Move external code to its own module

[martenson]

Idea spawned here: #617

Let's put together a list of these first:

• https://github.com/galaxyproject/galaxy/blob/dev/doc/patch.py
• https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/jstree.py
• https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/pastescript/serve.py
• https://github.com/galaxyproject/galaxy/blob/dev/lib/pkg_resources.py

[nsoranzo]

I'm not sure it makes sense to move the files (may break imports), but listing them somewhere is a good idea. I've added 3 files which were already in .ci/flake8_blacklist.txt .

[jxtx]

We can move them and import them to the old locations for backward compatibility.

[nsoranzo]

I think the code should reside where it is more logical, not per-license. If you are worried about license-compatibility, moving the files does not fix it.

Edit: if we want to acknowledge the code authors, this should be done per file/directory anyway.

[jxtx]

I think it is logical to separate core Galaxy code from 3rd party code.

[jmchilton]

👍 to separating out this code into a separate module.

[hexylena]

@jmchilton you've done some re-organising into packages recently. Should this be included in that?

[jmchilton]

We've removed patch.py and pkg_resources.py. We've modified jstree.py a bunch and I think we own it at this point - I think it is only used in one or two modules so imports aren't really a problem - it'd be fine to extract it or keep it where it is (xref #8058 though).

We still modify pastescript/serve.py - I'm sure a year or two from now it will be gone though as I can't imagine it will be the way we do things in a Python 3 only world.