Merge branch 'develop' into add_read_skew

4DNucleome · Oct 21, 2024 · 7fdfeef · 7fdfeef
2 parents f3e8a54 + 505808a
commit 7fdfeef
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Showing 115 changed files with 967 additions and 1,957 deletions.
diff --git a/.azure-pipelines/pyinstaller.yaml b/.azure-pipelines/pyinstaller.yaml
@@ -5,23 +5,23 @@ 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
     displayName: build
 
-  - task: PublishBuildArtifacts@1
+  - task: PublishPipelineArtifact@1
     inputs:
-      pathToPublish: dist2
-      artifactName: execs
+      targetPath: dist2
+      publishLocation: pipeline
   - script: ${{ parameters.test_path }}
     displayName: TestBuild
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/upload-artifact@v4.4.0
         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
@@ -22,12 +22,12 @@ 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"
       os: ${{ matrix.os }}
-      napari: "napari5"
+      napari: "napari54"
       qt_backend: ${{ matrix.qt_backend }}
       timeout: 10
 
@@ -36,10 +36,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        napari: ["napari417", "napari418"]
+        napari: ["napari419", "napari54"]
         qt_backend: ["PyQt5"]
         include:
-          - napari: "napari417"
+          - napari: "napari54"
             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
@@ -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
@@ -50,24 +50,27 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        os: ["ubuntu-20.04"]
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
+        os: ["ubuntu-24.04"]
         qt_backend: ["PyQt5"]
         tox_args: [ "" ]
         include:
-          - python_version: "3.9"
+          - python_version: "3.11"
             os: "macos-13"
             qt_backend: "PyQt5"
-          - python_version: "3.9"
-            os: "windows-2019"
+          - python_version: "3.12"
+            os: "macos-14"
+            qt_backend: "PyQt6"
+          - python_version: "3.11"
+            os: "windows-latest"
             qt_backend: "PyQt5"
-          - python_version: "3.9"
+          - python_version: "3.10"
             os: "ubuntu-20.04"
             qt_backend: "PySide2"
-          - python_version: "3.9"
-            os: "ubuntu-22.04"
-            qt_backend: "PySide6"
           - python_version: "3.10"
+            os: "ubuntu-24.04"
+            qt_backend: "PySide6"
+          - python_version: "3.12"
             os: "ubuntu-22.04"
             qt_backend: "PyQt6"
           - python_version: "3.10"
@@ -90,20 +93,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        os: ["ubuntu-20.04", "macos-13", "windows-2019"]
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
+        os: ["ubuntu-24.04", "macos-14", "windows-2022"]
         qt_backend: ["PySide2", "PyQt5"]
         include:
-          - python_version: "3.11"
+          - python_version: "3.12"
             qt_backend: "PyQt5"
             os: "ubuntu-22.04"
-          - python_version: "3.9"
+          - python_version: "3.10"
             os: "ubuntu-22.04"
             qt_backend: "PySide6"
-          - python_version: "3.9"
+          - python_version: "3.11"
             os: "ubuntu-22.04"
             qt_backend: "PyQt6"
-          - python_version: "3.10"
+          - python_version: "3.11"
             os: "ubuntu-22.04"
             qt_backend: "PyQt5"
             pydantic: "_pydantic_1"
@@ -112,20 +115,26 @@ 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
     uses: ./.github/workflows/base_test_workflow.yml
     with:
       test_data: True
-      python_version: "3.10"
-      tox_args: "-e py310-PyQt5-coverage"
+      python_version: "3.12"
+      tox_args: "-e py312-PyQt5-coverage"
       coverage: true
 
   test_minimal:
@@ -134,8 +143,8 @@ jobs:
     uses: ./.github/workflows/base_test_workflow.yml
     with:
       test_data: True
-      python_version: "3.8"
-      tox_args: "-e py38-PyQt5-minimal"
+      python_version: "3.9"
+      tox_args: "-e py39-PyQt5-minimal"
       coverage: true
 
   coverage_prepare:
@@ -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
@@ -35,7 +35,7 @@ jobs:
           pip install -U uv
           flags=(--extra pyqt6 --extra pyside2 --extra pyside6 --extra test --extra pyinstaller_base)
 
-          for pyv in 3.8 3.9 3.10 3.11 3.12; do
+          for pyv in 3.9 3.10 3.11 3.12; do
             uv pip compile --python-version ${pyv} --upgrade --output-file requirements/constraints_py${pyv}.txt pyproject.toml requirements/version_denylist.txt "${flags[@]}"
             uv pip compile --python-version ${pyv} --upgrade --output-file requirements/constraints_py${pyv}_pydantic_1.txt pyproject.toml requirements/version_denylist.txt "${flags[@]}" --constraint requirements/pydantic_1.txt
           done