Add full copy of zarr-python v2.18.7 under src/zarr/v2

Author: jni

src/zarr/v2/__init__.py

@@ -0,0 +1,70 @@
+# flake8: noqa
+from zarr.codecs import *
+from zarr.convenience import (
+    consolidate_metadata,
+    copy,
+    copy_all,
+    copy_store,
+    load,
+    open,
+    open_consolidated,
+    save,
+    save_array,
+    save_group,
+    tree,
+)
+from zarr.core import Array
+from zarr.creation import (
+    array,
+    create,
+    empty,
+    empty_like,
+    full,
+    full_like,
+    ones,
+    ones_like,
+    open_array,
+    open_like,
+    zeros,
+    zeros_like,
+)
+from zarr.errors import CopyError, MetadataError
+from zarr.hierarchy import Group, group, open_group
+from zarr.n5 import N5Store, N5FSStore
+from zarr._storage.store import v3_api_available
+from zarr.storage import (
+    ABSStore,
+    DBMStore,
+    DictStore,
+    DirectoryStore,
+    KVStore,
+    LMDBStore,
+    LRUStoreCache,
+    MemoryStore,
+    MongoDBStore,
+    NestedDirectoryStore,
+    RedisStore,
+    SQLiteStore,
+    TempStore,
+    ZipStore,
+)
+from zarr.sync import ProcessSynchronizer, ThreadSynchronizer
+from zarr.version import version as __version__
+
+# in case setuptools scm screw up and find version to be 0.0.0
+assert not __version__.startswith("0.0.0")
+
+if v3_api_available:
+    from zarr._storage.v3 import (
+        ABSStoreV3,
+        DBMStoreV3,
+        KVStoreV3,
+        DirectoryStoreV3,
+        LMDBStoreV3,
+        LRUStoreCacheV3,
+        MemoryStoreV3,
+        MongoDBStoreV3,
+        RedisStoreV3,
+        SQLiteStoreV3,
+        ZipStoreV3,
+    )

