Rewrite YAML + Markdown linting, use Prettier

[ewels]

YAML linting has been broken for ages, and since we fixed it recently it has now started throwing tonnes of errors everywhere and generally being annoying.

This extends to the latest pipeline sync, where PRs such as nf-core/pgdb#47 are failing CI with errors like this:

lint: info: yamllint on ..
lint: error: failed yamllint on ..
Warning: [comments] too few spaces before comment
Error: [empty-lines] too many blank lines (1 > 0)
Error: [trailing-spaces] trailing spaces
Error: [empty-lines] too many blank lines (1 > 0)
Error: [empty-lines] too many blank lines (1 > 0)
Error: [empty-lines] too many blank lines (1 > 0)
Error: [trailing-spaces] trailing spaces
Error: [indentation] wrong indentation: expected [10](https://github.com/nf-core/pgdb/runs/5560875515?check_suite_focus=true#step:4:10) but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8
Error: [indentation] wrong indentation: expected 10 but found 8

We can of course fix these errors in the template. But to be honest it feels like now is a good time to revisit this linting.

Proposal is to drop Markdown and YAML linting and instead use https://prettier.io - this does both and generally feels like a bit more of a polished tool. One major advantage is that Prettier can and does fix the linting errors for you, rather than just spitting out errors. There's also good editor plugin integrations available.

Whilst we're there, it would be good to revisit the automated PR comments. We have a weird setup for the nf-core lint results which were the result of a load of pain to do with GitHub Actions bot permissions, but the comments from the YAML and Markdown linting seem to be working now. So maybe we can simplify this a lot.

[ewels]

But the comments from the YAML and Markdown linting seem to be working now. So maybe we can simplify this a lot.

Correction, they're still broken:

Run mshick/add-pr-comment@v1
Error: Resource not accessible by integration

I must have been looking at a PR from a branch (eg. the sync) when I thought it was working.

Ok, but still stands - just need to make it the other way around: mimic the nf-core linting comment but for the other lint tests.

[mashehu]

#1413 (comment):

I looked a bit into switching to prettier over the weekend. I think we should stick with markdown-lint and yaml-lint for now, because most of our markdown rules (e.g. ul-indent,no-duplicate-header, etc.) can not be replicated in a prettier config as far as I can see. But if you say these rules are not that important we could switch.

[maxulysse]

Can't we then run prettier as a first test and then followed by YAML and Markdown lint?

[edmundmiller]

https://prettier.io/docs/en/options.html#print-width From our conversation about google docs in slack the other day.

[ewels]

I looked a bit into switching to prettier over the weekend. I think we should stick with markdown-lint and yaml-lint for now, because most of our markdown rules (e.g. ul-indent,no-duplicate-header, etc.) can not be replicated in a prettier config as far as I can see. But if you say these rules are not that important we could switch.

Sorry @mashehu only just seeing this now but yeah, I came to the same conclusion. But I think that those rules are not super important are were mostly to make the linter less strict. Prettier is less strict by default (whilst still being strict enough in my mind). So I think we're good, hopefully..