pirl-unc / hitlist / 25242722227
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v1.30.29: Audit cleanup -- prune version-history slop, refresh stale docs (#218)

Per audit pass review: code comments and docstrings had accumulated
PR-diff-style change-log narration ("v1.30.17 splits...", "v1.30.22
raised...", "v1.30.28 bumped...") that read fine in commit messages
but rotted as inline documentation -- forcing readers through three
versions of history before getting to the current rules.

Code/comment cleanups:

- hitlist/observations.py: severity-tier block now leads with the
  current four-tier table (class-I + class-II rules side-by-side)
  instead of listing the v1.30.17 -> .22 -> .28 evolution. The
  rationale paragraph below states the current rule, not how we
  arrived at it.
- hitlist/qc.py: discrepancies and curation_plan docstrings drop
  the "added in v1.30.X / #Y" narration. The version metadata is in
  the commit messages where it belongs. Also fixes a stale
  ">=31aa" threshold in the discrepancies docstring (v1.30.28
  raised it to >=45).
- hitlist/downloads.py: drop the inline qc.proteome_coverage
  origin story from the Mtb registry block.

README updates:

- Refresh stats (159 PMIDs, 633 ms_samples, 446 4-digit, 9 supps,
  22 species, 33 viral) -- previous numbers had drifted ~30-50%
  out of date.
- Fix the lookup_proteome("Mycobacterium tuberculosis") example:
  v1.30.24 added Mtb to the static SPECIES_PROTEOMES so the call
  no longer needs use_uniprot=True and resolves to UP000001584
  (H37Rv) instead of UP000001020 (CDC 1551).
- Add the three new export-observations CLI flags
  (--exclude-class-label-suspect, --exclude-class-label-implausible,
  --apm-only) to the filter table.
- Add a QC diagnostics CLI section listing all `hitlist qc`
  subcommands including the new proteome-coverage one.

No code-behavior changes; tests unchanged at 603 pass.

3711 of 5229 relevant lines covered (70.97%)

0.71 hits per line

Coverage Regressions

Lines Coverage ∆ File
74
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1
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Jobs
ID Job ID Ran Files Coverage
1 25242722227.1 27
70.97
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Source Files on build 25242722227