BUG: Fix failing to install optional dependencies during selective install

[jamesobutler]

Traceback:

Traceback (most recent call last):
  File "C:\Users\butlej30383\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py", line 3255, in tryWithErrorDisplay
    yield
  File "C:/Users/butlej30383/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 319, in onPackageUpgrade
    self.logic.setupPythonRequirements(upgrade=True)
  File "C:/Users/butlej30383/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 821, in setupPythonRequirements
    self.pipInstallSelective('nnunetv2', nnunetRequirement, packagesToSkip)
  File "C:/Users/butlej30383/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 706, in pipInstallSelective
    slicer.util.pip_install(requirement)
  File "C:\Users\butlej30383\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py", line 3887, in pip_install
    _executePythonModule("pip", args)
  File "C:\Users\butlej30383\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py", line 3848, in _executePythonModule
    logProcessOutput(proc)
  File "C:\Users\butlej30383\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py", line 3814, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Users/butlej30383/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', 'black;extra', '==', 'dev']' returned non-zero exit status 2.

importlib finds the optional dependencies where nnUNet has optional dependencies (see here) for dev usage for enforcing various linting rules. Although these don't need to be installed to run TotalSegmentator successfully, I've changed the code to continue to install all the optional dependencies when using the selective pip install action.

SlicerTotalSegmentator/TotalSegmentator/TotalSegmentator.py

Lines 679 to 681 in 3ca58b1

	# Install all dependencies but the ones listed in packagesToSkip
	import importlib.metadata
	requirements = importlib.metadata.requires(packageToInstall)

cc: @lassoan

---

This was originally brought up by @Keyn34 in Slicer/ExtensionsIndex#2127 (comment).

I also get an error while installing TotalSegmentator Extension for black;extra==dev. I did not investigate further, though.

[lassoan]

Thanks a lot @jamesobutler. I've just added two comments inline.

[lassoan]

Shouldn't we just skip the dependency if extra is dev?

[jamesobutler]

I considered it but optional dependencies appears to have no standard about group names within it. A project could calling it “linting” or “dev” or whatever and I didn’t want to add code to generic method pipInstallSelective that was unique to nnUnet. All optional dependencies will report as package_name; extra == “group_name”.

Alternatively the packagesToSkip could include known linting packages like black, ruff, pre-commit, however that list could arbitrarily grow and I didn’t want to start that precedent here either.

[lassoan]

Thank you for your contribution!