed; wheel contains tablassert/data/experimental_taxa.yaml
• uv run pyright → only pre-existing optional-import diagnostics remain for logger/loguru

[coderabbitai]

Important

• 🔍 Trigger review

This repository does not receive automatic reviews because it has fewer than 10 stars.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Advanced

Run ID: 90f09afb-6189-48f9-a5f1-6cf9e2abbba3

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}