Modules remove patch

[awgymer]

#1920

This is an initial commit of an example of how we could achieve this using exisiting functionality to apply a patch in reverse.

Would need significant improvements in error-handling.
May be better to do an update on the current sha?

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

❗ No coverage uploaded for pull request base (dev@e2ef749). Click here to learn what that means.
The diff coverage is 71.69%.

@@          Coverage Diff           @@
##             dev    #2216   +/-   ##
======================================
  Coverage       ?   72.98%           
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  Files          ?       77           
  Lines          ?     8396           
  Branches       ?        0           
======================================
  Hits           ?     6128           
  Misses         ?     2268           
  Partials       ?        0           

Impacted Files	Coverage Δ
nf_core/__main__.py	59.83% <40.00%> (ø)
nf_core/modules/modules_json.py	79.92% <66.66%> (ø)
nf_core/modules/patch.py	79.04% <76.92%> (ø)

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[mirpedrol]

Looks very good! :) Maybe we could add a recommendation to lint the module after that? And also an option to force the remove and skip the questionary.

[mirpedrol]

I would catch possible errors here before removing it from modules.json

[awgymer]

Yes, error handling needs to be added for sure!

[awgymer]

I've added some code to check if the reverted module matches the code for the known sha and if it doesn't we suggest a reinstall.
Still think this process is quite messy and not sure if deleting the patch and removing from the JSON followed by a reinstall would be better?

Not sure what the best way to write a test for this is either.

[mirpedrol]

Even if it would be the easiest, I think we should avoid reinstalling because we could lose track from the "installed_by" in modules.json
Regarding tests, we are already testing applying a reverse patch, so I would only test if this function deletes the file and removes it from modules.json.

[awgymer]

Failure due to an API rate-limit issue. Tests for 3.9 all passed though. Could I get a re-review on the test I implemented please @mirpedrol

[mirpedrol]

LGTM when tests pass 🙂 thanks!