Add a __class__ key to the demography .asdict methods

And convert list input to numpy array.

The __class__ key is useful because e.g. for events, the dictionary keys aren't enough to distinguish between the event types. This also means that the classes are properly output when saving provenance, aiding reproducibility.

Author: hyanwong

msprime/demography.py

@@ -223,7 +223,9 @@ class Population:
     """
 
     def asdict(self):
-        return dataclasses.asdict(self)
+        d = dataclasses.asdict(self)
+        d["__class__"] = f"{self.__module__}.{self.__class__.__name__}"
+        return d
 
     def validate(self):
         if self.initial_size < 0:
@@ -269,6 +271,15 @@ def __post_init__(self):
         if self.migration_matrix is None:
             N = self.num_populations
             self.migration_matrix = np.zeros((N, N))
+        else:
+            # convert to a numpy array if it's not already
+            if not isinstance(self.migration_matrix, np.ndarray):
+                self.migration_matrix = np.array(self.migration_matrix)
+        if self.events is not None:
+            for event in self.events:
+                if not isinstance(event, DemographicEvent):
+                    raise TypeError("Events must be instances of DemographicEvent")
+                event.demography = self
 
         # People might get cryptic errors from passing in copies of the same
         # population, so check for it.
@@ -1196,6 +1207,8 @@ def asdict(self):
             "populations": [pop.asdict() for pop in self.populations],
             "events": [event.asdict() for event in self.events],
             "migration_matrix": self.migration_matrix.tolist(),
+            "__class__": f"{self.__module__}.{self.__class__.__name__}",
+
         }
 
     def debug(self):
@@ -2882,6 +2895,8 @@ def asdict(self):
             initial_size=self.initial_size,
             growth_rate=self.growth_rate,
             metadata=self.metadata,
+            __class__=f"{self.__module__}.{self.__class__.__name__}",
+
         )
 
 
@@ -2914,11 +2929,14 @@ def _effect(self):
         raise NotImplementedError()
 
     def asdict(self):
-        return {
+        deprecated = {"population_id", "matrix_index", "destination"}
+        d = {
             key: getattr(self, key)
             for key in inspect.signature(self.__init__).parameters.keys()
-            if hasattr(self, key)
+            if hasattr(self, key) and key not in deprecated
         }
+        d["__class__"] = f"{self.__module__}.{self.__class__.__name__}"
+        return d
 
     def _convert_id(self, population_ref):
         """