WIP: Add support for Windows

[zivy]

Add support for building and testing on Windows OS in a consistent manner to Linux and macOS.
Repository URL and tag are specified in a shared
configuration file (SITK_CONFIG) which is used
by both the configure and configure.win scripts.
Testing is performed in CircleCI as it offers a
more powerful build machine under the free plan.

[Artur-man]

trying now with my local win, but it seems MAKEJ and ADDITIONAL_SITK_MODULES are not being passed to cmake at all.

[Artur-man]

as a side note, configure.vars does not apply to windows ... thus these variables have to be set as environmental variables before installation
https://support.posit.co/hc/en-us/articles/200486518-Customizing-Package-Build-Options-in-the-RStudio-IDE

Sys.setenv("ADDITIONAL_SITK_MODULES"="-DSIMPLEITK_USE_ELASTIX=ON")
Sys.setenv("MAKEJ"="6")
remotes::install_github("SimpleITK/SimpleITKRInstaller")

[Artur-man]

i think the issue is with Rtools not seeing the make, there seems to be a quick fix for that, which i check before installing the package.
https://github.com/BIMSBbioinfo/SimpleITKRInstaller/tree/release

UPDATE: getting close, it seems working with powershell instead of bash is solving the problem. An issue could be to write a separate workflow for windows, I will try unfying mac and win runs afterwards.

[Artur-man]

It is working!, since configure.win is (because we set as so) working on bash, I moved setting RTOOLS_HOME to configure.win directly. Everything else is in powershell.

[Artur-man]

It seems windows require a separate cmake setup because i am getting these compilation errors:

[ 59%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmext/csa.c.obj
[ 59%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmext/mec_mr3.c.obj
[ 59%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmext/mec_mr3_io.c.obj
C:/bld/Build/ITK/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmext/mec_mr3_io.c: In function 'aligned_alloc_impl':
C:/bld/Build/ITK/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmext/mec_mr3_io.c:146:15: error: implicit declaration of function 'posix_memalign' [-Wimplicit-function-declaration]
  146 |   int error = posix_memalign(&allocPtr, alignment, size);
      |               ^~~~~~~~~~~~~~
make[6]: *** [Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/build.make:1625: Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmext/mec_mr3_io.c.obj] Error 1

UPDATE: looked over the web but couldn't find any specific solution, caused by gdcm ? Using -DITK_USE_SYSTEM_ZLIB:BOOL=ON \ skips one of the compilations that invokes posix but then the same error occurs somewhere else still.

[Artur-man]

@zivy know any fix to this posix_memalign error ?

[blowekamp]

The following check looks suspicious for a mingw compiler:
https://github.com/InsightSoftwareConsortium/ITK/blob/5be898bdeadd8c7d2de6daa9962489ed391782e6/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmext/mec_mr3_io.c#L315-L323

I'll have to check to see if ITK has any current build with this compiler.

[Artur-man]

I have tried the win build on my local win machine too and i am getting the same error, thus I will also try GHA in
https://github.com/Artur-man/ITKR/blob/master/configure.win

Getting the same error with the ITK build:
https://github.com/Artur-man/ITKR/actions/runs/21477502152/job/61865100103

C:\Users\runneradmin\AppData\Local\Temp\Rtmp6FJg3S\R.INSTALL2188552d2b27\ITKR\src\itks\Modules\ThirdParty\GDCM\src\gdcm\Utilities\gdcmext\mec_mr3_io.c
C:\Users\runneradmin\AppData\Local\Temp\Rtmp6FJg3S\R.INSTALL2188552d2b27\ITKR\src\itks\Modules\ThirdParty\GDCM\src\gdcm\Utilities\gdcmext\mec_mr3_io.c: In function 'aligned_alloc_impl':
C:\Users\runneradmin\AppData\Local\Temp\Rtmp6FJg3S\R.INSTALL2188552d2b27\ITKR\src\itks\Modules\ThirdParty\GDCM\src\gdcm\Utilities\gdcmext\mec_mr3_io.c:146:15: error: implicit declaration of function 'posix_memalign' [-Wimplicit-function-declaration]
  146 |   int error = posix_memalign(&allocPtr, alignment, size);
      |               ^~~~~~~~~~~~~~
mingw32-make[3]: *** [Modules\ThirdParty\GDCM\src\gdcm\Source\MediaStorageAndFileFormat\CMakeFiles\gdcmMSFF.dir\build.make:1627: Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/CMakeFiles/gdcmMSFF.dir/__/__/Utilities/gdcmext/mec_mr3_io.c.obj] Error 1

[blowekamp]

What should be tested is building vanilla ITK with the mingw compiler.

I suspect that a the preprocessor logic around this function need adjustment:
https://github.com/search?q=repo%3Amalaterre%2FGDCM%20posix_memalign&type=code