COMP: Build against ITK main; repair ExternalData, baselines, and docs CI by hjmjohnson · Pull Request #456 · InsightSoftwareConsortium/ITKSphinxExamples

hjmjohnson · 2026-06-11T01:01:06Z

Builds the examples against ITK main (was v5.4.2), recreates 20 lost Core/Common visuals, and repairs everything that surfaced once the stricter toolchain and dashboard actually ran: ExternalData staging, Python baseline skew, ITK 6 deprecations, the warning gate, and the docs environment. All 13 CI checks are green.

Change inventory (10 commits)

Commit	What
COMP: Build against ITK main; sync ExternalData config	Superbuild `ITK_TAG` → `main`; pip `itk>=5.4.6`, `zarr>=3`; URL templates mirror ITK; zarr2 compat shim for itkwidgets in the docs venv; drops the imported `ExternalData_BINARY_ROOT` that mis-staged fixtures
ENH: ComputeFFTInOneDimension sha512 → cid	Legacy links converted; objects republished
DOC: Recreate lost Core/Common example visuals	20 figures from #440 were unrecoverable (ITKTestingData #63/#66 hold the new blobs)
COMP: Tolerate one intensity level in six baseline comparisons	itk 5.4.6 wheels vs ITK main round one gray-level apart at quantization boundaries
STYLE: Replace deprecated iterator GetIndex and RNG Initialize calls	Tree-wide sweep to `*WithIndex` iterators and `SetSeed()` (ITK 6 deprecations; GCC flags more sites than AppleClang)
COMP: Exempt benign lines from the warning gate	`UseITK.cmake` deprecation (~350 configure lines), pip cache notice, example/file names containing "Warning", missing-doxygen-class lookups
COMP: Configure CTestCustom into the superbuild dir, COPYONLY	The dashboard ctest runs at the superbuild root and never loaded the exceptions; `configure_file` without COPYONLY also substituted away the list's self-references
COMP: Add ITK-style pre-commit configuration	clang-format v19.1.7 (tracks ITK's pin), black 25.12.0 (matches super-linter), pyupgrade, standard hygiene hooks
STYLE: Apply pre-commit mechanical fixes	EOF/whitespace normalization, exec bits, black/pyupgrade output (117 files)
DOC: Store executed outputs in ConvertNumPyArrayToitkImage notebook + Sphinx warning fixes	nbsphinx now skips executing it (itkwidgets `view()` is zarr-2-only); title underline + literal-block lexing fixes

Known follow-ups

Migrate ~350 example CMakeLists from include(${ITK_USE_FILE}) to imported targets (UseITK deprecation currently exempted).
Nightly InsightDoxygen XML is missing itk::AddImageFilter and itk::Statistics::SampleToHistogramFilter (lookups exempted; needs an upstream ITK doxygen-artifact fix).
Five .ipynb files contain invalid JSON (adjacent-string concatenation); excluded from the JSON hook until repaired.
itkwidgets zarr 3 incompatibility tracked upstream; the venv shim and stored notebook outputs decouple this PR from it.

hjmjohnson · 2026-06-11T01:32:13Z

Finding from #455's re-run: the sha512→cid conversion here is required, not cosmetic — the top-level CMakeLists.txt data-staging glob matches *.cid only, so the 6 .sha512 content links were never staged into the binary tree (MouseLiverRF.mha does not exist), and the baseline-comparison macro's string(REPLACE .cid "") likewise passes literal .mha.sha512 paths as baselines. The FFT tests have been structurally unable to run since those links were added.

hjmjohnson · 2026-06-11T02:14:41Z

Folded the visual-cid fix from #455 (closed) into this PR as f759c48 — with ITKTestingData#63/#64/#65 all merged, every content link this PR's CI needs is now published. Remaining known blocker: the ITKReview/zlib link regression on ITK main hits the superbuild jobs (fix validated locally; ITK PR pending).

hjmjohnson · 2026-06-11T23:06:15Z

Fixed the 277-test failure from the previous run: the ExternalData config sync imported ITK's ExternalData_BINARY_ROOT=${PROJECT_BINARY_DIR}/ExternalData, but this project's test macros reference staged fixtures at ${CMAKE_CURRENT_BINARY_DIR}/<Example>/<file>, which requires the default binary root. Dropped the line (fixup into the config-sync commit). Verified locally: previously-failing GetImageSize/ReadAPointSet/ReadWriteVectorImage/Iterate* tests all pass.

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.

Last remaining hash-based links in the repository; blobs published under CID in ITKTestingData#64.

The 20 PNGs referenced since InsightSoftwareConsortium#440 were never published to ITKTestingData and are unrecoverable from any public source; every build of Module_SphinxExamples fails 20 ExternalData fetches. Point the .cid files at recreated diagrams (ITKTestingData#63) and fix the Operator.png/Operation.png reference mismatch.

The pip itk 5.4.6 wheels and ITK main round differently at quantization boundaries, leaving pixels one gray-level apart (plus sub-integer FFT float noise) between Python and C++ example outputs compared against shared baselines.

ITK main deprecates ImageConstIterator::GetIndex in favor of the WithIndex iterator variants, and MersenneTwister Initialize() in favor of SetSeed(). The zero-warning dashboard gate fails on these once the superbuild targets ITK main.

Every example includes ${ITK_USE_FILE}, which ITK main deprecates; migrating ~350 example CMakeLists to imported targets is follow-up work.

