Xlmod submodule

[mwalzer]

Removed cv folder contents, replaced with a git submodule

[mwalzer]

submodule updates via

git submodule update --remote --recursive --merge
git push

[edeutsch]

I don't understand how this works, but I hope it does! fine with me!

[mobiusklein]

Is the goal here is to make it so the previous URL https://github.com/HUPO-PSI/mzIdentML/blob/<commitish>/cv/XLMOD.obo resolvable, or to make it so git clone https://github.com/HUPO-PSI/mzIdentML still contains XLMOD.obo?

A submodule does not do the former since cv isn't a file as far as GitHub is concerned. A submodule could do the latter with the git clone --recurse-submodules. Submodules are imperfect solutions. I do not know if git subtree would work better. I don't remember which of the above goals we're trying to solve either.

[mwalzer]

Is the goal here is to make it so the previous URL https://github.com/HUPO-PSI/mzIdentML/blob/<commitish>/cv/XLMOD.obo resolvable, or to make it so git clone https://github.com/HUPO-PSI/mzIdentML still contains XLMOD.obo?

I think since XLMOD is now in a stand-alone project, it shouldn't resolve the XLMOD path for future commits in mzIdentML anymore.
And I also think it's okay that a default clone does not ship the CV. Developers should be aware of extra dependencies, and as such the submodule works for me and gives anyone the convenience to include XLMOD from the new sources with few extra steps.
But some documentation on this should be included in the PR - if we decide to go this route.

Submodules are imperfect solutions.

I tend to agree, but the alternative to leave an outdated 'hardcopy' in here I like even less. Maybe other alternatives exist, IDK how subtree would work.
@edeutsch Would removing it completely work, too?

[edeutsch]

@edeutsch Would removing it completely work, too?

I don't really know.

If any code such as the validator relies on XLMOD.obo being in this specific place (in the old repo) I would imagine it would be very easy to adjust it to a new scheme. And maybe that is preferable to trying to get fancy with submodules.