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kwrobot
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Sep 6, 2018
cmake_minimum_required(VERSION 3.9.5 FATAL_ERROR)
foreach(p
## Only policies introduced after the cmake_minimum_required
## version need to explicitly be set to NEW.
CMP0070 #3.10.0 Define ``file(GENERATE)`` behavior for relative paths.
CMP0071 #3.10.0 Let ``AUTOMOC`` and ``AUTOUIC`` process ``GENERATED`` files.
)
if(POLICY ${p})
cmake_policy(SET ${p} NEW)
endif()
endforeach()
Change-Id: I30c9a4f2401bf83bcdb56ba89d44b24ca8342853
kwrobot
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Mar 4, 2021
…n metric Fix uninitialized variable use in `ANTS` neighborhood correlation metric: ensure that `fixedImageGradient` and `movingImageGradient` have valid values before assigning them to the `scanMem` struct that scans over images. Fixes: ``` Run-Time Check Failure #3 - The variable 'fixedImageGradient' is being used without being initialized. ``` The bug was affecting a number of tests in the `ITKRegistrationMethodsv4Test` module. Signaled at https://open.cdash.org/viewTest.php?onlyfailed&buildid=7067466 and https://open.cdash.org/viewTest.php?onlyfailed&buildid=7069241
kwrobot
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Apr 29, 2024
Found with thread sanitizer (TSan) running the `itkANTSNeighborhoodCorrelationImageToImageRegistrationTest` unit test.
There was already a `m_ANTSAssociateOnceFlag` flag for use with `std::call_once`, so I just used that in this place too (it's already used elsewhere).
Partial backtrace from TSan:
```
WARNING: ThreadSanitizer: data race (pid=79176)
Write of size 8 at 0x000108f02240 by thread T2:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
Previous write of size 8 at 0x000108f02240 by thread T14:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
```
kwrobot
pushed a commit
that referenced
this pull request
May 30, 2024
Found with thread sanitizer (TSan) running the `itkANTSNeighborhoodCorrelationImageToImageRegistrationTest` unit test.
There was already a `m_ANTSAssociateOnceFlag` flag for use with `std::call_once`, so I just used that in this place too (it's already used elsewhere).
Partial backtrace from TSan:
```
WARNING: ThreadSanitizer: data race (pid=79176)
Write of size 8 at 0x000108f02240 by thread T2:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
Previous write of size 8 at 0x000108f02240 by thread T14:
#0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
#1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
#2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
#3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
#4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
```
The pre-commit-style.bash file should be runnable in stand-alone mode to allow testing failure cases in isolation outside of the commit process.
Template definition (InIm1) doesn't match regular expression
This file is not used and is empty.
The KWStyle for requiring namespace conformance is not needed for these two files.
DOC: Updates for release testing data uploads
The "while loop" always accesses vvec[0] which would be an access violation if the size is zero. Make a function that uses a for loop (with no iterations in the zero size case) to encapsulate the behavior.
If constexpr feature was introduced to allow compile-time branching based on constant expressions. Unlike regular if statements, which are evaluated at runtime, the if constexpr allows the compiler to discard branches of code that do not apply. It means only the branch of code for which the condition is true is compiled and other code branch is discarded during compilation.
The SetDoublePrecision function should never be overridden. This function was used in the construction and a warning indicating that calling virtual functions from constructors is runtime (aka dangerous) dependent.
Initial bug reported in SimpleITK/SimpleITK#2220. On 64-bit windows system, truncation to 32-bit (unsigned long) was occouring when setting VectorImages with over 4GB buffers.
BUG: Fix 32-bit truncation on VectorImage Accessor
FOR RELEASE BUG: Fix 32-bit truncation on VectorImage Accessor
Demonstrate community activity and motivate involvement. Add to the README and ReadTheDocs Contributing index.
Broken link.
Preallocate with reserve and use emplace. Removes copying of iterators.
DOC: Add repobeats stats to README, contributing docs
Additionally update to use std::vector range-based loop removing call to ProcessObject::GetNumberOfIndexedInputs.
Indexes were incorrectly accessed with pre-increment instead of post-increment
Use `ITK_TRY_EXPECT_NO_EXCEPTION` macro in `ImageCompose` tests: - Use `ITK_TRY_EXPECT_NO_EXCEPTION` macro when updating filters in lieu of `try/catch` blocks for the sake of readability and compactness, and to save typing/avoid boilerplate code. - Only place with the macro the code that might raise exceptions.
