chore: Update CI configuration to use more modern OS and python versi…

…ons (#1207) ## Summary by Sourcery Update CI configurations to use Ubuntu 24.04 and Python 3.12, ensuring compatibility with the latest environments and dependencies. Build: - Update Azure Pipelines and GitHub Actions to use Ubuntu 24.04 as the default operating system for CI jobs. CI: - Upgrade Python version to 3.12 across various CI workflows and update dependencies accordingly.  ## Summary by CodeRabbit - **Chores** - Updated testing workflows to utilize a newer operating system version (Ubuntu 24.04) and Python version (3.12) for enhanced testing capabilities. - Maintained existing job structures and configurations to ensure continuity in testing processes. - **New Features** - Enhanced compatibility with the latest dependencies and testing environments through updated configurations across various workflows, including broader Python version support (3.9, 3.10, 3.11, 3.12). - Introduced a new job for package checking in the testing workflow to ensure package integrity. - Added a new `SelectDirectoryDialog` class to improve file selection handling. - **Bug Fixes** - Improved dependency management in the environment configuration by removing outdated dependencies and refining the structure for better compatibility and functionality. - **Tests** - Enhanced clarity and specificity of tests for loading and saving dialogs, ensuring they accurately validate functionality with updated method signatures and additional test cases.
4DNucleome · Oct 21, 2024 · 505808a · 505808a
1 parent 895e629
commit 505808a
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Showing 16 changed files with 193 additions and 117 deletions.
diff --git a/.azure-pipelines/pyinstaller.yaml b/.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

diff --git a/.github/workflows/base_test_workflow.yml b/.github/workflows/base_test_workflow.yml
@@ -9,11 +9,15 @@ on:
       os:
         required: false
         type: string
-        default: "ubuntu-20.04"
+        default: "ubuntu-24.04"
       tox_args:
         required: false
         type: string
         default: ""
+      pytest_args:
+        required: false
+        type: string
+        default: ""
       napari:
         required: false
         type: string
@@ -38,6 +42,10 @@ on:
         required: false
         type: string
         default: ""
+      artifact_suffix:
+        required: false
+        type: string
+        default: ""
 
 
 jobs:
@@ -85,21 +93,56 @@ jobs:
           python -m pip install -r requirements/requirements_dev.txt tox-gh-actions>=2.12.0 tox-min-req tox-uv
           pip list
 
-      - name: Test with tox
+      - name: Test with tox PartSegImage
+        if: ${{ inputs.napari == 'latest' }}
+        run: python -m tox ${{ inputs.tox_args }} -- package/tests/test_PartSegImage ${{ inputs.pytest_args }}
+        env:
+          PYVISTA_OFF_SCREEN: True  # required for opengl on windows
+          NAPARI: ${{ inputs.napari }}
+          BACKEND: ${{ inputs.qt_backend }}
+          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
+          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
+
+      - name: Test with tox PartSegCore
+        if: ${{ inputs.napari == 'latest' }}
+        run: python -m tox ${{ inputs.tox_args }} --  package/tests/test_PartSegCore ${{ inputs.pytest_args }}
+        env:
+          PYVISTA_OFF_SCREEN: True  # required for opengl on windows
+          NAPARI: ${{ inputs.napari }}
+          BACKEND: ${{ inputs.qt_backend }}
+          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
+          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
+
+      - name: Test with tox PartSeg
+        if: ${{ inputs.napari == 'latest' }}
         uses: aganders3/headless-gui@v2
         timeout-minutes: ${{ inputs.timeout }}
         with:
-          run: python -m tox ${{ inputs.tox_args }}
+          run: python -m tox ${{ inputs.tox_args }} -- package/tests/test_PartSeg ${{ inputs.pytest_args }}
         env:
           PYVISTA_OFF_SCREEN: True  # required for opengl on windows
           NAPARI: ${{ inputs.napari }}
           BACKEND: ${{ inputs.qt_backend }}
           PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
           UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
 
+      - name: Test with tox all
+        if: ${{ inputs.napari != 'latest' }}
+        uses: aganders3/headless-gui@v2
+        timeout-minutes: ${{ inputs.timeout }}
+        with:
+          run: python -m tox ${{ inputs.tox_args }} -- ${{ inputs.pytest_args }}
+        env:
+          PYVISTA_OFF_SCREEN: True  # required for opengl on windows
+          NAPARI: ${{ inputs.napari }}
+          BACKEND: ${{ inputs.qt_backend }}
+          PIP_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
+          UV_CONSTRAINT: ${{ inputs.napari == 'latest' && format('requirements/constraints_py{0}{1}.txt', inputs.python_version, inputs.pydantic ) || '' }}
+
+
       - uses: actions/upload-artifact@v4
         with:
-          name: timing-report-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}-${{ inputs.coverage }}
+          name: timing-report-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}-${{ inputs.coverage }}${{ inputs.artifact_suffix }}
           path: |
             ./report-*.json
           retention-days: 7
@@ -108,7 +151,7 @@ jobs:
         uses: actions/[email protected]
         if: ${{ inputs.coverage }}
         with:
-          name: cov-reports-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}
+          name: cov-reports-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}${{ inputs.artifact_suffix }}
           include-hidden-files: 'true'
           path: |
             ./.coverage.*
diff --git a/.github/workflows/make_release.yml b/.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

diff --git a/.github/workflows/test_napari_repo.yml b/.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:

diff --git a/.github/workflows/test_napari_widgets.yml b/.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"

diff --git a/.github/workflows/test_prereleases.yml b/.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:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -51,21 +51,24 @@ 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"
@@ -91,7 +94,7 @@ jobs:
       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"
@@ -112,12 +115,18 @@ 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 }}
       os: ${{ matrix.os }}
       qt_backend: ${{ matrix.qt_backend }}
       pydantic: ${{ matrix.pydantic }}
+      artifact_suffix: "-main"
+      pytest_args: "-v"
 
   test_coverage:
     needs: download_data
@@ -182,7 +191,7 @@ 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
@@ -193,7 +202,7 @@ jobs:
           use-mamba: true
           channels: conda-forge
           channel-priority: strict
-          python-version: "3.11"
+          python-version: "3.12"
 
       - uses: tlambert03/setup-qt-libs@v1
 
@@ -236,7 +245,7 @@ jobs:
       - name: Test with tox
         uses: aganders3/headless-gui@v2
         with:
-          run: conda run -n test --no-capture-output tox -e py311-PySide2-conda
+          run: conda run -n test --no-capture-output tox -e py312-PySide2-conda
         timeout-minutes: 60
 
   check-package:

diff --git a/.github/workflows/upgrade-dependencies.yml b/.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

diff --git a/.readthedocs.yml b/.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:

diff --git a/azure-pipelines.yml b/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: '3.12'
           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'