v0.5.0

Add support for BCRs and gamma-delta TCRs

Backwards-incompatible changes:

• The data structure has changed. Column have been renamed from TRA_xxx and TRB_xxx to IR_VJ_xxx and IR_VDJ_xxx. Additionally a locus column has been added for each chain.
• All occurences of tcr in the function and class names have been replaced with ir. Aliases for the old names have been created and emit a FutureWarning.

Additions:

• There's now a mixed TCR/BCR example dataset (maynard2020) available (#211)
• BCR-related amendments to the documentation (#206)
• tl.chain_qc which supersedes chain_pairing. It additionally provides information about the receptor type.
• io.read_tracer now supports gamma-delta T-cells (#207)
• io.to_ir_objs allows to convert adata to a list of IrCells (#210)
• io.read_bracer allows to read-in BraCeR BCR data. (#208)
• The pp.merge_with_ir function now can handle the case when both the left and the right AnnData object contain immune receptor information. This is useful when integrating both TCR and BCR data into the same dataset. (#210)

Fixes:

• Fix a bug in vdj_usage which has been triggered by the new data structure (#203)

Minor changes:

• Removed the tqdm monkey patch, as the issue has been resolved upstream (#200)
• Add AIRR badge, as scirpy is now certified to comply with the AIRR software standard v1. (#202)
• Require pycairo >1.20 which provides a windows wheel, eliminating the CI problems.