docs(release): 8.1.6.01 release notes - #2074
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SpringSaLaD gets user documentation, and three things that told the user the wrong story get fixed. The headline is the documentation, because the gap was odd: VCell has been able to build and run SpringSaLaD models for over a year - the application, the Langevin solver, the molecular structure editor, the 3D trajectory viewer - and the help said nothing about any of it. Six pages now do, including the two errors a modeller meets before they meet the concept: what "the forward rate Kf is too large" means, and the fact that a transition condition is called something different here than in the standalone program. The three fixes are grouped in the notes because they share a shape - each one reported something that was not what had happened: - the progress dialog sat at zero while the server was computing progress and sending it, because the listener was registered after the call that waits; - a failed or cancelled time-series retrieval surfaced as an unrelated NullPointerException in a plotting step, the real cause gone; - a species named PROTEINA_A (with the accent) was accepted and saved, and the application then refused to generate math with an error naming an expression and nothing pointing at the species. The last is written under Changed rather than Fixed, and the API note says why: a name that was accepted before is now rejected at creation. Models already saved with one still open, and report the name as a problem instead. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019HAnpFxkzf9LmxBayDSANf
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Release-cut docs for 8.1.6.01, per
docs/RELEASING.md— landed before tagging so thetag points at a self-describing tree.
Covers everything on master since
8.1.5.01: #2059, #2061, #2064, #2065, #2066, #2067,#2073.
Highlight: SpringSaLaD user documentation, which did not exist. Six help pages,
including explanations of the two errors a modeller meets before they meet the concept —
"the forward rate Kf is too large", and the transition condition that is called something
different in VCell than in the standalone program.
Three fixes, grouped because they share a shape — each reported something other than
what happened: a progress dialog that sat at zero while progress was being computed and
sent (#2066); a failed or cancelled time-series retrieval that surfaced as an unrelated
NullPointerExceptionin a plotting step (#2065); and a species namedPROTEÍNA_Athatwas accepted, saved, and then failed math generation with an error naming an expression and
nothing pointing at the species (#2064).
That last one is under Changed, not Fixed, and the "Notes for API consumers" section
says why: a name that used to be accepted is now rejected at creation. Models already saved
with one still open — refusing them would take away the only way to rename the species —
and report the name as a problem instead.
Docs only; no code changes.
🤖 Generated with Claude Code
https://claude.ai/code/session_019HAnpFxkzf9LmxBayDSANf