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vtk: 9.2.6 -> 9.5.0#417613

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wegank merged 2 commits intoNixOS:masterfrom
qbisi:vtk-9.5
Jul 29, 2025
Merged

vtk: 9.2.6 -> 9.5.0#417613
wegank merged 2 commits intoNixOS:masterfrom
qbisi:vtk-9.5

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@qbisi
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@qbisi qbisi commented Jun 17, 2025

VTK introduces deprecated APIs in every minor release. These deprecated APIs are typically removed after two subsequent minor versions, which often leads to compatibility issues for downstream packages. Since VTK currently publishes a new minor version approximately every six months, I plan to start creating separate package variants for each minor release starting from VTK 9.5. I intend to maintain at least three concurrent minor versions of VTK.

changes:

  1. add headlessDisplayHook doing check for vtk. I will maintain the graphical test presonly.
  2. drop alias 'vtk_9', add alias 'vtk_9_5'.
  3. drop 'f3d_egl/vtk_9_egl'. As vtk_9_5 has been built with egl support by default and will not cause a headless display in f3d.

optional dependent pr:

  1. libLAS: propagate libgeotiff, libtiff and laszip_2 #415234
  2. python3Packages.nipy: fix build with deprecated numpy api #423726
  3. gdcm: 3.0.25 -> 3.0.26 #422597

dependent pr:

  1. python3Packages.wslink: init at 2.3.4 #416458
  2. openusd: propagate dependencies OpenGL #414827
  3. gdcm: fix deprecated api in vtk #417665
  4. Freecad: fix build with vtk 9.5 #421276
  5. viskores: init at 1.0.0 #422203
  6. Release v0.46 pyvista/pyvista#7690

Things done

  • Built on platform(s)
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
    • sandbox = relaxed
    • sandbox = true
  • Tested, as applicable:
  • Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
  • Tested basic functionality of all binary files (usually in ./result/bin/)
  • Nixpkgs 25.11 Release Notes (or backporting 24.11 and 25.05 Nixpkgs Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
  • NixOS 25.11 Release Notes (or backporting 24.11 and 25.05 NixOS Release notes)
    • (Module updates) Added a release notes entry if the change is significant
    • (Module addition) Added a release notes entry if adding a new NixOS module
  • Fits CONTRIBUTING.md, pkgs/README.md, maintainers/README.md and other contributing documentation in corresponding paths.

Add a 👍 reaction to pull requests you find important.

@github-actions github-actions bot added 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 101-500 This PR causes between 101 and 500 packages to rebuild on Linux. 6.topic: python Python is a high-level, general-purpose programming language. labels Jun 17, 2025
@qbisi qbisi mentioned this pull request Jun 30, 2025
13 tasks
@qbisi qbisi force-pushed the vtk-9.5 branch 2 times, most recently from 4a22fa1 to 101ab03 Compare July 1, 2025 23:47
@qbisi qbisi force-pushed the vtk-9.5 branch 9 times, most recently from 42ab35b to bf098e7 Compare July 9, 2025 09:27
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qbisi commented Jul 9, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 417613
Commit: bf098e71fca18596236a6ee35a32bd945c0d60b7


