pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "setuptools_scm[toml]>=7.1"]
build-backend = "setuptools.build_meta"

[project]
name = "qsprpred"
dynamic = ["version"]
description = "A cheminformatics package for training and testing QSAR/QSPR models"
readme = { file = "README.md", content-type = "text/markdown" }
requires-python = ">=3.10"
license = { file = "LICENSE" }
keywords = ["qsar", "machine learning", "cheminformatics"]
authors = [{ name = "Helle van den Maagdenberg", email = "h.w.van.den.maagdenberg@lacdr.leidenuniv.nl" },
    { name = "Linde Schoenmaker", email = "l.schoenmaker@lacdr.leidenuniv.nl" },
    { name = "Martin Sicho", email = "m.sicho@lacdr.leidenuniv.nl" },
    { name = "David Araripe", email = "d.figueiredo.vidal@lacdr.leidenuniv.nl" },
    { name = "Sohvi Luukkonen", email = "s.luukkonen@lacdr.leidenuniv.nl" },
    { name = "Olivier Béquignon", email = "o.j.m.bequignon@lacdr.leidenuniv.nl" },
    { name = "Marina Gorostiola Gonzalez", email = "m.gorostiola.gonzalez@lacdr.leidenuniv.nl" },
    { name = "Remco van den Broek", email = "r.l.van.den.broek@umail.leidenuniv.nl" },
    { name = "Gerard van Westen", email = "gerard@lacdr.leidenuniv.nl" }]
maintainers = [{ name = "Helle van den Maagdenberg", email = "h.w.van.den.maagdenberg@lacdr.leidenuniv.nl" },
    { name = "Linde Schoenmaker", email = "l.schoenmaker@lacdr.leidenuniv.nl" },
    { name = "Martin Sicho", email = "m.sicho@lacdr.leidenuniv.nl" },
    { name = "David Araripe", email = "d.figueiredo.vidal@lacdr.leidenuniv.nl" },
    { name = "Sohvi Luukkonen", email = "s.luukkonen@lacdr.leidenuniv.nl" },
    { name = "Olivier Béquignon", email = "o.j.m.bequignon@lacdr.leidenuniv.nl" },
    { name = "Marina Gorostiola Gonzalez", email = "m.gorostiola.gonzalez@lacdr.leidenuniv.nl" },
    { name = "Remco van den Broek", email = "r.l.van.den.broek@umail.leidenuniv.nl" },
    { name = "Gerard van Westen", email = "gerard@lacdr.leidenuniv.nl" }]
classifiers = [
    "Development Status :: 4 - Beta",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Chemistry",
]
dependencies = [
    "parameterized",
    "pebble",
    "numpy",
    "scikit-learn >= 1.0.2",
    "pandas >= 1.2.2",
    "matplotlib >= 2.0",
    "chembl_structure_pipeline >= 1.2.0",
    "rdkit",
    "optuna",
    "gitpython",
    "xgboost",
    "boruta",
    "tqdm",
    "ml2json",
    "jsonpickle",
    "papyrus_scripts",
    "gbmtsplits",
    "mlchemad",
    "mols2grid"
]

[project.optional-dependencies]

extra = [
    "mold2-pywrapper",
    "dask[distributed]",
    "padel-pywrapper >= 1.0.2.post1",
    "Mordred",
    "biopython",
    "prodec",
    "Signature-pywrapper",
]
deep = [
    "torch >= 1.7.0",
]
chemprop = [
    "rdkit < 2023.9.6",
    "chemprop >= 1.6.0, < 2.0.0",
]
full = [
    "qsprpred[deep]",
    "qsprpred[extra]",
    "qsprpred[chemprop]",
]
dev = [
    "qsprpred[full]",
    "pre-commit",
    "isort",
    "yapf",
    "ruff",
    "pytest"
]

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

[project.urls]
homepage = "https://github.com/CDDLeiden/QSPRpred"
repository = "https://github.com/CDDLeiden/QSPRpred"
documentation = "https://cddleiden.github.io/QSPRpred/docs/"

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

[tool.setuptools_scm]
write_to = "qsprpred/_version.py"

[tool.yapf]
based_on_style = "facebook"
column_limit = 88

[tool.isort]
profile = "black"
line_length = 88
multi_line_output = 3
skip_gitignore = true
honor_noqa = true
src_paths = ["qsprpred"]
known_first_party = 'qsprpred'

[tool.ruff]
line-length = 88
target-version = "py39"
fix = true
fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
unfixable = []

# inspired by the configuration used in the pandas project
select = [
    # pyflakes
    "F",
    # pycodestyle
    "E", "W",
    # flake8-2020
    "YTT",
    # flake8-bugbear
    "B",
    # flake8-quotes
    "Q",
    # flake8-debugger
    "T10",
    # flake8-gettext
    "INT",
    # pylint
    "PLC", "PLE", "PLR", "PLW",
    # misc lints
    "PIE",
    # flake8-pyi
    "PYI",
    # tidy imports
    "TID",
    # implicit string concatenation
    "ISC",
    # type-checking imports
    "TCH",
    # comprehensions
    "C4",
    # pygrep-hooks
    "PGH",
    # Ruff-specific rules
    "RUF",
]

ignore = [
    # line length - somes lines are just too long
    "E501",
    # we decided on having relative rather than absolute imports
    "TID252",
    # module level import not at top of file
    "E402",
    # do not assign a lambda expression, use a def
    "E731",
    # controversial
    "B006",
    # controversial
    "B007",
    # controversial
    "B008",
    # tests use assert False
    "B011",
    # tests use comparisons but not their returned value
    "B015",
    # false positives
    "B019",
    # Loop control variable overrides generator it iterates
    "B020",
    # Function definition does not bind loop variable
    "B023",
    # Only works with python >=3.10
    "B905",
    # Too many arguments to function call
    "PLR0913",
    # Too many returns
    "PLR0911",
    # Too many branches
    "PLR0912",
    # Too many statements
    "PLR0915",
    # Redefined loop name
    "PLW2901",
    # Global statements are discouraged
    "PLW0603",
    # Docstrings should not be included in stubs
    "PYI021",
    # No builtin `eval()` allowed
    "PGH001",
    # compare-to-empty-string
    "PLC1901",
    # pairwise-over-zipped (>=PY310 only)
    "RUF007",
    # Within an except clause, raise exceptions with ...
    "B904",
    # Use "collections.abc.*" instead of "typing.*" (PEP 585 syntax)
    # "PYI027",  # not yet implemented
    # while int | float can be shortened to float, the former is more explicit
    # "PYI041",  # not yet implemented
]

# Esclude a variety of commonly ignored dictionaries
exclude = [
    "docs/*.py",
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
]