vcell-mbsolver/pyproject.toml at main · virtualcell/vcell-mbsolver · GitHub

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[build-system]
requires = ["scikit-build-core>=0.8", "pybind11>=2.10"]
build-backend = "scikit_build_core.build"

[project]
name = "pyvcell_mbsolver"
description = "Python bindings for the VCell moving-boundary parabolic PDE solver"
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.10"
dynamic = ["version"]
classifiers = [
    "Programming Language :: C++",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
]

[project.urls]
Homepage = "https://github.com/virtualcell/vcell-mbsolver"
Repository = "https://github.com/virtualcell/vcell-mbsolver"

# ---------------------------------------------------------------------------
# scikit-build-core: drive the existing CMake build to produce the wheel.
#
# Only the `vcellmbsolver_py` extension and the pure-Python wrapper are placed
# in the wheel (the "python" install component); the static C++ library, the
# CLI binary, and the C++ headers are deliberately excluded. Tests and the
# job-status messaging (CURL) are turned off for wheel builds.
# ---------------------------------------------------------------------------
[tool.scikit-build]
cmake.version = ">=3.13"
build.targets = ["_core"]
install.components = ["python"]
wheel.packages = []          # the pyvcell_mbsolver package is installed by CMake, not auto-copied
wheel.license-files = ["LICENSE"]
sdist.include = ["CMakeLists.txt"]

[tool.scikit-build.cmake.define]
BUILD_TESTING = "OFF"
OPTION_TARGET_MESSAGING = "OFF"

# importlib import-mode prevents the source tree from shadowing the built/
# installed pyvcell_mbsolver package when running pytest directly.
[tool.pytest.ini_options]
addopts = ["--import-mode=importlib"]
testpaths = ["python/tests"]

# Keep the wheel version in lock-step with the CMake project() version.
[tool.scikit-build.metadata.version]
provider = "scikit_build_core.metadata.regex"
input = "CMakeLists.txt"
regex = '''project\(VCellMovingBoundary VERSION (?P<value>[0-9]+\.[0-9]+\.[0-9]+)'''

# ---------------------------------------------------------------------------
# cibuildwheel: build redistributable, repaired wheels across platforms.
# Native dependencies (HDF5, Boost) are installed per-platform in before-all.
# Wheel repair (auditwheel/delocate/delvewheel) vendors the shared HDF5 libs
# into the wheel so it is self-contained.
# ---------------------------------------------------------------------------
[tool.cibuildwheel]
build = "cp310-* cp311-* cp312-* cp313-* cp314-*"
skip = "*-musllinux_* *_i686 *-win32"
build-frontend = "build"
test-command = "python -c \"import pyvcell_mbsolver; from pyvcell_mbsolver import _core; print('import OK')\""

[tool.cibuildwheel.linux]
manylinux-x86_64-image = "manylinux_2_28"
manylinux-aarch64-image = "manylinux_2_28"
before-all = [
    "dnf install -y epel-release",
    "dnf install -y hdf5-devel boost-devel",
]

[tool.cibuildwheel.macos]
before-all = "brew install hdf5 boost"
# Homebrew bottles target the runner's macOS, so the vendored HDF5 libs require
# a recent minimum; matching it here keeps delocate's wheel repair happy. (This
# means the macOS wheels require macOS 15+, as with vcell-fvsolver.)
environment = { MACOSX_DEPLOYMENT_TARGET = "15.0" }

# Windows wheels: vcpkg provides HDF5/Boost/CURL via the x64-windows triplet.
# The "Install Windows vcpkg dependencies" step in wheels.yml runs
# `vcpkg install --triplet x64-windows` before cibuildwheel, and the
# CMAKE_ARGS below wire the toolchain file and explicit library hints into the
# scikit-build-core configure step. OPTION_TARGET_MESSAGING stays OFF via
# [tool.scikit-build.cmake.define] above.
#
# VCPKG_ROOT_FWD / GITHUB_WORKSPACE_FWD (set via GITHUB_ENV in the "Install
# Windows vcpkg dependencies" step) are forward-slash copies of
# VCPKG_INSTALLATION_ROOT / GITHUB_WORKSPACE. Using the backslash originals
# here would break the build: cibuildwheel expands $VAR references with a
# bash-syntax evaluator, and scikit-build-core then parses CMAKE_ARGS with
# Python's POSIX-mode shlex.split(), which silently strips backslashes out of
# Windows paths (e.g. "D:\a\repo" becomes "D:arepo"), corrupting HDF5_ROOT and
# friends so vcpkg/HDF5/Boost/CURL can no longer be found.
#
# Unlike Linux (auditwheel) and macOS (delocate), cibuildwheel's default
# repair-wheel-command on Windows is empty, so the wheel is left unrepaired
# by default: the built _core extension dynamically loads hdf5.dll /
# hdf5_cpp.dll / z.dll from vcpkg_installed/x64-windows/bin, which is not
# on PATH in the clean venv cibuildwheel uses to test the wheel, causing
# "ImportError: DLL load failed while importing _core". Explicitly repair
# with delvewheel, pointing --add-path at the vcpkg bin directory so it can
# find and vendor those DLLs into the wheel.
# %GITHUB_WORKSPACE_FWD% is set by the "Install Windows vcpkg dependencies"
# step in wheels.yml (see note above); this repair command is GitHub
# Actions-specific and assumes that step has already populated
# vcpkg_installed/x64-windows/bin. Unlike the CMAKE_ARGS below (expanded by
# cibuildwheel's own bash-syntax environment evaluator), repair-wheel-command
# is run via `shell=True`, which on Windows invokes cmd.exe: it only expands
# %VAR% references, not $VAR, so the cmd.exe syntax is required here.
[tool.cibuildwheel.windows]
before-build = "pip install delvewheel"
repair-wheel-command = "delvewheel repair --add-path %GITHUB_WORKSPACE_FWD%/vcpkg_installed/x64-windows/bin -w {dest_dir} {wheel}"

[tool.cibuildwheel.windows.environment]
CMAKE_ARGS = """\
    -DCMAKE_TOOLCHAIN_FILE=$VCPKG_ROOT_FWD/scripts/buildsystems/vcpkg.cmake \
    -DVCPKG_TARGET_TRIPLET=x64-windows \
    -DVCPKG_INSTALLED_DIR=$GITHUB_WORKSPACE_FWD/vcpkg_installed \
    -DVCPKG_MANIFEST_INSTALL=OFF \
    -DCMAKE_PREFIX_PATH=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows \
    -DBOOST_ROOT=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows \
    -DBOOST_INCLUDEDIR=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows/include \
    -DHDF5_ROOT=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows \
    -DHDF5_INCLUDE_DIR=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows/include \
    -DHDF5_CXX_INCLUDE_DIR=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows/include \
    -DHDF5_hdf5_cpp_LIBRARY=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows/lib/hdf5_cpp.lib \
    -DHDF5_hdf5_LIBRARY=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows/lib/hdf5.lib \
    -DCURL_ROOT=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows \
    -DCURL_INCLUDE_DIR=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows/include \
    -DCURL_LIBRARY=$GITHUB_WORKSPACE_FWD/vcpkg_installed/x64-windows/lib/libcurl.lib"""