x86_64-linux

✅ 187 packages built:
  • ants
  • appcsxcad
  • c3d
  • cloudcompare
  • csxcad
  • elastix
  • elmerfem
  • exhibit
  • expliot
  • expliot.dist
  • ezminc
  • f3d
  • f3d.man
  • freecad
  • gdcm
  • headlessDisplayHook
  • intensity-normalization (python313Packages.intensity-normalization)
  • intensity-normalization.dist (python313Packages.intensity-normalization.dist)
  • itk (itk_5)
  • itk_5_2
  • libsForQt5.qcsxcad (plasma5Packages.qcsxcad)
  • libsForQt5.qcsxcad.dev (plasma5Packages.qcsxcad.dev)
  • mirtk
  • mrtrix
  • octavePackages.dicom
  • openems
  • otb
  • pcl
  • python312Packages.dcmstack
  • python312Packages.dcmstack.dist
  • python312Packages.deid
  • python312Packages.deid.dist
  • python312Packages.dicom-numpy
  • python312Packages.dicom-numpy.dist
  • python312Packages.dicom2nifti
  • python312Packages.dicom2nifti.dist
  • python312Packages.dicomweb-client
  • python312Packages.dicomweb-client.dist
  • python312Packages.dipy
  • python312Packages.dipy.dist
  • python312Packages.f3d
  • python312Packages.f3d.man
  • python312Packages.fslpy
  • python312Packages.fslpy.dist
  • python312Packages.gdcm
  • python312Packages.heudiconv
  • python312Packages.heudiconv.dist
  • python312Packages.highdicom
  • python312Packages.highdicom.dist
  • python312Packages.intensity-normalization
  • python312Packages.intensity-normalization.dist
  • python312Packages.itk
  • python312Packages.mayavi
  • python312Packages.mayavi.dist
  • python312Packages.medpy
  • python312Packages.medpy.dist
  • python312Packages.medvol
  • python312Packages.medvol.dist
  • python312Packages.napari-nifti
  • python312Packages.napari-nifti.dist
  • python312Packages.nibabel
  • python312Packages.nibabel.dist
  • python312Packages.nilearn
  • python312Packages.nilearn.dist
  • python312Packages.nipy
  • python312Packages.nipy.dist
  • python312Packages.nipype
  • python312Packages.nipype.dist
  • python312Packages.nitime
  • python312Packages.nitime.dist
  • python312Packages.nitransforms
  • python312Packages.nitransforms.dist
  • python312Packages.niworkflows
  • python312Packages.niworkflows.dist
  • python312Packages.pybids
  • python312Packages.pybids.dist
  • python312Packages.pydicom
  • python312Packages.pydicom.dist
  • python312Packages.pylibjpeg
  • python312Packages.pylibjpeg-openjpeg
  • python312Packages.pylibjpeg-openjpeg.dist
  • python312Packages.pylibjpeg.dist
  • python312Packages.pymatgen
  • python312Packages.pymatgen.dist
  • python312Packages.pymedio
  • python312Packages.pymedio.dist
  • python312Packages.pynetdicom
  • python312Packages.pynetdicom.dist
  • python312Packages.pyorthanc
  • python312Packages.pyorthanc.dist
  • python312Packages.pyotb
  • python312Packages.pyotb.dist
  • python312Packages.pyradiomics
  • python312Packages.pyradiomics.dist
  • python312Packages.python-csxcad
  • python312Packages.python-csxcad.dist
  • python312Packages.python-openems
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  • python312Packages.simpleitk
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  • python312Packages.sumo
  • python312Packages.sumo.dist
  • python312Packages.templateflow
  • python312Packages.templateflow.dist
  • python312Packages.torchio
  • python312Packages.torchio.dist
  • python312Packages.trx-python
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  • python312Packages.vtk
  • python312Packages.xnatpy
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  • python313Packages.dcmstack
  • python313Packages.dcmstack.dist
  • python313Packages.deid
  • python313Packages.deid.dist
  • python313Packages.dicom-numpy
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  • python313Packages.dicom2nifti.dist
  • python313Packages.dicomweb-client
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  • python313Packages.dipy
  • python313Packages.dipy.dist
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  • python313Packages.f3d.man
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  • python313Packages.gdcm
  • python313Packages.highdicom
  • python313Packages.highdicom.dist
  • python313Packages.itk
  • python313Packages.mayavi
  • python313Packages.mayavi.dist
  • python313Packages.medpy
  • python313Packages.medpy.dist
  • python313Packages.medvol
  • python313Packages.medvol.dist
  • python313Packages.napari-nifti
  • python313Packages.napari-nifti.dist
  • python313Packages.nibabel
  • python313Packages.nibabel.dist
  • python313Packages.nilearn
  • python313Packages.nilearn.dist
  • python313Packages.nipy
  • python313Packages.nipy.dist
  • python313Packages.nitime
  • python313Packages.nitime.dist
  • python313Packages.nitransforms
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  • python313Packages.pynetdicom
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  • python313Packages.templateflow.dist
  • python313Packages.torchio
  • python313Packages.torchio.dist
  • python313Packages.trx-python
  • python313Packages.trx-python.dist
  • vtk-full (python313Packages.vtk)
  • python313Packages.xnatpy
  • python313Packages.xnatpy.dist
  • rtabmap
  • simpleitk
  • therion
  • viskores
  • vtk (vtk_9_5)
  • vtkWithQt5
  • vtkWithQt6

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qbisi commented Jul 9, 2025

@K900 when running test with xvfb backend, it complains

2025-07-10 07:07:01.941 (   0.004s) [    7FFFEFC74D00]vtkXOpenGLRenderWindow.:1452  WARN| Failed to load GLX. Please install OpenGL drivers.
libEGL warning: Not allowed to force software rendering when API explicitly selects a hardware device.
Segmentation fault (core dumped)

you can valid this by runing

$out/bin/vtkProbeOpenGLVersion 

Does xvfb backend has an optional opengl support that i can enable it in headlessDisplayHook.

