pirl-unc / hitlist / 27364016973
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v1.41.2: rewrite docs for accuracy + add a curation-process overview (#340)

The mkdocs site had drifted badly from the code and didn't explain the
curation pipeline as a whole:

- pmid-curation.md taught the DEPRECATED YAML schema the loader actively warns
  against (`label:`/`type:`/`n:`/`peptides_estimated:`), claimed "34 studies"
  (now 159) and "233 alleles / mhcgnomes 3.20.0", and used wrong proteome
  kwargs. Rewritten against the real schema: `study_label`, `rules`,
  `ms_samples` (`sample_label`/`n_samples`/`mhc`/`mhc_class`/`classification`/
  `override`/`reason`), provenance fills, `mono_allelic_host`, the full
  `override` vocabulary (incl. `ebv_lcl`, `noncancer_cell_line`), the rule
  condition-matching semantics, and per-donor attribution.
- index.md used a `tissue_overrides:` key that doesn't exist and a stale
  "14 datasets". Reworked into a coherent landing page that links the three
  deep-dive pages, with a real (verified) Löffler-CRC rules example.
- source-classification.md was missing real concepts: `noncancer_cell_line`,
  the EBV-LCL auto-correction, mono-allelic evidence, chimeric/engineered-MHC/
  xenograft, non-peptide ligands, and the three-axis species model. The
  deprecated `human_only` param is now flagged as such.
- New page curation-process.md ("How curation works") covers the
  scan → fill → classify → partition → build pipeline, supplementary
  ingestion, the reference registries, and the design principles — the
  internal process and ideas, end to end.
- mkdocs nav reordered: Home → How Curation Works → Source Classification →
  PMID Curation Overrides. `mkdocs build --strict` passes.

5721 of 7158 relevant lines covered (79.92%)

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1 27364016973.1 29
79.92
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Source Files on build 27364016973