Fixing the now extreme long time to pip install during gen doc, causing timeout failure on readthedoc

docs/requirements.txt

@@ -1,12 +1,8 @@
 Sphinx==4.1.2
 sphinx-autobuild==2021.3.14
-myst-parser==0.15.2
-numpy>=1.21.6
-matplotlib==3.3.4
-ipywidgets==7.6.4
-pandas==1.1.5
-nbclient==0.5.4
-myst-nb==0.13.0
+myst-nb==0.17.2  # this version is fine in python 3.8 and avoids pulling in multiple nbformat packages
+myst-parser==0.18.0
+lxml_html_clean  # needed by myst-nb
 linkify-it-py==1.0.1  # https://myst-parser.readthedocs.io/en/latest/syntax/optional.html?highlight=linkify#linkify
 sphinx-togglebutton==0.2.3
 sphinx-copybutton==0.4.0
@@ -18,17 +14,7 @@ ablog==0.10.19
 docutils==0.16  # 0.17 causes error. https://github.com/executablebooks/MyST-Parser/issues/343
 pydata_sphinx_theme==0.6.3
 sphinxemoji==0.1.8
-scipy
-scikit-image>=0.17.2
-plotly
-nibabel>=3.2.1
-monai>=1.0.0
 torch>=1.12.0
-numpy-stl>=2.12.0
-trimesh>=3.8.11
-pydicom
-PyPDF2>=2.11.1
-highdicom>=0.18.2
 sphinx-autodoc-typehints==1.12.0
 sphinxcontrib-applehelp==1.0.2
 sphinxcontrib-devhelp==1.0.2
@@ -37,4 +23,3 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
 sphinxcontrib-serializinghtml==1.1.5
 sphinxcontrib-mermaid==0.7.1
-lxml_html_clean

docs/source/conf.py

@@ -19,6 +19,9 @@
         f"{READTHEDOCS_PROJECT}/envs/{READTHEDOCS_VERSION}/bin/activate; ../../run setup read_the_docs'",
         shell=True,
     )
+    # Print LD_LIBRARY_PATH for verification
+    ld_library_path = os.environ.get("LD_LIBRARY_PATH", "")
+    print(f"LD_LIBRARY_PATH: {ld_library_path}")
     subprocess.call(
         "/bin/bash -c 'source /home/docs/checkouts/readthedocs.org/user_builds/"
         f"{READTHEDOCS_PROJECT}/envs/{READTHEDOCS_VERSION}/bin/activate; ../../run setup_gen_docs'",

run

@@ -302,10 +302,11 @@ get_package_info() {
 
 install_python_dev_deps() {
     local config="${1:-dev}"
+    local is_read_the_docs="false"
     if [ -n "${VIRTUAL_ENV}" ] || [ -n "${CONDA_PREFIX}" ]; then
         # Read the Docs site is using specific setuptools version so should not upgrade it.
         if [ "$config" = "read_the_docs" ]; then
-            run_command ${MONAI_PY_EXE} -m pip install -q -U pip wheel build
+            is_read_the_docs="true"
         else
             run_command ${MONAI_PY_EXE} -m pip install -q -U setuptools pip wheel build
         fi
@@ -329,6 +330,26 @@ install_python_dev_deps() {
     # fix_holoscan_import
 
     install_edit_mode
+
+    # Install packages overridden by Holoscan package if readthedocs is enabled
+    if [ ${is_read_the_docs} = "true" ]; then
+        # Upgrade pip overridden by Holoscan
+        run_command ${MONAI_PY_EXE} -m pip install -q -U pip wheel build
+        # Upgrade PyYAML to avoid the issue with the version installed by Holoscan
+        run_command ${MONAI_PY_EXE} -m pip install -U PyYAML
+
+        # Install cuda runtime dependency
+        run_command ${MONAI_PY_EXE} -m pip install nvidia-cuda-runtime-cu12
+
+        # Copy the cuda runtime library to the fixed location (workaround for readthedocs) so that
+        # we can leverage the existing LD_LIBRARY_PATH (configured by the readthedocs UI) to locate the cuda runtime library.
+        # (LD_LIBRARY_PATH is set to /home/docs/ for that purpose)
+        # Note that 'python3.8' is hard-coded here, it should be updated if the Python version changes by
+        # .readthedocs.yml or other configurations.
+        run_command ls -al /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.8/site-packages/nvidia/cuda_runtime/lib/
+        run_command cp /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.8/site-packages/nvidia/cuda_runtime/lib/*.so* /home/docs/
+        run_command ls -al /home/docs/
+    fi
 }
 
 fix_holoscan_import() {