HomoeoGWAS v2.1.3

HomoeoGWAS v2.1.3 is a patch release of v2.1.2 and the first v2 release on PyPI
(pip install homoeogwas==2.1.3).

Changed: common analysis traps now stop at preflight or are flagged by audit.
A homoeolog table that repeats a gene across groups is refused without naming a
bypass; interact.allow_duplicate_genes is removed, and only the data owner can
waive the check (written reason, named approver, bound to the table hash; not
exposed via MCP; flagged OVERRIDDEN_INPUT_CHECK). fit and interact record
the sample join and refuse to run when unmatched phenotype IDs match genotype IDs
after normalisation (leading zeros, case, whitespace, trailing .0); losing more
than 5% of phenotyped samples is flagged SAMPLE_JOIN_LOSS.
prep-homoeologs --method diamond-rbh refuses protein FASTAs with non-amino-acid
characters or unmatched headers, runs DIAMOND with a timeout and treats zero
reciprocal pairs as an error. fit checks .bed/.bim/.fam for every subgenome
before computing, prep-snps refuses empty subgenomes or chromosome names absent
from the .bim, and validate runs fit's phenotype checks without computing.
A trait equal to the mean of trials with different means is flagged
PHENOTYPE_RAW_TRIAL_AVERAGE. PVE_UNCERTAINTY_NOT_ASSESSED is now info.

Added: report_card_<result>.json next to every fit summary and interact
result, with the numbers to quote, the audit flags and the statements a report
must carry; it is built from the result and audit, no statistic is recomputed.

No statistical code changed. Estimates, p-values and decisions equal v2.1.2.
See the changelog for details.