First stab at nicely formatted cli help output using Rich.

[ewels]

Took code from rich-cli written by @willmcgugan and played around with until it worked for us.

It's so pretty 🤩

• Help strings are no longer truncated if they're a bit on the long side
• Text now stuff wraps onto multiple lines for narrow terminals and long help texts
• I've set it to use a maximum width of 100 chars, instead of the full terminal width. Personal preference.
• We have a custom @click.version_option() which doesn't seem to make it into the help, I don't know how to fix this.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

Before	Afer

[maxulysse]

<3

[ewels]

Don't merge yet - just figured out why the version wasn't printed. We're skipping the first argument because I copied over some code without understanding why it was there 👀

The rich-cli has a positional argument which I guess looked a bit ugly in the help, so was skipped. We also often have positional arguments but not always (in which case the first option flag is skipped), and in the future some commands may have more than one (in which case subsequent ones will be printed).

Now looking into a way to detect these and give them dedicated styling.

[ewels]

Ok, sorted it. I started adding support for a panel dedicated to arguments, but then realised that there isn't really much that we can print. click doesn't accept help strings for arguments and there are no options, so it's basically only the metavars. These are already printed in the usage string. So now the code just skips any parameters that are positional arguments.

It seems that this is intentional on the part of click. See relevant docs: https://click.palletsprojects.com/en/8.0.x/documentation/#documenting-arguments

[codecov]

Codecov Report

Merging #1403 (2351867) into dev (0ddcd23) will increase coverage by 0.10%.
The diff coverage is 85.33%.

@@            Coverage Diff             @@
##              dev    #1403      +/-   ##
==========================================
+ Coverage   66.78%   66.88%   +0.10%     
==========================================
  Files          50       50              
  Lines        5714     5762      +48     
==========================================
+ Hits         3816     3854      +38     
- Misses       1898     1908      +10     

Impacted Files	Coverage Δ
nf_core/__main__.py	58.07% <85.33%> (+2.46%)	⬆️

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