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Release notes

Release notes#

Version 0.10.0#

0.10.2 2024-04-15#

Features

  • adds the option to return the results for get.aggregate as sparse matrices if the input is sparse pr160 S Dicks

  • adds support for rapids-24.04 pr166 S Dicks

Performance

  • for pp.scale replaces array operation with an elementwise kernel to improve memory footprint pr159 S Dicks

Bug fixes

  • fixes small bugs with pandas in ligrec pr166 S Dicks

Misc

  • moves the notebooks from docs into a submodule pr164 S Dicks

  • moves tests to rapids-24.04 pr166 S Dicks

  • unpinned pandas version pr166 S Dicks

0.10.1 2024-04-03#

Bug fixes

  • updates the behavior of _check_gpu_X for require_cf. It now only works for pearson_residuals calcs and corrects instead of throwing an error pr154 S Dicks

  • Fixes the behavior of pp.scale with mask_obs and max_value. Now only the masked part gets clipped pr158 S Dicks

Misc

  • Updates CI to work with uv pr149 S Dicks

  • Adds Codespell pr155 S Dicks

0.10.0 2024-03-26#

Features

  • added get module pr100 S Dicks

  • switch utils functions to get pr100 S Dicks

  • added get.aggregated to create condensed anndata objects pr100 S Dicks

  • added pp.scrublet and pp.scrublet_simulate_doublets pr129 S Dicks

  • adds the option to return a copied AnnData for get.anndata_to_CPU & get.anndata_to_GPU pr134 S Dicks

  • adds mask argument to pp.scale and pp.pca pr135 S Dicks

  • adds the option to run pp.scale on sparse matrixes zero_center = False without densification pr135 S Dicks

  • updated ruff and now requires parameters by name/keyword in all public APIs pr140 S Dicks

  • adds the option to run pp.harmony with np.float32 pr145 S Dicks

Bug fixes

  • Fixes an issue where pp.normalize and pp.log1p now use copy and inplace correctly pr129 S Dicks

  • changes the graph constructor for tl.leiden and tl.louvain pr143 S Dicks

  • Added a test to handle zero features, that caused issues in the sparse pp.pca pr144 S Dicks

  • Added a test to check if sparse matrices are in canonical format. For now this only affects pp.highly_variable_genes, pp.scale and pp.normalize_pearson_residuals. pr146 S Dicks

Removals

  • Removed cunnData which was deprecated in 0.9.0. Please use AnnData from now on. pr130 S Dicks

Version 0.9.0#

0.9.6#

Bug fixes

Misc

  • Updates Conda yaml file to work with rapids-24.02 pr128 S Dicks

0.9.5#

Bug fixes

  • louvain() now has backward compatibility with older rapids versions pr114 S Dicks

Misc

  • Updates Conda yaml file to work with rapids-23.12 pr114 S Dicks

0.9.4#

Features

  • leiden() now provides random_state parameter for initializing the optimization pr102 J Pintar & S Dicks

  • louvain() now provides threshold parameter for setting the minimum modularity gain between levels pr103 J Pintar & S Dicks

  • added a kernel for sparse sum along the major axis pr112 S Dicks

  • calculate_qc_metrics() now uses less atomics and global memory during kernels pr113 S Dicks

0.9.3#

Features

  • neighbors now works with raft and better supports approximate search with cagra, ivfpq and ivfflat pr89 S Dicks

  • spatial_autocorr now works with sparse data matrices without densifying. It will use the sparse matrix by default. pr93 S Dicks

Bug fixes

  • Fixes an issue where pca didn’t write all parameters pr91 S Dicks

0.9.2#

Bug fixes

  • Fixes implicit conversion issue for Umap and neighbors pr82 S Dicks

0.9.1#

Features

Misc

  • Can now be installed against CUDA11 and CUDA12 with pip pr72 S Dicks

0.9.0#

Features

  • added support for GPU enabled AnnData pr60 S Dicks

  • added support for dense cupy.ndarray pr60 S Dicks

  • added support for 64 bit floats pr60 S Dicks

  • added rapids_singlecell.utils to help with AnnData GPU conversion pr60 S Dicks

  • renamed cunndata_funcs to pp pr60 S Dicks

  • renamed scanpy_gpu to tl pr60 S Dicks

  • switched neighbors() to pp pr60 S Dicks

  • switched harmony_integrate() to pp pr60 S Dicks

  • deprecated rapids_singlecell.cunnData.cunnData pr60 S Dicks

Docs

  • updated Usage_Principles pr60 L Heumos & S Dicks

  • added a release-notes pr60 P Angerer & S Dicks

  • changed notebooks to work with anndata pr60 S Dicks

Bug fixes

Misc

  • tests now work with anndata

Version 0.8.0#

0.8.1#

Bug fixes

  • fixed rsc.tl.neighbors for rapids-23.08 pr55 S Dicks

Misc

  • switched testing to rapids-23.08 with cuda-11.8

0.8.0#

Features

  • added support for umap() pr47 S Dicks

  • added support for neighbors pr50 S Dicks

Bug fixes

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