update tskit schema for individual metadata

molpopgen · Aug 16, 2023 · 162711b · 162711b
1 parent a928e37
commit 162711b
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Showing 3 changed files with 6 additions and 0 deletions.
diff --git a/fwdpy11/_types/diploid_population.py b/fwdpy11/_types/diploid_population.py
@@ -165,6 +165,7 @@ def liftover(input, output):
                     output['nodes'][i] = input[i].nodes
                     output['geography'][i] = input[i].geography
                     output['label'][i] = input[i].label
+                    output['id'][i] = input[i].id
             decoded_md = fwdpy11.tskit_tools.decode_individual_metadata(ts)
             # Take a writeable VIEW of the C++-side data...
             md = np.array(ll._diploid_metadata, copy=False)

diff --git a/fwdpy11/tskit_tools/metadata.py b/fwdpy11/tskit_tools/metadata.py
@@ -48,6 +48,8 @@ class DiploidMetadata(object):
     :type deme: int
     :param label: Index in the population at time of living/sampling
     :type label: int
+    :param id: Unique identifier for this individual
+    :type id: int
     :param alive: Individual is alive
     :type alive: bool
     :param preserved: Individual is preserved
@@ -70,6 +72,7 @@ class DiploidMetadata(object):
     sex: int
     deme: int
     label: int
+    id: int
     alive: bool = attr.ib(converter=bool)
     preserved: bool = attr.ib(converter=bool)
     first_generation: bool = attr.ib(converter=bool)

diff --git a/fwdpy11/tskit_tools/metadata_schema.py b/fwdpy11/tskit_tools/metadata_schema.py
@@ -71,6 +71,7 @@
             "sex": {"type": "number", "binaryFormat": "i"},
             "deme": {"type": "number", "binaryFormat": "i"},
             "label": {"type": "number", "binaryFormat": "Q"},
+            "id": {"type": "number", "binaryFormat": "L"},
             "parents": {
                 "type": "array",
                 "items": {"type": "number", "binaryFormat": "Q"},
@@ -154,6 +155,7 @@ def generate_individual_metadata(
         "sex": metadata.sex,
         "deme": metadata.deme,
         "label": metadata.label,
+        "id": metadata.id,
     }
     return d