New features! This doesn't change anything in the preprocessing/singularity workflow.
- new
write_10x
function withDandelion
class so that it can now format AIRR-formatted tables to 10x's input files (e.g. all_contig_annotations.csv and all_contig.fasta) - new saving mode - makes no difference to users but the new format is different in the backend as i have dropped the dependency on
pandas
- now it directly saves withh5py
, which means that the way the files can be accessed is different. files saves previously should still be possible to be read in - if resaved, it will overwrite with the new format. - downsampling in
generate_network
now can also downsample orphan VJ chains (previously it relied on VDJ chains primarily), and also works on alternativeclone_key
dandelion
is now compatible with python 3.12. Just in time before python 3.13 😩- compatibility with
AnnData
is fixed. @grst, you should be able to unpin dandelion in scirpy! - revamped the testing suite with micromamba with new caching options.
What's Changed
- Fix anndata compat by @zktuong in #408
- fix clone id key by @zktuong in #414
- new saving mode by @zktuong in #420
- fix downsampling logic in generate network by @zktuong in #424
- fix clone_key not respected properly if non-default clone_id by @zktuong in #429
- prepare for python 3.12 by @zktuong in #363
dependency updates
- pip prod(deps): update pandas requirement from <=2.2.2,>=1.0.3 to >=1.0.3,<=2.2.3 by @dependabot in #431
- pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.2.3 to <=2.4.4 by @dependabot in #430
- pip dev(deps-dev): update scirpy requirement from <=0.17.2 to <=0.18.0 by @dependabot in #426
Full Changelog: v0.3.8...v0.4.0