ENH: Ingest ITKCuberille into Modules/Filtering

[hjmjohnson]

Ingests Cuberille from the standalone remote module InsightSoftwareConsortium/ITKCuberille into ITK at Modules/Filtering/Cuberille/ using the v4 ingestion pipeline (PR #6204). Stacked on #6204 — that PR must merge first.

Local validation: pre-commit run --all-files clean; CuberilleTestDriver builds; 25/25 Cuberille tests pass locally in 5.3s.

Pipeline metrics

Metric	Value
Upstream commits → rewritten	200 → 106
Upstream merges → preserved	59 → 30 (no linearization, per feedback_ingest_merge_topology.md)
Blobs scanned in sanitize	148 (cxx=103, py=1, cmake=28, text=5, skip=11)
Blobs reformatted	95 (clang-format / black / gersemi / trailing-ws / EOF)
Commit subjects auto-prefixed	36
Merges visible in git log -- Modules/Filtering/Cuberille	6

v4 deny-pass bug surfaced and fixed during this run

The first attempt at this ingest leaked test/Docker/{Dockerfile,build.sh,run.sh,test.sh} into ITK history, because the v4 ingest driver had only a whitelist pass — no --invert-paths --path-glob deny-pass for CI/packaging scaffolding that lives inside whitelisted directories. Fixed in PR #6204 by porting v3's deny-glob list (Docker, Jenkinsfile, .github, azure-pipelines, .clang-format inside the module subtree, etc.). Re-running this ingest after the fix produced a clean tree with no scaffolding leakage.

Auto-prefix decisions (sample)

prefix counts across the 36 changed subjects:
  ENH:   28
  STYLE:  4
  COMP:   2
  BUG:    1
  DOC:    1

Every commit on the rewritten history starts with a valid ITK prefix (BUG:/COMP:/DOC:/ENH:/PERF:/STYLE:/WIP:). The Utilities/Maintenance/RemoteModuleIngest/sanitize-history.py log records the (sha, chosen-prefix, original-subject) for each decision so the operator can audit before merge.

Follow-up commits in this PR

After the merge commit (ENH: Ingest ITKCuberille into Modules/Filtering), the standard cleanup commits land on top:

• STYLE: Apply gersemi 0.19.3 to Cuberille wrapping test CMakeLists. The v4 sanitize pass runs gersemi 0.24.0; ITK's pre-commit pins 0.19.3. The post-merge pre-commit run --all-files gate caught one CMake file that 0.24.0 considered clean but 0.19.3 wanted re-formatted. Working as designed.
• DOC: Add Modules/Filtering/Cuberille/README.md pointing at the archived upstream.
• COMP: Remove Modules/Remote/Cuberille.remote.cmake (now in-tree).
• ENH: Enable Module_Cuberille:BOOL=ON in pyproject.toml configure-ci.

Phase B (upstream archival) — deferred

Per the v4 design (PR #6204), the upstream archival step is intentionally separated. After this PR merges into ITK main, run:

~/src/ITK/Utilities/Maintenance/RemoteModuleIngest/archive-remote-module.sh \
    Cuberille --itk-pr-number <THIS-PR-NUMBER>

That step pushes the deletion + MIGRATION_README.md → README.md promotion to upstream and flips archived=true. This PR makes no upstream changes; the upstream ITKCuberille repository remains live until the operator manually runs Phase B.

[greptile-apps]

Greptile Summary

This PR ingests ITKCuberille from its standalone remote module into Modules/Filtering/Cuberille/ using the new v4 ingestion pipeline, and adds the pipeline tooling (ingest-module-v4.sh, sanitize-history.py, archive-remote-module.sh) to Utilities/Maintenance/RemoteModuleIngest/. The in-tree module replaces Modules/Remote/Cuberille.remote.cmake and is enabled for CI in pyproject.toml.

• P1 — global #define macros in public header: DEBUG_PRINT, USE_GRADIENT_RECURSIVE_GAUSSIAN, USE_ADVANCED_PROJECTION, and USE_LINESEARCH_PROJECTION are #defined at file scope in the installed header, polluting the preprocessor namespace for all downstream consumers.
• P1 — incorrect >= / <= operators in VertexLookupNode: Both operators use >= / <= on the primary key (m_Y) in their first branch, causing them to short-circuit before checking m_X, which inverts results for equal-Y cases.

Confidence Score: 3/5

Two P1 issues in the ingested public header must be resolved before merge.

Two independent P1 findings both touch the same public header: global macro pollution is a present defect for any consumer that includes the header, and the operator bugs are logically wrong class-level API. The rest of the ingestion (CMake wiring, tests, tooling scripts) looks correct.

Modules/Filtering/Cuberille/include/itkCuberilleImageToMeshFilter.h requires fixes before merge.

Important Files Changed

Filename	Overview
Modules/Filtering/Cuberille/include/itkCuberilleImageToMeshFilter.h	Public header with two issues: four global #define macros that pollute the preprocessor namespace, and logically incorrect >= / <= operators in the private VertexLookupNode class.
Modules/Filtering/Cuberille/include/itkCuberilleImageToMeshFilter.hxx	1052-line header-only implementation; core algorithm looks correct. The four #define guards are consumed here but originate in the .h.
Modules/Filtering/Cuberille/test/CMakeLists.txt	25 CuberilleTest01 variants and CuberilleIssue66 use bare add_test rather than ITK's itk_add_test; the remaining 3 tests use itk_add_test correctly.
Modules/Filtering/Cuberille/itk-module.cmake	Module registration looks correct; DEPENDS and TEST_DEPENDS are appropriately specified; EXCLUDE_FROM_DEFAULT and ENABLE_SHARED match other in-tree modules.
Modules/Remote/Cuberille.remote.cmake	Correctly deleted as part of ingestion; module is now in-tree.
Utilities/Maintenance/RemoteModuleIngest/sanitize-history.py	New ingestion tooling; content-sniffing, formatter wrappers, and commit-callback logic look well-structured and fail-soft. No security concerns.
Utilities/Maintenance/RemoteModuleIngest/ingest-module-v4.sh	Phase A driver script; set -euo pipefail throughout, proper preflight checks, clean argument parsing — no obvious issues.
pyproject.toml	Adds -DModule_Cuberille:BOOL=ON to the CI configure line, enabling the new in-tree module for Python wheel builds.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[upstream ITKCuberille repo] -->|Phase A: ingest-module-v4.sh| B[git-filter-repo: path whitelist + deny-glob]
    B --> C[sanitize-history.py: clang-format / black / gersemi / prefix]
    C --> D[Mode-A merge into ITK main]
    D --> E[Modules/Filtering/Cuberille/]
    D --> F[Remove Modules/Remote/Cuberille.remote.cmake]
    D --> G[pyproject.toml: enable Module_Cuberille]
    E --> H[itk-module.cmake: DEPENDS / TEST_DEPENDS]
    E --> I[include/itkCuberilleImageToMeshFilter.h+.hxx]
    E --> J[test/ + wrapping/]
    D -->|Phase B: deferred post-merge| K[archive-remote-module.sh]
    K --> L[upstream: delete files + flip archived=true]

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_{Reviews (1): Last reviewed commit: "ENH: Enable Module_Cuberille in configur..." | Re-trigger Greptile}

[dzenanz]

Mostly looks good.