Fix incorrect assertions for called_with on mocks

[awgymer]

Closes #2890

fix: assertions for called_with/called_once_with were silently returning mocks before 3.12. Broken in 3.12.

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

[awgymer]

We need to resolve the issue with the patch on the schema lint tests.

I cannot for the life of me figure out what the correct way to patch the method call of the pipeline Schema object is. I think perhaps there is an issue with the fact the class is imported inside the cli function?

[codecov]

Codecov Report

Attention: Patch coverage is 88.88889% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 74.97%. Comparing base (221b683) to head (3fa8131).
Report is 4 commits behind head on dev.

Files	Patch %	Lines
nf_core/components/components_command.py	0.00%	1 Missing ⚠️

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[awgymer]

So is this good to merge now? It will make a lot of other PRs stop failing!

[mashehu]

I guess so😄