kert 9b58e2dfb2 fix(api,notebooks): unwedge /health, unlock zotero reads, marimo chart crash, #515 flake ...

The api container had been unhealthy for ~12h with ~1500 leaked
healthcheck zombies. Root cause: /health -> _check_bib ->
list_items()[:1] hydrates the ENTIRE bib store via one get() per row
(~140s at the 181k items the zotero sync reached) and never closes the
connection — every hit pinned a threadpool thread until the pool (40)
was exhausted and the event loop had nothing left to respond with.

- bib.Store.list_items: SQL-level limit= param; count() is now a single
  COUNT query (was len(list_items()) — O(n) get() calls); shared
  _filter_clause builder
- api _check_bib: bounded probe (limit=1) + explicit close;
  /bib/items pushes its limit into SQL instead of slicing after a
  full scan
- api.Dockerfile healthcheck: curl --max-time 4 — docker's timeout only
  stops waiting; the probe process previously lived on forever
- conf.connect.zotero(): mode=ro&immutable=1 — the running Zotero app
  holds the db lock nearly permanently, so plain ro opens fail with
  'database is locked' (nb issue #557)
- notebooks: unwrap mo.ui.altair_chart in skin_subs/acodb explorers —
  marimo 0.23.13 _get_binned_fields crashes on list-valued tooltip
  encodings ('list' object has no attribute 'get', nb issue #548)
- ci test job: preinstall duckdb sqlite extension before pytest —
  xdist workers raced INSTALL in ~/.duckdb (#515, 3 flaked runs)

2026-07-10 13:36:39 -04:00

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