Scirpy

Backwards-incompatible changes:

- Set more sensible defaults the the `cutoff` parameter in `ir_neighbors`. The default is now `2` for `hamming` and `levenshtein` distance metrics and `10` for the `alignment` distance metric.

Additions:

- Add Hamming-distance as additional distance metric for `ir_neighbors` (216 by ktpolanski)

Minor changes:

- Fix MacOS CI (221)
- Use mamba instead of conda in CI (216)

Backwards-incompatible changes:

- The [data structure](https://icbi-lab.github.io/scirpy/usage-principles.html#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.

- Include tests into main package (189)

- Fix pythonpublish CI action
- Update black version (and code style, accordingly)
- Changes for AIRR-complicance:
- Add support level to README
- Add Biocontainer instructions to README
- Add a minimal test suite to be ran on conda CI

- Adapt tcr_dist to support second array of sequences (166). This enables comparing CDR3 sequences against a list of reference sequences.
- Add `tl.clonotype_convergence` which helps to find evidence of convergent evolution (168)
- Optimize parallel sequence distance calculation (171). There is now less communication overhead with the worker processes.
- Fixed an error when runing `pp.tcr_neighbors` (177)
- Improve packaging. Use `setuptools_scm` instead of `get_version`. Remove redundant metadata. (180). More tests for conda (180).

- More extensive CI tests (now also testing on Windows, MacOS and testing the conda recipe) (136, 138)
- Add example images to API documentation (140)
- Refactor IO to expose TcrCell and TcrChain (139)
- Create data loading tutorial (139)
- Add a progressbar to TCR neighbors (143)
- Move clonotype_network_igraph to tools (144)
- Add `read_airr` to support the AIRR rearrangement format (147)
- Add option to take v-gene into account during clonotype definition (148)
- Store colors in AnnData to ensure consistent coloring across plots (151)
- Divide `define_clontoypes` into `define_clonotypes` and `define_clonotype_clusters` (152). Now, the user has to specify explicitly `sequence` and `metric` for both `tl.tcr_neighbors`, `tl.define_clonotype_clusters` and `tl.clonotype_network`. This makes it more straightforward to have multiple, different versions of the clonotype network at the same time. The default parameters changed to `sequence="nt"` and `metric="identity" to comply with the traditional definition of clonotypes. The changes are also reflected in the glossary and the tutorial.
- Update the workflow figure (154)
- Fix a bug that caused labels in the `repertoire_overlap` heatmap to be mixed up. (157)
- Add a label to the heatmap annotation in `repertoire_overlap` (158).