Update lshmm requirement to 0.0.5

Also update changed parameter names for lshmm 0.0.5

Author: jeromekelleher

c/tskit/haplotype_matching.c

@@ -1126,6 +1126,8 @@ tsk_ls_hmm_process_site_backward(tsk_ls_hmm_t *self, const tsk_site_t *site,
      * immediately before calling store_site in order to filter out -1 nodes,
      * and also (crucially) to ensure that the value transitions are listed
      * in preorder, which we rely on later for decoding.
+     *
+     * https://github.com/tskit-dev/tskit/issues/2803
      */
     ret = tsk_ls_hmm_compress(self);
     if (ret != 0) {

python/requirements/CI-complete/requirements.txt

@@ -3,7 +3,7 @@ coverage==7.2.7
 dendropy==4.6.1
 h5py==3.9.0
 kastore==0.3.2
-lshmm==0.0.4
+lshmm==0.0.5
 msgpack==1.0.5
 msprime==1.2.0
 networkx==3.1
@@ -12,4 +12,4 @@ pytest==7.4.0
 pytest-cov==4.1.0
 pytest-xdist==3.3.1
 tszip==0.2.2
-xmlunittest==0.5.0
+xmlunittest==0.5.0

python/requirements/CI-tests-pip/requirements.txt

@@ -1,4 +1,4 @@
-lshmm==0.0.4
+lshmm==0.0.5
 numpy==1.21.6; python_version < '3.11' # Held at 1.21.6 for Python 3.7 compatibility
 numpy==1.24.1; python_version > '3.10'
 pytest==7.1.3
@@ -12,4 +12,4 @@ dendropy==4.5.2
 networkx==2.6.3 # Held at 2.6.3 for Python 3.7 compatibility
 msgpack==1.0.4
 newick==1.3.2
-tszip==0.2.2
+tszip==0.2.2

python/requirements/development.txt

@@ -10,7 +10,7 @@ h5py>=2.6.0
 jsonschema>=3.0.0
 jupyter-book>=0.12.1
 kastore
-lshmm
+lshmm>=0.0.5
 matplotlib
 meson>=0.61.0
 msgpack>=1.0.0

python/tests/test_genotype_matching_fb.py

@@ -953,7 +953,7 @@ def verify(self, ts):
                 np.flip(G_check, axis=0),
                 np.flip(s, axis=1),
                 r_flip,
-                mutation_rate=np.flip(mu),
+                p_mutation=np.flip(mu),
                 scale_mutation_based_on_n_alleles=False,
             )
 
@@ -978,7 +978,7 @@ def verify(self, ts):
                 )
 
             F, c, ll = ls.forwards(
-                G_check, s, r, mutation_rate=mu, scale_mutation_based_on_n_alleles=False
+                G_check, s, r, p_mutation=mu, scale_mutation_based_on_n_alleles=False
             )
             cm_d = ls_forward_tree(s[0, :], ts_check, r, mu)
             self.assertAllClose(cm_d.decode(), F)
@@ -1004,14 +1004,14 @@ def verify(self, ts):
                 )
 
             F, c, ll = ls.forwards(
-                G_check, s, r, mutation_rate=mu, scale_mutation_based_on_n_alleles=False
+                G_check, s, r, p_mutation=mu, scale_mutation_based_on_n_alleles=False
             )
             B = ls.backwards(
                 G_check,
                 s,
                 c,
                 r,
-                mutation_rate=mu,
+                p_mutation=mu,
                 scale_mutation_based_on_n_alleles=False,
             )
 

python/tests/test_genotype_matching_viterbi.py

@@ -1055,14 +1055,14 @@ def verify(self, ts):
                 )
             ts_check = ts.simplify(range(1, n + 1), filter_sites=False)
             phased_path, ll = ls.viterbi(
-                G_check, s, r, mutation_rate=mu, scale_mutation_based_on_n_alleles=False
+                G_check, s, r, p_mutation=mu, scale_mutation_based_on_n_alleles=False
             )
             path_ll_matrix = ls.path_ll(
                 G_check,
                 s,
                 phased_path,
                 r,
-                mutation_rate=mu,
+                p_mutation=mu,
                 scale_mutation_based_on_n_alleles=False,
             )
 
