🗂 VCell solver refactoring / modernization

[jcschaff]

🗂 Master issue — VCell solver refactoring / modernization · on the VCell board.

Why — The solvers historically lived in the monolithic vcell-solvers. Extracting and modernizing each makes them independently buildable, portable, and usable both as standalone executables and from Python — and lets VCell adopt them in place of the legacy builds.

What — Extract each solver from the legacy vcell-solvers monorepo and modernize it.

Per-solver checklist: native execs (L/M/W) · Python wheels (L/M/W) · Docker container · libvcell input generator · native wired into the VCell client (vcell/pom.xml) · Docker wired into the VCell server (vcell-fluxcd/.../submit.env).

Per-solver progress grid (2026-07-07) — ✅ done · ❌ missing · ❓ unverified · ➖ n/a

Solver repo (latest)	nat·L	nat·M	nat·W	whl·L	whl·M	whl·W	Docker	lib	cli	srv
vcell-fvsolver (0.10.5)	✅	✅	✅	❓	❓	❓	✅	✅	❌	✅
vcell-ode (0.9.0)	✅	✅	✅	✅	✅	✅	✅	❌	❌	❌
vcell-stochastic (ci)	✅	✅	✅	❌	❌	❌	❌	❌	❌	❌
vcell-mbsolver (v1.0.3)	✅	✅	❌	✅	✅	❓	❌	✅	❌	❌
vcell-nfsim (v0.1.0)	❓	❓	❓	✅	✅	✅	❌	❌	❌	❌
cam-center/LangevinNoVis01 (1.4.7)	✅	✅	✅	➖	➖	➖	✅	➖	✅	✅

nat=native exec, whl=Python wheel (L/M/W=Linux/macOS/Windows); Docker=own/injected container; lib=libvcell input generator; cli=native in VCell client; srv=container in VCell server.

Server containers now: vcell-fvsolver:0.9.7 (dedicated) · vcell-solvers:v0.8.2 (ode/stochastic/mbsolver/nfsim) · vcell-batch:8.0.0.06 (Langevin native Linux exe injected in). Client natives all from the legacy vcell-solvers bundle (v0.0.44-dev4 mac/linux, v0.0.40 win) — except Langevin (1.4.7, its own, used by client + server).

Notes — libvcell supports fvsolver (vcml_to_finite_volume_input) + mbsolver (vcml_to_moving_boundary_input) via GraalVM native; nfsim publishes multi-platform wheels; ode advertises wheels + has a Dockerfile (server not cut over); mbsolver native is Linux/macOS only. Integration gap dominates: only fvsolver (server) and Langevin (client + server + Docker) are wired into VCell; the rest still run legacy.

Not in scope (Java solvers): RungeKutta{2,4,Fehlberg}, ForwardEuler, AdamsMoulton — Java solvers in the vcell repo, shipped in vcell-batch; never in the monorepo.

Scope also includes libvcell (legacy Java → native Python lib via GraalVM; the finite-volume + moving-boundary input generators; instrumental to vcell standalone + each solver's Python bindings). (vcell-fenics is its own initiative.)

Coordination inbox: comment with progress/handoffs (what moved + PR/commit links); the lead posts a periodic status summary.