New modules command: nf-core modules info <tool>

[ewels]

I know that there are more important issues, but it was the evening and I can't resist making a pretty thing ✨

This one is for you @jfy133 - closes #1427

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

[codecov]

Codecov Report

Merging #1447 (f3d4937) into dev (2492743) will decrease coverage by 0.91%.
The diff coverage is 24.21%.

@@            Coverage Diff             @@
##              dev    #1447      +/-   ##
==========================================
- Coverage   65.72%   64.81%   -0.92%     
==========================================
  Files          50       51       +1     
  Lines        5853     5977     +124     
==========================================
+ Hits         3847     3874      +27     
- Misses       2006     2103      +97     

Impacted Files	Coverage Δ
nf_core/modules/info.py	19.09% <19.09%> (ø)
nf_core/__main__.py	51.55% <41.66%> (-0.30%)	⬇️
nf_core/modules/module_utils.py	38.23% <75.00%> (+0.09%)	⬆️
nf_core/modules/__init__.py	100.00% <100.00%> (ø)
nf_core/modules/install.py	58.13% <100.00%> (-0.49%)	⬇️

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[jfy133]

😍 this is exactly what I was looking for, can't view the code, otherwise 👍👍👍

[mashehu]

Very nice!
the <code> style block looks a bit unoptimized for light mode. but I understand it is not easy to find a good color scheme which works for both dark and light backgrounds in the terminal.

[mashehu]

Is there some kind of caching happening? I fixed the formatting in controlfreec (nf-core/modules#1393) and it still throws the error:

│ /Users/mitochondrium/nf-core_tools/nf_core/modules/info.py:159 in generate_module_info_help                                                                │
│                                                                                                                                                            │
│   158 │   │   │   │   │   │   f"[orange1 on black] {key} [/][dim i] ({info['type']})",                                                                     │
│ ❱ 159 │   │   │   │   │   │   info["description"].replace("\n", " "),                                                                                      │
│   160 │   │   │   │   │   │   info.get("pattern", ""),                                                                                                     │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
AttributeError: 'NoneType' object has no attribute 'replace'

Which I guess comes from the old formatting. (also we probably want to keep the \n for code blocks, see nf-core/website#1069

[ewels]

Is the light mode bad enough to need changing? I actually think it looks kind of cool 😅

Right, instead of dropping the newlines I will parse as markdown then 👍🏻

[ewels]

Is there some kind of caching happening?

And yes, with requests_cache. I think I set it up to save in ~/.nfcore/ by default so if you wipe that you should be good to go 👍🏻

[ewels]

Ok, markdown should now be parsed. Also if you run in a local pipeline or clone of the modules repo, it should use the local copy (not get it from the web / caching issues etc). Turned out that the file path for modules was dodgy, so that's fixed now too. So now runs with the local variant as you edit it.

Controlfreec seems to be working locally for me now 👍🏻

[sateeshperi]

lgtm! excited to use this!