Severin Dicks

`normalize_total` with numba

3

### What kind of feature would you like to request? Other? ### Please describe your wishes This would speed up normalization

redesign UMAP to use this function once cuML's version is working

Make sure that neigbors works consitently with scanpy. Also investigate bbknn

lets umap run in parallel

2

Closes #3211 Lets you run all parts of UMAP in Parallel. Default will still be False for reproducibility. Benchmarks (95k Cells AMD5950X) `parallel = False` 33 s `parallel = True`...

Update pyproject.toml

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Test new upperlimit for dask for rapids 24.10. https://github.com/scverse/rapids_singlecell/actions/runs/11325725585/job/31493220507?pr=277

We are trying to implement numba-parallel execution of `simplicial_set_embedding`. The docs state that `parallel` will be ignored if a `random_state` is provided. However in our testing having both `parallel` and...

dask-version

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Needed for rapids-24.10

This pull request includes several enhancements to the Harmony algorithm implementation in the `rapids_singlecell` package. The changes introduce new kernels for avoiding GEMM and the one hot encoding batch matrix.

Title: GPL Dependencies as Hard Dependencies

2

Scirpy currently lists both igraph and python-Levenshtein as hard dependencies. Since these packages are licensed under the GPL, their inclusion could inadvertently impose GPL conditions on Scirpy, which is intended...