Publication Cleanup Log¶
Date: 2026-06-02
This log records repository cleanup decisions made before publication review. The goal was to reduce ambiguity without changing scientific assumptions, Parquet behavior, chunking, or restart-safe pipeline contracts.
Completed Decisions¶
| Feature request | Outcome |
|---|---|
| FR-001 generated artifacts | Moved tracked .DS_Store and Python bytecode files to deprecated/generated_artifacts/2026-06-02/ with original paths preserved. Added ignore rules so new local artifacts stay untracked. |
| FR-002 large deprecated data | Kept deprecated Megan unmixing data for provenance, documented its status, and excluded deprecated/ plus root gocmd from source distributions through MANIFEST.in. |
| FR-003 distribution contents | Added MANIFEST.in to include package data/docs/tests intentionally and exclude root staging data, deprecated archives, generated docs reports, and container-only helpers. |
| FR-004 root scripts | Kept root helper scripts because container and remote-storage workflows call them from unusual mount roots. Documented them in docs/dev/container-workflows.md. |
| FR-005 docs source of truth | Archived stale root draft pages with FILLME markers to deprecated/docs/publication_cleanup_2026-06-02/ and updated README links to current MkDocs pages. |
| FR-006 docs tooling | Updated scripts/check_docs_links.py to scan nested docs, ignore generated _build output, and make FILLME failure opt-in via --fail-on-fillme. |
| FR-007 README QA placeholder | Removed the “coming soon” placeholder and linked the checked-in workflow diagram that includes QA reports in the output contract. A renderer-produced QA PNG was not generated locally because this environment lacks matplotlib; QA fixture rendering remains covered by tests/CI. |
| FR-008 MicaSense tutorial | Rewrote the tutorial around the supported run_drone_pipeline local-H5 API and drone-native output names. |
| FR-009 stale reference examples | Rewrote docs/reference/extending.md around current extension points and archived the stale root docs/validation.md CSV-first draft. |
| FR-011 top-level orchestration exports | Added lazy top-level exports for go_forth_and_multiply and process_one_flightline, plus smoke coverage. |
| FR-012 generated docs drift reports | Moved tracked docs/_build/ reports to deprecated/generated_docs/2026-06-02/ and ignored future generated _build output. |
| FR-013 duplicated data locations | Documented root data/ as examples/local staging and src/spectralbridge/data/ as authoritative package data. |
| FR-014 publication checklist | Refreshed checklist items to reflect completed packaging, docs, tests, Ray, and cleanup work. |
Notes¶
- Unrelated external-repo PRISM artifacts were removed earlier in this cleanup because the user confirmed they belonged to a different repository.
- Ray is required and remains the default parallel engine. Thread and process engines remain explicit alternatives for runs that should avoid Ray initialization.
- Parquet remains the authoritative tabular output. CSV files, when present, are convenience sidecars only.
- Root
CONTRIBUTING.mdwas refreshed alongside MkDocs contributor guidance so public community files use current SpectralBridge naming and commands.