Add a --out flag so a caller can choose the output path - #21
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Closes #20. The output path is the one path a spec names that does not sit beside it: every other -- csv, title_md, chain_representation, a local structure -- is an input in the spec's own directory, so resolving out the same way forces a caller whose build system owns the output tree to write repository layout (`../../../results/...`) into a data file, and forces a Snakemake rule to parse the spec at DAG-construction time to learn its own output. --out resolves relative to the working directory, and is mutually exclusive with the spec's own out: exactly one must be given, checked in load_spec so the CLI and the Python API cannot disagree. out therefore leaves spec.SHARED_KEYS for the new OUT_KEY. Nothing downstream changes -- render already derives the report path from spec.out, so <stem>_report.txt follows --out and the .html check applies to it too. Existing specs are unaffected: a spec that names its own out stays valid, so the examples and scripts/build_examples.sh are untouched. Released as 0.2.0. Verified with scripts/check.sh, scripts/build_docs.sh (mkdocs --strict, which resolves the new anchor), and scripts/build_examples.sh, which re-renders examples/output/ byte-identically. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Closes #20, and bumps the version to 0.2.0.
What changed
--out PATHon the CLI, resolved relative to the working directory rather than to the spec file, and mutually exclusive with the spec's ownout— exactly one must be given:--outonlyoutonlyInputErrornaming both valuesInputErrorasking for oneThe check lives in
load_spec(path, out=None), the one place the CLI and the Python API both pass through, so they cannot disagree;render_file(spec_path, out=None)threads it.outleavesspec.SHARED_KEYSfor the newOUT_KEY, staying inOPTION_KEYSand in the allowed top-level keys.Spec.outis still a required dataclass field, populated from whichever source gave it, so nothing downstream changes:renderalready derives the report path fromspec.out, and<stem>_report.txttherefore follows--out,.htmlcheck included.Existing specs are unaffected — a spec that names its own
outstays valid — soexamples/*/spec.yamlandscripts/build_examples.share untouched. Theinputssubcommand discussed in the issue is deliberately not here.Docs
Meaning is written once, in a new Where the page is written section of
docs/spec.md, with the intro paragraph and the required-keys table corrected and one cross-reference each fromdocs/index.mdanddocs/python-api.md. The CLI docstring's "every option lives in that file rather than in a flag" andCLAUDE.md's "there are no flags" both stopped being true and are fixed.Verification
scripts/check.sh: 243 passed, ruff and black clean. New tests cover--outalone (page plus report), CWD-relative resolution against a spec in a subdirectory, both → error, neither → error, and--out foo.htm→ error. DroppingoutfromSHARED_KEYSremoves its case from the parametrizedtest_missing_shared_key_is_fatal; the two dedicatedtest_spec.pytests replace that coverage.examples/1f8b_active_site.scripts/build_examples.shre-rendersexamples/output/byte-identically.scripts/build_docs.sh(mkdocs build --strict) builds clean and resolves the new#where-the-page-is-writtenanchor.No
viewer.pyor template change, so no browser check applies.🤖 Generated with Claude Code