docs: Set "version" in Sphinx configuration

[tsibley]

This will allow us to display the specific version for "stable" on Read
the Docs (once nextstrain/sphinx-theme#16 is
merged).

Also sets "release" as the Sphinx documentation says¹:

If you don’t need the separation provided between version and
release, just set them both to the same value.

¹ https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-release

[corneliusroemer]

Probably not the right place but seeing this reminded me:

The __version__ PEP has been rejected a few months ago: https://www.python.org/dev/peps/pep-0396/#id14

Will we make the switch at some point to importlib.metadata.version(augur) as suggested: https://docs.python.org/3/library/importlib.metadata.html#distribution-versions

[tsibley]

Ah, but the rejection standardizing __version__ has little bearing on independently using a variable called __version__ internally in our own code?

[huddlej]

@corneliusroemer Could you create an issue for your recommended change as an enhancement? We can keep the current convention internally, but it would be nice to support the standard version interface, too.

[tsibley]

I think there's some confusion. We do support the standard version interface already. importlib.metadata.version() reads from the installed package metadata. In our case, we declare that in setup.py and during build it ends up in the source or wheel distribution metadata (e.g. nextstrain-augur-X.Y.Z/PKG-INFO or nextstrain_augur-X.Y.Z.dist-info/METADATA), which then gets installed alongside the code into site-packages (as *.dist-info/METADATA).

[tsibley]

By way of example:

$ nextstrain shell /var/empty
Entering the Nextstrain build environment

Mapped volumes:
  /nextstrain/build is from /var/empty

Run the command "exit" to leave the build environment.

nextstrain:/nextstrain/build $ python3
Python 3.7.12 (default, Jan 26 2022, 22:28:48) 
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from importlib_metadata import version
>>> version('nextstrain-augur')
'13.1.2'

[huddlej]

I think there's some confusion.

Yeah, thank you for clearing this up. I expected the following to work:

>>> from importlib.metadata import version
>>> version('augur')

since one always refers to Python packages in code by the actual modules exposed by a distribution and not the PyPI package name. But, I see now that this module is designed to get the version of a distribution.

[tsibley]

Yeah, it's a subtly. You can use packages_distributions() (and maybe other ways) to map packages (not modules) → distribution, e.g.

>>> from importlib_metadata import packages_distributions, version
>>> [version(dist) for dist in packages_distributions()['augur']]
['13.1.2']

[tsibley]

(and if need to go module → distribution, you do so by way of module.__package__, e.g. augur.io.__package__ == 'augur').