Merge pull request #7 from AstraZeneca/zarr-3

Upgrade to zarr-python 3
AstraZeneca · Feb 5, 2025 · 5588b60 · 5588b60
2 parents 3c4e50e + 13ed2b1
commit 5588b60
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diff --git a/.github/release.yml b/.github/release.yml
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -4,97 +4,67 @@ on:
   push:
     branches:
       - main
-    tags:
-      - 'v*'
   pull_request:
     branches:
       - main
   workflow_dispatch:
 
 env:
-  POETRY_VERSION: 1.6.1
+  UV_VERSION: '0.5.26'
 
 jobs:
   check:
     name: Check
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-
-      - name: Install poetry
-        run: pipx install poetry==$POETRY_VERSION
-
-      - name: Set up python
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+
+      # Note: We need to manually install uv because this action is not whitelisted.
+      # - name: Install uv
+      #   uses: astral-sh/setup-uv@v5
+      #   with:
+      #     version: ${{ env.UV_VERSION }}
+      #     enable-cache: true
+      #     cache-dependency-glob: 'uv.lock'
+      - name: Install uv
+        run: pipx install uv==$UV_VERSION
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-          cache: 'poetry'
+          python-version-file: '.python-version'
 
       - name: Install dependencies
-        run: poetry install
+        run: uv sync --all-extras --dev
 
       - name: Run checks
-        run: poetry run invoke check
+        run: uv run invoke check
 
   test:
     needs: [check]
     name: Test py${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11']
+        python-version: ['3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Install poetry
-        run: pipx install poetry==$POETRY_VERSION
+      - name: Install uv
+        run: pipx install uv==$UV_VERSION
 
       - name: Set up python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'poetry'
 
       - name: Install dependencies
         run: |
           sudo apt-get update
           sudo apt-get install qtbase5-dev xvfb
-          poetry install
-          poetry run pip install pyqt5
+          uv sync --all-extras --dev
 
       - name: Run tests
-        run: poetry run xvfb-run invoke test
-
-  release:
-    needs: [test]
-    name: Release
-    runs-on: ubuntu-latest
-    if: contains(github.ref, 'tags')
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Install poetry
-        run: pipx install poetry==$POETRY_VERSION
-
-      - name: Set up python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-
-      - name: Build distribution
-        run: poetry build
-
-      - name: Create release
-        run: |
-          VERSION="${GITHUB_REF/refs\/tags\/}" 
-          if [[ "$VERSION" != *"rc"* ]]; then
-            gh release create $VERSION --verify-tag --generate-notes
-          else
-            gh release create $VERSION --verify-tag --generate-notes --prerelease
-          fi
-          gh release upload $VERSION dist/*
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: xvfb-run uv run invoke test
diff --git a/.gitignore b/.gitignore
@@ -1,84 +1,23 @@
-# Byte-compiled / optimized / DLL files
+# Python
 __pycache__/
 *.py[cod]
-*$py.class
 
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
+# Distribution / Packaging
 dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
 
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
+# Caches
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
 
-# Unit test / coverage reports
-htmlcov/
-.tox/
+# Testing
 .coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-.napari_cache
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask instance folder
-instance/
-
-# Sphinx documentation
-docs/_build/
 
-# MkDocs documentation
-/site/
-
-# PyBuilder
-target/
-
-# Pycharm and VSCode
+# IDEs
+.conda/
 .idea/
+.venv/
 venv/
-.vscode/
-
-# IPython Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
 
 # OS
 .DS_Store
-
-# written by setuptools_scm
-**/_version.py
diff --git a/.napari-hub/DESCRIPTION.md b/.napari-hub/DESCRIPTION.md
@@ -1,36 +1,17 @@
 # Description
 
-This [napari] plugin provides a reader for various whole slide image formats.
-
-By default, any of the following formats is read using the [tifffile] library.
-If the image file contains a tag `GDAL_METADATA`, the [rasterio] library is used
-instead.
-
-- .bif
-- .ndpi
-- .qptiff
-- .scn
-- .svs
-- .tif
-- .tiff
+This [napari] plugin provides a widget for reading various whole-slide image
+formats using a common [zarr] store inteface, based on the libraries
+[openslide], [rasterio], and [wsidicom].
 
 # Quickstart
 
-From the terminal:
-
-```bash
-napari CMU-1.svs
-```
-
-From python:
-
-```python
-import napari
-
-viewer = napari.Viewer()
-viewer.open("CMU-1.svs")
-```
+After installation, open the `Plugins` menu in the viewer and select
+`WSI Reader` to open the widget. Then select a `Backend` to use, select a `Path`
+to open, and click `Load`.
 
 [napari]: https://github.com/napari/napari
+[openslide]: https://github.com/openslide/openslide-python
 [rasterio]: https://github.com/rasterio/rasterio
-[tifffile]: https://github.com/cgohlke/tifffile
+[wsidicom]: https://github.com/imi-bigpicture/wsidicom
+[zarr]: https://github.com/zarr-developers/zarr-python
diff --git a/.python-version b/.python-version
@@ -0,0 +1 @@
+3.11
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -21,24 +21,19 @@ example.
 
 ## Setting up a development environment
 
-This project uses [poetry] packaging and dependency management.
+This project uses [uv] for packaging and dependency management. To install the
+full set of dependencies needed for developement, run:
 
 ```bash
-poetry install
-poetry run pip install pyqt5
-poetry run napari
+uv sync --all-extras --dev
 ```
 
-Note: `pyqt5` is not a direct dependency of this plugin, but is necessary to run
-napari (see the [napari installation guide]).
-
-## Running checks and tests
+To run a code formatter, a linter and all unit tests, run:
 
 ```bash
-poetry run invoke check
-poetry run invoke test
+uv run invoke fix
+uv run invoke check
+uv run invoke test
 ```
 
-[napari installation guide]:
-  https://napari.org/stable/tutorials/fundamentals/installation.html#choosing-a-different-qt-backend
-[poetry]: https://python-poetry.org/
+[uv]: https://github.com/astral-sh/uv