test on multiple versions of python

Author: alpae

.github/workflows/run_example.yml

@@ -7,35 +7,36 @@ on:
 jobs:
   test-example-dataset:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout code
         uses: actions/checkout@v6
 
-      - name: Set up Python
-        uses: actions/setup-python@v6
+      - name: Install uv and set the Python version
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.10'
+          python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .
+      - name: Install the project
+        run: uv sync --all-extras --dev
 
       - name: Download LUCA.h5
         run: wget https://omabrowser.org/All/LUCA.h5
 
       - name: Run omamer search
         run: |
           mkdir output
-          omamer search \
+          uv run omamer search \
             --db LUCA.h5 \
             --query example_data/UP000005640_9606.fasta \
             --out output/UP000005640_9606.omamer
 
       - name: Run omark
         run: |
-          omark \
+          uv run omark \
             -f output/UP000005640_9606.omamer \
             -d LUCA.h5 \
             -o output/