CI fix, forgot to call bash #46
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| # Author - Stuart McAlpine - [email protected] - Jan 2023 | |
| name: DESC Legacy Blinding for Cosmosis | |
| # How does the workflow get triggered? | |
| on: | |
| # Triggers when push/pull-request made to the main branch. | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| # List of jobs for this workflow. | |
| jobs: | |
| # Our pytest job. | |
| legacy_blinding-pytest: | |
| # Our strategy lists the OS and Python versions we want to test on. | |
| strategy: | |
| # Don't quit all jobs if only one job fails. | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9"] | |
| os: [ubuntu-20.04, macos-latest] | |
| include: | |
| - os: ubuntu-20.04 | |
| INSTALL_DEPS: sudo apt-get update && sudo apt-get -y install gfortran-7 swig libopenmpi-dev openmpi-bin libopenblas-dev && sudo ln -s `which gfortran-7` /usr/local/bin/gfortran | |
| - os: macos-latest | |
| INSTALL_DEPS: brew update-reset && HOMEBREW_NO_AUTO_UPDATE=1 HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas && if [ ! -f /usr/local/bin/gfortran ]; then ln -s /usr/local/bin/gfortran-$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1) /usr/local/bin/gfortran; fi | |
| # What operating system is this job running on? | |
| runs-on: ${{ matrix.os }} | |
| # Our CI steps for this job. | |
| steps: | |
| # Check out this repository code. | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: cosmosis-env | |
| channels: conda-forge | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ matrix.pyversion }} | |
| - name: Install dependencies with conda | |
| shell: bash -l {0} | |
| run: mamba install -c conda-forge "cosmosis>=2.5" cosmosis-build-standard-library pytest | |
| # - name: Source cosmosis | |
| # # Install Python. | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Install dependencies | |
| # run: ${{ matrix.INSTALL_DEPS }} | |
| - name: Setup cosmosis standard library | |
| shell: bash -l {0} | |
| run: | | |
| source cosmosis-configure | |
| cosmosis-build-standard-library -i | |
| # Install our package. | |
| - name: Install legacy_blinding | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install . | |
| # Perform the unit test and outputs a coverage report | |
| - name: Test with pytest | |
| run: pytest --cov=blind_2pt_cosmosis --cov-report=xml ./tests | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |