Add support for BCEWithLogitsLoss in DiceCELoss
#22594
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |