Expand dask support

[flying-sheep]

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

Meta issue tracking scanpy functions without dask support

Related #921

First we should test things more generically:

• [x] add global array_type fixture to use in all tests for features below

  • 2595

@ivirshup came up with places where we should prioritize dask support:

• [x] normalize_total
  • seems to work: scverse/scanpy#2466
  • has tests: scverse/scanpy#1663
• [x] log1p, normalize_per_cell, filter_cells/*_genes:
  • [x] accept Dask arrays: scverse/scanpy#283
  • [x] Test that they are kept as Dask arrays throughout: scverse/scanpy#2814
• [x] sc.pp.pca: scverse/scanpy#2563
• [ ] sc.pp.calculate_qc_metrics
• sc.pp.highly_variable_genes:
  • [x] scverse/scanpy#2777
  • [x] scverse/scanpy#2807
  • [ ] scverse/scanpy#2808
  • [ ] experimental “pearson_residuals” flavor
• [x] sc.tl.rank_genes_groups: scverse/scanpy#2621
• [ ] Subsample
• [ ] Aggregate

Later:

• [ ] scale
• [ ] nearest-neighbors
• [ ] umap
• [ ] metrics

[mumichae]

For the highly_variable_genes dask support, are you also considering cases where the dask chunks are scipy sparse matrices?

[flying-sheep]

Not currently, but since the scope of that PR got reduced, it shouldn’t be too much work.