COMP: Build against ITK main; sync ExternalData config with ITK

Superbuild ITK_TAG v5.4.2 -> main, matching the C++ CI jobs and
picking up post-5.4.2 fixes behind the Python baseline mismatches.
pip itk pins -> >=5.4.6; zarr>=3.0.0 satisfies ngff-zarr OME-Zarr 0.5
(nbsphinx notebook execution failed without it).

ExternalData URL templates and module now mirror ITK main: adds the
Girder hashsum mirror (sole host of some legacy sha512 objects, e.g.
ComputeFFTInOneDimension), filebase and pinata public gateways, and
the WASI symlink guard; drops dead estuary.tech/w3s.link and the
released-root-CID gateways. The project-specific gin.g-node.org
mirror and ExternalData_LINK_CONTENT=CID are retained.

Author: hjmjohnson

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

@@ -264,7 +264,7 @@ jobs:
         run: |
             python -m pip install --upgrade pip
             python -m pip install ninja
-            python -m pip install itk>=5.4rc3
+            python -m pip install itk>=5.4.6
             python -m pip install matplotlib
             python -m pip install itkwidgets
             # Issues with 5.7.0

CMake/ExternalData.cmake

@@ -999,7 +999,6 @@ function(_ExternalData_get_from_object_store hash algo var_obj var_success)
   foreach(dir ${ExternalData_OBJECT_STORES})
     set(obj "${dir}/${algo}/${hash}")
     if(EXISTS "${obj}")
-      message(STATUS "Found object: \"${obj}\"")
       set("${var_obj}" "${obj}" PARENT_SCOPE)
       set("${var_success}" 1 PARENT_SCOPE)
       return()
@@ -1013,7 +1012,6 @@ function(_ExternalData_download_object name hash algo var_obj var_success var_er
   foreach(dir ${ExternalData_OBJECT_STORES})
     set(obj "${dir}/${algo}/${hash}")
     if(EXISTS "${obj}")
-      message(STATUS "Found object: \"${obj}\"")
       set("${var_obj}" "${obj}" PARENT_SCOPE)
       set("${var_success}" "${success}" PARENT_SCOPE)
       return()

CMake/ITKSphinxExamplesExternalData.cmake

@@ -1,3 +1,4 @@
+set(ExternalData_SOURCE_ROOT "${PROJECT_SOURCE_DIR}")
 get_filename_component(_ITKExternalData_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
 include(${_ITKExternalData_DIR}/ExternalData.cmake)
 
@@ -18,52 +19,38 @@ if(NOT ExternalData_OBJECT_STORES)
 endif()
 list(APPEND ExternalData_OBJECT_STORES
   # Local data store populated by the ITK pre-commit hook
-  "${CMAKE_SOURCE_DIR}/.ExternalData"
+  "${PROJECT_SOURCE_DIR}/.ExternalData"
   )
 
-set(ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID bafybeib6yijwyl52gkalx6griio2wsibowlrt3v5wmkkuqlnuvku64c3ra)
+set(ExternalData_BINARY_ROOT ${PROJECT_BINARY_DIR}/ExternalData)
 
+# Expands %(algo:lower)
 set(ExternalData_URL_ALGO_CID_lower cid)
+set(ExternalData_URL_ALGO_MD5_lower md5)
 set(ExternalData_URL_TEMPLATES "" CACHE STRING
   "Additional URL templates for the ExternalData CMake script to look for testing data. E.g.
 file:///var/bigharddrive/%(algo)/%(hash)")
 mark_as_advanced(ExternalData_URL_TEMPLATES)
 if(NOT ITK_FORBID_DOWNLOADS)
   list(APPEND ExternalData_URL_TEMPLATES
+    # Data published on GitHub Pages
+    "https://insightsoftwareconsortium.github.io/ITKTestingData/%(algo)/%(hash)"
     # Local IPFS gateway
     "http://127.0.0.1:8080/ipfs/%(hash)"
-
-    # Data published on GitHub Pages (note: not complete due to file size
-    # limit)
-    "https://insightsoftwareconsortium.github.io/ITKTestingData/%(algo)/%(hash)"
-
-    # Released data rsync'd to Kitware's Apache web server
-    "https://itk.org/files/ExternalData/%(algo)/%(hash)"
-
-    # Restricted gateway with released data
-    "https://itk.mypinata.cloud/ipfs/${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}/Objects/CID/%(hash)"
-
-    # New data on web3.storage
-    "https://w3s.link/ipfs/%(hash)"
-
-    # Released data on web3.storage
-    "https://${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}.ipfs.w3s.link/Objects/CID/%(hash)"
-
-    # Released data on estuary.tech
-    "https://api.estuary.tech/gw/ipfs/${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}/Objects/CID/%(hash)"
-
-    # Protocol Labs gateway
-    "https://${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}.ipfs.dweb.link/Objects/CID/%(hash)"
-
-    # Gateway for arbitrary new files, uploaded to web3.storage
-    "https://dweb.link/ipfs/%(hash)"
-
     # Protocol Labs gateway
     "https://ipfs.io/ipfs/%(hash)"
-
+    # Filebase gateway
+    "https://ipfs.filebase.io/ipfs/%(hash)"
+    # Gateway for data pinned on pinata
+    "https://gateway.pinata.cloud/ipfs/%(hash)"
     # Cloudflare gateway
     "https://cloudflare-ipfs.com/ipfs/%(hash)"
-
+    # Additional gateway (modern but has redirect)
+    "https://dweb.link/ipfs/%(hash)"
+    # Data published on Girder
+    "https://data.kitware.com:443/api/v1/file/hashsum/%(algo)/%(hash)/download"
+    # Data published by developers using git-gerrit-push.
+    "https://itk.org/files/ExternalData/%(algo)/%(hash)"
     # DataLad repository on gin.g-node.org
     "https://gin.g-node.org/InsightSoftwareConsortium/ITKSphinxExamplesData/raw/main/Objects/CID/%(hash)"
     )
@@ -73,7 +60,7 @@ endif()
 set(ExternalData_LINK_CONTENT CID)
 
 # Emscripten currently has difficulty reading symlinks.
-if(EMSCRIPTEN)
+if(EMSCRIPTEN OR WASI)
   set(ExternalData_NO_SYMLINKS 1)
 endif()
 

Superbuild/External-ITK.cmake

@@ -2,8 +2,8 @@
 # Get and build itk
 
 if(NOT ITK_TAG)
-  # ITK release 2025-01-02
-  set(ITK_TAG "v5.4.2")
+  # Track ITK main, matching the itk-git-tag used by the C++ CI jobs
+  set(ITK_TAG "main")
 endif()
 
 set(_vtk_args)

Superbuild/External-Python.cmake

@@ -18,6 +18,6 @@ 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>=5.4.2 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==7.2.6 six black nbsphinx ipywidgets sphinx-contributors ipykernel matplotlib itkwidgets[lab,notebook]>=1.0a51 pydata-sphinx-theme
   COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/ITKBlackConfig.cmake
   )