New CLI / Config

[36000]

The AFQ.api.AFQ.init docstring is now scraped to make a configuration file with all of the defaults and descriptions.
The scraping is done with: https://github.com/Chilipp/funcargparse

usage.rst can also be generated using updatedocs.py . If there were some way to call this automatically on server side for each commit, that could be cool.

[pep8speaks]

Hello @36000! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-08-11 19:53:27 UTC

[36000]

Looks like Cli2Gui, which primarily uses pysimplegui, is getting pyqt installed, not because pysimplegui requires it but because getostheme requires it.

Other than Cli2Gui, there is also Gooey, but that requires wxpython.

It may be simplest to just use pysimplegui directly.

[36000]

• Add back in "The default values of the configuration are" thats in master.
• Use toml instead of ini
• Remove GUI comments
• Generate usage.rst

[36000]

@arokem this is ready for review

[36000]

• Write a unit tests that makes sure the warnings of missing docstrings don't happen.
• Make sure lack of square brackets is handled as above.
• use custom sphinx extensions like in dipy (make usage.rst look like a template, generate the real one with update docs)
• change last .ini to .toml

[arokem]

OK - this works great locally for me.

Could you please:

1. Rebase on master
2. Add docs/source/usage.rst to the .gitignore file? Since that one's generated automatically, we'd like to avoid tracking it.

[arokem]

This is ready to go, I believe. I'll merge as soon as the CI comes back 🟢