ENH: Transition project configuration to `pyproject.toml` #162

jhlegarreta · 2024-06-22T21:29:32Z

ENH: Transition project configuration to `pyproject.toml
COMP: Update CI configuration for ITK 5.4

jhlegarreta · 2024-06-22T21:29:45Z

Depends on PR #161.

jhlegarreta · 2024-06-22T21:35:13Z

The long_description is not added: https://github.com/InsightSoftwareConsortium/ITKTubeTK/blob/master/setup.py#L16

Can we use the README.md file instead of duplicating its contents in another file?

aylward

I was just about to start the conversion - thank you!!!!

aylward · 2024-06-22T21:43:01Z

The long_description is not added: https://github.com/InsightSoftwareConsortium/ITKTubeTK/blob/master/setup.py#L16

Can we use the README.md file instead of duplicating its contents in another file?

Great idea!

aylward · 2024-06-22T21:47:44Z

The windows build failure has been an issue for awhile. It is building the shared lib, but trying to use the static lib when linking executable test drivers. I haven't had time to track it down - it builds fine on windows systems - just not dashboard machines :(

jhlegarreta · 2024-06-22T21:50:18Z

The windows build failure has been an issue for awhile. It is building the shared lib, but trying to use the static lib when linking executable test drivers. I haven't had time to track it down - it builds fine on windows systems - just not dashboard machines :(

Yes, I've seen that.

Not sure where this comes from, though:
https://github.com/InsightSoftwareConsortium/ITKTubeTK/actions/runs/9628422655/job/26556652788?pr=162#step:6:1507

@thewtex Maybe from https://github.com/search?q=repo%3AInsightSoftwareConsortium%2FITKPythonPackage%20setup.py&type=code ?

pyproject.toml

aylward · 2024-06-22T22:00:20Z

The windows build failure has been an issue for awhile. It is building the shared lib, but trying to use the static lib when linking executable test drivers. I haven't had time to track it down - it builds fine on windows systems - just not dashboard machines :(

Yes, I've seen that.

Not sure where this comes from, though: https://github.com/InsightSoftwareConsortium/ITKTubeTK/actions/runs/9628422655/job/26556652788?pr=162#step:6:1507

@thewtex Maybe from https://github.com/search?q=repo%3AInsightSoftwareConsortium%2FITKPythonPackage%20setup.py&type=code ?

Perhaps we need to updated the .github/workflow/build-test-package.yml to match https://github.com/KitwareMedical/ITKRLEImage/blob/main/.github/workflows/build-test-package.yml

jhlegarreta · 2024-06-22T22:12:45Z

Perhaps we need to updated the .github/workflow/build-test-package.yml to match https://github.com/KitwareMedical/ITKRLEImage/blob/main/.github/workflows/build-test-package.yml

Done. Let's see what the CI says. @aylward Please take over from here if this does not fix all issues. Thanks.

aylward · 2024-06-22T22:19:47Z

Done. Let's see what the CI says. @aylward Please take over from here if this does not fix all issues. Thanks.

Will do. Thank you very much for getting this started!

Transition project configuration to `pyproject.toml`. Used the `setup-py-to-pyproject-toml.py` script in the `ITKModuleTemplate` repository: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate as a starting base, then made manual changes as necessary. Transfer the dependencies in `docs/requirements.txt` to the `[doc]` optional dependencies section. Remove the `setup-readme.md` file: the project long description is read from `README.md` in `pyproject.toml` now.

Update CI configuration for ITK 5.4.

jhlegarreta · 2024-06-22T22:47:43Z

Re #162 (comment) removed file in last push-force. pyproject.toml takes README.md (provides a minimalhttps://github.com//pull/162#issuecomment-2184199452) for such purpose.

thewtex · 2024-06-23T19:24:19Z

LINK : fatal error LNK1181: cannot open input file 'D:\ITK-build\lib\itkTubeTK-5.4.lib'

I was able to reproduce this locally by using the Ninja generator.

