Transition remote modules configuration from `setup.py` to the modern `pyproject.toml`

[jhlegarreta]

Description

Transition remote modules configuration from setup.py to the modern pyproject.toml.

Impact analysis

pyproject.toml is the modern way to package projects using Python code:
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/
https://packaging.python.org/en/latest/guides/modernize-setup-py-project/#modernize-setup-py-project

Expected behavior

Transition all remote module's project configuration to a pyproject.toml file.

Actual behavior

Almost all remote module's project configuration dwells in a setup.py file.

Versions

N/A.

Environment

N/A.

Additional Information

Matt has contributed with a script that would help in the transition:
InsightSoftwareConsortium/ITKModuleTemplate#161

Also, there is this tool Matt has used to update the remote module CI config to ITK 5.4:
https://github.com/asottile/all-repos

Ongoing work:
thewtex@9e9d513

Remotes and PRs:

TODO:

• https://github.com/SCIInstitute/ITKCleaver: chore: Convert from setup.py to pyproject.toml SCIInstitute/ITKCleaver#56
• https://github.com/InsightSoftwareConsortium/scifio-imageio : Forked from scifio, the latter being ahead: needs to be managed

DONE:

• https://github.com/KitwareMedical/ITKHigherOrderAccurateGradient: Duplicate of ISC, the latter forked from KitwareMedical and being ahead; needs to be managed - Deleted 2025-02-03
• https://github.com/KitwareMedical/ITKContourInterpolation: PR ENH: Update setup.py to pyproject.toml KitwareMedical/ITKContourInterpolation#122
• https://github.com/KitwareMedical/ITKUltrasound PR chore: Convert from setup.py to pyproject.toml KitwareMedical/ITKUltrasound#239
• https://github.com/KitwareMedical/MultipleImageIterator: No Python packaging
• https://github.com/KitwareMedical/ITKIOScanco: ENH: Transition project configuration to pyproject.toml ITKIOScanco#85
• https://github.com/InsightSoftwareConsortium/ITKLabelErodeDilate: ENH: Transition project configuration to pyproject.toml ITKLabelErodeDilate#39
• https://github.com/InsightSoftwareConsortium/ITKMGHImageIO: PR ENH: Transition project configuration to pyproject.toml ITKMGHImageIO#41
• https://github.com/InsightSoftwareConsortium/ITKNDReg:
• https://github.com/InsightSoftwareConsortium/ITKOptimizationMonitor: ENH: Transition project configuration to pyproject.toml ITKOptimizationMonitor#6
• https://github.com/InsightSoftwareConsortium/ITKPolarTransform: PR ENH: Transition project configuration to pyproject.toml ITKPolarTransform#26
• https://github.com/InsightSoftwareConsortium/ITKPrincipalComponentsAnalysis: PR ENH: Transition project configuration to pyproject.toml ITKPrincipalComponentsAnalysis#37
• https://github.com/InsightSoftwareConsortium/ITKSimpleITKFilters PR chore: Convert from setup.py to pyproject.toml ITKSimpleITKFilters#22
• https://github.com/InsightSoftwareConsortium/ITKSkullStrip: PR ENH: Transition project configuration to pyproject.toml ITKSkullStrip#26
• https://github.com/InsightSoftwareConsortium/itkAnalyzeObjectMap: PR ENH: Transition project configuration to pyproject.toml ITKAnalyzeObjectMap#30
• https://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR: PR ENH: Transition project configuration to pyproject.toml ITKAnisotropicDiffusionLBR#55
• https://github.com/InsightSoftwareConsortium/ITKArrayFire: ENH: Transition project configuration to pyproject.toml ITKArrayFire#6
• https://github.com/InsightSoftwareConsortium/ITKBioCell: PR ENH: Transition project configuration to pyproject.toml ITKBioCell#28
• https://github.com/InsightSoftwareConsortium/ITKBoneEnhancement: PR ENH: Transition project configuration to pyproject.toml ITKBoneEnhancement#41
• https://github.com/InsightSoftwareConsortium/ITKBoneMorphometry: PR ENH: Transition project configuration to pyproject.toml ITKBoneMorphometry#56
• https://github.com/InsightSoftwareConsortium/ITKBSplineGradient: ENH: Transition project configuration to pyproject.toml ITKBSplineGradient#34
• https://github.com/InsightSoftwareConsortium/ITKColorNormalization: ENH: Transition project configuration to pyproject.toml ITKColorNormalization#43
• https://github.com/InsightSoftwareConsortium/ITKCuberille
• https://github.com/InsightSoftwareConsortium/ITKEntropyBasedIntensityCorrection: ENH: Transition project configuration to pyproject.toml ITKEntropyBasedIntensityCorrection#1
• https://github.com/InsightSoftwareConsortium/ITKFastBilateral: PR ENH: Transition project configuration to pyproject.toml ITKFastBilateral#5
• https://github.com/InsightSoftwareConsortium/ITKFixedPointInverseDisplacementField: PR ENH: Transition project configuration to pyproject.toml ITKFixedPointInverseDisplacementField#29
• https://github.com/InsightSoftwareConsortium/ITKFPFH
• https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator: PR ENH: Transition project configuration to pyproject.toml ITKGenericLabelInterpolator#37
• https://github.com/InsightSoftwareConsortium/ITKGrowCut: PR ENH: Transition project configuration to pyproject.toml ITKGrowCut#25
• https://github.com/InsightSoftwareConsortium/ITKHigherOrderAccurateGradient
• https://github.com/InsightSoftwareConsortium/ITKIOFDF: PR ENH: Transition project configuration to pyproject.toml ITKIOFDF#41
• https://github.com/InsightSoftwareConsortium/ITKIOOpenJPH
• https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF
