Handle dirty local module repos by force checkout of commits and branches if needed

[gregorysprenger]

Use a try/except block to catch GitCommandError errors when performing git checkout, where changes may need to be stashed or force the checkout. This should solve issues similar to #2656 and the need to use rm -rf ~/.config/nfcore/nf-core/modules/ where the following error is observed:

GitCommandError: Cmd('git') failed due to: exit code(1)
cmdline: git checkout master
stderr: 'error: Your local changes to the following files would be overwritten by checkout:

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: 7 lines in your changes are missing coverage. Please review.

Comparison is base (d7610a1) 73.53% compared to head (3e95d02) 73.61%.

❗ Current head 3e95d02 differs from pull request most recent head 77aa1cb. Consider uploading reports for the commit 77aa1cb to get more accurate results

Files	Patch %	Lines
nf_core/synced_repo.py	50.00%	7 Missing ⚠️

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[mashehu]

Thanks, that's a great addition, just tried to make it a bit more fail-safe.

@mirpedrol: do you think we should ask first before we overwrite changes?

[mashehu]

@nf-core-bot changelog

[gregorysprenger]

@mashehu Awesome, thanks! If you all would rather stash the changes and re-checkout, I'm more than happy to make those changes.

[mashehu]

A dirty local module repo is usually the result of an error during an installation/update, so nothing could actively be lost, maybe I am just a bit too paranoid... this is probably the better solution, instead of dragging an installation error along

[mirpedrol]

Looks good! but I agree with @mashehu I would prefer to first ask the user if they want to continue and delete changes.

[mashehu]

after a quick thought, new idea: because we use this function also in other contexts, we should check that we are in the modules repo in the if clause and then do a force checkout with a prompt and otherwise raise an errror to be on the save side