Scirpy

New Features

- Download IEDB and process it into an AnnData object by ausserh in https://github.com/scverse/scirpy/pull/377

Fixes

- Fix working with subplots (378) by grst in https://github.com/scverse/scirpy/pull/379

Documentation

- Fix typos in IR query by Zethson in https://github.com/scverse/scirpy/pull/374
- Fix a bunch of typos in the docs by grst in https://github.com/scverse/scirpy/pull/375

Internal changes

- Fix CI by grst in https://github.com/scverse/scirpy/pull/376

New Contributors

- Zethson made their first contribution in https://github.com/scverse/scirpy/pull/374
- ausserh made their first contribution in https://github.com/scverse/scirpy/pull/377

**Full Changelog**: https://github.com/scverse/scirpy/compare/v0.11.2...v0.12.0

Fixes

- Excluded broken python-igraph version (366)

Fixes

- Solve incompatibility with scipy v1.9.0 (360)

Internal changes

- do not autodeploy docs via CI (currently broken)
- updated patched version of scikit-learn

Additions

- Add data loader for BD Rhapsody single-cell immune-cell receptor data (`io.read_bd_rhapsody`) (351)

Fixes

- Fix type conversions in `from_dandelion` (349).
- Update minimal dandelion version

Documentation

- Rebranding to [scverse](https://scverse.org) (#324, 326)
- Add issue templates
- Fix IMGT typos (344 by emjbishop)

Internal changes

- Bump default CI python version to 3.9
- Use patched version of scikit-bio in CI until https://github.com/biocore/scikit-bio/pull/1813 gets merged

Fixes

- Fix bug in cellranger import (310 by ddemaeyer)
- Fix that VDJDB download failed when cache dir was not present (311)

Additions

This release adds a new feature to query reference databases (298) comprising

- an extension of `pp.ir_dist` to compute distances to a reference dataset,
- `tl.ir_query`, to match immune receptors to a reference database based on the distances computed with `ir_dist`,
- `tl.ir_query_annotate` and `tl.ir_query_annotate_df` to annotate cells based on the result of `tl.ir_query`, and
- `datasets.vdjdb` which conveniently downloads and processes the latest version of [VDJDB](https://vdjdb.cdr3.net/).

Fixes

- Bump minimal dependencies for networkx and tqdm (300)
- Fix issue with `repertoire_overlap` (Fix 302 via 305)
- Fix issue with `define_clonotype_clusters` (Fix 303 via 305)
- Suppress `FutureWarning`s from pandas in tutorials (307)

Internal changes

- Update sphinx to >= 4.1 (306)
- Update black version
- Update the internal folder structure: `tl`, `pp` etc. are now real packages instead of aliases