Execute notebooks at documentation generation (#102)

Author: anissa111

.github/workflows/build.yml

@@ -40,6 +40,10 @@ jobs:
         if: inputs.build_from_code_artifact != 'true'
         uses: actions/checkout@v4
 
+      - name: set environment variables
+        run: |
+          echo "TODAY=$(date +%Y-%m-%d)" >> $GITHUB_ENV
+
       - name: Download code artifact
         id: get_code_artifact
         if: inputs.build_from_code_artifact == 'true'
@@ -57,10 +61,23 @@ jobs:
           unzip pr_code.zip
           rm -f pr_code.zip
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install sphinx-book-theme myst-nb sphinx-design nbsphinx sphinxcontrib-bibtex pandas
+      - name: environment setup
+        id: env-setup
+        continue-on-error: true
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yml
+          cache-environment: true
+          cache-environment-key: "build-${{env.TODAY}}"
+
+      - name: retry environment set up if failed
+        if: steps.env-setup.outcome == 'failure'
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          download-micromamba: false
+          environment-file: environment.yml
+          cache-environment: true
+          cache-environment-key: "build-${{env.TODAY}}"
 
       - name: make html
         run: |