fix packaging

[NickleDave]

the current source code layout that we've evolved into since 0.6.0 release + setup.py causes a couple of issues:

• the article package that I added in src is getting added to the source distribution, because the setup.py file says "just include every package you find in the src/ directory"
• this causes a bunch of import errors -, if you don't do pip install .[article] to get dependencies like sklearn that are declared in the EXTRAS_REQUIRE of the setup.py
  • -> to reproduce, do $ python setup.py sdist and then pip install the generated tar.gz in the dist/ directory, then launch a REPL and try to import tweetynet
• the intent of the article package is not to be in the tweetynet distribution -- it just gives us a separate convenient package to work with for article-only code
• but the yarden2annot module is currently in that article package. vak needs access to it, to load the canary annotations.
• also this is all extra annoying to figure out how to fix, because we're still using an old-school setup.py which is not even well-documented any more on the setuptools site

fix:

• [ ] adopt a "monorepo" format where we actually have two sub-dirs (see below)
• [ ] switch to declarative setup.cfg instead of setup.py, or possibly switch to poetry and use pyproject.toml
• [ ] move yarden2annot into tweetynet package
• [ ] fix corresponding entry point in tweetynet/setup.cfg file upon doing so, so the format still gets installed for vak
• [ ] add install instructions for article code -- we shouldn't put article on PyPI but we should make it easy for an interested reader to install locally. Have a separate README in the "article" sub-directory for this

This is the structure I mean by "monorepo", I think this is the least-complicated solution. An alternative might be doing something fancy with setup.cfg and/or setup.py but I'm not sure if it's possible and if so worth it

tweetynet 
│   ├── tweetynet
│   │   ├── src
│   │   ├── setup.cfg 
│   │   └── tests/
│   └── article
│   │   ├── src
│   │   ├── setup.cfg 

[NickleDave]

Also, these issues are what's preventing me from testing whether the fix for newer versions of torch works. Hence the need to fix sooner rather than later

[NickleDave]

I ended up solving this differently.

• [x] remove yarden2annot and added that directly to crowsetta, and then released a new version of crowsetta; because I was running into issues with circular imports trying to keep the yarden2annot module in, and the other workarounds I came up with would have been weird and fragile. Also because we want it to be easy for people to be able to work with those annotations, without needing to install tweetynet necessarily
• [x] keep the tweetynet/src repo at the same level -- this is the "package" that this repo can be used to build
• [x] add the article folder and just move all related things into that folder. It will be easy to install but it's not set up to build into a distribution package, which is fine
• [x] keep pyproject.toml but use flit to develop -- the pyproject.toml is the standard used by more projects and I find it much more readable than setup.cfg so I would rather use it