[build-system]
requires = ["setuptools>=77", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[tool.uv]
required-version = ">=0.12.8"

[project]
name = "datamol"
description = "A python library to work with molecules. Built on top of RDKit."
authors = [{ name = "Hadrien Mary", email = "hadrien@valencediscovery.com" }]
readme = "README.md"
dynamic = ["version"]
requires-python = ">=3.11"
license = "Apache-2.0"
license-files = ["LICENSE"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Healthcare Industry",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
    "Natural Language :: English",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
]
dependencies = [
    "tqdm>=4.66",
    "loguru>=0.7",
    "joblib>=1.3",
    "fsspec[http]>=2023.9.2",
    "pandas>=2.2",
    "numpy>=1.26",
    "scipy>=1.11",
    "platformdirs>=4",
    "scikit-learn>=1.4",
    "packaging>=23.2",
    "rdkit>=2024.9.1",
    # I/O backends: cloud filesystems, Excel and Parquet.
    "gcsfs>=2024.3",
    "s3fs>=2024.3",
    "openpyxl>=3.1",
    "xlsxwriter>=3.2",
    "pyarrow>=15",
    # Visualization.
    "matplotlib>=3.8",
    "networkx>=3.2",
    "nglview>=3.1",
    "pillow>=10",
    # SELFIES conversion.
    "selfies>=2.1",
]

[project.optional-dependencies]
test = [
    "ipykernel>=6.29",
    "ipywidgets>=8.1",
    "nbconvert>=7.16",
    "nbformat>=5.10",
    "pytest>=8",
    "pytest-cov>=6",
    "pytest-xdist>=3.6",
]
docs = [
    "markdown-include>=0.8.1",
    "mdx-truly-sane-lists>=1.3",
    "mike>=2",
    "mkdocs>=1.6",
    "mkdocs-jupyter>=0.25",
    "mkdocs-material>=9.5",
    "mkdocs-material-extensions>=1.3",
    "mkdocstrings[python]>=0.30",
    "seaborn>=0.13",
]
dev = [
    "black>=25",
    "build>=1.2",
    "mypy>=1.15",
    "pre-commit>=4",
    "pyright>=1.1.400",
    "ruff>=0.11",
    "twine>=6",
]

[project.urls]
Website = "https://datamol.io"
"Source Code" = "https://github.com/datamol-io/datamol"
"Bug Tracker" = "https://github.com/datamol-io/datamol/issues"
Documentation = "https://docs.datamol.io"

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

[tool.setuptools_scm]
fallback_version = "0.0.0"

[tool.setuptools.packages.find]
where = ["."]
include = ["datamol", "datamol.*"]
exclude = []
namespaces = true

[tool.setuptools.package-data]
"datamol.data" = ["*"]

[tool.black]
line-length = 100
target-version = ['py311']
include = '\.pyi?$'

[tool.pytest.ini_options]
minversion = "8.0"
addopts = "--verbose --cov=datamol --cov-fail-under=85 --cov-report xml --cov-report term --durations=10 -n auto"
testpaths = ["tests"]
markers = [
    "integration: runs the executable tutorial suite",
    "notebook: executes a tutorial notebook",
]
filterwarnings = [
    "ignore::DeprecationWarning:rdkit.Chem.MolStandardize",
    "ignore::DeprecationWarning:jupyter_client",
    "ignore::DeprecationWarning:pkg_resources",
    "ignore::DeprecationWarning:joblib.externals.loky.backend",
    "ignore::DeprecationWarning:dateutil.tz.tz",
    "ignore::DeprecationWarning:joblib._utils",
    "ignore::DeprecationWarning:openpyxl.packaging.core",
    "ignore::DeprecationWarning:tqdm.std",
]

[tool.coverage.run]
source = ["datamol/"]
disable_warnings = ["no-data-collected"]
data_file = ".coverage/coverage"

[tool.coverage.report]
omit = ["datamol/__init__.py", "datamol/_version.py"]

[tool.coverage.xml]
output = "coverage.xml"

[tool.mypy]
exclude = []
ignore_missing_imports = true
python_version = "3.11"

[tool.pyright]
reportShadowedImports = false

[tool.ruff]
line-length = 110
target-version = "py311"

[tool.ruff.lint]
select = ["E4", "E7", "E9", "F"]
ignore = [
    "E501", # Never enforce `E501` (line length violations).
    "E731", # Do not assign a lambda expression, use a def
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = [
    "F401", # imported but unused
    "E402", # Module level import not at top of file
]

[tool.ruff.lint.pycodestyle]
max-doc-length = 150