From 1d2d2c1ff53c55353ca92aaab6b6992ea232a17c Mon Sep 17 00:00:00 2001
From: Miles Roberts <69371202+milesroberts-123@users.noreply.github.com>
Date: Mon, 30 Jun 2025 15:22:14 -0400
Subject: [PATCH] Update diversity definition

Just updating the documentation of the diversity() function in popgen.py to clarify that diversity is the mean number of differences between a pair of sequences, as opposed to other diversity estimators.
---
 sgkit/stats/popgen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sgkit/stats/popgen.py b/sgkit/stats/popgen.py
index e201dfc98..af9884aa8 100644
--- a/sgkit/stats/popgen.py
+++ b/sgkit/stats/popgen.py
@@ -29,7 +29,7 @@ def diversity(
     cohort_allele_count: Hashable = variables.cohort_allele_count,
     merge: bool = True,
 ) -> Dataset:
-    """Compute diversity from cohort allele counts.
+    """Compute diversity as the average number of differences between a pair of sequences from cohort allele counts.
 
     By default, values of this statistic are calculated per variant.
     To compute values in windows, call :func:`window_by_position` or :func:`window_by_variant` before calling