Upgrade python support to 3.10-3.12, fix deprecation errors

.github/workflows/test_and_deploy.yml

@@ -1,14 +1,11 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: test and deploy
 
 on:
   push:
     branches:
       - main
     tags:
-      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+      - "v*"
   pull_request:
     branches:
       - main
@@ -18,76 +15,109 @@ jobs:
   test:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.platform }}
+
     strategy:
+      fail-fast: false
       matrix:
-# platform: [ubuntu-latest, windows-latest] # , macos-latest
-        platform: [ubuntu-latest]
-        python-version: ['3.8', '3.9'] #issues with monai and 3.10; pausing for now. users should use python 3.9
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
+          cache: pip
 
-# these libraries enable testing on Qt on linux
-      - uses: tlambert03/setup-qt-libs@v1
+      - name: Install Qt libraries on Linux
+        if: runner.os == 'Linux'
+        uses: tlambert03/setup-qt-libs@v1
 
-# strategy borrowed from vispy for installing opengl libs on windows
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
+        shell: pwsh
         run: |
           git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
-          powershell gl-ci-helpers/appveyor/install_opengl.ps1
-          if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {Exit 0} else {Exit 1}
-
-# note: if you need dependencies from conda, considering using
-# setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-# and
-# tox-conda: https://github.com/tox-dev/tox-conda
-      - name: Install dependencies
+          ./gl-ci-helpers/appveyor/install_opengl.ps1
+          if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {
+            exit 0
+          } else {
+            exit 1
+          }
+
+      - name: Install tox
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools tox tox-gh-actions
-          python -m pip install tifffile
-          python -m pip install monai[nibabel,einops,tifffile]
-#         pip install git+https://github.com/lucasb-eyer/pydensecrf.git@master#egg=pydensecrf
-
-# this runs the platform-specific tests declared in tox.ini
-      - name: Test with tox
-        uses: GabrielBB/xvfb-action@v1 # aganders3/headless-gui@v1
+          python -m pip install tox tox-gh-actions
+
+      - name: Test with tox on Linux
+        if: runner.os == 'Linux'
+        uses: GabrielBB/xvfb-action@v1
         with:
           run: python -m tox
         env:
           PLATFORM: ${{ matrix.platform }}
+          QT_API: pyqt6
+          PYTEST_QT_API: pyqt6
+          VISPY_USE_APP: pyqt6
+          QT_OPENGL: software
+          PYVISTA_OFF_SCREEN: true
 
-      - name: Coverage
-        uses: codecov/codecov-action@v2
+      - name: Test with tox on Windows/macOS
+        if: runner.os != 'Linux'
+        run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+          QT_API: pyqt6
+          PYTEST_QT_API: pyqt6
+          VISPY_USE_APP: pyqt6
+          QT_OPENGL: software
+          PYVISTA_OFF_SCREEN: true
+
+      - name: Upload coverage
+        if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: codecov/codecov-action@v6
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   deploy:
-# this will run when you have tagged a commit, starting with "v*"
-# and requires that you have put your twine API key in your
-# github secrets (see readme for details)
     needs: [test]
     runs-on: ubuntu-latest
-    if: contains(github.ref, 'tags')
+    if: startsWith(github.ref, 'refs/tags/v')
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
+        with:
+            fetch-depth: 0
+
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.x"
-      - name: Install dependencies
+          python-version: "3.12"
+
+      - name: Install build tools
         run: |
           python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine build
-      - name: Build and publish
+          python -m pip install build twine
+
+      - name: Build package
+        run: |
+          python -m build
+
+      - name: Check package
+        run: |
+          python -m twine check dist/*
+
+      - name: Publish to PyPI
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
         run: |
-          git tag
-          python -m build .
           twine upload dist/*

napari_cellseg3d/__init__.py

@@ -1,3 +1,8 @@
 """napari-cellseg3d - napari plugin for cell segmentation."""
 
-__version__ = "0.2.2"
+try:
+    from napari_cellseg3d._version import version as __version__
+except ImportError:
+    from importlib.metadata import version
+
+    __version__ = version("napari_cellseg3d")