Use text format for jupyter notebooks using jupytext

.github/workflows/unit-tests.yml

@@ -34,10 +34,9 @@ jobs:
           pip install --upgrade pip
           # note: installing torch and torchvision together ensures their version compatibility
           pip install torch==2.8.0 torchvision --index-url https://download.pytorch.org/whl/cpu
-          pip install pytest
-          pip install -e .[cpu]
-          pip install -r test-requirements.txt
           pip install jupyter nbconvert pandas matplotlib
+          pip install -r test-requirements.txt
+          pip install -e .[cpu]
       - name: Test with pytest
         shell: bash
         run: |
@@ -59,6 +58,6 @@ jobs:
         shell: bash
         run: |
           export JAX_PLATFORMS=cpu
-          for FILE in $(find docs -name '*.ipynb'); do
-            jupyter nbconvert --to notebook --execute $FILE;
+          for FILE in $(find docs -name '*.py'); do
+              python $FILE
           done

.gitignore

@@ -2,6 +2,8 @@
 __pycache__/
 *.py[codz]
 *$py.class
+*.ipynb  # notebooks should use jupytext, and check in .py / .md format
+docs/site/
 
 # C extensions
 *.so
@@ -195,9 +197,9 @@ cython_debug/
 .abstra/
 
 # Visual Studio Code
-#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
 #   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
 #   you could uncomment the following to ignore the entire vscode folder
 # .vscode/