Handle incomplete SoftMax kinetic exports in SpectraMax parser

[wasimxyz]

Summary

When SoftMax stops a Kinetic run early, the plate header’s num_readings can exceed the exported groups. The old loop kept consuming the summary (or hit ~End badly). The new path:

1. Stops at ~End / EOF (_at_plate_end)
2. For Kinetic only, requires an elapsed-time token in the next group window (_kinetic_reading_present + _ELAPSED_TIME_RE, including D.HH:MM:SS)

Applied in both flat and grid layouts. Tests cover overstated count + summary, day-prefixed times, and stop-at-~End without summary. AGENTS.md adds a no-internal-secrets-in-PRs rule (sensible; slightly orthogonal to the parser fix).

Changes

• SoftMax Pro can declare more Kinetic readings in the plate header than it exports when a run stops early; the SpectraMax parser now stops at the summary table or ~End instead of raising IndexError.
• Add unit coverage for overstated num_readings, including day-prefixed elapsed times after 24 h (D.HH:MM:SS).
• Document in AGENTS.md that agents must not put internal-environment secrets, signed URLs, or instrument/run/file IDs into commits or PRs.

Test plan

• uv run pytest lambda/tests/spectramax_plate_reader/test_parse_raw_well_data.py -q
• Reprocess a previously failing incomplete Kinetic plate-reader file after deploy and confirm it reaches processed status

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Project	Deployment	Actions	Updated (UTC)
data-hub	Ready	Preview	Jul 30, 2026 10:46pm