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

.github/workflows/build.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         os: ['windows-latest', 'macos-latest', 'ubuntu-latest']
     steps:
       - uses: actions/checkout@v4
@@ -27,7 +27,9 @@ jobs:
         run: tox --conf tox.ini
 
       - name: Upload code coverage
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           file: ./coverage.xml
           fail_ci_if_error: true

.github/workflows/pre.yml

@@ -17,8 +17,8 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {os: windows-latest, python_Version: '3.9', toxenv: 'py39'}
-          - {os: macos-latest, python_Version: '3.8', toxenv: 'py38'}
+          - {os: windows-latest, python_Version: '3.11', toxenv: 'py311'}
+          - {os: macos-latest, python_Version: '3.10', toxenv: 'py310'}
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/publish_pypi.yml

@@ -8,13 +8,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
       - name: Build a binary wheel and a source tarball
         run: |
-          python -mpip install wheel build
+          python -mpip install build
           python -m build
       - name: Publish distribution to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@v1.3.0
+        uses: pypa/gh-action-pypi-publish@v1.8.14
         with:
           password: ${{ secrets.PYPI_PASSWORD }}

.isort.cfg

@@ -1,5 +1,5 @@
 [settings]
-known_third_party = dask,numcodecs,numpy,pytest,scipy,skimage,zarr
+known_third_party = dask,fsspec,numcodecs,numpy,pytest,scipy,skimage,zarr
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0

.pre-commit-config.yaml

@@ -12,20 +12,20 @@ repos:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 24.2.0
+    rev: 24.10.0
     hooks:
       - id: black
         args: [--target-version=py36]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.1
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         args:
-          - --py36-plus
+          - --py39-plus
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: .bumpversion.cfg
@@ -45,14 +45,14 @@ repos:
           - --autofix
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         additional_dependencies: [
           # flake8-blind-except, FIXME
           flake8-builtins,
           flake8-rst-docstrings,
-          flake8-logging-format,
+          # flake8-logging-format, FIXME
         ]
         args: [
           # default black line length is 88
@@ -61,12 +61,13 @@ repos:
           # Conflicts with PEP8 and black:
           # W503 line break before binary operator
           # Does not recognize deprecated directive in docstrings
-          "--ignore=E203,RST303, W503",
+          "--ignore=E203,RST303,W503",
+          "--builtins-allowed-modules=csv,io,types",
           "--rst-roles=class,func,ref,mod,meth,const",
         ]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.13.0
     hooks:
       - id: mypy
         args: [--config-file=mypy.ini]
@@ -79,6 +80,6 @@ repos:
         #
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell

CHANGELOG.md

@@ -1,7 +1,18 @@
-# 0.8.4 (unreleased)
+# Unreleased
+
+- Drop support for Python 3.8.
+- Document parameters and return value of `parse_url`.
+
+# 0.9.0 (May 2024)
 
 - Correctly specify maximum compatible fsspec version. ([#338](https://github.com/ome/ome-zarr-py/pull/338))
 - Add tests on Python 3.12. ([#338](https://github.com/ome/ome-zarr-py/pull/338))
+- Write OMERO metadata. ([#261](https://github.com/ome/ome-zarr-py/pull/261))
+- Fixed chunking when a scalar value for chunks is given. Previously
+  passing ``storage_options={"chunks": <int>}`` only set the chunk
+  size of the final dimension. Now the chunk size of all dimensions is
+  set to this value, which is identical behaviour to ``zarr-python``.
+  ([#365](https://github.com/ome/ome-zarr-py/pull/365))
 
 # 0.8.3 (November 2023)
 

README.rst

@@ -6,7 +6,7 @@ ome-zarr-py
 
 Tools for multi-resolution images stored in Zarr filesets, according to the `OME NGFF spec`_.
 
-See `Documentation <https://ome-zarr.readthedocs.io/>`_ for usage information.
+See `Readthedocs <https://ome-zarr.readthedocs.io/>`_ for usage information.
 
