Add custom json encoder and decoder

zarr/meta.py

@@ -166,6 +166,9 @@ def encode_fill_value(v, dtype):
     if v is None:
         return v
     if dtype.kind == 'f':
+        # these cases are handled in the ZarrJsonEncoder now,
+        # but there may be cases where the metadata was not parsed
+        # with this encoder (?), so better to leave it here
         if np.isnan(v):
             return 'NaN'
         elif np.isposinf(v):

zarr/tests/test_attrs.py

@@ -4,6 +4,7 @@
 
 import pytest
 
+import numpy as np
 from zarr.attrs import Attributes
 from zarr.tests.util import CountingDict
 
@@ -218,3 +219,15 @@ def test_caching_off(self):
         assert 'spam' not in a
         assert 10 == store.counter['__getitem__', 'attrs']
         assert 3 == store.counter['__setitem__', 'attrs']
+
+    def test_special_values(self):
+        a = self.init_attributes(dict())
+
+        a['nan'] = np.nan
+        assert np.isnan(a['nan'])
+
+        a['pinf'] = np.PINF
+        assert np.isposinf(a['pinf'])
+
+        a['ninf'] = np.NINF
+        assert np.isneginf(a['ninf'])

zarr/util.py

@@ -19,15 +19,44 @@
 }
 
 
+class ZarrJsonEncoder(JsonEncoder):
+    """Encode json input
+    """
+    def default(self, obj):
+        if np.isnan(obj):
+            return "NaN"
+        elif np.isposinf(obj):
+            return "Infinity"
+        elif np.isneginf(obj):
+            return "-Infinity"
+        # we could also allow for passing numpy dtypes:
+        # if isinstance(obj, np.dtype):
+        #    return obj.item()
+        return super().default(obj)
+
+
+class ZarrJsonDecoder(JsonEncoder):
+    """Decode json input
+    """
+    def default(self, obj):
+        if obj == "NaN":
+            return np.nan
+        elif obj == "Infinity":
+            return np.PINF
+        elif obj == "-Infinity":
+            return np.NINF
+        return super().default(obj)
+
+
 def json_dumps(o):
     """Write JSON in a consistent, human-readable way."""
     return json.dumps(o, indent=4, sort_keys=True, ensure_ascii=True,
-                      separators=(',', ': ')).encode('ascii')
+                      separators=(',', ': '), cls=ZarrJsonEncoder).encode('ascii')
 
 
 def json_loads(s):
     """Read JSON in a consistent way."""
-    return json.loads(ensure_text(s, 'ascii'))
+    return json.loads(ensure_text(s, 'ascii'), cls=ZarrJsonDecoder)
 
 
 def normalize_shape(shape):