updated read_hdf() --> create a new HDFStore only if arg filepath_or_buffer is not already an HDFStore

Author: alixdamman

larray/inout/array.py

@@ -496,31 +496,40 @@ def read_hdf(filepath_or_buffer, key, fill_value=np.nan, na=np.nan, sort_rows=Fa
 
     key = _translate_key_hdf(key)
     res = None
-    with pd.HDFStore(filepath_or_buffer, **kwargs) as store:
-        pd_obj = store.get(key)
-        attrs = store.get_storer(key).attrs
-        # for backward compatibility but any object read from an hdf file should have an attribute 'type'
-        _type = attrs.type if 'type' in dir(attrs) else 'LArray'
-        if _type == 'LArray':
-            res = df_aslarray(pd_obj, sort_rows=sort_rows, sort_columns=sort_columns, fill_value=fill_value, parse_header=False)
-        elif _type == 'Axis':
-            if name is None:
-                name = str(pd_obj.name)
-            if name == 'None':
-                name = None
-            res = Axis(labels=pd_obj.values, name=name)
-            if 'wildcard' not in dir(attrs):
-                raise ValueError("Attribute 'wildcard' is missing for axis {}".format(key))
-            res._iswildcard = attrs['wildcard']
-        elif _type == 'Group':
-            if name is None:
-                name = str(pd_obj.name)
-            if name == 'None':
-                name = None
-            if 'axis_key' not in dir(attrs):
-                raise ValueError("Attribute 'axis_key' is missing for group {}".format(key))
-            axis = read_hdf(filepath_or_buffer, attrs['axis_key'])
-            res = LGroup(key=pd_obj.values, name=name, axis=axis)
+    if isinstance(filepath_or_buffer, pd.HDFStore):
+        if not filepath_or_buffer.is_open:
+            raise IOError('The HDFStore must be open for reading.')
+        store = filepath_or_buffer
+        close_store = False
+    else:
+        store = pd.HDFStore(filepath_or_buffer, mode='r')
+        close_store = True
+    pd_obj = store.get(key)
+    attrs = store.get_storer(key).attrs
+    # for backward compatibility but any object read from an hdf file should have an attribute 'type'
+    _type = attrs.type if 'type' in dir(attrs) else 'LArray'
+    if _type == 'LArray':
+        res = df_aslarray(pd_obj, sort_rows=sort_rows, sort_columns=sort_columns, fill_value=fill_value, parse_header=False)
+    elif _type == 'Axis':
+        if name is None:
+            name = str(pd_obj.name)
+        if name == 'None':
+            name = None
+        res = Axis(labels=pd_obj.values, name=name)
+        if 'wildcard' not in dir(attrs):
+            raise ValueError("Attribute 'wildcard' is missing for axis {}".format(key))
+        res._iswildcard = attrs['wildcard']
+    elif _type == 'Group':
+        if name is None:
+            name = str(pd_obj.name)
+        if name == 'None':
+            name = None
+        if 'axis_key' not in dir(attrs):
+            raise ValueError("Attribute 'axis_key' is missing for group {}".format(key))
+        axis = read_hdf(filepath_or_buffer, attrs['axis_key'])
+        res = LGroup(key=pd_obj.values, name=name, axis=axis)
+    if close_store:
+        store.close()
     return res
 
 @deprecate_kwarg('nb_index', 'nb_axes', arg_converter=lambda x: x + 1)