Rename TreePosition to TreeIndexes

Author: benjeffery

python/tests/test_coalrate.py

@@ -68,7 +68,7 @@ def _nonmissing_window_span(ts, windows):
     missing = 0.0
     num_edges = 0
     w = 0
-    position = tsutil.TreePosition(ts)
+    position = tsutil.TreeIndexes(ts)
     while position.interval.right < sequence_length:
         position.next()
         left, right = position.interval.left, position.interval.right
@@ -272,7 +272,7 @@ def _pair_coalescence_stat(
     sample_counts = nodes_sample.copy()
 
     w = 0
-    position = tsutil.TreePosition(ts)
+    position = tsutil.TreeIndexes(ts)
     while position.interval.right < sequence_length:
         position.next()
         left, right = position.interval.left, position.interval.right

python/tests/test_extend_haplotypes.py

@@ -414,7 +414,7 @@ def merge_paths(self, c, left, right):
         self.add_or_extend_edge(p_out, child, left, right)
 
     def extend_haplotypes(self):
-        tree_pos = tsutil.TreePosition(self.ts)
+        tree_pos = tsutil.TreeIndexes(self.ts)
         if self.direction == 1:
             valid = tree_pos.next()
         else:

python/tests/test_haplotype_matching.py

@@ -113,8 +113,8 @@ def __init__(
         self.N = np.zeros(ts.num_nodes, dtype=int)
         # Efficiently compute the allelic state at a site
         self.allelic_state = np.zeros(ts.num_nodes, dtype=int) - 1
-        # TreePosition so we can can update T and T_index between trees.
-        self.tree_pos = tsutil.TreePosition(ts)
+        # TreeIndexes so we can can update T and T_index between trees.
+        self.tree_pos = tsutil.TreeIndexes(ts)
         self.parent = np.zeros(self.ts.num_nodes, dtype=int) - 1
         self.tree = tskit.Tree(self.ts)
         self.output = None

python/tests/test_ld_matrix.py

@@ -1769,7 +1769,7 @@ class TreeState:
     enables easy copying of the state for computing a matrix.
     """
 
-    pos: tsutil.TreePosition  # current position in the tree sequence
+    pos: tsutil.TreeIndexes  # current position in the tree sequence
     parent: np.ndarray  # parent node of a given node (connected by an edge)
     branch_len: np.ndarray  # length of the branch above a particular child node
     node_samples: BitSet  # samples that exist under a given node, this is a
@@ -1784,7 +1784,7 @@ class TreeState:
     edges_in: List[int]  # list of edges added during iteration
 
     def __init__(self, ts, sample_sets, num_sample_sets, sample_index_map):
-        self.pos = tsutil.TreePosition(ts)
+        self.pos = tsutil.TreeIndexes(ts)
         self.parent = -np.ones(ts.num_nodes, dtype=np.int64)
         self.branch_len = np.zeros(ts.num_nodes, dtype=np.float64)
         self.node_samples = BitSet(ts.num_samples, ts.num_nodes * num_sample_sets)

python/tests/test_relatedness_vector.py

@@ -297,7 +297,7 @@ def relatedness_vector(ts, sample_weights, windows=None, nodes=None, **kwargs):
     if drop_dimension:
         windows = [0, ts.sequence_length]
 
-    tree_pos = tsutil.TreePosition(ts)
+    tree_pos = tsutil.TreeIndexes(ts)
     breakpoints = np.fromiter(ts.breakpoints(), dtype="float")
     index = np.searchsorted(breakpoints, windows[0])
     if breakpoints[index] > windows[0]:

python/tests/test_tree_positioning.py

@@ -44,7 +44,7 @@ class StatefulTree:
 
     def __init__(self, ts):
         self.ts = ts
-        self.tree_pos = tsutil.TreePosition(ts)
+        self.tree_pos = tsutil.TreeIndexes(ts)
         self.parent = [-1 for _ in range(ts.num_nodes)]
 
     def __str__(self):
@@ -158,7 +158,7 @@ def iter_backward(self, index):
 def check_iters_forward(ts):
     alg_t_output = tsutil.algorithm_T(ts)
     lib_tree = tskit.Tree(ts)
-    tree_pos = tsutil.TreePosition(ts)
+    tree_pos = tsutil.TreeIndexes(ts)
     sample_count = np.zeros(ts.num_nodes, dtype=int)
     sample_count[ts.samples()] = 1
     parent1 = [-1 for _ in range(ts.num_nodes)]
@@ -208,7 +208,7 @@ def check_iters_back(ts):
     i = len(alg_t_output) - 1
 
     lib_tree = tskit.Tree(ts)
-    tree_pos = tsutil.TreePosition(ts)
+    tree_pos = tsutil.TreeIndexes(ts)
     parent1 = [-1 for _ in range(ts.num_nodes)]
 
     lib_tree.last()
@@ -422,35 +422,35 @@ def test_seek_backward_out_range_is_empty(self, index):
         check_seek_backward_out_range_is_empty(ts, index)
 
 
-class TestTreePositionStep:
+class TestTreeIndexesStep:
     def ts(self):
         return tsutil.all_trees_ts(3)
 
     @pytest.mark.parametrize("index", [0, 1, 2])
     def test_tree_position_step_forward(self, index):
         ts = self.ts()
-        tree1_pos = tsutil.TreePosition(ts)
+        tree1_pos = tsutil.TreeIndexes(ts)
         tree1_pos.seek_forward(index)
         tree1_pos.step(direction=1)
-        tree2_pos = tsutil.TreePosition(ts)
+        tree2_pos = tsutil.TreeIndexes(ts)
         tree2_pos.seek_forward(index + 1)
         tree1_pos.assert_equal(tree2_pos)
 
     @pytest.mark.parametrize("index", [1, 2, 3])
     def test_tree_position_step_backward(self, index):
         ts = self.ts()
-        tree1_pos = tsutil.TreePosition(ts)
+        tree1_pos = tsutil.TreeIndexes(ts)
         tree1_pos.seek_backward(index)
         tree1_pos.step(direction=-1)
-        tree2_pos = tsutil.TreePosition(ts)
+        tree2_pos = tsutil.TreeIndexes(ts)
         tree2_pos.seek_backward(index - 1)
         tree1_pos.assert_equal(tree2_pos)
 
     def test_tree_position_step_invalid_direction(self):
         ts = self.ts()
         # Test for unallowed direction
         with pytest.raises(ValueError, match="Direction must be FORWARD"):
-            tsutil.TreePosition(ts).step(direction="foo")
+            tsutil.TreeIndexes(ts).step(direction="foo")
 
 
 class TestSeeking:

python/tests/tsutil.py

@@ -1737,7 +1737,7 @@ class EdgeRange:
     order: typing.List
 
 
-class TreePosition:
+class TreeIndexes:
     def __init__(self, ts):
         self.ts = ts
         self.index = -1