Feature/test datasets

[JulianFlesch]

This is a DRAFT.

This PR adds functionality to list and search the nf-core/test-datasets github repository via a new subcommand test-datasets. Closes #3487 where this feature was requested.

Changes:

• Adds new subcommands: test-datasets search, test-datasets list, test-datasets list-branches
• Adds new test-datasets folder with command and utility functions

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

[mirpedrol]

I made some comments especially about the structure of the files, but it is looking good! 😄

[mirpedrol]

To follow the same structure as in other commands, the main functions of each sub-command should be moved to its own script. utils should only contain the functions that are common to all these scripts.

[JulianFlesch]

I restructured all logic into search.py and list.py 👍 But I would suggest keeping all functions in utils.py in the same plce, as they are either exported by more than one other file, or depend on each other.

[mirpedrol]

And one last comment. When we print the list of files or branches, we could use a rich table like we do here

[jfy133]

Noooo no rich stuff!!!!! Makes it much harder to copy and paste 😭🫠🫠😭🫠😭🫠😭

[JulianFlesch]

I'm on the fence on this one. Usually I also prefer plain text output because it is just easier to pipe, but rich is used a lot in nf-core, right?
How about another flag -t, --plain-text to print plain text output instead of a rich table? Or we could always default to plain text, if -u or -g is given.

[jfy133]

I'm on the fence on this one. Usually I also prefer plain text output because it is just easier to pipe, but rich is used a lot in nf-core, right?
How about another flag -t, --plain-text to print plain text output instead of a rich table? Or we could always default to plain text, if -u or -g is given.

Latter is probably best I think, as makes me and you happy but default sticks with the typical nf-core convention

[JulianFlesch]

Oh and one more general question: Whats our stance on type hints @mirpedrol ? Should I add them?
Their use across nf-core seemed a bit inconsistent to me, at first. But now I see them more and more :D

[mirpedrol]

We are slowly adopting them when we add new code or modify old code, so yes, you should add them 😄