openvax / topiary / 24488580857

90%

push

github

Add SelfProteome — nearest-self lookup architecture — v5.8.0 (#135)

Part A of #124.  SelfProteome class with from_peptides / from_fasta /
from_ensembl constructors.  SIMD-vectorized Hamming nearest search,
scope="all" | "non_cta" (pirlygenes for human, explicit cta_source
for non-human), composite reference_version, TopiaryPredictor
integration (self_proteome= kwarg, self_nearest_* columns attached
before filter/sort).

25 tests covering construction, nearest lookup, scope resolution,
tie-breaking, TopiaryPredictor integration on both named-sequences
and fragment paths.

Deferred to parts B/C (#124): scope="protected_tissues", 1aa indels,
BLOSUM62, self_mimic_* binding-aware axes, seed-and-extend indexing,
bundled prediction artifacts.

179 of 203 new or added lines in 3 files covered. (88.18%)

3603 of 4085 relevant lines covered (88.2%)

2.65 hits per line