Bump flask from 1.0.4 to 2.3.2 in /website #172
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| name: Tests | |
| on: [push] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| env: | |
| MYSQL_USER: root | |
| MYSQL_PASSWORD: password | |
| services: | |
| mysql: | |
| image: mysql:8 | |
| env: | |
| # see https://hub.docker.com/_/mysql | |
| MYSQL_ROOT_PASSWORD: ${{ env.MYSQL_PASSWORD }} | |
| ports: | |
| - 3306:3306 | |
| options: >- | |
| --health-cmd="mysqladmin ping" | |
| -health-interval=10s | |
| --health-timeout=5s | |
| --health-retries=5 | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set Python 3.7 and mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh | |
| # Python 3.7 EOL: 27 Jun 2023 | |
| python-version: 3.7 | |
| activate-environment: test | |
| - name: Cache conda | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | | |
| test-${{ hashFiles('environment.yml', 'website/requirements.txt', 'website/tests/requirements.txt') }} | |
| restore-keys: | | |
| test | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get remove r-base r-base-core | |
| mamba env update --file environment.yml --name test | |
| - name: List all packages | |
| run: | | |
| conda list | |
| - name: Display R config | |
| run: | | |
| conda activate test | |
| R -e '.libPaths()' --vanilla -q | |
| - name: Run setup script | |
| run: | | |
| bash setup.sh | |
| env: | |
| MYSQL_PORT: ${{ job.services.mysql.ports['3306'] }} | |
| - name: Check for syntax errors | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| - name: Run deployment script | |
| run: | | |
| cd website | |
| bash deploy.sh | |
| - name: Run tests that can run in parallel | |
| run: | | |
| NPM_BIN=$(npm bin) | |
| cd website | |
| PATH="$PATH:$NPM_BIN" python3 -m pytest | |
| - name: Run sequential tests | |
| run: | | |
| NPM_BIN=$(npm bin) | |
| cd website | |
| PATH="$PATH:$NPM_BIN" python3 -m pytest --cov-append -m 'serial' | |
| - name: Coveralls | |
| run: | | |
| cd website | |
| coveralls | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| lint: | |
| name: Lint code | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set Python 3.7 and mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh | |
| python-version: 3.7 | |
| activate-environment: test | |
| - name: Install dependencies | |
| run: | | |
| conda install flake8 | |
| - name: Lint code with Flake8 | |
| run: flake8 . --count --statistics |