The weird thing is that itkTubeTK-5.4.dll and itkTubeTK-5.4.pdb exist, but itkTubeTK-5.4.lib does not. It is referenced in build.ninja:

# =============================================================================
# Link build statements for SHARED_LIBRARY target TubeTK


#############################################
# Link the shared library D:\ITK-build\bin\itkTubeTK-5.4.dll

build D$:\ITK-build\bin\itkTubeTK-5.4.dll D$:\ITK-build\lib\itkTubeTK-5.4.lib: CXX_SHARED_LIBRARY_LINKER__TubeTK_Release src\CMakeFiles\TubeTK.dir\Common\tubeIndent.cxx.obj src\CMakeFiles\TubeTK.dir\Common\tubeObject.cxx.obj src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaClassPDF.cxx.obj src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaLDA.cxx.obj src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaNJetLDA.cxx.obj src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaRidgeSeed.cxx.obj src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaTubeExtractor.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeBrentOptimizer1D.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeGoldenMeanOptimizer1D.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeOptimizer1D.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeOptimizerND.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeParabolicFitOptimizer1D.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeSpline1D.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeSplineApproximation1D.cxx.obj src\CMakeFiles\TubeTK.dir\Numerics\tubeSplineND.cxx.obj src\CMakeFiles\TubeTK.dir\ObjectDocuments\tubeMetaDocument.cxx.obj src\CMakeFiles\TubeTK.dir\ObjectDocuments\tubeMetaObjectDocument.cxx.obj src\CMakeFiles\TubeTK.dir\ObjectDocuments\tubeOptionList.cxx.obj | D$:\ITK-build\lib\itkhdf5_cpp-shared-5.4.lib D$:\ITK-build\lib\itkhdf5_hl-shared-5.4.lib D$:\ITK-build\lib\ITKIOTransformBase-5.4.lib D$:\ITK-build\lib\ITKMetaIO-5.4.lib D$:\ITK-build\lib\ITKRegionGrowing-5.4.lib D$:\ITK-build\lib\ITKSmoothing-5.4.lib D$:\ITK-build\lib\ITKTestKernel-5.4.lib D$:\ITK-build\lib\ITKSpatialObjects-5.4.lib D$:\ITK-build\lib\ITKPath-5.4.lib D$:\ITK-build\lib\itkMinimalPathExtraction-5.4.lib D$:\ITK-build\lib\itkhdf5-shared-5.4.lib D$:\ITK-build\lib\ITKTransformFactory-5.4.lib D$:\ITK-build\lib\ITKFFT-5.4.lib D$:\ITK-build\lib\ITKIOBMP-5.4.lib D$:\ITK-build\lib\ITKIOGDCM-5.4.lib D$:\ITK-build\lib\ITKIOGIPL-5.4.lib D$:\ITK-build\lib\ITKIOJPEG-5.4.lib D$:\ITK-build\lib\ITKIOMeshBYU-5.4.lib D$:\ITK-build\lib\ITKIOMeshFreeSurfer-5.4.lib D$:\ITK-build\lib\ITKIOMeshGifti-5.4.lib D$:\ITK-build\lib\ITKIOMeshOBJ-5.4.lib D$:\ITK-build\lib\ITKIOMeshOFF-5.4.lib D$:\ITK-build\lib\ITKIOMeshVTK-5.4.lib D$:\ITK-build\lib\ITKIOMeshBase-5.4.lib D$:\ITK-build\lib\ITKQuadEdgeMesh-5.4.lib D$:\ITK-build\lib\ITKMesh-5.4.lib D$:\ITK-build\lib\ITKIOMeta-5.4.lib D$:\ITK-build\lib\ITKMetaIO-5.4.lib D$:\ITK-build\lib\itkzlib-5.4.lib D$:\ITK-build\lib\ITKIONIFTI-5.4.lib D$:\ITK-build\lib\ITKTransform-5.4.lib D$:\ITK-build\lib\ITKIONRRD-5.4.lib D$:\ITK-build\lib\ITKIOPNG-5.4.lib