Update buildsystem to support customapp bundling #149

jcfr · 2023-01-13T11:48:12Z

No description provided.

This commit updates default to account for Slicer/Slicer@dedb6c04d (COMP: Require at least C++17)

This commit fixes warnings like the following: CMake Deprecation Warning at /path/to/Slicer-Release/VTK-build/lib/cmake/vtk-9.1/vtk-config.cmake:75 (message): The new name for the 'vtkIOLegacy' component is 'IOLegacy'

This commit fixes the following warning: CMake Deprecation Warning at /path/to/Slicer-Release/VTK-build/lib/cmake/vtk-9.1/vtk-use-file-deprecated.cmake:1 (message): The `VTK_USE_FILE` is no longer used starting with 8.90. Call Stack (most recent call first): UKFTractography.cmake:34 (include) CMakeLists.txt:97 (include)

File ITKSetStandardCompilerFlags copied from ITK v5.1b01 This commit fixes the following error: CMake Error at /path/to/Slicer-build/ITK/CMake/ITK_CheckCCompilerFlag.cmake:29 (check_c_compiler_flag): Unknown CMake command "check_c_compiler_flag". Adapted from: * NIRALUser/ShapePopulationViewer@53edc736d (Fix configuration updating ITKSetStandardCompilerFlags) * NIRALUser/ShapePopulationViewer@aecbfec22 (COMP: Fix inconsistent dll linkage error on windows)

Update PreventInSourceBuilds module to reference Github instead of SVN repository. Adapted from: * NIRALUser/ShapePopulationViewer@e7c97d75c (COMP: Fix Qt5 build and update SuperBuild layout using ExternalProjectDependency)

This commit removes obsolete copy of the module originally introduced in 2013 through 6ac1ecf (COMP: Switch to NamicExternalProjects SuperBuild) and instead rely on the module provided by CMake.

jcfr · 2023-01-13T11:50:45Z

@yrathi Once this is integrated, we will rebase & consolidate change associated with #143 and #146

cc: @pieper @LucasGandel

pieper · 2023-01-13T17:34:11Z

Thank you @jcfr 🙏

@yrathi it's hard to review these changes but I think we should accept to keep the code current or it will fall far behind. Old code and binaries will still be available in the case that something unusual is introduced.

jcfr · 2023-01-13T17:38:21Z

The white space changes can be excluded from the review appending ?w=1 to the URL.

For example, see https://github.com/pnlbwh/ukftractography/pull/149/files?w=1

Or by explicitly toggling the option:


See https://github.blog/changelog/2021-10-14-hiding-whitespace-is-now-remembered-for-each-pull-request/

tashrifbillah · 2023-01-13T17:42:05Z

Please wait ... we are dealing with failed storage at our office now.

LucasGandel · 2023-01-18T12:58:00Z

Tested on Windows with VS2019. Works like a charm after adding the following changes:
UKF_diff.txt

cc: @jcfr

tashrifbillah · 2023-01-18T14:40:00Z

What GCC did you use to test it on CentOS 7? Are you able to build it using the native 4.8.5?

See https://en.wikipedia.org/wiki/Microsoft_Visual_C%2B%2B#Internal_version_numbering and https://github.com/scikit-build/cmake-FindVcvars/blob/v1.6/FindVcvars.cmake#L124 Co-authored-by: Lucas Gandel <lucas.gandel@kitware.com>

References: * https://www.boost.org/doc/libs/1_81_0/tools/build/doc/html/index.html#bbv2.reference.tools.compiler.msvc * https://github.com/scikit-build/cmake-FindVcvars/blob/v1.6/FindVcvars.cmake#L124 * https://en.wikipedia.org/wiki/Microsoft_Visual_C%2B%2B#Internal_version_numbering

References: * https://en.wikipedia.org/wiki/Microsoft_Visual_C%2B%2B#Internal_version_numbering * https://github.com/scikit-build/cmake-FindVcvars/blob/v1.6/FindVcvars.cmake#L124

…ject Streamline maintenance ensuring each project repository and version are set in the corresponding external project file.

… possible

Remove outdated comments and logic for old MacOSX platforms that are no longer supported. Adapted from Slicer/Slicer@ac191b40f

jcfr · 2023-08-02T15:01:58Z

Can we move forward with the integration ?

