Merge branch 'ome:master' into master

.github/workflows/build.yml

@@ -4,67 +4,30 @@ on: [push, pull_request]
 
 jobs:
   test:
-    name: Test ${{ matrix.os }} / ${{ matrix.toxenv }}
+    name: Test ${{ matrix.os }}-python${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - {os: windows-latest, python_Version: '3.11', toxenv: 'py311'}
-          - {os: windows-latest, python_Version: '3.10', toxenv: 'py310'}
-          - {os: windows-latest, python_Version: '3.8', toxenv: 'py38'}
-          - {os: windows-latest, python_Version: '3.9', toxenv: 'py39'}
-          - {os: ubuntu-latest, python_Version: '3.11', toxenv: 'py311'}
-          - {os: ubuntu-latest, python_Version: '3.10', toxenv: 'py310'}
-          - {os: ubuntu-latest, python_Version: '3.8', toxenv: 'py38'}
-          - {os: ubuntu-latest, python_Version: '3.9', toxenv: 'py39'}
-          - {os: macos-latest, python_Version: '3.11', toxenv: 'py311'}
-          - {os: macos-latest, python_Version: '3.10', toxenv: 'py310'}
-          - {os: macos-latest, python_Version: '3.8', toxenv: 'py38'}
-          # missing numcodecs wheels on 3.9. conda not yet an option. see gh-51
-          # {os: macos-latest, python_Version: '3.9', toxenv: 'py39'}
-
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        os: ['windows-latest', 'macos-latest', 'ubuntu-latest']
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
-        name: Install Python ${{ matrix.python_version }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python_version }}
-
-      - name: Install ubuntu libraries
-        if: startsWith(matrix.os, 'ubuntu')
-        run: "\
-            sudo apt-get install -y \
-            libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
-            libxcb-image0 libxcb-keysyms1 libxcb-randr0 \
-            libxcb-render-util0 libxcb-xinerama0 \
-            libxcb-xinput0 libxcb-xfixes0"
-
-      - name: Install & test
-        run: |
-          python -m pip install tox
-          tox -e ${{ matrix.toxenv }}
-
-  test_coverage:
-    name: Test coverage
-    runs-on: macos-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-        name: Install Python '3.10'
-        with:
-          python-version: '3.10'
+          python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
-          python -m pip install -r requirements/requirements-dev.txt
-
-      - name: Test
-        run: tox -e  'py310-coverage'
+            python -m pip install --upgrade pip
+            python -m pip install tox tox-gh-actions
+      - name: Test with tox
+        run: tox --conf tox.ini
 
-      - uses: codecov/codecov-action@v2
+      - name: Upload code coverage
+        uses: codecov/codecov-action@v2
         with:
           file: ./coverage.xml
-          fail_ci_if_error: false
+          fail_ci_if_error: true

.gitignore

@@ -6,3 +6,8 @@ build
 dist/
 target/
 docs/build/
+
+# Testing files
+.tox*
+.coverage*
+coverage.xml

.pre-commit-config.yaml

@@ -7,18 +7,18 @@ repos:
       - id: seed-isort-config
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.2.0
     hooks:
       - id: black
         args: [--target-version=py36]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.1
     hooks:
       - id: pyupgrade
         args:
@@ -45,7 +45,7 @@ repos:
           - --autofix
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         additional_dependencies: [
@@ -66,13 +66,13 @@ repos:
         ]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         args: [--config-file=mypy.ini]
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         # args: [--config-data=relaxed]

CHANGELOG.md

@@ -1,3 +1,8 @@
+# 0.8.4 (unreleased)
+
+- 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))
+
 # 0.8.3 (November 2023)
 
 - Fix reading HCS file on AWS S3 ([#322](https://github.com/ome/ome-zarr-py/pull/322))

docs/source/python.rst

@@ -11,7 +11,7 @@ By default, a pyramid of resolution levels will be created by down-sampling the
 of 2 in the X and Y dimensions.
 
 Alternatively, the :py:func:`ome_zarr.writer.write_multiscale` can be used, which takes a
-"pyramid" `numpy` arrays.
+"pyramid" of pre-computed `numpy` arrays.
 
