Add miiv_demo

.gitattributes

@@ -1,5 +1,10 @@
 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/eicu_demo/features.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
+tests/testdata/mimic_demo/sta.parquet filter=lfs diff=lfs merge=lfs -text
+tests/testdata/mimic_demo/features.parquet filter=lfs diff=lfs merge=lfs -text
+tests/testdata/miiv_demo/dyn.parquet filter=lfs diff=lfs merge=lfs -text
+tests/testdata/miiv_demo/sta.parquet filter=lfs diff=lfs merge=lfs -text
+tests/testdata/miiv_demo/features.parquet filter=lfs diff=lfs merge=lfs -text

.github/workflows/ci.yaml

@@ -30,15 +30,29 @@ jobs:
         run: python -m pip install --no-build-isolation --no-deps --disable-pip-version-check -e .
       - name: install icd-mappings
         run: pip install icd-mappings
+      - name: Move features.parquet out of the way
+        run: |
+          mv tests/testdata/eicu_demo/features.parquet tests/testdata/eicu_demo/old_features.parquet
+          mv tests/testdata/mimic_demo-carevue/features.parquet tests/testdata/mimic_demo-carevue/old_features.parquet
+          mv tests/testdata/miiv_demo/features.parquet tests/testdata/miiv_demo/old_features.parquet
       - 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
+      - name: feature engineering for mimic_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: feature engineering for miiv_demo
+        run: |
+          python icu_features/icd_codes.py --data_dir "tests/testdata" --dataset "miiv_demo"
+          python icu_features/feature_engineering.py --dataset "miiv_demo" --data_dir "tests/testdata"
+      # - name: compare new to old features.parquet
+      #   run: |
+      #     python -c "import pyarrow.parquet as pq;old = pq.read_table('tests/testdata/eicu_demo/old_features.parquet');new = pq.read_table('tests/testdata/eicu_demo/features.parquet');assert old.equals(new)"
+      #     python -c "import pyarrow.parquet as pq;old = pq.read_table('tests/testdata/mimic_demo-carevue/old_features.parquet');new = pq.read_table('tests/testdata/mimic_demo-carevue/features.parquet');assert old.equals(new)"
+      #     python -c "import pyarrow.parquet as pq;old = pq.read_table('tests/testdata/miiv_demo/old_features.parquet');new = pq.read_table('tests/testdata/miiv_demo/features.parquet');assert old.equals(new)"
       - name: Pytest
         run: pytest tests
 

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python>=3.12
+  - python==3.12
   - setuptools
   - pip
   - click