Reformat

astheeggeggs · Apr 19, 2024 · b98cdc7 · b98cdc7
1 parent 820e582
commit b98cdc7
Showing 1 changed file with 16 additions and 21 deletions.
diff --git a/tests/lsbase.py b/tests/lsbase.py
@@ -33,10 +33,7 @@ def get_examples_haploid(self, ts):
         H = ts.genotype_matrix()
         s = H[:, 0].reshape(1, H.shape[0])
         H = H[:, 1:]
-        haplotypes = [
-            s,
-            H[:, -1].reshape(1, H.shape[0])
-        ]
+        haplotypes = [s, H[:, -1].reshape(1, H.shape[0])]
         s_miss_last = s.copy()
         s_miss_last[0, -1] = core.MISSING
         s_miss_mid = s.copy()
@@ -77,16 +74,16 @@ def get_examples_pars_haploid(self, ts, scale_mutation=True, seed=42):
         m = ts.num_sites
         n = H.shape[1]
         rs = [
-            np.zeros(m) + 0.01, # Equal recombination and mutation
-            np.zeros(m) + 0.999,    # Extreme
-            np.zeros(m) + 1e-6, # Extreme
+            np.zeros(m) + 0.01,  # Equal recombination and mutation
+            np.zeros(m) + 0.999,  # Extreme
+            np.zeros(m) + 1e-6,  # Extreme
             np.random.rand(m),  # Random
         ]
         mus = [
-            np.zeros(m) + 0.01, # Equal recombination and mutation
+            np.zeros(m) + 0.01,  # Equal recombination and mutation
             np.zeros(m) + 0.2,  # Extreme
-            np.zeros(m) + 1e-6, # Extreme
-            np.random.rand(m) * 0.2,    # Random
+            np.zeros(m) + 1e-6,  # Extreme
+            np.random.rand(m) * 0.2,  # Random
         ]
         for s, r, mu in itertools.product(haplotypes, rs, mus):
             r[0] = 0
@@ -108,7 +105,7 @@ def get_examples_diploid(self, ts, seed=42):
         H = H[:, 2:]
         genotypes = [
             s,
-            H[:, -1].reshape(1, H.shape[0]) + H[:, -2].reshape(1, H.shape[0])
+            H[:, -1].reshape(1, H.shape[0]) + H[:, -2].reshape(1, H.shape[0]),
         ]
         s_miss_last = s.copy()
         s_miss_last[0, -1] = core.MISSING
@@ -142,25 +139,23 @@ def get_examples_pars_diploid(self, ts, seed=42):
         m = ts.num_sites
         n = H.shape[1]
         rs = [
-            np.zeros(m) + 0.01, # Equal recombination and mutation
-            np.zeros(m) + 0.999,    # Extreme
-            np.zeros(m) + 1e-6, # Extreme
+            np.zeros(m) + 0.01,  # Equal recombination and mutation
+            np.zeros(m) + 0.999,  # Extreme
+            np.zeros(m) + 1e-6,  # Extreme
             np.random.rand(m),  # Random
         ]
         mus = [
-            np.zeros(m) + 0.01, # Equal recombination and mutation
-            np.zeros(m) + 0.33, # Extreme
-            np.zeros(m) + 1e-6, # Extreme
-            np.random.rand(m) * 0.33,   # Random
+            np.zeros(m) + 0.01,  # Equal recombination and mutation
+            np.zeros(m) + 0.33,  # Extreme
+            np.zeros(m) + 1e-6,  # Extreme
+            np.random.rand(m) * 0.33,  # Random
         ]
         for s, r, mu in itertools.product(genotypes, rs, mus):
             r[0] = 0
             e = self.get_emission_matrix_diploid(mu, m)
             yield n, m, G, s, e, r, mu
 
-    def get_examples_pars_larger_diploid(
-        self, ts, mean_r=1e-5, mean_mu=1e-5, seed=42
-    ):
+    def get_examples_pars_larger_diploid(self, ts, mean_r=1e-5, mean_mu=1e-5, seed=42):
         np.random.seed(seed)
         H, G, genotypes = self.get_examples_diploid(ts)
         m = H.shape[0]