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chanzuckerberg/cellxgene: Release 0.15.0

Colin Megill; Bruce Martin; Charlotte Weaver; Sidney Bell; Severiano Badajoz; Matt Weiden; Justin Kiggins; Jeremy Freeman; fionagriffin; bmccandless; Marcus Kinsella; Snyk bot; Prete; Philipp A.; Marcio von Muhlen; James Taylor; Isaac Virshup; Gökçen Eraslan; GenevieveHaliburton; Alex Wolf

Summary: 0.15 resolves incompatibilities with the current anndata/scanpy releases, improves ontology-driven label input in user annotations, moves annotations to a supported feature, and resolves a number of miscellaneous bugs and UI issues.

Added:

  • User annotations feature has moved to a fully supported feature, and is no longer experimental (nb. command line params have changed, and annotations are enabled by default - see documentation for more information).

  • Experimental support for ontology-driven annotation/label input was further enhanced. Users can now pick from an ontology or define their own label in a single dialog, and ontologies are available for both label and category creation and editing.

  • Code coverage reports added to the github repo CI pipeline

  • Significant additions to unit & smoke tests and configuration testing in the CI pipeline

  • Added experimental support computed re-embedding on user-selected cell sets.

  • Better handling of annotations with very large number of categorical values.

Changed:

  • Resolved incompatibility with annata 0.7 and remove pinned Python dependencies for anndata, h5py and tables modules. This resolves several compatibility issues with H5AD files. #1157, #1202

  • Reset UI replaced with Subset and Unsubset (#1183), and unsubset no longer deletes genes in the right side bar (fixes #1171).

  • Work in preparation for a web-hosted cellxgene (not yet available or complete), including:

    • Incremental loading of data on the front end

    • Refactoring the back-end to support a cloud-native data format built upon tiledb.

    • #1140, #1163, #1200

  • Javascript and Python package dependencies updated.

  • Variety of small UI improvements throughout the application, including more readable data labels on the main graph (#1141, #1160), better handling of long strings (#1206), improved enable/disable state on buttons, etc.

Fixed:

  • Datasets with more than 32 annotations would occasionally cause the crossfilter to get confused, and selection state to be lost (#1162)

  • Undo/redo was not working correctly with color-by-annotation and other UI actions (#1165)

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