Looking at your requirements files, I notice that sphinx itself isn't…

… explicitly listed in either requirements file. While some dependencies might pull it in as a secondary dependency, it's better to explicitly specify it.

I'd suggest updating your docs/requirements.txt to

I see the issue now. There are a few potential problems:
The sphinx-notes/pages@v3 action you're using is quite minimal and might not be installing all required dependencies. Your documentation requires several extensions (numpydoc, m2r2, etc.).
The mdinclude directive you're using in index.rst comes from m2r2, but the dependencies need to be properly installed.
I'd recommend modifying your sphinx-to-github-pages.yml workflow to explicitly install the dependencies:

.github/workflows/sphinx-to-github-pages.yml

@@ -17,5 +17,18 @@ jobs:
       pages: write
       id-token: write
     steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r docs/requirements.txt
+
     - id: deployment
       uses: sphinx-notes/pages@v3

docs/requirements.txt

@@ -1,4 +1,5 @@
 -e .
+sphinx>=4.0
 numpydoc
 m2r2
 sphinxcontrib.mermaid