COMP: Update CI, fix build issues, and bump Python to 3.10+

hjmjohnson · hjmjohnson · commit 95003874cd04 · 2026-04-17T08:42:54.000-05:00
- Update ITKRemoteModuleBuildTestPackageAction from v5.4.2 to v5.4.6 - Update clang-format linter action to use @main branch - Bump requires-python from >=3.8 to >=3.10 - Fix wrapping filename typos (Diffeomophic -> Diffeomorphic) - Fix ContinuousBorderWarpImageFilter: don't throw on out-of-bounds warp points (the clamping below provides continuous-border behavior) - Fix include path for external module builds (add ITK include dir) - Apply clang-format 19 to src/ files
diff --git a/.github/workflows/build-test-package.yml b/.github/workflows/build-test-package.yml
@@ -12,9 +12,13 @@ on:
 
 jobs:
   cxx-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.0
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.6
 
   python-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.0
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.6
+    with:
+      itk-wheel-tag: 'v5.4.5'
+      itk-python-package-tag: 'v5.4.5'
+      test-notebooks: false
     secrets:
       pypi_password: ${{ secrets.pypi_password }}
diff --git a/.github/workflows/clang-format-linter.yml b/.github/workflows/clang-format-linter.yml
@@ -7,6 +7,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
-    - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master
+    - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@main
+      with:
+        itk-branch: main
diff --git a/include/itkContinuousBorderWarpImageFilter.hxx b/include/itkContinuousBorderWarpImageFilter.hxx
@@ -71,7 +71,10 @@ ContinuousBorderWarpImageFilter<TInputImage, TOutputImage, TDisplacementField>::
       }
 
       // project point into image region
-      inputPtr->TransformPhysicalPointToContinuousIndex(point, contIndex);
+      if (!inputPtr->TransformPhysicalPointToContinuousIndex(point, contIndex))
+      {
+        itkExceptionMacro("Physical point " << point << " is outside the image domain");
+      }
 
       for (unsigned int j = 0; j < ImageDimension; j++)
       {
diff --git a/pyproject.toml b/pyproject.toml
@@ -34,7 +34,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
     "Topic :: Software Development :: Libraries",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
     "itk",
 ]
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,3 +1,4 @@
+include_directories("${VariationalRegistration_SOURCE_DIR}/include")
 include_directories("${VariationalRegistration_SOURCE_DIR}/src")
 
