PyUp Safety actively tracks 362,670 Python packages for vulnerabilities and notifies you when to upgrade.
New features - Introduced CLI parameter [--X-approximate-distribution](https://github.com/chanzuckerberg/cellxgene/issues/2282) for users to specify the distribution of their data, and override the default heuristic determination - For categories with the number of labels over the number set by --max-category-items (default 1000), we now include a label that aggregates all labels over the limit instead of truncating the list of labels Breaking changes - Removed support for experimental features (--experimental-annotations-ontology, --experimental-annotations-ontology-obo and --experimental-enable-reembedding) Bug fixes - Fixed a [bug](https://github.com/chanzuckerberg/cellxgene/issues/2211) in differential expression calculation by changing the t-test calculation to consistently assume normally distributed data, and to log data when data is not normally distributed based on a heuristic - Fixed a [bug](https://github.com/chanzuckerberg/cellxgene/issues/2225) in --max-category-items
This release contains a new major feature: gene sets! A gene set is a list of genes. You will now be able to visualize the mean expression of a gene set and create and edit gene sets from the UI. Check out our user guide under docs for more information and how to get started. We’ve also improved differential expression functionality. Now when you run differential expression, 2 lists will be created: one list of 50 highly expressed genes in group 1 and one list of 50 highly expressed genes in group 2. Please note we will be deprecating Safari support with this release. Please use Chrome, Edge, or Firefox for the best experience.
**Summary**: There were two packages that had major updates that caused incompatibility issues with cellxgene: `flatbuffers` and `Flask`. In this release, we have pinned both packages to be below the latest 2.0 versions to avoid these incompatibilities (issue 2197).
**Summary:** This release contains bug fixes for a few issues with mismatched colors between the left sidebar and the main canvas (issues 2007 and 2011), and improved error handling for —experimental-annotations-ontology (issue 2024).
**Summary:** We fixed [an issue](https://github.com/chanzuckerberg/cellxgene/issues/1959) caused by a h5py major version change. As a result, [h5py is now restricted to < 3.0.0](https://github.com/chanzuckerberg/cellxgene/pull/1960)
**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
0.15.0 not secure
0.14.1 not secure
Fixed: * 1137 - labels do not correctly pan/zoom
0.14.0 not secure
0.13.0 not secure
0.12.0 not secure
0.11.2 not secure
Fixed * FIx matplotlib incompatibility error(877)
0.11.0 not secure
Summary This release implements a requested cellxgene feature: histograms on categorical values vis a vis continuous (see: 762, 616). Color by any continuous variable, like a gene, and see the breakdown of distributions by opening any categorical menu item. This answers questions such as “which clusters expressed which gene?” “What was the breakdown of total gene counts by tissue?” among others. Added Added mini histograms to categorical selection, displaying continuous metadata distribution (827) Added prepare example, updated demo dataset (810, 803, 547, 529) Documentation regarding hosted instances (807) Hover on label increases point size of associated cells in graph (809 833) Changed Updated roadmap (825) Menu bar code cleanup, logo (804) Fixed Fixed broken URL in docs (801, 802) Fixed jest tests by removing async (805)
0.10.1 not secure
Changed * Pinned python requirement 'tables==3.5.1' to work around installation failure in recently release of tables 3.5.2 Fixed * Improved main graph scaling and centering of embedding (784)
0.10.0 not secure
0.9.3 not secure
Fixed * Fixed `ImportError: cannot import name 'IndexMixin'` by excluding conflicting scipy version (770)
0.9.2 not secure
Fixed * Correctly handle column slicing of csr data (754)
0.9.1 not secure
Fixed * __init__.py file missing from new module (748)
Added * “Clip” to percentile range for continuous data - (metadata and expression) outside of range will be excluded from histograms and grayed out on layout. This improves handling of zero-heavy distributions, or other cases where outliers need to be suppressed (570, 672) * Prepare calculates and adds QC metrics as to continuous metadata (uses new ScanPy 'calculate_qc_metrics') (697) Changed * Documentation updates (691, 706, 649, 702) * Color-by buttons toggle if clicked twice (693) * ScanPy requirements updated to 1.3.7(688) * Server-side refactoring in prep for PyQt & notebook support (711) * Performance improvements accessing large sparse expression data (719) Fixed * Undo/redo improvements - histogram and graph selection now correctly interacts with undo/redo (679, 663) * Selection of continuous data dimensions containing NaN values would select incorrect cells (715) * Graph pan/zoom and selection now stay in sync (622) * Graph selection paints correctly when window resized (203) * Gene name type-ahead no longer clears text on blur (573) * Would fail if simplejson was installed in python environment (700)
0.8.0 not secure
Added * Python 3.7 support * Redo/Undo * (falexwolf) Support additional graph layouts * Menu with FAQ, etc Changed * When selected embedding has more than two components cellxgene UI truncates to the first two instead of failing Fixed * Various UI bug fixes * Histograms no longer allow tiny/invisible selections
0.7.0 not secure
This is largely a performance and refactoring release, with a few small bug fixes. Changes: * Performance improvements throughout application, due to introduction of a new internal data model and other refactoring (588, 590, 611) * 610 fixed - Reset slow for large datasets * 617 fixed - negative scalar annotation and expression values were incorrectly displayed
0.6.1 not secure
Fixed * Failed pypi upload due to previously deleted version
Added * Lasso selection tool * Add list of genes Fixed * (ivirshup) Serving cellxgene through reverse proxy * Does not error if Content-Type header also include charset * De-duped -d CLI option alias for launch: kept the alias for --diffexp, removed from --debug
0.5.1 not secure
Fixed * ModuleNotFoundError: No module named 'server.app.util.fbs'
0.5.0 not secure
Added * Performance improvements facilitated by switching to binary (using flatbuffers) for data transport * Scatterplot any two genes * Async busy indicators on slow operations * Non-finite values displayed as gray on graph when coloring by a field and elided from histograms Fixed * Can now run cellxgene container on remote host * Disable cell set buttons until differential expression is cleared Removed * CLI param --nan-to-num removed (non-finite values can be serialized after switching to binary transport)
0.4.0 not secure
Changes * Add cluster occupancy - when coloring by categorical metadata, stacked barchart shows proportional breakdown of other categorical fields. E.g. color by gender, evaluate gender makeup of each cluster * Add Docker support
0.3.0 not secure
Changes: - Add a typeahead, with fuzzy string search, on the Selected Gene text box - Improve error handling and detection of ScanPy data containing NaN or Infinite values. - Add `--nan-to-num` command line parameter to convert NaN/Infinite to finite floating point values. - Minor improvements to startup speed Breaking changes: - Added `--host` command line option, replacing `--listen-all`. The equivalent of `--listen-all` can now be accomplished with `--host 0.0.0.0`