HomoeoGWAS v2.0.1

HomoeoGWAS v2.0.1 unifies homoeolog interaction analysis across polyploid
species and adds the evidence, stability, provenance, and runtime safeguards
needed for publication-grade use.

Highlights:

• One canonical mode: group, statistic: omniB engine now covers two or
  more subgenomes. Pair edges are the shared primitive: two copies yield one
  edge, three yield three, and four yield six. Four-copy groups aggregate
  their six pair edges; HomoeoGWAS never fits or claims a direct four-way
  coefficient.
• Edge and group hypotheses can be calibrated as one declared
  experiment-wide bootstrap-minP family. Results record adjusted p-values,
  family hashes and counts, the complete ranking, and the evidence-driving
  omniB component.
• Canonical omniB scoring and material/environment deletion follow-up now use
  observable POSIX worker processes with one native numerical thread per
  worker. Requested and effective jobs, backend, and worker PIDs are recorded,
  while bootstrap streams, checkpoint identities, score arrays, and FWER
  decisions remain unchanged.
• homoeogwas audit writes JSON, TSV, and Markdown reports that distinguish
  computational validity, internal familywise discovery, component-level
  interpretation, and replication status.
• Complete component-aware rankings retain minor-allele burden, PC1, and
  kernel-Hadamard evidence. Components localize a combined omniB signal; they
  are not treated as separate discoveries.
• Optional fitted-model bootstrap intervals quantify uncertainty in the
  per-subgenome PVE partition, including boundary rates, refit success, and
  component-rank stability.
• Biallelic PAV, SV, and haplotype pseudo-markers now require explicit marker
  encodings and exact BIM-linked manifests. Scan and GRM inputs are validated
  independently; binary absence/presence must be encoded as 0/2.
• The experimental triad3 statistic remains available as an opt-in
  exact-three-copy sensitivity analysis. The canonical publication claim is
  encoding-robust omnibus pairwise interaction evidence within a homoeolog
  group, not a third- or fourth-order causal or physical mechanism.

Validation:

• Clean-checkout test suite: 771 passed, 4 skipped, and 1 deselected.
• GitHub Actions passed Ruff, CPU tests on Python 3.10, 3.11, and 3.12, and
  source/wheel package builds.
• Cross-species production checks cover wheat, cotton, peanut, and rapeseed
  through the same canonical group-omniB configuration and runtime contract.

Important upgrade notes:

• Use interact.mode: group, statistic: omniB, and one declared
  bootstrap-minP family for new two-, three-, and four-copy analyses. Legacy
  burden analyses remain accepted only when explicitly requested.
• Regenerate legacy SNP-to-gene NPZ files with the analysis BED using
  homoeogwas prep-snps; unverified mappings or BIM fingerprint mismatches are
  refused.
• Raw or multi-allelic copy-number states are not accepted as diploid SNP
  surrogates. Convert them into defensible biallelic features with a marker
  manifest or use a model designed for copy number.
• A significant group result supports omnibus pairwise interaction evidence
  within that homoeolog group. It does not establish a direct multi-protein
  complex or higher-order causal coefficient.

Paper analysis code, frozen configs, figure sources, and result fingerprints
remain in the separate
HomoeoGWAS-reproducibility
repository.