--- a +++ b/pyproject.toml @@ -0,0 +1,69 @@ +[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" +]