[trissim]

Scope

Refs #172. Sole source owner for the Opera initialization defect; parent remains integration/merge and installed-acceptance owner. Target is main, as requested. Started from parent PR #206 at 5ce9e30 with PolyStore PR #20 (91fd7e8); paired #206/#16 were pending at dispatch and are now normally merged. This branch normally merged current main e690c3b, including the merged PolyStore pin 84f322e4; only this owned source fix/test/receipt/evidence remain in the PR diff. This PR is draft and parent will integrate/merge. Keep #172 open.

The original installed MCP raw Opera 1x1 generation (no --openhcs-format) warned plate_grid_dimensions_unavailable; complete empty PipelineDocument artifact-plan failed OperaPhenixXmlContentError: Could not determine grid size from XML data. Its XML is unchanged and the original exception is preserved in source evidence.

Implementation

• Extend the existing XML parser's finite field-coordinate decoding for both grid and field-remapping readers.
• Accept any nonempty valid coordinate population, including one field and colocated channels/planes, without cached mutation or a special singleton path.
• Keep numeric well/channel/plane populations separate, existing axis quantization and first multi-image group precedence.
• Delete unreachable field-ID square/factor guessing; do not infer geometry from field numbers.
• No generator, filename, microscope-base, metadata store, environment, installed package or parent-worktree edits.

Evidence and limits

Eleven pure-source XML tests pass in a one-CPU, <=512 MiB, <=60s shard. Unchanged original installed-reproducer XML now yields (1, 1) and {1: 1} remapping, with fresh-parser reopen and original SHA256 retained. All three unchanged CI structural-ratchet roots pass: -4 string-key reads, -14 long-chain terms, no new dispatch or exceptions. Peak observed combined RSS is 83.55 MiB; longest shard 17.71s. Git tree identity proves normal main integration did not change qualified production/test source. Focused current-archive AST/census is recorded separately, with zero parser failures; no full NRA or global R1 certificate claimed.

This proves the parser source boundary only: no public-package discovery, scientific/native runtime, installed MCP or live UI acceptance. Worktree dependency gitlinks remain deliberately uninitialized. Original failures and all source evidence are archived and byte-verified before disposable scratch/tool-worktree cleanup.

docs/validation/opera_singleton_172.rst records pattern IDs, ownership witnesses, exact new-case experiments and resources. Separate A01 persisted metadata versus R01C01 filename inventory mismatch remains tracked under #172: its generator/catalog producer is outside this stage-coordinate owner. Parent retains original installed receipts and performs integration/live acceptance.

[trissim]

Parent installed acceptance now passes on candidate de09ed00e40d1dada99cf5a020e4fe4bda5e6e45 (exact PR329 parser plus merged PR332 skill). Real installed MCP continuous journey: raw Opera 1x1 generation → native auto-detected inspection (one R01C01 well) → complete empty-document workspace initialization → canonical 8x8 sample → reopened inspection and artifact plan → final healthy unchanged process → clean exit 0. Original failing XML unchanged. Initialization warning retained; reopened route has no errors/warnings. Generic PolyStore metadata filename did not override openhcs_metadata.json. No JVM/viewer/biology acceptance claimed. First source-shadowed launch failure retained separately. Full persistent receipt: /home/ts/wt/openhcs-issue-batch-20260929/opera-installed-20261001/ACCEPTANCE.rst and original installed-live logs. Targeted fix is ready to merge under owner no-hosted-CI-wait instruction; keep #172 open for the separately owned generator inventory defect.

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