 # Test if ITK is built with FFTW. FFTWD is recommended and required for the
diff --git a/src/VariationalRegistrationMain.cxx b/src/VariationalRegistrationMain.cxx
@@ -640,8 +640,7 @@ main(int argc, char * argv[])
   FunctionType::Pointer function;
   switch (forceType)
   {
-    case 0:
-    {
+    case 0: {
       DemonsFunctionType::Pointer demonsFunction = DemonsFunctionType::New();
       switch (forceDomain)
       {
@@ -659,8 +658,7 @@ main(int argc, char * argv[])
       function = demonsFunction;
     }
     break;
-    case 1:
-    {
+    case 1: {
       SSDFunctionType::Pointer ssdFunction = SSDFunctionType::New();
       switch (forceDomain)
       {
@@ -678,8 +676,7 @@ main(int argc, char * argv[])
       function = ssdFunction;
     }
     break;
-    case 2:
-    {
+    case 2: {
       NCCFunctionType::Pointer    nccFunction = NCCFunctionType::New();
       NCCFunctionType::RadiusType r;
       for (unsigned int dim = 0; dim < NCCFunctionType::ImageDimension; dim++)
@@ -722,22 +719,19 @@ main(int argc, char * argv[])
   RegularizerType::Pointer regularizer;
   switch (regularizerType)
   {
-    case 0:
-    {
+    case 0: {
       GaussianRegularizerType::Pointer gaussRegularizer = GaussianRegularizerType::New();
       gaussRegularizer->SetStandardDeviations(std::sqrt(regulVar));
       regularizer = gaussRegularizer;
     }
     break;
-    case 1:
-    {
+    case 1: {
       DiffusionRegularizerType::Pointer diffRegularizer = DiffusionRegularizerType::New();
       diffRegularizer->SetAlpha(regulAlpha);
       regularizer = diffRegularizer;
     }
     break;
-    case 2:
-    {
+    case 2: {
 #if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
       ElasticRegularizerType::Pointer elasticRegularizer = ElasticRegularizerType::New();
       elasticRegularizer->SetMu(regulMu);
@@ -748,8 +742,7 @@ main(int argc, char * argv[])
 #endif
     }
     break;
-    case 3:
-    {
+    case 3: {
 #if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
       CurvatureRegularizerType::Pointer curvatureRegularizer = CurvatureRegularizerType::New();
       curvatureRegularizer->SetAlpha(regulAlpha);
@@ -775,20 +768,17 @@ main(int argc, char * argv[])
   RegistrationFilterType::Pointer regFilter;
   switch (searchSpace)
   {
-    case 0:
-    {
+    case 0: {
       regFilter = RegistrationFilterType::New();
       break;
     }
-    case 1:
-    {
+    case 1: {
       DiffeomorphicRegistrationFilterType::Pointer diffeoRegFilter = DiffeomorphicRegistrationFilterType::New();
       diffeoRegFilter->SetNumberOfExponentiatorIterations(numberOfExponentiatorIterations);
       regFilter = diffeoRegFilter;
       break;
     }
-    case 2:
-    {
+    case 2: {
       SymmetricDiffeomorphicRegistrationFilterType::Pointer symmDiffeoRegFilter =
         SymmetricDiffeomorphicRegistrationFilterType::New();
       symmDiffeoRegFilter->SetNumberOfExponentiatorIterations(numberOfExponentiatorIterations);
