Merge branch 'main' of github.com:zarr-developers/zarr-python into feat/read-funcs

Author: d-v-b

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.3
+    rev: v0.8.0
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
@@ -28,10 +28,8 @@ repos:
         files: src|tests
         additional_dependencies:
           # Package dependencies
-          - asciitree
-          - crc32c
           - donfig
-          - numcodecs
+          - numcodecs[crc32c]
           - numpy
           - typing_extensions
           - universal-pathlib

README.md

@@ -78,6 +78,13 @@
 	</td>
 </tr>
 <tr>
+	<td>Funding</td>
+	<td>
+		<a href="https://chanzuckerberg.com/eoss/">
+			<img src="https://img.shields.io/badge/funded%20by-EOSS-FF414B.svg?logo=data:image/svg+xml;base64,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" alt="CZI's Essential Open Source Software for Science">
+		</a>
+	</td>
+</tr>
 	<td>Citation</td>
 	<td>
 		<a href="https://doi.org/10.5281/zenodo.3773450">

docs/guide/storage.rst

@@ -2,7 +2,7 @@ Storage
 =======
 
 Zarr-Python supports multiple storage backends, including: local file systems,
-Zip files, remote stores via ``fspec`` (S3, HTTP, etc.), and in-memory stores. In
+Zip files, remote stores via ``fsspec`` (S3, HTTP, etc.), and in-memory stores. In
 Zarr-Python 3, stores must implement the abstract store API from
 :class:`zarr.abc.store.Store`. 
 
@@ -19,9 +19,9 @@ to Zarr's top level API will result in the store being created automatically.
 .. code-block:: python
 
    >>> import zarr
-   >>> zarr.open("data/foo/bar", mode="r")  # implicitly creates a LocalStore
+   >>> zarr.open("data/foo/bar", mode="r")  # implicitly creates a read-only LocalStore
    <Group file://data/foo/bar>
-   >>> zarr.open("s3://foo/bar", mode="r")  # implicitly creates a RemoteStore
+   >>> zarr.open("s3://foo/bar", mode="r")  # implicitly creates a read-only RemoteStore
    <Group s3://foo/bar>
    >>> data = {}
    >>> zarr.open(data, mode="w")  # implicitly creates a MemoryStore
@@ -43,7 +43,7 @@ filesystem.
 .. code-block:: python
 
    >>> import zarr
-   >>> store = zarr.storage.LocalStore("data/foo/bar", mode="r")
+   >>> store = zarr.storage.LocalStore("data/foo/bar", read_only=True)
    >>> zarr.open(store=store)
    <Group file://data/foo/bar>
 
@@ -72,7 +72,7 @@ that implements the `AbstractFileSystem` API,
 .. code-block:: python
 
    >>> import zarr
-   >>> store = zarr.storage.RemoteStore.from_url("gs://foo/bar", mode="r")
+   >>> store = zarr.storage.RemoteStore.from_url("gs://foo/bar", read_only=True)
    >>> zarr.open(store=store)
    <Array <RemoteStore(GCSFileSystem, foo/bar)> shape=(10, 20) dtype=float32>
 
@@ -86,7 +86,7 @@ Zarr data (metadata and chunks) to a dictionary.
 
    >>> import zarr
    >>> data = {}
-   >>> store = zarr.storage.MemoryStore(data, mode="w")
+   >>> store = zarr.storage.MemoryStore(data)
    >>> zarr.open(store=store, shape=(2, ))
    <Array memory://4943638848 shape=(2,) dtype=float64>
 

docs/tutorial.rst

@@ -330,10 +330,10 @@ representation of the hierarchy, e.g.::
 
     >>> root.tree()
     /
-     └── foo
-         └── bar
-             ├── baz (10000, 10000) int32
-             └── quux (10000, 10000) int32
+    └── foo
+        └── bar
+            ├── baz (10000, 10000) int32
+            └── quux (10000, 10000) int32
 
 The :func:`zarr.convenience.open` function provides a convenient way to create or
 re-open a group stored in a directory on the file-system, with sub-groups stored in
@@ -424,6 +424,12 @@ Groups also have the :func:`zarr.hierarchy.Group.tree` method, e.g.::
          ├── bar (1000000,) int64
          └── baz (1000, 1000) float32
 
+
+.. note::
+
+   :func:`zarr.Group.tree` requires the optional `rich <https://rich.readthedocs.io/en/stable/>`_
+   dependency. It can be installed with the ``[tree]`` extra.
+
 If you're using Zarr within a Jupyter notebook (requires
 `ipytree <https://github.com/QuantStack/ipytree>`_), calling ``tree()`` will generate an
 interactive tree representation, see the `repr_tree.ipynb notebook