upgrade CI configuartio to use more recent python and runners

.azure-pipelines/pyinstaller.yaml

@@ -5,15 +5,15 @@ parameters:
   type: string
 
 steps:
-  - {task: UsePythonVersion@0, inputs: {versionSpec: '3.11', architecture: x64}}
+  - {task: UsePythonVersion@0, inputs: {versionSpec: '3.12', architecture: x64}}
   - template: pip_cache.yaml
     parameters:
-      key: pyinstaller | requirements/constraints_py3.9.txt | "$(Agent.OS)" | "$(PY)"
+      key: pyinstaller | requirements/constraints_py3.12.txt | "$(Agent.OS)" | "$(PY)"
       path:  ${{ parameters.cache_dir }}
   - bash: |
       python -m pip install -U pip wheel setuptools
     displayName: install libs
-  - bash: python -m pip install .[pyinstaller] -c requirements/constraints_py3.11.txt
+  - bash: python -m pip install .[pyinstaller] -c requirements/constraints_py3.12.txt
     displayName: install partseg
   - bash: |
       python  build_utils/create_and_pack_executable.py --no-simple-zip

.github/workflows/base_test_workflow.yml

@@ -9,7 +9,7 @@ on:
       os:
         required: false
         type: string
-        default: "ubuntu-20.04"
+        default: "ubuntu-24.04"
       tox_args:
         required: false
         type: string

.github/workflows/make_release.yml

@@ -34,7 +34,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
       - uses: tlambert03/setup-qt-libs@v1
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
@@ -44,12 +44,12 @@ jobs:
           if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {Exit 0} else {Exit 1}
         shell: powershell
       - name: Install PartSeg
-        run: python -m pip install --editable ".[pyinstaller]" --constraint requirements/constraints_py3.10.txt
+        run: python -m pip install --editable ".[pyinstaller]" --constraint requirements/constraints_py3.12.txt
 
       - name: compile numpy on macos-14
         if: ${{ matrix.os == 'macos-14' }}
         run: |
-          python -m pip install --no-binary numpy numpy --force-reinstall --constraint requirements/constraints_py3.10.txt
+          python -m pip install --no-binary numpy numpy --force-reinstall --constraint requirements/constraints_py3.12.txt
 
       - name: Build PartSeg bundle
         run: python build_utils/create_and_pack_executable.py

.github/workflows/test_napari_repo.yml

@@ -14,7 +14,7 @@ on:
 jobs:
   download_data:
     name: Download test data
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
       - shell: bash
@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ ubuntu-22.04 ]
+        platform: [ ubuntu-24.04 ]
         python: ['3.9' , '3.10', '3.11', '3.12']
         napari_version: ['repo']
     steps:

.github/workflows/test_napari_widgets.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         qt_backend: ["PyQt5", "PySide2"]
-        os: ["ubuntu-22.04"]
+        os: ["ubuntu-24.04"]
     uses: ./.github/workflows/base_test_workflow.yml
     with:
       python_version: "3.10"

.github/workflows/test_prereleases.yml

@@ -21,7 +21,7 @@ on:
 jobs:
   download_data:
     name: Download test data
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
       - shell: bash
@@ -41,7 +41,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [windows-2022, macos-14, ubuntu-22.04]
+        platform: [windows-2022, macos-14, ubuntu-24.04]
         python: [3.12]
     steps:
       - uses: actions/checkout@v4
@@ -108,9 +108,9 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
-      name: Install Python 3.11
+      name: Install Python 3.12
       with:
-        python-version: 3.11
+        python-version: 3.12
     - uses: tlambert03/setup-qt-libs@v1
     - name: Install dependencies
       run: |
@@ -146,7 +146,7 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         PLATFORM: "linux"
-        PYTHON: "3.11"
+        PYTHON: "3.12"
         RUN_ID: ${{ github.run_id }}
         TITLE: '[test-bot] pyinstaller bundle --pre is failing'
       with:

