Merge remote-tracking branch 'gh/zarr_v3' into zarr_v3

.github/workflows/publish_pypi.yml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.11'
       - name: Build a binary wheel and a source tarball
         run: |
           python -mpip install build

.isort.cfg

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

CHANGELOG.md

@@ -1,7 +1,12 @@
-# Unreleased
+# 0.10.2 (November 2024)
 
 - Drop support for Python 3.8.
 - Document parameters and return value of `parse_url`.
+* Write metadata using delayed that depends on writing array(s)
+* Document return values of sample data
+* Simplify Python tutorial
+* pin zarr at < 3
+* Update version of pyupgrade
 
 # 0.9.0 (May 2024)
 

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

pyproject.toml

@@ -0,0 +1,64 @@
+[build-system]
+requires = [
+    "setuptools>=64",
+    "setuptools-scm>=8.0",
+]
+build-backend = "setuptools.build_meta"
+
+[tools.setuptools.dynamic]
+version = {attr = "ome_zarr.__version__"}
+
+[project]
+name = "ome-zarr"
+readme = "README.rst"
+dynamic = ["version"]
+description="Implementation of images in Zarr files."
+
+requires-python = ">3.10"
+
+dependencies = [
+    "numpy",
+    "dask",
+    "distributed",
+    "zarr==v3.0.0-beta.3",
+    "fsspec[s3]>=0.8,!=2021.07.0",
+    # See https://github.com/fsspec/filesystem_spec/issues/819
+    "aiohttp<4",
+    "requests",
+    "scikit-image",
+    "toolz",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: BSD License",
+]
+
+authors = [
+    {name = "The Open Microscopy Team"},
+]
+
+[project.entry-points."console_scripts"]
+ome_zarr = "ome_zarr.cli:main"
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+]
+
+[project.urls]
+Documentation = "https://ome-zarr.readthedocs.io"
+Repository = "https://github.com/ome/ome-zarr-py"
+Changelog = "https://github.com/ome/ome-zarr-py/blob/master/CHANGELOG.md"
+
+[tool.setuptools]
+packages = ["ome_zarr"]
+py-modules = ["ome_zarr"]
+
+[tool.setuptools_scm]
+version_file = "ome_zarr/_version.py"

tox.ini

@@ -1,11 +1,9 @@
 [tox]
-envlist = py{39,310,311,312}
+envlist = py{311,312}
 
 
 [gh-actions]
 python =
-    3.9: py39
-    3.10: py310
     3.11: py311
     3.12: py312