Run notebooks in CI

.github/workflows/notebooks.yml

@@ -0,0 +1,33 @@
+name: Notebooks
+
+on:
+    push:
+      branches: [ develop ]
+    pull_request:
+      branches: [ main, develop ]
+
+jobs:
+    build:
+      runs-on: ubuntu-latest
+
+      steps:
+        - uses: actions/checkout@v4
+        - name: Initialize Python
+          uses: actions/[email protected]
+          with:
+            python-version: '3.11'
+        - name: Setup Python
+          run: |
+            python -m pip install --upgrade pip jupyter
+            python -m pip install .
+            python -m ipykernel install --user --name run-notebook --display-name "Run notebook"
+        - name: Run notebooks
+          run: |
+            # The functional annotation of RPGRIP1, STXBP1, and KBG takes too long.
+            # However, we can add them later, if we will really want that.
+            cohorts=(MAPK8IP3 PPP2R1A SUOX)
+            for cohort in ${cohorts[@]}; do
+              nb="notebooks/${cohort}/${cohort}.ipynb"
+              printf "Processing notebook at %s\n" ${nb}
+              jupyter execute --kernel_name run-notebook ${nb}
+            done