 The following code creates a 3D Image in OME-Zarr::
 

ome_zarr/axes.py

@@ -1,5 +1,6 @@
 """Axes class for validating and transforming axes
 """
+
 from typing import Any, Dict, List, Union
 
 from .format import CurrentFormat, Format

ome_zarr/cli.py

@@ -1,4 +1,5 @@
 """Entrypoint for the `ome_zarr` command-line tool."""
+
 import argparse
 import logging
 import sys

ome_zarr/data.py

@@ -1,4 +1,5 @@
 """Functions for generating synthetic data."""
+
 from random import randrange
 from typing import Callable, List, Optional, Tuple, Union
 

ome_zarr/io.py

@@ -166,27 +166,45 @@ def get_json(self, subpath: str) -> JSONDict:
             return {}
 
     def parts(self) -> List[str]:
-        if self.__store.fs.protocol == "file":
+        if self._isfile():
             return list(Path(self.__path).parts)
         else:
             return self.__path.split("/")
 
     def subpath(self, subpath: str = "") -> str:
-        if self.__store.fs.protocol == "file":
+        if self._isfile():
             filename = Path(self.__path) / subpath
             filename = filename.resolve()
             return str(filename)
-        if self.__store.fs.protocol in ["http", "https"]:
+        elif self._ishttp():
             url = str(self.__path)
             if not url.endswith("/"):
                 url = f"{url}/"
             return urljoin(url, subpath)
         else:
+            # Might require a warning
             if self.__path.endswith("/"):
                 return f"{self.__path}{subpath}"
             else:
                 return f"{self.__path}/{subpath}"
 
+    def _isfile(self) -> bool:
+        """
+        Return whether the current underlying implementation
+        points to a local file or not.
+        """
+        return self.__store.fs.protocol == "file" or self.__store.fs.protocol == (
+            "file",
+            "local",
+        )
+
+    def _ishttp(self) -> bool:
+        """
+        Return whether the current underlying implementation
+        points to a URL
+        """
+        return self.__store.fs.protocol in ["http", "https"]
+
 
 def parse_url(
     path: Union[Path, str], mode: str = "r", fmt: Format = CurrentFormat()

ome_zarr/reader.py

@@ -62,10 +62,12 @@ def __init__(
 
     @overload
     def first(self, spectype: Type["Well"]) -> Optional["Well"]:
+        # Handled by the generic case
         ...
 
     @overload
     def first(self, spectype: Type["Plate"]) -> Optional["Plate"]:
+        # Handled by the generic case
         ...
 
     def first(self, spectype: Type["Spec"]) -> Optional["Spec"]:

ome_zarr/scale.py

@@ -2,6 +2,7 @@
 
 See the :class:`~ome_zarr.scale.Scaler` class for details.
 """
+
 import inspect
 import logging
 import os

ome_zarr/writer.py

@@ -1,6 +1,7 @@
 """Image writer utility
 
 """
+
 import logging
 import warnings
 from pathlib import Path

requirements/requirements-dev.txt

@@ -1,4 +1,4 @@
-fsspec==2023.6.0
+fsspec
 black
 cython >= 0.29.16
 numpy >= 1.16.0

requirements/requirements-test.txt

@@ -1,3 +1,2 @@
 pytest
 pytest-cov
-codecov

setup.py

@@ -19,7 +19,7 @@ def read(fname):
 install_requires += (["dask"],)
 install_requires += (["distributed"],)
 install_requires += (["zarr>=2.8.1"],)
-install_requires += (["fsspec[s3]>=0.8,!=2021.07.0,!=2023.09.0"],)
+install_requires += (["fsspec[s3]>=0.8,!=2021.07.0"],)
 # See https://github.com/fsspec/filesystem_spec/issues/819
 install_requires += (["aiohttp<4"],)
 install_requires += (["requests"],)

tox.ini

@@ -1,26 +1,18 @@
-# tox (https://tox.readthedocs.io/) is a tool for running tests
-# in multiple virtualenvs. This configuration file will run the
-# test suite on all supported python versions. To use it, "pip install tox"
-# and then run "tox" from this directory.
-
 [tox]
-envlist = py{38,39,310,311}
+envlist = py{38,39,310,311,312}
+
+
+[gh-actions]
+python =
+    3.8: py38
+    3.9: py39
+    3.10: py310
+    3.11: py311
+    3.12: py312
 
 [testenv]
-# passenv = DISPLAY XAUTHORITY
-passenv = GITHUB_ACTIONS
 deps =
-    -rrequirements/requirements-dev.txt
-    pytest-xvfb ; sys_platform == 'linux'
-
-commands =
-    pytest {posargs:tests -s}
+    -r requirements/requirements-test.txt
 
-[testenv:py310-coverage]
-passenv =
-    CI
-    GITHUB_ACTIONS
-usedevelop = true
 commands =
-    pytest --cov-report=xml --cov=./ome_zarr  --cov-append {posargs:-v}
-    codecov -f codecov.xml
+    pytest --cov-report=xml --cov=./ome_zarr  --cov-append {posargs}