Modules lint output sorting

[awgymer]

The current modules lint behaviour sorts the test messages by message then by module_name (this is done by python string-sorting i.e. alphabetically).

Personally I find this somewhat unintuitive to grok.

Current output:

This PR changes the default sort order to use the lint_test test name, then the module_name, then finally the message.

It also adds the option to order by module_name first. This is a personal preference - feel free to quibble the inclusion.

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 #2077 (e8aa448) into dev (ea9dd92) will increase coverage by 0.01%.
The diff coverage is 91.66%.

@@            Coverage Diff             @@
##              dev    #2077      +/-   ##
==========================================
+ Coverage   67.98%   67.99%   +0.01%     
==========================================
  Files          43       43              
  Lines        5597     5602       +5     
==========================================
+ Hits         3805     3809       +4     
- Misses       1792     1793       +1     

Impacted Files	Coverage Δ
nf_core/modules/lint/__init__.py	83.24% <87.50%> (-0.27%)	⬇️
nf_core/__main__.py	58.65% <100.00%> (+0.13%)	⬆️

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[mashehu]

Not sure about the different shades of the row. It was alternating between rows before, but now seems to group them. Do we need the different shades? @ewels 👀

[awgymer]

You know I didn't actually notice how that changed, I would need to look at the logic to see how it decides what to highlight. But personally I do like that it seems to highlight the "groups" of rows.

I think it alternates highlighting between groups based on the module name.

[ewels]

Can't remember how the varying colours works now. I added it to try to aid readability, which is pretty poor for this output.

[ewels]

This is for nf-core modules lint but maybe you also want it for nf-core lint?

[awgymer]

Added to pipeline linting. Called it sort_by for consistency across commands but did consider if it should be module_sort_by in pipeline lint

[mirpedrol]

I personally like sort_by more, I find module_sort_by a bit more confusing. Should we merge? are you happy with it @awgymer ?

[awgymer]

Ok that's good then. Happy to merge if this gets an approving review

[mirpedrol]

sorry, I thought it was already approved 😅

[mashehu]

Can't remember how the varying colours works now. I added it to try to aid readability, which is pretty poor for this output.

btw. this is the source for the alternating colors:

https://github.com/nf-core/tools/blob/dev/nf_core/modules/lint/__init__.py#L377

[awgymer]

Can't remember how the varying colours works now. I added it to try to aid readability, which is pretty poor for this output.

btw. this is the source for the alternating colors:

https://github.com/nf-core/tools/blob/dev/nf_core/modules/lint/__init__.py#L377

Indeed it colours rows in grouping of module name. I don't think it was ever guaranteed to be alternating every row.

If you (or anyone) has a preference for changing it then happy to implement something different in future but will merge this PR now.

[mashehu]

Oh, we forgot to mention that new option in the changelog. Can you open a PR for that, @awgymer?