Merge pull request #2826 from jeromekelleher/test_infrastructure_maint

Test infrastructure maint

Author: jeromekelleher

.github/workflows/tests.yml

@@ -60,7 +60,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: [ 3.7, 3.9, "3.11" ]
+        python: [ 3.8, 3.9, "3.11" ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:

python/tests/test_highlevel.py

@@ -4625,7 +4625,7 @@ class TestSeekDirection:
     def ts(self):
         return tsutil.all_trees_ts(3)
 
-    def setup(self):
+    def get_tree_pair(self):
         ts = self.ts()
         t1 = tskit.Tree(ts)
         t2 = tskit.Tree(ts)
@@ -4638,7 +4638,7 @@ def setup(self):
     def test_index_from_different_directions(self, index):
         # Check that we get different orderings of the children arrays
         # for all trees when we go in different directions.
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         while t1.index != index:
             t1.next()
         while t2.index != index:
@@ -4647,7 +4647,7 @@ def test_index_from_different_directions(self, index):
 
     @pytest.mark.parametrize("position", [0, 1, 2, 3])
     def test_seek_from_null(self, position):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         t1.clear()
         t1.seek(position)
         t2.first()
@@ -4656,7 +4656,7 @@ def test_seek_from_null(self, position):
 
     @pytest.mark.parametrize("index", range(3))
     def test_seek_next_tree(self, index):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         while t1.index != index:
             t1.next()
             t2.next()
@@ -4666,7 +4666,7 @@ def test_seek_next_tree(self, index):
 
     @pytest.mark.parametrize("index", [3, 2, 1])
     def test_seek_prev_tree(self, index):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         while t1.index != index:
             t1.prev()
             t2.prev()
@@ -4675,52 +4675,52 @@ def test_seek_prev_tree(self, index):
         assert_trees_identical(t1, t2)
 
     def test_seek_1_from_0(self):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         t1.first()
         t1.next()
         t2.first()
         t2.seek(1)
         assert_trees_identical(t1, t2)
 
     def test_seek_1_5_from_0(self):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         t1.first()
         t1.next()
         t2.first()
         t2.seek(1.5)
         assert_trees_identical(t1, t2)
 
     def test_seek_1_5_from_1(self):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         for _ in range(2):
             t1.next()
             t2.next()
         t2.seek(1.5)
         assert_trees_identical(t1, t2)
 
     def test_seek_3_from_null(self):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         t1.last()
         t2.seek(3)
         assert_trees_identical(t1, t2)
 
     def test_seek_3_from_null_prev(self):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         t1.last()
         t1.prev()
         t2.seek(3)
         t2.prev()
         assert_trees_identical(t1, t2)
 
     def test_seek_3_from_0(self):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         t1.last()
         t2.first()
         t2.seek(3)
         assert_trees_identical(t1, t2)
 
     def test_seek_0_from_3(self):
-        t1, t2 = self.setup()
+        t1, t2 = self.get_tree_pair()
         t1.last()
         t1.first()
         t2.last()

python/tests/tsutil.py

@@ -201,7 +201,7 @@ def insert_multichar_mutations(ts, seed=1, max_len=10):
 
 
 def insert_random_ploidy_individuals(
-    ts, min_ploidy=0, max_ploidy=5, max_dimension=3, samples_only=False, seed=1
+    ts, min_ploidy=0, max_ploidy=5, max_dimension=3, samples_only=True, seed=1
 ):
     """
     Takes random contiguous subsets of the samples and assigns them to individuals.