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Implement scverse datastucture

Open grst opened this issue 2 years ago • 0 comments

Implementing the changes suggested in #327.

Close #327 Close #184

Requires

  • pre-release version of awkward array
  • Anndata installed from the val_shape branch

TODO

  • [ ] store index pointing to primary and secondary chains somehwere
  • [ ] update all tests and test data
  • [ ] update example data in scirpy.datasets
  • [ ] phase out support for the scirpy <0.7 data structure. The additional effort maintaining this is not worth it.
  • [ ] update the _check_upgrade_schema() wrappers to detect the 0.7 < x <= 0.11 data structure.
  • [ ] conversion from old schema to new datastructure
  • [ ] instructions how to use the new AIRR/awkward array anndata with muon
  • [ ] Go through tutorials
  • [ ] Go through docstrings
  • [ ] keep public functions that were not deprecated before and add stub functions
  • [ ] do i still need has_ir and multichain columns?

grst avatar Aug 13 '22 17:08 grst