Add nf-core configs create sub command (attempt 2)

[jfy133]

Closes #2731

Supersedes: https://github.com/nf-core/tools/pull/2852/files#

Unresolved TODOs:

• Find a way to make TextInput more generic and move to common location (uses a specific ValidateConfig function)
• Find a way to make ValidateConfig more generic and move to common location (calls CreateConfig)
• Investigate whether make the TextInput widget not displayed given a particular context (see: https://textual.textualize.io/styles/visibility/), rather than just disable
• Add check if config file already exists before writing
• In 2d7863a added issue where unless everything filled in on basic details screen all elements in params dict get sets to none causing failure due to can't NonType + str error when trying to create the file

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

Attention: Patch coverage is 11.93182% with 310 lines in your changes missing coverage. Please review.

Project coverage is 74.78%. Comparing base (52dfee6) to head (227abc2).
Report is 4 commits behind head on dev.

Files with missing lines	Patch %	Lines
nf_core/configs/create/utils.py	0.00%	112 Missing ⚠️
nf_core/configs/create/__init__.py	0.00%	51 Missing ⚠️
nf_core/configs/create/basicdetails.py	0.00%	37 Missing ⚠️
nf_core/configs/create/create.py	0.00%	36 Missing ⚠️
nf_core/configs/create/final.py	0.00%	20 Missing ⚠️
nf_core/configs/create/configtype.py	0.00%	15 Missing ⚠️
nf_core/configs/create/nfcorequestion.py	0.00%	15 Missing ⚠️
nf_core/configs/create/welcome.py	0.00%	13 Missing ⚠️
nf_core/__main__.py	67.74%	10 Missing ⚠️
nf_core/configs/__init__.py	0.00%	1 Missing ⚠️

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[jfy133]

Two now identified problems:

Major

• [ ]Problem
  • Failed fields with validation does not block continuing with dialogue screens (i.e. pressing next)
  • Because validation has failed, the tool 'fails' to run CreateConfig with remaining fields (i.e., the resulting object is still created, but 'force' sets all entries to None)
  • Because we can proceed after pressing 'next', we can get to to the end of the questions and tool attempts to write a file. However as config name is now set to None , it fails with a can't None + str error.

Probably due to bad classmethods in utils.py

• Preferred behavior:
  • Validation only occurs if something filled in. If nothing filled in, returns a valid 'no info' entry (which can be subsequently ignored)
  • If validation fails, block next button (unless again reset to empty, or filled in with valid information)

Minor:

• Description always gets written "" even though it should not be written (if description != "" or not None:)

[jfy133]

@mirpedrol I don't know if that sync is because you plan to continue on this branch or not, but it's probably easier to start from scratch 😅.

Let me know if you ever want a top-level planning meeting or anything

[mirpedrol]

I was starting to work on this, yes! 😄 It was not very outdated since it's a mostly independent command so I think it is ok to continue working on this PR.
I remember we had a document describing the functionality we wanted on this tool. do you have the link? And is this still valid? Thanks!

[jfy133]

I was starting to work on this, yes! 😄 It was not very outdated since it's a mostly independent command so I think it is ok to continue working on this PR.
I remember we had a document describing the functionality we wanted on this tool. do you have the link? And is this still valid? Thanks!

Ok cool!

It's probably on the configbuilder channel on slack, I'll ping you