add cache_attrs to API

Author: alimanfoo

zarr/core.py

@@ -43,7 +43,7 @@ class Array(object):
     synchronizer : object, optional
         Array synchronizer.
     cache_metadata : bool, optional
-        If True, array configuration metadata will be cached for the
+        If True (default), array configuration metadata will be cached for the
         lifetime of the object. If False, array metadata will be reloaded
         prior to all data access and modification operations (may incur
         overhead depending on storage and data access pattern).

zarr/creation.py

@@ -16,8 +16,8 @@
 def create(shape, chunks=True, dtype=None, compressor='default',
            fill_value=0, order='C', store=None, synchronizer=None,
            overwrite=False, path=None, chunk_store=None, filters=None,
-           cache_metadata=True, read_only=False, object_codec=None,
-           **kwargs):
+           cache_metadata=True, cache_attrs=True, read_only=False,
+           object_codec=None, **kwargs):
     """Create an array.
 
     Parameters
@@ -54,6 +54,10 @@ def create(shape, chunks=True, dtype=None, compressor='default',
         lifetime of the object. If False, array metadata will be reloaded
         prior to all data access and modification operations (may incur
         overhead depending on storage and data access pattern).
+    cache_attrs : bool, optional
+        If True (default), user attributes will be cached for attribute read
+        operations. If False, user attributes are reloaded from the store prior
+        to all attribute read operations.
     read_only : bool, optional
         True if array should be protected against modification.
     object_codec : Codec, optional
@@ -115,7 +119,7 @@ def create(shape, chunks=True, dtype=None, compressor='default',
 
     # instantiate array
     z = Array(store, path=path, chunk_store=chunk_store, synchronizer=synchronizer,
-              cache_metadata=cache_metadata, read_only=read_only)
+              cache_metadata=cache_metadata, cache_attrs=cache_attrs, read_only=read_only)
 
     return z
 
@@ -342,8 +346,9 @@ def array(data, **kwargs):
 
 
 def open_array(store, mode='a', shape=None, chunks=True, dtype=None, compressor='default',
-               fill_value=0, order='C', synchronizer=None, filters=None, cache_metadata=True,
-               path=None, object_codec=None, **kwargs):
+               fill_value=0, order='C', synchronizer=None, filters=None,
+               cache_metadata=True, cache_attrs=True, path=None, object_codec=None,
+               **kwargs):
     """Open an array using file-mode-like semantics.
 
     Parameters
@@ -377,6 +382,10 @@ def open_array(store, mode='a', shape=None, chunks=True, dtype=None, compressor=
         lifetime of the object. If False, array metadata will be reloaded
         prior to all data access and modification operations (may incur
         overhead depending on storage and data access pattern).
+    cache_attrs : bool, optional
+        If True (default), user attributes will be cached for attribute read
+        operations. If False, user attributes are reloaded from the store prior
+        to all attribute read operations.
     path : string, optional
         Array path within store.
     object_codec : Codec, optional
@@ -465,7 +474,7 @@ def open_array(store, mode='a', shape=None, chunks=True, dtype=None, compressor=
 
     # instantiate array
     z = Array(store, read_only=read_only, synchronizer=synchronizer,
-              cache_metadata=cache_metadata, path=path)
+              cache_metadata=cache_metadata, cache_attrs=cache_attrs, path=path)
 
     return z
 

zarr/hierarchy.py

@@ -35,6 +35,10 @@ class Group(MutableMapping):
     chunk_store : MutableMapping, optional
         Separate storage for chunks. If not provided, `store` will be used
         for storage of both chunks and metadata.
+    cache_attrs : bool, optional
+        If True (default), user attributes will be cached for attribute read
+        operations. If False, user attributes are reloaded from the store prior
+        to all attribute read operations.
     synchronizer : object, optional
         Array synchronizer.
 
