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openvax / topiary
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Repo Added 05 Jan 2018 08:34PM UTC
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LAST BUILD ON BRANCH fix-declared-deps-and-dead-surface
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15 Sep 2026 01:07AM UTC coverage: 92.262% (+0.1%) from 92.154%
34915990000-1

Pull #319

github

iskandr
Rename the ranking allele validator apart from the mhcgnomes normalizers

Three functions were called _normalize_alleles, doing two different
jobs. Two canonicalize allele names through mhcgnomes as a reader builds
a frame (io_pvacseq, io_lens). The third validates the *shape* of a
declared allele set - None, callable, Mapping or non-empty sequence with
no blank entries - and returns the names exactly as the caller spelled
them.

Verified it transforms no strings: ['HLA-A2', 'hla-a*02:01',
'HLA-A*02:01'] comes back unchanged.

That one is now _validate_declared_alleles, with a docstring saying why
it is deliberately not mhcgnomes normalization: declared alleles are
matched against whatever spelling the frame already carries, so
canonicalizing one side only would stop equal alleles comparing equal.
The shared name invited exactly the opposite conclusion - that this was
a site where the mhcnames-to-mhcgnomes migration had been missed.

Claude-Session: https://claude.ai/code/session_015pMD1uiTztbB2bTQ1FkY8m
Pull Request #319: Make declared dependencies and exported surface match the code (#314, #315)

9 of 10 new or added lines in 5 files covered. (90.0%)

115 existing lines in 3 files now uncovered.

7118 of 7715 relevant lines covered (92.26%)

0.92 hits per line

Relevant lines Covered
Build:
Build:
7715 RELEVANT LINES 7118 COVERED LINES
0.92 HITS PER LINE
Source Files on master
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Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
34915990... fix-declared-deps-and-dead-surface Rename the ranking allele validator apart from the mhcgnomes normalizers Three functions were called _normalize_alleles, doing two different jobs. Two canonicalize allele names through mhcgnomes as a reader builds a frame (io_pvacseq, io_lens). T... Pull #319 15 Sep 2026 01:14AM UTC iskandr github
92.26
34915993... fix-declared-deps-and-dead-surface Merge 00b527db1 into 862b6ade6 Pull #319 15 Sep 2026 01:14AM UTC web-flow github
92.26
34914989... fix-declared-deps-and-dead-surface Make declared dependencies and exported surface match the code (#314, #315) Two mechanical issues from today's review. Every claim verified before changing anything. Dependencies (#315): - mhcnames was a hard dependency with no importer anywher... Pull #319 15 Sep 2026 12:58AM UTC iskandr github
92.26
34904426... master Give CachedPredictorCoverageError a __str__; catch RuntimeError in the CLI (#311) * Give CachedPredictorCoverageError a __str__; catch RuntimeError in the CLI A review of 5.56.1 found that my "test gap closed" claim was only half true, and that ... push 14 Sep 2026 10:35PM UTC web-flow github
92.15
34869603... fix-coverage-error-str-and-cli-handling Narrow to PredictorSetupError; bare RuntimeError masked real bugs A second review of this branch caught it contradicting its own principle: it argued a narrow type is how you avoid hiding bugs, then caught bare RuntimeError across the whole predi... Pull #311 14 Sep 2026 05:00PM UTC iskandr github
92.15
34867372... fix-coverage-error-str-and-cli-handling Merge b5f54c7c6 into cd37e3a42 Pull #311 14 Sep 2026 04:39PM UTC web-flow github
92.13
34867658... deslop/readme README: drop release narration, fix stale facts - Isovar extra requires 1.8.0 (pyproject), not 1.7.10 - Remove the mhctools 3.7.0 compatibility paragraph; requirements pin >=3.39 - column(name) example showed the bare form - Drop the comparison t... Pull #318 14 Sep 2026 04:28PM UTC iskandr github
92.14
34867367... fix-coverage-error-str-and-cli-handling Give CachedPredictorCoverageError a __str__; catch RuntimeError in the CLI A review of 5.56.1 found that my "test gap closed" claim was only half true, and that the fix sat at the wrong layer. Both confirmed by running them. The vacuous assertio... Pull #311 14 Sep 2026 04:22PM UTC iskandr github
92.13
34803732... master Report a missing input file's message, not its errno (5.56.0 regression) (#309) Reviewing 5.56.0's own diff turned up a bug it introduced. Its CLI handler unwrapped e.args[0] for every exception it caught, to strip the extra layer of repr quoting... push 14 Sep 2026 03:51AM UTC web-flow github
92.14
34803217... fix-cli-oserror-message-regression Report a missing input file's message, not its errno (5.56.0 regression) Reviewing 5.56.0's own diff turned up a bug it introduced. Its CLI handler unwrapped e.args[0] for every exception it caught, to strip the extra layer of repr quoting str() ... Pull #309 14 Sep 2026 03:42AM UTC iskandr github
92.14
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