Merge branch 'experiments' of github-personal:Lagergren-Lab/victree i…

…nto experiments

src/inference/victree.py

@@ -535,12 +535,13 @@ def make_input(data: anndata.AnnData | str, cc_layer: str | None = 'copy',
     # default params
     tree_nodes = n_nodes if fix_tree is None else fix_tree.number_of_nodes()
     obs_bins, obs_cells = obs.shape
+    qT_temp = 1. if fix_tree is not None else obs_bins
 
     if config is None:
         config = Config(chain_length=obs_bins, n_cells=obs_cells, n_nodes=tree_nodes,
                         chromosome_indexes=dh.get_chr_idx(), debug=debug, step_size=step_size,
                         sieving_size=sieving[0], n_sieving_iter=sieving[1], wis_sample_size=wis_sample_size,
-                        split=split, qT_temp=obs_bins)
+                        split=split, qT_temp=qT_temp)
     else:
         config.chromosome_indexes = dh.get_chr_idx()
 

tests/test_vardists/test_qc.py

@@ -91,6 +91,7 @@ def test_entropy_lower_for_random_transitions_than_uniform_transitions(self):
         print(f"Entropy random eta_2: {rand_res} - uniform eta_2: {uniform_res}")
         self.assertLess(rand_res, uniform_res)
 
+    @unittest.skip("wrong code")
     def test_cross_entropy_lower_for_random_transitions_than_deterministic_transitions(self):
         K = 3
         M = 5
@@ -103,6 +104,7 @@ def test_cross_entropy_lower_for_random_transitions_than_deterministic_transitio
         cross_entropy_rand = qc_1.neg_cross_entropy_arc(q_eps, 0, 1)
         print(f"Random: {cross_entropy_rand}")
         qc_2 = qC(config_1).initialize()
+        # FIXME: m goes over two cycles but only used once
         for k in range(K):
             for m in range(M - 1):
                 qc_2.eta1 = torch.log(torch.zeros(K, A) + 0.001)