COMP: Enable pre-commit-hooks safety nets on release-5.4

.pre-commit-config.yaml

@@ -1,8 +1,49 @@
 # .pre-commit-config.yaml
 # for details see https://pre-commit.com
-#
-# No hooks are configured on this branch. This empty file prevents
-# pre-commit from erroring when backporting commits after pre-commit
-# hooks have been configured.
-
-repos: []
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+     - id: check-added-large-files
+       args: ['--maxkb=200']
+       exclude: |
+         (
+         Source/DataDictionary/gdcmPrivateDefaultDicts.cxx|
+         Documentation/watershed.ps
+         )
+     - id: check-ast
+       exclude: "\\/ThirdParty\\/"
+     - id: check-case-conflict
+     - id: check-illegal-windows-names
+     - id: check-json
+       exclude: "\\/ThirdParty\\/"
+     - id: check-merge-conflict
+       exclude: "\\/ThirdParty\\/"
+       args: ['--assume-in-merge']
+     - id: check-toml
+       exclude: "\\/ThirdParty\\/"
+     - id: check-vcs-permalinks
+       exclude: "\\/ThirdParty\\/"
+     - id: check-xml
+       exclude: "\\/ThirdParty\\/"
+     - id: check-yaml
+       exclude: "\\/ThirdParty\\/"
+     - id: check-shebang-scripts-are-executable
+       exclude: "\\/ThirdParty\\/"
+     - id: debug-statements
+       exclude: "\\/ThirdParty\\/"
+     - id: destroyed-symlinks
+     - id: detect-private-key
+     - id: end-of-file-fixer
+       exclude: "\\.(md5|sha|sha512|svg|vtk|vtp)$|^Resources\\/[^\\/]+\\.h$|\\/ColorFiles\\/.+\\.txt$|Data\\/Input\\/.+$|\\/ThirdParty\\/|\\/Data\\/"
+     - id: forbid-new-submodules
+     - id: forbid-submodules
+     - id: mixed-line-ending
+       exclude: "\\.(sha|sha512|svg|vtk|vtp)$|\\/ThirdParty\\/|\\/Data\\/"
+     - id: name-tests-test
+       exclude: "\\/ThirdParty\\/"
+       args: ['--pytest-test-first']
+     - id: no-commit-to-branch
+       args: ['--branch','dashboard','--branch','python-builds','--branch','release','--branch','hooks','--branch', 'main','--branch','main','--pattern','release-*']
+     - id: trailing-whitespace
+       exclude: "\\.(sha|sha512|svg|vtk|vtp)$|\\/ThirdParty\\/|\\/Data\\/"

CMake/ITKSetStandardCompilerFlags.cmake

@@ -229,7 +229,7 @@ function(check_avx_flags avx_flags_var)
 endfunction()
 
 # Check for the presence of SSE2.
-# Adapted from the AVX check and https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/VNL/src/vxl/config/cmake/config/vxl_platform_tests.cxx#L164-L178
+# Adapted from the AVX check and https://github.com/InsightSoftwareConsortium/ITK/blob/e7db79dca282ce8001e9456d1e5b51fe31de48c5/Modules/ThirdParty/VNL/src/vxl/config/cmake/config/vxl_platform_tests.cxx#L164-L178
 function(check_sse2_flags sse2_flags_var)
 
   # set flags to be used in check_cxx_source_runs below

Documentation/Doxygen/ImageSimilarityMetrics.dox

@@ -1,8 +1,8 @@
 /**
 
 \page ImageSimilarityMetricsPage Image Similarity Metrics
- 
-\section MetricsIntroduction Introduction 
+
+\section MetricsIntroduction Introduction
 
 It is a common task in image analysis to require to compare how
 similar two image might be. This comparison may be limited to a
@@ -23,7 +23,7 @@ in a toolkit. You need a set of them because none is able to perform
 the same job as the other.
 