@@ -86,7 +90,7 @@ class Group(MutableMapping):
     """
 
     def __init__(self, store, path=None, read_only=False, chunk_store=None,
-                 synchronizer=None):
+                 cache_attrs=True, synchronizer=None):
 
         self._store = store
         self._chunk_store = chunk_store
@@ -115,7 +119,7 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
         # setup attributes
         akey = self._key_prefix + attrs_key
         self._attrs = Attributes(store, key=akey, read_only=read_only,
-                                 synchronizer=synchronizer)
+                                 cache=cache_attrs, synchronizer=synchronizer)
 
         # setup info
         self._info = InfoReporter(self)
@@ -320,10 +324,12 @@ def __getitem__(self, item):
         path = self._item_path(item)
         if contains_array(self._store, path):
             return Array(self._store, read_only=self._read_only, path=path,
-                         chunk_store=self._chunk_store, synchronizer=self._synchronizer)
+                         chunk_store=self._chunk_store,
+                         synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
         elif contains_group(self._store, path):
             return Group(self._store, read_only=self._read_only, path=path,
-                         chunk_store=self._chunk_store, synchronizer=self._synchronizer)
+                         chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
+                         synchronizer=self._synchronizer)
         else:
             raise KeyError(item)
 
@@ -403,6 +409,7 @@ def groups(self):
             if contains_group(self._store, path):
                 yield key, Group(self._store, path=path, read_only=self._read_only,
                                  chunk_store=self._chunk_store,
+                                 cache_attrs=self.attrs.cache,
                                  synchronizer=self._synchronizer)
 
     def array_keys(self):
@@ -447,6 +454,7 @@ def arrays(self):
             if contains_array(self._store, path):
                 yield key, Array(self._store, path=path, read_only=self._read_only,
                                  chunk_store=self._chunk_store,
+                                 cache_attrs=self.attrs.cache,
                                  synchronizer=self._synchronizer)
 
     def visitvalues(self, func):
@@ -649,7 +657,8 @@ def _create_group_nosync(self, name, overwrite=False):
                    overwrite=overwrite)
 
         return Group(self._store, path=path, read_only=self._read_only,
-                     chunk_store=self._chunk_store, synchronizer=self._synchronizer)
+                     chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
+                     synchronizer=self._synchronizer)
 
     def create_groups(self, *names, **kwargs):
         """Convenience method to create multiple groups in a single call."""
@@ -692,7 +701,8 @@ def _require_group_nosync(self, name, overwrite=False):
                        overwrite=overwrite)
 
         return Group(self._store, path=path, read_only=self._read_only,
-                     chunk_store=self._chunk_store, synchronizer=self._synchronizer)
+                     chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
+                     synchronizer=self._synchronizer)
 
     def require_groups(self, *names):
         """Convenience method to require multiple groups in a single call."""
@@ -760,6 +770,7 @@ def _create_dataset_nosync(self, name, data=None, **kwargs):
 
         # determine synchronizer
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
 
         # create array
         if data is None:
@@ -804,9 +815,10 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 
             synchronizer = kwargs.get('synchronizer', self._synchronizer)
             cache_metadata = kwargs.get('cache_metadata', True)
+            cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
             a = Array(self._store, path=path, read_only=self._read_only,
                       chunk_store=self._chunk_store, synchronizer=synchronizer,
-                      cache_metadata=cache_metadata)
+                      cache_metadata=cache_metadata, cache_attrs=cache_attrs)
             shape = normalize_shape(shape)
             if shape != a.shape:
                 raise TypeError('shape do not match existing array; expected {}, got {}'
@@ -834,6 +846,7 @@ def create(self, name, **kwargs):
     def _create_nosync(self, name, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return create(store=self._store, path=path, chunk_store=self._chunk_store,
                       **kwargs)
 
@@ -845,6 +858,7 @@ def empty(self, name, **kwargs):
     def _empty_nosync(self, name, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return empty(store=self._store, path=path, chunk_store=self._chunk_store,
                      **kwargs)
 
@@ -856,6 +870,7 @@ def zeros(self, name, **kwargs):
     def _zeros_nosync(self, name, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return zeros(store=self._store, path=path, chunk_store=self._chunk_store,
                      **kwargs)
 
