VCell Moving Boundary Solver

A C++ solver library for moving-boundary problems in biological systems. A single build produces three artifacts:

Artifact	Description
`MovingBoundarySolver`	Standalone command-line binary
`libMovingBoundaryLib`	Linkable static (or shared) library
`vcellmbsolver_py`	Python extension module (pybind11)

Prerequisites

All platforms

Dependency	Notes
CMake ≥ 3.13	https://cmake.org/download/
C++14 compiler	GCC 7+, Clang 6+, MSVC 2017+
HDF5 (C + C++)	See platform sections below
Python 3 + headers	Python 3.8+ recommended
pybind11	`pip install pybind11` or system package
All former VCell monorepo dependencies (FronTier, ExpressionParser,
vcommons) are bundled in this repo and built automatically — no external
paths required.

Building

Ubuntu / Debian

# System dependencies
sudo apt-get install cmake libhdf5-dev python3-dev python3-pip
pip3 install pybind11

# Configure (substitute your actual library paths)
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release

# Build everything
cmake --build build --parallel

Output files land in build/bin/:

build/bin/
  MovingBoundarySolver        # binary
  libMovingBoundaryLib.a      # static library
  vcellmbsolver_py.cpython-*.so  # Python module

macOS

# Dependencies via Homebrew
brew install cmake hdf5 python pybind11

# Configure
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release

# Build everything
cmake --build build --parallel

For Apple Silicon the build system detects the architecture automatically and sets -DCMAKE_OSX_ARCHITECTURES=arm64. On Intel Macs it sets x86_64.

Windows (Visual Studio)

Install prerequisites:

CMake
Python 3 (check "Add to PATH")
HDF5: use the official HDF Group Windows installer or vcpkg (vcpkg install hdf5)
pybind11: pip install pybind11 or vcpkg (vcpkg install pybind11)

cmake -S . -B build

cmake --build build --config Release --parallel

If using vcpkg, add -DCMAKE_TOOLCHAIN_FILE=C:\vcpkg\scripts\buildsystems\vcpkg.cmake to the configure step so CMake finds the vcpkg-installed packages automatically.

Output files land in build\bin\Release\.

Build options

CMake variable	Default	Description
`CMAKE_BUILD_TYPE`	`Release`	`Release`, `Debug`, `RelWithDebInfo`, `MinSizeRel`
`BUILD_SHARED_LIBS`	`OFF`	Build `libMovingBoundaryLib` as a shared library instead of static
`BUILD_TESTING`	`ON`	Also build the `TestMovingBoundary` test executable
`VARIABLE_SPECIES_STORAGE`	`OFF`	Enable dynamic species storage (`-DMB_VARY_MASS`)

Example — debug build, shared library, no tests:

cmake -S . -B build \
  -DCMAKE_BUILD_TYPE=Debug \
  -DBUILD_SHARED_LIBS=ON \
  -DBUILD_TESTING=OFF \
cmake --build build --parallel

Running the tests

Tests are built by default (BUILD_TESTING=ON). After a successful build:

cd build
ctest --output-on-failure

Test suites

All three suites run automatically when you invoke ctest. The Python tests require pytest (pip install pytest).

Suite	Name in ctest	Framework
Moving boundary unit tests (~150 cases)	`TestMovingBoundary.*`	Google Test
Expression parser smoke test	`ExpressionParserTest`	custom main
Python wrapper tests	`PyVcellMbSolver`	pytest

Python test prerequisites

No manual setup required. CMake creates an isolated virtual environment in build/python_venv/ at configure time and installs pytest into it automatically. The venv is recreated on every cmake -S . -B build run.

The Python tests import vcellmbsolver_py (the compiled extension) and vcellmbsolver (the pure-Python wrapper in python/). ctest sets PYTHONPATH so both are importable from the build tree without installation.

Useful ctest options

# Run in parallel
ctest --output-on-failure -j$(nproc)

# Run only tests whose name matches a pattern
ctest --output-on-failure -R "algo"
ctest --output-on-failure -R "ExpressionParser"
ctest --output-on-failure -R "PyVcellMbSolver"

# List all registered tests without running them
ctest -N

# Show full output even for passing tests
ctest -V

Running the Python tests directly

After configuring, the venv already has pytest installed. Run the suite directly using the venv's Python:

PYTHONPATH=build/bin:python build/python_venv/bin/python -m pytest python/tests -v

On Windows, substitute build\python_venv\Scripts\python.exe.

Skipping tests

Pass -DBUILD_TESTING=OFF at configure time to skip building and registering the test executables entirely (this also disables the Python tests):

cmake -S . -B build -DBUILD_TESTING=OFF

Using the binary

./build/bin/MovingBoundarySolver <input.xml> <output.h5>

The input file format is described in metadata/MovingBoundarySolverInputFile.docx and validated by Solver/MovingBoundarySetup.xsd.

