Allow Demography init from provenance with preset pop IDs

CHANGELOG.md

@@ -3,6 +3,10 @@
 
 ## [1.3.5] - 2025-XX-XX
 
+**New features**
+
+- Demography objects can now be created from provenance entries ({pr}`{2369}, {user}`hyanwong`)
+
 **Breaking changes**:
 
 - The `.asdict()` methods for Demography, Population, and Event classes in the

msprime/provenance.py

@@ -31,6 +31,7 @@
 import tskit
 
 from . import ancestry
+from . import demography
 from msprime import _msprime
 
 __version__ = "undefined"
@@ -188,10 +189,21 @@ def hook(obj):
             elif "__npgeneric__" in obj:
                 return numpy.array([obj["__npgeneric__"]]).astype(obj["dtype"])[0]
             elif "__class__" in obj:
-                module, cls = obj["__class__"].rsplit(".", 1)
+                module, cls = obj.pop("__class__").rsplit(".", 1)
                 module = importlib.import_module(module)
-                del obj["__class__"]
-                return getattr(module, cls)(**obj)
+                cls = getattr(module, cls)
+                if cls == demography.Demography:
+                    # the Demography class normally generates its own population IDs, but
+                    # allow fixed IDs here to ensure they match e.g. IDs in event objects
+                    demography_object = object.__new__(cls)
+                    try:
+                        demography_object.__init__(**obj)
+                    except ValueError as e:
+                        if str(e).startswith("Population ID should not be set"):
+                            return demography_object  # This is the allowed fixed ID err
+                        else:
+                            raise
+                return cls(**obj)
             return obj
 
         return json.JSONDecoder(object_hook=hook).decode(s)

tests/test_provenance.py

@@ -244,6 +244,39 @@ def test_current_ts(self):
         assert command == "sim_mutations"
         assert prov["tree_sequence"] == ts1
 
+    def test_demography(self):
+        demography = msprime.Demography.island_model([1, 1], 1 / 3)
+        ts = msprime.sim_ancestry(
+            demography=demography,
+            samples=[
+                msprime.SampleSet(1, population=0),
+                msprime.SampleSet(1, population=1),
+            ],
+            random_seed=3,
+        )
+        command, prov = msprime.provenance.parse_provenance(ts.provenance(-1), ts)
+        assert command == "sim_ancestry"
+        assert prov["demography"] == demography
+
+    def test_bad_demography(self):
+        demography = msprime.Demography.island_model([1, 1], 1 / 3)
+        ts = msprime.sim_ancestry(
+            demography=demography,
+            samples=[
+                msprime.SampleSet(1, population=0),
+                msprime.SampleSet(1, population=1),
+            ],
+            random_seed=3,
+        )
+        prov = ts.provenance(-1)
+        record = json.loads(prov.record)
+        # Corrupt the provenance record
+        assert len(record["parameters"]["demography"]["migration_matrix"]) == 2
+        record["parameters"]["demography"]["migration_matrix"] = [1, 0, 0]
+        prov.record = json.dumps(record)
+        with pytest.raises(ValueError, match="Migration matrix must be square"):
+            msprime.provenance.parse_provenance(prov, ts)
+
 
 class TestRoundTrip:
     """