aggregate - out of core#395
Merged
Merged
Conversation
* test map_blocks * add dense prototype * update kernels * make nicer * fix 64_bit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
for more information, see https://pre-commit.ci
ilan-gold
reviewed
Jul 14, 2025
Comment on lines
+49
to
+53
| for i in range(4): | ||
| c = ["sum", "mean", "var", "count_nonzero"][i] | ||
| a = out_in_memory.layers[c] | ||
| b = out_dask.layers[c] | ||
| cp.testing.assert_allclose(a, b) |
Contributor
There was a problem hiding this comment.
Curious what happens if you run compute under a processes scheduler because for us, it actually produced inconsistent results variance sparse-in-dask (and to rectify the problem, I had to call compute on the mean within the variance calculation for sparse-in-dask).
| adata_2 = adata_2.raw.to_adata() | ||
| adata_1.X = cusparse.csr_matrix(adata_1.X.astype(np.float64)) | ||
| adata_2.X = as_sparse_cupy_dask_array(adata_2.X.astype(np.float64)) | ||
| elif data_kind == "dense": |
Contributor
There was a problem hiding this comment.
No C vs F contiguous in dask ?
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
#385
This PR updates aggregate to work with dask matrices. Also Allows for CSC based aggr to dense and F based aggr