Enable resuming the importance sampler #426
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Continuous Integration | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| schedule: | |
| # run this every week at 12 noon on Monday | |
| - cron: '0 12 * * 1' | |
| jobs: | |
| build-and-test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9, "3.10", 3.11] | |
| # macos13 runs on until and macos14 now runs on arm64 | |
| os: [ubuntu-20.04, macos-latest, macos-13] | |
| exclude: | |
| # Python 3.7 is not available on M1 Mac homebrew | |
| - os: macos-latest | |
| python-version: 3.7 | |
| include: | |
| - os: ubuntu-20.04 | |
| INSTALL_DEPS: sudo apt-get update && sudo apt-get -y install gfortran-7 swig libopenmpi-dev openmpi-bin libopenblas-dev && sudo ln -s `which gfortran-7` /usr/local/bin/gfortran | |
| - os: macos-latest | |
| # Different versions of homebrew put the gfortran in different | |
| INSTALL_DEPS: > | |
| brew update-reset | |
| && HOMEBREW_NO_AUTO_UPDATE=1 HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas | |
| && COSMOSIS_GCC_VER=$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1) | |
| && GFORTRAN_PATH1=/usr/local/bin/gfortran | |
| && GFORTRAN_PATH2=/usr/local/bin/gfortran-${COSMOSIS_GCC_VER} | |
| && GFORTRAN_PATH3=/opt/homebrew/bin/gfortran | |
| && GFORTRAN_PATH4=/opt/homebrew/bin/gfortran-${COSMOSIS_GCC_VER} | |
| && if ! which -s gfortran | |
| ; then if [ -f $GFORTRAN_PATH2 ]; then ln -s $GFORTRAN_PATH2 $GFORTRAN_PATH1; echo Linking gfortran from /usr/local | |
| ; elif [ -f $GFORTRAN_PATH4 ]; then ln -s $GFORTRAN_PATH4 $GFORTRAN_PATH3; echo Linking gfortran from /opt/homebrew | |
| ; else echo "gfortran not found" && exit 1 | |
| ; fi | |
| ; fi | |
| && echo "gfortran now at $(which -a gfortran)" | |
| - os: macos-13 | |
| # Different versions of homebrew put the gfortran in different | |
| INSTALL_DEPS: > | |
| brew update-reset | |
| && HOMEBREW_NO_AUTO_UPDATE=1 HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas | |
| && COSMOSIS_GCC_VER=$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1) | |
| && GFORTRAN_PATH1=/usr/local/bin/gfortran | |
| && GFORTRAN_PATH2=/usr/local/bin/gfortran-${COSMOSIS_GCC_VER} | |
| && GFORTRAN_PATH3=/opt/homebrew/bin/gfortran | |
| && GFORTRAN_PATH4=/opt/homebrew/bin/gfortran-${COSMOSIS_GCC_VER} | |
| && if ! which -s gfortran | |
| ; then if [ -f $GFORTRAN_PATH2 ]; then ln -s $GFORTRAN_PATH2 $GFORTRAN_PATH1; echo Linking gfortran from /usr/local | |
| ; elif [ -f $GFORTRAN_PATH4 ]; then ln -s $GFORTRAN_PATH4 $GFORTRAN_PATH3; echo Linking gfortran from /opt/homebrew | |
| ; else echo "gfortran not found" && exit 1 | |
| ; fi | |
| ; fi | |
| && echo "gfortran now at $(which -a gfortran)" | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' # caching pip dependencies | |
| cache-dependency-path: 'setup.py' | |
| - name: Install dependencies | |
| run: ${{ matrix.INSTALL_DEPS }} | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -v . | |
| pip install --no-binary=mpi4py mpi4py astropy pytest pytest-cov | |
| - name: Install PocoMC | |
| if: matrix.python-version != '3.7' | |
| run: | | |
| pip install pocomc==1.2.2 | |
| - name: Test nautilus alone | |
| if: (matrix.python-version == '3.11' || matrix.python-version =='3.10') && (matrix.os == 'macos-13') | |
| run: | | |
| # On some systems it seems like nautilus runs out of | |
| # memory when run with the full test suite. | |
| python cosmosis/test/test_samplers.py test_nautilus | |
| - name: Test with pytest | |
| run: | | |
| cosmosis --version | |
| if [[ "${{ matrix.os }}" == 'macos-13' && ("${{ matrix.python-version }}" == '3.10' || "${{ matrix.python-version }}" == '3.11') ]]; then | |
| export SKIP_NAUTILUS=1 | |
| fi | |
| mkdir tmp && cd tmp && pytest --pyargs cosmosis --cov cosmosis --cov-report=xml | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| if: matrix.python-version == '3.9' && matrix.os == 'ubuntu-20.04' | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |