Change setup configuration for pip

[smoia]

This is a proposed internal setup makeover.

Proposed Changes

• Add a setup.cfg file for pip to better handle the requirements installation
• Move most of setup.py content into setup.cfg
• Remove the packaged six and docopt, add them as requirements during installation.
• Update imports to reflect the above-mentioned change
• Add "extra" modules installation (e.g. h5py and scipy can be installed with pip install bioread[hdf5/mat/all]

Things that may be interesting to discuss about

• At the moment, most of the requirements don't have minimal version indication. It might be interesting to add them.
• ordereddict is still packaged, mainly due to the fact that it becomes deprecated with python > 3.6, but then some refactoring is necessary to drop the dependency. It's still a possibility!

[smoia]

Basically, this is what changes:

[njvack]

Hmmmm... it's probably worth dropping ordereddict, and with it the entirety of python2 support. Which means we can also drop six.

Also! It looks like we might really want a pyproject.toml file instead of a setup.cfg file. I could even be talked into the idea that the version number belongs both there and in _metadata.py though it makes my soul cry, just a little bit. Though this offers some hope — looks like maybe introspecting with importlib is a reasonable thing to do?

Anyhow, I'm gonna merge this for now, as it's better than what I'm doing now, and on the right track to being The Right Thing, I think.

[njvack]

Well, on a clean vagrant box, after installing I now get:

$ acq_info
Traceback (most recent call last):
  File "/home/vagrant/.local/bin/acq_info", line 11, in <module>
    load_entry_point('bioread==1.0.5', 'console_scripts', 'acq_info')()
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 480, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 2693, in load_entry_point
    return ep.load()
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 2324, in load
    return self.resolve()
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 2330, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/vagrant/.local/lib/python3.6/site-packages/bioread/__init__.py", line 13, in <module>
    from bioread import reader
  File "/home/vagrant/.local/lib/python3.6/site-packages/bioread/reader.py", line 31, in <module>
    from bioread import headers as bh
  File "/home/vagrant/.local/lib/python3.6/site-packages/bioread/headers.py", line 11, in <module>
    from bioread.struct_dict import StructDict
  File "/home/vagrant/.local/lib/python3.6/site-packages/bioread/struct_dict.py", line 13, in <module>
    from bioread.vendor.ordereddict import OrderedDict
ModuleNotFoundError: No module named 'bioread.vendor'

so something is Not Quite Right yet

[smoia]

Aw, sorry for that! It might be because it's not initiating the vendor folder. Let me open a second PR. @rmarkello set up versioneer for phys2bids. We could try to do the same here and drop _metadata.py.

Also, I think that the issue with vendor is due to the fact that I accidentally removed the __init__.py library from that folder. I can put it back. Would you like to setup a CI to test that these things won't happen?

[njvack]

I 100% would love to set up CI, though I haven't done so in yonks and have mostly forgotten how to do it :/

It looks like Github has its own solution for this now?

Also, hi, @rmarkello!

[njvack]

Yes it turns out that re-adding __init__.py to vendor/ makes this better, I've just done it.

[smoia]

Great, sorry for the bug! Github does have CI solutions now! We still use Travis and azure (still thanks to our great @rmarkello), but why not stay in house? (Probably there's a reason, but I don't know it)

[smoia]

Well, let me know if you cut a release for pypi any time soon, I can't wait to update our installation to make it flawless!

[njvack]

It looks like versioneer expects to be making a _version.py file which won't be compatible with updating a pypyroject.toml file... we'll figure something out though

[njvack]

Okay! I've upload 1.0.5 to pypi, let me know if it makes life better. There's more stuff to do here, but this might make your life better now.

[njvack]

As a little aside: I've set up a CI build with Github Actions and it works a charm. I'm gonna release a 2.0 (only supporting py3.6+) probably today... the last major change to make there is going to be to use pyproject.toml and make setup.py a stub.

[njvack]

Okay again! Just FYI, I've yanked 1.0.5 from pypi and replaced it with a full-on 2.0. I figured that a major release was good for the whole "dropping support for a major language version" thing.

Now I am 100% done commenting on this closed PR.