chanzuckerberg/cellxgene: Release 0.15.0

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)