D$:\ITK-build\lib\ITKIOTIFF-5.4.lib D$:\ITK-build\lib\ITKIOVTK-5.4.lib D$:\ITK-build\lib\ITKIOImageBase-5.4.lib D$:\ITK-build\lib\ITKOptimizers-5.4.lib D$:\ITK-build\lib\ITKStatistics-5.4.lib D$:\ITK-build\lib\itkNetlibSlatec-5.4.lib D$:\ITK-build\lib\ITKPath-5.4.lib D$:\ITK-build\lib\ITKCommon-5.4.lib D$:\ITK-build\lib\itksys-5.4.lib D$:\ITK-build\lib\ITKVNLInstantiation-5.4.lib D$:\ITK-build\lib\itkvnl_algo-5.4.lib D$:\ITK-build\lib\itkvnl-5.4.lib D$:\ITK-build\lib\itkv3p_netlib-5.4.lib D$:\ITK-build\lib\itkvcl-5.4.lib D$:\ITK-build\lib\ITKFastMarching-5.4.lib
  LANGUAGE_COMPILE_FLAGS = /DWIN32 /D_WINDOWS /GR /EHsc  /bigobj /O2 /Ob2 /DNDEBUG -MD
  LINK_FLAGS = /machine:x64  /INCREMENTAL:NO
  LINK_LIBRARIES = D:\ITK-build\lib\itkhdf5_cpp-shared-5.4.lib  D:\ITK-build\lib\itkhdf5_hl-shared-5.4.lib  D:\ITK-build\lib\ITKIOTransformBase-5.4.lib  D:\ITK-build\lib\ITKMetaIO-5.4.lib  D:\ITK-build\lib\ITKRegionGrowing-5.4.lib  D:\ITK-build\lib\ITKSmoothing-5.4.lib  D:\ITK-build\lib\ITKTestKernel-5.4.lib  D:\ITK-build\lib\ITKSpatialObjects-5.4.lib  D:\ITK-build\lib\ITKPath-5.4.lib  D:\ITK-build\lib\itkMinimalPathExtraction-5.4.lib  D:\ITK-build\lib\itkhdf5-shared-5.4.lib  D:\ITK-build\lib\ITKTransformFactory-5.4.lib  D:\ITK-build\lib\ITKFFT-5.4.lib  D:\ITK-build\lib\ITKIOBMP-5.4.lib  D:\ITK-build\lib\ITKIOGDCM-5.4.lib  D:\ITK-build\lib\ITKIOGIPL-5.4.lib  D:\ITK-build\lib\ITKIOJPEG-5.4.lib  D:\ITK-build\lib\ITKIOMeshBYU-5.4.lib  D:\ITK-build\lib\ITKIOMeshFreeSurfer-5.4.lib  D:\ITK-build\lib\ITKIOMeshGifti-5.4.lib  D:\ITK-build\lib\ITKIOMeshOBJ-5.4.lib  D:\ITK-build\lib\ITKIOMeshOFF-5.4.lib  D:\ITK-build\lib\ITKIOMeshVTK-5.4.lib  D:\ITK-build\lib\ITKIOMeshBase-5.4.lib  D:\ITK-build\lib\ITKQuadEdgeMesh-5.4.lib  D:\ITK-build\lib\ITKMesh-5.4.lib  D:\ITK-build\lib\ITKIOMeta-5.4.lib  D:\ITK-build\lib\ITKMetaIO-5.4.lib  D:\ITK-build\lib\itkzlib-5.4.lib  comctl32.lib  wsock32.lib  D:\ITK-build\lib\ITKIONIFTI-5.4.lib  D:\ITK-build\lib\ITKTransform-5.4.lib  D:\ITK-build\lib\ITKIONRRD-5.4.lib  D:\ITK-build\lib\ITKIOPNG-5.4.lib  D:\ITK-build\lib\ITKIOTIFF-5.4.lib  D:\ITK-build\lib\ITKIOVTK-5.4.lib  D:\ITK-build\lib\ITKIOImageBase-5.4.lib  D:\ITK-build\lib\ITKOptimizers-5.4.lib  D:\ITK-build\lib\ITKStatistics-5.4.lib  D:\ITK-build\lib\itkNetlibSlatec-5.4.lib  D:\ITK-build\lib\ITKPath-5.4.lib  D:\ITK-build\lib\ITKCommon-5.4.lib  D:\ITK-build\lib\itksys-5.4.lib  ws2_32.lib  dbghelp.lib  psapi.lib  D:\ITK-build\lib\ITKVNLInstantiation-5.4.lib  D:\ITK-build\lib\itkvnl_algo-5.4.lib  D:\ITK-build\lib\itkvnl-5.4.lib  D:\ITK-build\lib\itkv3p_netlib-5.4.lib  D:\ITK-build\lib\itkvcl-5.4.lib  D:\ITK-build\lib\ITKFastMarching-5.4.lib  kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib
  OBJECT_DIR = src\CMakeFiles\TubeTK.dir
  POST_BUILD = cd .
  PRE_LINK = cd .
  RESTAT = 1
  TARGET_COMPILE_PDB = src\CMakeFiles\TubeTK.dir\
  TARGET_FILE = D:\ITK-build\bin\itkTubeTK-5.4.dll
  TARGET_IMPLIB = D:\ITK-build\lib\itkTubeTK-5.4.lib
  TARGET_PDB = D:\ITK-build\bin\itkTubeTK-5.4.pdb

