Refactor nf-core modules commands

[ErikDanielsson]

Refactored pipeline_modules.py into one file file per nf-core modules command.

• Removed pipeline_modules.py
• Created base class ModuleCommand for modules commands to inherit from.
• Created classes for list, install and remove commands.

The modules commands are all now found in <command>.py.

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 #1124 (c1dce02) into dev (c196325) will increase coverage by 0.16%.
The diff coverage is 63.69%.

@@            Coverage Diff             @@
##              dev    #1124      +/-   ##
==========================================
+ Coverage   70.41%   70.58%   +0.16%     
==========================================
  Files          45       48       +3     
  Lines        4797     4827      +30     
==========================================
+ Hits         3378     3407      +29     
- Misses       1419     1420       +1     

Impacted Files	Coverage Δ
nf_core/__main__.py	62.11% <0.00%> (+1.13%)	⬆️
nf_core/modules/test_yml_builder.py	45.94% <50.00%> (ø)
nf_core/modules/install.py	53.38% <53.38%> (ø)
nf_core/modules/module_utils.py	76.08% <60.00%> (+12.98%)	⬆️
nf_core/modules/list.py	61.11% <61.11%> (ø)
nf_core/modules/modules_command.py	78.20% <78.20%> (ø)
nf_core/modules/remove.py	81.25% <81.25%> (ø)
nf_core/modules/__init__.py	100.00% <100.00%> (ø)
nf_core/modules/lint/__init__.py	75.96% <100.00%> (+0.84%)	⬆️
nf_core/modules/lint/module_changes.py	78.26% <0.00%> (ø)
... and 4 more

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[KevinMenden]

Hi @ErikDanielsson , overall I think this is a nice idea!

One thing that is a bit tricky with the modules commands though is that some of them (mostly lint at the moment) can be run on pipelines and on the nf-core/modules repository. So I would suggest to add a repo_type field to the base class and a method to identify the repo class (we have this in the lint code, just need to copy+paste and adapt a little). And then other methods such has has_valid_pipeline will need to be adapted accordingly.

But other than that I think this is nice! But would be nice to hear what @ewels thinks about this :)

[ErikDanielsson]

Thanks, I'll take a look at the lint code.

[KevinMenden]

LGTM!

[ewels]

On my phone, didn't get very far with the review sorry. But concept sounds great! I'm happy to merge if it LGTM you guys. Especially as high risk for merge conflicts.

[ewels]

Can we raise an exception instead and catch it in the cli code? I prefer not to have exits anywhere but there if possible.

[ewels]

Other checks just return false. So that would also be fine.