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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=64", "setuptools-scm>=8.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "MEDS_transforms"
dynamic = ["version"]
authors = [
{ name="Matthew McDermott", email="[email protected]" },
]
description = "MEDS ETL and transformation functions leveraging a sharding-based parallelism model & polars."
readme = "README.md"
requires-python = ">=3.11"
classifiers = [
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
]
dependencies = [
"polars~=1.14", "pyarrow", "nested_ragged_tensors>=0.0.8", "loguru", "hydra-core", "numpy", "meds==0.3.3",
]
[tool.setuptools_scm]
[project.optional-dependencies]
dev = ["pre-commit<4"]
tests = ["pytest", "pytest-cov", "rootutils", "hydra-joblib-launcher"]
local_parallelism = ["hydra-joblib-launcher"]
slurm_parallelism = ["hydra-submitit-launcher"]
docs = [
"mkdocs==1.6.0", "mkdocs-material==9.5.31", "mkdocstrings[python,shell]==0.25.2", "mkdocs-gen-files==0.5.0",
"mkdocs-literate-nav==0.6.1", "mkdocs-section-index==0.3.9", "mkdocs-git-authors-plugin==0.9.0",
"mkdocs-git-revision-date-localized-plugin==1.2.6"
]
[project.scripts]
# MEDS_extract
MEDS_extract-split_and_shard_subjects = "MEDS_transforms.extract.split_and_shard_subjects:main"
MEDS_extract-shard_events = "MEDS_transforms.extract.shard_events:main"
MEDS_extract-convert_to_sharded_events = "MEDS_transforms.extract.convert_to_sharded_events:main"
MEDS_extract-merge_to_MEDS_cohort = "MEDS_transforms.extract.merge_to_MEDS_cohort:main"
MEDS_extract-extract_code_metadata = "MEDS_transforms.extract.extract_code_metadata:main"
MEDS_extract-finalize_MEDS_metadata = "MEDS_transforms.extract.finalize_MEDS_metadata:main"
MEDS_extract-finalize_MEDS_data = "MEDS_transforms.extract.finalize_MEDS_data:main"
# MEDS_transform
## General
MEDS_transform-aggregate_code_metadata = "MEDS_transforms.aggregate_code_metadata:main"
MEDS_transform-fit_vocabulary_indices = "MEDS_transforms.fit_vocabulary_indices:main"
MEDS_transform-reshard_to_split = "MEDS_transforms.reshard_to_split:main"
## Filters
MEDS_transform-filter_measurements = "MEDS_transforms.filters.filter_measurements:main"
MEDS_transform-filter_subjects = "MEDS_transforms.filters.filter_subjects:main"
## Transforms
MEDS_transform-reorder_measurements = "MEDS_transforms.transforms.reorder_measurements:main"
MEDS_transform-add_time_derived_measurements = "MEDS_transforms.transforms.add_time_derived_measurements:main"
MEDS_transform-extract_values = "MEDS_transforms.transforms.extract_values:main"
MEDS_transform-normalization = "MEDS_transforms.transforms.normalization:main"
MEDS_transform-occlude_outliers = "MEDS_transforms.transforms.occlude_outliers:main"
MEDS_transform-tensorization = "MEDS_transforms.transforms.tensorization:main"
MEDS_transform-tokenization = "MEDS_transforms.transforms.tokenization:main"
# Runner
MEDS_transform-runner = "MEDS_transforms.runner:main"
[project.urls]
Homepage = "https://github.com/mmcdermott/MEDS_transforms"
Issues = "https://github.com/mmcdermott/MEDS_transforms/issues"