diff --git a/.github/workflows/meds-etl-test.yml b/.github/workflows/meds-etl-test.yml new file mode 100644 index 0000000..634c793 --- /dev/null +++ b/.github/workflows/meds-etl-test.yml @@ -0,0 +1,51 @@ +name: Run MEDS-ETL tests + +on: + push: + branches: [ "main" ] + pull_request: + branches: [ "main" ] + +jobs: + build: + + runs-on: ubuntu-latest + + strategy: + matrix: + python-version: ["3.10"] + + steps: + - uses: actions/checkout@v3 + + # Clone the MEDS-ETL repository + - name: Clone MEDS-ETL repository + run: git clone https://github.com/Medical-Event-Data-Standard/meds_etl.git + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest + + # Install MEDS-ETL + - name: Install MEDS-ETL + run: | + cd meds_etl + python -m pip install . + + # Download MIMIC-IV-Demo (v2.2) + - name: Download MIMIC-IV-Demo (v2.2) + run: | + cd meds_etl + wget -r -N -c --no-host-directories --cut-dirs=1 -np -P tests/data https://physionet.org/files/mimic-iv-demo/2.2/ + + # Run MEDS-ETL tests + - name: Run MEDS-ETL tests + run: | + cd meds_etl + pytest -v