@@ -867,6 +882,7 @@ def ones(self, name, **kwargs):
     def _ones_nosync(self, name, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return ones(store=self._store, path=path, chunk_store=self._chunk_store, **kwargs)
 
     def full(self, name, fill_value, **kwargs):
@@ -877,6 +893,7 @@ def full(self, name, fill_value, **kwargs):
     def _full_nosync(self, name, fill_value, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return full(store=self._store, path=path, chunk_store=self._chunk_store,
                     fill_value=fill_value, **kwargs)
 
@@ -888,6 +905,7 @@ def array(self, name, data, **kwargs):
     def _array_nosync(self, name, data, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return array(data, store=self._store, path=path, chunk_store=self._chunk_store,
                      **kwargs)
 
@@ -899,6 +917,7 @@ def empty_like(self, name, data, **kwargs):
     def _empty_like_nosync(self, name, data, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return empty_like(data, store=self._store, path=path,
                           chunk_store=self._chunk_store, **kwargs)
 
@@ -910,6 +929,7 @@ def zeros_like(self, name, data, **kwargs):
     def _zeros_like_nosync(self, name, data, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return zeros_like(data, store=self._store, path=path,
                           chunk_store=self._chunk_store, **kwargs)
 
@@ -921,6 +941,7 @@ def ones_like(self, name, data, **kwargs):
     def _ones_like_nosync(self, name, data, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return ones_like(data, store=self._store, path=path,
                          chunk_store=self._chunk_store, **kwargs)
 
@@ -932,6 +953,7 @@ def full_like(self, name, data, **kwargs):
     def _full_like_nosync(self, name, data, **kwargs):
         path = self._item_path(name)
         kwargs.setdefault('synchronizer', self._synchronizer)
+        kwargs.setdefault('cache_attrs', self.attrs.cache)
         return full_like(data, store=self._store, path=path,
                          chunk_store=self._chunk_store, **kwargs)
 
@@ -971,7 +993,8 @@ def _normalize_store_arg(store, clobber=False):
     return normalize_store_arg(store, clobber=clobber, default=DictStore)
 
 
-def group(store=None, overwrite=False, chunk_store=None, synchronizer=None, path=None):
+def group(store=None, overwrite=False, chunk_store=None,
+          cache_attrs=True, synchronizer=None, path=None):
     """Create a group.
 
     Parameters
@@ -984,6 +1007,10 @@ def group(store=None, overwrite=False, chunk_store=None, synchronizer=None, path
     chunk_store : MutableMapping, optional
         Separate storage for chunks. If not provided, `store` will be used
         for storage of both chunks and metadata.
+    cache_attrs : bool, optional
+        If True (default), user attributes will be cached for attribute read
+        operations. If False, user attributes are reloaded from the store prior
+        to all attribute read operations.
     synchronizer : object, optional
         Array synchronizer.
     path : string, optional
@@ -1021,10 +1048,10 @@ def group(store=None, overwrite=False, chunk_store=None, synchronizer=None, path
                    path=path)
 
     return Group(store, read_only=False, chunk_store=chunk_store,
-                 synchronizer=synchronizer, path=path)
+                 cache_attrs=cache_attrs, synchronizer=synchronizer, path=path)
 
 
-def open_group(store, mode='a', synchronizer=None, path=None):
+def open_group(store, mode='a', cache_attrs=True, synchronizer=None, path=None):
     """Open a group using file-mode-like semantics.
 
     Parameters
@@ -1036,6 +1063,10 @@ def open_group(store, mode='a', synchronizer=None, path=None):
         read/write (must exist); 'a' means read/write (create if doesn't
         exist); 'w' means create (overwrite if exists); 'w-' means create
         (fail if exists).
+    cache_attrs : bool, optional
+        If True (default), user attributes will be cached for attribute read
+        operations. If False, user attributes are reloaded from the store prior
+        to all attribute read operations.
     synchronizer : object, optional
         Array synchronizer.
     path : string, optional
@@ -1093,4 +1124,5 @@ def open_group(store, mode='a', synchronizer=None, path=None):
     # determine read only status
     read_only = mode == 'r'
 
-    return Group(store, read_only=read_only, synchronizer=synchronizer, path=path)
+    return Group(store, read_only=read_only, cache_attrs=cache_attrs,
+                 synchronizer=synchronizer, path=path)