Migrate list command to components

[mashehu]

What if we used component command classes actually? 👿

[awgymer]

I'm never sure on when it is really necessary to have a method within a method, but this feels like it could (and should) be a standalone method outside the class. I find it particularly confusing that keywords is used in the scope of this internal method whilst being defined in the enclosing method directly above.

[mashehu]

partially fixed in 7a2fa10

[mirpedrol]

I like it with these levels of inheritance :)
I am not sure if this will be possible in all commands as some of them have different functionalities in ModulesCommand or SubworkflowsCommand, but we can try 💪

[awgymer]

Do we need to add tests/subworkflows/list? I didn't see it in the diff

[awgymer]

I like it with these levels of inheritance :) I am not sure if this will be possible in all commands as some of them have different functionalities in ModulesCommand or SubworkflowsCommand, but we can try 💪

I just looked and I think after this only check_patch_paths will be a method on ModulesCommand and SubworkflowsCommand just sets component_type='subworkflows' in the init, so we could probably move to drop the Subworkflows/ModulesCommand classes and just use Componet<X>Command subclasses or direct subclassing of ComponentCommand where there is no shared functionality between the particular modules and subworkflows commands.

[codecov]

Codecov Report

Merging #1995 (3f8863e) into dev (7848faa) will increase coverage by 0.87%.
The diff coverage is 54.19%.

@@            Coverage Diff             @@
##              dev    #1995      +/-   ##
==========================================
+ Coverage   62.50%   63.37%   +0.87%     
==========================================
  Files          43       44       +1     
  Lines        4902     5030     +128     
==========================================
+ Hits         3064     3188     +124     
- Misses       1838     1842       +4     

Impacted Files	Coverage Δ
nf_core/components/components_command.py	67.92% <4.54%> (-16.60%)	⬇️
nf_core/__main__.py	59.59% <48.27%> (-0.41%)	⬇️
nf_core/components/list.py	69.62% <69.62%> (ø)
nf_core/subworkflows/install.py	85.00% <100.00%> (+62.50%)	⬆️
nf_core/modules/modules_repo.py	81.46% <0.00%> (+1.95%)	⬆️

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