feat: add Array API support via array-api-compat - #4179
Draft
amalia-k510 wants to merge 31 commits into
Draft
Conversation
❌ 15 Tests Failed:
View the top 3 failed test(s) by shortest run time
To view more test analytics, go to the Test Analytics Dashboard |
flying-sheep
self-requested a review
June 25, 2026 14:58
flying-sheep
requested changes
Jun 26, 2026
flying-sheep
left a comment
flying-sheep
left a comment
Member
There was a problem hiding this comment.
OK, please remember the comments from the fast-array-utils PR, e.g. we agreed to handle singledispatch functions like this: https://github.com/scverse/fast-array-utils/blob/febaf245ecd6da849c2331638219f649935d5a21/src/fast_array_utils/stats/_power.py#L38-L39
We also need tests. There’s MAP_ARRAY_TYPES which should gain an entry, which will make many many tests run with the type you add. We can discuss how to best exclude certain tests, for starters you can just add it and make some of the tests fail – that’ll show you where things aren’t working yet (and might or might not be fixed in this PR)
Please also add a release note (hatch run towncrier:create 4179.feat.md)
for more information, see https://pre-commit.ci
…lia-k510/scanpy into array-api-compat-integration
for more information, see https://pre-commit.ci
flying-sheep
changed the title
flying-sheep
requested changes
Jul 17, 2026
…lia-k510/scanpy into array-api-compat-integration
…lia-k510/scanpy into array-api-compat-integration
Member
There was a problem hiding this comment.
Looking good! Just nitpicks left in the code that’s there.
One big change we should do is updating the array type metadata so it lists Array API support.
The docs currently have one central table and each function has its own little info box.
Since you know what’s going to be supported, you should update the metadata by adding an aa tag and filling out the support here (so far, np means numpy, sp means scipy sparse, da means dask, da[...] means “... in dask”, and sp[csc] means “scipy sparse with csc format”):
Lines 178 to 210 in fc0b419
If you want, you can also update the Sphinx code, but you don’t need to learn how to do that if you don’t want to. I’ll happily do that myself.
flying-sheep
requested changes
Aug 11, 2026
| svd_solvers = {"auto", "full", "arpack", "randomized", "covariance_eigh"} | ||
| case (helpers.asarray, False): | ||
| case (helpers.asarray | helpers.as_dense_jax_array, True): | ||
| svd_solvers = {"auto", "full", "arpack", "randomized"} | SKLEARN_ADDITIONAL |
Member
There was a problem hiding this comment.
this doesn’t exist and breaks the tests
Member
There was a problem hiding this comment.
Why did you resolve this? SKLEARN_ADDITIONAL still doesn’t exist and breaks the tests.
Comment on lines
+884
to
+886
| # rank_genes_groups uses numba kernels internally, so need convert at entry. | ||
| if isinstance(adata.X, HasArrayNamespace) and not isinstance(adata.X, np.ndarray): | ||
| adata.X = np.asarray(adata.X) |
Member
There was a problem hiding this comment.
This isn’t the right approach, as it modifies an object the user passed. Why not do this in _RankGenes.__init__?
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This adds Array API support to scanpy's preprocessing pipeline, where I am planning to use JAX as the test case. The goal is for someone to put a JAX array into
adata.Xand run the usual pipeline without the array getting silently pulled to CPU partway through. It builds on the recentfast-array-utilswork, which means a lot of the heavy lifting (sums, means, variances) already works across backends.