Scirpy

Additions

- Add a `mask_obs` argument to `tl.clonotype_network` that allows to compute the clonotype networks on a subset of the cells ([557](https://github.com/scverse/scirpy/pull/557)).
- Add `datasets.stephenson2021_5k`, an example dataset for the upcoming BCR tutorial ([565](https://github.com/scverse/scirpy/pull/565))

Fixes

- Add all optional dependencies required for testing to the `[test]` dependency group ([562](https://github.com/scverse/scirpy/pull/562)).
- Unpin AnnData version ([551](https://github.com/scverse/scirpy/pull/551))

Additions

- Isotypically included B cells are now labelled as `receptor_subtype="IGH+IGK/L"` instead of `ambiguous` in `tl.chain_qc` ([537](https://github.com/scverse/scirpy/pull/537)).
- Added the `normalized_hamming` metric to `pp.ir_dist` that accounts for differences in CDR3 sequence length ([512](https://github.com/scverse/scirpy/pull/512)).
- `tl.define_clonotype_clusters` now has an option to require J genes to match (`same_j_gene=True`) in addition to `same_v_gene`. ([470](https://github.com/scverse/scirpy/pull/470)).

Performance improvements

- The hamming distance has been reimplemented with numba, achieving a significant speedup ([512](https://github.com/scverse/scirpy/pull/512)).
- Clonotype clustering has been accelerated leveraging sparse matrix operations ([470](https://github.com/scverse/scirpy/pull/470)).

Fixes

- Fix that `pl.clonotype_network` couldn't use non-standard obsm key ([545](https://github.com/scverse/scirpy/pull/545)).

Other changes

- Make `parasail` an optional dependency since it is hard to install it on ARM CPUs. `TCRdist` is now the
recommended default distance metric which is much faster than parasail-based pairwise sequence alignments while
providing very similar results ([547](https://github.com/scverse/scirpy/pull/547)).
- Drop support for Python 3.9 in accordance with [SPEC0](https://scientific-python.org/specs/spec-0000/) ([#546](https://github.com/scverse/scirpy/pull/546))

Fixes

- Detection of CPU count in `define_clonotype_clusters` was broken ([527](https://github.com/scverse/scirpy/pull/527))

Fixes

- Compatibility with numpy 2.0 ([525](https://github.com/scverse/scirpy/pull/525))

Chore

- scverse template update to v0.4 ([519](https://github.com/scverse/scirpy/pull/519))

Additions

- Add "TCRdist" as new metric ([502](https://github.com/scverse/scirpy/pull/502))

Fixes

- Fix issue with detecting the number of available CPUs on MacOS ([518](https://github.com/scverse/scirpy/pull/502))

Fixes

- Fix default value for `n_jobs` in `ir.tl.ir_query` that could lead to an error ([498](https://github.com/scverse/scirpy/pull/498)).
- Update description of D50 diversity metric in documentation ([499](https://github.com/scverse/scirpy/pull/498)).
- Fix `clonotype_modularity` not being able to store result in MuData in some cases ([504](https://github.com/scverse/scirpy/pull/504)).
- Fix issue with creating sparse matrices from generators with the latest scipy version ([504](https://github.com/scverse/scirpy/pull/504))