BioNetGen BNGL import enhancement#1698
Merged
Merged
Conversation
jcschaff
approved these changes
May 20, 2026
Member
jcschaff
left a comment
jcschaff
left a comment
There was a problem hiding this comment.
Approved, per Michael's request and your implementation
jcschaff
added a commit
that referenced
this pull request
May 21, 2026
CHANGELOG.md (Keep-a-Changelog format, per-build engineer-track log): - [Unreleased] section with #1698 BNGL preprocessor fix queued for the next tag cut - [8.0.0.02] and [8.0.0.01] per-build sections covering the current 8.0.0 line - [7.7] consolidated backfill section covering all 78 builds of the 7.7 line (2024-09-27 → 2026-05-11), with a marketing-epoch breakdown table mapping prod-roll dates to the three named 7.7 release events - [7.6-patches] consolidated backfill section covering 7.6.x patches rolled to prod between the VCell 7.6 marketing release (2024-07-12, build 7.6.0.19) and the 7.7 line opening (2024-09-27, build 7.7.0.0) release-notes/major/ (user-facing marketing-grade narratives, one file per marketing release): - 8.0.0.md — VCell 8.0.0 SpringSaLaD GA, with Michalski & Loew (2016) citation; covers SpringSaLaD GA, Structural Sites, multi-run, batch-results visualization, Plot Options, Quick Run guardrails, admincli report toolkit, BNGL preprocessor - 7.7.md — index file pointing at the three named 7.7 epoch files (rendered on vcell.org as three separate accordion entries) - 7.7-initial-release.md — Sept 2024 launch (Java-native CLI plotting, initial Quarkus REST, OIDC/Auth0, HDF5 modernization, native pyvcell foundations, first-pass SpringSaLaD UI redesign) - 7.7-feature-update.md — Feb 2026 (the big bundle: complete Quarkus REST endpoints, install-without-admin-privileges, SpringSaLaD multi-run + SLURM array, parameter estimation REST migration, generalized stochastic of non-mass-action reactions, Pathway Commons upgrade) - 7.7-stability-update.md — Apr-May 2026 (JMS failover watchdog, OOM exit handler, DNS negative-cache fix, charset-aware Oracle CLOB reads, unit-formatting thread-safety, NPE fixes in math mapping, /loki-query tooling) SpringSaLaD is consistently described as a beta-test-feature-flag release throughout the 7.7 line (on by default in non-production deployments, off by default on the release site), with the flag removed in 8.0.0 where SpringSaLaD becomes enabled across all deployments. The 7.7-line marketing narrative is restructured around three named release events corresponding to actual prod rollouts (per vcell-fluxcd/kustomize/overlays/prod history), rather than treating the 20-month line as a single release event. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jcschaff
added a commit
that referenced
this pull request
May 21, 2026
Per docs/RELEASING.md, the tag should point at a tree where CHANGELOG.md reflects the release. [8.0.0.03] covers the queued BNGL preprocessor change (#1698) and is the release that accompanies the SpringSaLaD GA marketing event in release-notes/major/8.0.0.md. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
BioNetGen BNGL import enhancement
replace ~ with ~s
Closes #1697