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K900 commented Jul 10, 2025

Can we skip that one test instead? Or is it all of them?

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qbisi commented Jul 10, 2025

Saddly nearly half of the tests (1500+) require x server backend with opengl support.

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K900 commented Jul 10, 2025

Then we just have to skip those I think, because there's no OpenGL in the sandbox.

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qbisi commented Jul 10, 2025

vtk and pyvista do their headless check on ubuntu server with xvfb backend, is nixpkgs#xvfb diff from that xvfb in debian/ubuntu in lacking opengl support?
also, are you against or for if i choose weston as a replacement of xvfb for doing headless display check.

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K900 commented Jul 10, 2025

That's not the problem, the problem is that it's trying to explicitly specify a hardware render device when we're trying to force it to software. I don't think Weston will help here.

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qbisi commented Jul 10, 2025

I have checked with the weston xwayland backend in combine with llvmpipe hook, and nealy all the tests passed, only 4 failed(fail reason are given)

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K900 commented Jul 10, 2025

OK, I guess we need to build xvfb with GLX support for this to work, which is now possible.

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qbisi commented Jul 10, 2025

OK, I guess we need to build xvfb with GLX support for this to work, which is now possible.

I am not familiar with xvfb, swiching --disable-glx to --enable-glx does not yield a success build for xvfb. Waiting for your contribution.
And, what should i do before that, just simply disable the tests? Or use weston as a temporary solution.

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Is this split actually necessary?

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IMO, neccessary to keep multi vtk instance.
some downstream packages (e.g. gdcm) may react slow to vtk api change. While some (e.g. paraview) want's the latest vtk version.

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Can we not have more Qt5 stuff added?

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rtabmap, qcsxcad, appcsxcad, elmerfem depend on vtkWithQt5.
I am not familiar with rtabmap, qcsxcad, appcsxcad, but i am sure elmerfem require vtkWithQt5 and does not work with vtkWithQt6.

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qbisi commented Jul 19, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 417613
Commit: 47ab1b2c838c9fdfdddd4e1f8963b5a6820ba925


x86_64-linux

❌ 6 packages failed to build:
  • python312Packages.fast-simplification
  • python312Packages.fast-simplification.dist
  • python312Packages.pyvista
  • python312Packages.pyvista.dist
  • python312Packages.sfepy
  • python312Packages.sfepy.dist
✅ 185 packages built:
  • ants
  • appcsxcad
  • c3d
  • cloudcompare
  • csxcad
  • elastix
  • elmerfem
  • exhibit
  • expliot
  • expliot.dist
  • ezminc
  • f3d
  • f3d.man
  • freecad
  • gdcm
  • intensity-normalization (python313Packages.intensity-normalization)
  • intensity-normalization.dist (python313Packages.intensity-normalization.dist)
  • itk (itk_5)
  • itk_5_2
  • libsForQt5.qcsxcad (plasma5Packages.qcsxcad)
  • libsForQt5.qcsxcad.dev (plasma5Packages.qcsxcad.dev)
  • mirtk
  • mrtrix
  • octavePackages.dicom
  • openems
  • otb
  • pcl
  • python312Packages.dcmstack
  • python312Packages.dcmstack.dist
  • python312Packages.deid
  • python312Packages.deid.dist
  • python312Packages.dicom-numpy
  • python312Packages.dicom-numpy.dist
  • python312Packages.dicom2nifti
  • python312Packages.dicom2nifti.dist
  • python312Packages.dicomweb-client
  • python312Packages.dicomweb-client.dist
  • python312Packages.dipy
  • python312Packages.dipy.dist
  • python312Packages.f3d
  • python312Packages.f3d.man
  • python312Packages.fslpy
  • python312Packages.fslpy.dist
  • python312Packages.gdcm
  • python312Packages.heudiconv
  • python312Packages.heudiconv.dist
  • python312Packages.highdicom
  • python312Packages.highdicom.dist
  • python312Packages.intensity-normalization
  • python312Packages.intensity-normalization.dist
  • python312Packages.itk
  • python312Packages.mayavi
  • python312Packages.mayavi.dist
  • python312Packages.medpy
  • python312Packages.medpy.dist
  • python312Packages.medvol
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  • python312Packages.napari-nifti
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  • python312Packages.nibabel
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  • python312Packages.nilearn
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  • rtabmap
  • simpleitk
  • therion
  • vtk (vtk_9_5)
  • vtkWithQt5
  • vtkWithQt6

