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.gitattributes
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CITATION.cff
CONTRIBUTING.md
LICENSE
README.md
codecov.yml
conftest.py
mkdocs.yml
pyproject.toml
uv.lock
.github/actions/setup/action.yaml
.github/workflows/code-quality-main.yaml
.github/workflows/code-quality-pr.yaml
.github/workflows/docs.yaml
.github/workflows/python-build.yaml
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docs/gen_ref_pages.py
docs/gen_stage_docs.py
docs/gen_static_assets.py
docs/index.md
docs/ingestion_pathways.md
docs/hooks/silence_griffe_missing_type_warnings.py
docs/javascripts/mathjax.js
example/README.md
example/messy.yaml
example/pipeline.yaml
example/expected_output/data/held_out/0.parquet
example/expected_output/data/train/0.parquet
example/expected_output/data/tuning/0.parquet
example/expected_output/metadata/.shards.json
example/expected_output/metadata/codes.parquet
example/expected_output/metadata/subject_splits.parquet
example/raw_data/diagnoses.csv
example/raw_data/lab_descriptions.csv
example/raw_data/labs_vitals.csv
example/raw_data/medication_classes.csv
example/raw_data/medications.csv
example/raw_data/patients.csv
example/raw_data/stays.csv
src/MEDS_extract/__init__.py
src/MEDS_extract/_cli.py
src/MEDS_extract/_stage_example.py
src/MEDS_extract/config.py
src/MEDS_extract/io.py
src/MEDS_extract.egg-info/PKG-INFO
src/MEDS_extract.egg-info/SOURCES.txt
src/MEDS_extract.egg-info/dependency_links.txt
src/MEDS_extract.egg-info/entry_points.txt
src/MEDS_extract.egg-info/requires.txt
src/MEDS_extract.egg-info/scm_file_list.json
src/MEDS_extract.egg-info/scm_version.json
src/MEDS_extract.egg-info/top_level.txt
src/MEDS_extract/configs/__init__.py
src/MEDS_extract/configs/_extract.yaml
src/MEDS_extract/convert_to_MEDS_events/__init__.py
src/MEDS_extract/convert_to_MEDS_events/config.yaml
src/MEDS_extract/convert_to_MEDS_events/convert_to_MEDS_events.py
src/MEDS_extract/convert_to_MEDS_events/examples/default/README.md
src/MEDS_extract/convert_to_MEDS_events/examples/default/cfg.yaml
src/MEDS_extract/convert_to_MEDS_events/examples/default/in.yaml
src/MEDS_extract/convert_to_MEDS_events/examples/default/out_data.yaml
src/MEDS_extract/convert_to_MEDS_events/examples/default/pipeline_cfg.yaml
src/MEDS_extract/convert_to_parquet/__init__.py
src/MEDS_extract/convert_to_parquet/config.yaml
src/MEDS_extract/convert_to_parquet/convert_to_parquet.py
src/MEDS_extract/convert_to_parquet/examples/default/in.yaml
src/MEDS_extract/convert_to_parquet/examples/default/out_data.yaml
src/MEDS_extract/convert_to_parquet/examples/default/pipeline_cfg.yaml
src/MEDS_extract/convert_to_subject_sharded/__init__.py
src/MEDS_extract/convert_to_subject_sharded/convert_to_subject_sharded.py
src/MEDS_extract/convert_to_subject_sharded/examples/aggregated_join/README.md
src/MEDS_extract/convert_to_subject_sharded/examples/aggregated_join/in.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/aggregated_join/out_data.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/aggregated_join/pipeline_cfg.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/default/README.md
src/MEDS_extract/convert_to_subject_sharded/examples/default/in.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/default/out_data.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/default/pipeline_cfg.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/join/README.md
src/MEDS_extract/convert_to_subject_sharded/examples/join/in.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/join/out_data.yaml
