Initial Zarr v3 Support

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-ARG PYTHON_VERSION=3.12
+ARG PYTHON_VERSION=3.13
 ARG LINUX_DISTRO=bookworm
 
 FROM mcr.microsoft.com/devcontainers/python:1-${PYTHON_VERSION}-${LINUX_DISTRO}

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Upgrade pip
         run: |

.github/workflows/tests.yml

@@ -12,21 +12,20 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { python: "3.12", os: "ubuntu-latest", session: "pre-commit" }
-          - { python: "3.12", os: "ubuntu-latest", session: "safety" }
+          - { python: "3.13", os: "ubuntu-latest", session: "pre-commit" }
+          - { python: "3.13", os: "ubuntu-latest", session: "safety" }
+          #          - { python: "3.13", os: "ubuntu-latest", session: "mypy" }
           #          - { python: "3.12", os: "ubuntu-latest", session: "mypy" }
           #          - { python: "3.11", os: "ubuntu-latest", session: "mypy" }
-          #          - { python: "3.10", os: "ubuntu-latest", session: "mypy" }
+          - { python: "3.13", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
-          - { python: "3.10", os: "ubuntu-latest", session: "tests" }
-          - { python: "3.12", os: "windows-latest", session: "tests" }
-          - { python: "3.12", os: "macos-latest", session: "tests" }
+          - { python: "3.13", os: "windows-latest", session: "tests" }
+          - { python: "3.13", os: "macos-latest", session: "tests" }
+          #          - { python: "3.13", os: "ubuntu-latest", session: "typeguard" }
           #          - { python: "3.12", os: "ubuntu-latest", session: "typeguard" }
           #          - { python: "3.11", os: "ubuntu-latest", session: "typeguard" }
-          #          - { python: "3.10", os: "ubuntu-latest", session: "typeguard" }
-          #          - { python: "3.10", os: "ubuntu-latest", session: "xdoctest" }
-          - { python: "3.12", os: "ubuntu-latest", session: "docs-build" }
+          - { python: "3.13", os: "ubuntu-latest", session: "docs-build" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
@@ -121,7 +120,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Upgrade pip
         run: |

noxfile.py

@@ -24,8 +24,8 @@
 
 
 package = "mdio"
-python_versions = ["3.12", "3.11", "3.10"]
-nox.needs_version = ">= 2022.1.7"
+python_versions = ["3.13", "3.12", "3.11"]
+nox.needs_version = ">= 2024.10.9"
 nox.options.sessions = (
     "pre-commit",
     "safety",

pyproject.toml

@@ -6,16 +6,16 @@ authors = [{ name = "Altay Sansal", email = "[email protected]" }]
 license = "Apache-2.0"
 readme = "README.md"
 keywords = ["mdio", "multidimio", "seismic", "wind", "data"]
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.11,<3.14"
 dependencies = [
     "click (>=8.1.7,<9.0.0)",
     "click-params (>=0.5.0,<0.6.0)",
-    "zarr (>=2.18.2,<3.0.0)",
+    "zarr (>=3.0.2,<4.0.0)",
     "dask (>=2024.12.0)",
     "tqdm (>=4.67.0,<5.0.0)",
     "psutil (>=6.1.0,<7.0.0)",
     "fsspec (>=2024.10.0)",
-    "segy (>=0.3.1,<0.4.0)",
+    "segy (>=0.4.0,<1.0.0)",
     "rich (>=13.9.4,<14.0.0)"
 ]
 

src/mdio/api/accessor.py

@@ -186,32 +186,33 @@ def _validate_store(self, storage_options):
         if storage_options is None:
             storage_options = {}
 
-        self.store = process_url(
+        self.url = process_url(
             url=self.url,
-            mode=self.mode,
-            storage_options=storage_options,
-            memory_cache_size=self._memory_cache_size,
             disk_cache=self._disk_cache,
         )
 
-    def _connect(self):
-        """Open the zarr root."""
         try:
-            if self.mode in {"r", "r+"}:
-                self.root = zarr.open_consolidated(store=self.store, mode=self.mode)
-            elif self.mode == "w":
-                self.root = zarr.open(store=self.store, mode="r+")
-            else:
-                msg = f"Invalid mode: {self.mode}"
-                raise ValueError(msg)
-        except KeyError as e:
+            self.store = zarr.open(
+                self.url, mode=self.mode, storage_options=storage_options
+            ).store
+        except FileNotFoundError as e:
             msg = (
-                f"MDIO file not found or corrupt at {self.store.path}. "
+                f"MDIO file not found or corrupt at {self.url}. "
                 "Please check the URL or ensure it is not a deprecated "
                 "version of MDIO file."
             )
             raise MDIONotFoundError(msg) from e
 
+    def _connect(self):
+        """Open the zarr root."""
+        if self.mode in {"r", "r+"}:
+            self.root = zarr.open_consolidated(store=self.store, mode=self.mode)
+        elif self.mode == "w":
+            self.root = zarr.open(store=self.store, mode="r+")
+        else:
+            msg = f"Invalid mode: {self.mode}"
+            raise ValueError(msg)
+
     def _deserialize_grid(self):
         """Deserialize grid from Zarr metadata."""
         self.grid = Grid.from_zarr(self.root)
@@ -375,12 +376,12 @@ def stats(self, value: dict) -> None:
     @property
     def _metadata_group(self) -> zarr.Group:
         """Get metadata zarr.group handle."""
-        return self.root.metadata
+        return self.root["metadata"]
 
     @property
     def _data_group(self) -> zarr.Group:
         """Get data zarr.Group handle."""
-        return self.root.data
+        return self.root["data"]
 
     def __getitem__(self, item: int | tuple) -> npt.ArrayLike | da.Array | tuple:
         """Data getter."""

src/mdio/api/convenience.py

@@ -5,8 +5,8 @@
 from typing import TYPE_CHECKING
 
 import zarr
+from numcodecs import Blosc
 from tqdm.auto import tqdm
-from zarr import Blosc
 
 from mdio.api.io_utils import process_url
 from mdio.core.indexing import ChunkIterator
@@ -51,20 +51,22 @@ def copy_mdio(  # noqa: PLR0913
             Default is None (will assume anonymous).
         overwrite: Overwrite destination or not.
 
