Scarf

CHANGELOG

**Improvements**
- Added `keep_bounds` parameter in `Metadata.sift` and `DataStore.filter_cells`

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

CHANGELOG

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).

CHANGELOG

**Improvements**
- Added assertion checks and changed overwrite behaviour in `ZarrMerge`

CHANGELOG

**Bug fixes**
- Log message formatting in `RNAassay.mark_hvgs`

**New features**
- Added `CSVReader`
- Added `CSVtoZarr`