Merge remote-tracking branch 'origin/master' into zarr_v3

.gitignore

@@ -6,7 +6,7 @@ build
 dist/
 target/
 docs/build/
-
+*.DS_Store
 # Testing files
 .tox*
 .coverage*

.readthedocs.yml

@@ -10,17 +10,11 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-    # You can also specify other tool versions:
-    # nodejs: "16"
-    # rust: "1.55"
-    # golang: "1.17"
 
+# Build documentation in the docs/ directory with Sphinx
 sphinx:
   fail_on_warning: true
-
-# Build documentation in the docs/ directory with Sphinx
-# sphinx:
-#    configuration: docs/conf.py
+  configuration: docs/source/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:

CHANGELOG.md

@@ -1,3 +1,9 @@
+# 0.10.3 (Janbuary 2025)
+
+- Document Scaler attributes ([#418](https://github.com/ome/ome-zarr-py/pull/418))
+- Fix dimension separator when downloading files ([#419](https://github.com/ome/ome-zarr-py/pull/419))
+- Exclude bad version of fsspec in deps ([#420](https://github.com/ome/ome-zarr-py/pull/420))
+
 # 0.10.2 (November 2024)
 
 - Drop support for Python 3.8.

README.rst

@@ -64,10 +64,8 @@ Distributed under the terms of the `BSD`_ license,
 
 .. |docs| image:: https://readthedocs.org/projects/ome-zarr/badge/?version=stable
     :alt: Documentation Status
-    :scale: 100%
     :target: https://ome-zarr.readthedocs.io/en/stable/?badge=stable
 
 .. |coverage| image:: https://codecov.io/gh/ome/ome-zarr-py/branch/master/graph/badge.svg
     :alt: Test coverage
-    :scale: 100%
     :target: https://codecov.io/gh/ome/ome-zarr-py

docs/requirements.txt

@@ -1,7 +1,7 @@
 sphinx==8.1.3
 sphinx-rtd-theme==3.0.2
-fsspec==2023.6.0
-zarr==v3.0.0-beta.3
+fsspec
+zarr>=v3.0.0
 dask
 numpy
 scipy

ome_zarr/scale.py

@@ -39,6 +39,21 @@ class Scaler:
     choices. These values can be returned by the
     :func:`~ome_zarr.scale.Scaler.methods` method.
 
+    Attributes:
+        copy_metadata:
+            If `True`, copy Zarr attributes from the input array to the new group.
+        downscale:
+            Downscaling factor.
+        in_place:
+            Does not do anything.
+        labeled:
+            If `True`, check that the values in the downsampled levels are a subset
+            of the values found in the input array.
+        max_layer:
+            The maximum number of downsampled layers to create.
+        method:
+            Downsampling method
+
     >>> import numpy as np
     >>> data = np.zeros((1, 1, 1, 64, 64))
     >>> scaler = Scaler()

ome_zarr/utils.py

@@ -129,7 +129,9 @@ def download(input_path: str, output_dir: str = ".") -> None:
                     for dataset, data in reversed(list(zip(datasets, resolutions))):
                         LOGGER.info("resolution %s...", dataset)
                         with pbar:
-                            data.to_zarr(str(target_path / dataset))
+                            data.to_zarr(
+                                str(target_path / dataset), dimension_separator="/"
+                            )
             else:
                 # Assume a group that needs metadata, like labels
                 zarr.group(str(target_path))

pyproject.toml

@@ -20,8 +20,8 @@ dependencies = [
     "numpy",
     "dask",
     "distributed",
-    "zarr==v3.0.0-beta.3",
-    "fsspec[s3]>=0.8,!=2021.07.0",
+    "zarr>=v3.0.0",
+    "fsspec[s3]>=0.8,!=2021.07.0,!=2023.9.0",
     # See https://github.com/fsspec/filesystem_spec/issues/819
     "aiohttp<4",
     "requests",

tests/test_cli.py

@@ -8,6 +8,16 @@
 from ome_zarr.utils import strip_common_prefix
 
 
+def directory_items(directory: Path):
+    """
+    Get all items (files and folders) in a directory, relative to that directory.
+    """
+    if not directory.is_dir():
+        raise ValueError(f"{directory} is not a directory")
+
+    return sorted([p.relative_to(directory) for p in directory.glob("*")])
+
+
 class TestCli:
     @pytest.fixture(autouse=True)
     def initdir(self, tmpdir):
@@ -40,6 +50,24 @@ def test_astronaut_download(self, tmpdir):
         main(["download", filename, f"--output={out}"])
         main(["info", f"{out}/{basename}"])
 
+        assert directory_items(Path(out) / "data-3") == [
+            Path(".zattrs"),
+            Path(".zgroup"),
+            Path("0"),
+            Path("1"),
+            Path("2"),
+            Path("3"),
+            Path("4"),
+            Path("labels"),
+        ]
+
+        assert directory_items(Path(out) / "data-3" / "1") == [
+            Path(".zarray"),
+            Path("0"),
+            Path("1"),
+            Path("2"),
+        ]
+
     def test_s3_info(self, s3_address):
         main(["info", s3_address])