It's saying the branch has conflicts.

Also, this is a very wide change, that accomplishes much more than just updating setup.py, so perhaps it's best if split into multiple commits? Specially the (welcome) code -> singularity dir renaming should be in its own commit.

Better now?

I'm ok with it, but I want some other opinions.

MANIFEST.in misses a new-line character at the end of the file. Some editors may be confused or even crash if that line is not there. But else, it looks green to me. :-) Nice work.

Care to rebase this patch so we can merge it?

rebased.

Can you rebase it ?

I tried and it seemed like a nontrivial rebase with some code moves, and to be honest I did this so long ago I don't really remember the details of what I did, will finish the rebase later.

Yes, I am doing a lot of change. Thanks.

Since a lot of refactoring and change will be come next, if you can't do it in one time, I suggest you to wait I freeze before release.

Fixed in aba8ba6 based on commits by @rardiol.

@rardiol Thanks for your initial work on this task!