Conform to ITK style guidelines in test ending message across the `ImageCompose` module test files: add it where missing and use the same message consistently. Take advantage of the commit to remove unnecessary comments about objects being destroyed when exiting the test main method.
Conform to ITK style guidelines in test argument check message across the `ImageCompose` module test files: add the missing argument message where missing and use the same message consistently.
Perform first the test input argument check across the `ImageCompose` module test files. Take advantage of the commit to add the missing argument message where missing and use the same message consistently.
Remove unnecessary/uninformative comment block in `ImageCompose` module test.
Do not capitalize variable first letter: adhere to ITK style guidelines.
STYLE: Miscellaneous `ImageCompose` test style enhancements
This is a follow-up to bbffe4f.
Moved the member function definitions of member functions that have an empty
member function definition from their "itk*.hxx" file to the corresponding
"itk*.h" file, and into their class definition.
Found by regular expression `^..[^:,].+\)\r\n{}` in "itk*.hxx" files.
- Follow-up to pull request #5198
commit b94770d
"STYLE: Move empty member functions with empty param list from .hxx to .h"
Closes #5179. To address warnings of the style: ...ITK/Modules/Core/Common/include/itkImageBoundaryCondition.h:123: warning: argument 'outputRequestedRegion' of command @param is not found in the argument list of itk::ImageBoundaryCondition< TInputImage, TOutputImage >::GetInputRequestedRegion(const RegionType &inputLargestPossibleRegion, const RegionType &) const
…ation Closes #2481. Avoid itkLegacyMacro from appearing in the API docs.
Add to Wrapping/DoxygenConfig.cmake the two lines that were recently added to Utilities/Doxygen/DoxygenConfig.cmake.
To prevent warnings about large graphs. Closes #5184.
When in the automatically generated module / topics page there were no dependencies present there was still the word "Dependencies".
This extra style sheet is no longer needed. 77e28a7 greatly expanded it size. It is unclear whether that was needed.
Second PR out of N, converting raw inline citations with various styles to using a bibliography database and the doxygen cite command. Bibtex file was formatted using bibtex-tidy (https://github.com/FlamingTempura/bibtex-tidy). This tool can be used as a pre-commit hook but currently does not have an option for just performing compliance checking so not added to .pre-commit-config.yaml file.
DOC: Convert from raw in-code citations to bibtex (2/N)
With the newer versions of doxygen (i.e. 1.9.8 and newer) the old modules pages is missing. As of doxygen 1.9.8 the modules have been renamed to topics to prevent confusion with C++ modules.
Third PR out of N, converting raw inline citations with various styles to using a bibliography database and the doxygen cite command. Bibtex file was formatted using bibtex-tidy (https://github.com/FlamingTempura/bibtex-tidy). This tool can be used as a pre-commit hook but currently does not have an option for just performing compliance checking so not added to .pre-commit-config.yaml file.
DOC: Convert from raw in-code citations to bibtex (3/N)
Fourth and final PR, converting raw inline citations with various styles to using a bibliography database and the doxygen cite command. Bibtex file was formatted using bibtex-tidy (https://github.com/FlamingTempura/bibtex-tidy). This tool can be used as a pre-commit hook but currently does not have an option for just performing compliance checking so not added to .pre-commit-config.yaml file.
DOC: Convert from raw in-code citations to bibtex (4/4)
Moved the member function definitions of `const`member functions that have an empty
member function definition from their "itk*.hxx" file to the corresponding
"itk*.h" file, and into their class definition.
Found by regular expression `^..[^:,].+\) const\r\n{}` in "itk*.hxx" files.
- Follow-up to pull request #5198
commit b94770d
"STYLE: Move empty member functions with empty param list from .hxx to .h"
The problem is a result of filtering and as the dox files don't contain "C++" code but just comments, there is no need to run them through the "grouping filter".
The old code was flipping left/right axis instead of anterior/posterior. The bug was introduced with the original feature on November 22, 2005: 15372e8
Addresses warning about incorrect usage of the `@cite` command like: `Modules/Segmentation/LevelSets/include/itkCurvesLevelSetFunction.h:49: warning: Illegal command '@cite' found as part of a title section`
The warning addressed: Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h:139: warning: Found unknown command '\dennis1983'
By upgrading doxygen version from 1.9.6 to 1.13.2, the defaults for these settings changed from: GENERATE_TREEVIEW = NO DISABLE_INDEX = NO to GENERATE_TREEVIEW = YES DISABLE_INDEX = YES Co-authored-by: Albert GitHub <[email protected]>
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