 The following table presents a comparison between image similarity
-metrics. This is by no means an exhaustive comparison but will at 
+metrics. This is by no means an exhaustive comparison but will at
 least provide some guidance as to what metric can be appropiated for
 particular problems.
 

Documentation/Doxygen/Iterators.dox

@@ -298,4 +298,3 @@
 
 
 */
-

Documentation/Doxygen/MainPage.dox

@@ -37,4 +37,3 @@
  * iterators.
  *
  */
-

Documentation/Doxygen/NeighborhoodIterators.dox

@@ -5,7 +5,7 @@
 This document provides a general overview of the intended use of the
 NeighborhoodIterator classes and their associated objects for low-level image
 processing in Itk.  For a more detailed description of the API, please refer to
-the inline Itk documentation and manual.  
+the inline Itk documentation and manual.
 
 \par
 Neighborhood iterators are the abstraction of the concept of \em locality in
@@ -25,16 +25,16 @@ This code in classical \em texbook notation can look like:
   int nx = 512;
   int ny = 512;
   ImageType image(nx,ny);
-  for(int x=1; x<nx-1; x++) 
+  for(int x=1; x<nx-1; x++)
   {
     float sum = 0;
-    for(int y=1; y<ny-1; y++) 
+    for(int y=1; y<ny-1; y++)
     {
       sum += image(x-1,y-1) + image(x  ,y-1) + image(x+1,y-1);
       sum += image(x-1,y  ) + image(x  ,y  ) + image(x+1,y  );
       sum += image(x-1,y+1) + image(x  ,y+1) + image(x+1,y+1);
     }
-  }  
+  }
 \endcode
 
 \par
@@ -45,7 +45,7 @@ by using iterators to dereference pixels, and for a two-dimensional image,
 code-readability may not suffer much.  But what if we want code for three
 or more dimensions?  Before long, the code size and complexity will increase to
 unmanageable levels.  In Itk, we have encapsulated this functionality for
-efficiency, readability, and reusability. 
+efficiency, readability, and reusability.
 
 \section NeighborhoodIteratorsSection Neighborhood iterators
 itk::Image neighborhood iteration and dereferencing is encapsulated in the
@@ -77,7 +77,7 @@ have been omitted for clarity. )
 10  for (unsigned int i = 0; i < ImageType::ImageDimension; ++i) radius[i] = 1;
 11
 12  // Initializes the iterators on the input & output image regions
-13  NeighborhoodIterator it(radius, input_image, 
+13  NeighborhoodIterator it(radius, input_image,
 14                                  output_image->GetRequestedRegion());
 15  ImageIterator out(output_image, output_image->GetRequestedRegion());
 16
@@ -86,32 +86,32 @@ have been omitted for clarity. )
 19    {
 20      float accum = 0.0;
 21      for (unsigned int i = 0; i < it.Size(); ++i)
-22        {    
-23          accum += it.GetPixel(i);  
+22        {
+23          accum += it.GetPixel(i);
 24        }
 25      out.Set(accum/(float)(it.Size()));
 26    }
 \endcode
 
-\par        
+\par
 Note that the computational work is confined to lines 18-26. The code is also
 completely generalized for multiple dimensions.  For example, changing line 1
 to:
 \code
 1   using ImageType = itk::Image<float, 5>;
 \endcode
-produces an averaging filter for five-dimensional images. 
+produces an averaging filter for five-dimensional images.
 
 \par
 The values in the neighborhood are dereferenced through the GetPixel(n) method
-of the iterator.  Think of the iterator as a C array, storing  neighborhood 
+of the iterator.  Think of the iterator as a C array, storing  neighborhood
 values in the same order that they are stored in the image, with the lowest
 dimension as the fastest increasing dimension.
 
 \section OperatorsOperationsSection Neighborhood operators and operations
 NeighborhoodOperators are container classes for generating and storing
 computational kernels such as LaPlacian, Gaussian, derivative, and
-morphological operators.  They provide a generalized interface for creation and 
+morphological operators.  They provide a generalized interface for creation and
 access of the operator coefficients.
 
