Update train_ms2deepscore_wrapper to use new ms2deepscore training fu… #1274
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| name: CI Build | |
| on: | |
| push: | |
| pull_request: | |
| types: [opened, reopened] | |
| jobs: | |
| thorough_check: | |
| name: Thorough code check / python-3.8 / ubuntu-latest | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Python info | |
| run: | | |
| which python | |
| python --version | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e .[dev] | |
| - name: Show pip list | |
| run: | | |
| pip list | |
| - name: Run test with coverage | |
| run: pytest --cov --cov-report term --cov-report xml -m "not integration" | |
| - name: Check style against standards using prospector | |
| run: prospector -o grouped -o pylint:pylint-report.txt | |
| - name: Check whether import statements are used consistently | |
| run: isort --check-only --diff . | |
| - name: SonarCloud Scan | |
| uses: sonarsource/sonarcloud-github-action@master | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| basic_checks: | |
| name: Basic code checks / python-${{ matrix.python-version }} / ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu-latest', 'macos-latest', 'windows-latest'] | |
| python-version: ['3.8', '3.9'] | |
| exclude: | |
| # already tested in first_check job | |
| - python-version: 3.8 | |
| os: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Python info | |
| run: | | |
| which python | |
| python --version | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e .[dev] | |
| - name: Show pip list | |
| run: | | |
| pip list | |
| - name: Run tests | |
| run: | | |
| pytest -m "not integration" | |
| integration_checks: | |
| name: Integration code checks / python-${{ matrix.python-version }} / ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu-latest'] | |
| python-version: ['3.8'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Python info | |
| run: | | |
| which python | |
| python --version | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e .[dev] | |
| - name: Show pip list | |
| run: | | |
| pip list | |
| - name: Run tests | |
| run: | | |
| pytest -m "integration" | |
| yml_checks: | |
| name: envionment.yml checks / python-${{ matrix.python-version }} / ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| runs-on: 'ubuntu-latest' | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: ms2query | |
| environment-file: ./environment.yml | |
| python-version: 3.8 | |
| - name: activate conda environment | |
| run: | | |
| conda activate ms2query | |
| - name: Show conda list | |
| run: | | |
| conda info | |
| conda list | |
| - name: Run tests | |
| run: | | |
| pytest -m "not integration" |