Merge pull request #215 from IFB-ElixirFr/api_v2_jsonLD #644
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| # 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 and test | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: [dev_alban, dev_thomas, master, pre_deploy_1.1] | |
| pull_request: | |
| branches: [dev_alban, dev_thomas, master, pre_deploy_1.1] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| #---------------------------------------------- | |
| # ----- install & configure conda | |
| #---------------------------------------------- | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: 3.8 | |
| conda-build-version: "*" | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| - shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda config --show-sources | |
| conda config --show | |
| printenv | sort | |
| - shell: bash -l {0} | |
| run: | | |
| conda env update -n test --file environment.yml | |
| - name: Create mongoDB Docker container | |
| run: sudo docker run -d -p 27017:27017 mongo:latest | |
| #---------------------------------------------- | |
| # Code quality check | |
| #---------------------------------------------- | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda activate test | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --exclude=.venv,.git --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --exclude=.venv,.git --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| #---------------------------------------------- | |
| # run test suite | |
| #---------------------------------------------- | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda activate test | |
| coverage run --omit '.venv/*' -m pytest tests | |
| coverage report -m |