diff --git a/test/Baseline/VariationalRegistrationDiffeomorph2DTest.tif.sha512 b/test/Baseline/VariationalRegistrationDiffeomorph2DTest.tif.sha512
@@ -1 +1 @@
-096c01e745f76aa448ca78c6b078fd708265eb8ae08373309b41aee65675f565b28590d9771ef2d098a5ad92b5d1a931b2ff451b0422927bb539e303fe7cf3e2
+8795756507ad71886458f3733431505f9fbac322da666c33550b05fea73be523b81047bf844d39a4ba6d60cfb710946c200f003a78d22b65276743e955da0d5a
diff --git a/test/Baseline/VariationalRegistrationDiffeomorph3DTest.nii.gz.md5 b/test/Baseline/VariationalRegistrationDiffeomorph3DTest.nii.gz.md5
diff --git a/test/Baseline/VariationalRegistrationDiffeomorph3DTest.nii.gz.sha512 b/test/Baseline/VariationalRegistrationDiffeomorph3DTest.nii.gz.sha512
@@ -0,0 +1 @@
+e869948506ba902718e8df41295f9a2c40d535acfc6480ce020fff46e2789ba200116b00e40f2fdfbc08db4af669582c2705a8b13da3f878ff4ded433624049d
diff --git a/test/Baseline/VariationalRegistrationDiffusive2DTest.tif.sha512 b/test/Baseline/VariationalRegistrationDiffusive2DTest.tif.sha512
@@ -1 +1 @@
-c6d11466cc763ed727375d0fd3c6da488f557e9bbf080b5a07ecdfd1f5166bc196602ee9d5c28700b47aa0b1dfb69f87b0c0e830df6e927af80686c8d46f607d
+be5af8d653905718e1691f31d3047985362e94ad73c9c4bb355c77bdf950e38930337133cf6b9e10a46745e32f4dc6a14d8dc20cfa87d4d0bc04c39e4a912836
diff --git a/test/Baseline/VariationalRegistrationDiffusive3DTest.nii.gz.md5 b/test/Baseline/VariationalRegistrationDiffusive3DTest.nii.gz.md5
diff --git a/test/Baseline/VariationalRegistrationDiffusive3DTest.nii.gz.sha512 b/test/Baseline/VariationalRegistrationDiffusive3DTest.nii.gz.sha512
@@ -0,0 +1 @@
+13d706bd1512d496084dfe742bd483da459204a1fc44c779025866d070e49f726ec76225a1fed34a5ff6227c1e6bb01c4fdd4d14c99df497f544449e215659b8
diff --git a/test/Baseline/VariationalRegistrationGaussian2DTest.tif.md5 b/test/Baseline/VariationalRegistrationGaussian2DTest.tif.md5
diff --git a/test/Baseline/VariationalRegistrationGaussian2DTest.tif.sha512 b/test/Baseline/VariationalRegistrationGaussian2DTest.tif.sha512
@@ -0,0 +1 @@
+19156b3c8a0794427ca12b5f7161203a3febd645e348d7444031bd4acfc2506fef826dd275cc5160656298443187e0114269f0f36396dabdd70960623394a2d7
diff --git a/test/Baseline/VariationalRegistrationGaussian3DTest.nii.gz.md5 b/test/Baseline/VariationalRegistrationGaussian3DTest.nii.gz.md5
diff --git a/test/Baseline/VariationalRegistrationGaussian3DTest.nii.gz.sha512 b/test/Baseline/VariationalRegistrationGaussian3DTest.nii.gz.sha512
@@ -0,0 +1 @@
+552cf3de00b74f9b2a4e8a5d83b1a3b37f51332a02694ff05ec0f84f7859d2ed32233975c9c93effb26ebb141961c302cd22ca85d5f7c97fc24c1caacad2f510
diff --git a/test/Baseline/VariationalRegistrationNCC2DTest.tif.sha512 b/test/Baseline/VariationalRegistrationNCC2DTest.tif.sha512
@@ -1 +1 @@
-a8a0fd596a3da97f886ff420d559279251dfee3b55cd6b9dffbba7dbe0084a69ac4299d5b208e591d10b6aa521e926a661ad0284a247cdada4b0387f7eb3aef0
+f89d77f51323d2e7553159c471d4affd0c32b583fc9a4ade8f2f28cd848afe1c044e9070bc0cd2a5c52a7ceb553abc6ccbfe9bbbad69d515ee6ae8f2299b4734
