MTN fix tests #135
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: ci | |
| on: | |
| pull_request: | |
| push: | |
| branches: main | |
| tags: | |
| - '*' | |
| jobs: | |
| # flake8 linting | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Run flake8 | |
| run: | | |
| pip install flake8 | |
| flake8 | |
| # check manifest/sources consistency | |
| check-manifest: | |
| 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 | |
| - name: Install dependencies | |
| run: pip install check-manifest | |
| - name: Check MANIFEST | |
| run: check-manifest | |
| # unit tests | |
| test: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| mpi_install: [system, conda] | |
| python: [3.8, 3.9] | |
| env: | |
| DICODILE_DATA_HOME: /home/runner/data | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge | |
| - name: Cache test data | |
| uses: actions/cache@v2 | |
| env: | |
| cache-name: cache-test-data | |
| with: | |
| path: ${{ env.DICODILE_DATA_HOME }} | |
| key: ${{ env.cache-name }} | |
| - name: Install MPI | |
| run: | | |
| conda --version | |
| which python | |
| ./ci/install_mpi.sh | |
| env: | |
| MPI_INSTALL: ${{ matrix.mpi_install }} | |
| - name: Run unit tests | |
| run: | | |
| pip install -e .[test] | |
| echo "localhost slots=16">hostfile | |
| export OMPI_MCA_btl_tcp_if_exclude="docker0" | |
| pytest --cov-report=xml --cov=dicodile | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| flags: unittests | |
| fail_ci_if_error: true | |
| verbose: true | |
| # build and publish to PyPI and TestPyPi | |
| build-n-publish: | |
| name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI | |
| runs-on: ubuntu-20.04 | |
| needs: [lint, test, check-manifest] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install pypa/build | |
| run: >- | |
| python -m | |
| pip install | |
| build | |
| --user | |
| - name: Build a binary wheel and a source tarball | |
| run: >- | |
| python -m | |
| build | |
| --sdist | |
| --wheel | |
| --outdir dist/ | |
| - name: Publish distribution 📦 to Test PyPI | |
| if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags')) && github.repository == 'tomMoral/dicodile' | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| # do not fail if the TestPyPi release already | |
| # exists | |
| skip_existing: true | |
| - name: Publish distribution 📦 to PyPI | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') && github.repository == 'tomMoral/dicodile' | |
| uses: pypa/gh-action-pypi-publish@v1.4.2 | |
| with: | |
| password: ${{ secrets.PYPI_API_TOKEN }} |