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docs: replace arrow notation with plain prose for readability - #217
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Rewrites the chained '->' arrows that read as AI-generated text across README.md and docs/ into natural sentences, comma lists, and 'to'/'then' phrasing. Python return-type annotations, the quick_map example f-string, and KGX '--[predicate]-->' edge notation are code and stay untouched. - QC stage lists (exact -> fuzzy -> abbreviation -> SapBERT) become comma-separated stage names in README.md, docs/installation.md, docs/tutorial.md, docs/cli.md, and docs/api/qc.md - Pipeline and dataflow arrows in docs/fullmap.md, docs/cli.md, docs/api/fullmap.md become prose or comma lists - Input/output example arrows in config docs and code comments become 'becomes'/'maps to'/'yields' - Bidirectional '<->' pair notation becomes plain 'X / Y' or 'X and Y' - Schema-migration 'v3->v4' wording and the '[CLI Reference -> build-fullmap]' link label reworded No behavior change; markdown only.
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SkyeAv
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Oct 15, 2026
Cut 21.0.0 and bump the package version in pyproject.toml, CITATION.cff, and uv.lock. Major: two breaking changes ship since 20.0.0. Derived-path builds emit section source record URLs on the upstream repository supporting sources entry (infores:pubmed-central for PMC sections) instead of the primary graph-infores entry, and the inlined supporting Study is named after the table config file plus its 1-based section index (#220); validate-infores is folded into validate-kgx as the knowledge-source identity half, and the standalone validate-infores command is gone (#218). Also adds no_map on NodeEncoding to pass subject/object CURIEs through verbatim (#219) and normalizes documentation prose to plain ASCII (#217). Changelog: - Versioned the Unreleased section as 21.0.0 - 2026-10-15. - Added the missing #218 (breaking, with migration note), #219, and #217 entries so no merged PR ships unmentioned. Docs: none needed here; the release commit only versions existing prose. Testing: - make check -> ruff clean, pyright 0 errors, pytest 1239 passed + 1 skipped, cargo test ok, cargo clippy --all-targets -- -D warnings clean - uv run mkdocs build --strict -> pass
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Replaces the chained
->arrows acrossREADME.mdanddocs/with plain prose so the documentationreads as human-written text rather than generated output.
What changed
exact -> fuzzy -> abbreviation -> SapBERTlists inREADME.md,docs/installation.md,docs/tutorial.md,docs/cli.md, anddocs/api/qc.mdbecome comma-separated stage names ("exact match, fuzzy match, abbreviation expansion, then SapBERT").Loading Tables -> Extracting Sections -> ...(docs/cli.md) and the normalization/fetch chains indocs/fullmap.mdanddocs/api/fullmap.mdbecome prose or comma lists; tuning-table outcomes (Lower -> less RAM, more run files) become sentences."123" -> "CUSTOM:123") become "becomes" / "maps to" / "yields"; bidirectional<->pair notation becomes plain "X / Y" or "X and Y" phrasing.[CLI Reference -> build-fullmap]link label and thev3->v4schema-migration wording indocs/fullmap.mdare reworded.Kept as code
-> str,-> pl.LazyFrame) indocs/api/*.mdare syntax, not style, and stay.print(f"{row['gene_name']} -> {row['gene']}")example indocs/api/lib.mdis executable code.Lactobacillus rhamnosus --[correlated_with]--> 13C-tamoxifen) indocs/configuration/advanced-example.mdis not an arrow tell.Testing
uv run mkdocs build --strict-> passuv run pytest tests/test_docs_cli_coverage.py tests/test_docs_examples.py tests/test_docs_source_of_truth.py -q->192 passedrg -n -- '->' README.md docs/-> only the three code categories above remain (10 lines, all syntax)