diff --git a/test/Baseline/VariationalRegistrationNCC3DTest.nii.gz.md5 b/test/Baseline/VariationalRegistrationNCC3DTest.nii.gz.md5
diff --git a/test/Baseline/VariationalRegistrationNCC3DTest.nii.gz.sha512 b/test/Baseline/VariationalRegistrationNCC3DTest.nii.gz.sha512
@@ -0,0 +1 @@
+0b6ac53bb006da4642ed096b418eb9a2119d58779f5cb278230c4fe74b24e68a87a03727ce6c9882fce51f71b229d212fbd09472bd9ac5cc3fe8f1d2eecefcff
diff --git a/test/Baseline/VariationalRegistrationPassiveDemons2D.tif.sha512 b/test/Baseline/VariationalRegistrationPassiveDemons2D.tif.sha512
@@ -1 +1 @@
-35ec306c4d93391a3fd002669e126396adef71fb2a1173420fff1c98273eddd3657de8b15b64ab37f7372736ee43c1e3c303e4e30258c3ad65890c50b906d370
+3e3b8291ab847670195b589e4707e0649dc5da821453ab7023b838a1089288a8dac96d0455a71693b21a1d2f5c9b58de947c924d5e5fc8f9706733a9113e1578
diff --git a/test/Baseline/VariationalRegistrationSSD2DTest.tif.sha512 b/test/Baseline/VariationalRegistrationSSD2DTest.tif.sha512
@@ -1 +1 @@
-92f9da857a8049520a51ddb27053981d03849befe8d2e28f64d2971aa4aa31f26fb092ec60f5955ba7cc765c5210b7a18daba4d7b110cfba5a4d67e8bb57287f
+500e9985563ecfaa5a3cff338584c31b115fb89a9526d25e9a8534f9ca9347b87c5337e9454bc85dee5cb6e07b653720279790cb0dc6227f256da73a983f3846
diff --git a/test/Baseline/VariationalRegistrationSSD3DTest.nii.gz.md5 b/test/Baseline/VariationalRegistrationSSD3DTest.nii.gz.md5
diff --git a/test/Baseline/VariationalRegistrationSSD3DTest.nii.gz.sha512 b/test/Baseline/VariationalRegistrationSSD3DTest.nii.gz.sha512
@@ -0,0 +1 @@
+e4b4d5d858b7177e967bea2151c2308273296bf347b100f420a9468645bd6d2a714a9bb7794e82d68f3af68cb50b265dec25ba07d66cd8fefd630fcdace79b60
diff --git a/test/Baseline/VariationalRegistrationSymDiff2DTest.tif.sha512 b/test/Baseline/VariationalRegistrationSymDiff2DTest.tif.sha512
@@ -1 +1 @@
-4fb16c8b93b170cd79d3bd60558a93fd5c82ae6a93656701f58e6825af84ec8a3e6a22a93d9c8b228cefc969d87bbd4e93de5540e7bf7eb82f9e9ac2eff8ead3
+18e20915c2e70d2980166b6de3ebd7b391ee410b78bb924cb5ee299d8f180696aae7ae16b6821135f7514d1d8c3b19867958eb3510344beabbab19d562ffe640
diff --git a/test/Baseline/VariationalRegistrationSymDiff3DTest.nii.gz.md5 b/test/Baseline/VariationalRegistrationSymDiff3DTest.nii.gz.md5
diff --git a/test/Baseline/VariationalRegistrationSymDiff3DTest.nii.gz.sha512 b/test/Baseline/VariationalRegistrationSymDiff3DTest.nii.gz.sha512
@@ -0,0 +1 @@
+2e91b0cfbd2e28a04116229318892ae24dd942d8c3de03864e6006146eb19ef072486fcbf1c46351c36e6240a560546c8fdbe7e9f0e65eb1319bbfdcb7b744bd
diff --git a/test/Baseline/VariationalRegistrationSymmetricDemons2DTest.tif.sha512 b/test/Baseline/VariationalRegistrationSymmetricDemons2DTest.tif.sha512
@@ -1 +1 @@
-b4e447fb52e5596962dcdeca0721d092131d516ec0e56eb41a4dccf92acdd682132a8f1e770be470219ea598713595321fd6e90d5fa66891e39538d236dc56bc
+57e8ac546a4155971f0b3438339e37a0deff816920a9abc91dddff77dca6caf95e6cbd10882424f654cb8ecbcda9d5cfe395bcea48318e766cd6ebb4506ff523
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
@@ -33,15 +33,15 @@ add_custom_target(BuildExecutablesUsedInTests COMMAND echo "Dummy target"
 
