v0.4.1

• 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

v0.4

• 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).

v0.3

• 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).

v0.2

• 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).

v0.1.2

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

v0.1.1

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

v0.1

Initial release for pre-print