swapped function name

popsim-consortium · Oct 29, 2021 · 4467f53 · 4467f53
1 parent 7e7f27f
commit 4467f53
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Showing 4 changed files with 18 additions and 18 deletions.
diff --git a/stdpopsim/genomes.py b/stdpopsim/genomes.py
@@ -325,7 +325,7 @@ def all_intervals_array(self):
         all_intervals = stdpopsim.utils.build_intervals_array(all_intervals)
         return all_intervals
 
-    def clear_features(self):
+    def clear_DFEs(self):
         """
         convenience function to clear dfe_list and interval_list
         """
@@ -343,7 +343,7 @@ def add_DFE(self, intervals, DFE, fill_neutral=True):
         if len(self.dfe_list) >= 2:
             raise ValueError("only single DFE + neutral sites implemented")
         if fill_neutral:
-            self.clear_features()
+            self.clear_DFEs()
         stdpopsim.utils.check_intervals_validity(intervals)
         self.dfe_list.append(DFE)
         self.interval_list.append(intervals)

diff --git a/tests/test_engines.py b/tests/test_engines.py
@@ -111,7 +111,7 @@ def test_non_neutral_contig(self):
         model = species.get_demographic_model("AshkSub_7G19")
         samples = model.get_samples(10)
         contig = stdpopsim.Contig.basic_contig(length=100)
-        contig.clear_features()
+        contig.clear_DFEs()
         props = [1]
         mt = [stdpopsim.ext.MutationType(distribution_type="f", distribution_args=[1])]
         dfes = [
@@ -128,7 +128,7 @@ def test_non_neutral_contig(self):
         with pytest.raises(ValueError):
             engine.simulate(model, contig, samples, seed=1)
         # okay now change selection coefficient to neutral
-        contig.clear_features()
+        contig.clear_DFEs()
         props = [1]
         mt = [stdpopsim.ext.MutationType(distribution_type="f", distribution_args=[0])]
         dfes = [

diff --git a/tests/test_genomes.py b/tests/test_genomes.py
@@ -35,7 +35,7 @@ def test_add_DFE_errors(self):
 
     def test_add_DFE(self):
         contig = stdpopsim.Contig.basic_contig(length=100)
-        contig.clear_features()
+        contig.clear_DFEs()
         props = [0.3, 0.7]
         mt = [stdpopsim.ext.MutationType() for _ in props]
         dfes = [
@@ -57,7 +57,7 @@ def test_add_DFE(self):
 
     def test_is_neutral(self):
         contig = stdpopsim.Contig.basic_contig(length=100)
-        contig.clear_features()
+        contig.clear_DFEs()
         props = [0.3, 0.7]
         mt = [
             stdpopsim.ext.MutationType(distribution_type="f", distribution_args=[1])
@@ -81,7 +81,7 @@ def test_is_neutral(self):
 
     def test_is_neutral2(self):
         contig = stdpopsim.Contig.basic_contig(length=100)
-        contig.clear_features()
+        contig.clear_DFEs()
         props = [0.3, 0.7]
         mt = [stdpopsim.ext.MutationType() for _ in props]
         dfes = [
@@ -102,7 +102,7 @@ def test_is_neutral2(self):
 
     def test_is_neutral3(self):
         contig = stdpopsim.Contig.basic_contig(length=100)
-        contig.clear_features()
+        contig.clear_DFEs()
         props = [0.3, 0.7]
         mt = [
             stdpopsim.ext.MutationType(distribution_type="e", distribution_args=[1])
@@ -126,7 +126,7 @@ def test_is_neutral3(self):
 
     def test_too_many_dfes(self):
         contig = stdpopsim.Contig.basic_contig(length=100)
-        contig.clear_features()
+        contig.clear_DFEs()
         props = [0.3, 0.7]
         mt = [
             stdpopsim.ext.MutationType(distribution_type="e", distribution_args=[1])
@@ -307,7 +307,7 @@ def test_simulation_runs(self):
             length=10000,
             mutation_rate=1e-6,  # Ne=1e3 and length=1e4 so theta=40
         )
-        contig.clear_features()
+        contig.clear_DFEs()
         contig.add_DFE(
             intervals=np.array([[0, contig.length / 2]], dtype="int"),
             DFE=self.dfe,

diff --git a/tests/test_slim_engine.py b/tests/test_slim_engine.py
@@ -695,7 +695,7 @@ def test_single_genomic_element_type_in_script(self):
     def test_multiple_genomic_element_types_in_script(self):
         contig = get_test_contig()
         engine = stdpopsim.get_engine("slim")
-        contig.clear_features()
+        contig.clear_DFEs()
         contig.add_DFE(
             np.array([[0, 100]]), stdpopsim.dfe.neutral_DFE(), fill_neutral=False
         )
@@ -781,7 +781,7 @@ def test_unweighted_mutations_are_not_simulated_by_slim(self):
             proportions=[0, 0],
             mutation_types=mt,
         )
-        contig.clear_features()
+        contig.clear_DFEs()
         contig.add_DFE(
             np.array([[0, contig.length]], dtype="int32"), test_d, fill_neutral=False
         )
@@ -807,7 +807,7 @@ def test_unweighted_mutations_are_not_simulated_by_slim(self):
             proportions=[0, 0],
             mutation_types=mt,
         )
-        contig.clear_features()
+        contig.clear_DFEs()
         contig.add_DFE(
             np.array([[10, contig.length]], dtype="int32"), test_d, fill_neutral=True
         )
@@ -1624,14 +1624,14 @@ def test_add_dfe_misc(self):
             proportions=[0, 1],
             mutation_types=mt,
         )
-        contig.clear_features()
+        contig.clear_DFEs()
         contig.add_DFE(
             np.array([[contig.length - 1, contig.length]], dtype="int32"),
             test_d,
             fill_neutral=True,
         )
         assert contig.interval_list[1].shape == (1, 2)
-        contig.clear_features()
+        contig.clear_DFEs()
         contig.add_DFE(
             np.array([[contig.length - 2, contig.length - 1]], dtype="int32"),
             test_d,
@@ -1661,7 +1661,7 @@ def test_slim_fractions(self):
         proportions = ([0, 1.0], [0.5, 0.5], [0, 0], [0.2, 0])
         for props in proportions:
             slim_frac = np.array(sum(props))
-            contig.clear_features()
+            contig.clear_DFEs()
             test_d.proportions = props
             contig.add_DFE(test_int, test_d, fill_neutral=False)
             assert (slim_frac == stdpopsim.slim_engine.get_slim_fractions(contig)).all()
@@ -1708,7 +1708,7 @@ def test_complex_mutation_rate_maps(self):
             mutation_types=mt,
         )
         for prop1, prop2 in ((0.3, 0.7), (0.7, 0.3), (1.0, 0.0)):
-            contig.clear_features()
+            contig.clear_DFEs()
             test_d.proportions = [prop1]
             contig.add_DFE(np.array([[10, 100]]), test_d, fill_neutral=True)
             contig.dfe_list[1].proportions = [0]
@@ -1734,7 +1734,7 @@ def test_complex_mutation_rate_maps(self):
                 np.isclose(np.array(obs_slim_rates), np.array(exp_slim_rates))
             ).all()
 
-            contig.clear_features()
+            contig.clear_DFEs()
             contig.add_DFE(np.array([[0, 50]]), test_d, fill_neutral=False)
             test_d2 = stdpopsim.DFE(
                 id="test",