Preparing release 3.10 #533
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Merge pull request #427 from theislab/dev
Signed-off-by: zethson <lukas.heumos@posteo.net>
* made trainer paths more flexible
Co-authored-by: davidsebfischer <david.seb.fischer@gmail.com>
* added data loader dno_doi_luecken * improved CLI and documentation
* rewrote batch_schedule to work directly on the supplied indicies
* added torch.utils.data.IterableDataset and torch Dataset class * added adpator unit test * cached query of assembly name to ensembl ftp server file query was already cached, but assembly name retrieval based on release version was not cached * added random rounding in intercalated batch data laoder * updated test splitting * enabled store loading from multiple paths * deprecated optional dependency of Dataset attributes on meta data files * fixed d10_1038_s41586_019_1631_3 * relaxed required arguments for DistributedStoreAnndata * added a full data set batch schedule * feature / added method to persist dask.array of DaoStroage into memory + small bug fixes (#447) * dask.array of DaoStore can now be persisted into memory in CSR format * improved docstring documentation for .adataptor * extended store docs * refactored distributedstore to store and minor obs indexing and cart default fixes * fixed obs indexing bug with empty single cart within multi cart Co-authored-by: felix0097 <47145207+felix0097@users.noreply.github.com>
* 10.1038/s41467-020-15543-y
* datasets can be shuffled now before writing dao store
…tDask (#476) * random_batch_schedule for DaskCart now matches dask partitions * rearanged imports + removed debugging assertion statement
* str obs data is now stored and processed as categorical * fixed check for categorical dtype
* put column 3 back into var dataframe and named column feature_class
* refactored estimator code into tf.keras code and base estimator code. this prepares side-by-side keras and torch code. * added torch losses and metrics
* improved guidance through CLI pipeline through action messages and error messages * improved curation documentation * relabled export phase in summary * CLI: add automatic detection of container for path handling * CLI: adapt path checking to container usecase * CLI: make env variables usable also without containers * CLI: add automatic PR submission in container * fix template creation CLI run * switched data library, CLI and curation annotation to yaml version 1.2 (#528) * improved curation docs * improved guidance in sfaira create-dataloader * improved reaction to existing loaders * improved data loader linting in CLI * support for count and processed data matrices in same loader, deprecates "normalization" * support for feature type annotation, allows for ATAC and CITE data (feature_type) * support for based genetic modification meta data (gm) * support for basic treatment meda data (treatment) * support for cell tracking in meta studies (source_doi) * support for spatial data * support for VDJ data * support for velocity data * support for reference genome annotation * support for arbirtrary organisms in genome container * added phase Pe * Data/10.1126/science.abj4008 (#531) * d10_1126_science_abj4008 #530 * added validate to template checking * improvements to VDJ interface * d10_1126_science_abe6474 (#532) * fixed sfaira structure DOI input to annotate * annotated GEO look up * d10_1126_sciimmunol_abd1554 (#471) * d10_1126_sciimmunol_abd1554 * dno_doi_luecken neurips loader update (#472) * fixed rich printing in CLI * added documentation of compressed and r file reading * Fix d10_1016_j_cell_2021_01_053 to work with GEO (#469) * added validation statement at the end of finalize * d10_1038_s41591_020_1061_7 * updated required meta data section in docs * disabled default cellxgene collection meta data caching which resulted in bug when collection were updated on remote Co-authored-by: davidsebfischer <david.seb.fischer@gmail.com> Co-authored-by: le-ander <20015434+le-ander@users.noreply.github.com> Co-authored-by: Laura Martens <laura.d.martens@icloud.com> Co-authored-by: xlancelottx <33050110+xlancelottx@users.noreply.github.com>
* added new figures
davidsebfischer
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Feb 9, 2022
This reverts commit 7241ee5.
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