Antpack

Bug fixes (the rare substr error). Added option to build msa to
add unobserved positions. Rewrote algorithm for paired chain annotator
to improve support for single chains supplied by accident (or
intentionally). Added prefiltering for alignment which improves speed
by roughly 2x. Updated CLI to include unobserved positions by default
and to include percent identity.

Minor changes to docstrings in 0.3.5.

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.

Added cibuildwheel support to build cross-platform automatically.

Updated the VJ gene tool to return BOTH the assigned V and J genes and the
percent identity.

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.