Standard hygiene hooks plus clang-format v19.1.7 (must track ITK main's pin; the lint CI job resolves it from ITK at run time), black, and pyupgrade for Python.

end-of-file/trailing-whitespace normalization, exec bits on shebang scripts, black and pyupgrade modernization of utility and example Python.

nbsphinx (execute=auto) skips notebooks with stored outputs, matching the other five notebooks; executing this one in the docs environment fails because itkwidgets view() requires the zarr 2 API.

review-notebook-app · 2026-06-12T08:43:48Z

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Lengthen a short title underline, lex the FFT output block as text, and exempt doxygenclass lookups for classes absent from the current nightly InsightDoxygen XML.

thewtex

Amazing, Hans!!

hjmjohnson · 2026-06-12T10:28:50Z

@greptileai review

dzenanz

Mostly looks good.

dzenanz · 2026-06-12T12:35:07Z

@@ -0,0 +1,53 @@
+# Mirrors ITK's .pre-commit-config.yaml style gates for C++ and Python.


Are these file mode changes intentional? Why make these ~30 .py files executable? All of them should have the same file mode.

hjmjohnson

This is a stable starting point.

github-actions Bot added area:Filtering Issues affecting the Filtering module type:Compiler Compiler support or related warnings type:Infrastructure Infrastructure/ecosystem related changes, such as CMake or buildbots type:Data Changes to example data (usually displayed images) labels Jun 11, 2026

hjmjohnson marked this pull request as ready for review June 11, 2026 01:08

github-actions Bot added area:Core Issues affecting the Core module area:Documentation Issues affecting the Documentation module labels Jun 11, 2026

hjmjohnson mentioned this pull request Jun 11, 2026

ENH: Add CID blob for ITKSphinxExamples FilterImageRegion.png InsightSoftwareConsortium/ITKTestingData#66

Merged

hjmjohnson force-pushed the fix/ci-itk-pin-and-deps branch from f759c48 to d2521d3 Compare June 11, 2026 02:30

hjmjohnson mentioned this pull request Jun 11, 2026

COMP: Recover lost ExternalData objects from actions cache (do not merge) #457

Closed

hjmjohnson force-pushed the fix/ci-itk-pin-and-deps branch from d2521d3 to cc33939 Compare June 11, 2026 23:05

github-actions Bot added area:Segmentation Issues affecting the Segmentation module language:C++ Changes to C++ examples labels Jun 12, 2026

hjmjohnson force-pushed the fix/ci-itk-pin-and-deps branch 2 times, most recently from 6585d6f to 3be442b Compare June 12, 2026 01:34

hjmjohnson force-pushed the fix/ci-itk-pin-and-deps branch 5 times, most recently from 53fc455 to a8eb989 Compare June 12, 2026 03:58

hjmjohnson force-pushed the fix/ci-itk-pin-and-deps branch 5 times, most recently from 7cc9ccd to 3411ef0 Compare June 12, 2026 07:30

hjmjohnson added 8 commits June 12, 2026 02:57

ENH: Convert ComputeFFTInOneDimension content links from sha512 to cid

45a6f2d

Last remaining hash-based links in the repository; blobs published under CID in ITKTestingData#64.

COMP: Exempt the UseITK.cmake deprecation from the warning gate

52d5b26

Every example includes ${ITK_USE_FILE}, which ITK main deprecates; migrating ~350 example CMakeLists to imported targets is follow-up work.

COMP: Add ITK-style pre-commit configuration

3711827

Standard hygiene hooks plus clang-format v19.1.7 (must track ITK main's pin; the lint CI job resolves it from ITK at run time), black, and pyupgrade for Python.

STYLE: Apply pre-commit mechanical fixes across the tree

7658627

end-of-file/trailing-whitespace normalization, exec bits on shebang scripts, black and pyupgrade modernization of utility and example Python.

hjmjohnson force-pushed the fix/ci-itk-pin-and-deps branch from 3411ef0 to 7658627 Compare June 12, 2026 07:57

DOC: Store executed outputs in ConvertNumPyArrayToitkImage notebook

fa9225c

nbsphinx (execute=auto) skips notebooks with stored outputs, matching the other five notebooks; executing this one in the docs environment fails because itkwidgets view() requires the zarr 2 API.

github-actions Bot added the type:Python Notebook Changes to Python Notebook examples label Jun 12, 2026

DOC: Fix Sphinx warnings surfaced by the documentation gate

9ca80aa

Lengthen a short title underline, lex the FFT output block as text, and exempt doxygenclass lookups for classes absent from the current nightly InsightDoxygen XML.

thewtex approved these changes Jun 12, 2026

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hjmjohnson changed the title ~~COMP: Build against ITK main; sync ExternalData config; fix docs env~~ COMP: Build against ITK main; repair ExternalData, baselines, and docs CI Jun 12, 2026

dzenanz reviewed Jun 12, 2026

View reviewed changes

hjmjohnson commented Jun 12, 2026

View reviewed changes

hjmjohnson merged commit c9be6b0 into InsightSoftwareConsortium:main Jun 12, 2026
13 checks passed

hjmjohnson mentioned this pull request Jun 12, 2026

COMP: Update Doxygen artifacts to v6.0b01; revert doxygenclass warning suppression #458

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COMP: Build against ITK main; repair ExternalData, baselines, and docs CI#456

COMP: Build against ITK main; repair ExternalData, baselines, and docs CI#456
hjmjohnson merged 10 commits into
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hjmjohnson:fix/ci-itk-pin-and-deps

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		@@ -0,0 +1,53 @@
		# Mirrors ITK's .pre-commit-config.yaml style gates for C++ and Python.

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