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Merge branch 'Project-MONAI:dev' into dev
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‎.dockerignore‎

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__pycache__/
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docs/
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.vscode
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.git
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.mypy_cache
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.ruff_cache
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.pytype
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.coverage
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.coverage.*
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.coverage/
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coverage.xml
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.readthedocs.yml
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*.toml
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!README.md

‎.github/workflows/build_docs.yml‎

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name: build_docs
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on:
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push:
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branches:
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- dev
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- main
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- releasing/*
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pull_request:
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branches:
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- dev
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- main
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- releasing/*
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concurrency:
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# automatically cancel the previously triggered workflows when there's a newer version
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group: build-docs-${{ github.event.pull_request.number || github.ref }}
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cancel-in-progress: true
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jobs:
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build-docs:
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runs-on: ubuntu-latest
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env:
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# minimum supported version of Python
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PYTHON_VER1: '3.10'
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steps:
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- uses: actions/checkout@v6
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- name: Set up Python ${{ env.PYTHON_VER1 }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ env.PYTHON_VER1 }}
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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 --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/
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make clean
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make html 2>&1 | tee tmp_log
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if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "Found errors"; grep "ERROR:" tmp_log; exit 1; fi
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sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log # monai#7133
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if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "Found warnings"; grep "WARNING:" tmp_log; exit 1; fi
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shell: bash

