openvax / topiary / 36363955353-1

93%

master: 93%

Pull #422

github

Run --protein-change, and fix the help it contradicts (5.84.0)

The flag, its parser and its tests have existed for years, but nothing
called the parser: alone it reported "No variants loaded", and beside
--variant it was silently dropped. Fragment building required
effect.variant.short_description, which a named protein change has no
variant for, so it now uses getattr and leaves the variant column empty
rather than inventing a coordinate. Combining it with genomic inputs is
refused: those rows can carry read-level evidence and these cannot.

--predict-wt's help named wt_affinity, which parses as affinity from a
predictor called "wt" and then fails; it now names the wt.* scope
forms. The deprecated RNA flags print a visible line instead of a
DeprecationWarning Python hides.

Closes #322. Union of input modes tracked in #421.

Claude-Session: https://claude.ai/code/session_016qyxwku965ujmfSRxnmDb7

16 of 16 new or added lines in 3 files covered. (100.0%)

8402 of 9013 relevant lines covered (93.22%)

0.93 hits per line