Merge branch 'cicd_test_update' of github.com:ericspod/MONAI into cicd_test_update

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Author: ericspod

.dockerignore

@@ -3,11 +3,15 @@
 __pycache__/
 docs/
 
+.vscode
+.git
+.mypy_cache
+.ruff_cache
+.pytype
 .coverage
 .coverage.*
 .coverage/
 coverage.xml
 .readthedocs.yml
-*.toml
 
 !README.md

.github/workflows/chatops.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: dispatch
-        uses: peter-evans/slash-command-dispatch@v5.0.0
+        uses: peter-evans/slash-command-dispatch@v5.0.2
         with:
           token: ${{ secrets.PR_MAINTAIN }}
           reaction-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/cicd_tests.yml

@@ -48,21 +48,12 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+        cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
-    - name: Lint and type check with "./runtests.sh --build --${{ matrix.opt }}"
+        python -m pip install --no-build-isolation -r requirements-dev.txt
+    - name: Lint and type check
       run: |
         # clean up temporary files
         $(pwd)/runtests.sh --build --clean
@@ -186,23 +177,11 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
+        cache: 'pip'
     - name: Prepare pip wheel
       run: |
         which python
         python -m pip install --upgrade pip wheel
-        python -m pip install --user more-itertools>=8.0
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-      shell: bash
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: ${{ steps.pip-cache.outputs.dir }}
-        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
@@ -216,14 +195,14 @@ jobs:
         python -m pip install --user --upgrade pip wheel
         python -m pip install torch==2.5.1 torchvision==0.20.1
         cat "requirements-dev.txt"
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation -r requirements-dev.txt
         python -m pip list
-        python setup.py develop  # test no compile installation
+        python -m pip install -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ runner.os }})
       run: |
-        python setup.py develop --uninstall
-        BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
+        python -m pip uninstall -y monai
+        BUILD_MONAI=1 python -m pip install -e .  # compile the cpp extensions
       shell: bash
     - name: Run quick tests
       run: |
@@ -255,25 +234,14 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+        cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --user --upgrade pip setuptools wheel twine packaging
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch\>=2.5.1 torchvision
+        python -m pip install torch>=2.5.1 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Check packages
       run: |
         pip uninstall monai
@@ -302,7 +270,7 @@ jobs:
       working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
       run: |
         # install from wheel
-        python -m pip install monai*.whl
+        python -m pip install monai*.whl --extra-index-url https://download.pytorch.org/whl/cpu
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'
         python -m pip uninstall -y monai
@@ -313,7 +281,7 @@ jobs:
         # install from tar.gz
         name=$(ls *.tar.gz | head -n1)
         echo $name
-        python -m pip install $name[all]
+        python -m pip install $name[all] --extra-index-url https://download.pytorch.org/whl/cpu
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'
     - name: Quick test
@@ -323,7 +291,30 @@ jobs:
         cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
         cp -r ${{ steps.root.outputs.pwd }}/tests .
         ls -al
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu
         python -m unittest -v
       env:
         PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
+
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.10'
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r docs/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu
+    - name: Make html
+      run: |
+        cd docs/
+        make clean
+        make html 2>&1 | tee tmp_log
+        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi
+        sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
+        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
+      shell: bash

.github/workflows/cron-ngc-bundle.yml

@@ -26,7 +26,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: ~/.cache/pip

.github/workflows/docker.yml

@@ -37,7 +37,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: _version.py
           path: build/lib/monai/_version.py

.github/workflows/integration.yml

@@ -22,7 +22,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: |
@@ -98,7 +98,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: |

.github/workflows/release.yml

@@ -66,7 +66,7 @@ jobs:
 
     - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
       name: Upload artifacts
-      uses: actions/upload-artifact@v5
+      uses: actions/upload-artifact@v6
       with:
         name: dist
         path: dist/
@@ -109,7 +109,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: _version.py
           path: build/lib/monai/_version.py

.github/workflows/setupapp.yml

@@ -35,7 +35,7 @@ jobs:
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
       if: ${{ startsWith(github.ref, 'refs/heads/dev') }}
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: |
@@ -90,23 +90,12 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ steps.pip-cache.outputs.datew }}
+        cache: pip
     - name: Install the dependencies
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation -r requirements-dev.txt
     - name: Run quick tests CPU ubuntu
       env:
         NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
@@ -115,8 +104,8 @@ jobs:
       run: |
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        BUILD_MONAI=0 ./runtests.sh --build --quick --unittests
-        BUILD_MONAI=1 ./runtests.sh --build --quick --min
+        BUILD_MONAI=0 ./runtests.sh --build --coverage --quick --unittests
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --quick --min
         coverage xml --ignore-errors
     - name: Upload coverage
       uses: codecov/codecov-action@v5
@@ -136,7 +125,7 @@ jobs:
       run: |
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: |

.github/workflows/weekly-preview.yml

@@ -21,7 +21,7 @@ jobs:
       run: |
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: ~/.cache/pip

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -27,46 +27,18 @@ repos:
       - id: end-of-file-fixer
       - id: mixed-line-ending
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.14.11
     hooks:
-    -   id: ruff
-        args:
-        - --fix
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.0
-    hooks:
-      - id: pyupgrade
-        args: [--py39-plus, --keep-runtime-typing]
-        name: Upgrade code with exceptions
+    -   id: ruff-check
+        args: ["--fix"]
         exclude: |
           (?x)(
               ^versioneer.py|
-              ^monai/_version.py|
-              ^monai/networks/| # avoid typing rewrites
-              ^monai/apps/detection/utils/anchor_utils.py| # avoid typing rewrites
-              ^tests/test_compute_panoptic_quality.py # avoid typing rewrites
+              ^monai/_version.py
           )
 
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.5.0
-    hooks:
-      - id: yesqa
-        name: Unused noqa
-        additional_dependencies:
-          - flake8>=3.8.1
-          - flake8-bugbear<=24.2.6
-          - flake8-comprehensions
-          - pep8-naming
-        exclude: |
-          (?x)^(
-              monai/__init__.py|
-              docs/source/conf.py|
-              tests/utils.py
-          )$
-
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.5.0
+    rev: v2.6.0
     hooks:
       - id: pycln
         args: [--config=pyproject.toml]