src/MEDS_extract/convert_to_subject_sharded/examples/join/pipeline_cfg.yaml
src/MEDS_extract/download/README.md
src/MEDS_extract/download/__init__.py
src/MEDS_extract/download/_cli.yaml
src/MEDS_extract/download/_paths.py
src/MEDS_extract/download/cli.py
src/MEDS_extract/download/source.py
src/MEDS_extract/download/spec.py
src/MEDS_extract/download/unarchive.py
src/MEDS_extract/download/backends/__init__.py
src/MEDS_extract/download/backends/fsspec.py
src/MEDS_extract/download/backends/http.py
src/MEDS_extract/download/backends/physionet.py
src/MEDS_extract/extract_code_metadata/__init__.py
src/MEDS_extract/extract_code_metadata/config.yaml
src/MEDS_extract/extract_code_metadata/extract_code_metadata.py
src/MEDS_extract/extract_code_metadata/examples/default/README.md
src/MEDS_extract/extract_code_metadata/examples/default/in.yaml
src/MEDS_extract/extract_code_metadata/examples/default/out_metadata.yaml
src/MEDS_extract/extract_code_metadata/examples/default/pipeline_cfg.yaml
src/MEDS_extract/finalize_MEDS_data/__init__.py
src/MEDS_extract/finalize_MEDS_data/finalize_MEDS_data.py
src/MEDS_extract/finalize_MEDS_data/examples/default/README.md
src/MEDS_extract/finalize_MEDS_data/examples/default/in.yaml
src/MEDS_extract/finalize_MEDS_data/examples/default/out_data.yaml
src/MEDS_extract/finalize_MEDS_metadata/__init__.py
src/MEDS_extract/finalize_MEDS_metadata/finalize_MEDS_metadata.py
src/MEDS_extract/finalize_MEDS_metadata/examples/default/README.md
src/MEDS_extract/finalize_MEDS_metadata/examples/default/in.yaml
src/MEDS_extract/finalize_MEDS_metadata/examples/default/out_metadata.yaml
src/MEDS_extract/finalize_MEDS_metadata/examples/default/pipeline_cfg.yaml
src/MEDS_extract/merge_to_MEDS_cohort/__init__.py
src/MEDS_extract/merge_to_MEDS_cohort/config.yaml
src/MEDS_extract/merge_to_MEDS_cohort/merge_to_MEDS_cohort.py
src/MEDS_extract/merge_to_MEDS_cohort/examples/default/README.md
src/MEDS_extract/merge_to_MEDS_cohort/examples/default/in.yaml
src/MEDS_extract/merge_to_MEDS_cohort/examples/default/out_data.yaml
src/MEDS_extract/merge_to_MEDS_cohort/examples/default/pipeline_cfg.yaml
src/MEDS_extract/run/__init__.py
src/MEDS_extract/run/_cli.yaml
src/MEDS_extract/run/cli.py
src/MEDS_extract/split_and_shard_subjects/__init__.py
src/MEDS_extract/split_and_shard_subjects/config.yaml
src/MEDS_extract/split_and_shard_subjects/split_and_shard_subjects.py
src/MEDS_extract/split_and_shard_subjects/examples/default/README.md
src/MEDS_extract/split_and_shard_subjects/examples/default/cfg.yaml
src/MEDS_extract/split_and_shard_subjects/examples/default/in.yaml
src/MEDS_extract/split_and_shard_subjects/examples/default/out_metadata.yaml
src/MEDS_extract/split_and_shard_subjects/examples/default/pipeline_cfg.yaml
src/MEDS_extract/split_and_shard_subjects/examples/join/README.md
src/MEDS_extract/split_and_shard_subjects/examples/join/cfg.yaml
src/MEDS_extract/split_and_shard_subjects/examples/join/in.yaml
src/MEDS_extract/split_and_shard_subjects/examples/join/out_metadata.yaml
src/MEDS_extract/split_and_shard_subjects/examples/join/pipeline_cfg.yaml
static/logo_dark.svg
static/logo_light.svg
tests/__init__.py
tests/_fetcher_sigint_child.py
tests/test_config.py
tests/test_convert_to_parquet.py
tests/test_download.py
tests/test_download_cli.py
tests/test_download_fsspec.py
tests/test_example.py
tests/test_extract_code_metadata.py
tests/test_inprocess_pipeline.py
tests/test_merge_properties.py
tests/test_pipeline.py
tests/test_run.py
tests/test_run_example.py
tests/test_stage_examples.py