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Merge branch 'dev' into refactor/remap-labels-sequential
2 parents d999603 + c44ea23 commit b69af40

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13 files changed

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‎.github/workflows/chatops.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: dispatch
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uses: peter-evans/[email protected].0
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uses: peter-evans/[email protected].2
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with:
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token: ${{ secrets.PR_MAINTAIN }}
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reaction-token: ${{ secrets.GITHUB_TOKEN }}

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

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

‎.github/workflows/docker.yml‎

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

‎.github/workflows/integration.yml‎

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

‎.github/workflows/pythonapp-min.yml‎

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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: cache for pip
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uses: actions/cache@v4
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uses: actions/cache@v5
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id: cache
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: cache for pip
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uses: actions/cache@v4
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uses: actions/cache@v5
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id: cache
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: cache for pip
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uses: actions/cache@v4
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uses: actions/cache@v5
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id: cache
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with:
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path: ${{ steps.pip-cache.outputs.dir }}

‎.github/workflows/pythonapp.yml‎

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@@ -33,16 +33,7 @@ jobs:
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uses: actions/setup-python@v6
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with:
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python-version: '3.9'
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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- name: cache for pip
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uses: actions/cache@v4
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id: cache
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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uses: actions/setup-python@v6
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with:
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python-version: '3.9'
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cache: 'pip'
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- name: Prepare pip wheel
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run: |
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which python
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python -m pip install --upgrade pip wheel
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: cache for pip
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uses: actions/cache@v4
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id: cache
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
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- if: runner.os == 'windows'
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name: Install torch cpu from pytorch.org (Windows only)
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run: |
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uses: actions/setup-python@v6
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with:
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python-version: '3.9'
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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- name: cache for pip
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uses: actions/cache@v4
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id: cache
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with:
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path: |
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~/.cache/pip
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~/.cache/torch
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key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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python -m pip install --user --upgrade pip setuptools wheel twine packaging
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# install the latest pytorch for testing
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# however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
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# fresh torch installation according to pyproject.toml
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python -m pip install torch>=2.5.1 torchvision
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python -m pip install torch>=2.5.1 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
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- name: Check packages
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run: |
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pip uninstall monai
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working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
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run: |
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# install from wheel
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python -m pip install monai*.whl
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python -m pip install monai*.whl --extra-index-url https://download.pytorch.org/whl/cpu
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python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
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python -c 'import monai; print(monai.__file__)'
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python -m pip uninstall -y monai
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# install from tar.gz
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name=$(ls *.tar.gz | head -n1)
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echo $name
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python -m pip install $name[all]
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python -m pip install $name[all] --extra-index-url https://download.pytorch.org/whl/cpu
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python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
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python -c 'import monai; print(monai.__file__)'
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- name: Quick test
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cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
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cp -r ${{ steps.root.outputs.pwd }}/tests .
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ls -al
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python -m pip install -r requirements-dev.txt
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python -m pip install -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu
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python -m unittest -v
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PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354
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uses: actions/setup-python@v6
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with:
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python-version: '3.9'
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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- name: cache for pip
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uses: actions/cache@v4
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id: cache
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with:
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path: |
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~/.cache/pip
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~/.cache/torch
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key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip wheel
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python -m pip install -r docs/requirements.txt
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python -m pip install -r docs/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu
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- name: Make html
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run: |
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cd docs/

‎.github/workflows/release.yml‎

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- if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
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name: Upload artifacts
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uses: actions/upload-artifact@v5
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uses: actions/upload-artifact@v6
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name: dist
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path: dist/
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python setup.py build
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cat build/lib/monai/_version.py
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- name: Upload version
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uses: actions/upload-artifact@v5
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uses: actions/upload-artifact@v6
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with:
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name: _version.py
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path: build/lib/monai/_version.py

‎.github/workflows/setupapp.yml‎

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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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- name: cache for pip
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if: ${{ startsWith(github.ref, 'refs/heads/dev') }}
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uses: actions/cache@v4
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uses: actions/cache@v5
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id: cache
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with:
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path: |
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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- name: cache for pip
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uses: actions/cache@v4
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uses: actions/cache@v5
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id: cache
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with:
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path: |
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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- name: cache for pip
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uses: actions/cache@v4
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uses: actions/cache@v5
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id: cache
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with:
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path: |

‎.github/workflows/weekly-preview.yml‎

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

‎monai/bundle/scripts.py‎

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import re
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import urllib
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import warnings
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import zipfile
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from collections.abc import Mapping, Sequence
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from functools import partial
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from pathlib import Path
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from torch.cuda import is_available
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from monai._version import get_versions
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from monai.apps.utils import _basename, download_url, extractall, get_logger
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from monai.apps.utils import _basename, _extract_zip, download_url, extractall, get_logger
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from monai.bundle.config_parser import ConfigParser
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from monai.bundle.utils import DEFAULT_INFERENCE, DEFAULT_METADATA, merge_kv
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from monai.bundle.workflows import BundleWorkflow, ConfigWorkflow
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if remove_prefix:
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filename = _remove_ngc_prefix(filename, prefix=remove_prefix)
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extract_path = download_path / f"{filename}"
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with zipfile.ZipFile(zip_path, "r") as z:
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z.extractall(extract_path)
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logger.info(f"Writing into directory: {extract_path}.")
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_extract_zip(zip_path, extract_path)
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logger.info(f"Writing into directory: {extract_path}.")
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def _get_ngc_token(api_key, retry=0):

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