pirl-unc / hitlist / 27799766194
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coverage: 80.37% (+0.05%) from 80.324%
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Fix silent-wrong-result bugs in the data/observations layer (#344)

Six correctness fixes surfaced by a holistic review (all reproduced, regression
tests added):

- observations: mhc_allele_in_set was silently skipped when the caller's
  columns= omitted mhc_allele_set (the post-load guard saw no column and the
  filter no-op'd, returning the full unfiltered table). Add the read dependency
  + drop the helper column post-filter (mirrors serotypes).
- observations: a NaN host/source/mhc_species became the literal "nan"/"None"
  string (astype(str) before the no-op dropna), creating a phantom species.
  fillna("") first.
- scanner: rows with a blank Assay IRI collapsed to one (the dedupe seeded ""
  into the seen-set); only dedupe present IRIs, and use _safe_col for short rows.
- downloads: a clean 200 with an empty body (withdrawn proteome) was cached as a
  valid 0-byte file forever. Reject size==0 as a retryable error.
- downloads: a transient UniProt failure was cached as a permanent not_found,
  excluding that organism from every later build. Let transport errors
  propagate and skip caching a negative on them.
- VersionedDatasetRegistry: manifest write was non-atomic (direct write_text);
  an interrupted/concurrent write truncates manifest.json and _read_manifest
  silently returns {}, losing all provenance. Use the atomic temp+os.replace
  pattern (matches _save_manifest, #331).

Bumps 1.43.0 -> 1.43.1.

5863 of 7295 relevant lines covered (80.37%)

0.8 hits per line

Coverage Regressions

Lines Coverage ∆ File
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Jobs
ID Job ID Ran Files Coverage
1 27799766194.1 29
80.37
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Source Files on build 27799766194