try to make tests faster. Triggered #836

fwdpy11/src/functions/add_mutation.cc

@@ -319,6 +319,11 @@ add_mutation(const fwdpy11::GSLrng_t& rng, const double left, const double right
                 }
         }
 
+    for(auto & d : pop.diploids)
+    {
+        if(pop.haploid_genomes[d.first].n == 0) { throw std::runtime_error("bad1a"); }
+        if(pop.haploid_genomes[d.second].n == 0) { throw std::runtime_error("bad2a"); }
+    }
     std::size_t new_mutation_key = std::numeric_limits<std::size_t>::max();
     auto candidates = generate_canidate_list(left, right, ndescendants, deme, pop);
 

tests/test_selective_sweeps.py

@@ -30,12 +30,12 @@
 
 
 def make_pop_with_msprime_ancestry(seed):
-    N = 500
+    N = 100
     rho = 1000
     L = 1.0
     initial_ts = msprime.sim_ancestry(
         samples=N,
-        population_size=1000,
+        population_size=2 * N,
         recombination_rate=rho / 4 / N,
         random_seed=seed,
         sequence_length=L,
@@ -59,15 +59,15 @@ def run_selective_sweep(
     msprime_seed,
     fp11_seed,
     ndescendants,
-    N=500,
+    N=100,
     alpha=1000,  # 2Ns
     rho=100,
     L=1.0,
     max_attempts=100,
 ):
     for initial_ts in msprime.sim_ancestry(
         samples=N,
-        population_size=1000,
+        population_size=2 * N,
         recombination_rate=rho / 4 / N,
         random_seed=msprime_seed,
         sequence_length=1.0,
@@ -91,6 +91,13 @@ def run_selective_sweep(
         if idx is None:
             continue
 
+        c = 0
+        for dip in pop.diploids:
+            for genome in [dip.first, dip.second]:
+                if idx in pop.haploid_genomes[genome].smutations:
+                    c += 1
+        assert c == ndescendants
+
         # Make sure we've chosen a valid time
         assert (
             pop.mutations[idx].g <= pop.tables.nodes[pop.tables.mutations[0].node].time
@@ -135,7 +142,7 @@ def test_sweep_from_new_mutation(msprime_seed, fp11_seed):
 
 @pytest.mark.parametrize("msprime_seed", seed_list(135123, 5))
 @pytest.mark.parametrize("fp11_seed", seed_list(5130125, 5))
-@pytest.mark.parametrize("ndescendants", [2, 7, 10, 23, 100, 257])
+@pytest.mark.parametrize("ndescendants", [2, 7, 10, 23, 12, 100])
 def test_sweep_from_standing_variation(msprime_seed, fp11_seed, ndescendants):
     pop_with_fixation, idx = run_selective_sweep(msprime_seed, fp11_seed, ndescendants)
     if pop_with_fixation is not None:
@@ -162,11 +169,7 @@ def test_sweep_from_new_mutation_using_API(msprime_seed, fp11_seed, alpha):
         "window": (0.49, 0.51),
     }
     rng = fwdpy11.GSLrng(fp11_seed)
-    (
-        pop_with_fixation,
-        idx,
-        _,
-    ) = fwdpy11.conditional_models.selective_sweep(
+    (pop_with_fixation, idx, _,) = fwdpy11.conditional_models.selective_sweep(
         rng,
         pop,
         params,
@@ -181,7 +184,7 @@ def test_sweep_from_new_mutation_using_API(msprime_seed, fp11_seed, alpha):
 
 @pytest.mark.parametrize("msprime_seed", seed_list(135123, 5))
 @pytest.mark.parametrize("fp11_seed", seed_list(5130125, 5))
-@pytest.mark.parametrize("ndescendants", [2, 7, 10, 23, 100, 257])
+@pytest.mark.parametrize("ndescendants", [2, 7, 10, 23, 12, 100])
 @pytest.mark.parametrize("alpha", [1000.0])
 def test_sweep_from_standing_variation_using_API(
     msprime_seed, fp11_seed, ndescendants, alpha
@@ -200,13 +203,10 @@ def test_sweep_from_standing_variation_using_API(
         "data": fwdpy11.NewMutationData(effect_size=alpha / 2 / pop.N, dominance=1.0),
         "window": (0.49, 0.51),
     }
+    finished = False
+    rng = fwdpy11.GSLrng(fp11_seed)
     try:
-        rng = fwdpy11.GSLrng(fp11_seed)
-        (
-            pop_with_fixation,
-            idx,
-            _,
-        ) = fwdpy11.conditional_models.selective_sweep(
+        (pop_with_fixation, idx, _,) = fwdpy11.conditional_models.selective_sweep(
             rng,
             pop,
             params,
@@ -217,6 +217,7 @@ def test_sweep_from_standing_variation_using_API(
         if pop_with_fixation is not None:
             assert pop_with_fixation.mcounts[idx] == 2 * pop_with_fixation.N
             _ = pop_with_fixation.dump_tables_to_tskit()
+            finished = True
     except fwdpy11.conditional_models.AddMutationFailure as a:
         pass
     except Exception as e:
@@ -334,11 +335,7 @@ def test_sweep_from_new_mutation_in_singe_deme_using_API(fp11_seed, demes_yaml,
         "window": (0.49, 0.51),
     }
     rng = fwdpy11.GSLrng(fp11_seed)
-    (
-        pop_with_fixation,
-        idx,
-        _,
-    ) = fwdpy11.conditional_models.selective_sweep(
+    (pop_with_fixation, idx, _,) = fwdpy11.conditional_models.selective_sweep(
         rng,
         pop,
         params,
@@ -389,11 +386,7 @@ def test_sweep_from_new_mutation_with_demography_using_API(
         "window": (0.49, 0.51),
     }
     rng = fwdpy11.GSLrng(fp11_seed)
-    (
-        pop_with_fixation,
-        idx,
-        _,
-    ) = fwdpy11.conditional_models.selective_sweep(
+    (pop_with_fixation, idx, _,) = fwdpy11.conditional_models.selective_sweep(
         rng,
         pop,
         params,
@@ -438,11 +431,7 @@ def test_origination_deme1_fixation_in_deme_2(fp11_seed, demes_yaml, alpha):
         "window": (0.49, 0.51),
     }
     rng = fwdpy11.GSLrng(fp11_seed)
-    (
-        pop_with_fixation,
-        idx,
-        _,
-    ) = fwdpy11.conditional_models.selective_sweep(
+    (pop_with_fixation, idx, _,) = fwdpy11.conditional_models.selective_sweep(
         rng,
         pop,
         params,
@@ -547,11 +536,7 @@ def test_origination_deme2_fixation_in_deme_2_no_migration(
         "window": (0.49, 0.51),
     }
     rng = fwdpy11.GSLrng(fp11_seed)
-    (
-        pop_with_fixation,
-        idx,
-        _,
-    ) = fwdpy11.conditional_models.selective_sweep(
+    (pop_with_fixation, idx, _,) = fwdpy11.conditional_models.selective_sweep(
         rng,
         pop,
         params,