Scirpy

- 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).

- Documentation overhaul. A lot of docstrings got corrected and improved and the formatting of the documentation now matches scanpy's.
- Experimental function to assess bias in clonotype abundance between conditions (92)
- Scirpy now has a logo (123)
- Update default parameters for `clonotype_network`:
- Edges are now only automatically displayed if plotting < 1000 nodes
- If plotting variables with many categories, the legend is hidden.
- Update default parameters for alignment-based `tcr_neighbors`
- The gap extend penalty now equals the gap open penalty (`11`).

- Make 10x csv and json import consistent (109)
- Fix version requirements (112)
- Fix compatibility issues with pandas > 1 (112)
- Updates to tutorial and README

- Update documentation about T-cell receptor model (4, 10)
- Update README
- Fix curve plots (31)
- Host datasets on GitHub (104)

Initial release for pre-print