thewtex · 2024-06-23T19:25:10Z

itkTubeTK-5.4.lib should be generated -- this is the "import library" that is linked against on Windows at build time to use the corresponding *.dll at runtime.

thewtex · 2024-06-23T19:25:59Z

CC @aylward @jhlegarreta

aylward · 2024-06-23T20:04:13Z

This bug exists prior to conversion to pyproject, so I merged this and will start a separate PR for fixing this bug...when we have some insight.

It is happening when compiling two executables I use during testing: CompareImage and CompareTextFiles in TubeTK/test/CompareTools.

Instead of building those two as test drivers, I am going to try building them as executables. Perhaps that will create the necessary cmake/build/link dependencies?

thewtex · 2024-06-23T21:59:46Z

@aylward 🥇 👍 good plan!

aylward · 2024-06-27T22:52:29Z

itkTubeTK-5.4.lib should be generated -- this is the "import library" that is linked against on Windows at build time to use the corresponding *.dll at runtime.

Hi Matt (@thewtex) - this does not happen on the two windows 11 machines I have. Compiling using vs2022 and ninja 1.11.0. It also doesn't happen for me on Ubuntu 22.04 with ninja. This is when I am doing things manually (cmake-gui version 3.27.7 for config, and typing ninja to compile). But I'm not building shared libs. Will try adding that option and seeing what happens. Other suggestions are welcomed!

Thanks,

aylward · 2024-06-27T23:27:38Z

Yes - only happens with BUILD_SHARED_LIBS ON

aylward · 2024-06-28T01:03:29Z

Seems like TubeTK is not creating any exports.

See the documentation on /IMPLIB here:
https://learn.microsoft.com/en-us/cpp/build/reference/implib-name-import-library?view=msvc-170

The correct command is being generated by cmake/ninja, but the "/implib lib/itkTubeTK-6.0.lib' file isn't being generated even though it is being correctly specified. There is a bug in the class defs of tubetk. Below is the ninja / cmake command that should be generating the lib.

