EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310)

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Make the EUCAST Clinical Breakpoint Tables import (2019-2026) fail-safe:

- Add blocking rows (NA breakpoints, reason in `note`) where EUCAST gives
  no breakpoint for an organism (IE, "-", Note, brackets, "except"
  clauses, table scope), so as.sir() no longer falls back to broader taxa
- Apply restrictions from EUCAST notes via a curated rule table with a
  completeness guard (e.g. zone diameters for E. coli only)
- Import PK-PD (non-species related) breakpoints 2019-2023, H.
  parainfluenzae MIC breakpoints, and explicit screening thresholds from
  notes (high-level aminoglycosides, cefoxitin MIC, unidentified CoNS)
- Parser fixes: lost Staphylococcus sheets 2019/2020, note keys and
  bodies, struck-through cells, hidden sheets, missing disk contents,
  organism groups, site vocabulary, MIC dilution levels, off-scale
  breakpoints stored as 0.0001
- Keep EUCAST antifungal breakpoints 2019-2025 from WHONET; code WHONET
  streptomycin as STR1 instead of STR (streptoduocin)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

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Matthijs BerendsandClaude Opus 5.5 authored and GitHub committed 2026-10-02 06:01:58 +02:00

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