• https://github.com/InsightSoftwareConsortium/ITKIOOpenSlide: PR ENH: Transition project configuration to pyproject.toml ITKIOOpenSlide#30
• https://github.com/InsightSoftwareConsortium/ITKIOMeshSTL: PR ENH: Transition project configuration to pyproject.toml ITKIOMeshSTL#49
• https://github.com/InsightSoftwareConsortium/ITKIOMeshSWC: ENH: Transition project configuration to pyproject.toml ITKIOMeshSWC#3
• https://github.com/InsightSoftwareConsortium/ITKIOMeshMZ3
• https://github.com/InsightSoftwareConsortium/ITKIOTransformDCMTK: ENH: Transition project configuration to pyproject.toml ITKIOTransformDCMTK#13
• https://github.com/InsightSoftwareConsortium/ITKIsotropicWavelets: PR ENH: Transition project configuration to pyproject.toml ITKIsotropicWavelets#159
• https://github.com/InsightSoftwareConsortium/ITKMeshNoise: PR ENH: Transition project configuration to pyproject.toml ITKMeshNoise#31
• https://github.com/InsightSoftwareConsortium/ITKMeshToPolyData
• https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction: PR ENH: Transition project configuration to pyproject.toml ITKMinimalPathExtraction#105
• https://github.com/InsightSoftwareConsortium/ITKMontage
  ENH: Transition project configuration to pyproject.toml ITKNDReg#24
• https://github.com/InsightSoftwareConsortium/ITKNeuralNetworks: ENH: Transition project configuration to pyproject.toml ITKNeuralNetworks#15
• https://github.com/InsightSoftwareConsortium/ITKParabolicMorphology
• https://github.com/InsightSoftwareConsortium/ITKPyTorch chore: Convert from setup.py to pyproject.toml ITKPyTorch#22
• https://github.com/InsightSoftwareConsortium/ITKRANSAC
• https://github.com/InsightSoftwareConsortium/ITKRingArtifact: PR ENH: Transition project configuration to pyproject.toml ITKRingArtifact#10
• https://github.com/InsightSoftwareConsortium/ITKRobustPredicate
• https://github.com/InsightSoftwareConsortium/ITKSmoothingRecursiveYvvGaussianFilter: ENH: Transition project configuration to pyproject.toml ITKSmoothingRecursiveYvvGaussian#32
• https://github.com/InsightSoftwareConsortium/ITKSplitComponents: PR ENH: Transition project configuration to pyproject.toml ITKSplitComponents#78
• https://github.com/InsightSoftwareConsortium/ITKSubdivisionQuadEdgeMeshFilter: PR ENH: Transition project configuration to pyproject.toml ITKSubdivisionQuadEdgeMeshFilter#41
• https://github.com/InsightSoftwareConsortium/ITKTextureFeatures: ENH: Transition project configuration to pyproject.toml ITKTextureFeatures#101
• https://github.com/InsightSoftwareConsortium/ITKThickness3D: ENH: Transition project configuration to pyproject.toml ITKThickness3D#51
• https://github.com/InsightSoftwareConsortium/ITKThinShellDemons: PR ENH: Transition project configuration to pyproject.toml ITKThinShellDemons#22
• https://github.com/InsightSoftwareConsortium/ITKTotalVariation: PR ENH: Transition project configuration to pyproject.toml ITKTotalVariation#50
• https://github.com/InsightSoftwareConsortium/ITKTrimmedPointSetRegistration: ENH: Transition project configuration to pyproject.toml ITKTrimmedPointSetRegistration#2
• https://github.com/InsightSoftwareConsortium/ITKTubeTK: PR ENH: Transition project configuration to pyproject.toml ITKTubeTK#162
• https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration: PR ENH: Transition project configuration to pyproject.toml ITKTwoProjectionRegistration#29
• https://github.com/InsightSoftwareConsortium/ITKVariationalRegistration
• https://github.com/InsightSoftwareConsortium/ITKVkFFTBackend: PR ENH: Transition project configuration to pyproject.toml ITKVkFFTBackend#67
• https://github.com/InsightSoftwareConsortium/ITKVtkGlue: PR ENH: Transition project configuration to pyproject.toml ITKVtkGlue#41
• https://github.com/InsightSoftwareConsortium/ITKWavelet
• https://github.com/InsightSoftwareConsortium/LesionSizingToolkit: ENH: Transition project configuration to pyproject.toml LesionSizingToolkit#45
• https://github.com/KitwareMedical/HASI chore: Convert from setup.py to pyproject.toml KitwareMedical/HASI#85
• https://github.com/KitwareMedical/ITKDICOM
• https://github.com/KitwareMedical/ITKHalideFilters
• https://github.com/KitwareMedical/ITKPhaseSymmetry
• https://github.com/KitwareMedical/ITKRLEImage
• https://github.com/KitwareMedical/ITKStrain: PR ENH: Transition project configuration to pyproject.toml KitwareMedical/ITKStrain#70
• https://github.com/RTKConsortium/RTK
• https://github.com/scifio/scifio-imageio: No Python packaging
• https://github.com/slicersalt/ITKShape: PR chore: Convert from setup.py to pyproject.toml slicersalt/ITKShape#30
• https://github.com/blowekamp/itkBinShrink: No Python packaging
• https://github.com/blowekamp/itkOBBLabelMap: No Python packaging
• https://github.com/blowekamp/itkScaleSpace: No Python packaging
• https://github.com/blowekamp/itkStreamingSinc: No Python packaging
• https://github.com/blowekamp/itkSuperPixel (integrated into ITK/tree/master/Modules/Segmentation/SuperPixel at ITK v5)
• https://github.com/blowekamp/itkTextureAnalysis: No Python packaging
• https://github.com/ntustison/ITKAdaptiveDenoising: PR chore: Convert from setup.py to pyproject.toml ntustison/ITKAdaptiveDenoising#18
• https://github.com/anmaithien/Retinal-Images-Mosaicking : MATLAB code
• https://github.com/argaja10/Liver-tumor-segmentation: No Python packaging (Python, Jupyter code)
• https://github.com/dyollb/ITKDissolve
• https://github.com/dyollb/ITKLabelPointSet
• https://github.com/dyollb/ITKTopologyControl

