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Update outcomes, add script for ICD codes, update load function #7

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Merged
mlondschien merged 16 commits into from
Jul 4, 2025
Merged

Update outcomes, add script for ICD codes, update load function #7

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574c2a4
Update outcomes, add script for ICD codes, update load function.
mlondschien Jun 12, 2025
a72dfe9
Add remaining los back in
mlondschien Jun 12, 2025
6e32c1e
Merge branch 'main' into update-outcomes
mlondschien Jun 12, 2025
d17699d
Format and cleanup.
mlondschien Jul 4, 2025
a123af8
Update test files
mlondschien Jul 4, 2025
1362ac0
Add code to split datasets mimic->mimic-carevue and mimic-metavision.
mlondschien Jul 4, 2025
669f49c
Refer to icu_features.
mlondschien Jul 4, 2025
8ec0c41
Compute icd codes in CI
mlondschien Jul 4, 2025
503d54c
Fix code.
mlondschien Jul 4, 2025
bb56e00
Test mimic_demo as well
mlondschien Jul 4, 2025
61c09b0
Pin polars.
mlondschien Jul 4, 2025
445a085
Fix ci.
mlondschien Jul 4, 2025
9fb45e7
Fix unit tests.
mlondschien Jul 4, 2025
d215e87
Split into unit and integration tests.
mlondschien Jul 4, 2025
92071a0
Revert splitting.
mlondschien Jul 4, 2025
744aaa1
Test mimic_demo-carevue as well
mlondschien Jul 4, 2025
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3 changes: 3 additions & 0 deletions .gitattributes
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Original file line number Diff line number Diff line change
@@ -1,2 +1,5 @@
tests/testdata/eicu_demo/dyn.parquet filter=lfs diff=lfs merge=lfs -text
tests/testdata/eicu_demo/sta.parquet filter=lfs diff=lfs merge=lfs -text
tests/testdata/eicu_demo/hospital.parquet filter=lfs diff=lfs merge=lfs -text
tests/testdata/mimic_demo/dyn.parquet filter=lfs diff=lfs merge=lfs -text
tests/testdata/mimic_demo/sta.parquet filter=lfs diff=lfs merge=lfs -text
16 changes: 12 additions & 4 deletions .github/workflows/ci.yaml
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Expand Up @@ -5,7 +5,7 @@ on:
pull_request:

jobs:
unittest:
integration-tests:
name: Unit tests - ${{ matrix.PYTHON_VERSION }}
runs-on: ubuntu-latest
strategy:
Expand All @@ -28,12 +28,20 @@ jobs:
environment-file: environment.yml
- name: Install repository
run: python -m pip install --no-build-isolation --no-deps --disable-pip-version-check -e .
- name: Run feature_engineering.py
run: python icu_features/feature_engineering.py --dataset "eicu_demo" --data_dir "tests/testdata"
- name: install icd-mappings
run: pip install icd-mappings
- name: feature engineering for eicu_demo
run: |
python icu_features/icd_codes.py --data_dir "tests/testdata" --dataset "eicu_demo"
python icu_features/feature_engineering.py --dataset "eicu_demo" --data_dir "tests/testdata"
- name: feature engineering for eicu_demo
run: |
python icu_features/split_datasets.py --data_dir "tests/testdata"
python icu_features/icd_codes.py --data_dir "tests/testdata" --dataset "mimic_demo-carevue"
python icu_features/feature_engineering.py --dataset "mimic_demo-carevue" --data_dir "tests/testdata"
- name: Pytest
run: pytest tests


pre-commit-checks:
name: "Linux - pre-commit checks - Python 3.12"
timeout-minutes: 30
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2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -8,6 +8,6 @@ dependencies:
- pip
- click
- numpy>=2.1
- polars
- polars==1.26
- pytest
- pyarrow
3 changes: 3 additions & 0 deletions icu_features/__init__.py
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@@ -0,0 +1,3 @@
from .load import load

__all__ = ["load"]
3 changes: 1 addition & 2 deletions icu_features/constants.py
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Expand Up @@ -2,7 +2,7 @@

VARIABLE_REFERENCE_PATH = Path(__file__).parents[1] / "resources" / "variables.tsv"

HORIZONS = [8, 24, 72]
HORIZONS = [8, 24]

CAT_MISSING_NAME = "(MISSING)"

Expand Down Expand Up @@ -124,7 +124,6 @@

CONTINUOUS_FEATURES = [
"mean",
"sq_mean",
"std",
"slope",
"fraction_nonnull",
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