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db.save_database() requires a positional directory argument not shown in the ingest skill templates #100

Description

@kelle

Where: astrodb-ingest-publications skill's references/ingest_publication_api.md, "Saving" section, and scripts/ingest_publication.py template — both call db.save_database() with no arguments.

What happened: Running the generated script with SAVE_DB = True raised TypeError: Database.save_database() missing 1 required positional argument: 'directory'. The installed astrodbkit version requires save_database(directory, clear_first=True, reference_directory="reference", source_directory="source").

Workaround: Called db.save_database("data/") (matching database.toml's data_path) in both ingest scripts.

Suggested change: Update references/ingest_publication_api.md and scripts/ingest_publication.py (and any other ingest skill's template making the same call — astrodb-ingest-sources, astrodb-ingest-photometry should be checked too) to show db.save_database("data/") or explicitly note the directory argument is required and should match database.toml's data_path.


Reported from a gotchas.md log filed by a skill user (2026-08-28).

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