Merge branch 'develop' into docs/plugin_create

4DNucleome · Apr 22, 2024 · d011273 · d011273
2 parents c3280b4 + f014ed4
commit d011273
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diff --git a/.azure-pipelines/tests.yaml b/.azure-pipelines/tests.yaml
@@ -3,10 +3,10 @@ parameters:
   type: string
 
 steps:
-  - {task: UsePythonVersion@0, inputs: {versionSpec: '3.9'}}
+  - {task: UsePythonVersion@0, inputs: {versionSpec: '3.11'}}
   - template: pip_cache.yaml
     parameters:
-      key: test | requirements/constraints_py3.9.txt | "$(Agent.OS)" | "$(PY)"
+      key: test | requirements/constraints_py3.11.txt | "$(Agent.OS)" | "$(PY)"
       path: ${{ parameters.cache_dir }}
   - task: DownloadPipelineArtifact@2
     inputs:
@@ -16,7 +16,7 @@ steps:
       pip install -U pip wheel setuptools virtualenv
       pip install -r requirements/requirements_dev.txt
     displayName: "Install deps"
-  - script: tox -e py39-PyQt5-azure
+  - script: tox -e py311-PyQt5-azure
     displayName: "Run Tox"
     env:
       CODECOV_TOKEN: $(codecov_token_secret)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -6,3 +6,7 @@ updates:
       interval: "weekly"
 
     target-branch: "develop"
+    groups:
+      github-actions:
+        patterns:
+          - "actions/*"
diff --git a/.github/workflows/base_test_workflow.yml b/.github/workflows/base_test_workflow.yml
@@ -1,3 +1,5 @@
+name: Base Test Workflow
+
 on:
   workflow_call:
     inputs:
@@ -32,6 +34,10 @@ on:
         required: false
         type: number
         default: 60
+      pydantic:
+        required: false
+        type: string
+        default: ""
 
 
 jobs:
@@ -40,12 +46,12 @@ jobs:
     runs-on: ${{ inputs.os }}
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python ${{ inputs.python_version }}
         with:
           python-version: ${{ inputs.python_version }}
           cache: 'pip'
-          cache-dependency-path: 'setup.cfg'
+          cache-dependency-path: 'pyproject.toml'
 
 #      - name: Install ubuntu libraries
 #        if: runner.os == 'Linux'
@@ -69,7 +75,7 @@ jobs:
 
       - name: Download test data
         if: ${{ inputs.test_data }}
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -80,34 +86,27 @@ jobs:
           pip list
 
       - name: Test with tox
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         timeout-minutes: ${{ inputs.timeout }}
         with:
           run: python -m tox ${{ inputs.tox_args }}
         env:
           PYVISTA_OFF_SCREEN: True  # required for opengl on windows
           NAPARI: ${{ inputs.napari }}
           BACKEND: ${{ inputs.qt_backend }}
-          PIP_CONSTRAINT: requirements/constraints_py${{ inputs.python_version }}.txt
+          PIP_CONSTRAINT: requirements/constraints_py${{ inputs.python_version }}${{ inputs.pydantic }}.txt
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: upload pytest timing reports as json
+          name: timing-report-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}-${{ inputs.coverage }}
           path: |
             ./report-*.json
           retention-days: 7
 
-      - uses: actions/upload-artifact@v3
+      - name: Upload coverage data
+        uses: actions/upload-artifact@v4
         if: ${{ inputs.coverage }}
         with:
-          name: coverage_report ${{ inputs.tox_args }}
+          name: cov-reports-${{ inputs.os }}-py-${{ inputs.python_version }}-${{ inputs.napari }}-${{ inputs.qt_backend }}
           path: |
-            ./htmlcov
-          retention-days: 7
-
-      - uses: codecov/codecov-action@v3
-        if: ${{ inputs.coverage }}
-        with:
-          file: ./coverage.xml
-          fail_ci_if_error: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+            ./.coverage.*
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -47,7 +47,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -58,7 +58,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -72,4 +72,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
diff --git a/.github/workflows/semgrep.yml b/.github/workflows/semgrep.yml
@@ -28,7 +28,7 @@ jobs:
 
