enhances auto3dseg data analyzer info #22212
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| # Jenkinsfile.monai-premerge | |
| name: premerge | |
| on: | |
| # quick tests for pull requests and the releasing branches | |
| push: | |
| branches: | |
| - dev | |
| - main | |
| - releasing/* | |
| pull_request: | |
| concurrency: | |
| # automatically cancel the previously triggered workflows when there's a newer version | |
| group: build-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| # caching of these jobs: | |
| # - docker-py3-pip- (shared) | |
| # - ubuntu py37 pip- | |
| # - os-latest-pip- (shared) | |
| flake8-py3: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| opt: ["codeformat", "pytype", "mypy"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.8' | |
| - name: cache weekly timestamp | |
| id: pip-cache | |
| run: | | |
| echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT | |
| - name: cache for pip | |
| uses: actions/cache@v3 | |
| id: cache | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| python -m pip install -r requirements-dev.txt | |
| - name: Lint and type check | |
| run: | | |
| # clean up temporary files | |
| $(pwd)/runtests.sh --build --clean | |
| # Github actions have 2 cores, so parallelize pytype | |
| $(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2 | |
| quick-py3: # full dependencies installed tests for different OS | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [windows-latest, macOS-latest, ubuntu-latest] | |
| timeout-minutes: 120 | |
| steps: | |
| - if: runner.os == 'windows' | |
| name: Config pagefile (Windows only) | |
| uses: al-cheb/[email protected] | |
| with: | |
| minimum-size: 8GB | |
| maximum-size: 16GB | |
| disk-root: "D:" | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.8' | |
| - name: Prepare pip wheel | |
| run: | | |
| which python | |
| python -m pip install --upgrade pip wheel | |
| - name: cache weekly timestamp | |
| id: pip-cache | |
| run: | | |
| echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT | |
| echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: cache for pip | |
| uses: actions/cache@v3 | |
| id: cache | |
| with: | |
| path: ${{ steps.pip-cache.outputs.dir }} | |
| key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }} | |
| - if: runner.os == 'windows' | |
| name: Install torch cpu from pytorch.org (Windows only) | |
| run: | | |
| python -m pip install torch==1.13.1+cpu torchvision==0.14.1+cpu -f https://download.pytorch.org/whl/torch_stable.html | |
| - if: runner.os == 'Linux' | |
| name: Install itk pre-release (Linux only) | |
| run: | | |
| python -m pip install --pre -U itk | |
| - name: Install the dependencies | |
| run: | | |
| python -m pip install torch==1.13.1 torchvision==0.14.1 | |
| cat "requirements-dev.txt" | |
| python -m pip install -r requirements-dev.txt | |
| python -m pip list | |
| python setup.py develop # test no compile installation | |
| shell: bash | |
| - name: Run compiled (${{ runner.os }}) | |
| run: | | |
| python setup.py develop --uninstall | |
| BUILD_MONAI=1 python setup.py develop # compile the cpp extensions | |
| shell: bash | |
| - name: Run quick tests (CPU ${{ runner.os }}) | |
| run: | | |
| python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' | |
| python -c "import monai; monai.config.print_config()" | |
| python -m unittest -v | |
| env: | |
| QUICKTEST: True | |
| PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 | |
| packaging: | |
| runs-on: ubuntu-latest | |
| env: | |
| QUICKTEST: True | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.8' | |
| - name: cache weekly timestamp | |
| id: pip-cache | |
| run: | | |
| echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT | |
| - name: cache for pip | |
| uses: actions/cache@v3 | |
| id: cache | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| ~/.cache/torch | |
| key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --user --upgrade pip setuptools wheel twine | |
| # install the latest pytorch for testing | |
| # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated | |
| # fresh torch installation according to pyproject.toml | |
| python -m pip install torch>=1.9 torchvision | |
| - name: Check packages | |
| run: | | |
| pip uninstall monai | |
| pip list | grep -iv monai | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| set -e | |
| # build tar.gz and wheel | |
| python setup.py check -m -s | |
| python setup.py sdist bdist_wheel | |
| python -m twine check dist/* | |
| - run: echo "pwd=$PWD" >> $GITHUB_OUTPUT | |
| id: root | |
| - run: echo "tmp_dir=$(mktemp -d)" >> $GITHUB_OUTPUT | |
| id: mktemp | |
| - name: Move packages | |
| run: | | |
| printf ${{ steps.root.outputs.pwd }} | |
| printf ${{ steps.mktemp.outputs.tmp_dir }} | |
| # move packages to a temp dir | |
| cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}" | |
| rm -r build dist monai.egg-info | |
| cd "${{ steps.mktemp.outputs.tmp_dir }}" | |
| ls -al | |
| - name: Install wheel file | |
| working-directory: ${{ steps.mktemp.outputs.tmp_dir }} | |
| run: | | |
| # install from wheel | |
| python -m pip install monai*.whl | |
| python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown" | |
| python -c 'import monai; print(monai.__file__)' | |
| python -m pip uninstall -y monai | |
| rm monai*.whl | |
| - name: Install source archive | |
| working-directory: ${{ steps.mktemp.outputs.tmp_dir }} | |
| run: | | |
| # install from tar.gz | |
| name=$(ls *.tar.gz | head -n1) | |
| echo $name | |
| python -m pip install $name[all] | |
| python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown" | |
| python -c 'import monai; print(monai.__file__)' | |
| - name: Quick test | |
| working-directory: ${{ steps.mktemp.outputs.tmp_dir }} | |
| run: | | |
| # run min tests | |
| cp ${{ steps.root.outputs.pwd }}/requirements*.txt . | |
| cp -r ${{ steps.root.outputs.pwd }}/tests . | |
| ls -al | |
| python -m pip install -r requirements-dev.txt | |
| python -m unittest -v | |
| env: | |
| PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 | |
| build-docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.8' | |
| - name: cache weekly timestamp | |
| id: pip-cache | |
| run: | | |
| echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT | |
| - name: cache for pip | |
| uses: actions/cache@v3 | |
| id: cache | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| ~/.cache/torch | |
| key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| python -m pip install -r docs/requirements.txt | |
| - name: Make html | |
| run: | | |
| cd docs/ | |
| make clean | |
| make html 2>&1 | tee tmp_log | |
| if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi | |
| if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi | |
| shell: bash |