[build-system]

requires = ["setuptools >= 69.0", "setuptools-scm>=8.0"]

build-backend = "setuptools.build_meta"

[project]

name = "femr"

description = "Framework for Electronic Medical Records. A python package for building models using EHR data."

readme = "README.md"

dependencies = [

    "numpy >= 1.22",

    "scipy >= 1.6",

    "scikit-learn >= 0.24",

    "tqdm >= 4.60.0",

    "zstandard >= 0.18",

    "icecream == 2.1.3",

    "nptyping == 2.4.1",

    "msgpack >= 1.0.5",

    "meds == 0.1.3",

    "meds_etl == 0.1.0",

    "torch >= 2.1.2",

    "transformers >= 4.25",

    "datasets >= 2.15",

    "polars >= 0.20",

    "dill >= 0.3.7",

]

requires-python=">3.9"

dynamic = ["version"]

[tool.setuptools_scm]

version_file = "src/femr/_version.py"

[project.scripts]

femr_stanford_omop_fixer = "femr.post_etl_pipelines.stanford:femr_stanford_omop_fixer_program"

[project.optional-dependencies]

build = [

    "pytest >= 5.2",

    "flake8-future-import >= 0.4.6",

    "black >= 19.10b0",

    "isort >= 5.3.2",

    "mypy >= 0.782",

    "flake8 >= 3.8.3",

    "sphinx >= 3.2.1",

    "sphinx-rtd-theme >= 0.5.0",

    "sphinx-autoapi >= 1.5.1",

    "torchtyping == 0.1.4",

]

[tool.isort]

multi_line_output = 3

include_trailing_comma = true

force_grid_wrap = 0

use_parentheses = true

ensure_newline_before_comments = true

line_length = 120

[tool.black]

line_length = 120

target_version = ['py310']

[tool.pydocstyle]

match = "src/.*\\.py"

[tool.pytest.ini_options]

pythonpath = [

    "tests"

]