Error logs: `x86_64-linux`
python312Packages.pyvista
adding 'pyvista/utilities/regression.py'
adding 'pyvista/utilities/sphinx_gallery.py'
adding 'pyvista/utilities/transformations.py'
adding 'pyvista/utilities/wrappers.py'
adding 'pyvista/utilities/xvfb.py'
adding 'pyvista-0.45.2.dist-info/licenses/AUTHORS.rst'
adding 'pyvista-0.45.2.dist-info/licenses/LICENSE'
adding 'pyvista-0.45.2.dist-info/METADATA'
adding 'pyvista-0.45.2.dist-info/WHEEL'
adding 'pyvista-0.45.2.dist-info/top_level.txt'
adding 'pyvista-0.45.2.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built pyvista-0.45.2-py3-none-any.whl
Finished creating a wheel...
Finished executing pypaBuildPhase
Running phase: pythonRuntimeDepsCheckHook
@nix { "action": "setPhase", "phase": "pythonRuntimeDepsCheckHook" }
Executing pythonRuntimeDepsCheck
Checking runtime dependencies for pyvista-0.45.2-py3-none-any.whl
  - vtk<9.5.0 not satisfied by version 9.5.0

@nixpkgs-ci nixpkgs-ci bot added the 2.status: merge conflict This PR has merge conflicts with the target branch label Jul 24, 2025
@nixpkgs-ci nixpkgs-ci bot removed the 2.status: merge conflict This PR has merge conflicts with the target branch label Jul 27, 2025
K900
K900 previously requested changes Jul 27, 2025
@qbisi qbisi force-pushed the vtk-9.5 branch 4 times, most recently from 85317a1 to 47556b5 Compare July 27, 2025 14:50
@nix-owners nix-owners bot requested a review from wegank July 28, 2025 13:33
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qbisi commented Jul 28, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 417613
Commit: 9b615580583a072b1fb8018fe92f622554afc11a


aarch64-darwin

❌ 1 package failed to build:
  • therion
✅ 41 packages built:
  • ants
  • elmerfem
  • f3d
  • gdcm
  • itk (itk_5)
  • itk_5_2
  • octavePackages.dicom
  • pcl
  • python312Packages.f3d
  • python312Packages.fast-simplification
  • python312Packages.fast-simplification.dist
  • python312Packages.gdcm
  • python312Packages.gstools
  • python312Packages.gstools.dist
  • python312Packages.mayavi
  • python312Packages.mayavi.dist
  • python312Packages.pykrige
  • python312Packages.pykrige.dist
  • python312Packages.pymatgen
  • python312Packages.pymatgen.dist
  • python312Packages.pyvista
  • python312Packages.pyvista.dist
  • python312Packages.sfepy
  • python312Packages.sfepy.dist
  • python312Packages.sumo
  • python312Packages.sumo.dist
  • python312Packages.vtk
  • python313Packages.f3d
  • python313Packages.fast-simplification
  • python313Packages.fast-simplification.dist
  • python313Packages.gdcm
  • python313Packages.gstools
  • python313Packages.gstools.dist
  • python313Packages.pykrige
  • python313Packages.pykrige.dist
  • python313Packages.pyvista
  • python313Packages.pyvista.dist
  • vtk-full (python313Packages.vtk)
  • vtk (vtk_9_5)
  • vtkWithQt5
  • vtkWithQt6

