Initial release.
Added Kabat, Martin schemes.
Added sequence scoring functionality for humanness. Updated all numbering tools to improve behavior in the presence of N-terminal deletions.
Fixed bug that caused gapped scoring (scoring where all gaps are ignored) to yield masked scores only.
Added scoring with a user-supplied mask, so that the user can filter out regions they would like to not include in the score. Also default to -O3 when compiling.
Minor updates to alignment; fixed a bug relevant to old versions of GCC that prevents compilation with old versions of GCC; removed the scipy dependency; fixed the double-normalization issue.
Added MultiChainAnnotator, LiabilitySearchTool and VJGeneTool. This considerably expands the capabilities of the library to cover most basic antibody amino acid sequence analysis tasks. Removed BioPython as a dependency (it is not necessary to include a fasta file generator in SingleChainAnnotator since any users using Biopython can easily add this themselves.)
Added the sort position codes function to SingleChainAnnotator, which enables the user to sort a list of position codes (this is useful and convenient when merging many lists of numbers). Set SingleChainAnnotator up to return a list indicating whether each position is cdr or framework if the user so requests.
Updated the VJ gene tool to return BOTH the assigned V and J genes and the percent identity.
Added cibuildwheel support to build cross-platform automatically.
Revised and updated API for PairedChainAnnotator, SingleChainAnnotator. Added bug fix for unusual alignment errors. Updated numbering tools to accept letter X in input. Converted PairedChainAnnotator, SingleChainAnnotator, VJGeneTool to C++. Updated vj gene assignment to use either e-value or percent identity and either IMGT or OGRDB, and to report multiple matches if multiple equivalent matches are found. Switched C++ wrapping to Nanobind. Rewrote core alignment code to produce a 30% improvement in numbering speed / efficiency. Added Aho numbering scheme. Added code to convert between numbering schemes when assigning VJ so that VJ can be assigned using any scheme not just IMGT. Added command line interface for easy use on fasta files from the command line.
Minor changes to docstrings in 0.3.5.