sfaira overhaul

Updating codebase, introducing new data fields and fixing many bugs.

Bug fixes to feature streamlining

What's Changed

• improvements to CLI and documentation of phase 5, 6
• bug fixes in feature streamlining

Curators

@davidsebfischer

Full Changelog: v0.3.11...v0.3.12

Extended CLI functionalities

What's Changed

• improvements to CLI
• improved data curation docs
• bug fixes resulting from meta data updates

Curators

@davidsebfischer
@le-ander
@felix0097

Full Changelog: v0.3.10...v0.3.11

Improved curation, store and meta data schema 1.2

What's Changed

• improvements to store API inclugind torch support
• improvements to CLI
• improved data curation docs
• meta schema update to version 1.2, including multimodal support and further new meta data

Curators

@davidsebfischer
@le-ander
@lauradmartens

Full Changelog: v0.3.9...v0.3.10

Fixing package installation, synapse interface and regressions

What's Changed

• add manifest file by @le-ander in #424
• fix data store subsetting regression introduced in 0.3.8 and cleanup deprecated files by @le-ander in #425
• fix synapse data download interface by @le-ander in #426

Full Changelog: v0.3.8...v0.3.9

Blocked generators, custom cache locations and performance

What's Changed

• added blocked generator by @davidsebfischer in #383
• bug fixes and performance improvements by @felix0097 in #419 and #409
• cache migration to settings container by @le-ander in #418
• many more bugfixes and minor improvements by @giovp @davidsebfischer and @le-ander

New Contributors

• @felix0097 made their first contribution in #411
  Full Changelog: v0.3.7...v0.3.8

Data streamlining and UI

• Added dataset:
  10.1016/j.cell.2021.01.053 Covid PBMC dataloader (#363)
  1235fe0
  10.1038/s41590-021-00933-1 T cell tuberculosis dataloader (#362)
• UI Fixes
• Adopted cellxgene schema v2.0 streamlining
• Minor improvements

Minor improvements to v0.3.5

• Recovered fast store access that broke in generator refactor.
• Fixed bugs related to Universe loading.
• Enabled map_fn vectorisation in Generators.

Improved CLI, store, ontologies and testing

• improvements to CLI
• improvements to stores and new generator interface
• ontology bug fixes and verioning improvements
• improved unit testing using mock data

Full description: #356

Improvments to commit history

Merge pull request #311 from theislab/dev

Dev