Notes:

• I did not bump the versions for the remotes while opening the PRs. @thewtex let me know your thoughts. Major, minor, patch, none?
• May of the remotes used all-capitals ITK as a keyword, as well as InsightToolkit, and capitalized the first letter of other keywords. The module template contains itk all lowercase: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate/blob/main/%7B%7Bcookiecutter.project_name%7D%7D/pyproject.toml#L15 Can be a good moment to make these consistent.

[thewtex]

@jhlegarreta thank you for your help with this! 💯 🥇

I did not bump the versions for the remotes while opening the PRs. @thewtex let me know your thoughts. Major, minor, patch, none?

I think we should bump the major version. Experience has shown that the packages are not binary compatible across itk major or minor releases. Following semantic versioning, this is a major bump.

In the process of updating these, we could consider also changing the default branch from master to main,

[jhlegarreta]

Re #4748 (comment)

I am not bumping to newer ITK versions when transitioning to pyproject.toml: I am leaving unmodified the ITK dependency version that is transferred automatically from setup.py to pyproject.toml. Do you want me to require "itk>=5.4" for all of them while adopting pyproject.toml?

In the process of updating these, we could consider also changing the default branch from master to main,

Can do that right after the PRs are merged.

[thewtex]

I am not bumping to newer ITK versions when transitioning to pyproject.toml: I am leaving unmodified the ITK dependency version that is transferred automatically from setup.py to pyproject.toml. Do you want me to require "itk>=5.4" for all of them while adopting pyproject.toml?

Yes, please. itk == 5.4.* to be specific (or itk-core == 5.4.* if it only requires itk-core, etc.) We should update the script to do so automatically, too.

[jhlegarreta]

Yes, please. itk == 5.4.* to be specific (or itk-core == 5.4.* if it only requires itk-core, etc.) We should update the script to do so automatically, too.

OK, done. The script does update to itk == 5.4.* in most cases (e.g. it does not when no specific version of itk has been specified, for example).

Edit: leaving bumping version of ITKTubeTK to @aylward.