pyproject.toml

[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "byteff2"
version = "1.1.0"
description = "ByteFF and ByteFF-Pol source package"
readme = "README.md"
requires-python = ">=3.11"
license = { file = "LICENSE" }
dependencies = [
    "rdkit~=2026.3",
    "ase~=3.29.0",
    "torch~=2.11.0",
    "torch-geometric~=2.8.0",
    "sella~=2.3",
    "gitpython~=3.1",
    "mdanalysis~=2.10",
    "h5py~=3.16",
    "numpy~=2.4",
    "pandas~=3.0",
    "pyyaml~=6.0",
    "scipy~=1.17",
    "tqdm~=4.67",
    "torchmetrics>=1.9.0",
]

[dependency-groups]
dev = [
    "pre-commit>=4.0.0",
    "pytest~=9.1.1",
    "pytest-cov~=7.1",
    "pytest-xdist~=3.8",
    "pytest-random-order~=1.2",
    "ruff>=0.16",
]
[tool.setuptools.packages.find]
include = ["byteff2*"]

[tool.setuptools.package-data]
"byteff2.bytemol.toolkit.infer_molecule" = ["bond_length_ref.csv"]

[tool.pytest.ini_options]
log_format = "%(asctime)s %(levelname)s %(message)s"
log_date_format = "%Y-%m-%d %H:%M:%S"
log_cli = true
log_level = "INFO"
filterwarnings = ["always"]
markers = ["serial"]

[tool.ruff]
target-version = "py311"
line-length = 120
exclude = ["**/deprecated/**", "**/debug/**", "scripts/**", "submodules/openmm"]

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors: indentation, whitespace, blank lines, etc.
    "F",   # Pyflakes: unused imports, undefined names, duplicate keys, etc.
    "W",   # pycodestyle warnings: trailing whitespace, missing newline, invalid escapes, etc.
    "PLE", # pylint errors: runtime errors (yield in __init__, invalid signatures, etc.
    "PLW", # pylint warnings: suspicious patterns, unspecified encoding, etc.
    "PLR", # pylint refactoring: too many branches/args/statements, collapsible else-if, etc.
    "PLC", # pylint conventions: naming, import aliases, __slots__ style, etc.
    "I",   # isort: import sorting and formatting
]
ignore = [
    "PLW1514", # open() without explicit encoding argument
    "E402",    # module-level import not at top of file
    "E741",    # Checks for the use of the characters 'l', 'O', or 'I' as variable names.
    "PLC0415", # import outside top-level scope
    "PLR0402", # use "from X import Y" instead of "import X as X"
    "PLR0904", # too many public methods
    "PLR0912", # too many branches (default max 12)
    "PLR0915", # too many statements
    "PLR1711", # useless return / return None at end of function
    "PLR2004", # magic numbers
    "PLR5501", # collapsible else-if (use elif)
    "PLR0913", # too many arguments in function definition
    "PLR0911", # too many return statements
]

[tool.ruff.lint.pylint]
max-args = 12
max-locals = 50

[tool.ruff.lint.isort]
known-first-party = ["byteff2", "example", "scripts"]
force-sort-within-sections = true
order-by-type = false
combine-as-imports = true
lines-after-imports = 2

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