.github/workflows/tests.yml

@@ -51,28 +51,28 @@ jobs:
       fail-fast: false
       matrix:
         python_version: ["3.9", "3.10", "3.11", "3.12"]
-        os: ["ubuntu-20.04"]
+        os: ["ubuntu-24.04"]
         qt_backend: ["PyQt5"]
         tox_args: [ "" ]
         include:
           - python_version: "3.11"
             os: "macos-13"
             qt_backend: "PyQt5"
+          - python_version: "3.12"
+            os: "macos-14"
+            qt_backend: "PyQt6"
           - python_version: "3.11"
-            os: "windows-2019"
+            os: "windows-latest"
             qt_backend: "PyQt5"
           - python_version: "3.10"
             os: "ubuntu-20.04"
             qt_backend: "PySide2"
           - python_version: "3.10"
-            os: "ubuntu-22.04"
+            os: "ubuntu-24.04"
             qt_backend: "PySide6"
           - python_version: "3.12"
             os: "ubuntu-22.04"
             qt_backend: "PyQt6"
-          - python_version: "3.12"
-            os: "ubuntu-24.04"
-            qt_backend: "PyQt5"
           - python_version: "3.10"
             os: "ubuntu-22.04"
             qt_backend: "PyQt5"
@@ -87,14 +87,14 @@ jobs:
 
   base-test-main:
     name: Base py${{ matrix.python_version }}
-    if: github.event_name == 'push'
+    if: github.event_name == 'push' || contains(github.event.pull_request.files, '.github/workflows/test.yml')
     uses: ./.github/workflows/base_test_workflow.yml
     needs: download_data
     strategy:
       fail-fast: false
       matrix:
         python_version: ["3.9", "3.10", "3.11", "3.12"]
-        os: ["ubuntu-20.04", "macos-13", "windows-2019"]
+        os: ["ubuntu-24.04", "macos-14", "windows-2022"]
         qt_backend: ["PySide2", "PyQt5"]
         include:
           - python_version: "3.12"
@@ -115,6 +115,10 @@ jobs:
             qt_backend: "PySide2"
           - python_version: "3.12"
             qt_backend: "PySide2"
+          - os: "macos-14"
+            qt_backend: "PySide2"
+          - os: macos-14
+            python_version: "3.9"
     with:
       test_data: True
       python_version: ${{ matrix.python_version }}
@@ -185,7 +189,7 @@ jobs:
 
   test_conda:
     name: Test PartSeg conda
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     needs: download_data
     steps:
       - uses: actions/checkout@v4
@@ -196,7 +200,7 @@ jobs:
           use-mamba: true
           channels: conda-forge
           channel-priority: strict
-          python-version: "3.11"
+          python-version: "3.12"
 
       - uses: tlambert03/setup-qt-libs@v1
 

.github/workflows/upgrade-dependencies.yml

@@ -25,7 +25,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: pip
           cache-dependency-path: 'pyproject.toml'
       - name: Upgrade Python dependencies

.readthedocs.yml

@@ -19,15 +19,15 @@ formats: all
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
   apt_packages:
     - graphviz
 
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: requirements/constraints_py3.11_docs.txt
+    - requirements: requirements/constraints_py3.12_docs.txt
     - method: pip
       path: .
       extra_requirements:

azure-pipelines.yml

@@ -17,13 +17,13 @@ stages:
   - stage: GetTestData
     jobs:
     - job: linux
-      pool: {vmImage: 'Ubuntu-22.04'}
+      pool: {vmImage: 'Ubuntu-24.04'}
       steps:
         - script: bash build_utils/download_data.sh
           displayName: "download data"
         - task: UsePythonVersion@0
           inputs:
-            versionSpec: '3.11'
+            versionSpec: '3.2'
           displayName: 'Use Python $(python.version)'
         - script: python build_utils/cut_changelog.py changelog_cut.md
           displayName: "Cut changelog"
@@ -59,9 +59,9 @@ stages:
       - job: manifest_check
         pool: {vmImage: 'Ubuntu-latest'}
         steps:
-          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.10', architecture: x64}}
+          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.12', architecture: x64}}
           - bash: |
-              python -m pip install check-manifest==0.49 numpy==1.22.3
+              python -m pip install check-manifest==0.50 numpy==2.0.2
             displayName: InstallDeps
           - bash: check-manifest
             displayName: check-manifest
@@ -74,10 +74,10 @@ stages:
         variables:
           pip_cache_dir: $(Pipeline.Workspace)/.pip
         steps:
-          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.11', architecture: x64}}
+          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.12', architecture: x64}}
           - template: .azure-pipelines/pip_cache.yaml
             parameters:
-              key: doc | requirements/constraints_py3.11_docs.txt | "$(PY)"
+              key: doc | requirements/constraints_py3.12_docs.txt | "$(PY)"
               path: $(pip_cache_dir)
           - bash: |
               python -m pip install tox
@@ -91,24 +91,24 @@ stages:
               artifactName: docs
 
