Dependencies not installed with "install dependencies" button

[shai-ikko]

Hi,

When you install the dependencies for MuscleMap using the extension, you consistently use the --no-deps flag to pip.
As a result, some dependencies (higher-level dependencies for the Slicer extension) are not installed. E.g. starting from a fresh Slicer 5.12, installing MuscleMap, installing pytorch using its extension, and pushing the "Install MuscleMap dependencies" button, you get (after some time) a message that the dependencies are all installed. But if you try to create a segmentation, you discover that dependencies like "narwhals" and "psutils" are still missing.

SlicerMuscleMap/WholeBodyMuscleSegmentation/WholeBodyMuscleSegmentation.py

Line 460 in 45c59de

slicer.util.pip_install(["--no-deps", pkg])

SlicerMuscleMap/WholeBodyMuscleSegmentation/WholeBodyMuscleSegmentation.py

Line 466 in 45c59de

slicer.util.pip_install(["--no-deps", "git+https://github.com/MuscleMap/MuscleMap.git"])

[Eddowesselink]

Dear @shai-ikko,

Thanks for the detailed report. Fix pushed. It now installs the runtime dependencies with their dependencies (no more --no-deps), so transitive packages resolve automatically. They're left unpinned so it doesn't fight Slicer's bundled numpy/scikit-learn/pandas, while torch (from the PyTorch extension) and numpy stay protected via a pip constraints file so they're never up/downgraded.

It should be available in Slicer tomorrow after the nightly build.

Would you be willing to give it a try once it's out and let me know if it works on your end? That would be a great final confirmation. Thanks!

Cheers,
Eddo