pirl-unc / tsarina / 35649005655
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coverage: 77.281% (+0.2%) from 77.117%
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Report panel proteoform groups under oncoref's preferred symbol (#165) (#166)

Closes #165. personalize started reporting identical-protein CTA groups
as NY-ESO-1 / XAGE1A/B / SSX2/B in #164; panel still printed the raw
members label (CTAG1A/CTAG1B, XAGE1A/XAGE1B), so the two workflows
named the same antigen differently.

Display-only, as planned on the issue. The members label stays the
internal key everywhere it is load-bearing: _CTA_GROUPS and
_cta_member_symbols (which resolves a label *back* into symbols through
that dict and would quietly return ("NY-ESO-1",) for a renamed one),
_GROUP_ALIAS_TO_LABEL / _cta_display_name, the selection allowlist, and
the identical-pMHC / peptide-set grouping keys. Every selection,
filtering, grouping and ranking decision runs exactly as before.

_apply_display_labels() rewrites the outward-facing labels in a single
pass after grouping and ranking finish, covering selected["cta"],
cta_list, cta_groups, cta_rank_values, empty_ctas and input_cta_list
together -- they have to agree, since the wide pivot reindexes
selected["cta"] against cta_list and a half-applied rename silently
yields an all-NaN matrix.

Only groups oncoref actually registers are renamed. proteoform_symbol()
is safe on arbitrary strings, but panel also builds ad-hoc groups at
runtime from CTAs with identical selected pMHCs or peptide sets, and
contracting one of those would invent a name like MAGEA1/4 claiming an
identical protein sequence those genes don't have.

Also fixes round-tripping, which was needed for this to be usable:
panel prints these labels, so --ctas <printed label> has to resolve, and
9 of 17 didn't (CGB3/5/8, GAGE12C/D/E, TSPY10/3, ...). The 8 that worked
only coincided with a curated anchor alias. _build_group_alias_map() now
registers each group's display symbol too.

--proteoform-labels {symbol,members} (default symbol) restores the old
strings for anyone with a script keyed on them.

Bumps 1.30.1 -> 1.31.0.

Claude-Session: ht... (continued)

3218 of 4164 relevant lines covered (77.28%)

0.77 hits per line

Coverage Regressions

Lines Coverage ∆ File
83
91.66
 0.24% spanning.py
23
86.19
 0.08% cli_spanning.py
Jobs
ID Job ID Ran Files Coverage
1 35649005655.1 39
77.28
 GitHub Action Run
Source Files on build 35649005655