‎.github/workflows/cicd_tests.yml‎

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name: tests
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on:
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# quick tests for pull requests and the releasing branches
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push:
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branches:
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- dev
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- main
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- releasing/*
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paths-ignore: # skip if only docs are modified
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- '**.md'
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- '**.rst'
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- 'docs/**'
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pull_request:
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branches:
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- dev
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- main
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- releasing/*
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paths-ignore: # skip if only docs are modified
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- '**.md'
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- '**.rst'
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- 'docs/**'
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concurrency:
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# automatically cancel the previously triggered workflows when there's a newer version
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group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
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cancel-in-progress: true
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# Supported versions of Python and PyTorch are listed here for use below and as documentation
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env:
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# supported versions of Python
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PYTHON_VER1: '3.10'
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PYTHON_VER2: '3.11'
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PYTHON_VER3: '3.12'
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PYTHON_VER4: '3.13'
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# PYTHON_VER5: '3.14' # TODO: not compatible with Torchscript, re-enable once Torchscript removed from MONAI
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# supported versions of PyTorch
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PYTORCH_VER1: '2.8.0'
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PYTORCH_VER2: '2.9.1'
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PYTORCH_VER3: '2.10.0'
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PYTORCH_VER4: '2.11.0'
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TORCHVISION_VER1: '0.23.0' # used for testing with lowest PyTorch version (PYTORCH_VER1), update as needed
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# versions of PyTorch/Torchvision to use for full-dep Windows tests, needed to get around a gloo bug
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WIN_FULLDEP_VER: '2.11.0'
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WIN_FULLDEP_VISION_VER: '0.26.0'
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PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354
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# These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
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# Python and PyTorch in many places using the above environment variables but also hard coded where necessary.
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# When support is dropped for a version it is important to update these as appropriate.
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jobs:
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static-checks: # Perform static type and other checks using runtests.sh
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runs-on: ubuntu-latest
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strategy:
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matrix:
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opt: ["codeformat", "pytype", "mypy"]
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steps:
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- name: Clean unused tools
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf /usr/local/lib/android
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sudo rm -rf /opt/ghc /usr/local/.ghcup
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sudo docker system prune -f
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- uses: actions/checkout@v6
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- name: Set up Python ${{ env.PYTHON_VER1 }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ env.PYTHON_VER1 }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip wheel
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python -m pip install --no-build-isolation -r requirements-dev.txt
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- name: Lint and type check
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run: |
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# clean up temporary files
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$(pwd)/runtests.sh --build --clean
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# Github actions have multiple cores, so parallelize pytype
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$(pwd)/runtests.sh --build --${{ matrix.opt }} -j $(nproc --all)
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min-dep: # Test with minumum dependencies installed for different OS, Python, and PyTorch combinations
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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# Base test cases are to test on all three OSes with the lowest versions of Python and PyTorch, other cases are
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# added below as special cases to cover other Python and PyTorch versions under Ubuntu
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os: [windows-latest, macOS-latest, ubuntu-latest]
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python-version: ['3.10']
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pytorch-version: ['2.8.0']
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include:
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# Test Python versions under Ubuntu with lowest PyTorch version supported
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- os: ubuntu-latest
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pytorch-version: '2.8.0'
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python-version: '3.11'
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- os: ubuntu-latest
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pytorch-version: '2.8.0'
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python-version: '3.12'
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- os: ubuntu-latest
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pytorch-version: '2.8.0'
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python-version: '3.13'
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# - os: ubuntu-latest
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# pytorch-version: '2.9.1'
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# python-version: '3.14'
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# Test PyTorch versions under Ubuntu with lowest Python version supported
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- os: ubuntu-latest
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python-version: '3.10'
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pytorch-version: '2.9.1'
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- os: ubuntu-latest
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python-version: '3.10'
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pytorch-version: '2.10.0'
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- os: ubuntu-latest
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python-version: '3.10'
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pytorch-version: '2.11.0'
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timeout-minutes: 40
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steps:
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- if: runner.os == 'Linux'
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name: Clean unused tools
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf /usr/local/lib/android
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sudo rm -rf /opt/ghc /usr/local/.ghcup
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sudo docker system prune -f
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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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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Prepare pip wheel
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run: |
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which python
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python -m pip install --upgrade pip wheel
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python -m pip install --user more-itertools>=8.0
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- name: Install the minimum dependencies
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run: |
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# min. requirements
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python -m pip install torch==${{ matrix.pytorch-version }}
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python -m pip install -r requirements-min.txt
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python -m pip list
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BUILD_MONAI=0 python setup.py develop # no compile of extensions
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shell: bash
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- if: matrix.os == 'linux-gpu-runner'
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name: Print GPU Info
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run: |
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nvidia-smi
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python -c 'import torch; print(torch.rand(2,2).to("cuda:0"))'
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shell: bash
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- name: Run quick tests
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run: |
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python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
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python -c "import monai; monai.config.print_config()"
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./runtests.sh --min
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shell: bash
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env:
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QUICKTEST: True
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NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
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NGC_ORG: ${{ secrets.NGC_ORG }}
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NGC_TEAM: ${{ secrets.NGC_TEAM }}
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full-dep: # Test with full dependencies installed for different OS runners
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [windows-latest, macOS-latest, ubuntu-latest]
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timeout-minutes: 120
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env:
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QUICKTEST: True
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steps:
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- if: runner.os == 'Linux'
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name: Clean unused tools
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf /usr/local/lib/android
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sudo rm -rf /opt/ghc /usr/local/.ghcup
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sudo docker system prune -f
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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@v1.5
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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@v6
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- name: Set up Python ${{ env.PYTHON_VER1 }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ env.PYTHON_VER1 }}
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cache: 'pip'
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- name: Prepare pip wheel
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run: |
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which python
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python -m pip install --upgrade pip wheel
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- if: runner.os == 'windows'
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name: Install torch cpu from pytorch.org (Windows only)
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run: |
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python -m pip install torch==${WIN_FULLDEP_VER} torchvision==${WIN_FULLDEP_VISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
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shell: bash
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- if: runner.os != 'windows'
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name: Install torch gpu
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run: |
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# install the lowest version of PyTorch supported
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python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
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shell: bash
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- if: runner.os == 'Linux'
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name: Install itk pre-release (Linux only)
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run: |
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python -m pip install --pre -U itk
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shell: bash
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- name: Install the complete dependencies
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run: |
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python -m pip install --user --upgrade pip wheel pybind11 # TODO: pybind11 added for macOS, may not be needed
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#python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
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cat "requirements-dev.txt"
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python -m pip install --no-build-isolation -r requirements-dev.txt
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python -m pip list
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python -m pip install -e . # test no compile installation
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shell: bash
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- name: Run compiled (${{ runner.os }})
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run: |
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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
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run: |
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python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
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python -c "import monai; monai.config.print_config()"
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python -m unittest -v
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shell: bash
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packaging: # Test package generation
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runs-on: ubuntu-latest
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env:
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QUICKTEST: True
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steps:
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- name: Clean unused tools
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf /usr/local/lib/android
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sudo rm -rf /opt/ghc /usr/local/.ghcup
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sudo docker system prune -f
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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 ${{ env.PYTHON_VER1 }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ env.PYTHON_VER1 }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --user --upgrade pip setuptools wheel twine packaging
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# install the latest pytorch for testing
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# however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
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# fresh torch installation according to pyproject.toml
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python -m pip install torch==${PYTORCH_VER1} 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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pip list | grep -iv monai
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git fetch --depth=1 origin +refs/tags/*:refs/tags/*
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set -e
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# build tar.gz and wheel
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python setup.py check -m -s
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python setup.py sdist bdist_wheel
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python -m twine check dist/*
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- run: echo "pwd=$PWD" >> $GITHUB_OUTPUT
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id: root
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- run: echo "tmp_dir=$(mktemp -d)" >> $GITHUB_OUTPUT
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id: mktemp
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- name: Move packages
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run: |
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printf ${{ steps.root.outputs.pwd }}
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printf ${{ steps.mktemp.outputs.tmp_dir }}
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# move packages to a temp dir
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cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}"
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rm -r build dist monai.egg-info
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cd "${{ steps.mktemp.outputs.tmp_dir }}"
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ls -al
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- name: Install wheel file
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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 --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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rm monai*.whl
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- name: Install source archive
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working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
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run: |
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for name in *.tar.gz; do break; done
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echo $name
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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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working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
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run: |
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# run min tests
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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 --no-build-isolation -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu
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python -m unittest -v

‎.github/workflows/conda.yml‎

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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: ["3.9", "3.10"]
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python-version: ["3.10", "3.11"]
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runs-on: ${{ matrix.os }}
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timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
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env:
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run: |
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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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rm -rf /usr/share/dotnet/
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- uses: conda-incubator/setup-miniconda@v3
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- uses: conda-incubator/setup-miniconda@v4
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}

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