7.7.0.77

What's Changed

• Don't cache failed DNS lookups in the desktop client by @jcschaff in #1684

Full Changelog: 7.7.0.76...7.7.0.77

7.7.0.76

What's Changed

• Add /loki-query slash command for VCell log access by @jcschaff in #1680
• Exit JVM and dump heap on OutOfMemoryError for server containers by @jcschaff in #1683
• Document direct kubectl logs as fallback for /loki-query by @jcschaff in #1682
• Add JmsFailoverWatchdog and bound failover reconnect by @jcschaff in #1681

Full Changelog: 7.7.0.75...7.7.0.76

7.7.0.75

What's Changed

• Tooling for support-email log processing and triage by @jcschaff in #1670
• Fix Oracle CLOB read: charset-aware character stream by @jcschaff in #1679
• Use UTF-8 explicitly when reading SBML/SED-ML XML by @jcschaff in #1676
• Validate XML chars in name and sbmlName setters by @jcschaff in #1677
• Add scan-xml-control-chars admin CLI by @jcschaff in #1678

Full Changelog: 7.7.0.74...7.7.0.75

PDE Export Panel Improvements

What's Changed

• Fix NPE in StochMathMapping for symbol-less rate expressions by @jcschaff in #1672
• Fix NPE in ParticleMathMapping for non-mass-action kinetics by @jcschaff in #1671
• Make InternalUnitDefinition.round thread-safe by @jcschaff in #1669
• Partial upgrade of libsedml, fixed cli plot bugs by @CodeByDrescher in #1627
• Changed Spatial Results Export Selection to be CheckBox based by @CodeByDrescher in #1667

Full Changelog: 7.7.0.73...7.7.0.74

7.7.0.73

First master release with pre-built Apptainer SIF support and parameter estimation migration.

Pre-built Apptainer SIF for SLURM containers

• Container image properties renamed from *_docker_name to *_apptainer_image with ORAS URL values
• SlurmProxy derives local SIF filenames from ORAS URLs; fail-fast on missing SIF
• CI build-and-publish-sif job publishes vcell-opt + vcell-batch SIFs to GHCR via ORAS
• See docs/apptainer-image-build.md for operational reference

Parameter estimation migration (parest-bug branch)

• Database-backed job tracking (vc_optjob table)
• REST endpoints: POST/GET /api/v1/optimization
• Cross-protocol Artemis messaging (AMQP 1.0 ↔ OpenWire JMS)
• Desktop client rewritten to use generated OptimizationResourceApi
• Legacy /api/v0/optimization endpoints and socket server removed
• COPASI upgraded (basico 0.40→0.86, python-copasi 4.37→4.46)

Other fixes

• Fix CodeQL partial path traversal alert #226
• Restore executable permission on langevin_x64 in batch container
• Fail fast when notarytool submit fails
• Increase optimization polling timeout to 10 minutes

Companion changes required

• vcell-fluxcd: rename properties in submit.env, add htc_singularity_imagedir, add vcell-sif-prepull k8s Job
• One-time: bootstrap vcell-solvers + vcell-fvsolver SIFs to GHCR via ORAS

UI improvements (PR #1666)

• New renderers, extra options, dimming on mouse over, crosshair snap node highlight

7.7.0.72

Same as 7.7.0.71 with CI fix: correct setup-apptainer action reference (eWaterCycle/setup-apptainer, not apptainer/setup-apptainer).

7.7.0.71

Pre-built Apptainer SIF for SLURM containers

Eliminates the ~5 minute per-job SIF rebuild from docker:// that was causing parameter estimation timeouts and adding latent overhead to all simulations.

Changes

• Rename container image properties from *_docker_name to *_apptainer_image with ORAS URL values
• SlurmProxy derives local SIF filenames from ORAS URLs; emits fail-fast checks in SLURM scripts
• New build-and-publish-sif CI job builds and publishes vcell-opt + vcell-batch SIFs to GHCR via ORAS
• New htc_singularity_imagedir property for the cluster SIF directory
• Updated all 12 SLURM test fixtures for SIF-path form
• Operational reference: docs/apptainer-image-build.md

Also includes (from earlier commits on this branch)

• Fix CodeQL partial path traversal alert #226
• Restore executable permission on langevin_x64 in batch container
• Fail fast when notarytool submit fails

Companion changes needed

• vcell-fluxcd: rename properties in submit.env, add htc_singularity_imagedir, add vcell-sif-prepull Kubernetes Job manifest
• One-time bootstrap: manually build and push vcell-solvers + vcell-fvsolver SIFs to GHCR via ORAS

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