cmd.exe /C "cd . && "C:\Program Files\CMake\bin\cmake.exe" -E vs_link_dll --intdir=Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir --rc=C:\PROGRA~~2\WI3CF2~~1\10\bin\100226~~1.0\x64\rc.exe --mt=C:\PROGRA~~2\WI3CF2~~1\10\bin\100226~~1.0\x64\mt.exe --manifests -- C:\PROGRA~~1\MIB055~~1\2022\COMMUN~~1\VC\Tools\MSVC\1437~~1.328\bin\Hostx64\x64\link.exe /nologo Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Common\tubeIndent.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Common\tubeObject.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaClassPDF.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaLDA.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaNJetLDA.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaRidgeSeed.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\MetaIO\itktubeMetaTubeExtractor.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeBrentOptimizer1D.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeGoldenMeanOptimizer1D.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeOptimizer1D.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeOptimizerND.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeParabolicFitOptimizer1D.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeSpline1D.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeSplineApproximation1D.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\Numerics\tubeSplineND.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\ObjectDocuments\tubeMetaDocument.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\ObjectDocuments\tubeMetaObjectDocument.cxx.obj Modules\Remote\TubeTK\src\CMakeFiles\TubeTK.dir\ObjectDocuments\tubeOptionList.cxx.obj /out:Wrapping\Generators\Python\itk\itkTubeTK-6.0.dll /implib:lib\itkTubeTK-6.0.lib /pdb:Wrapping\Generators\Python\itk\itkTubeTK-6.0.pdb /dll /version:1.0 /machine:x64 /INCREMENTAL:NO lib\itkhdf5_cpp-shared-6.0.lib lib\itkhdf5_hl-shared-6.0.lib lib\ITKIOTransformBase-6.0.lib lib\ITKMetaIO-6.0.lib lib\ITKRegionGrowing-6.0.lib lib\ITKSmoothing-6.0.lib lib\ITKTestKernel-6.0.lib lib\ITKSpatialObjects-6.0.lib lib\ITKPath-6.0.lib lib\itkMinimalPathExtraction-6.0.lib lib\itkhdf5-shared-6.0.lib lib\ITKTransformFactory-6.0.lib lib\ITKFFT-6.0.lib lib\ITKIOBMP-6.0.lib lib\ITKIOGDCM-6.0.lib lib\ITKIOGIPL-6.0.lib lib\ITKIOJPEG-6.0.lib lib\ITKIOMeshBYU-6.0.lib lib\ITKIOMeshFreeSurfer-6.0.lib lib\ITKIOMeshGifti-6.0.lib lib\ITKIOMeshOBJ-6.0.lib lib\ITKIOMeshOFF-6.0.lib lib\ITKIOMeshVTK-6.0.lib lib\ITKIOMeshBase-6.0.lib lib\ITKQuadEdgeMesh-6.0.lib lib\ITKMesh-6.0.lib lib\ITKIOMeta-6.0.lib lib\ITKMetaIO-6.0.lib lib\itkzlib-6.0.lib comctl32.lib wsock32.lib lib\ITKIONIFTI-6.0.lib lib\ITKTransform-6.0.lib lib\ITKIONRRD-6.0.lib lib\ITKIOPNG-6.0.lib lib\ITKIOTIFF-6.0.lib lib\ITKIOVTK-6.0.lib lib\ITKIOImageBase-6.0.lib lib\ITKOptimizers-6.0.lib lib\ITKStatistics-6.0.lib lib\itkNetlibSlatec-6.0.lib lib\ITKPath-6.0.lib lib\ITKCommon-6.0.lib lib\itksys-6.0.lib ws2_32.lib dbghelp.lib psapi.lib lib\ITKVNLInstantiation-6.0.lib lib\itkvnl_algo-6.0.lib lib\itkvnl-6.0.lib lib\itkv3p_netlib-6.0.lib lib\itkvcl-6.0.lib lib\ITKFastMarching-6.0.lib kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib && cd ."

aylward · 2024-06-28T10:44:17Z

Simple fix explained and being investigated via PR #167.

jhlegarreta mentioned this pull request Jun 22, 2024

WIP: ENH: Add script to migrate setup.py to pyproject.toml InsightSoftwareConsortium/ITKModuleTemplate#161

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jhlegarreta force-pushed the TransitionToPyprojectToml branch from 99cdf8d to 8c92dde Compare June 22, 2024 21:57

jhlegarreta added 2 commits June 22, 2024 18:43

COMP: Update CI configuration for ITK 5.4

70c64c3

Update CI configuration for ITK 5.4.

jhlegarreta force-pushed the TransitionToPyprojectToml branch from 03d9c6c to 70c64c3 Compare June 22, 2024 22:44

jhlegarreta mentioned this pull request Jun 23, 2024

Transition remote modules configuration from setup.py to the modern pyproject.toml InsightSoftwareConsortium/ITK#4748

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aylward merged commit 5b9b4d8 into InsightSoftwareConsortium:master Jun 23, 2024
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ENH: Transition project configuration to `pyproject.toml` #162

ENH: Transition project configuration to `pyproject.toml` #162

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ENH: Transition project configuration to pyproject.toml #162

ENH: Transition project configuration to pyproject.toml #162

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ENH: Transition project configuration to `pyproject.toml` #162

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