Cellprofiler app + plugin #3544
Workflow file for this run
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| # Copyright (c) MONAI Consortium | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: build | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| 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: | |
| deps_check: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [windows-latest, ubuntu-latest] | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install -r requirements.txt | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| MONAI_ZOO_AUTH_TOKEN: ${{ github.token }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install openslide-tools -y | |
| python -m pip install --upgrade pip wheel | |
| pip install -r requirements-dev.txt | |
| - name: Clean | |
| run: | | |
| $(pwd)/runtests.sh --clean | |
| - name: PyType | |
| run: | | |
| echo $(pwd)/runtests.sh --pytype | |
| - name: Unit Tests | |
| run: | | |
| $(pwd)/runtests.sh --unittests | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: false | |
| file: ./coverage.xml | |
| packaging: | |
| runs-on: ubuntu-latest | |
| env: | |
| MONAI_ZOO_AUTH_TOKEN: ${{ github.token }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-node@v4 | |
| - name: Set up Python | |
| 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: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install openslide-tools -y | |
| python -m pip install --user --upgrade pip setuptools wheel | |
| python -m pip install torch>=1.7 torchvision | |
| - name: Build Package | |
| run: | | |
| ./runtests.sh --clean | |
| BUILD_OHIF=true python setup.py sdist bdist_wheel | |
| ls -l dist | |
| - name: Verify Package | |
| run: | | |
| tmp_dir=$(mktemp -d) | |
| cp dist/monailabel* "$tmp_dir" | |
| rm -r build monailabel*.egg-info | |
| # install from wheel | |
| python -m pip install "$tmp_dir"/monailabel*.whl | |
| python -c 'import monailabel; monailabel.print_config()' 2>&1 | grep -iv "unknown" | |
| python -c 'import monailabel; print(monailabel.__file__)' | |
| # install test utilities | |
| python -m pip install pytest | |
| # start the monailabel server in the background and run the integration tests | |
| ./runtests.sh --net | |
| # cleanup | |
| python -m pip uninstall -y monailabel | |
| rm -r "$tmp_dir" | |
| env: | |
| shell: bash | |
| build-docs: | |
| runs-on: ubuntu-latest | |
| env: | |
| MONAI_ZOO_AUTH_TOKEN: ${{ github.token }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| 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: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install openslide-tools -y | |
| python -m pip install --upgrade pip wheel | |
| python -m pip install -r docs/requirements.txt | |
| - name: Make html | |
| run: | | |
| export PYTHONPATH=$(pwd) | |
| cd docs/ | |
| make clean | |
| make html 2>&1 | tee tmp_log | |
| if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi | |
| shell: bash |