version bump

CHANGELOG.rst

@@ -1,5 +1,5 @@
 ***************************
-[1.0.2] - 2023-06-20
+[1.0.3] - 2023-06-21
 ***************************
 
 **Bugfixes**:
@@ -17,6 +17,12 @@
     are not at the same time as the others. (:user:`petrelharp`, :pr:`308`)
 
 
+***************************
+[1.0.2] - 2023-06-20
+***************************
+
+This was a bugfix release that was pushed out without the actual bug fix.
+Please don't use this one.
 
 ***************************
 [1.0.1] - 2022-09-23

pyslim/_version.py

@@ -1,5 +1,5 @@
 # coding: utf-8
-pyslim_version = '1.0.2'
+pyslim_version = '1.0.3'
 slim_file_version = '0.8'
 # other file versions that require no modification
 compatible_slim_file_versions = ['0.8']

pyslim/methods.py

@@ -92,10 +92,7 @@ def recapitate(ts,
         # since that's when all the linages are at, and otherwise the event
         # won't apply to them
         demography.add_population_split(
-                np.nextafter(
-                    ts.metadata['SLiM']['tick'],
-                    2 * ts.metadata['SLiM']['tick'],
-                ),
+                np.nextafter( recap_time, 2 * recap_time),
                 derived=derived_names,
                 ancestral=ancestral_name,
         )

tests/test_tree_sequence.py

@@ -4,6 +4,7 @@
 import random
 import numpy as np
 import os
+import json
 
 import pytest
 import tskit
@@ -88,7 +89,7 @@ class TestRecapitate(tests.PyslimTestCase):
     Tests for recapitation.
     '''
 
-    def check_recap_consistency(self, ts, recap):
+    def check_recap_consistency(self, ts, recap, with_ancestral_Ne=True):
         assert ts.metadata['SLiM']['tick'] == recap.metadata['SLiM']['tick']
         assert ts.metadata['SLiM']['cycle'] == recap.metadata['SLiM']['cycle']
         assert ts.metadata['SLiM']['stage'] == recap.metadata['SLiM']['stage']
@@ -98,6 +99,26 @@ def check_recap_consistency(self, ts, recap):
         if ts.has_reference_sequence():
             assert ts.reference_sequence.data == recap.reference_sequence.data
 
+        root_times = list(set([ts.node(n).time for t in ts.trees() for n in t.roots]))
+        assert len(root_times) == 1
+        if with_ancestral_Ne:
+            # check that time recorded in provenance is correct
+            assert recap.num_provenances == 2
+            recap_prov = json.loads(recap.provenance(1).record)
+            recap_events = recap_prov['parameters']['demography']['events']
+            assert len(recap_events) == 1
+            recap_time = recap_events[0]['time']
+            assert np.allclose(recap_time, root_times[0])
+            # the oldest nodes in all trees with SLiM provenance should be at that time
+            if recap.num_nodes <= 500: # takes a long time otherwise
+                for t in recap.trees():
+                    for n in t.nodes():
+                        rn = recap.node(n)
+                        if rn.metadata is not None:
+                            p = t.parent(n)
+                            if p == tskit.NULL or recap.node(p).metadata is None:
+                                assert rn.time == root_times[0]
+
         ts_samples = list(ts.samples())
         for u in recap.samples():
             n1 = recap.node(u)
@@ -218,7 +239,7 @@ def test_with_demography(self, recipe):
                 extra_metadata={"slim_id": ts.num_populations},
         )
         demography.add_population_split(
-                time=ts.metadata["SLiM"]["tick"] + 1.0,
+                time=ts.metadata["SLiM"]["tick"] + 20.0,
                 derived=[p.name for p in demography.populations if p.name != "ancestral"],
                 ancestral="ancestral",
         )
@@ -228,7 +249,7 @@ def test_with_demography(self, recipe):
                 recombination_rate=recomb_rate,
                 random_seed=333,
         )
-        self.check_recap_consistency(ts, recap)
+        self.check_recap_consistency(ts, recap, with_ancestral_Ne=False)
 
     @pytest.mark.parametrize('recipe', recipe_eq(exclude="long"), indirect=True)
     def test_first_gen_nodes(self, recipe):