Fix PyPI package generation

[gaurav]

I found a bug in the PyPI package generation -- the generated .whl and .tar.gz files didn't actually contain the crdch_model.py program. Luckily, it was a pretty easy fix, and crdch-model v1.1.1 contains the files and seems to work with the Example Data Workflow.

I don't think the data files are being included, either; there's some example syntax in https://setuptools.pypa.io/en/latest/userguide/declarative_config.html that might help.

Closes #69.

[turbomam]

@sujaypatil96 and I were playing around with packages = find: b ut this is better.

[gaurav]

We definitely need to add linkml-model as a prereq in the generated PyPI model.

[gaurav]

Okay, I think I've added linkml-runtime as a prereq.

@turbomam I haven't been able to figure out how to get setup.cfg to include crdch_model as the top-level object (i.e. you would still need from crdch_model import crdch_model to access the objects in it. However, I have figured out how to do that with Poetry (PR #127). It might be worth switching over to that if that feature is really important to you.

Another option would be to rename the file from crdch_model/crdch_model.py to crdch/model.py. That way, you'll need to run from crdch import model, which... works better? Maybe? I dunno.

I'd love to know your thoughts, and if we need more time, we can discuss this on the Thursday call.

[gaurav]

@turbomam Oh, I should have mentioned:

• https://pypi.org/project/crdch-model/1.1.2/ is what it looks like when you publish using setup.py using this branch.
• https://pypi.org/project/crdch-model/1.1.3/ is what it looks like when you publish using poetry using PR Switch from setup.py to poetry for Python Data Class installation #127.

[turbomam]

from crdch_model import crdch_model is fine with me, I just kept forgetting to write it that way. @sujaypatil96 is making a good case for Poetry, so I wouldn't object to that either. I'm looking at the 1.1.2 and 1.1.3 packages now.

[turbomam]

I can access BodySite() after importing 1.1.2, 1.1.3 or 1.1.5 now.

[sujaypatil96]

Looks good @gaurav.🚀 I tried the importing the module and the associated dataclasses like from crdch_model import crdch_model and everything works as expected.

Right, +1 for PR #127, I think this is all the more reason to start adopting poetry.

[sujaypatil96]

Actually, I think I figured out what's causing the problem:

package_dir=
    =crdch_model
packages=find:

[options.packages.find]
where=crdch_model

By adding the above snippet, we can import crdch_model in the same way as PR #127.

[sujaypatil96]

Commits from PR #138 have been added to this PR, so this is ready to be merged.