v0.6.0

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)

v0.5.0

Add support for BCRs and gamma-delta TCRs

Backwards-incompatible changes:

• The 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.

data release: BCR example data

The assets of this release contain the example datasets compatible
with v0.5.

v0.4.2

• Include tests into main package (#189)

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)