Reconfigure for jupyter build execute (#57)

* Refactor data loading

* Refactor data loading

* Reconfigure for jupyter execution

Author: mathieuboudreau

.github/workflows/deploy.yml

@@ -34,20 +34,30 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-          
+      - name: Install system dependencies for Jupyter
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
       # Install Python dependencies
       - name: Install Python dependencies
         run: |
           python -m venv venv
           source venv/bin/activate
           pip install -r binder/requirements.txt
+      - name: Install and configure Jupyter
+        run: |
+          python -m ipykernel install --user
+          jupyter kernelspec list --json
       - uses: actions/setup-node@v4
         with:
           node-version: 18.x
       - name: Install MyST Markdown
         run: npm install -g mystmd
       - name: Build HTML Assets
-        run: myst build --execute --html
+        run: |
+          export JUPYTER_PATH=$(python -c "import jupyter_core; print(jupyter_core.paths.jupyter_path()[0])")
+          mkdir -p $JUPYTER_PATH
+          myst build --execute --html
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:

binder/requirements.txt

@@ -11,4 +11,7 @@ nbformat>=4.2.0
 pandas
 nibabel
 jupyter
-scikit-learn
+scikit-learn
+ipykernel 
+myst-nb
+jupyter-cache