Merge pull request #505 from grahamgower/numpy-str

Fix use of numpy strings for deme names

demes/demes.py

@@ -2369,21 +2369,27 @@ def filt(attrib, value):
                 or (not (hasattr(value, "__len__") and len(value) == 0))
             ) and attrib.name != "_deme_map"
 
-        def coerce_numbers(inst, attribute, value):
-            # Explicitly convert numeric types to int or float, so that they
+        def coerce_types(inst, attribute, value):
+            # Explicitly convert numeric and string types, so that they
             # don't cause problems for the YAML and JSON serialisers.
-            # E.g. numpy int32/int64 are part of Python's numeric tower as
+            # Numpy int32/int64 are part of Python's numeric tower as
             # subclasses of numbers.Integral, similarly numpy's float32/float64
             # are subclasses of numbers.Real. There are yet other numeric types,
             # such as the standard library's decimal.Decimal, which are not part
             # of the numeric tower, but provide a __float__() method.
-            if isinstance(value, numbers.Integral):
+            # Likewise, string subclasses such as numpy.str_ aren't recognised
+            # by the YAML serialiser, so we explicitly convert them to str.
+            # We check for 'str' first, because numpy.str_ also has a
+            # __float__() method.
+            if isinstance(value, str):
+                value = str(value)
+            elif isinstance(value, numbers.Integral):
                 value = int(value)
             elif isinstance(value, numbers.Real) or hasattr(value, "__float__"):
                 value = float(value)
             return value
 
-        data = attr.asdict(self, filter=filt, value_serializer=coerce_numbers)
+        data = attr.asdict(self, filter=filt, value_serializer=coerce_types)
         # translate to spec data model
         for deme in data["demes"]:
             for epoch in deme["epochs"]:

tests/test_load_dump.py

@@ -575,6 +575,16 @@ def test_float_subclass(self):
         )
         self.check_dump_load_roundtrip(b.resolve())
 
+    def test_str_subclass(self):
+        # Check that numpy.str_ are round-trippable.
+        b = demes.Builder(defaults=dict(epoch=dict(start_size=1)))
+        names = np.array(["a", "b"])
+        b.add_deme(names[0])
+        b.add_deme(names[1], ancestors=[names[0]], start_time=50)
+        b.add_pulse(sources=[names[0]], dest=names[1], time=10, proportions=[0.1])
+        b.add_migration(source=names[0], dest=names[1], rate=1e-3)
+        self.check_dump_load_roundtrip(b.resolve())
+
     def test_json_infinities_get_stringified(self):
         b = demes.Builder()
         b.add_deme("a", epochs=[dict(start_size=1)])