src/zarr/v2/_storage/__init__.py

@@ -0,0 +1,293 @@
+"""This module contains storage classes related to Azure Blob Storage (ABS)"""
+
+from typing import Optional
+import warnings
+
+from numcodecs.compat import ensure_bytes
+from zarr.util import normalize_storage_path
+from zarr._storage.store import (
+    _get_metadata_suffix,
+    data_root,
+    meta_root,
+    Store,
+    StoreV3,
+    V3_DEPRECATION_MESSAGE,
+)
+from zarr.types import DIMENSION_SEPARATOR
+
+__doctest_requires__ = {
+    ("ABSStore", "ABSStore.*"): ["azure.storage.blob"],
+}
+
+
+class ABSStore(Store):
+    """Storage class using Azure Blob Storage (ABS).
+
+    Parameters
+    ----------
+    container : string
+        The name of the ABS container to use.
+
+        .. deprecated::
+           Use ``client`` instead.
+
+    prefix : string
+        Location of the "directory" to use as the root of the storage hierarchy
+        within the container.
+
+    account_name : string
+        The Azure blob storage account name.
+
+        .. deprecated:: 2.8.3
+           Use ``client`` instead.
+
+    account_key : string
+        The Azure blob storage account access key.
+
+        .. deprecated:: 2.8.3
+           Use ``client`` instead.
+
+    blob_service_kwargs : dictionary
+        Extra arguments to be passed into the azure blob client, for e.g. when
+        using the emulator, pass in blob_service_kwargs={'is_emulated': True}.
+
+        .. deprecated:: 2.8.3
+           Use ``client`` instead.
+
+    dimension_separator : {'.', '/'}, optional
+        Separator placed between the dimensions of a chunk.
+
+    client : azure.storage.blob.ContainerClient, optional
+        And ``azure.storage.blob.ContainerClient`` to connect with. See
+        `here <https://docs.microsoft.com/en-us/python/api/azure-storage-blob/azure.storage.blob.containerclient?view=azure-python>`_  # noqa
+        for more.
+
+        .. versionadded:: 2.8.3
+
+    Notes
+    -----
+    In order to use this store, you must install the Microsoft Azure Storage SDK for Python,
+    ``azure-storage-blob>=12.5.0``.
+    """  # noqa: E501
+
+    def __init__(
+        self,
+        container=None,
+        prefix="",
+        account_name=None,
+        account_key=None,
+        blob_service_kwargs=None,
+        dimension_separator: Optional[DIMENSION_SEPARATOR] = None,
+        client=None,
+    ):
+        warnings.warn(
+            V3_DEPRECATION_MESSAGE.format(store=self.__class__.__name__),
+            FutureWarning,
+            stacklevel=3,
+        )
+
+        self._dimension_separator = dimension_separator
+        self.prefix = normalize_storage_path(prefix)
+        if client is None:
+            # deprecated option, try to construct the client for them
+            msg = (
+                "Providing 'container', 'account_name', 'account_key', and 'blob_service_kwargs'"
+                "is deprecated. Provide and instance of 'azure.storage.blob.ContainerClient' "
+                "'client' instead."
+            )
+            warnings.warn(msg, FutureWarning, stacklevel=2)
+            from azure.storage.blob import ContainerClient
+
+            blob_service_kwargs = blob_service_kwargs or {}
+            client = ContainerClient(
+                f"https://{account_name}.blob.core.windows.net/",
+                container,
+                credential=account_key,
+                **blob_service_kwargs,
+            )
+
+        self.client = client
+        self._container = container
+        self._account_name = account_name
+        self._account_key = account_key
+
+    @staticmethod
+    def _warn_deprecated(property_):
+        msg = (
+            "The {} property is deprecated and will be removed in a future "
+            "version. Get the property from 'ABSStore.client' instead."
+        )
+        warnings.warn(msg.format(property_), FutureWarning, stacklevel=3)
+
+    @property
+    def container(self):
+        self._warn_deprecated("container")
+        return self._container
+
+    @property
+    def account_name(self):
+        self._warn_deprecated("account_name")
+        return self._account_name
+
+    @property
+    def account_key(self):
+        self._warn_deprecated("account_key")
+        return self._account_key
+
+    def _append_path_to_prefix(self, path):
+        if self.prefix == "":
+            return normalize_storage_path(path)
+        else:
+            return "/".join([self.prefix, normalize_storage_path(path)])
+
+    @staticmethod
+    def _strip_prefix_from_path(path, prefix):
+        # normalized things will not have any leading or trailing slashes
+        path_norm = normalize_storage_path(path)
+        prefix_norm = normalize_storage_path(prefix)
+        if prefix:
+            return path_norm[(len(prefix_norm) + 1) :]
+        else:
+            return path_norm
+
+    def __getitem__(self, key):
+        from azure.core.exceptions import ResourceNotFoundError
+
+        blob_name = self._append_path_to_prefix(key)
+        try:
+            return self.client.download_blob(blob_name).readall()
+        except ResourceNotFoundError as e:
+            raise KeyError(f"Blob {blob_name} not found") from e
+
+    def __setitem__(self, key, value):
+        value = ensure_bytes(value)
+        blob_name = self._append_path_to_prefix(key)
+        self.client.upload_blob(blob_name, value, overwrite=True)
+
+    def __delitem__(self, key):
+        from azure.core.exceptions import ResourceNotFoundError
+
+        try:
+            self.client.delete_blob(self._append_path_to_prefix(key))
+        except ResourceNotFoundError as e:
+            raise KeyError(f"Blob {key} not found") from e
+
+    def __eq__(self, other):
+        return (
+            isinstance(other, ABSStore)
+            and self.client == other.client
+            and self.prefix == other.prefix
+        )
+
+    def keys(self):
+        return list(self.__iter__())
+
+    def __iter__(self):
+        if self.prefix:
+            list_blobs_prefix = self.prefix + "/"
+        else:
+            list_blobs_prefix = None
+        for blob in self.client.list_blobs(list_blobs_prefix):
+            yield self._strip_prefix_from_path(blob.name, self.prefix)
+
+    def __len__(self):
+        return len(self.keys())
+
+    def __contains__(self, key):
+        blob_name = self._append_path_to_prefix(key)
+        return self.client.get_blob_client(blob_name).exists()
+
+    def listdir(self, path=None):
+        dir_path = normalize_storage_path(self._append_path_to_prefix(path))
+        if dir_path:
+            dir_path += "/"
+        items = [
+            self._strip_prefix_from_path(blob.name, dir_path)
+            for blob in self.client.walk_blobs(name_starts_with=dir_path, delimiter="/")
+        ]
+        return items
+
+    def rmdir(self, path=None):
+        dir_path = normalize_storage_path(self._append_path_to_prefix(path))
+        if dir_path:
+            dir_path += "/"
+        for blob in self.client.list_blobs(name_starts_with=dir_path):
+            self.client.delete_blob(blob)
+
+    def getsize(self, path=None):
+        store_path = normalize_storage_path(path)
+        fs_path = self._append_path_to_prefix(store_path)
+        if fs_path:
+            blob_client = self.client.get_blob_client(fs_path)
+        else:
+            blob_client = None
+
+        if blob_client and blob_client.exists():
+            return blob_client.get_blob_properties().size
+        else:
+            size = 0
+            if fs_path == "":
+                fs_path = None
+            elif not fs_path.endswith("/"):
+                fs_path += "/"
+            for blob in self.client.walk_blobs(name_starts_with=fs_path, delimiter="/"):
+                blob_client = self.client.get_blob_client(blob.name)
+                if blob_client.exists():
+                    size += blob_client.get_blob_properties().size
+            return size
+
+    def clear(self):
+        self.rmdir()
+
+
+class ABSStoreV3(ABSStore, StoreV3):
+    def list(self):
+        return list(self.keys())
+
+    def __eq__(self, other):
+        return (
+            isinstance(other, ABSStoreV3)
+            and self.client == other.client
+            and self.prefix == other.prefix
+        )
+
+    def __setitem__(self, key, value):
+        self._validate_key(key)
+        super().__setitem__(key, value)
+
+    def rmdir(self, path=None):
+        if not path:
+            # Currently allowing clear to delete everything as in v2
+
+            # If we disallow an empty path then we will need to modify
+            # TestABSStoreV3 to have the create_store method use a prefix.
+            ABSStore.rmdir(self, "")
+            return
+
+        meta_dir = meta_root + path
+        meta_dir = meta_dir.rstrip("/")
+        ABSStore.rmdir(self, meta_dir)
+
+        # remove data folder
+        data_dir = data_root + path
+        data_dir = data_dir.rstrip("/")
+        ABSStore.rmdir(self, data_dir)
+
+        # remove metadata files
+        sfx = _get_metadata_suffix(self)
+        array_meta_file = meta_dir + ".array" + sfx
+        if array_meta_file in self:
+            del self[array_meta_file]
+        group_meta_file = meta_dir + ".group" + sfx
+        if group_meta_file in self:
+            del self[group_meta_file]
+
+    # TODO: adapt the v2 getsize method to work for v3
+    #       For now, calling the generic keys-based _getsize
+    def getsize(self, path=None):
+        from zarr.storage import _getsize  # avoid circular import
+
+        return _getsize(self, path)
+
+
+ABSStoreV3.__doc__ = ABSStore.__doc__