@@ -1077,7 +1077,7 @@ def verify(self, ts):
                 s,
                 np.transpose(path_tree_dict),
                 r,
-                mutation_rate=mu,
+                p_mutation=mu,
                 scale_mutation_based_on_n_alleles=False,
             )
 

python/tests/test_haplotype_matching.py

@@ -455,6 +455,7 @@ def compute_next_probability(self, site_id, p_next, is_match, node):
     def process_site(self, site, haplotype_state, s):
         # FIXME see nodes in the C code for why we have two calls to
         # compress
+        # https://github.com/tskit-dev/tskit/issues/2803
         self.compress()
         self.output.store_site(
             site.id,
@@ -928,7 +929,7 @@ def verify(self, ts):
                 np.flip(H, axis=0),
                 np.flip(s, axis=1),
                 r_flip,
-                mutation_rate=np.flip(mu),
+                p_mutation=np.flip(mu),
                 scale_mutation_based_on_n_alleles=False,
             )
 
@@ -952,7 +953,7 @@ def verify(self, ts):
                         H,
                         s,
                         r,
-                        mutation_rate=mu,
+                        p_mutation=mu,
                         scale_mutation_based_on_n_alleles=scale_mutation,
                     )
                 # Note, need to remove the first sample from the ts, and ensure
@@ -977,14 +978,14 @@ class TestForwardBackwardTree(FBAlgorithmBase):
     def verify(self, ts):
         for n, H, s, r, mu in self.example_parameters_haplotypes(ts):
             F, c, ll = ls.forwards(
-                H, s, r, mutation_rate=mu, scale_mutation_based_on_n_alleles=False
+                H, s, r, p_mutation=mu, scale_mutation_based_on_n_alleles=False
             )
             B = ls.backwards(
                 H,
                 s,
                 c,
                 r,
-                mutation_rate=mu,
+                p_mutation=mu,
                 scale_mutation_based_on_n_alleles=False,
             )
 
@@ -1017,7 +1018,7 @@ class TestTreeViterbiHap(VitAlgorithmBase):
     def verify(self, ts):
         for n, H, s, r, mu in self.example_parameters_haplotypes(ts):
             path, ll = ls.viterbi(
-                H, s, r, mutation_rate=mu, scale_mutation_based_on_n_alleles=False
+                H, s, r, p_mutation=mu, scale_mutation_based_on_n_alleles=False
             )
             ts_check = ts.simplify(range(1, n + 1), filter_sites=False)
             cm = ls_viterbi_tree(s[0, :], ts_check, r, mu)
@@ -1032,7 +1033,7 @@ def verify(self, ts):
                 s,
                 path_tree,
                 r,
-                mutation_rate=mu,
+                p_mutation=mu,
                 scale_mutation_based_on_n_alleles=False,
             )
             self.assertAllClose(ll, ll_check)
@@ -1055,7 +1056,7 @@ def check_viterbi(ts, h, recombination=None, mutation=None):
         G,
         h.reshape(1, m),
         recombination,
-        mutation_rate=mutation,
+        p_mutation=mutation,
         scale_mutation_based_on_n_alleles=False,
     )
     assert np.isscalar(ll)
@@ -1073,7 +1074,7 @@ def check_viterbi(ts, h, recombination=None, mutation=None):
         h.reshape(1, m),
         path_tree,
         recombination,
-        mutation_rate=mutation,
+        p_mutation=mutation,
         scale_mutation_based_on_n_alleles=False,
     )
     nt.assert_allclose(ll_check, ll)
@@ -1109,7 +1110,7 @@ def check_forward_matrix(ts, h, recombination=None, mutation=None):
         G,
         h.reshape(1, m),
         recombination,
-        mutation_rate=mutation,
+        p_mutation=mutation,
         scale_mutation_based_on_n_alleles=False,
     )
     assert F.shape == (m, n)
@@ -1154,7 +1155,7 @@ def check_backward_matrix(ts, h, forward_cm, recombination=None, mutation=None):
         h.reshape(1, m),
         forward_cm.normalisation_factor,
         recombination,
-        mutation_rate=mutation,
+        p_mutation=mutation,
         scale_mutation_based_on_n_alleles=False,
     )