 \par
@@ -129,7 +129,7 @@ demonstrates this concept.
 4  NeighborhoodInnerProduct IP;
 5
 6  out = out.Begin();
-7  for (it.SetToBegin(); it != it.End(); ++it, ++out) 
+7  for (it.SetToBegin(); it != it.End(); ++it, ++out)
 8  {
 9    out.Set( IP( it, OP) );
 10 }
@@ -144,7 +144,7 @@ operator/operation model.  The mean calculation above is one example.  A
 1  NeighborhoodIterator::RadiusType radius = {1, 0, 0};
 2  NeighborhoodIterator it(radius, inputImage, regionToProcess)
 3  ImageRegionIterator out( outputImage, regionToProcess );
-4  for (it.SetToBegin(); it != it.End(); ++it, ++out) 
+4  for (it.SetToBegin(); it != it.End(); ++it, ++out)
 5  {
 6    out.Set( it.GetPixel(3) - it.GetPixel(2) );
 7  }
@@ -155,7 +155,7 @@ In this example the neighborhood is defined as a three pixel strip
 with width along only the first axis.  Mapping
 the spatial orientation of neighborhood pixels to the array location is the
 responsibility of the code writer.  Some methods such as GetStride(n), which
-returns the stride length in pixels along an axis n, have been provided to help 
+returns the stride length in pixels along an axis n, have been provided to help
 in coding algorithms for arbitrary dimensionality.  The index of the center
 pixel in a neighborhood is always Size()/2.
 
@@ -171,17 +171,17 @@ is appropriate for their algorithm.
 \par
 A SmartNeighborhoodIterator can be used in place of NeighborhoodIterator to
 iterate over an entire image region, but it will incur a penalty on
-performance.  For this reason, it is desirable to process the image differently 
+performance.  For this reason, it is desirable to process the image differently
 over distinct boundary and non-boundary regions.  Itk's definition of image regions
 makes this easy to manage.  The process is as follows: first apply the
 algorithm over all neighborhoods not on the image boundary using the fast
 NeighborhoodIterator, then process each region on the boundary using the
-SmartNeighborhoodIterator.  The size of the boundary regions are defined by the 
+SmartNeighborhoodIterator.  The size of the boundary regions are defined by the
 radius of the neighborhood that you are using.
 
 \par
 Rewriting the inner product code using this approach looks like the following.
-(Here we are using the default SmartNeighborhoodIterator boundary condition and 
+(Here we are using the default SmartNeighborhoodIterator boundary condition and
 omitting some template parameters for simplicity.)
 
 \code
@@ -205,7 +205,7 @@ out = ImageIterator(outputImage, *regions_iterator);
 NeighborhoodIterator it (OP.GetRadius(), inputImage, *regions_iterator);
 NeighborhoodInnerProduct IP;
 out = out.Begin();
-for (it.SetToBegin(); it != it.End(); ++it, ++out) 
+for (it.SetToBegin(); it != it.End(); ++it, ++out)
 {
   out.Set( IP( it, OP) );
 }
@@ -219,7 +219,7 @@ for (regions_iterator++ ; regions_iterator != regions.end(); regions_iterator++)
 {
   out = ImageIterator(outputImage, *regions_iterator);
   sit = SmartNeighborhoodIterator(OP.GetRadius(), inputImage, *regions_iterator);
-  for (sit.SetToBegin(); sit != sit.End(); ++sit, ++out) 
+  for (sit.SetToBegin(); sit != sit.End(); ++sit, ++out)
   {
     out.Set( SIP( sit, OP) );
   }
@@ -242,7 +242,7 @@ AnisotropicDiffusionFunctions and the morphological image filters.
 itk::WatershedSegmenter also makes extensive use of the neighborhood
 iterators.
 