     steps:
       # Fetch project source with GitHub Actions Checkout.
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # Run the "semgrep ci" command on the command line of the docker image.
       - run: semgrep ci
         env:

diff --git a/.github/workflows/test_napari_repo.yml b/.github/workflows/test_napari_repo.yml
@@ -15,7 +15,7 @@ jobs:
       - shell: bash
         run: bash build_utils/download_data.sh
       - name: Upload test data
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -29,13 +29,13 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ ubuntu-22.04 ]
-        python: ['3.8', '3.9' , '3.10']
-        napari_version: [repo]
+        python: ['3.8', '3.9' , '3.10', '3.11']
+        napari_version: ['repo']
     steps:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 
@@ -54,14 +54,14 @@ jobs:
           pip install setuptools tox tox-gh-actions
 
       - name: Download test data
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: test_data
           path: test_data
 
       - name: Test with tox
         # run tests using pip install --pre
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         timeout-minutes: 60
         with:
           run: tox

diff --git a/.github/workflows/test_napari_widgets.yml b/.github/workflows/test_napari_widgets.yml
@@ -27,7 +27,7 @@ jobs:
     with:
       python_version: "3.10"
       os: ${{ matrix.os }}
-      napari: "napari417"
+      napari: "napari419"
       qt_backend: ${{ matrix.qt_backend }}
       timeout: 10
 
@@ -36,10 +36,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        napari: ["napari414", "napari415", "napari416"]
+        napari: ["napari417", "napari418"]
         qt_backend: ["PyQt5"]
         include:
-          - napari: "napari414"
+          - napari: "napari417"
             qt_backend: "PySide2"
     if: github.event_name == 'push'
     uses: ./.github/workflows/base_test_workflow.yml

diff --git a/.github/workflows/test_prereleases.yml b/.github/workflows/test_prereleases.yml
@@ -8,9 +8,13 @@ on:
     branches:
       - master
       - develop
-      - bugfix/fix_pre_tests
   schedule:
     - cron: '0 */12 * * *'  # every 12 hours
+  pull_request:
+    paths:
+      - '.github/workflows/test_prereleases.yml'
+      - 'pyproject.toml'
+      - 'requirements/pre_test_problematic_version.txt'
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
@@ -23,7 +27,7 @@ jobs:
       - shell: bash
         run: bash build_utils/download_data.sh
       - name: Upload test data
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -43,11 +47,11 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: 'pip'
-          cache-dependency-path: 'setup.cfg'
+          cache-dependency-path: 'pyproject.toml'
 
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
@@ -59,7 +63,7 @@ jobs:
       - uses: tlambert03/setup-qt-libs@v1
 
       - name: Download test data
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: test_data
           path: test_data
@@ -71,7 +75,7 @@ jobs:
 
       - name: Test with tox linux
         # run tests using pip install --pre
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         timeout-minutes: 60
         with:
           run: python -m tox -v --pre
@@ -80,6 +84,7 @@ jobs:
           PYVISTA_OFF_SCREEN: True  # required for opengl on windows
           NAPARI: latest
           BACKEND: PyQt5
+          PIP_CONSTRAINT: requirements/pre_test_problematic_version.txt
 
       # If something goes wrong, we can open an issue in the repo
       - name: Report Failures
@@ -100,7 +105,7 @@ jobs:
     runs-on: "ubuntu-latest"
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       name: Install Python 3.9
       with:
         python-version: 3.9
@@ -111,23 +116,23 @@ jobs:
         pip install pip-tools
     - name: Compile and install PyInstaller requirements
       run: |
-        pip-compile --upgrade -o requirements.txt setup.cfg --extra pyinstaller  --pre
+        pip-compile --upgrade -o requirements.txt pyproject.toml requirements/pre_test_problematic_version.txt --extra pyinstaller  --pre
         pip-sync
         pip install .
     - name: upload requirements
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: requirements
         path: requirements.txt
     - name: Run PyInstaller
       run: python  build_utils/create_and_pack_executable.py
     - name: Upload bundle
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: bundle
         path: dist2/
     - name: Test bundle
-      uses: aganders3/headless-gui@v1
+      uses: aganders3/headless-gui@v2
       timeout-minutes: 60
       with:
         run: dist/PartSeg/PartSeg _test