Fix NA issues after Pandas update #210
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| name: pytest/codecov | |
| on: | |
| push: | |
| # Only perform codecov if autometa or tests have changed... | |
| paths: | |
| - "autometa/**" | |
| - "tests/**" | |
| - "pytest.ini" | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| # Only perform codecov if autometa or tests have changed... | |
| paths: | |
| - "autometa/**" | |
| - "tests/**" | |
| - "pytest.ini" | |
| branches: | |
| - main | |
| - dev | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: [3.8] | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python-version }} | |
| name: pytest & codecov | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Cache conda | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{ hashFiles('tests/environment.yml') }} | |
| - name: Cache test data | |
| uses: actions/cache@v2 | |
| with: | |
| path: tests/data/test_data.json | |
| key: ${{ runner.os }}-test-data | |
| - name: Setup mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: true | |
| activate-environment: autometa | |
| environment-file: tests/environment.yml | |
| - name: Conda config info | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda config --show-sources | |
| conda config --show | |
| printenv | sort | |
| - name: Download test data | |
| shell: bash -l {0} | |
| run: gdown https://drive.google.com/uc\?\id=1bSlPldaq3C6Cf9Y5Rm7iwtUDcjxAaeEk -O tests/data/test_data.json | |
| - name: Install Autometa | |
| shell: bash -l {0} | |
| run: python -m pip install . --ignore-installed --no-deps -vv | |
| - name: Run pytest | |
| shell: bash -l {0} | |
| run: python -m pytest --cov-report=xml --cov=autometa tests/ | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| env_vars: OS,PYTHON | |
| flags: unittests | |
| verbose: true |