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qbisi commented Jul 28, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 417613
Commit: 9b615580583a072b1fb8018fe92f622554afc11a


x86_64-linux

❌ 4 packages failed to build:
  • python312Packages.pymatgen
  • python312Packages.pymatgen.dist
  • python312Packages.sumo
  • python312Packages.sumo.dist
✅ 197 packages built:
  • ants
  • appcsxcad
  • c3d
  • cloudcompare
  • csxcad
  • elastix
  • elmerfem
  • exhibit
  • expliot
  • expliot.dist
  • ezminc
  • f3d
  • f3d.man
  • freecad
  • gdcm
  • intensity-normalization (python313Packages.intensity-normalization)
  • intensity-normalization.dist (python313Packages.intensity-normalization.dist)
  • itk (itk_5)
  • itk_5_2
  • libsForQt5.qcsxcad (plasma5Packages.qcsxcad)
  • libsForQt5.qcsxcad.dev (plasma5Packages.qcsxcad.dev)
  • mirtk
  • mrtrix
  • octavePackages.dicom
  • openems
  • otb
  • pcl
  • python312Packages.dcmstack
  • python312Packages.dcmstack.dist
  • python312Packages.deid
  • python312Packages.deid.dist
  • python312Packages.dicom-numpy
  • python312Packages.dicom-numpy.dist
  • python312Packages.dicom2nifti
  • python312Packages.dicom2nifti.dist
  • python312Packages.dicomweb-client
  • python312Packages.dicomweb-client.dist
  • python312Packages.dipy
  • python312Packages.dipy.dist
  • python312Packages.f3d
  • python312Packages.f3d.man
  • python312Packages.fast-simplification
  • python312Packages.fast-simplification.dist
  • python312Packages.fslpy
  • python312Packages.fslpy.dist
  • python312Packages.gdcm
  • python312Packages.gstools
  • python312Packages.gstools.dist
  • python312Packages.heudiconv
  • python312Packages.heudiconv.dist
  • python312Packages.highdicom
  • python312Packages.highdicom.dist
  • python312Packages.intensity-normalization
  • python312Packages.intensity-normalization.dist
  • python312Packages.itk
  • python312Packages.mayavi
  • python312Packages.mayavi.dist
  • python312Packages.medpy
  • python312Packages.medpy.dist
  • python312Packages.medvol
  • python312Packages.medvol.dist
  • python312Packages.napari-nifti
  • python312Packages.napari-nifti.dist
  • python312Packages.nibabel
  • python312Packages.nibabel.dist
  • python312Packages.nilearn
  • python312Packages.nilearn.dist
  • python312Packages.nipy
  • python312Packages.nipy.dist
  • python312Packages.nipype
  • python312Packages.nipype.dist
  • python312Packages.nitime
  • python312Packages.nitime.dist
  • python312Packages.nitransforms
  • python312Packages.nitransforms.dist
  • python312Packages.niworkflows
  • python312Packages.niworkflows.dist
  • python312Packages.pybids
  • python312Packages.pybids.dist
  • python312Packages.pydicom
  • python312Packages.pydicom.dist
  • python312Packages.pykrige
  • python312Packages.pykrige.dist
  • python312Packages.pylibjpeg
  • python312Packages.pylibjpeg-openjpeg
  • python312Packages.pylibjpeg-openjpeg.dist
  • python312Packages.pylibjpeg.dist
  • python312Packages.pymedio
  • python312Packages.pymedio.dist
  • python312Packages.pynetdicom
  • python312Packages.pynetdicom.dist
  • python312Packages.pyorthanc
  • python312Packages.pyorthanc.dist
  • python312Packages.pyotb
  • python312Packages.pyotb.dist
  • python312Packages.pyradiomics
  • python312Packages.pyradiomics.dist
  • python312Packages.python-csxcad
  • python312Packages.python-csxcad.dist
  • python312Packages.python-openems
  • python312Packages.python-openems.dist
  • python312Packages.pyvista
  • python312Packages.pyvista.dist
  • python312Packages.sfepy
  • python312Packages.sfepy.dist
  • python312Packages.simpleitk
  • python312Packages.simpleitk.dist
  • python312Packages.templateflow
  • python312Packages.templateflow.dist
  • python312Packages.torchio
  • python312Packages.torchio.dist
  • python312Packages.trx-python
  • python312Packages.trx-python.dist
  • python312Packages.vtk
  • python312Packages.xnatpy
  • python312Packages.xnatpy.dist
  • python313Packages.dcmstack
  • python313Packages.dcmstack.dist
  • python313Packages.deid
  • python313Packages.deid.dist
  • python313Packages.dicom-numpy
  • python313Packages.dicom-numpy.dist
  • python313Packages.dicom2nifti
  • python313Packages.dicom2nifti.dist
  • python313Packages.dicomweb-client
  • python313Packages.dicomweb-client.dist
  • python313Packages.dipy
  • python313Packages.dipy.dist
  • python313Packages.f3d
  • python313Packages.f3d.man
  • python313Packages.fast-simplification
  • python313Packages.fast-simplification.dist
  • python313Packages.fslpy
  • python313Packages.fslpy.dist
  • python313Packages.gdcm
  • python313Packages.gstools
  • python313Packages.gstools.dist
  • python313Packages.highdicom
  • python313Packages.highdicom.dist
  • python313Packages.itk
  • python313Packages.medpy
  • python313Packages.medpy.dist
  • python313Packages.medvol
  • python313Packages.medvol.dist
  • python313Packages.napari-nifti
  • python313Packages.napari-nifti.dist
  • python313Packages.nibabel
  • python313Packages.nibabel.dist
  • python313Packages.nilearn
  • python313Packages.nilearn.dist
  • python313Packages.nipy
  • python313Packages.nipy.dist
  • python313Packages.nitime
  • python313Packages.nitime.dist
  • python313Packages.nitransforms
  • python313Packages.nitransforms.dist
  • python313Packages.pybids
  • python313Packages.pybids.dist
  • python313Packages.pydicom
  • python313Packages.pydicom.dist
  • python313Packages.pykrige
  • python313Packages.pykrige.dist
  • python313Packages.pylibjpeg
  • python313Packages.pylibjpeg-openjpeg
  • python313Packages.pylibjpeg-openjpeg.dist
  • python313Packages.pylibjpeg.dist
  • python313Packages.pymedio
  • python313Packages.pymedio.dist
  • python313Packages.pynetdicom
  • python313Packages.pynetdicom.dist
  • python313Packages.pyorthanc
  • python313Packages.pyorthanc.dist
  • python313Packages.pyotb
  • python313Packages.pyotb.dist
  • python313Packages.pyradiomics
  • python313Packages.pyradiomics.dist
  • python313Packages.python-csxcad
  • python313Packages.python-csxcad.dist
  • python313Packages.pyvista
  • python313Packages.pyvista.dist
  • python313Packages.simpleitk
  • python313Packages.simpleitk.dist
  • python313Packages.templateflow
  • python313Packages.templateflow.dist
  • python313Packages.torchio
  • python313Packages.torchio.dist
  • python313Packages.trx-python
  • python313Packages.trx-python.dist
  • vtk-full (python313Packages.vtk)
  • python313Packages.xnatpy
  • python313Packages.xnatpy.dist
  • rtabmap
  • simpleitk
  • therion
  • vtk (vtk_9_5)
  • vtkWithQt5
  • vtkWithQt6

