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Merge branch 'dev' into fix-6840
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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/slash-command-dispatch@v4.0.0
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uses: peter-evans/slash-command-dispatch@v5.0.2
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with:
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token: ${{ secrets.PR_MAINTAIN }}
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reaction-token: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/codeql-analysis.yml‎

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steps:
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- name: Checkout repository
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL

‎.github/workflows/conda.yml‎

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steps:
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- if: runner.os == 'windows'
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name: Config pagefile (Windows only)
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uses: al-cheb/configure-pagefile-action@v1.4
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uses: al-cheb/configure-pagefile-action@v1.5
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with:
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minimum-size: 8GB
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maximum-size: 16GB
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disk-root: "D:"
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Clean up disk space
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;

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

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if: github.repository == 'Project-MONAI/MONAI'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Set up Python 3.9
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uses: actions/setup-python@v6
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with:
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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/cron.yml‎

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options: "--gpus all"
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runs-on: [self-hosted, linux, x64, common]
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: apt install
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run: |
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apt-get update
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options: "--gpus all"
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runs-on: [self-hosted, linux, x64, integration]
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Install APT dependencies
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run: |
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apt-get update
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options: "--gpus all"
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runs-on: [self-hosted, linux, x64, integration]
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Install the dependencies
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options: "--gpus all --ipc=host"
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runs-on: [self-hosted, linux, x64, integration]
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Install MONAI
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id: monai-install
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run: |

‎.github/workflows/docker.yml‎

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if: ${{ false }} # disable docker build job project-monai/monai#7450
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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# full history so that we can git describe
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with:
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ref: dev
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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
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needs: versioning_dev
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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with:
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ref: dev
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- name: Download version

‎.github/workflows/integration.yml‎

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@@ -13,7 +13,7 @@ jobs:
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runs-on: [self-hosted, linux, x64, command]
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steps:
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# checkout the pull request branch
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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with:
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token: ${{ secrets.PR_MAINTAIN }}
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repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
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id: pip-cache
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run: echo "datew=$(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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runs-on: [self-hosted, linux, x64, command1]
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steps:
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# checkout the pull request branch
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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with:
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token: ${{ secrets.PR_MAINTAIN }}
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repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
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id: pip-cache
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run: echo "datew=$(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-gpu.yml‎

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options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true # workaround for unsatisfied condition: cuda>=11.6
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runs-on: [self-hosted, linux, x64, common]
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: apt install
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if: github.event.pull_request.merged != true
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run: |

‎.github/workflows/pythonapp-min.yml‎

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os: [windows-latest, macOS-latest, ubuntu-latest]
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timeout-minutes: 40
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Set up Python 3.9
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uses: actions/setup-python@v6
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with:
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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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python-version: ['3.9', '3.10', '3.11', '3.12']
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timeout-minutes: 40
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6
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with:
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echo "dir=$(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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path: ${{ steps.pip-cache.outputs.dir }}
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pytorch-version: ['2.5.1', '2.6.0', '2.7.1', '2.8.0']
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timeout-minutes: 40
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Set up Python 3.9
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uses: actions/setup-python@v6
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with:
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echo "dir=$(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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matrix:
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opt: ["codeformat", "pytype", "mypy"]
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Set up Python 3.9
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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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python -m pip install --upgrade pip wheel
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python -m pip install -r requirements-dev.txt
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python -m pip install --no-build-isolation -r requirements-dev.txt
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- name: Lint and type check
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run: |
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# clean up temporary files
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steps:
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- if: runner.os == 'windows'
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name: Config pagefile (Windows only)
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uses: al-cheb/configure-pagefile-action@v1.4
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uses: al-cheb/configure-pagefile-action@v1.5
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with:
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minimum-size: 8GB
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maximum-size: 16GB
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disk-root: "D:"
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Set up Python 3.9
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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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python -m pip install --user --upgrade pip wheel
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python -m pip install torch==2.5.1 torchvision==0.20.1
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cat "requirements-dev.txt"
108-
python -m pip install -r requirements-dev.txt
88+
python -m pip install --no-build-isolation -r requirements-dev.txt
10989
python -m pip list
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python setup.py develop # test no compile installation
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python -m pip install -e . # test no compile installation
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shell: bash
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- name: Run compiled (${{ runner.os }})
11393
run: |
114-
python setup.py develop --uninstall
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BUILD_MONAI=1 python setup.py develop # compile the cpp extensions
94+
python -m pip uninstall -y monai
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BUILD_MONAI=1 python -m pip install -e . # compile the cpp extensions
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shell: bash
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- name: Run quick tests (CPU ${{ runner.os }})
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run: |
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QUICKTEST: True
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shell: bash
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Set up Python 3.9
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uses: actions/setup-python@v6
137117
with:
138118
python-version: '3.9'
139-
- name: cache weekly timestamp
140-
id: pip-cache
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run: |
142-
echo "datew=$(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
146-
with:
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path: |
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~/.cache/pip
149-
~/.cache/torch
150-
key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
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cache: 'pip'
151120
- name: Install dependencies
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run: |
153122
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
155124
# install the latest pytorch for testing
156125
# however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
157126
# fresh torch installation according to pyproject.toml
158-
python -m pip install torch>=2.5.1 torchvision
127+
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: |
161130
pip uninstall monai
@@ -184,7 +153,7 @@ jobs:
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working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
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run: |
186155
# install from wheel
187-
python -m pip install monai*.whl
156+
python -m pip install monai*.whl --extra-index-url https://download.pytorch.org/whl/cpu
188157
python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
189158
python -c 'import monai; print(monai.__file__)'
190159
python -m pip uninstall -y monai
@@ -195,7 +164,7 @@ jobs:
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# install from tar.gz
196165
name=$(ls *.tar.gz | head -n1)
197166
echo $name
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python -m pip install $name[all]
167+
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
@@ -205,35 +174,24 @@ jobs:
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cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
206175
cp -r ${{ steps.root.outputs.pwd }}/tests .
207176
ls -al
208-
python -m pip install -r requirements-dev.txt
177+
python -m pip install --no-build-isolation -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu
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python -m unittest -v
210179
env:
211180
PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354
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213182
build-docs:
214183
runs-on: ubuntu-latest
215184
steps:
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- uses: actions/checkout@v5
185+
- uses: actions/checkout@v6
217186
- name: Set up Python 3.9
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uses: actions/setup-python@v6
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with:
220189
python-version: '3.9'
221-
- name: cache weekly timestamp
222-
id: pip-cache
223-
run: |
224-
echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
225-
- name: cache for pip
226-
uses: actions/cache@v4
227-
id: cache
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with:
229-
path: |
230-
~/.cache/pip
231-
~/.cache/torch
232-
key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
190+
cache: 'pip'
233191
- name: Install dependencies
234192
run: |
235193
python -m pip install --upgrade pip wheel
236-
python -m pip install -r docs/requirements.txt
194+
python -m pip install -r docs/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu
237195
- name: Make html
238196
run: |
239197
cd docs/

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