 Documentation
 -------------
@@ -56,13 +56,7 @@ Distributed under the terms of the `BSD`_ license,
 "ome-zarr-py" is free and open source software
 
 .. _`OME NGFF spec`: https://github.com/ome/ngff
-.. _`@napari`: https://github.com/napari
 .. _`BSD`: https://opensource.org/licenses/BSD-2-Clause
-.. _`Apache Software License 2.0`: http://www.apache.org/licenses/LICENSE-2.0
-.. _`Mozilla Public License 2.0`: https://www.mozilla.org/media/MPL/2.0/index.txt
-.. _`napari`: https://github.com/napari/napari
-.. _`napari-ome-zarr`: https://github.com/ome/napari-ome-zarr
-.. _`ome-zarr`: https://pypi.org/project/ome-zarr/
 
 .. |pypi| image:: https://badge.fury.io/py/ome-zarr.svg
     :alt: PyPI project

docs/source/cli.rst

@@ -1,3 +1,5 @@
+.. highlight:: bash
+
 
 Command-line tool
 -----------------
@@ -7,50 +9,53 @@ The examples below use the image at http://idr.openmicroscopy.org/webclient/?sho
 
 All examples can be made more or less verbose by passing `-v` or `-q` one or more times::
 
-    # ome_zarr -vvv ...
+    ome_zarr -vvv ...
 
 
 info
 ====
 
-Use the `ome_zarr` command to interrogate Zarr datasets::
+Use the `ome_zarr` command to interrogate Zarr datasets.
+
+Remote data::
 
-    # Remote data
-    $ ome_zarr info https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/
+    ome_zarr info https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/
 
-    # Local data (after downloading as below)
-    $ ome_zarr info 6001240.zarr/
+Local data::
+
+    ome_zarr info 6001240.zarr/
 
 view
 ====
 
 Use the `ome_zarr` command to view Zarr data in the https://ome.github.io/ome-ngff-validator::
 
-    # Local data (after downloading as below)
-    $ ome_zarr view 6001240.zarr/
+    ome_zarr view 6001240.zarr/
 
 download
 ========
 
-To download all the resolutions and metadata for an image::
+To download all the resolutions and metadata for an image use ``ome_zarr download``. This creates ``6001240.zarr`` locally::
+
+    ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/
 
-    # creates local 6001240.zarr/
-    $ ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/
+Specify a different output directory::
 
-    # Specify output directory
-    $ ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ --output image_dir
+    ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ --output image_dir
 
 create
 ======
 
-To create sample OME-Zarr image from the `skimage coins <https://scikit-image.org/docs/stable/api/skimage.data.html#skimage.data.coins>`_
-image::
+To create sample OME-Zarr image from the `skimage <https://scikit-image.org/docs/stable/api/skimage.data.html>`_
+data.
 
-    # Create an OME-Zarr image in coinsdata/ dir:
-    $ ome_zarr create coinsdata
+Create an OME-Zarr image in coinsdata/ dir::
 
-    # Create an rgb image from skimage astronaut in testimage dir:
-    $ ome_zarr create testimage --method=astronaut
+    ome_zarr create coinsdata
+
+Create an rgb image from skimage astronaut in testimage dir::
+
+    ome_zarr create testimage --method=astronaut
 
 csv to labels
 =============
@@ -75,13 +80,13 @@ to specify the data-type for each column (string by default).
  - `s`: `StringColumn`, for text
  - `b`: `BoolColumn`, for true/false
 
-Use e.g. `#d` as a suffix in the column name to denote a `float` column, no spaces etc.:
-```
-"area#d,label_text#s,Width#l,Height#l"
-```
+Use e.g. `#d` as a suffix in the column name to denote a `float` column, no spaces etc.::
+
+    "area#d,label_text#s,Width#l,Height#l"
+
 
 For example, to take values from columns named `area`, `label_text`, `Width` and `Height`
 within a CSV file named `labels_data.csv` with an ID column named `shape_id` and add these
 values to label properties with an ID key of `omero:shapeId` in an Image or Plate named `123.zarr`::
 
