scirpy
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Implement scverse datastucture
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?