Add moving-boundary solver support#53
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Author and run VCell moving-boundary simulations from pyvcell via libvcell (>= 0.0.16) and the pyvcell-mbsolver package. Authoring API (models_app): - Application.add_moving_boundary_sim(): a simulation with Solver="MovingB" and MovingBoundarySolverOptions. - Application.set_moving_boundary_front(): the prescribed front velocity (FrontVelocity / SurfaceKinematics). - Simulation.solver / .moving_boundary_options / .is_moving_boundary. Writer/reader round-trip the Solver attribute and MovingBoundarySolverOptions. Runtime: - vc.simulate_moving_boundary(biomodel, sim) drives the pipeline: to_vcml_str (round-trip 1 -> VCell auto-generates SpatialObjects) -> inject SurfaceKinematics front velocity -> vcml_to_vcml (round-trip 2 -> moving-boundary math) -> vcml_to_moving_boundary_input -> run pyvcell_mbsolver. - Output is collected via solver observers (no HDF5 file is written by the binding) into MovingBoundaryResult: per output time, the moving front polygon plus per-element (x, y, grid_i, grid_j, concentration) on the moving mesh, subsampled to output_time_step. Packaging: new `mb` extra (pyvcell-mbsolver, gated to Python < 3.14), added to `all`; lazy imports with a clear "install pyvcell[mb]" hint. The `native` extra is held at >=0.0.15.3 until libvcell 0.0.16 is published to PyPI, so a release should wait for that even though the PR can merge. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
pyvcell-mbsolver 1.0.1 ships a py.typed marker, so the package now type-checks natively. Bump the `mb` extra pin to >=1.0.1 and remove the workarounds that covered the untyped 1.0.0 wheel: - the [[tool.mypy.overrides]] for pyvcell_mbsolver - the `# type: ignore[misc]` on class _Collector(mb.SimulationObserver) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Both moving-boundary dependencies now ship Python 3.14-compatible wheels: - libvcell 0.0.17 publishes universal py3-none-<platform> wheels (installable on every Python including 3.14) and includes moving-boundary support, so `native` requires >=0.0.17 and the code calls vcml_to_moving_boundary_input directly. - pyvcell-mbsolver 1.0.3 adds cp314 wheels and _core.pyi stubs, so the `mb` extra drops its temporary `python_version < '3.14'` gate and requires >=1.0.3. With both packages present and typed on all CI Python versions, the temporary mypy workarounds (pyvcell_mbsolver ignore_missing_imports + disallow_subclassing_any) are removed; mypy passes natively. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Author and run VCell moving-boundary simulations from pyvcell, via
libvcell(≥ 0.0.16) and thepyvcell-mbsolverpackage.Authoring API (
models_app)Application.add_moving_boundary_sim(...)— a simulation withSolver="MovingB"andMovingBoundarySolverOptions.Application.set_moving_boundary_front(velocity_x, velocity_y, ...)— the prescribed front velocity (FrontVelocity→ aSurfaceKinematicsprocess).Simulation.solver/.moving_boundary_options/.is_moving_boundary.The writer and (lenient) reader round-trip the
Solverattribute and theMovingBoundarySolverOptionsblock.Runtime
vc.simulate_moving_boundary(biomodel, sim)drives the pipeline:to_vcml_str(round-trip 1 → VCell computes geometry regions and auto-generates the canonicalSpatialObjects)SurfaceVelocity+ inject theSurfaceKinematicsfront velocityvcml_to_vcml(round-trip 2 → moving-boundary math: aMembraneSubDomainwith a velocity)vcml_to_moving_boundary_input→MovingBoundarySetupXML → runpyvcell_mbsolverMovingBoundaryResult: per output time, the moving-front polygon plus per-element(x, y, grid_i, grid_j, concentration)on the moving mesh — mirroring vcell-core's element/species model rather than the fixed-grid zarrResult. Snapshots are subsampled tooutput_time_step.Packaging
mboptional extra (pyvcell-mbsolver, gated to Python < 3.14 since there is no cp314 wheel), added toall.install pyvcell[mb]hint; validation errors surface without the solver extras installed.pyvcell_mbsolvermypy override + one# type: ignore[misc]cover the current 1.0.0 wheel which lackspy.typed; both can be removed once a typed wheel is published.Authoring moving-boundary input requires libvcell ≥ 0.0.16, which is not yet published (latest on PyPI is 0.0.15.4). The
nativeextra is intentionally held at>=0.0.15.3and the requirement is documented. The PR can merge, but a release should wait for 0.0.16.Verification
make checkclean:uv lock --check, ruff, ruff-format, mypy (strict), deptry.pytest: 111 passed, 11 skipped, including a gated end-to-end moving-boundary solve (a circular front undersin(t)/cos(t): 11 output frames, moving front, per-element concentrations). The end-to-end test skips automatically whenlibvcell< 0.0.16 orpyvcell-mbsolveris unavailable.🤖 Generated with Claude Code