-    ome_zarr csv_to_labels labels_data.csv shape_id "area#d,label_text#s,Width#l,Height#l" 123.zarr omero:shapeId```
+    ome_zarr csv_to_labels labels_data.csv shape_id "area#d,label_text#s,Width#l,Height#l" 123.zarr omero:shapeId

docs/source/python.rst

@@ -17,13 +17,11 @@ The following code creates a 3D Image in OME-Zarr::
 
     import numpy as np
     import zarr
-    import os
 
     from ome_zarr.io import parse_url
     from ome_zarr.writer import write_image
 
     path = "test_ngff_image.zarr"
-    os.mkdir(path)
 
     size_xy = 128
     size_z = 10

ome_zarr/axes.py

@@ -1,7 +1,7 @@
 """Axes class for validating and transforming axes
 """
 
-from typing import Any, Dict, List, Union
+from typing import Any, Union
 
 from .format import CurrentFormat, Format
 
@@ -11,7 +11,7 @@
 class Axes:
     def __init__(
         self,
-        axes: Union[List[str], List[Dict[str, str]]],
+        axes: Union[list[str], list[dict[str, str]]],
         fmt: Format = CurrentFormat(),
     ) -> None:
         """
@@ -41,15 +41,15 @@ def validate(self) -> None:
 
     def to_list(
         self, fmt: Format = CurrentFormat()
-    ) -> Union[List[str], List[Dict[str, str]]]:
+    ) -> Union[list[str], list[dict[str, str]]]:
         if fmt.version == "0.3":
             return self._get_names()
         return self.axes
 
     @staticmethod
     def _axes_to_dicts(
-        axes: Union[List[str], List[Dict[str, str]]]
-    ) -> List[Dict[str, str]]:
+        axes: Union[list[str], list[dict[str, str]]]
+    ) -> list[dict[str, str]]:
         """Returns a list of axis dicts with name and type"""
         axes_dicts = []
         for axis in axes:
@@ -74,7 +74,7 @@ def _validate_axes_types(self) -> None:
                 "Too many unknown axes types. 1 allowed, found: %s" % unknown_types
             )
 
-        def _last_index(item: str, item_list: List[Any]) -> int:
+        def _last_index(item: str, item_list: list[Any]) -> int:
             return max(loc for loc, val in enumerate(item_list) if val == item)
 
         if "time" in axes_types and _last_index("time", axes_types) > 0:
@@ -88,7 +88,7 @@ def _last_index(item: str, item_list: List[Any]) -> int:
         ) > axes_types.index("space"):
             raise ValueError("'space' axes must come after 'channel'")
 
-    def _get_names(self) -> List[str]:
+    def _get_names(self) -> list[str]:
         """Returns a list of axis names"""
         axes_names = []
         for axis in self.axes:

ome_zarr/cli.py

@@ -3,7 +3,7 @@
 import argparse
 import logging
 import sys
-from typing import List, Union
+from typing import Union
 
 from .csv import csv_to_zarr
 from .data import astronaut, coins, create_zarr
@@ -81,7 +81,7 @@ def csv_to_labels(args: argparse.Namespace) -> None:
     csv_to_zarr(args.csv_path, args.csv_id, args.csv_keys, args.zarr_path, args.zarr_id)
 
 
-def main(args: Union[List[str], None] = None) -> None:
+def main(args: Union[list[str], None] = None) -> None:
     """Run appropriate function with argparse arguments, handling errors."""
     parser = argparse.ArgumentParser()
     parser.add_argument(

ome_zarr/conversions.py

@@ -1,9 +1,7 @@
 """Simple conversion helpers."""
 
-from typing import List
 
-
-def int_to_rgba(v: int) -> List[float]:
+def int_to_rgba(v: int) -> list[float]:
     """Get rgba (0-1) e.g. (1, 0.5, 0, 1) from integer.
     >>> print(int_to_rgba(0))
     [0.0, 0.0, 0.0, 0.0]
@@ -13,7 +11,7 @@ def int_to_rgba(v: int) -> List[float]:
     return [x / 255 for x in v.to_bytes(4, signed=True, byteorder="big")]
 
 
-def int_to_rgba_255(v: int) -> List[int]:
+def int_to_rgba_255(v: int) -> list[int]:
     """Get rgba (0-255) from integer.
     >>> print(int_to_rgba_255(0))
     [0, 0, 0, 0]