pirl-unc / tsarina / 27096219887
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coverage: 72.115% (+0.6%) from 71.478%
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Audit hygiene: drop dead HPA fraction path, harden tissue derivation (P3) (#99)

Follow-up to the tissue-derivation audit. Four low-risk fixes:

- hpa.py: remove the dead, divergent deflated reproductive-fraction
  implementation (reproductive_fraction_weighted, deflated_ntpm_map, the
  rna_reproductive_fraction_weighted__core/__extended columns, the
  rna_repro_frac_ge_* flags, adaptive_rna_fraction_required, and
  hpa_adaptive_confidence_restricted). These columns had no consumer or
  test (evidence.py only uses rna_tissue_ntpm_map) and used EXTENDED while
  the live filter (scripts/add_cta_gene.py) uses CORE -- a maintainer trap.
  The bundled table's passes_filters is produced solely by the scripts.

- tiers.py: add 'spinal cord' to SAFETY_TISSUE_GROUPS['brain'] (it is a
  consensus tissue, previously in no safety group) and document that the
  brain group spans two HPA vocabularies (10 consensus names drive the RNA
  flag; medulla oblongata/pons/thalamus/white matter are consensus-absent
  but feed the MS vital-organ screen).

- tissues.py: harden adaptive_rna_threshold to strip/casefold the tier
  label so a non-canonical string (' Enhanced ') maps to its tier instead
  of silently falling to the strict 0.97 'Missing' floor.

No behavior change to the bundled gene sets (stored columns unchanged);
the spinal-cord addition affects only future regeneration + the MS screen
(already covered by the drift-guard test). 402 tests pass.

2493 of 3457 relevant lines covered (72.11%)

0.72 hits per line

Coverage Regressions

Lines Coverage ∆ File
39
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 0.0% hpa.py
39
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Jobs
ID Job ID Ran Files Coverage
1 27096219887.1 35
72.11
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Source Files on build 27096219887