openvax / topiary / 24905071717

90%

push

github

Inline BLOSUM62 matrix to drop biopython dependency (#146)

topiary.self_proteome imported BLOSUM62 via
Bio.Align.substitution_matrices.load (added in v5.9.0), but biopython
was not declared as a dependency and adding it just for a 400-integer
constant is overkill. Inline the standard 20x20 matrix as a numpy
constant; values verified to match biopython's BLOSUM62 exactly.

Fixes the 17 ModuleNotFoundError: No module named 'Bio' failures on
the #138 self_proteome tests that block CI on all open PRs.

2 of 2 new or added lines in 1 file covered. (100.0%)

3686 of 4170 relevant lines covered (88.39%)

2.65 hits per line