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Use pathlib for path handling #57

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merged 1 commit into from
Oct 24, 2024
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tsmbland
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@tsmbland tsmbland commented Oct 23, 2024

This PR aims to make full use of the inbuilt pathlib module to handle paths, which were previously being passed around as strings. Mostly this is to ensure compatibility on different operating systems, but the syntax is also tidier and makes the code a bit more readable.

The tests pass locally, although the testing suite is minimal, so I'm sure someone will want to try this out more thoroughly before merging

Close #39

@tsmbland tsmbland marked this pull request as ready for review October 23, 2024 13:34
@tsmbland tsmbland mentioned this pull request Oct 23, 2024
@alexdewar
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Thanks for this @tsmbland!

The only problem is that this PR and your other one are likely to cause merge conflicts with @Thomas-Rowlands' mega-PR (#20). We've got a meeting with the team today, so hopefully we'll be able to figure out a strategy to get all the PRs merged together.

With your pre-commit PR, were a lot of manual fixes required or were they mostly automated? I'm just wondering how much work it would be to re-fix things after merging #20.

@tsmbland
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Ah ok I didn't spot that!

Very few manual fixes were required. See this commit

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Yeah, sorry I didn't make it clear in the issue descriptions 😞. Hopefully we should just be able to merge it with your work.

@Thomas-Rowlands Thomas-Rowlands self-requested a review October 24, 2024 11:44
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Tested and looks good :)

@Thomas-Rowlands Thomas-Rowlands merged commit 39dc6ce into omicsNLP:main Oct 24, 2024
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@alexdewar
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@Thomas-Rowlands There are now a bunch of merge conflicts with #20. See my comments above

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Indeed, #20 is very old at this point and has such a large amount of changes I would expect nothing less. Unfortunately as #20 also contains intended changes to the way table processing is handled, for example, I'm not certain the regression test would be a guarantee of success. #20 will need to be picked through with a fine-toothed comb after merging locally, so this may take a while.

Speak shortly in the Teams meeting.

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Okey doke. Speak soon then.

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Convert to using Pathlib
4 participants