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Combining tests
Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
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‎.github/workflows/cicd_tests.yml‎

Lines changed: 220 additions & 147 deletions
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name: premerge-min
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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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cancel-in-progress: true
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jobs:
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static-checks:
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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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- uses: actions/checkout@v4
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- name: Set up Python 3.9
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uses: actions/setup-python@v5
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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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- 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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- name: Lint and type check
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run: |
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# clean up temporary files
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$(pwd)/runtests.sh --build --clean
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# Github actions have 2 cores, so parallelize pytype
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$(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2
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min-dep: # min dependencies installed tests for different OS
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runs-on: ${{ matrix.os }}
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strategy:
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NGC_ORG: ${{ secrets.NGC_ORG }}
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NGC_TEAM: ${{ secrets.NGC_TEAM }}
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# # caching of these jobs:
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# # - docker-py3-pip- (shared)
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# # - ubuntu py37 pip-
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# # - os-latest-pip- (shared)
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# min-dep-os: # min dependencies installed tests for different OS
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# runs-on: ${{ matrix.os }}
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# strategy:
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# fail-fast: false
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# matrix:
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# os: [windows-latest, macOS-latest, ubuntu-latest]
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# timeout-minutes: 40
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# steps:
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# - uses: actions/checkout@v4
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# - name: Set up Python 3.9
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# uses: actions/setup-python@v5
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# with:
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# python-version: '3.9'
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# - name: Prepare pip wheel
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# run: |
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# which python
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# python -m pip install --upgrade pip wheel
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# - name: cache weekly timestamp
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# id: pip-cache
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# run: |
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# echo "datew=$(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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# - name: Install the dependencies
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# run: |
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# # min. requirements
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# python -m pip install torch --index-url https://download.pytorch.org/whl/cpu
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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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# - name: Run quick tests (CPU ${{ runner.os }})
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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: # full dependencies installed tests for different OS
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [windows-latest, macOS-latest, ubuntu-latest]
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timeout-minutes: 120
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steps:
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- if: runner.os == 'windows'
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name: Config pagefile (Windows only)
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uses: al-cheb/configure-pagefile-action@v1.4
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with:
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minimum-size: 8GB
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maximum-size: 16GB
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disk-root: "D:"
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- uses: actions/checkout@v4
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- name: Set up Python 3.9
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uses: actions/setup-python@v5
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with:
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python-version: '3.9'
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- name: Prepare pip wheel
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run: |
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which python
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python -m pip install --upgrade pip wheel
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(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 torch==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
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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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find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
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- name: Install the dependencies
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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"
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python -m pip install -r requirements-dev.txt
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python -m pip list
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python setup.py develop # 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 setup.py develop --uninstall
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BUILD_MONAI=1 python setup.py develop # compile the cpp extensions
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shell: bash
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- name: Run quick tests (CPU ${{ runner.os }})
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run: |
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python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
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python -c "import monai; monai.config.print_config()"
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# python -m unittest -v
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env:
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QUICKTEST: True
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PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354
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packaging:
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runs-on: ubuntu-latest
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env:
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QUICKTEST: True
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shell: bash
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python 3.9
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uses: actions/setup-python@v5
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with:
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python-version: '3.9'
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(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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- 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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- 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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# min-dep-py3: # min dependencies installed tests for different python
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# runs-on: ubuntu-latest
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# strategy:
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# fail-fast: false
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# matrix:
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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@v4
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# - name: Set up Python ${{ matrix.python-version }}
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# uses: actions/setup-python@v5
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# with:
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# python-version: ${{ matrix.python-version }}
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# - name: Prepare pip wheel
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# run: |
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# which python
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# python -m pip install --user --upgrade pip setuptools wheel
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# - name: cache weekly timestamp
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# id: pip-cache
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# run: |
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# echo "datew=$(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: ${{ steps.pip-cache.outputs.dir }}
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# key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
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# - name: Install the dependencies
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# run: |
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# # min. requirements
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# python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
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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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# - name: Run quick tests (CPU ${{ runner.os }})
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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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# 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: ${{ secrets.NGC_TEAM }}
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# build tar.gz and wheel
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python setup.py check -m -s
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python setup.py sdist bdist_wheel
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python -m twine check dist/*
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- run: echo "pwd=$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
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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: ${{ steps.mktemp.outputs.tmp_dir }}
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run: |
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# install from tar.gz
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name=$(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 -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 -r requirements-dev.txt
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python -m unittest -v
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env:
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PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354
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# min-dep-pytorch: # min dependencies installed tests for different pytorch
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# runs-on: ubuntu-latest
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# strategy:
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# fail-fast: false
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# matrix:
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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@v4
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# - name: Set up Python 3.9
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# uses: actions/setup-python@v5
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# with:
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# python-version: '3.9'
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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 --user --upgrade pip setuptools 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: ${{ steps.pip-cache.outputs.dir }}
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# key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
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# - name: Install the 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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# - name: Run quick tests (pytorch ${{ matrix.pytorch-version }})
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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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# 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: ${{ secrets.NGC_TEAM }}
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build-docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.9
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uses: actions/setup-python@v5
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with:
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python-version: '3.9'
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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- name: cache for pip
295+
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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- 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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- 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

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