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fix: fix & refactor miRNA extension script #144
fix: fix & refactor miRNA extension script #144
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Of course you can also update/add the tests first, in this branch, so that the tests pass. Probably makes more sense :) |
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Here are some small comments; besides the last one, everything is related to the docstrings .
In the meantime, if it's alright, I'll be working on fixing the unit tests and static code analyses for this PR.
Awesome, thanks a lot :) Will you address these points when you are adding the tests etc? 🙏 |
On it! The unit tests will take me the rest of today, luckily not that much of tomorrow. Just a small comment. The following line has more than 80 char therefore, it fails the static code analysis:
black suggests to apply the following style:
I find it horrible. So I want to know which one of the following approach you want me to follow:
I'd rather go with the first one but it's up to you :) |
The changes applied in the last push are:
@uniqueg I cannot put you as a reviewer as you created this PR. But please, have a look. I'll wait for your feedback :)) |
Either way is fine by me :) |
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A few comments...
@uniqueg the pushed changes are:
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LGTM :) |
* fix: fix & refactor miRNA extension script (#144) * fix: fix & refactor miRNA extension script * feat: add name modification method * test: update 'test_mirna_extension.py * ci: update expected output * refactor: add custom exception * test: add unit test for illegal pos * test: add illegal coords test file * test: fix for static code analysis * Update mirna_quantification.py --------- Co-authored-by: deliaBlue <[email protected]> --------- Co-authored-by: Alex Kanitz <[email protected]>
I had a bit of time and felt like coding, so I refactored the script a bit (well, maybe a bit more than a bit).
It should now do what it's supposed to do, I hope. Or in any case, it's broken down into more, simpler steps, so if it isn't fully there yet (the tests would show), then it should be easy enough to change.
I suppose you could merge this in your branch, if you like, and then update the tests to match and cover all edge cases. Note that I have included two or three specific error checks that were not covered before, so apart from refactoring, you'd probably need to add a couple more tests to check for these.