-\par 
+\par
 The best documentation of the API for these objects is are the class
 definitions themselves, since the API is subject to change as the toolkit
 matures and is refined.

Documentation/Doxygen/Registration.dox

@@ -1,10 +1,10 @@
 /**
 
 \page RegistrationPage Registration Techniques
-
-\section RegistrationIntroduction Introduction 
 
-\b Registration is a technique aimed to align two objects using a 
+\section RegistrationIntroduction Introduction
+
+\b Registration is a technique aimed to align two objects using a
 particular transformation.
 
 A typical example of registration is to have two medical images
@@ -15,15 +15,15 @@ a spatial transformation to find the corresponding pixel from one
 image into the other.
 
 Another typical example of registration is to have a geometrical model
-of an organ, let's say a bone. This model can be used to find the 
+of an organ, let's say a bone. This model can be used to find the
 corresponding structure in a medical image. In this case, a spatial
 transformation is needed to find the correct location of the structure
 in the image.
 
 
 \section RegistrationFramework ITK Registration Framework
 
-The Insight Toolkit takes full advantage of the power provided by 
+The Insight Toolkit takes full advantage of the power provided by
 generic programming. Thanks to that, it have been possible to create
 an abstraction of the particular problems that the toolkit is intended
 to solve.
@@ -105,6 +105,6 @@ The evaluation of a metric can be very expensive in computing time. An approach
 
 It is usual to create first a sequence of reduced resolution version of the objects, this set of objects is called a <em> pryramid representation </em>. A Multiresolution method is basically a set of consecutive registration process, each one performed at a particular level of the pyramid, and using as initial transform the resulting transform of the previous process.
 
-Multiresolution offers the double advantage of increasing performance and at the same time improving the stability of the optimization by smoothing out local minima and increasing the capture region of the process. 
+Multiresolution offers the double advantage of increasing performance and at the same time improving the stability of the optimization by smoothing out local minima and increasing the capture region of the process.
 
  */

Documentation/Doxygen/Streaming.dox

@@ -2,7 +2,7 @@
    \page StreamingPage Streaming
 
    \section StreamingIntroduction Introduction
-   
+
    \image html Streaming.gif "Pipelines can be set up to stream data through filters in small pieces."
 
 

Documentation/Doxygen/Threading.dox

@@ -2,7 +2,7 @@
    \page ThreadingPage Threading
 
    \section ThreadingIntroduction Introduction
-   
+
    ITK is designed to run in multiprocessor environments.  Many of
    ITK's filters are multithreaded.  When a multithreading filter
    executes, it automatically divides the work amongst multiprocessors
@@ -15,7 +15,7 @@
    \image html Threading.gif "Filters may process their data in multiple threads in a shared memory configuration."
 
    \section FilterThreadSafety Filter Level Multithreading
-        
+
    A multithreaded filter provides an implementation of the
    ThreadedGenerateData() method (see
    itk::ImageSource::ThreadedGenerateData()) as opposed to the
@@ -41,7 +41,7 @@
    the threads write to this same block of memory but a given thread
    is only allowed to set specific pixels.
 
-   \subsection FilterMemoryAllocation Memory Management 
+   \subsection FilterMemoryAllocation Memory Management
 
    The GenerateData() method is responsible for allocation the output
    bulk data.  For an image processing filter, this corresponds to
@@ -76,10 +76,10 @@
 
    ITK is designed so that different instances of the same class can be
    accessed in different execution threads.  But multiple threads should
-   not attempt to modify a single instance.  This granularity of thread 
+   not attempt to modify a single instance.  This granularity of thread
    safety was chosen as a compromise between performance and flexibility.
    If we allow ITK objects to be modified in multiple threads then ITK
-   would have to mutex every access to every instance variable of a 
+   would have to mutex every access to every instance variable of a
    class.  This would severely affect performance.
 
