Fix-up fixable tests

Author: jeromekelleher

sc2ts/inference.py

@@ -503,7 +503,7 @@ def add_matching_results(
     date,
     num_mismatches,
     max_hmm_cost,
-    min_group_size,
+    min_group_size=1,
     show_progress=False,
 ):
     if num_mismatches is None:
@@ -611,7 +611,7 @@ def add_matching_results(
     # print(ts.draw_text())
     ts = coalesce_mutations(ts, attach_nodes)
 
-    return ts, excluded_samples, added_samples
+    return ts # , excluded_samples, added_samples
 
 
 def fetch_samples_from_pickle_file(date, num_past_days=None, in_dir=None):

tests/test_inference.py

@@ -8,12 +8,11 @@
 import util
 
 
-@pytest.mark.skip("add_matching_results broken")
 class TestAddMatchingResults:
     def add_matching_results(
         self, samples, ts, date="2020-01-01", num_mismatches=None, max_hmm_cost=None
     ):
-        ts2, _ = sc2ts.add_matching_results(
+        ts2 = sc2ts.add_matching_results(
             samples=samples,
             ts=ts,
             date=date,
@@ -77,7 +76,7 @@ def test_one_sample_recombinant_filtered(self):
         x = L / 2
         samples = util.get_samples(ts, [[(0, x, 2), (x, L, 3)]])
         # Note that it is calling the function in the main module.
-        ts2, _ = sc2ts.add_matching_results(
+        ts2 = sc2ts.add_matching_results(
             samples, ts, "2021", num_mismatches=1e3, max_hmm_cost=1e3 - 1
         )
         assert ts2.num_trees == 1
@@ -98,7 +97,7 @@ def test_two_samples_recombinant_one_filtered(self):
             ],  # Filtered
         ]
         samples = util.get_samples(ts, new_paths)
-        ts2, _ = sc2ts.add_matching_results(
+        ts2 = sc2ts.add_matching_results(
             samples, ts, "2021", num_mismatches=3, max_hmm_cost=4
         )
         assert ts2.num_trees == 2
@@ -125,7 +124,7 @@ def test_one_sample_one_mutation_filtered(self):
         samples = util.get_samples(
             ts, [[(0, ts.sequence_length, 1)]], mutations=[[(0, "X")]]
         )
-        ts2, _ = sc2ts.add_matching_results(
+        ts2 = sc2ts.add_matching_results(
             samples, ts, "2021", num_mismatches=0.0, max_hmm_cost=0.0
         )
         assert ts2.num_trees == ts.num_trees
@@ -149,7 +148,7 @@ def test_two_samples_one_mutation_one_filtered(self):
             paths=new_paths,
             mutations=new_mutations,
         )
-        ts2, _ = sc2ts.add_matching_results(
+        ts2= sc2ts.add_matching_results(
             samples, ts, "2021", num_mismatches=3, max_hmm_cost=1
         )
         assert ts2.num_trees == ts.num_trees

tests/test_utils.py

@@ -18,7 +18,6 @@ def test_initial(self):
         self.check_site_padding(sc2ts.initial_ts())
 
 
-@pytest.mark.skip("match_tsinfer broken")
 class TestDetachSingletonRecombinants:
     def make_recombinant_tree(self, num_samples=1):
         # Make a tree sequence by adding num_samples samples under a
@@ -35,7 +34,7 @@ def make_recombinant_tree(self, num_samples=1):
         L = ts.sequence_length
         x = L / 2
         samples = util.get_samples(ts, [[(0, x, 2), (x, L, 3)]] * num_samples)
-        ts_rec, _ = sc2ts.add_matching_results(
+        ts_rec = sc2ts.add_matching_results(
             samples, ts, "2021", num_mismatches=None, max_hmm_cost=None
         )
         assert ts_rec.num_trees == 2