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fix: stop rendering phantom --empty-* flags in help - #202
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SkyeAv
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September 29, 2026 22:33
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SkyeAv
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Cyclopts auto-generates an --empty-<name> reset flag for every list parameter and gives it its own help row; agent's --empty-pmc-ids even rendered [required], reading as a mandatory flag. quick-map's terms and filter lists and agent's pmc_ids/local now set Parameter(negative="") to opt out, and a sweep test asserts no command's --help contains an --empty- row so a future list parameter cannot reintroduce the noise.
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Cut 19.4.0 and bump the package version in pyproject.toml, CITATION.cff, and the uv.lock self-entry. Minor: one new capability plus four help/UX fixes since 19.3.0. Enum-ranged qualifier columns are now audited against their closed Biolink vocabulary at build time, failing with `qualifier-vocabulary-violation` (#198). The CLI help surface got a sweep: `distill-weigh`'s `--policy` becomes a `Literal` with a full docstring Args section (#199), `build-kg`/`validate`/`validate-kgx` gain per-flag help matching docs/cli.md (#200), `build-fullmap`'s shadowed `--version` flag is renamed to `--babel-version` (#201), and phantom `--empty-*` list-reset flags no longer render in any help (#202). Changelog: - Versioned the Unreleased section as 19.4.0, added the missing Fixed entries for #199, #200, and #202 with PR links. Docs: none needed here; docs/cli.md and the flag docs shipped with the feature PRs, and mkdocs builds strict. Testing: - make check -> All checks passed! (1663 passed, 52 skipped; rust: 127/11/17/1 ok) - uv run --no-sync mkdocs build --strict -> pass
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Cyclopts auto-generates an
--empty-<name>reset flag for every list parameter and gives it its own help row; onagent,--empty-pmc-idseven rendered[required], reading as a mandatory flag an agent must pass. List parameters now opt out, and a sweep test keeps the help pages phantom-free.Suppression
agent'spmc_idsandlocal, andquick-map'sterms,prioritize,avoid,exclude_prefixes, andexclude_regex, setParameter(negative="")insrc/tablassert/cli.py, which stops cyclopts from generating the unused reset negation.tests/test_cli_help_friendly.py::test_no_help_page_renders_a_phantom_empty_flagrenders all eight commands'--helpand fails on any--empty-row, so a future list parameter cannot reintroduce the noise.Changelog
CHANGELOG.mdUnreleased entry's PR link (#201), which could not be written before the stack existed.Testing
uv run --extra cli pytest tests/test_cli_help_friendly.py -q->8 passeduv run pytest -q(dev + agent + optimize + distill + cli + qc + log extras) ->1760 passed, 3 skipped;uv run pyright->0 errors;uv run ruff check .anduv run ruff format --check .-> clean[aria2]extra installed trips a pre-existingtests/test_fullmap.py::test_build_fullmap_cli_function_smokefailure (the test monkeypatches only the Python downloader; auto-selection switches to aria2c). Unrelated to this stack: the diff touches none of the downloader-selection code.