Make new release notes for vcell 7.7

[jcschaff]

Create release notes for vcell.org for vcell 7.7.0.47 (below is up to 7.7.0.39 - need to regenerate the verbose list and distill manually).

when we publish the release notes, we should

[jcschaff]

Generated Release notes - need proof reading.

Detailed Release notes (based solely on Github commit messages and PRs)

VCell Release Notes (7.7.0.15 → 7.8.0)

466 commits, 55+ PRs merged since Feb 5, 2025

Major Features

New Export System Overhaul (PRs #1568, #1596)

• Migrated export system to Quarkus REST API
• Replaced ApacheMQ with ArtemisMQ for export queue
• Separate Docker image for export service
• Now uses N5 format exclusively
• Improved concurrency and error handling

SpringSaLaD/Langevin Solver Improvements (PRs #1439, #1446, #1454, #1478, #1492, #1525, #1532, #1558, #1584, #1588)

• Upgraded Langevin solver: 1.4.0 → 1.4.2 → 1.4.4
• SLURM array job support for multiple trials
• Post-processing statistics (averages, std dev, min/max)
• Physical limit validation for sites, diffusion rates, partitions
• SpringSaLaD enabled by default (later disabled by default in property enableSpringSaLaD is false by default #1584)

Field Data System Rewrite (PRs #1457, #1463, #1466, #1477, #1484, #1490, #1499)

• Server-side field data processing (moved from client)
• New REST endpoints for field data creation
• Fixed field data creation from simulations
• Improved memory management
• Copy field data from BioModel functionality

Quarkus REST API Expansion (PRs #1500, #1506, #1512, #1514, #1523, #1526, #1533, #1544)

• BioModel save/delete/info endpoints
• MathModel endpoints (save, delete, get, info)
• Geometry endpoints
• VCImage resource endpoints
• Improved error handling architecture with proper HTTP codes
• OpenAPI spec CI testing

Bug Fixes

• Fixed OutputFunctions being ignored in spatial CLI data (Fixed bug where OutputFunctions were ignored #1595)
• Fixed Math Model export error (Fix Math Model Export Error #1594)
• Fixed PubMed links in Annotations tab (PubMed links disappeared from Annotations tabs #1576)
• Fixed Google login (Add Parameter that Prompts Login #1520)
• Fixed VCell reconnection/token refresh failure (VCell Connection Failure Fix #1471)
• Fixed NPE when inserting compartment (Fix NPE when inserting compartment. #1541)
• Fixed concurrent modification in simulation results display (NullPointerException in TreeMap because of concurrent modification #1465)
• Fixed geometry viewer cropping bug (Fixed bug with cropping in geometry viewer #1437)
• Typo fix: "Constructed" → "Constructive" solid geometry (Typo fix: Constructed -> Constructive #1561)

Infrastructure & Maintenance

• Added VCell Support role for support staff (Add VCell Support Role #1536)
• SSH command options now configurable for SLURM migration (Changes to VCell to support migration to new Slurm cluster #1467)
• Native library compilation via GraalVM for pyvcell (native compilation of new vcell-nativelib for pyvcell #1452, prepare for nativelib deployment through libvcell repo #1455)
• BioSimulations: plots now reported as Reports for compatibility (As required by BioSimulations, plots reported as Reports #1444)
• Upgraded Pathway Commons integration to BioPAX level 3 (Upgrade Pathway commons #1574, replaced Map with linkedHashMap, evaluate work for biopax lvl 3 #1586)
• XML security hardening (XXE attack prevention) (Clean XML #1531)
• Removed deprecated/dead code and unused DB files
• Updated JAI Core repository

[jcschaff]

update release notes.

[jcschaff]

@ACowan0105 @vcellmike here are release notes for vcell 7.7