pyproject.toml

[build-system]
requires = ["setuptools>=68.0", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "q2mm"
dynamic = ["version"]
description = "Quantum-guided molecular mechanics force field optimization"
readme = "README.md"
requires-python = ">=3.10"
license = { text = "MIT" }
authors = [
    { name = "Eric Hansen" },
]
keywords = [
    "force-field",
    "molecular-mechanics",
    "optimization",
    "transition-state",
    "computational-chemistry",
    "Q2MM",
    "OpenMM",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Chemistry",
]
dependencies = [
    "numpy",
    "pyyaml",
]

[tool.setuptools_scm]
# Version derived from git tags: git tag v5.0.0 → version 5.0.0
version_scheme = "guess-next-dev"
local_scheme = "no-local-version"

[project.optional-dependencies]
amber = [
    "parmed",
]
openmm = [
    "openmm",
]
openmm-cuda = [
    "openmm",
    "OpenMM-CUDA-12; platform_system != 'Darwin'",
]
optimize = [
    "scipy",
]
qm = [
    "pint",
]
jax = [
    "jax",
    "jaxlib",
    "jaxopt",
    "optax",
    "scipy",
]
jax-md = [
    "jax-md; sys_platform != 'win32'",
    "jax; sys_platform != 'win32'",
    "jaxlib; sys_platform != 'win32'",
    "scipy",
]
gpu = [
    "jax[cuda12]; sys_platform != 'win32'",
    "jaxopt; sys_platform != 'win32'",
    "scipy",
]
qcel = [
    "qcelemental",
]
qcengine = [
    "qcengine",
]
ase = [
    "ase",
]
dev = [
    "pytest",
    "pytest-benchmark",
    "pytest-cov",
    "ruff",
    "mypy",
    "scipy",
    "parmed",
    "qcelemental",
    "qcengine",
    "ase",
    "openmm",
    "build",
    "tomli; python_version < '3.11'",
]
docs = [
    "properdocs",
    "mkdocs-material",
    "mkdocstrings[python]",
    "mkdocs-gen-files",
    "mkdocs-literate-nav",
    "mkdocs-section-index",
]
all = [
    "openmm",
    "parmed",
    "pint",
    "scipy",
    "qcelemental",
    "qcengine",
    "ase",
    "jax",
    "jaxlib",
    "jax-md; sys_platform != 'win32'",
]

[project.scripts]
q2mm-benchmark = "q2mm.benchmarks.cli:main"

[project.urls]
Homepage = "https://github.com/ericchansen/q2mm"
Documentation = "https://ericchansen.github.io/q2mm/"
Repository = "https://github.com/ericchansen/q2mm"
Issues = "https://github.com/ericchansen/q2mm/issues"
Changelog = "https://github.com/ericchansen/q2mm/releases"

[tool.setuptools.packages.find]
include = ["q2mm*"]
namespaces = false

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

[tool.setuptools.package-data]
q2mm = [
    "py.typed",
    "data/sn2/manifest.json",
    "data/sn2/*.npy",
    "data/sn2/*.npz",
    "data/sn2/*.txt",
    "data/sn2/*.xyz",
]

[tool.pytest.ini_options]
testpaths = ["test"]
addopts = ""
markers = [
    "benchmark: performance benchmark tests (requires pytest-benchmark; use --benchmark-enable to collect timing)",
    "cross_backend: parity tests that execute two or more backend implementations",
    "integration: backend integration tests ~1-10s each (requires --run-integration)",
    "validation: correctness validation with no optimizer loops ~1-30s each (requires --run-validation)",
    "nightly: heavy tests with optimizer loops or large systems ~1-10min each (requires --run-nightly)",
]

[tool.ruff]
line-length = 120
target-version = "py310"
extend-exclude = ["*.ipynb"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"

[tool.ruff.lint]
select = [
    "E", "F", "W",      # pycodestyle + pyflakes
    "UP",                # pyupgrade
    "SIM",               # flake8-simplify
    "ANN",               # flake8-annotations (type hints)
    "D",                 # pydocstyle (docstrings)
    "ERA",               # eradicate (commented-out code)
]
ignore = [
    "E402",   # module-import-not-at-top (conditional imports)
    "E501",   # line too long (let formatter handle)
    "E701",   # multiple statements on one line
    "E741",   # ambiguous variable name (common in scientific code)
    "F841",   # unused variable (common in scientific iteration / tuple unpacking)
    "SIM102", # collapsible-if (readability preference)
    "SIM108", # ternary (readability preference in scientific code)
    "ANN401", # any-type (too strict for scientific code with numpy/openmm)
    "D105",   # undocumented-magic-method (usually obvious)
    "D107",   # undocumented-public-init (docstring goes on class)
    "D203",   # incorrect-blank-line-before-class (conflicts with D211)
    "D213",   # multi-line-summary-second-line (conflicts with D212)
]

[tool.ruff.lint.per-file-ignores]
"test/**" = [
    "D100", # undocumented-public-module (test modules)
    "D101", # undocumented-public-class (test classes)
    "D102", # undocumented-public-method (test methods — name is the doc)
    "D103", # undocumented-public-function (test helpers)
    "D104", # undocumented-public-package
]

[tool.mypy]
# Target 3.12 (the CI Lint job's Python) as a single source of truth so plain
# `python -m mypy q2mm/` matches CI locally. numpy>=2.5 ships PEP 695 `type`
# aliases in its stubs that mypy rejects under python_version=3.10 (a fatal
# stub parse error that halts all checking), so 3.10 is not a usable target
# here. The >=3.10 runtime floor is still enforced by ruff (target-version=
# py310) and the 3.10 test-core matrix.
python_version = "3.12"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false  # too strict for existing codebase
check_untyped_defs = true
ignore_missing_imports = true

# Grandfathered modules: mypy is enforced repo-wide via the CI Lint job, but
# the modules listed below carry pre-existing type errors. They are still
# followed for type info, but their own errors are not reported — so any NEW
# module, or any module removed from this list, must be mypy-clean.
# Un-grandfather modules one at a time as their errors are fixed.
# See https://mypy.readthedocs.io/en/stable/existing_code.html
[[tool.mypy.overrides]]
ignore_errors = true
module = [
  "q2mm.backends.mm",
  "q2mm.backends.mm._jax_common",
  "q2mm.backends.mm.batched",
  "q2mm.backends.mm.jax_engine",
  "q2mm.backends.mm.jax_md_engine",
  "q2mm.backends.mm.openmm",
  "q2mm.backends.mm.tinker",
  "q2mm.backends.qm.psi4",
  "q2mm.backends.registry",
  "q2mm.io._helpers",
  "q2mm.io.amber",
  "q2mm.io.cmap",
  "q2mm.io.gaussian",
  "q2mm.io.jaguar",
  "q2mm.io.macromodel",
  "q2mm.io.mm3",
  "q2mm.io.mol2",
  "q2mm.io.openmm",
  "q2mm.io.reference",
  "q2mm.io.tinker",
  "q2mm.models.forcefield",
  "q2mm.models.hessian",
  "q2mm.models.molecule",
  "q2mm.models.seminario",
  "q2mm.optimizers.cycling",
  "q2mm.optimizers.jax_multistart",
  "q2mm.optimizers.jaxopt_opt",
  "q2mm.optimizers.optax",
  "q2mm.optimizers.scipy_opt",
  "q2mm.workflows.method_e2",
]