Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands.
The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema.
The second takes an h5ad and checks if it follows the schema version written into its metadata.
Both are currently marked as "experimental" as the primary intended users are still at CZI.
* split out config
* add tests for base and app config, refactor client config out of app config
* refactor default config retrieval
* create config test class and helper functions
* move default_config into server to fix import issue
Many of our matrices are log normalized, which tends to eliminate
the number of non zero values (if there were any). This prevents
the matrix from being stored as a sparse matrix. The solution here
is to use a simple transformation to make it sparse again. The most
common value from each column is subtracted from that column. These
values that were subtracted are saved in an array called X_col_shift.
The cellxgene code needs to understand how to undo the transformation when
operating over the X matrix.
- added script to create a synthetic dataset for testing
- added a script to convert an existing CXG dataset to a sparse CXG dataset
Support for sparse tiledb arrays for the X matrix
1. cxgtool can now output sparse matrices
2. cxg_adaptor and diffexp_cxg updated to handle sparse matrices
3. added a test in test_diffexp to test sparse diffexp and get_X_array
* Add user-defined category-label colors
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152
As described in https://github.com/chanzuckerberg/cellxgene/issues/1307
* Respond to feedback from @bkmartinjr in nodejs
* Respond to feedback from @bkmartinjr in python
* Add tests to the server module
* Autoformat python, run linter
* Make colors_get error handling specific
* Respond to feedback from @bkmartinjr
* Respond to feedback from @bkmartinjr
* Fix whitespace
* Fix python lint errrors
* Update documentation
* Add --disable-user-colors option to launch and cxgtool.py
* Fix python formatting
* Rename '--disable-user-colors' to '--disable-custom-colors'
* Add user-generated annotations tests to the server
Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969
* Auto-format python code
* @skip_if: passing lambdas > than property strings
* Respond to feedback from @bkmartinjr
Marcus Kinsella