WIP

tests/lsbase.py

@@ -160,8 +160,6 @@ def get_examples_parameters_diploid(self, ts, seed=42):
         rs = [np.zeros(m) + 0.999, np.zeros(m) + 1e-6, np.random.rand(m)]
         mus = [np.zeros(m) + 0.33, np.zeros(m) + 1e-6, np.random.rand(m) * 0.33]
 
-        e = self.get_emission_prob_matrix_diploid(mu, m)
-
         for s, r, mu in itertools.product(genotypes, rs, mus):
             r[0] = 0
             e = self.get_emission_prob_matrix_diploid(mu, m)

tests/test_API.py

@@ -1,23 +1,12 @@
-import itertools
-import pytest
-
-import numpy as np
-
-import msprime
-import tskit
-
 from . import lsbase
 import lshmm as ls
-import lshmm.core as core
 import lshmm.fb_diploid as fbd
 import lshmm.fb_haploid as fbh
 import lshmm.vit_diploid as vd
 import lshmm.vit_haploid as vh
 
 
 class TestMethodsHaploid(lsbase.FBAlgorithmBase):
-    """Test that the computed likelihood is the same across all implementations."""
-
     def test_simple_n_10_no_recombination(self):
         ts = self.get_simple_n_10_no_recombination()
         self.verify(ts)

tests/test_API_multiallelic.py

@@ -7,6 +7,22 @@
 
 
 class TestMethodsHaploid(lsbase.FBAlgorithmBase):
+    def test_multiallelic_n_10_no_recombination(self):
+        ts = self.get_multiallelic_n_10_no_recombination()
+        return ts
+
+    def test_multiallelic_n_6(self):
+        ts = self.get_multiallelic_n_6()
+        return ts
+
+    def test_multiallelic_n_8(self):
+        ts = self.get_multiallelic_n_8()
+        return ts
+
+    def test_multiallelic_n_16(self):
+        ts = self.get_multiallelic_n_16()
+        return ts
+
     def verify(self, ts):
         for n, m, H_vs, s, e_vs, r, mu in self.get_examples_parameters_haploid(ts):
             F_vs, c_vs, ll_vs = fbh.forwards_ls_hap(n, m, H_vs, s, e_vs, r)
@@ -34,6 +50,22 @@ def verify(self, ts):
 
 
 class TestViterbiHaploid(lsbase.ViterbiAlgorithmBase):
+    def test_multiallelic_n_10_no_recombination(self):
+        ts = self.get_multiallelic_n_10_no_recombination()
+        return ts
+
+    def test_multiallelic_n_6(self):
+        ts = self.get_multiallelic_n_6()
+        return ts
+
+    def test_multiallelic_n_8(self):
+        ts = self.get_multiallelic_n_8()
+        return ts
+
+    def test_multiallelic_n_16(self):
+        ts = self.get_multiallelic_n_16()
+        return ts
+
     def verify(self, ts):
         for n, m, H_vs, s, e_vs, r, mu in self.get_examples_parameters_haploid(ts):
             V_vs, P_vs, ll_vs = vh.forwards_viterbi_hap_lower_mem_rescaling(