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()

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Did sitkUtils.PullVolumeFromSlicer() break with Slicer 5.2?

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