0.23.4

CHANGELOG

Bug fixes

• Added PyPi README to Manifest

0.23.3

CHANGELOG

Bug fixes

• Changed location of PyPi README

0.23.2

CHANGELOG

Bug fixes

• Changed README for PyPi

0.23.1

CHANGELOG

Improvements

• Added keep_bounds parameter in Metadata.sift and DataStore.filter_cells

0.23.0

CHANGELOG

Breaking changes introduced ⚠️

Improvements

• save_normed_for_query now uses parallel writing.
• modified iter_normed_feature_wise to export multiple formats (dataframe or ndarray).
• multiple fixes in docstrings.
• improved chunk sizing in smoothen_dists in knn_utils.
• changed the location of mu and sigma in Zarr hierarchy to avoid recomputation.
• optimized ann index saving for non local zarr

New functionality

• Added bed_to_sparse_array to writers module.
• Major rewrite of run_marker_search to include multiple summary stats about marker genes

0.22.2

CHANGELOG

Since 0.21.0

Bug fixes

• Fixes in tqdm usage
• Bug fixes and performance improvement in SparseToZarr

Improvements

• Reading obsm slot from H5ad file now supported.
• removed dependency on sparse library. Switched to scipy.sparse.coo_matrix

0.21.0

CHANGELOG

Bug fixes

• The index in anndata object obtained from to_anndata is now set to ids column to avoid name duplication.

Improvements

• The 'var', 'obs' and 'obsm' column in H5ad file are populated as expected when using to_h5ad. Known issue: PCA is still not exported (need to find a solution to generate PCA coords for this purpose).

0.20.1

CHANGELOG

Improvements

• Added assertion checks and changed overwrite behaviour in ZarrMerge

0.20.0

CHANGELOG

Bug fixes

• Log message formatting in RNAassay.mark_hvgs

New features

• Added CSVReader
• Added CSVtoZarr

0.19.8

CHANGELOG

redeploy to due Pypi sync error