[jpfeuffer]

Bumps the sync-openms retag to the official OpenMS dev build develop-2026.10.28-f940a46542. The build is containerdeploy run https://github.com/OpenMS/OpenMS/actions/runs/40679593583, from OpenMS develop @ f940a46542, which is the merge commit of OpenMS/OpenMS#10450. Once merged, it is published as ghcr.io/bigbio/openms-tools-thirdparty:2026.10.28 (Docker and SIF).

The Docker index and the SIF come from the same run. The SIF was built from docker://ghcr.io/openms/openms-tools-thirdparty:develop-2026.10.28-f940a46542.

• Docker index: ghcr.io/openms/openms-tools-thirdparty@sha256:c9b4b871f8c5edcc588ffa7759eb709eb827713e44c003066b6436bae5899637
  • amd64: e31f0ab1…
  • arm64: ad6e78d1…
• SIF: oras://ghcr.io/openms/openms-tools-thirdparty-sif@sha256:0cdb19e52d3ff534390ffdedcb19c242fe30ae3b3dcd0e47c1ca1788030a8cac
• Verified in the image: ProSE reports Revision: f940a46; -out accepts idXML/idparquet; ONNX Runtime and the PeptDeep models are present; there is no Bruker SDK.

The tag is pinned by digest. This avoids a race with the mutable latest nightly, which currently predates OpenMS/OpenMS#10450.

Retag change: docker pull/tag/push of an index digest republished only the runner's platform (amd64). The job now uses docker buildx imagetools create. It copies the full multi-arch index unchanged, and a check confirms the bigbio tag resolves to the source digest. The latest-on-release step referenced @sha256:${OPENMS_VERSION}, which is not a valid reference; it now uses the same copy.

Compared with 2026.10.04 it adds:

• ProSE with in-process rescoring (-Search:rescore, [API,PARAM,TEST] ProSE: Percolator rescoring in ProSEAlgorithm, on by default OpenMS/OpenMS#10578)
• native .idparquet -out ([FEATURE,PARAM] ProSE: write per-file .idparquet via new -out (deprecate -out_idxml) OpenMS/OpenMS#10450)
• consistent FDR and per-file outputs ([FIX] ProSE: consistent FDR outcomes (mixed rescoring, PSM FDR without decoys, protein groups, duplicate/unbalanced databases) OpenMS/OpenMS#10714, [FIX] ProSE: FDR:protein switches between final results and intermediates; outputs agree; full parameter names; run-view counts; c/z test OpenMS/OpenMS#10745)
• ONNX Runtime and PeptDeep models ([BUILD] Docker: ONNX Runtime + PeptDeep models (no Bruker SDK) OpenMS/OpenMS#10462, Add PeptDeep prediction-based rescoring features to ProSE (+3.7% / +15.0% PSMs at 1% FDR) OpenMS/OpenMS#9975)
• SDK-free Bruker m/z calibration ([FIX,IO] BrukerTimsFile: compute m/z from the MzCalibration table OpenMS/OpenMS#10469)
• vendor files readable through symlinks
• ProteomicsLFQ -feat_dir checkpoint fixes

bigbio/quantms#740 needs this image. It currently pins the OpenMS digests above and will repin to the bigbio tag after this PR merges.

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