.editorconfig
.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
LICENSE
README.md
mkdocs.yml
pyproject.toml
.github/workflows/code-quality-main.yaml
.github/workflows/code-quality-pr.yaml
.github/workflows/python-build.yaml
.github/workflows/tests.yaml
docs/gen_ref_pages.py
docs/index.md
docs/pipeline_configuration.md
docs/preprocessing_operation_prototypes.md
docs/terminology.md
docs/tokenization_tensorization.md
docs/javascripts/mathjax.js
src/MEDS_transforms/__init__.py
src/MEDS_transforms/aggregate_code_metadata.py
src/MEDS_transforms/fit_vocabulary_indices.py
src/MEDS_transforms/parser.py
src/MEDS_transforms/reshard_to_split.py
src/MEDS_transforms/runner.py
src/MEDS_transforms/utils.py
src/MEDS_transforms.egg-info/PKG-INFO
src/MEDS_transforms.egg-info/SOURCES.txt
src/MEDS_transforms.egg-info/dependency_links.txt
src/MEDS_transforms.egg-info/entry_points.txt
src/MEDS_transforms.egg-info/requires.txt
src/MEDS_transforms.egg-info/top_level.txt
src/MEDS_transforms/configs/__init__.py
src/MEDS_transforms/configs/_extract.yaml
src/MEDS_transforms/configs/_pipeline.yaml
src/MEDS_transforms/configs/_preprocess.yaml
src/MEDS_transforms/configs/_runner.yaml
src/MEDS_transforms/configs/stage_configs/__init__.py
src/MEDS_transforms/configs/stage_configs/add_time_derived_measurements.yaml
src/MEDS_transforms/configs/stage_configs/convert_to_sharded_events.yaml
src/MEDS_transforms/configs/stage_configs/count_code_occurrences.yaml
src/MEDS_transforms/configs/stage_configs/extract_code_metadata.yaml
src/MEDS_transforms/configs/stage_configs/filter_measurements.yaml
src/MEDS_transforms/configs/stage_configs/filter_subjects.yaml
src/MEDS_transforms/configs/stage_configs/finalize_MEDS_data.yaml
src/MEDS_transforms/configs/stage_configs/finalize_MEDS_metadata.yaml
src/MEDS_transforms/configs/stage_configs/fit_normalization.yaml
src/MEDS_transforms/configs/stage_configs/fit_outlier_detection.yaml
src/MEDS_transforms/configs/stage_configs/fit_vocabulary_indices.yaml
src/MEDS_transforms/configs/stage_configs/merge_to_MEDS_cohort.yaml
src/MEDS_transforms/configs/stage_configs/occlude_outliers.yaml
src/MEDS_transforms/configs/stage_configs/reorder_measurements.yaml
src/MEDS_transforms/configs/stage_configs/reshard_to_split.yaml
src/MEDS_transforms/configs/stage_configs/shard_events.yaml
src/MEDS_transforms/configs/stage_configs/split_and_shard_subjects.yaml
src/MEDS_transforms/extract/README.md
src/MEDS_transforms/extract/__init__.py
src/MEDS_transforms/extract/convert_to_sharded_events.py
src/MEDS_transforms/extract/extract_code_metadata.py
src/MEDS_transforms/extract/finalize_MEDS_data.py
src/MEDS_transforms/extract/finalize_MEDS_metadata.py
src/MEDS_transforms/extract/merge_to_MEDS_cohort.py
src/MEDS_transforms/extract/shard_events.py
src/MEDS_transforms/extract/split_and_shard_subjects.py
src/MEDS_transforms/extract/utils.py
src/MEDS_transforms/filters/README.md
src/MEDS_transforms/filters/__init__.py
src/MEDS_transforms/filters/filter_measurements.py
src/MEDS_transforms/filters/filter_subjects.py
src/MEDS_transforms/mapreduce/__init__.py
src/MEDS_transforms/mapreduce/mapper.py
src/MEDS_transforms/mapreduce/utils.py
src/MEDS_transforms/transforms/__init__.py
src/MEDS_transforms/transforms/add_time_derived_measurements.py
src/MEDS_transforms/transforms/extract_values.py
src/MEDS_transforms/transforms/normalization.py
src/MEDS_transforms/transforms/occlude_outliers.py
src/MEDS_transforms/transforms/reorder_measurements.py
src/MEDS_transforms/transforms/tensorization.py
src/MEDS_transforms/transforms/tokenization.py
tests/__init__.py
tests/test_with_runner.py
tests/utils.py
tests/MEDS_Extract/__init__.py
tests/MEDS_Extract/test_convert_to_sharded_events.py
tests/MEDS_Extract/test_extract.py
tests/MEDS_Extract/test_extract_code_metadata.py
tests/MEDS_Extract/test_extract_no_metadata.py
tests/MEDS_Extract/test_finalize_MEDS_data.py
tests/MEDS_Extract/test_finalize_MEDS_metadata.py
tests/MEDS_Extract/test_merge_to_MEDS_cohort.py
tests/MEDS_Extract/test_shard_events.py
tests/MEDS_Extract/test_split_and_shard_subjects.py
tests/MEDS_Transforms/__init__.py
tests/MEDS_Transforms/test_add_time_derived_measurements.py
tests/MEDS_Transforms/test_aggregate_code_metadata.py
tests/MEDS_Transforms/test_extract_values.py
tests/MEDS_Transforms/test_filter_measurements.py
tests/MEDS_Transforms/test_filter_subjects.py
tests/MEDS_Transforms/test_fit_vocabulary_indices.py
tests/MEDS_Transforms/test_multi_stage_preprocess_pipeline.py
tests/MEDS_Transforms/test_normalization.py
tests/MEDS_Transforms/test_occlude_outliers.py
tests/MEDS_Transforms/test_reorder_measurements.py
tests/MEDS_Transforms/test_reshard_to_split.py
tests/MEDS_Transforms/test_tensorization.py
tests/MEDS_Transforms/test_tokenization.py
tests/MEDS_Transforms/transform_tester_base.py