To help move forward, I can split the style commits (STYLE: Strip trailing spaces and STYLE: Convert tabs to spaces) into their own pull request, let me know how you would like to move forward.

tashrifbillah · 2023-08-02T15:05:32Z

#149 (comment)

comment unaddressed.

jcfr · 2023-08-02T15:20:06Z

What GCC did you use to test it on CentOS 7?

Testing was done using GCC 7, see latest environment described at https://github.com/Slicer/SlicerBuildEnvironment#supported-build-environments (itself based of https://github.com/dockbuild/dockbuild#compiling-environments)

Are you able to build it using the native 4.8.5?

Instead of using the outdated 4.8.5 compiler on Centos 7, we recommend upgrading your build environment leveraging the RedHat developer toolset.

Doing so allows to use modern compiler while being being compatible with older GlibC.

tashrifbillah · 2023-08-02T15:25:48Z

we recommend upgrading your build environment leveraging the RedHat developer toolset.

Hard to follow this recommendation in our workstation and cluster environment. They are all CentOS 7 and GCC 4.8.5 based. We shall discuss it internally.

tashrifbillah · 2023-08-02T15:26:45Z

In any case, does your PR supersede #143?
@hjmjohnson

jcfr · 2023-08-02T15:30:58Z

As described in #149 (comment)

@yrathi Once this is integrated, we will rebase & consolidate change associated with #143 and #146

tashrifbillah · 2023-08-02T15:35:01Z

I think I can run the extra mile to install GCC-7 in our environments and see if it builds. Did you add any new tests that would confirm that your builds did not break the underlying algebra/arithmetic?

jcfr · 2023-08-02T15:59:16Z

Did you add any new tests that would confirm that your builds did not break the underlying algebra/arithmetic?

Since these set of changes only focus on updating the build-system so that it is more consistent and maintainable, there were no tests added (All commits are labelled COMP or STYLE)

jcfr · 2023-08-02T17:01:09Z

Once this PR is integrated, we will take care of re-basing and addressing issues associated with the other ones.

tashrifbillah · 2023-08-16T14:16:16Z

Building in progress ...
cc @dheshanm

dheshanm · 2023-08-17T13:49:30Z

Building the current codebase as-is with cmake-3.23.0-rc3-linux-x86_64 and gcc-9.3.0 results in the following cmake errors:

-- Setting C++ standard
-- Setting C++ standard - C++17
CMake Error at CMake/ExternalProjectDependency.cmake:75 (message):
  Failed to initialize variable SUPERBUILD_TOPLEVEL_PROJECT.  Variable
  CMAKE_PROJECT_NAME is not defined.
Call Stack (most recent call first):
  Common.cmake:2 (include)
  CMakeLists.txt:97 (include)


-- Configuring incomplete, errors occurred!

Steps to reproduce:

git clone git@github.com:jcfr/ukftractography.git -b update-buildsystem-to-support-customapp-bundling
cd ukftractography
mkdir build && cd build
cmake ../

I can further confirm that the same configuration, with the same steps builds master branch at pnlbwh/ukftractography without issue.

jcfr · 2023-08-22T18:03:22Z

UKFTractography.cmake

@@ -20,18 +19,16 @@ include(${ITK_USE_FILE})
 #-----------------------------------------------------------------------------
 set(VTK_FOUND OFF)
 find_package(VTK COMPONENTS


Suggested change

find_package(VTK COMPONENTS

find_package(VTK 9 COMPONENTS

This will make thing unambiguous

dheshanm · 2023-08-22T18:48:05Z

I was able to get the build to succeed by making the following changes:

Move include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake) after project definition on CMakeLists.txt
Reverting changes to VTK on UKFTractography.cmake
Using 'git' instead of ${GIT_EXECUTABLE} on ukf/CMakeLists.txt

More Details

1. Move `include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake)` after project definition on CMakeLists.txt

ukftractography/CMakeLists.txt

Lines 97 to 108 in 32ec799

    
           include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake) #<-- All feature options for top superbuild and inner product build 
        
           if(${PRIMARY_PROJECT_NAME}_SUPERBUILD) 
        
             project(SuperBuild_${PRIMARY_PROJECT_NAME} LANGUAGES C CXX)  # <- NOTE: Project name for pre-requisites is different form main project 
        
             include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake") 
        
             return() 
        
           else() 
        
             # Building against Slicer 
        
             project(${PRIMARY_PROJECT_NAME} LANGUAGES C CXX)             # <- NOTE: Here is the main project name setting 
        
             include("${CMAKE_CURRENT_SOURCE_DIR}/${PRIMARY_PROJECT_NAME}.cmake") 
        
             return() 
        
           endif()

Move include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake) after project definition.

