Fix Sphinx autodoc by setting ANNDATA_CUPY=0 and adding comprehensive mock imports

Author: Andrew Ramirez

.github/workflows/documentation.yml

@@ -29,6 +29,7 @@ jobs:
               uses: astral-sh/setup-uv@v6
             - name: Sphinx build
               run: |
+                  export ANNDATA_CUPY=0
                   uv run --group dev sphinx-build -v docs docs/_build
             - name: Setup Pages
               uses: actions/configure-pages@v5

docs/conf.py

@@ -1,8 +1,12 @@
 """Configuration file for the Sphinx documentation builder."""
 
+import os
 import sys
 from pathlib import Path
 
+# Disable cupy in anndata to avoid import errors during doc build
+os.environ['ANNDATA_CUPY'] = '0'
+
 # Add the parent directory to the path so we can import RISE
 # This allows Sphinx to find the RISE package
 project_root = Path(__file__).parent.parent.resolve()
@@ -57,8 +61,18 @@
     "cupy",
     "torch",
     "scvi",
+    "datashader",
+    "colorcet",
+    "holoviews",
+    "pacmap",
+    "parafac2",
+    "tensorly",
+    "tlviz",
 ]
 
+# Suppress warnings during autodoc
+suppress_warnings = ["app.add_directive"]
+
 # Intersphinx mapping for external documentation
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),