v0.3.7 #396
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v0.3.7 #396
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Co-authored-by: David S. Fischer <david.seb.fischer@gmail.com>
* added 10.1016/j.cell.2021.01.053 dataloader and coarse annotation
* added 10.1038/s41590-021-00933-1 dataloader and annotation
* Added questionaire for gene symbols * changed check to gene_id_symbols_var_key * Format data field year as integer * fixed annotate-dataloader * Added template_data to gitignore * amended data_template test * set default_embedding default value to blank * fixed linting * fixed linting
Signed-off-by: zethson <lukas.heumos@posteo.net>
* add unit tests for UI * fix ui * store sfaira_repo_url in sfaira.consts * remove capitalisation of gene symbols when streamlining features * extend unit test to check that gene symbols match the genome container after feature streamlining * added check that genome assemblies are the same between celltype and embedding zoo * making sure var_names are automatically set according to schema in ui * keep original obs_names when loading a dataset through the ui
* when streamlining uns: ensure list can be sorted by converting to all-strings * ramove any appearances of np.sort( following np.unique( as the latter already sorts the array * fix some new dataloaders
Added feature and meta data streamlining for cellxgene schema version 2.0.0 and fixed small bugs * * switched EFO to obo * switched MMUSDV to obo * switched HSAPDV to obo * switched MONDO to obo * switched sex to PATO and obo * updated CL version * updated UBERON version * updated human and mouse genome versions * added feature streamlining version containers * relaxed numba * added default embedding in cellxgene export and fixed feature export * fixed default disease label in cellxgene export * added cell type map update unit test * updated CL throughout * fixed subsetting by cell * added primary data meta data entries * added minimal number of cells required to add embedding in cellxgene output * fixed mismatch between reference genome in test data simuation and test model
preparing v0.3.7
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