Error logs: `x86_64-linux`
python312Packages.pymatgen
SKIPPED [1] tests/transformations/test_advanced_transformations.py:540: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:549: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:97: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:617: mcsqs not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:638: mcsqs not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:656: icet not installed.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:670: icet not installed.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:681: icet not installed.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:874: hiphive not present
SKIPPED [1] tests/transformations/test_standard_transformations.py:256: enum_lib not present.
SKIPPED [1] tests/transformations/test_standard_transformations.py:274: enum_lib not present.
SKIPPED [1] tests/transformations/test_standard_transformations.py:280: enum_lib not present.
SKIPPED [1] tests/io/vasp/test_sets.py:1759: TODO: need someone to fix this
SKIPPED [1] tests/transformations/test_advanced_transformations.py:607: mcsqs not present.
SKIPPED [1] tests/transformations/test_standard_transformations.py:239: enum_lib not present.
SKIPPED [1] tests/io/vasp/test_outputs.py:1666: h5py required for HDF5 support.
SKIPPED [1] tests/io/test_phonopy.py:243: Phonopy not present
SKIPPED [1] tests/core/test_xcfunc.py:56: TODO:
SKIPPED [1] tests/transformations/test_site_transformations.py:213: enum_lib not present.
7 failed, 2998 passed, 215 skipped, 445105 warnings in 277.50s (0:04:37)

@qbisi
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qbisi commented Jul 28, 2025

Build failure of pymatgen should be fixed with #429040.
None of vtk's business

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qbisi commented Jul 28, 2025

@wegank, should we wait for pyvista 0.46? though it seems like will be soon, but no due time are given. pyvista/pyvista#7690

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wegank commented Jul 28, 2025

@wegank, should we wait for pyvista 0.46? though it seems like will be soon, but no due time are given. pyvista/pyvista#7690

Definitely not.