#-----------------------------------------------------------------------------
# Superbuild script
#-----------------------------------------------------------------------------

if(${PRIMARY_PROJECT_NAME}_SUPERBUILD)
  project(SuperBuild_${PRIMARY_PROJECT_NAME} LANGUAGES C CXX)  # <- NOTE: Project name for pre-requisites is different form main project

 # ===== MOVED HERE BELOW =====
  include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake) #<-- All feature options for top superbuild and inner product build
 # ===== MOVED HERE ABOVE =====

  include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
  return()
else()
  # Building against Slicer
  project(${PRIMARY_PROJECT_NAME} LANGUAGES C CXX)             # <- NOTE: Here is the main project name setting
  include("${CMAKE_CURRENT_SOURCE_DIR}/${PRIMARY_PROJECT_NAME}.cmake")
  return()
endif()
message(FATAL_ERROR "You should never reach this point !")

2. Reverting changes to VTK on UKFTractography.cmake

ukftractography/UKFTractography.cmake

Lines 20 to 31 in 32ec799

    
           set(VTK_FOUND OFF) 
        
           find_package(VTK COMPONENTS 
        
             CommonSystem 
        
             CommonCore 
        
             CommonSystem 
        
             CommonMath 
        
             CommonMisc 
        
             CommonTransforms 
        
             IOLegacy 
        
             IOXML 
        
             REQUIRED 
        
             )

Reverting changes to VTK back to

  set(VTK_FOUND OFF)
  find_package(VTK COMPONENTS
    vtkCommonSystem
    vtkCommonCore
    vtkCommonSystem
    vtkCommonMath
    vtkCommonMisc
    vtkCommonTransforms
    vtkIOLegacy
    vtkIOXML
    REQUIRED)
  if(VTK_USE_FILE)
    include(${VTK_USE_FILE})
  endif()

3. Using 'git' instead of ${GIT_EXECUTABLE} on ukf/CMakeLists.txt

ukftractography/ukf/CMakeLists.txt

Line 14 in 32ec799

    
           COMMAND                                  ${GIT_EXECUTABLE} rev-parse HEAD                       >> "${UKF_GITVER_TEMP}"

Instead using COMMAND git rev-parse HEAD >> "${UKF_GITVER_TEMP}"

Further

Will try building with the proposed find_package(VTK 9 COMPONENTS again.

tashrifbillah · 2023-08-22T18:55:40Z

Move include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake) after project definition on CMakeLists.txt

@jcfr Jean, I think this is another major problem. Feel free to propose a solution.

dheshanm · 2023-08-22T19:54:45Z

Tried building with proposed find_package(VTK 9 COMPONENTS results in the following build error:

CMake Error at UKFTractography.cmake:21 (find_package):
  Could not find a configuration file for package "VTK" that is compatible
  with requested version "9".

  The following configuration files were considered but not accepted:

    /build/VTK-build/VTKConfig.cmake, version: 7.1.1

Call Stack (most recent call first):
  CMakeLists.txt:110 (include)

Note: This build used the modifications 1 and 3 as outlined from the above comment, and used the proposed find_package(VTK 9 COMPONENTS for the 2nd issue instead of reverting.

jcfr · 2023-08-22T20:02:54Z

That makes sense since I initially tried to avoid updating VTK external project .. which is still building VTK 7.

I will follow in the next few days with an update. Thanks for the review

tashrifbillah · 2023-08-23T02:13:52Z

That makes sense since I initially tried to avoid updating VTK external project .. which is still building VTK 7.

Were you able to successfully build this PR before proposing it? @jcfr

tashrifbillah · 2024-04-01T15:42:20Z

@jcfr , @LucasGandel , @pieper :

UKFTractography headquarter is moving to RedHat 9 OS. Is this PR still of interest? If yes, we can try to build it. For the record, we tried it in CentOS 7 but did not work.

pieper · 2024-04-01T15:54:51Z

I'd be fine with whatever builds best on modern systems.

