vcell-fvsolver

Virtual Cell Finite Volume solver virtualcell/vcell-fvsolver is a reaction-diffusion-advection PDE solver for computational cell biology. This solver is used within the Virtual Cell modeling and simulation application virtualcell/vcell and as a component in the Virtual Cell Python API virtualcell/pyvcell (coming soon).

The Virtual Cell Project

The Virtual Cell is a modeling and simulation framework for computational biology. For details see http://vcell.org and http://github.com/virtualcell.

Releases, Docker image and SIF

Each release vX.Y.Z carries linux64.tgz, linux64arm.tgz, mac64.tgz (universal), win64.zip and SHA256SUMS, each with FiniteVolume_x64 and smoldyn_x64 at the archive root. The solvers are also published as the multi-arch image ghcr.io/virtualcell/vcell-fvsolver:X.Y.Z and, for VCell's cluster, the SIF oras://ghcr.io/virtualcell/vcell-fvsolver_singularity:X.Y.Z:

docker run --rm ghcr.io/virtualcell/vcell-fvsolver:latest            # version and executables
docker run --rm -v "$PWD:/simdata" ghcr.io/virtualcell/vcell-fvsolver:latest \
    FiniteVolume_x64 /simdata/SimID_1_0_.fvinput

See SOLVER-RELEASE.md for the release contract: asset layout, the entrypoint, messaging (-tid), and the CI smoke test. Builds: .github/workflows/cd.yml (macOS, Windows, wheels) and .github/workflows/container.yml (Linux archives, image and SIF, from the top-level Dockerfile).

Python API - pyvcell_fvsolver

The Python API for the VCell Finite Volume solver is a low level wrapper which accepts VCell solver input files (.fvinput, .vcg) and generates the output files (.log, .zip, .mesh, .meshmetrics, .hdf5). The .functions file is not used by the solver, but is helpful for interpreting the results in the context of the original model.

This package is intended to be used by the Virtual Cell Python API virtualcell/pyvcell (coming soon).

pyvcell_fvsolver requires Python >= 3.12. The extension is built with nanobind against the Python stable ABI, so each release ships one cp312-abi3 wheel per platform (macOS arm64 and x86_64, manylinux_2_28 x86_64 and aarch64, Windows x86_64) that installs on CPython 3.12 and every later version. CI tests each wheel on 3.12 and 3.14 and checks it with abi3audit.

Changes

• Unreleased: the Python binding moved from pybind11 to nanobind with the stable ABI (abi3). Python >= 3.12 is required (3.10 and 3.11 are dropped); the 25 per-version wheels become one cp312-abi3 wheel per platform. The Python API (solve, version, __version__) and its exceptions are unchanged. The release archives (linux64.tgz, linux64arm.tgz, mac64.tgz, win64.zip) are unchanged.