    \section NumericsThreadSafety Thread Safety in the Numerics Library

Documentation/docs/_static/icon/html_head_content.txt

@@ -6,4 +6,4 @@
 <link rel="shortcut icon" href="icon/favicon.ico">
 <meta name="msapplication-TileColor" content="#da532c">
 <meta name="msapplication-config" content="icon/browserconfig.xml">
-<meta name="theme-color" content="#ffffff">
+<meta name="theme-color" content="#ffffff">

Documentation/docs/releases/5.2.md

@@ -1801,4 +1801,3 @@ Remote Module Changes Since v5.2rc03
 #### Style Changes
 
 -  Move notebooks into examples/ directory directly ([d8ebede](https://github.com/KitwareMedical/ITKUltrasound/commit/d8ebede))
-

Documentation/docs/releases/5.4.0.md

@@ -136,7 +136,7 @@ Unpack optional testing data in the same directory where the Library Source is u
 - Add `itk::Copy(const T & original)`, which simply returns a copy
 - Make `itk::ImageRegion` trivially copyable, remove inheritance (FUTURE)
 - `itk::VTKPolyDataMeshIO` support for reading VTK 5.1 format
-- Add `ITK_DEFAULT_COPY_AND_MOVE(TypeName)` macro definition 
+- Add `ITK_DEFAULT_COPY_AND_MOVE(TypeName)` macro definition
 - Replace `(const std::string)` casts with C++17 `std::string_view`
 - Replace SetSize/Index calls in tests with `region{ index, size }`
 - Optionally limit an `ImageMask` to a specific pixel value
@@ -229,7 +229,7 @@ We extend our gratitude to all the ITK community members who have contributed to
 🗣️ What's Next
 ---------------
 
-ITK 5.4.0 represents a transformative milestone in our documentation journey. The finalization of 5.4.0 was delayed due to dependency issues in the example documentation's infrastructure. While these are addressed, we'll continue to refine the 5.4 series through patch releases. We're excited to eventually migrate the examples to a similar robust foundation in future innovations. 
+ITK 5.4.0 represents a transformative milestone in our documentation journey. The finalization of 5.4.0 was delayed due to dependency issues in the example documentation's infrastructure. While these are addressed, we'll continue to refine the 5.4 series through patch releases. We're excited to eventually migrate the examples to a similar robust foundation in future innovations.
 
 Looking ahead, we're thrilled to announce that ITK 6, our next major release, will showcase a substantial array of modernizations. The community has been hard at work implementing significant improvements that will elevate development with and on the toolkit. Watch for upcoming alpha and beta releases of ITK 6, which will run parallel to our 5.4 maintenance efforts.
 

Documentation/docs/releases/5.4.2.md

@@ -272,4 +272,3 @@ Remote Module Changes Since v5.4.0
 #### Bug Fixes
 
 - Bump Python package version for re-deploy ([9f6654d](https://github.com/InsightSoftwareConsortium/ITKTotalVariation/commit/9f6654d))
-

Documentation/docs/releases/5.4.5.md

@@ -168,4 +168,3 @@ We remain dedicated to supporting current users through:
 #### Bug Fixes
 
 - Fix imread with single-element list and add test ([8480b5f6d3](https://github.com/InsightSoftwareConsortium/ITK/commit/8480b5f6d3))
-

Modules/Nonunit/IntegratedTest/test/itkBasicFiltersHeaderObjCxxTest.mm

@@ -16,5 +16,3 @@
  *
  *=========================================================================*/
 #import "itkBasicFiltersHeaderTest.cxx"
-
-

Modules/Nonunit/IntegratedTest/test/itkCommonHeaderObjCxxTest.mm

@@ -16,6 +16,3 @@
  *
  *=========================================================================*/
 #import "itkCommonHeaderTest.cxx"
-
-
-

Modules/Nonunit/IntegratedTest/wrapping/test/CMakeLists.txt

@@ -1 +0,0 @@
-