tskit 1.0

CHANGELOG.md

@@ -4,6 +4,8 @@
 
 - Add support for Python 3.13, minimum version is now 3.10.
 
+- Make tsdate compatible with tskit 1.0.0.
+
 ## [0.2.3] - 2025-06-07
 
 **Breaking changes**

pyproject.toml

@@ -46,7 +46,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [
-    "tskit>=0.5.8",
+    "tskit>=1.0.0",
     "numpy",
     "scipy>=1.13.0",
     "numba>=0.58.1",
@@ -91,7 +91,7 @@ docs = [
     "pandas==2.3.2",
     "stdpopsim==0.3.0",
     "tsinfer==0.4.1",
-    "tskit==0.6.4",
+    "tskit==1.0.0",
     "jupyter-book==1.0.4.post1",
     "sphinx-issues==5.0.1",
     "sphinx-argparse==0.5.2",

tests/test_inference.py

@@ -415,6 +415,9 @@ def test_multiple_mutations_same_node_and_pos(self):
         tables.mutations.add_row(site=s, node=1, derived_state="1", time=1.5)
         tables.mutations.add_row(site=s, node=1, derived_state="2", time=1)
         tables.mutations.add_row(site=s, node=1, derived_state="3", time=0.5)
+        tables.sort()
+        tables.build_index()
+        tables.compute_mutation_parents()
         ts = tsdate.date(tables.tree_sequence(), mutation_rate=1)
         assert np.all(np.diff(ts.mutations_time) < 0)
         for m in ts.mutations():

tests/utility_functions.py

@@ -979,9 +979,9 @@ def single_tree_ts_2mutations_n3():
     )
     mutations = io.StringIO(
         """\
-    site    node    derived_state
-    0       3       1
-    0       1       0
+    site    node    derived_state parent
+    0       3       1             -1
+    0       1       0             0
     """
     )
     return tskit.load_text(

tsdate/evaluation.py

@@ -144,6 +144,8 @@ def remove_edges(ts, edge_id_remove_list):
                     tables.edges.append(e)
     assert len(new_edges) == 0
     tables.sort()
+    tables.build_index()
+    tables.compute_mutation_parents()
     return tables.tree_sequence()
 
 

tsdate/phasing.py

@@ -463,4 +463,6 @@ def rephase_singletons(ts, use_node_times=True, random_seed=None):
     tables.mutations.node = mutations_node
     tables.mutations.time = mutations_time
     tables.sort()
+    tables.build_index()
+    tables.compute_mutation_parents()
     return tables.tree_sequence()

tsdate/util.py

@@ -580,6 +580,8 @@ def split_disjoint_nodes(ts, *, record_provenance=None):
     # Update the mutations table
     tables.mutations.node = mutations_node
     tables.sort()
+    tables.build_index()
+    tables.compute_mutation_parents()
 
     assert np.array_equal(
         tables.nodes.time[tables.mutations.node], ts.nodes_time[ts.mutations_node]