pyproject.toml

[project]
name = "molcrafts-molpy"
dynamic = ["version"]
description = "Modern Python framework for molecular simulation and analysis"
readme = "README.md"
requires-python = ">=3.12"
license = { text = "BSD-3-Clause" }
authors = [{ name = "Roy Kid", email = "lijichen365@gmail.com" }]
maintainers = [{ name = "Roy Kid", email = "lijichen365@gmail.com" }]
keywords = [
    "molecular-simulation",
    "computational-chemistry",
    "molecular-dynamics",
    "force-fields",
    "scientific-computing",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Typing :: Typed",
]
# Runtime: numpy (scientific baseline) + MolCrafts ecosystem only.
# No lark / zarr / RDKit / etc. as hard deps — those live in molrs or optional extras.
dependencies = [
    "numpy>=2.0",
    "molcrafts-molrs>=0.14.0,<0.15",
    "molcrafts-mollog>=1.0.0",
    "molcrafts-molcfg>=1.2.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=6.0.0",
    "pytest-xdist>=3.0",
    "ruff==0.16.1",
    "ty==0.0.65",
    "tox>=4.23",
]
rdkit = ["rdkit"]  # optional: exercises the RDKitAdapter example only
doc = [
    "zensical>=0.0.53",
    # 0.2.9: equal chart margins + plain VL fences (no annotation passthrough).
    # 0.2.8+ required for ``$file`` data refs in molplot fences.
    "molcrafts-zensical-theme>=0.2.9",
    "mkdocstrings[python]>=0.24.0",
]
all = ["molcrafts-molpy[dev,doc]"]

[project.scripts]
molpy = "molpy.cli:main"

# Formats molpy owns, published for any molcrafts viewer to read. Declaring
# them here rather than importing a host keeps the arrow one-way: molpy says
# what it can parse, and a platform picks it up at install time.
[project.entry-points."molcrafts.metric_readers"]
lammps_log = "molpy.integrations.metric_readers:LammpsLogReader"
mrec = "molpy.integrations.metric_readers:MrecReader"
mlp_jsonl = "molpy.integrations.metric_readers:MlpJsonlReader"

[project.urls]
Homepage = "https://github.com/MolCrafts/molpy"
Documentation = "https://molpy.molcrafts.org"
Repository = "https://github.com/MolCrafts/molpy.git"
Issues = "https://github.com/MolCrafts/molpy/issues"

[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
package-dir = { "" = "src" }

[tool.setuptools.dynamic]
version = { attr = "molpy.version.version" }

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
"molpy.data" = ["README.md"]
"molpy.data.forcefield" = ["*.xml", "*.ff"]

[tool.ruff]
# Matches requires-python: the lint gate must reject syntax the floor
# (3.12) cannot parse — PEP 758 `except A, B:` slipped in exactly this way.
target-version = "py312"
line-length = 88

[tool.ruff.lint]
# Keep the historical default-style gate (E4/E7/E9/F); ruff 0.16 still honors
# an explicit select so we do not inherit future default expansions mid-release.
select = ["E4", "E7", "E9", "F", "RUF100"]
# E402: readers/writers import lazily inside functions by design (layering);
# E741: single-letter names in the maths-heavy kernels stay.
ignore = ["E402", "E741"]

[tool.ty.environment]
python-version = "3.14"
root = ["./src"]

[tool.ty.rules]
all = "warn"
# ty 0.0.65 is stricter; keep release gate green while types catch up.
missing-override-decorator = "ignore"
missing-type-argument = "ignore"
unresolved-import = "ignore"
invalid-argument-type = "ignore"
invalid-assignment = "ignore"
invalid-method-override = "ignore"
invalid-return-type = "ignore"
unsupported-operator = "ignore"
not-iterable = "ignore"
unknown-argument = "ignore"
invalid-type-arguments = "ignore"
not-subscriptable = "ignore"
index-out-of-bounds = "ignore"
no-matching-overload = "ignore"
missing-argument = "ignore"
division-by-zero = "ignore"
invalid-parameter-default = "ignore"
too-many-positional-arguments = "ignore"
invalid-type-form = "ignore"
call-non-callable = "ignore"
redundant-cast = "ignore"

[tool.ty.terminal]
output-format = "full"

[tool.pytest.ini_options]
testpaths = ["tests"]
# No __init__.py under tests/: same basenames (four test_lammps.py) resolve by path.
addopts = "--import-mode=importlib"
pythonpath = ["src"]
filterwarnings = [
    "error",
    "ignore::pytest.PytestUnraisableExceptionWarning",
]

# No [tool.uv.sources] override: molcrafts-molrs 0.14.0 is on PyPI, so the pin in
# [project] dependencies resolves everywhere, including a CI runner, which has no
# sibling checkout to point at. Do not reintroduce a path or git source without
# removing it again before the next release: it silently disables
# .pre-commit/check_molrs_pin_on_pypi.py, and uv honours a path dependency's own
# sources transitively, so a downstream that points at this directory inherits
# them (that is how molhub once got a molrs without `molrs.io.mrec`).

[tool.tox]
requires = ["tox>=4.23"]
env_list = ["lint"]

[tool.tox.env.lint]
skip_install = true
base_python = ["python3.14"]
deps = ["ruff==0.16.1", "ty==0.0.65"]
commands = [
    ["ruff", "format", "--check", "src/", "tests/"],
    ["ruff", "check", "src/", "tests/"],
    ["ty", "check", "src/molpy/"],
]