How to configure autopep8?

Hi, I am trying to use autopep8 but it doesn't work as I was expecting. When doing `Code Format: Format Code` some parts of my code are formatted and others aren't. I tried the autopep8 command in CLI and it formatted a lot more my code which is what I was looking for. I also tried using atom-beautify and it also did a lot more formatting.

So, I would like to know:
1) Why isn't ide-python formatting as much as autopep8 on CLI or atom-beautify?
2) Is there a configuration that is preventing ide-python to do this?
3) Is there a configuration file I should change (or create) to have the formatting I would like?

I am fairly new to autopep8 and I haven't used much this package but I think there should be a little more documentation on these topics as someone new to them. I feel a little lost on what steps to take to have this package working as I'd like.

Notes:
`python -m pyls --help` shows the desired output
I'm on macOS 10.13.6
Atom version 1.29.0
When seeing a Python file in Atom, pycodestyle shows a lot of errors that aren't corrected by the autopep8 setting.

まず、`Code Format: Format Code` の動作を autopep8 CLI および `python -m pyls --help` の出力と比較します。どの設定がフォーマットを制御するのか、その設定方法、そして pycodestyle のエラーが残る可能性がある理由を文書化します。新しく参加する人が、文書化された手順に従って期待されるフォーマットを得られるようになれば完了です。

索引モデルが issue の本文から書いたものです。