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Preserve partner-recovery progress around slow queries - #105
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Large mate/SA recovery queries currently lose the entire partner query's progress when one slow region causes a timeout. Add optional partner batches, query-count limits and a separate partner timeout; with
on_timeout="incomplete", completed batches survive and later batches continue. Failed locations remain unresolved and never become evidence of absence. Default request/cache identities and record matching are preserved.On the first Sid PacBio audit batch, the existing combined query timed out after 300 seconds with 404,697 retained seed records. A bounded-query pilot finished in 78 seconds with 404,699 verified records and explicit incomplete status. The audit is still tuning query sizes; this PR provides bounded progress without claiming complete template recovery.
Validation: 395 tests pass; ruff and strict MkDocs build pass; wheel/sdist build and Twine checks pass. New tests cover a timeout followed by a recoverable late mate, exact multiplicity, retry, query budgets, default cache identity, and invalid policy values. Version 0.15.1.
Fixes #104. Needed by openvax/isovar#433.