Change tskit_tools.MutationMetadata to "union typed" metadata.

tskit_tools.decode_mutation_metadata allows for None

Add test of decoding empty/None metadata from msprime.mutate
(Tests only run on 3.7 or later due to issues with msprime < 1.0)

fwdpy11/tskit_tools/metadata.py

@@ -21,7 +21,7 @@
 import attr
 import tskit
 
-from .._fwdpy11 import Mutation, MutationVector
+from .._fwdpy11 import Mutation
 from ._flags import (INDIVIDUAL_IS_ALIVE, INDIVIDUAL_IS_FIRST_GENERATION,
                      INDIVIDUAL_IS_PRESERVED)
 
@@ -108,41 +108,51 @@ def decode_individual_metadata(tc: tskit.TableCollection):
     return rv
 
 
-def decode_mutation_metadata(tc: tskit.TableCollection) -> MutationVector:
+def decode_mutation_metadata(
+    tc: tskit.TableCollection,
+) -> typing.List[typing.Optional[Mutation]]:
     """
-    Decodes a :class:`tskit.MutationTable`.
+    Decodes metadata from a :class:`tskit.MutationTable`.
 
     :param tc: A table collection
     :type tc: :class:`tskit.TableCollection`
 
     :returns: Mutations
-    :rtype: :class:`fwdpy11.MutationVector`
+    :rtype: list
 
     .. versionadded:: 0.12.0
+
+    .. versionchanged:: 0.14.2
+
+        Return type is now a list, allowing
+        some elements to be `None`.
     """
-    mutations = MutationVector()
+    mutations = []
     for m in tc.mutations:
         md = m.metadata
-        if "esizes" not in md:
-            mutations.append(
-                Mutation(
-                    pos=tc.sites.position[m.site],
-                    s=md["s"],
-                    h=md["h"],
-                    g=md["origin"],
-                    label=md["label"],
+        if md is not None:
+            if "esizes" not in md:
+                mutations.append(
+                    Mutation(
+                        pos=tc.sites.position[m.site],
+                        s=md["s"],
+                        h=md["h"],
+                        g=md["origin"],
+                        label=md["label"],
+                    )
                 )
-            )
-        else:
-            mutations.append(
-                Mutation(
-                    pos=tc.sites.position[m.site],
-                    s=md["s"],
-                    h=md["h"],
-                    g=md["origin"],
-                    esizes=md["esizes"],
-                    heffects=md["heffects"],
-                    label=md["label"],
+            else:
+                mutations.append(
+                    Mutation(
+                        pos=tc.sites.position[m.site],
+                        s=md["s"],
+                        h=md["h"],
+                        g=md["origin"],
+                        esizes=md["esizes"],
+                        heffects=md["heffects"],
+                        label=md["label"],
+                    )
                 )
-            )
+        else:
+            mutations.append(None)
     return mutations

fwdpy11/tskit_tools/metadata_schema.py

@@ -73,7 +73,7 @@
 MutationMetadata = tskit.metadata.MetadataSchema(
     {
         "codec": "struct",
-        "type": "object",
+        "type": ["object", "null"],
         "name": "Mutation metadata",
         "properties": {
             "s": {"type": "number", "binaryFormat": "d"},

tests/test_metadata_roundtrips_via_simulation.py

@@ -19,11 +19,11 @@
 
 import json
 
+import fwdpy11
+import msprime
 import numpy as np
 import pytest
 
-import fwdpy11
-
 
 @pytest.fixture
 def pdict(request):
@@ -55,6 +55,8 @@ def inception():
 @pytest.mark.parametrize("pdict", [{"simlen": 10}], indirect=["pdict"])
 @pytest.mark.parametrize("pop", [{"N": 100, "L": 1}], indirect=["pop"])
 def test_metadata_roundtrip_single_sim(rng, pdict, pop):
+    import sys
+
     params = fwdpy11.ModelParams(**pdict)
 
     r = fwdpy11.RandomAncientSamples(seed=42, samplesize=2, timepoints=[3])
@@ -63,6 +65,14 @@ def test_metadata_roundtrip_single_sim(rng, pdict, pop):
 
     ts = pop.dump_tables_to_tskit()
 
+    if sys.version_info.minor > 6:
+        # FIXME: this is a hack to avoid the test failing with msprime < 1.0
+        # add neutral mutations w/no metadata
+        ts = msprime.mutate(ts, rate=1.0, random_seed=654321)
+        # bulk decode the mutation metadata, which is all None
+        mutation_md = fwdpy11.tskit_tools.decode_mutation_metadata(ts.tables)
+        assert all([i is None for i in mutation_md])
+
     assert len(ts.tables.individuals) == pop.N + 2
     first = 0
     preserved = 0