pyproject.toml

[project]
name = "acellera-htmd"
description = "High throughput molecular dynamics (HTMD)"
authors = [{ name = "Acellera", email = "info@acellera.com" }]
readme = "README.md"
license = "LicenseRef-Acellera-Not-for-Profit"
license-files = ["LICENSE"]
requires-python = ">=3.11"
dynamic = ["version"]
classifiers = [
  "Programming Language :: Python :: 3",
  "Operating System :: POSIX :: Linux",
]
dependencies = [
  "ambertools-unofficial>=26.0.0; sys_platform != 'win32' and sys_platform != 'emscripten'",
  "deeptime>=0.4.5; sys_platform != 'emscripten'",
  "h5py>=3.15.1; sys_platform != 'emscripten'",
  "joblib>=1.5.3",
  "jobqueues>=1.0.13; sys_platform != 'emscripten'",
  "matplotlib>=3.10.8",
  "moleculekit>=1.16.11",
  "natsort>=8.4.0",
  "networkx>=3.4.2",
  "numpy>=2.2.6",
  "pandas>=2.3.3",
  "parmed>=4.3.1",
  "pint>=0.24.4",
  "protocolinterface>=0.4.7",
  "scikit-learn>=1.7.2",
  "scipy>=1.15.3",
  "tqdm>=4.67.3",
]

[project.optional-dependencies]
interactive = [
  "ipython",
  "jupyter_console",
  "notebook",
  "ipywidgets>=8.1.8",
  "nglview>=4.0.1",
]
# pymol-open-source publishes wheels only (no sdist) and tags them cp39-cp313,
# so it cannot be installed or built on 3.14+. Marked rather than dropped: the
# extra stays installable everywhere and simply contributes nothing on 3.14+.
pymol = ["pymol-open-source; python_version < '3.14'"]
openff = [
  "openmm",
  "acellera-openmmforcefields",
  "acellera-openff-interchange",
  "acellera-openff-toolkit>=0.18.0.post2",
  "acellera-openff-units>=0.3.2.post3",
  "acellera-openff-utilities>=0.1.16.post1",
  "acellera-openforcefields",
  "cachetools>=7.1.2",
  "pydantic>=2.13.4",
  "xmltodict>=1.0.4",
  # openff-toolkit's rdkit_wrapper imports `constraint` (E/Z stereo CSP) but
  # declares no Python deps of its own (conda-first upstream), so we supply it.
  # python-constraint 1.4.0's only artifact is a non-PEP 625 .tar.bz2, which
  # uv >= 0.12 refuses; python-constraint2 is the maintained fork of the same
  # module.
  "python-constraint2>=2.6",
  "lxml>=5.0.0",
  "acellera-openff-amber-ff-ports>=2025.9.0",
]
# NAGL is opt-in: it pulls torch (~1GB+ wheel with CUDA libs) and
# pytorch-lightning, which the openff backend does not otherwise need.
# Users who want AM1-BCC-equivalent charges via the OpenFF NAGL GNN
# surrogate (``charge_method="nagl"``) install with:
#     pip install acellera-htmd[nagl]   (or uv sync --extra nagl)
nagl = [
  "acellera-openff-nagl",
  "acellera-openff-nagl-models",
  "torch",
  "pytorch-lightning",
]

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

[project.scripts]
htmd_register = "htmd.license:htmd_register"

[tool.setuptools]
include-package-data = false

[tool.setuptools.packages.find]
where = [""]
include = ["htmd*"]
exclude = ["htmd.share*"]
namespaces = false

[tool.setuptools.package-data]
htmd = ["share/**/*", "logging.ini"]

[tool.setuptools_scm]

[build-system]
requires = ["setuptools", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

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

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

[dependency-groups]
test = ["acellera-htmd[openff,nagl]", "acemd", "flake8>=7.3.0", "pytest>=9.0.2"]
dev = [{ include-group = "test" }, "ffevaluation>=0.2.6", "ipython>=8.38.0"]
docs = [
  "acellera-docs-theme @ git+https://github.com/Acellera/acellera-docs-theme.git",
  "sphinx>=7",
  "myst-nb>=1.1",
  "sphinx-design>=0.6",
  "sphinx-copybutton>=0.5",
  "sphinxcontrib-mermaid>=1.0",
  "sphinx-autodoc-typehints>=2.0",
  "sphinx-argparse>=0.5",
  "sphinx-notfound-page>=1.0",
  "sphinx-sitemap>=2.6",
  "jupytext>=1.19.3",
  "nbconvert>=7.17.1",
]