ezarr 1.0.0

Tools for easily working with Zarr groups and arrays

eZarr

Easily store any Python object inside zarr hierarchies. This package defines proxies for regular Python lists (EZList) and dicts (EZDict), built as wrappers around zarr Arrays and Groups. It also defines a Protocol for writing and loading any object in zarr hierarchies.

EZList

An EZlist is a proxy for a Python list built on top of a zarr.Array. It allows storing mixed arbitrary objects in a 1 dimensional sequence.

Examples

>>> from ezarr import EZList
>>> from pathlib import Path

# EZList creation from a zarr.Array:
>>> EZList(zarr.array([1, 2, 3]))
EZList[1, 2, 3]

# EZList creation from a list:
>>> data = [1, "some text", Path("some/path.txt")]
>>> ez_list = EZList.from_list(data, store={}, name="data")
                                      #    ~~        ~~~~ a name for the list inside the store
                                      #    |
                                      #    or any zarr StoreLike object to store the list

>>> ez_list
EZList[1, 'some text', PosixPath('some/path.txt')]

# EZLists support general list methods:
>>> ez_list[0]
1

>>> del ez_list[1]
>>> ez_list
EZList[1, PosixPath('some/path.txt')]

>>> ez_list.append(3.14)
>>> ez_list
EZList[1, PosixPath('some/path.txt'), 3.14]

>>> ez_list.insert(0, [1, 2, 3])
>>> ez_list
EZList[[1, 2, 3], 1, PosixPath('/some/path.txt'), 3.14]

# EZList save to zarr store:
>>> ez_list.save("path/to/store", name="saved_list")

# EZList load from zarr store:
>>> EZList.open("path/to/store", name="saved_list")
EZList[[1, 2, 3], 1, PosixPath('/some/path.txt'), 3.14]

# EZList conversion to a regular list:
>>> ez_list.copy()
[[1, 2, 3], 1, PosixPath('some/path.txt'), 3.14]

EZDict

An EZDict is a proxy for a Python dict built on top of a zarr.Group. It expands zarr.Groups to store and retrieve arbitrary objects.

Examples

>>> from ezarr import EZDict

# EZdDct creation for a zarr.Group:
>>> EZDict(zarr.open_group({}))
EZDict{}

# EZDict creation for a dict:
>>> data = {"a": 1, "b": [1, 2, 3], "c": {"d": "some text"}}
>>> ez_dict = EZDict.from_dict(data, store={})
                                    #      ~~ or any zarr StoreLike object to store the dict into                                    #      |

# EZDict lazy representation:
>>> ez_dict
EZDict{
        a: 1,
        b: [1 2 3],
        c: {...}                    # <-- note the nested dict was not loaded for the representation
}

# EZDict save to zarr store:
>>> ez_dict.save("path/to/store", name="saved_dict")

# EZDict load from zarr store:
>>> EZDict.open("path/to/store", name="saved_dict")
EZDict{
        a: 1,
        b: [1 2 3],
        c: {...}
}

# EZDict conversion to a regular dict:
>>> ez_dict.copy()
{'a': np.int64(1), 'b': array([1, 2, 3]), 'c': {'d': np.str_('some text')}}

SupportsEZReadWrite

The SupportsEZReadWrite protocol, once implemented on an object, allows it to be store in and retrieved from a zarr hierarchy.

@runtime_checkable
class SupportsEZRead(Protocol):
    @classmethod
    def __ez_read__(cls, grp: zarr.Group) -> Self: ...


@runtime_checkable
class SupportsEZWrite(Protocol):
    def __ez_write__(self, grp: zarr.Group) -> None: ...


@runtime_checkable
class SupportsEZReadWrite(SupportsEZRead, SupportsEZWrite, Protocol): ...

This protocol has 2 parts:

• SupportsEZRead defines the classmethod __ez_read__(cls, grp: zarr.Group) -> Self for reconstructing an object from a zarr.Group.
• SupportsEZWrite defines the method __ez_write__(self, grp: zarr.Group) -> None for storing an object in a zarr.Group.

Once implemented on an object, this protocol allows that object to be automatically saved and loaded in EZLists and EZDicts.