Linking the library

Add to your project's CMakeLists.txt:

find_library(MB_LIB MovingBoundaryLib HINTS /path/to/vcell-mbsolver/build/bin)
find_path(MB_INCLUDE MovingBoundaryParabolicProblem.h
    HINTS /path/to/vcell-mbsolver/Solver/include)

target_link_libraries(my_target PRIVATE ${MB_LIB})
target_include_directories(my_target PRIVATE ${MB_INCLUDE})

Or install the project first and use the installed headers under <prefix>/include/vcell-mbsolver/.

Using the Python module

The bindings are shipped as the pyvcell_mbsolver package: the compiled extension is the private submodule pyvcell_mbsolver._core, and the high-level wrapper (MovingBoundarySolver, observer base classes) is the package itself.

import sys
sys.path.insert(0, "/path/to/vcell-mbsolver/build/bin")

import pyvcell_mbsolver
from pyvcell_mbsolver import MovingBoundarySolver   # high-level wrapper
from pyvcell_mbsolver import _core                  # low-level C++ API
# See python/pyvcellmbsolver.cpp for the exposed _core API

After cmake --install build --prefix /usr/local, the package is installed to the active Python's site-packages and importable directly:

import pyvcell_mbsolver

Python package & wheels

The repository also ships a PEP 517 build configuration (pyproject.toml, using the scikit-build-core backend) that drives the same CMake build to produce an installable Python wheel. The wheel contains only the pyvcell_mbsolver package (the _core extension and its pure-Python wrapper) — not the C++ library, CLI binary, or headers.

Install from a downloaded wheel

CI builds redistributable wheels for Linux (x86_64 + arm64) and macOS (x86_64 + arm64, macOS 15+) and uploads them as workflow artifacts (see the Wheels GitHub Actions workflow). Download the wheel for your platform/Python version and:

pip install pyvcell_mbsolver-<version>-<tags>.whl
python -c "import pyvcell_mbsolver; from pyvcell_mbsolver import _core; print('ok')"

The wheels are self-contained: the shared HDF5 libraries are vendored in by the wheel-repair step (auditwheel / delocate), so no system HDF5 install is required to use a wheel.

Windows is not currently supported. The bundled FronTier library is Unix/GCC code that does not compile under MSVC (its POINT/boolean types clash with the Windows SDK and it relies on GCC anonymous-struct extensions). Windows users can build/run under WSL using the Linux wheels.

Build a wheel locally

Building from source still needs the native toolchain and dependencies from the Prerequisites section (CMake, a C++14 compiler, HDF5, Boost):

pip install build
python -m build --wheel          # writes dist/vcellmbsolver-*.whl
pip install dist/vcellmbsolver-*.whl

pip install . works too. Wheel builds set BUILD_TESTING=OFF and OPTION_TARGET_MESSAGING=OFF automatically (see [tool.scikit-build] in pyproject.toml).

Publishing to PyPI

The Wheels workflow has a publish job that uploads the built wheels and sdist to PyPI via trusted publishing (OIDC — no stored API token). It runs only on v* tag pushes and stays dormant until a one-time setup is done on PyPI:

Register the project on PyPI (claim the pyvcell_mbsolver name).
Under the project's Publishing settings, add a trusted publisher:
- Owner: virtualcell, Repository: vcell-mbsolver
- Workflow: wheels.yml, Environment: pypi
Create the pypi environment in the repo settings (optionally with reviewers/branch protection).

Once configured, pushing a vX.Y.Z tag builds all wheels and publishes them. Until then, normal pushes and PRs simply produce downloadable wheel artifacts.

Dry run on TestPyPI first (recommended)

The workflow also has a publish-testpypi job to rehearse the release against TestPyPI before touching real PyPI. It runs only when the workflow is manually dispatched with the testpypi flag, and needs its own one-time setup mirroring the above:

Create a TestPyPI account (separate from PyPI; 2FA required).
At https://test.pypi.org/manage/account/publishing/, add a pending publisher:
- PyPI Project Name: pyvcell_mbsolver
- Owner: virtualcell, Repository: vcell-mbsolver
- Workflow: wheels.yml, Environment: testpypi
Create a testpypi environment in the repo settings.

Then trigger the dry run (no tag needed):

gh workflow run wheels.yml -f testpypi=true

(or Actions → Wheels → Run workflow, check the box). It builds all wheels + sdist and uploads them to TestPyPI; skip-existing keeps repeat runs of the same version from failing. Verify at https://test.pypi.org/project/pyvcell-mbsolver/, then do the real release by tagging vX.Y.Z.

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pyvcell-mbsolver 1.0.1

VCell Moving Boundary Solver

Prerequisites

All platforms

Building

Ubuntu / Debian

macOS

Windows (Visual Studio)

Build options

Running the tests

Test suites

Python test prerequisites

Useful ctest options

Running the Python tests directly

Skipping tests

Using the binary

Linking the library

Using the Python module

Python package & wheels

Install from a downloaded wheel

Build a wheel locally

Publishing to PyPI

Dry run on TestPyPI first (recommended)

Project links

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1 maintainer

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