       - job: Notebook_check
-        pool: {vmImage: 'Ubuntu-22.04'}
+        pool: {vmImage: 'Ubuntu-24.04'}
         continueOnError: true
         variables:
           DATA_PATH: typy_neuronow2
           pip_cache_dir: $(Pipeline.Workspace)/.pip
         steps:
-          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.11', architecture: x64}}
+          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.12', architecture: x64}}
           - template: .azure-pipelines/pip_cache.yaml
             parameters:
-              key: notebook | requirements/constraints_py3.11.txt | "$(PY)"
+              key: notebook | requirements/constraints_py3.12.txt | "$(PY)"
               path: $(pip_cache_dir)
           - bash: |
               python -m pip install tox
             displayName: "Install tox"
           - bash: tox -e jupyter
             displayName: "Run Notebook"
             env:
-              PIP_CONSTRAINT: requirements/constraints_py3.11.txt
+              PIP_CONSTRAINT: requirements/constraints_py3.12.txt
 
   - stage: Tests_linux
     dependsOn: [GetTestData, formatting_check]
@@ -117,7 +117,7 @@ stages:
       pip_cache_dir: $(Pipeline.Workspace)/.pip
     jobs:
     - job: test_linux
-      pool: { vmImage: 'ubuntu-22.04' }
+      pool: { vmImage: 'ubuntu-24.04' }
       variables:
         AZURE_PIPELINES: 1
         DISPLAY: ':99.0'

build_utils/create_environment_yml.sh

@@ -10,6 +10,6 @@ channels:
   - conda-forge
 dependencies:
 $dependencies
-  - pyside2
-  - python=3.11
+  - pyqt6
+  - python=3.12
 EOF

requirements/constraints_py3.11_docs.txt → requirements/constraints_py3.12_docs.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --python-version 3.11 --output-file requirements/constraints_py3.11_docs.txt pyproject.toml --extra docs --extra pyqt6
+#    uv pip compile --python-version 3.12 --output-file requirements/constraints_py3.12_docs.txt pyproject.toml --extra docs --extra pyqt6
 alabaster==1.0.0
     # via sphinx
 annotated-types==0.7.0
@@ -12,6 +12,8 @@ appdirs==1.4.4
     #   napari
     #   npe2
     #   pint
+appnope==0.1.4
+    # via ipykernel
 asttokens==2.4.1
     # via stack-data
 attrs==24.2.0
@@ -43,7 +45,7 @@ comm==0.2.2
     # via ipykernel
 czifile==2019.7.2
     # via partseg (pyproject.toml)
-dask==2024.9.1
+dask==2024.10.0
     # via napari
 debugpy==1.8.7
     # via ipykernel
@@ -89,8 +91,6 @@ imageio==2.36.0
     #   scikit-image
 imagesize==1.4.1
     # via sphinx
-importlib-metadata==8.5.0
-    # via dask
 in-n-out==0.2.1
     # via app-model
 ipykernel==6.29.5
@@ -218,7 +218,7 @@ partsegdata==0.10.0
     # via partseg (pyproject.toml)
 pexpect==4.9.0
     # via ipython
-pillow==10.4.0
+pillow==11.0.0
     # via
     #   imageio
     #   napari
@@ -233,7 +233,7 @@ pooch==1.8.2
     # via scikit-image
 prompt-toolkit==3.0.48
     # via ipython
-psutil==6.0.0
+psutil==6.1.0
     # via
     #   ipykernel
     #   napari
@@ -263,7 +263,7 @@ pydantic-compat==0.1.2
     # via app-model
 pydantic-core==2.23.4
     # via pydantic
-pydantic-settings==2.5.2
+pydantic-settings==2.6.0
     # via autodoc-pydantic
 pygments==2.18.0
     # via
@@ -343,7 +343,7 @@ scipy==1.14.1
     #   partseg (pyproject.toml)
     #   napari
     #   scikit-image
-sentry-sdk==2.16.0
+sentry-sdk==2.17.0
     # via partseg (pyproject.toml)
 shellingham==1.5.4
     # via typer
@@ -428,7 +428,6 @@ typing-extensions==4.12.2
     #   app-model
     #   flexcache
     #   flexparser
-    #   ipython
     #   magicgui
     #   napari
     #   pint
@@ -455,5 +454,3 @@ xlrd==2.0.1
     # via partseg (pyproject.toml)
 xlsxwriter==3.2.0
     # via partseg (pyproject.toml)
-zipp==3.20.2
-    # via importlib-metadata