Scirpy

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

Fixes

- Scirpy can now import additional columns from Cellranger 6 (279 by naity)
- Fix minor issue with `include_fields` in `AirrCell` (297)

Documentation

- Fix broken link in README (296)
- Add developer documentation (294)

Additions

- Add the new "clonotype modularity" tool which ranks clonotypes by how strongly connected their gene expression neighborhood graph is. (282).

The below example shows three clonotypes (164, 1363, 942), two of which consist of cells that are transcriptionally related.

<table>
<tr>
<th>
example clonotypes
</th>
<th>
clonotype modularity vs. FDR
</th>
</tr>
<tr>
<td>
<img src="https://user-images.githubusercontent.com/7051479/132355883-2608af74-8d2c-420f-871a-9fa006c4cfd8.png">
</td>
<td>
<img src="https://user-images.githubusercontent.com/7051479/132355941-927e0a9e-5a7c-4df4-b339-1be9535c4279.png">
</td>
</tr>
</table>

Deprecations

- `tl.clonotype_imbalance` is now deprecated in favor of the new clonotype modularity tool.

Fixes

- Fix calling locus from gene name in some cases (288)
- Compatibility with `networkx>=2.6` (292)

Minor updates

- Fix some links in README (284)
- Fix old instances of clonotype in docs (should be clone_id) (287)