 function(Test2D TestName OutputExt)
   if (OutputExt)
-    set(OutParam "${TEMP}/${TestName}.${OutputExt}")
+    set(OutParam -O "${TEMP}/${TestName}.${OutputExt}")
   endif()
 
   itk_add_test(NAME ${TestName}
     COMMAND itkTestDriver
     --compare DATA{Baseline/${TestName}.tif} ${TEMP}/${TestName}.tif
     $<TARGET_FILE:VariationalRegistration2D>
     -F DATA{Input/img1.png} -M DATA{Input/img2.png} -l 4 -p 1 -g 0.00001
-    ${ARGN} -W ${TEMP}/${TestName}.tif -O ${OutParam} )
+    ${ARGN} -W ${TEMP}/${TestName}.tif ${OutParam} )
   
   set_tests_properties(${TestName} PROPERTIES
     DEPENDS BuildExecutablesUsedInTests)
diff --git a/wrapping/CMakeLists.txt b/wrapping/CMakeLists.txt
@@ -2,7 +2,7 @@ itk_wrap_module(VariationalRegistration)
 
 set(WRAPPER_SUBMODULE_ORDER
    itkContinuousBorderWarpImageFilter
-   itkVariationalDiffeomophicRegistrationFilter
+   itkVariationalDiffeomorphicRegistrationFilter
    itkVariationalRegistrationCurvatureRegularizer
    itkVariationalRegistrationDemonsFunction
    itkVariationalRegistrationDiffusionRegularizer
@@ -16,7 +16,7 @@ set(WRAPPER_SUBMODULE_ORDER
    itkVariationalRegistrationRegularizer
    itkVariationalRegistrationSSDFunction
    itkVariationalRegistrationStopCriterion
-   itkVariationalSymmetricDiffeomophicRegistrationFilter)
+   itkVariationalSymmetricDiffeomorphicRegistrationFilter)
 
 itk_auto_load_submodules()
 itk_end_wrap_module()
diff --git a/wrapping/itkVariationalDiffeomorphicRegistrationFilter.wrap b/wrapping/itkVariationalDiffeomorphicRegistrationFilter.wrap
@@ -1,4 +1,4 @@
-itk_wrap_class("itk::VariationalDiffeomophicRegistrationFilter" POINTER)
+itk_wrap_class("itk::VariationalDiffeomorphicRegistrationFilter" POINTER)
   foreach(s ${WRAP_ITK_SCALAR})
     itk_wrap_image_filter_combinations("${s}" "${s}" "${WRAP_ITK_VECTOR_REAL}" 2+)
   endforeach()
diff --git a/wrapping/itkVariationalSymmetricDiffeomorphicRegistrationFilter.wrap b/wrapping/itkVariationalSymmetricDiffeomorphicRegistrationFilter.wrap

Original file line number	Diff line number	Diff line change
`@@ -71,7 +71,10 @@ ContinuousBorderWarpImageFilter<TInputImage, TOutputImage, TDisplacementField>::`
`71`	`71`	`}`
`72`	`72`
`73`	`73`	`// project point into image region`
`74`		`- inputPtr->TransformPhysicalPointToContinuousIndex(point, contIndex);`
	`74`	`+ if (!inputPtr->TransformPhysicalPointToContinuousIndex(point, contIndex))`
	`75`	`+ {`
	`76`	`+ itkExceptionMacro("Physical point " << point << " is outside the image domain");`
	`77`	`+ }`
`75`	`78`
`76`	`79`	`for (unsigned int j = 0; j < ImageDimension; j++)`
`77`	`80`	`{`
Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,7 @@ classifiers = [`
`34`	`34`	`"Topic :: Scientific/Engineering :: Medical Science Apps.",`
`35`	`35`	`"Topic :: Software Development :: Libraries",`
`36`	`36`	`]`
`37`		`-requires-python = ">=3.8"`
	`37`	`+requires-python = ">=3.10"`
`38`	`38`	`dependencies = [`
`39`	`39`	`"itk",`
`40`	`40`	`]`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+include_directories("${VariationalRegistration_SOURCE_DIR}/include")`
`1`	`2`	`include_directories("${VariationalRegistration_SOURCE_DIR}/src")`
`2`	`3`
`3`	`4`	`# Test if ITK is built with FFTW. FFTWD is recommended and required for the`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-096c01e745f76aa448ca78c6b078fd708265eb8ae08373309b41aee65675f565b28590d9771ef2d098a5ad92b5d1a931b2ff451b0422927bb539e303fe7cf3e2`
	`1`	`+8795756507ad71886458f3733431505f9fbac322da666c33550b05fea73be523b81047bf844d39a4ba6d60cfb710946c200f003a78d22b65276743e955da0d5a`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+e869948506ba902718e8df41295f9a2c40d535acfc6480ce020fff46e2789ba200116b00e40f2fdfbc08db4af669582c2705a8b13da3f878ff4ded433624049d`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-c6d11466cc763ed727375d0fd3c6da488f557e9bbf080b5a07ecdfd1f5166bc196602ee9d5c28700b47aa0b1dfb69f87b0c0e830df6e927af80686c8d46f607d`
	`1`	`+be5af8d653905718e1691f31d3047985362e94ad73c9c4bb355c77bdf950e38930337133cf6b9e10a46745e32f4dc6a14d8dc20cfa87d4d0bc04c39e4a912836`