@jcfr is this still useful for you?

jcfr · 2024-04-01T16:31:42Z

The changes are expected to be general and still relevant, while I was actively working on this, I had started to further improve the PR to address both the "standalone" and "bundled" case but had to pause due to other constraints.

Waiting for when I have time to address those, I will submit smaller PR with stylistic changes and alike.

tashrifbillah · 2024-04-09T15:46:44Z

That makes sense since I initially tried to avoid updating VTK external project .. which is still building VTK 7.

I will follow in the next few days with an update. Thanks for the review

@jcfr , this PR does not build on RHEL 9 either. I get Dheshan's error: #149 (comment)

He already proposed his solution here: #149 (comment)
Can you follow up with a revision?

jcfr added 9 commits January 13, 2023 05:01

STYLE: Strip trailing spaces

465a87f

STYLE: Convert tabs to spaces

3a52fbb

COMP: Fix configuration against Slicer by updating default C++ version

22e2907

This commit updates default to account for Slicer/Slicer@dedb6c04d (COMP: Require at least C++17)

COMP: Specify VTK component using updated convention

1990f30

This commit fixes warnings like the following: CMake Deprecation Warning at /path/to/Slicer-Release/VTK-build/lib/cmake/vtk-9.1/vtk-config.cmake:75 (message): The new name for the 'vtkIOLegacy' component is 'IOLegacy'

COMP: Update CMake/PreventIn* modules

d1ebd42

Update PreventInSourceBuilds module to reference Github instead of SVN repository. Adapted from: * NIRALUser/ShapePopulationViewer@e7c97d75c (COMP: Fix Qt5 build and update SuperBuild layout using ExternalProjectDependency)

COMP: Remove copy of ExternalData CMake module

6db1f5c

This commit removes obsolete copy of the module originally introduced in 2013 through 6ac1ecf (COMP: Switch to NamicExternalProjects SuperBuild) and instead rely on the module provided by CMake.

COMP: Remove unused NAMICExternalProjectsExternalData CMake module

af99662

jcfr and others added 10 commits January 25, 2023 11:47

COMP: Update Boost external project to support VS 2019

ca9c8fa

See https://en.wikipedia.org/wiki/Microsoft_Visual_C%2B%2B#Internal_version_numbering and https://github.com/scikit-build/cmake-FindVcvars/blob/v1.6/FindVcvars.cmake#L124 Co-authored-by: Lucas Gandel <lucas.gandel@kitware.com>

COMP: Update Boost external project adding support for VS 2022

f98bc9b

References: * https://en.wikipedia.org/wiki/Microsoft_Visual_C%2B%2B#Internal_version_numbering * https://github.com/scikit-build/cmake-FindVcvars/blob/v1.6/FindVcvars.cmake#L124

STYLE: Set Eigen repository and version in corresponding external pro…

65d7480

…ject Streamline maintenance ensuring each project repository and version are set in the corresponding external project file.

COMP: Remove unused and obsolete UKFTractography_USE_GIT_PROTOCOL option

2b1840c

COMP: Ensure GIT_EXECUTABLE is passed to inner build

aea46e1

COMP: Include "Common.cmake" in top-level CMakeLists.txt

df25884

COMP: Execute PreventIn(BuildInstalls|SourceBuilds) check as early as…

8b9795f

… possible

COMP: Simplify OSX Deployment target setting

1cb59ea

Remove outdated comments and logic for old MacOSX platforms that are no longer supported. Adapted from Slicer/Slicer@ac191b40f

COMP: Require at least macOS 10.13

32ec799

jcfr commented Aug 22, 2023

View reviewed changes

pnlbwh deleted a comment from jhlegarreta Aug 22, 2023

jcfr mentioned this pull request Apr 1, 2024

Strip trailing spaces and convert tabs to spaces #157

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Update buildsystem to support customapp bundling #149

Update buildsystem to support customapp bundling #149

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tashrifbillah commented Apr 9, 2024

Update buildsystem to support customapp bundling #149

Are you sure you want to change the base?

Update buildsystem to support customapp bundling #149

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Steps to reproduce:

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dheshanm commented Aug 22, 2023

More Details

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