Cellxgene

**Summary**: We fixed an [issue](https://github.com/chanzuckerberg/cellxgene/issues/1848) where some of the continuous attributes of cell data were not visible in the right hand side bar as well as an [issue](https://github.com/chanzuckerberg/cellxgene/issues/1922) with experimental re-embeddings failing.

**Summary:** We fix an issue with colors in the left sidebar not matching the colors in the main canvas area. The Docker contained was updated following a breaking change. We updated the way that static assets are served such that cellxgene can be used behind a proxy. We also corrected an issue with re-embeddings that was broken was small gene counts.

**Summary**: 0.16.2 corrects a couple of breaking changes from 0.16.0. We fix the bug with gene expression scatterplots where the x and y axes were swapped and we also fix the support of launching cellxgene with the `--experimental-enable-reembedding` flag.

**Summary**: 0.16.0 introduced a number of refinements to the cellxgene application. We have added a number of UI enhancements such as histogram coloring, improvements to the differential expression user experience, and re-embeddings. This release also includes a large number of bug fixes and small performance improvements.

*We are currently testing an alpha version of a hosted cellxgene at [cellxgene.cziscience.com](https://cellxgene.cziscience.com). While it is not yet feature complete, any feedback would be welcome.*

**Added**
- Support for coloring right-side histograms 1218
- Config file that provides the ability to set various parameters of launching cellxgene via either the server or the launch CLI command. 1264
- Tooltip for category names 1278
- Compression of HTTP responses for servers launched via the CLI 1285
- Differential expression UI and config visibility improvements 1336
- Support for user-defined category-label colors 1402
- Added ability to select labels for differential expression instead of only subsets 1494
- Improvement to lasso “can close” visual feedback 1550
- Categorial UI improvements including support for renaming the annotations file 1649, 1660
- Support for re-embedding 1679 - experimental. Functionality may change in the future.

**Changed**
- Show single value instead of entire histogram if the minimum and the maximum are the same 1554
- Major refactor to use lazy data loading from the server side using react-async 1571

**Fixed**
- Added a workaround to accommodate a bug in AnnData `make_index_unique` that does not work under certain conditions. 1260
- Assorted small UI fixes: proper truncation 1320
- Various histogram fixes like x-axis labeling 1363, performance improvement 1390
- Fix for brushing subset of a gene distribution after subsetting data 1409
- Fix to cache crossfilter when embedding type is changed 1493
- De-duping gene sets 1490

**Security**
- Removed `client` package that introduced security vulnerabilities 1248

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)

Fixed:
* 1137 - labels do not correctly pan/zoom