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Added approximate KNN backend #791

Merged
merged 8 commits into from
Nov 14, 2024
Merged

Added approximate KNN backend #791

merged 8 commits into from
Nov 14, 2024

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nicolassidoux
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I had to from scanpy.neighbors._types import KnnTransformerLike, _KnownTransformer to make transformer argument of neighbors() consistent with scanpy. But _types is protected...

@nicolassidoux nicolassidoux linked an issue Aug 24, 2024 that may be closed by this pull request
@nicolassidoux nicolassidoux marked this pull request as ready for review August 24, 2024 14:04
@Zethson Zethson requested a review from eroell August 25, 2024 22:15
@eroell
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eroell commented Aug 26, 2024

@Zethson what is your stance on importing private variables from scanpy, as we are doing elsewhere too?

I remember in the past you've added a fix of a previously imported, external private variable by defining the required variable ourselves.

I lean towards doing this here too

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Zethson commented Aug 26, 2024

@Zethson what is your stance on importing private variables from scanpy, as we are doing elsewhere too?

I remember in the past you've added a fix of a previously imported, external private variable by defining the required variable ourselves.

I lean towards doing this here too

Yeah, we should try to avoid importing internals so I think that's a good option.

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eroell commented Aug 26, 2024

Thank you so much @nicolassidoux !
One thing I realized here was that we should add tests for the pass through function calls of scanpy...

But this is from our side so far a lacking suite of tests (as we as of now have been closely eyeing scanpy), and hence no test suite at this point to add to here :)

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eroell commented Oct 18, 2024

ready for me to take a quick look again or are you still doing stuff? :)

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Hi @eroell, ready for re-review!

@eroell eroell self-requested a review November 14, 2024 10:26
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eroell commented Nov 14, 2024

Added the intersphinx mappings for pynndescent, and linked the reference to the scanpy knn tutorial with a readable text; Also added a more wordy description on the arguments, more wordy than scanpy...
So direct commit of suggestions instead of knitty-gritty review comments to save your time, what is your take on these additions @nicolassidoux? Would you as user think this is more clear now, or worse?

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@eroell
Yes, direct commit is a good idea indeed!
In regard with documentation stuff, I really let you decide whatever suits, I definitely don't have the skills to judge from a user perspective 😄 But AFAIK the description looks good!
I let you close the PR if you think all is good!

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eroell commented Nov 14, 2024

great - this is a nice addition, thank you @nicolassidoux !

@eroell eroell merged commit 5336a2e into main Nov 14, 2024
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@eroell eroell deleted the enhancement/issue-759 branch November 14, 2024 14:10
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Add approximate KNN backend
3 participants