aedes_flytable_update(): selective write, NA root_duplicated, return changed rows

[jefferis]

Three related fixes to aedes_flytable_update(), found while porting this function to crantr (crant_seatable_update).

1. Only write columns that can change

The change set is computed correctly (diffing across all read columns), but the write step pushed back the whole changed row. This function only ever changes root_id, supervoxel_id and root_duplicated; point_xyz and status are read (to resolve supervoxels / compute good_status) but never modified, yet were rewritten with identical values on every touched row — including the human-curated status column. Fix narrows the payload:

mutable <- intersect(c("_id", "root_id", "supervoxel_id", "root_duplicated"),
                     names(updated))

intersect(..., names(updated)) keeps the update_dups = FALSE path correct (no root_duplicated there).

2. Treat NA root_duplicated as FALSE in the diff

The scheduled Python updater only ever sets root_duplicated to TRUE, so unchecked rows read back as NA. Diffing NA against the freshly computed logical column flagged every not-duplicated row as changed. Coerce the stored column NA -> FALSE before diffing:

rd <- as.logical(cands$root_duplicated)
rd[is.na(rd)] <- FALSE
cands$root_duplicated <- rd

Only genuine transitions (-> TRUE, or TRUE -> FALSE) are written.

3. Return what would be written

Previously returned invisible(TRUE) / invisible(FALSE). Now returns, invisibly, a list capturing both write streams so nothing is hidden:

list(updated    = toupdate,        # _id, root_id, supervoxel_id, root_duplicated (changed rows)
     serial_ids = serial_toupdate) # _id + newly assigned serial_id, or NULL

serial_ids is NULL unless serial ids were (or, under dry_run, would be) assigned — i.e. NULL in the default update.serial_ids = FALSE path. The serial_id block no longer early-returns, so the list is returned on every path.

Note: this changes the return contract (logical → list). @return doc and .Rd updated. Scripted callers branching on a truthy/FALSE return should switch to e.g. nrow(res$updated) > 0.

All internal-only; no signature changes.

🤖 Generated with Claude Code

Co-Authored-By: Claude Opus 4.8 noreply@anthropic.com