7.7.0.70

• Restore executable permission on langevin_x64 in vcell-batch container (regressed by CI matrix parallelization where actions/upload-artifact@v4 strips POSIX perms)
• Fail fast when notarytool submit fails instead of polling 5 minutes with empty UUID

7.7.0.69

Merge master into parest-bug and fix CodeQL partial path traversal alert #226.

• Fix CodeQL alert #226 (java/partial-path-traversal-from-remote): replace getCanonicalPath().startsWith(String) with Path.startsWith(Path) in OptimizationBatchServer, SlurmProxy, and OpenWireOptSubmitStub
• Merge latest master (JFreeChart removal, logger cleanup, dan-ss-display PR #1661)

7.7.0.68

What's Changed

• Add publish endpoint and webapp UI for marking models as published by @jcschaff in #1651
• Springsalad batch run results visualization by @danv61 in #1661

Full Changelog: 7.7.0.52...7.7.0.68

7.7.0.67

Fix CodeQL path traversal warnings in SlurmProxy and OpenWireOptSubmitStub test stub.

7.7.0.66

Legacy optimization removal and improvements

• Remove legacy /api/v0/optimization — deleted socket server (port 8877), OptMessage.java, OptimizationRunServerResource, VCellOptClient, and related code (~1,010 lines)
• Remove dead config — vcell.submit.service.host property, Dockerfile ENV, K8s port 8877
• Upgrade COPASI — basico 0.40→0.86, python-copasi 4.37→4.46, Dockerfile bullseye→bookworm
• Fix progress buffering — confirm_overwrite=False enables incremental COPASI report flushing
• Increase client timeout — 200 seconds → 10 minutes
• Rewrite design doc — simplified to maintenance reference

7.7.0.65

Upgrade COPASI/basico and modernize vcell-opt

• Upgrade copasi-basico 0.40 → 0.86, python-copasi 4.37.264 → 4.46.300
• Set minimum Python to 3.10 (matches Dockerfile and CI)
• Fix report separator format for new basico API
• Upgrade Dockerfile base from Debian bullseye (EOL) to bookworm
• Add gcc/python3-dev to Dockerfile for psutil compilation

7.7.0.64

Parameter Estimation Fixes

• Fix COPASI progress buffering: Set confirm_overwrite=False in basico.assign_report() so COPASI flushes progress lines incrementally during execution, enabling real-time progress updates in the client
• Remove broken mkdir in SlurmProxy: The redundant mkdir on the external NFS path failed inside the vcell-submit container (harmless but noisy error log)
• Add incremental progress test: Uses multiprocessing to verify COPASI writes progress during execution
• Add debug logging to client-side optimization polling loop
• Update design doc with requirements section and post-migration notes

7.7.0.63

Fixes

• Fix progress reporting for all active optimization states — server now reads the progress report file for SUBMITTED/QUEUED states and auto-promotes to RUNNING when progress appears on disk; client dispatches progress to the UI graph for all active states

Docs

• Update parameter estimation design doc — rewritten architecture diagram, new sections on cross-protocol messaging, real-time progress reporting, and filesystem-driven status promotion

7.7.0.62

Fixes

• Fix CI build — remove unused ActiveMQConnectionFactory import from QuarkusStartUpTasks.java that failed compile when activemq-client is test-scope only

7.7.0.61

Fixes

• Fix ANYCAST routing for AMQP channels — add capabilities=queue to SmallRye AMQP channel configs so Artemis routes messages correctly between AMQP 1.0 (vcell-rest) and OpenWire JMS (vcell-submit)

Tests

• Add cross-protocol integration test — exercises the full AMQP 1.0 ↔ OpenWire JMS round-trip through an Artemis testcontainer, with an OpenWire stub that mirrors OptimizationBatchServer.handleSubmitRequest()