@wegank wegank dismissed K900’s stale review July 28, 2025 20:20

Resolved

@qbisi
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qbisi commented Jul 28, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 417613
Commit: 9b615580583a072b1fb8018fe92f622554afc11a


x86_64-linux

✅ 201 packages built:
  • ants
  • appcsxcad
  • c3d
  • cloudcompare
  • csxcad
  • elastix
  • elmerfem
  • exhibit
  • expliot
  • expliot.dist
  • ezminc
  • f3d
  • f3d.man
  • freecad
  • gdcm
  • intensity-normalization (python313Packages.intensity-normalization)
  • intensity-normalization.dist (python313Packages.intensity-normalization.dist)
  • itk (itk_5)
  • itk_5_2
  • libsForQt5.qcsxcad (plasma5Packages.qcsxcad)
  • libsForQt5.qcsxcad.dev (plasma5Packages.qcsxcad.dev)
  • mirtk
  • mrtrix
  • octavePackages.dicom
  • openems
  • otb
  • pcl
  • python312Packages.dcmstack
  • python312Packages.dcmstack.dist
  • python312Packages.deid
  • python312Packages.deid.dist
  • python312Packages.dicom-numpy
  • python312Packages.dicom-numpy.dist
  • python312Packages.dicom2nifti
  • python312Packages.dicom2nifti.dist
  • python312Packages.dicomweb-client
  • python312Packages.dicomweb-client.dist
  • python312Packages.dipy
  • python312Packages.dipy.dist
  • python312Packages.f3d
  • python312Packages.f3d.man
  • python312Packages.fast-simplification
  • python312Packages.fast-simplification.dist
  • python312Packages.fslpy
  • python312Packages.fslpy.dist
  • python312Packages.gdcm
  • python312Packages.gstools
  • python312Packages.gstools.dist
  • python312Packages.heudiconv
  • python312Packages.heudiconv.dist
  • python312Packages.highdicom
  • python312Packages.highdicom.dist
  • python312Packages.intensity-normalization
  • python312Packages.intensity-normalization.dist
  • python312Packages.itk
  • python312Packages.mayavi
  • python312Packages.mayavi.dist
  • python312Packages.medpy
  • python312Packages.medpy.dist
  • python312Packages.medvol
  • python312Packages.medvol.dist
  • python312Packages.napari-nifti
  • python312Packages.napari-nifti.dist
  • python312Packages.nibabel
  • python312Packages.nibabel.dist
  • python312Packages.nilearn
  • python312Packages.nilearn.dist
  • python312Packages.nipy
  • python312Packages.nipy.dist
  • python312Packages.nipype
  • python312Packages.nipype.dist
  • python312Packages.nitime
  • python312Packages.nitime.dist
  • python312Packages.nitransforms
  • python312Packages.nitransforms.dist
  • python312Packages.niworkflows
  • python312Packages.niworkflows.dist
  • python312Packages.pybids
  • python312Packages.pybids.dist
  • python312Packages.pydicom
  • python312Packages.pydicom.dist
  • python312Packages.pykrige
  • python312Packages.pykrige.dist
  • python312Packages.pylibjpeg
  • python312Packages.pylibjpeg-openjpeg
  • python312Packages.pylibjpeg-openjpeg.dist
  • python312Packages.pylibjpeg.dist
  • python312Packages.pymatgen
  • python312Packages.pymatgen.dist
  • python312Packages.pymedio
  • python312Packages.pymedio.dist
  • python312Packages.pynetdicom
  • python312Packages.pynetdicom.dist
  • python312Packages.pyorthanc
  • python312Packages.pyorthanc.dist
  • python312Packages.pyotb
  • python312Packages.pyotb.dist
  • python312Packages.pyradiomics
  • python312Packages.pyradiomics.dist
  • python312Packages.python-csxcad
  • python312Packages.python-csxcad.dist
  • python312Packages.python-openems
  • python312Packages.python-openems.dist
  • python312Packages.pyvista
  • python312Packages.pyvista.dist
  • python312Packages.sfepy
  • python312Packages.sfepy.dist
  • python312Packages.simpleitk
  • python312Packages.simpleitk.dist
  • python312Packages.sumo
  • python312Packages.sumo.dist
  • python312Packages.templateflow
  • python312Packages.templateflow.dist
  • python312Packages.torchio
  • python312Packages.torchio.dist
