Replace flake with flakeheaven for linting

[matteopilz]

The pyproject.toml needs to be configured. We can also optionally exclude not linted file types automatically and end the action early https://github.com/tj-actions/changed-files.

[jpfeuffer]

It says missing plugins. And you need to test with some actual changes in this PR

[matteopilz]

I have added the plugins and tested it on push. It still needs to be configured and I don't know which settings we want.

[jpfeuffer]

Any settings are fine for me. @OpenMS/core What do you think about auto-applying linting changes with e.g., https://github.com/adamchainz/blacken-docs

[timosachsenberg]

+1 if it doesn’t break it ;)

[matteopilz]

Does blacken-docs work only for code blocks?

[jpfeuffer]

Yes, what else do you want to lint?

[matteopilz]

The markdown in the rst files, basically apply the suggested changes for errors or warnings from flakeheaven automatically. I guess this would be too insecure.

[jpfeuffer]

I think flakeheaven also just looks at python and pycon code blocks. Rst would need another linter (e.g. rst-lint) but I find that sphinx does a decent job with its warnings.

[matteopilz]

Do we then actually still need flakeheaven, if we correct code blocks anyway?

[jpfeuffer]

If we agree to auto-apply, no, sorry. I was actually assuming that flake heaven can auto-apply.

[matteopilz]

blacken needs pre-commit (https://pre-commit.com/#install) installed on the machine to register a commit and actually change something beforehand. How should we handle this? If we install it with a commit on a runner, it kind of defeats the purpose because nothing will be changed.

[jpfeuffer]

you can also just run it in an action. Pre-commit is just the preferred way for most users, since they want to leave the choice to developers I guess.

[jpfeuffer]

python -m pip install blacken-docs && blacken-docs -l 80 docs/source/*.rst

[jpfeuffer]

That's how I did #333

[jpfeuffer]

By the way, I changed my mind for line length as you can see. BEcause this is for documentation. And it should be visible on mobile as well. No one is developing in there.

[jpfeuffer]

You need to somehow suggest or even directly push the changes. I guess the former (suggesting) is a nice middle ground. And for follow up PRs probably not to huge.

https://github.com/reviewdog/action-suggester

[jpfeuffer]

If you only use pull_request as a trigger, which is fine in this case actually, you will not be able to test it. Unless someone does a PR against YOUR branch. (your action is not on master, against which this PR is made)

[jpfeuffer]

Do a PR with the yml only and I will merge it.

[matteopilz]

I think action-suggester works only on pull_request. I'm currently not sure, if it will work, but we can try it. I'm removing the other files.

[matteopilz]

It didn't work, blacken still exits with an error.

[matteopilz]

It looks like flakeheaven would actually report in the output format, action-suggester expects...

[jpfeuffer]

I doubt it, since it is not able to make any changes. You might be able to comment with the comments. But this is almost useless. You have to go back to the code, search the place where the comments were etc. I just want to click on accept suggestion and be done with it.

[jpfeuffer]

Also: flakeheaven is also bugged: https://github.com/flakeheaven/flakeheaven/issues/165