Change deprecated scipy.ndimage namespaces in optional imports (#7847) #3
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| # Jenkinsfile.monai-postmerge | |
| name: deploy | |
| on: | |
| # full tests for all the important branches | |
| push: | |
| branches: | |
| - main | |
| - releasing/* | |
| - feature/* | |
| - dev | |
| concurrency: | |
| # automatically cancel the previously triggered workflows when there's a newer version | |
| group: deploy-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| # caching of these jobs: | |
| # - docker-py3-pip- (shared) | |
| # - ubuntu 37 38 39 310-pip- | |
| # - os-latest-pip (shared) | |
| coverage-py3: | |
| # if: github.repository == 'Project-MONAI/MONAI' | |
| if: ${{ false }} # disable self-hosted job project-monai/monai#7039 | |
| container: | |
| image: nvcr.io/nvidia/pytorch:22.04-py3 | |
| options: --gpus all | |
| runs-on: [self-hosted, linux, x64, integration] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: cache weekly timestamp | |
| id: pip-cache | |
| run: | | |
| echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT | |
| - name: cache for pip | |
| if: ${{ startsWith(github.ref, 'refs/heads/dev') }} | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| ~/.cache/torch | |
| key: docker-py3-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install the dependencies | |
| run: | | |
| which python | |
| python -m pip install --upgrade pip wheel | |
| python -m pip install --upgrade torch torchvision | |
| python -m pip install -r requirements-dev.txt | |
| - name: Run unit tests report coverage | |
| run: | | |
| python -m pip list | |
| git config --global --add safe.directory /__w/MONAI/MONAI | |
| git clean -ffdx | |
| df -h | |
| # python -m pip cache info | |
| nvidia-smi | |
| export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1) | |
| echo $CUDA_VISIBLE_DEVICES | |
| trap 'if pgrep python; then pkill python; fi;' ERR | |
| python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null & | |
| python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))" | |
| python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))' | |
| BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests # unit tests with coverage report | |
| BUILD_MONAI=1 ./runtests.sh --build --coverage --net # integration tests with coverage report | |
| coverage xml --ignore-errors | |
| if pgrep python; then pkill python; fi | |
| shell: bash | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: false | |
| files: ./coverage.xml | |
| test-py3x: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: cache weekly timestamp | |
| id: pip-cache | |
| run: | | |
| echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT | |
| - name: cache for pip | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| ~/.cache/torch | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install the dependencies | |
| run: | | |
| find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \; | |
| python -m pip install --upgrade pip wheel | |
| python -m pip install -r requirements-dev.txt | |
| - name: Run quick tests CPU ubuntu | |
| run: | | |
| python -m pip list | |
| python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' | |
| BUILD_MONAI=0 ./runtests.sh --build --quick --unittests | |
| BUILD_MONAI=1 ./runtests.sh --build --quick --min | |
| coverage xml --ignore-errors | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: false | |
| files: ./coverage.xml | |
| install: # pip install from github url, the default branch is dev | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.8' | |
| - name: cache weekly timestamp | |
| id: pip-cache | |
| run: | | |
| echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT | |
| - name: cache for pip | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| ~/.cache/torch | |
| key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install the default branch no build (dev branch only) | |
| if: github.ref == 'refs/heads/dev' | |
| run: | | |
| BUILD_MONAI=0 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI | |
| python -c 'import monai; monai.config.print_config()' | |
| cd $(python -c 'import monai; import os; print(os.path.dirname(monai.__file__))') | |
| ls . | |
| pip uninstall -y monai | |
| - name: Install the default branch with build (dev branch only) | |
| if: github.ref == 'refs/heads/dev' | |
| run: | | |
| find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \; | |
| BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI | |
| python -c 'import monai; monai.config.print_config()' | |
| - name: Get the test cases (dev branch only) | |
| if: github.ref == 'refs/heads/dev' | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: dev | |
| - name: Quick test installed (dev branch only) | |
| if: github.ref == 'refs/heads/dev' | |
| run: | | |
| cd $GITHUB_WORKSPACE | |
| rm -rf monai/ | |
| ls -al . | |
| python -m pip install -r requirements-min.txt | |
| python -m tests.min_tests | |
| env: | |
| QUICKTEST: True |