stop using modextrapaths to update $PYTHONPATH with standard path to installed Python packages (lib/python%(pyshortver)s/site-packages)

[Micket]

All the trivial cases cleaned up here. Some others i could potentially partly clean up, which uses a mix of several PYTHONPATH (standard + nonstandard location, Spark is an example of such an easyconfig).

Should of course not be merged until the corresponding framework PR is merged.

• depends on prepend to $PYTHONPATH or $EBPYTHONPREFIXES in generated module files by automatically scanning for Python site package directories (as configured via prefer-python-search-path) easybuild-framework#4539

[Flamefire]

That reminds me of an old PR of mine: #13385

However all but 1 of the ECs are now deprecated and that one is fixed here. However there was also an enhancement to CI which I extracted to #20963

And a regexp I used which you might try in your tree: grep -E ": 'lib/python[^/]+/site-packages'" $(grep --files-with-matches -Er "\\beasyblock = '(ConfigureMakePythonPackage|PythonBundle)'")

[Flamefire]

CI requires #21405 (which requires easybuilders/easybuild-framework#4644) after easybuilders/easybuild-framework#4634

[Flamefire]

ec.get has a resolve parameter defaulting to True, so it seems the value is already resolved at this point, isn't it?

If it was indeed required I'd suggest putting it below the check to avoid resolving every value without using almost any

[boegel]

Ah, maybe, I didn't actually verify that tbh... Will check

[boegel]

Test report by @boegel
FAILED
Build succeeded for 207 out of 209 (201 easyconfigs in total)
node3573.doduo.os - Linux RHEL 8.8, x86_64, AMD EPYC 7552 48-Core Processor, Python 3.6.8
See https://gist.github.com/boegel/7aa02cde418f967a759fb7895d895a0d for a full test report.

[boegel]

The two failures have nothing to do the changes being made here:

For BUSCO-5.4.5-foss-2022a.eb:

024-10-06 23:52:05 ERROR:	A run with the name /arcanine/scratch/gent/vo/000/gvo00002/vsc40023/easybuild_tests/RHEL8-eb5dev-rpath/zen2-ib/software/BUSCO/5.4.5-foss-2022a/test_eukaryota.out already exists...
	If you are sure you wish to overwrite existing files, please use the -f (force) option
2024-10-06 23:52:05 ERROR:	BUSCO analysis failed!

For FunGAP-1.1.1-foss-2022a.eb:

Missing modules for dependencies (use --robot?): BUSCO/5.4.5-foss-2022a

So it won't let it block this PR...

[boegel]

Going in, thanks @Micket!

[Flamefire]

Updated the PR for adding the CI check: #19061