Did sitkUtils.PullVolumeFromSlicer() break with Slicer 5.2?

lassoan · December 21, 2022, 2:50am

Setting an exact version requirement for a Python package in a complex system is a really bad idea. Dependencies can be so tangled that by setting exact version requirements for a few packages can almost guarantee a failure somewhere. Usually exact version requirement are not even necessary, but it is just because developers are cutting corners (because setting an exact known version is simpler for a developer than exploring what range of versions work).

We ran into the same issue with TotalSegmentator and SimpleITK. If you cannot fix the problem in the package that sets the exact version requirement then you can use this technique to prevent replacement of SimpleITK:

github.com

lassoan/SlicerTotalSegmentator/blob/70271651d7639bba716dcbd91dcc6e209b3fcdf1/TotalSegmentator/TotalSegmentator.py#L550-L594


      
          # TotalSegmentator requires an exact SimpleITK version (2.0.2).
          # Simply installing TotalSegmentator would uninstall Slicer's SimpleITK, which would break
          # image IO plugins (in particular, the in-memory image transfer IO plugin).
          
          
# As a workaround, TotalSegmentator installed without dependencies, then
          # SimpleITK is removed from dependencies (from METADATA file)
          # and then install TotalSegmentator with dependencies.
          
          
totalSegmentatorPackage = "git+https://github.com/wasserth/TotalSegmentator.git"
          
          
# Install TotalSegmentator without dependencies
          # (because we need to remove SimpleITK requirement before installing dependencies,
          # as it would replace Slicer's SimpleITK)
          slicer.util.pip_install(totalSegmentatorPackage + " --no-deps" + (" --upgrade" if upgrade else ""))
          
          
# Get path to site-packages\TotalSegmentator-1.4.0.dist-info\METADATA
          import importlib.metadata
          metadataPath = [p for p in importlib.metadata.files('TotalSegmentator') if 'METADATA' in str(p)][0]
          metadataPath.locate()

This file has been truncated. show original

Topic		Replies	Views
sitkUtils.PullVolumeFromSlicer makes Slicer crash Development bug	45	1747	February 13, 2020
Reproducible Slicer crash when pushing to some volume nodes using sitkUtils PushVolumeToSlicer Development	3	352	January 29, 2021
Trying to update a slicer volume node from SimpleITKImage Support mrml , sitk	6	2011	March 1, 2021
Possible malfunction with Slicer kernel for Jupyter notebook? Support jupyter	0	311	July 3, 2022
vtkMRMLScalarVolumeNode to SimpleITK image Development extensions-manager , vtk	2	1065	July 7, 2017

Did sitkUtils.PullVolumeFromSlicer() break with Slicer 5.2?

Related Topics