improve update.py

[fabianegli]

Main edits by @ErikDanielsson

• Refactor code into methods
• Always use a temporary directory when updating. This makes the code simpler, and reduces the risk that the files are removed before the update has shown to be successful.

This is a work in progress, do not merge.

Refactoring, bugfixes and other improvements.

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 #1536 (22f9ca7) into dev (1d427a2) will increase coverage by 0.35%.
The diff coverage is 73.39%.

@@            Coverage Diff             @@
##              dev    #1536      +/-   ##
==========================================
+ Coverage   67.88%   68.24%   +0.35%     
==========================================
  Files          56       56              
  Lines        6677     6694      +17     
==========================================
+ Hits         4533     4568      +35     
+ Misses       2144     2126      -18     

Impacted Files	Coverage Δ
nf_core/__main__.py	53.06% <ø> (ø)
nf_core/modules/update.py	73.76% <71.98%> (+8.70%)	⬆️
nf_core/modules/install.py	72.72% <100.00%> (-0.35%)	⬇️
nf_core/modules/modules_json.py	63.13% <100.00%> (-0.13%)	⬇️
nf_core/modules/modules_repo.py	81.52% <100.00%> (+0.23%)	⬆️
nf_core/utils.py	80.48% <100.00%> (+0.11%)	⬆️

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[ewels]

Just had a quick read through on my phone and all looks good so far 👌🏻 Thanks!

I've converted the PR to a draft. When you're ready for it to be reviewed + merged, drop the label and remove the draft status 👍🏻

[ErikDanielsson]

The main issue with doing it that way is that we need to report the errors in different ways. But I'm still working on it, so I'll have a look on how we can reduce the code bloat.

[ErikDanielsson]

Couldn't get_all_modules_info() use get_single_module_info() internally?

It is convenient when reporting skipped and overridden directories in get_all_modules_info due to entries in the .nf-core.yml to loop through the file at the repo level. We could not do this as easy if we were to try to reuse the code from get_single_module_info. Therefore I don't think it is worth to change currently.

[ErikDanielsson]

I think this PR is mature enough now to be merged. update.py might benefint from more refactoring in the future, but I think this is good start at least.

[fabianegli]

The docs are out of date: https://nf-co.re/tools/#update-modules-in-a-pipeline

[mirpedrol]

Looks good to me, thanks!

[ErikDanielsson]

Great, thanks for the review! Are you happy merging @fabianegli?

[fabianegli]

Yes, I think it is fine now. Thank you @mirpedrol for the review and @ErikDanielsson for the refactoring.