pyproject.toml

[project]
name = "moleculekit"
description = "A molecule reading/writing and manipulation package."
authors = [{ name = "Stefan Doerr", email = "s.doerr@acellera.com" }]
readme = "README.md"
# Floor is 3.11 because the extensions are built against the CPython Stable ABI and
# Py_buffer, which our memoryviews need, only entered the limited API in 3.11.
requires-python = ">=3.11"
dynamic = ["version"]
classifiers = [
  "Programming Language :: Python :: 3",
  "Operating System :: POSIX :: Linux",
]
dependencies = [
  "numpy>=1.23.5",
  "pandas>=1.1.2",
  "networkx",
  "tqdm",
  "msgpack",
  "requests",
  "matplotlib",
  "rdkit>=2020.09.5",
  "mdtraj",
  "acellera-propka",  # Remove once they make a new release
  # "openbabel>=3.1.1",
  # post2 is the floor because earlier releases depend on upstream propka, which
  # installs over acellera-propka's files. Whichever lands last wins, and when
  # upstream wins the Python 3.14 annotations fix is silently lost.
  "acellera-pdb2pqr>=3.7.1.post2",
  "biopython",
]

[project.urls]
"Homepage" = "https://github.com/Acellera/moleculekit"
"Bug Tracker" = "https://github.com/Acellera/moleculekit/issues"

[tool.setuptools.packages.find]
include = ["moleculekit*"]

[tool.setuptools.package-data]
"moleculekit.share" = ["**/*"]
"moleculekit.viewer.molstar" = ["static/**/*"]

[tool.setuptools.exclude-package-data]
"*" = ["*.c", "*.cpp", "*.cxx", "*.h", "*.pyx", "*.pxd", ".gitignore"]

[tool.setuptools_scm]

[build-system]
requires = [
  "setuptools",
  "numpy>=2.0.0rc1",
  "Cython>=0.29.21",
  "setuptools-scm>=8",
]
build-backend = "setuptools.build_meta"

[project.optional-dependencies]
openmm = [
  "nvidia-cuda-cupti-cu12<12.7",
  "nvidia-cuda-nvcc-cu12<12.7",
  "nvidia-cuda-nvrtc-cu12<12.7",
  "nvidia-cuda-runtime-cu12<12.7",
  "nvidia-nvjitlink-cu12<12.7",
  "openmm[cuda12]>=8.5.0",
]
notebook = ["molviewspec"]

[dependency-groups]
test = [
  "pytest>=8.4.2",
  "pytest-xdist",
  "jupytext",
  "nbclient",
  "ipykernel",
  "acellera-docs-theme @ git+https://github.com/Acellera/acellera-docs-theme.git",
]
docs = [
  "acellera-docs-theme @ git+https://github.com/Acellera/acellera-docs-theme.git",
  "sphinx",
  "myst-nb",
  "sphinx-design",
  "sphinx-copybutton",
  "sphinxcontrib-mermaid",
  "sphinx-autodoc-typehints",
  "sphinx-argparse",
  "sphinx-notfound-page",
  "sphinx-sitemap",
  "openmm>=8.5.0",
]
dev = [{ include-group = "test" }, "ipython>=8.18.1"]

[tool.uv]
# pdb2pqr 3.6.x pins docutils<0.18 but Sphinx needs newer; pdb2pqr works fine at runtime
# with current docutils, so override the constraint.
override-dependencies = ["docutils>=0.20"]

[tool.pytest.ini_options]
testpaths = ["tests"]


[tool.cibuildwheel]
# The extensions target the Stable ABI, so cibuildwheel compiles cp311 once and
# then reuses that cp311-abi3 wheel for every later version rather than rebuilding
# ("Found previously built wheel ... Skipping build step"), leaving a single wheel
# per platform in the output. It still runs test-command against the reused wheel
# on each version, and abi3audit over the result. requires-python already sets the
# floor, so no explicit build selector is needed here.
# Disable PyPy builds due to our Cython code not being compatible with it yet
# Disable Windows 32 builds, Musllinux builds due to rdkit not building on it
# Disable i686, ppc64le, s390x, universal2, armv7l due to numpy not building on them
skip = [
  # rdkit ships no cp315 wheel yet, so the test install fails. Remove when it does.
  "cp315-*",
  # Free-threaded builds cannot use the Stable ABI: setuptools rejects
  # py_limited_api when Py_GIL_DISABLED is set, so these fail outright.
  # See https://github.com/python/cpython/issues/111506
  "cp3*t-*",
  "pp*",
  "*win32",
  "*armv7l",
  "*_i686",
  "*_ppc64le",
  "*_s390x",
  "*_universal2",
  "*musllinux_x86_64",
  "*musllinux_aarch64",
]
test-requires = ["pytest", "pytest-xdist"]
test-command = "pytest -n auto {project}/tests"
# Only one binary is produced, so testing the ends of the range is what matters:
# 3.11 is the version actually compiled and 3.14 the newest, and a failure confined
# to an interior version while both ends pass is not a Stable ABI failure mode.
# Interior versions are covered by test.yml, which builds from source on 3.11 to
# 3.14 across all three OSes on every non-tag push. Each version tested here costs
# four more full suite runs on every release.
test-skip = "cp312-* cp313-*"
manylinux-x86_64-image = "manylinux_2_28"
manylinux-aarch64-image = "manylinux_2_28"
# build-frontend = "build[uv]"

[tool.cibuildwheel.linux]
# The manylinux CPython compiles extensions with -g, so the .so files ship with
# DWARF debug symbols that inflate the wheel ~2.5x (e.g. _ckdtree.so 8.8MB -> 0.8MB).
# Strip them during the repair step.
repair-wheel-command = "auditwheel repair --strip -w {dest_dir} {wheel}"

# [tool.uv.sources]
# acellera-pdb2pqr = { path = "../pdb2pqr", editable = true }