From c5f63b8bf7082f12c15712930589c2d9d22d867d Mon Sep 17 00:00:00 2001
From: "Kevin R. Thornton" <krthornt@uci.edu>
Date: Thu, 21 Nov 2024 16:04:47 -0800
Subject: [PATCH] Raise error when simulations w/neutral mutations are badly
 specified

---
 lib/evolve_discrete_demes/evolvets.cc         |  4 +--
 ...t_tree_sequences_with_neutral_mutations.py | 34 +++++++++++++++++++
 2 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/lib/evolve_discrete_demes/evolvets.cc b/lib/evolve_discrete_demes/evolvets.cc
index 20fc1a8cf..98440cdfa 100644
--- a/lib/evolve_discrete_demes/evolvets.cc
+++ b/lib/evolve_discrete_demes/evolvets.cc
@@ -255,12 +255,12 @@ evolve_with_tree_sequences(
         {
             if (options.track_mutation_counts_during_sim)
                 {
-                    if (simplification_interval != 1)
+                    if (simplification_interval != 1 or options.suppress_edge_table_indexing == true)
                         {
                             throw std::invalid_argument(
                                 "when track_mutation_counts is True and simulating "
                                 "neutral mutations, the simplification interval must be "
-                                "1");
+                                "1 and edge table indexing must not be suppressed");
                         }
                 }
         }
diff --git a/tests/test_tree_sequences_with_neutral_mutations.py b/tests/test_tree_sequences_with_neutral_mutations.py
index 2993a1659..c6f7865a7 100644
--- a/tests/test_tree_sequences_with_neutral_mutations.py
+++ b/tests/test_tree_sequences_with_neutral_mutations.py
@@ -2,6 +2,7 @@
 import unittest
 
 import numpy as np
+import pytest
 
 import fwdpy11
 from test_tree_sequences import set_up_quant_trait_model, set_up_standard_pop_gen_model
@@ -183,5 +184,38 @@ def test_trigger_final_simplification_with_fixations_to_remove():
     )
 
 
+def test_track_mutation_counts():
+    burnin = 10
+    N = 100
+    pdict = {
+        # Add a region for neutral mutations:
+        "nregions": [fwdpy11.Region(0, 1, 1)],
+        "sregions": [fwdpy11.ExpS(beg=0, end=1, weight=1, mean=0.2)],
+        "recregions": [fwdpy11.PoissonInterval(0, 1, 1e-2)],
+        "gvalue": [fwdpy11.Multiplicative(2.0)],
+        "rates": (1e-3, 1e-3, None),
+        "simlen": burnin * N,
+        "demography": fwdpy11.ForwardDemesGraph.tubes(
+            [N], burnin=10 * N, burnin_is_exact=True
+        ),
+        "prune_selected": True,
+    }
+    params = fwdpy11.ModelParams(**pdict)
+    pop = fwdpy11.DiploidPopulation(N, 1.0)
+    rng = fwdpy11.GSLrng(54321)
+
+    with pytest.raises(ValueError):
+        fwdpy11.evolvets(
+            rng,
+            pop,
+            params,
+            1,
+            # This is the bad thing...
+            suppress_table_indexing=True,
+            # ...combined with this
+            track_mutation_counts=True,
+        )
+
+
 if __name__ == "__main__":
     unittest.main()