MEDS_Tabular_AutoML/pyproject.toml at main · mmcdermott/MEDS_Tabular_AutoML · GitHub

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[build-system]
requires = ["setuptools>=61.0", "setuptools-scm>=8.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "meds-tab"
dynamic = ["version"]
authors = [
  { name="Matthew McDermott", email="mattmcdermott8@gmail.com" },
  { name="Nassim Oufattole", email="noufattole@gmail.com" },
  { name="Teya Bergamaschi", email="teyabergamaschi@gmail.com" },
]
description = "Scalable Tabularization of MEDS format Time-Series data"
readme = "README.md"
requires-python = ">=3.11"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dependencies = [
  "polars~=1.26.0",
  "pyarrow",
  "hydra-core==1.3.2",
  "numpy",
  "scipy<1.14.0",
  "pandas",
  "tqdm",
  "xgboost",
  "scikit-learn",
  "hydra-optuna-sweeper",
  "hydra-joblib-launcher",
  "ml-mixins",
  "meds~=0.4.0",
  "meds-transforms~=0.5.0",
  "meds-evaluation",
]

[tool.setuptools_scm]

[project.scripts]
meds-tab-describe = "MEDS_tabular_automl.scripts.describe_codes:main"
meds-tab-tabularize-static = "MEDS_tabular_automl.scripts.tabularize_static:main"
meds-tab-tabularize-time-series = "MEDS_tabular_automl.scripts.tabularize_time_series:main"
meds-tab-cache-task = "MEDS_tabular_automl.scripts.cache_task:main"
meds-tab-xgboost = "MEDS_tabular_automl.scripts.launch_model:main"
meds-tab-model = "MEDS_tabular_automl.scripts.launch_model:main"
meds-tab-autogluon = "MEDS_tabular_automl.scripts.launch_autogluon:main"
generate-subsets = "MEDS_tabular_automl.scripts.generate_subsets:main"


[project.optional-dependencies]
dev = ["pre-commit<4", "ruff"]
tests = ["pytest", "pytest-cov[toml]"]
profiling = ["mprofile", "matplotlib"]
autogluon = ["autogluon; python_version=='3.11.*'"]  # Environment marker to restrict AutoGluon to Python 3.11
docs = [
    "mkdocs==1.6.0",
    "mkdocs-gen-files==0.5.0",
    "mkdocs-get-deps==0.2.0",
    "mkdocs-git-authors-plugin==0.9.0",
    "mkdocs-git-revision-date-localized-plugin==1.2.7",
    "mkdocs-literate-nav==0.6.1",
    "mkdocs-material==9.5.33",
    "mkdocs-material-extensions==1.3.1",
    "mkdocs-section-index==0.3.9",
    "mkdocs-snippets==1.3.0",
    "mkdocstrings==0.25.2",
    "mkdocstrings-python==1.10.8"
]


[project.urls]
Homepage = "https://github.com/mmcdermott/MEDS_Tabular_AutoML"
Issues = "https://github.com/mmcdermott/MEDS_Tabular_AutoML/issues"

[tool.pytest.ini_options]
addopts = [
  "--color=yes",
  "--doctest-modules",
  "--ignore=docs",
  "--doctest-glob=*.md",
]
python_classes = "!TestEnv"
doctest_optionflags = ["NORMALIZE_WHITESPACE", "ELLIPSIS"]

[tool.coverage.report]
exclude_also = [
  "logger\\.debug", "except ImportError:", "if TYPE_CHECKING:",
  "if __name__ == .__main__.:",
]

[tool.ruff]
target-version = "py312"
line-length = 110
extend-exclude = ["docs/index.md"]

# Enable linters
[tool.ruff.lint]
select = [
    "E",   # pycodestyle
    "F",   # pyflakes
    "I",   # isort
    "UP",  # pyupgrade
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "DTZ", # flake8-datetimez
    "RUF", # Ruff-specific rules
    "SIM", # flake8-simplify
    "TCH", # flake8-type-checking
    "N",   # pep8-naming
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]  # Unused imports in __init__ files

[tool.ruff.lint.pep8-naming]
extend-ignore-names = ["X*", "MEDS*"]