+    Raises:
+        NotImplementedError: because Zarr v3 doesn't support copy.
     """
     if storage_options is None:
         storage_options = {}
 
     dest_store = process_url(
         url=dest_path_or_buffer,
-        mode="w",
-        storage_options=storage_options,
-        memory_cache_size=0,
         disk_cache=False,
     )
 
     if_exists = "replace" if overwrite is True else "raise"
 
+    # TODO(Altay): Update this function when Zarr v3 supports copy.
+    raise NotImplementedError("Zarr version 3.0.0+ does not support copy yet.")
+
     zarr.copy_store(
         source=source.store,
         dest=dest_store,
@@ -242,6 +244,7 @@ def rechunk_batch(
     write_rechunked_values(source, suffix_list, *plan)
 
 
+# TODO(Altay): This needs to be validated
 def rechunk(
     source: MDIOAccessor,
     chunks: tuple[int, ...],

src/mdio/api/io_utils.py

@@ -2,40 +2,27 @@
 
 from __future__ import annotations
 
-from typing import Any
-
 import dask.array as da
 import zarr
-from zarr.storage import FSStore
 
 
 def process_url(
     url: str,
-    mode: str,
-    storage_options: dict[str, Any],
-    memory_cache_size: int,
     disk_cache: bool,
-) -> FSStore:
+) -> str:
     """Check read/write access to FSStore target and return FSStore with double caching.
 
-    It can use an in-memory Least Recently Used (LRU) cache implementation from
-    Zarr, and optionally, a file cache (`simplecache` protocol from FSSpec) that
-    is useful for remote stores.
-
-    File cache is only valid for remote stores. The LRU caching works
-    on both remote and local.
+    It can optionally use a file cache (`simplecache` protocol from fsspec) that
+    is useful for remote stores. File cache is only useful for remote stores.
 
     The `storage_options` argument represents a set of parameters to be passed
-    to the FSSpec backend. Note that the format of `storage_options` is
+    to the fsspec backend. Note that the format of `storage_options` is
     different if `disk_cache` is enabled or disabled, since `disk_cache`
     interanlly uses the simplecache protocol.
 
     Args:
-        url: FSSpec compliant url
-        mode: Toggle for overwriting existing store
-        storage_options: Storage options for the storage backend.
-        memory_cache_size: Maximum in memory LRU cache size in bytes.
-        disk_cache: This enables FSSpec's `simplecache` if True.
+        url: fsspec compliant url
+        disk_cache: This enables fsspec's `simplecache` if True.
 
     Returns:
         Store with augmentations like cache, write verification etc.
@@ -52,7 +39,6 @@ def process_url(
         ...     url="s3://bucket/key",
         ...     mode="r",
         ...     storage_options={"key": "my_key", "secret": "my_secret"},
-        ...     memory_cache_size=0,
         ...     disk_cache=False,
         ... )
 
@@ -64,7 +50,6 @@ def process_url(
         ...     url="s3://bucket/key",
         ...     mode="r",
         ...     storage_options={"s3": {"key": "my_key", "secret": "my_secret"}},
-        ...     memory_cache_size=0,
         ...     disk_cache=True,
         ... )
 
@@ -77,35 +62,13 @@ def process_url(
         ...         "s3": {"key": "my_key", "secret": "my_secret"},
         ...         "simplecache": {"cache_storage": "custom/local/cache/path"},
         ...     },
-        ...     memory_cache_size=0,
         ...     disk_cache=True,
         ... )
     """
     if disk_cache is True:
         url = "::".join(["simplecache", url])
 
-    # Strip whitespaces and slashes from end of string
-    url = url.rstrip("/ ")
-
-    # Flag for checking write access
-    check = True if mode == "w" else False
-
-    # TODO: Turning off write checking now because zarr has a bug.
-    #  Get rid of this once bug is fixed.
-    check = False
-
-    store = FSStore(
-        url=url,
-        check=check,
-        create=check,
-        mode=mode,
-        **storage_options,
-    )
-
-    if memory_cache_size != 0:
-        store = zarr.storage.LRUStoreCache(store=store, max_size=memory_cache_size)
-
-    return store
+    return url
 
 
 def open_zarr_array(group_handle: zarr.Group, name: str) -> zarr.Array:

src/mdio/commands/info.py

@@ -95,7 +95,7 @@ def parse_grid(grid: Grid) -> dict[str, dict[str, int | str]]:
 def parse_access_patterns(reader: MDIOReader) -> dict[str, Any]:
     """Extract access patterns and their info."""
     access_pattern_dict = {}
-    for name, array in reader._data_group.items():
+    for name, array in reader._data_group.arrays():
         pattern = name.replace("chunked_", "")
         chunks = str(array.chunks)
         format_ = str(array.dtype)