  • python312Packages.trx-python
  • python312Packages.trx-python.dist
  • python312Packages.vtk
  • python312Packages.xnatpy
  • python312Packages.xnatpy.dist
  • python313Packages.dcmstack
  • python313Packages.dcmstack.dist
  • python313Packages.deid
  • python313Packages.deid.dist
  • python313Packages.dicom-numpy
  • python313Packages.dicom-numpy.dist
  • python313Packages.dicom2nifti
  • python313Packages.dicom2nifti.dist
  • python313Packages.dicomweb-client
  • python313Packages.dicomweb-client.dist
  • python313Packages.dipy
  • python313Packages.dipy.dist
  • python313Packages.f3d
  • python313Packages.f3d.man
  • python313Packages.fast-simplification
  • python313Packages.fast-simplification.dist
  • python313Packages.fslpy
  • python313Packages.fslpy.dist
  • python313Packages.gdcm
  • python313Packages.gstools
  • python313Packages.gstools.dist
  • python313Packages.highdicom
  • python313Packages.highdicom.dist
  • python313Packages.itk
  • python313Packages.medpy
  • python313Packages.medpy.dist
  • python313Packages.medvol
  • python313Packages.medvol.dist
  • python313Packages.napari-nifti
  • python313Packages.napari-nifti.dist
  • python313Packages.nibabel
  • python313Packages.nibabel.dist
  • python313Packages.nilearn
  • python313Packages.nilearn.dist
  • python313Packages.nipy
  • python313Packages.nipy.dist
  • python313Packages.nitime
  • python313Packages.nitime.dist
  • python313Packages.nitransforms
  • python313Packages.nitransforms.dist
  • python313Packages.pybids
  • python313Packages.pybids.dist
  • python313Packages.pydicom
  • python313Packages.pydicom.dist
  • python313Packages.pykrige
  • python313Packages.pykrige.dist
  • python313Packages.pylibjpeg
  • python313Packages.pylibjpeg-openjpeg
  • python313Packages.pylibjpeg-openjpeg.dist
  • python313Packages.pylibjpeg.dist
  • python313Packages.pymedio
  • python313Packages.pymedio.dist
  • python313Packages.pynetdicom
  • python313Packages.pynetdicom.dist
  • python313Packages.pyorthanc
  • python313Packages.pyorthanc.dist
  • python313Packages.pyotb
  • python313Packages.pyotb.dist
  • python313Packages.pyradiomics
  • python313Packages.pyradiomics.dist
  • python313Packages.python-csxcad
  • python313Packages.python-csxcad.dist
  • python313Packages.pyvista
  • python313Packages.pyvista.dist
  • python313Packages.simpleitk
  • python313Packages.simpleitk.dist
  • python313Packages.templateflow
  • python313Packages.templateflow.dist
  • python313Packages.torchio
  • python313Packages.torchio.dist
  • python313Packages.trx-python
  • python313Packages.trx-python.dist
  • vtk-full (python313Packages.vtk)
  • python313Packages.xnatpy
  • python313Packages.xnatpy.dist
  • rtabmap
  • simpleitk
  • therion
  • vtk (vtk_9_5)
  • vtkWithQt5
  • vtkWithQt6

@wegank wegank merged commit 658c6aa into NixOS:master Jul 29, 2025
25 of 27 checks passed
@wegank wegank mentioned this pull request Jul 29, 2025
13 tasks
@qbisi qbisi mentioned this pull request Jul 29, 2025
13 tasks
@bcdarwin bcdarwin mentioned this pull request Aug 20, 2025
13 tasks
imath
c-blosc
unixODBC
postgresql
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@wolfgangwalther wolfgangwalther Sep 2, 2025

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This added quite a few reverse dependencies to postgresql - which is something we'd like to avoid to lower rebuilds for these updates.

Given that it uses libmysqlclient below, I assume this only needs libpq, it should be tried with that instead.

Trying in #439715.

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6.topic: python Python is a high-level, general-purpose programming language. 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 101-500 This PR causes between 101 and 500 packages to rebuild on Linux.

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4 participants