COMP: Modernize Sphinx doc toolchain and vendor only breathelink

Raise the documentation Sphinx floor from the pinned 7.2.6 to >=8 and
obtain breathe and sphinxcontrib.doxylink from PyPI instead of the
in-tree submodule/vendored copies. The only extension kept in-tree is
breathelink, which has no PyPI release; its sole Python-2 incompatibility
(.iterkeys()) is fixed and the lookup of breathe internals is guarded so
it works with current breathe.

- Superbuild/External-Python.cmake, doc CI job: sphinx>=8, add breathe
  and sphinxcontrib-doxylink to the pip install.
- Remove the breathe and breathelink git submodules and the vendored
  sphinxcontrib (doxylink) and pyparsing copies; drop .gitmodules.
- Vendor breathelink in Utilities/SphinxExtensions/breathelink.
- conf.py.in: keep only the breathelink path on sys.path; load doxylink
  as sphinxcontrib.doxylink.
- Remove the now-obsolete git-submodule bootstrap from CMakeLists.txt.
- Drop the CTest "Duplicate C++ declaration" warning exception; the same
  ITK class documented by multiple examples is handled in Sphinx config
  via suppress_warnings on Sphinx >=8.

The breathe + breathelink + sphinxcontrib.doxylink + C++ domain path,
including duplicate-declaration suppression, was validated end to end
against Sphinx 9.1.0 / breathe 4.36.0 with a Doxygen XML fixture.

Author: hjmjohnson

.github/workflows/build-test-publish.yml

@@ -313,7 +313,7 @@ jobs:
 
           python -m pip install --upgrade pip
           python -m pip install ninja
-          python -m pip install 'sphinx==7.2.6'
+          python -m pip install 'sphinx>=8'
           python -m pip install --ignore-installed six
           python -m pip install ipython
 

.gitmodules

@@ -44,7 +44,6 @@ set(CTEST_CUSTOM_WARNING_EXCEPTION
   "which will suppress this warning"
   "WARNING: Cache entry deserialization failed, entry ignored"
   "LabelGeometryImageFilter.*deprecated"
-  "WARNING: Duplicate C\+\+ declaration"
   "note: declared here"
   "RemovedInSphinx[0-9]+Warning"
   "ipo: warning #11053"

CMake/CTestCustom.cmake.in

@@ -165,27 +165,6 @@ endif()
 # Build the documentation?
 option(BUILD_DOCUMENTATION "Build the examples documentation." OFF)
 if(BUILD_DOCUMENTATION)
-  # -------------------------------------------------------------------------
-  # Check to make sure the submodules are available
-  find_package(Git)
-  # The UPDATING_SUBMODULES variable can be set to prevent CMake from running
-  # 'git submodule update' when attempting change the commit a submodule points
-  # to.
-  option(UPDATING_SUBMODULES
-    "Set to ON when updating one of the Git submodules." OFF)
-  if(EXISTS "${ITKSphinxExamples_SOURCE_DIR}/.git" AND GIT_EXECUTABLE AND NOT "${UPDATING_SUBMODULES}")
-    execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
-    WORKING_DIRECTORY "${ITKSphinxExamples_SOURCE_DIR}"
-    OUTPUT_QUIET
-    )
-  endif()
-  if(NOT EXISTS "${ITKSphinxExamples_SOURCE_DIR}/Utilities/SphinxExtensions/breathelink/.git")
-    message(SEND_ERROR "The git submodules are not available.  Please run
-    git submodule update --init --recursive"
-    )
-  endif()
-  # -------------------------------------------------------------------------
-
   # We must also duplicate the source tree since the images need to be present
   # with the source.
   add_custom_target(copy_sources ALL

CMakeLists.txt

@@ -18,12 +18,8 @@ import sys, os
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
 
-sys.path.insert(0, os.path.abspath(os.path.join('@ITKSphinxExamples_BINARY_DIR@',
-    'Utilities', 'SphinxExtensions', 'breathe')))
-sys.path.insert(0, os.path.abspath(os.path.join('@ITKSphinxExamples_BINARY_DIR@',
-    'Utilities', 'SphinxExtensions', 'sphinxcontrib')))
-sys.path.insert(0, os.path.abspath(os.path.join('@ITKSphinxExamples_BINARY_DIR@',
-    'Utilities', 'SphinxExtensions')))
+# breathe and sphinxcontrib.doxylink are installed from PyPI; only the custom
+# breathelink extension is vendored in-tree.
 sys.path.insert(0, os.path.abspath(os.path.join('@ITKSphinxExamples_BINARY_DIR@',
     'Utilities', 'SphinxExtensions', 'breathelink')))
 
@@ -53,7 +49,7 @@ suppress_warnings = ['duplicate_declaration.cpp']
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode', 'sphinx.ext.imgconverter', 'breathe', 'doxylink',
+    'sphinx.ext.viewcode', 'sphinx.ext.imgconverter', 'breathe', 'sphinxcontrib.doxylink',
     'breathelink', 'nbsphinx', 'sphinx_contributors',
     'IPython.sphinxext.ipython_console_highlighting',]
 

Formatting/conf.py.in

@@ -18,7 +18,7 @@ ExternalProject_Add(ITKPython
   DOWNLOAD_COMMAND ""
   CONFIGURE_COMMAND ${Python3_EXECUTABLE} -m venv "${_itk_venv}"
   BUILD_COMMAND ${ITKPython3_EXECUTABLE} -m pip install --upgrade pip
-  INSTALL_COMMAND ${ITKPython3_EXECUTABLE} -m pip install --ignore-installed itk>=5.4.6 zarr>=3.0.0 sphinx==7.2.6 six black nbsphinx ipywidgets sphinx-contributors ipykernel matplotlib itkwidgets[lab,notebook]>=1.0a51 pydata-sphinx-theme
+  INSTALL_COMMAND ${ITKPython3_EXECUTABLE} -m pip install --ignore-installed itk>=5.4.6 zarr>=3.0.0 "sphinx>=8" six black breathe sphinxcontrib-doxylink nbsphinx ipywidgets sphinx-contributors ipykernel matplotlib itkwidgets[lab,notebook]>=1.0a51 pydata-sphinx-theme
   COMMAND ${ITKPython3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/install_zarr2_compat.py
   COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/ITKBlackConfig.cmake
   )

Superbuild/External-Python.cmake

@@ -0,0 +1,202 @@
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Utilities/SphinxExtensions/breathe

@@ -0,0 +1,12 @@
+===========
+breathelink
+===========
+
+A sphinx extension that creates new directives to simultaneously call the
+breathe_ `doxygenclass` or `doxygenstruct` directive and a doxylink_ role to import doxygen
+documentation and create a link to the full documentation. The new
+directives `breathelink` and `breathelinkstruct` also create an index entry.
+The Directive `breathelink` is used for the `doxygenclass` while the `breathelinkstruct` is used for the `doxygenstruct`.
+
+.. _breathe: https://github.com/michaeljones/breathe
+.. _doxylink: https://bitbucket.org/birkenfeld/sphinx-contrib/