let claude add tht tutorials

Author: AnneHartebrodt

.github/workflows/static.yaml

@@ -18,13 +18,19 @@ jobs:
         with:
           python-version: '3.x'
 
+      - name: Install pandoc
+        run: sudo apt-get install -y pandoc
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints furo
+          pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints furo nbsphinx
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           pip install . # Install the local package to make it importable
-          
+
+      - name: Copy tutorial notebooks from examples
+        run: cp examples/*.ipynb docs/source/tutorials/
+
       - name: Build Sphinx Documentation
         run: |
           sphinx-build -b html docs/source docs/build/html

docs/source/api.rst

@@ -10,5 +10,10 @@ API Reference
    netmap.model
    netmap.grn
    netmap.masking
-   netmap.downstream
+   netmap.downstream.clustering
+   netmap.downstream.edge_selection
+   netmap.downstream.gene_clustering
+   netmap.downstream.markers
+   netmap.downstream.plotting
+   netmap.downstream.regulon
    netmap.utils

docs/source/conf.py

@@ -25,8 +25,13 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.intersphinx',
     'sphinx_autodoc_typehints',
+    'nbsphinx',
 ]
 
+# Never re-execute notebooks during the Sphinx build.
+# Notebooks must be pre-run (outputs saved) before committing.
+nbsphinx_execute = 'never'
+
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
     'numpy': ('https://numpy.org/doc/stable', None),

docs/source/index.rst

@@ -37,6 +37,12 @@ Installation
    # pip — GPU dependencies must be added manually
    pip install -e .
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Tutorials
+
+   tutorials/index
+
 .. toctree::
    :maxdepth: 4
    :caption: API Reference

docs/source/tutorials/index.rst

@@ -0,0 +1,11 @@
+Tutorials
+=========
+
+Step-by-step notebooks demonstrating the full NETMAP pipeline.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Tutorials
+
+   1-preprocess-data
+   3-downstream