install numpy for testing scripts #41
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| name: Test | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '42 4 5,20 * *' | |
| jobs: | |
| Test: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 20 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8, 3.9, '3.10', 3] | |
| MPI: ['mpich', 'openmpi', 'no'] | |
| defaults: | |
| run: | |
| # this is needed, because otherwise conda env is not available | |
| shell: bash -l {0} | |
| steps: | |
| - name: Install build dependencies | |
| run: | | |
| sudo apt-get update && sudo apt-get -y --no-install-recommends install -y -qq libblas{3,-dev} liblapack{3,-dev} libatlas-base-dev cmake build-essential git gfortran | |
| - name: Install openmpi | |
| if: ${{ matrix.MPI == 'openmpi' }} | |
| run: | | |
| sudo apt-get install -qq openmpi-bin libopenmpi-dev python3-mpi4py | |
| update-alternatives --list mpi|grep "${{ matrix.MPI }}" | xargs -rt sudo update-alternatives --set mpi | |
| update-alternatives --list mpirun|grep "${{ matrix.MPI }}" | xargs -rt sudo update-alternatives --set mpirun | |
| - name: Install mpich | |
| if: ${{ matrix.MPI == 'mpich' }} | |
| run: | | |
| sudo apt-get install -qq mpich libmpich-dev python3-mpi4py | |
| update-alternatives --list mpi|grep "${{ matrix.MPI }}" | xargs -rt sudo update-alternatives --set mpi | |
| update-alternatives --list mpirun|grep "${{ matrix.MPI }}" | xargs -rt sudo update-alternatives --set mpirun | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| channels: conda-forge | |
| python-version: ${{ matrix.python-version }} | |
| #mamba-version: "*" | |
| - name: Install mamba | |
| run: conda install -y -c conda-forge mamba | |
| - name: Install python dependencies | |
| run: | | |
| mamba install --quiet --file conda-requirements.txt corner coveralls numpy | |
| pip install git+https://github.com/JohannesBuchner/coverage-lcov | |
| #sed --in-place -e 's,"report_include",,g' -e 's,"report_omit",,g' /usr/share/miniconda/envs/*/lib/python*/site-packages/coverage_lcov/converter.py | |
| conda list | |
| conda info -a | |
| - name: install mpi4py | |
| if: ${{ matrix.MPI != 'no' }} | |
| run: | | |
| pip install --user mpi4py | |
| python -c 'import mpi4py' | |
| - name: Install MultiNest | |
| run: | | |
| git clone https://github.com/JohannesBuchner/MultiNest | |
| mkdir -p MultiNest/build; pushd MultiNest/build; cmake .. && make && popd | |
| test -e MultiNest/lib/libmultinest.so | |
| echo LD_LIBRARY_PATH=MultiNest/lib/:${LD_LIBRARY_PATH} >> $GITHUB_ENV | |
| echo RDMAV_FORK_SAFE=1 >> $GITHUB_ENV | |
| - name: Install PyMultiNest | |
| run: | | |
| python setup.py install --user | |
| - name: Test imports | |
| run: | | |
| python -c 'import pymultinest' | |
| rm -rf chains/ | |
| - name: No-MPI tests | |
| if: ${{ matrix.MPI == 'no' }} | |
| run: | | |
| # do not test pycuba, it is broken | |
| rm tests/pycuba_test.py | |
| coverage run setup.py test | |
| coverage report | |
| coverage-lcov | |
| python pymultinest_demo_minimal.py | |
| python pymultinest_demo.py | |
| - name: MPI tests | |
| if: ${{ matrix.MPI == 'openmpi' }} | |
| run: | | |
| mpiexec -np 4 --oversubscribe python pymultinest_demo_minimal.py | |
| mpiexec -np 4 --oversubscribe python pymultinest_demo.py | |
| - name: MPI tests | |
| if: ${{ matrix.MPI == 'mpich' }} | |
| run: | | |
| mpiexec -np 4 python pymultinest_demo_minimal.py | |
| mpiexec -np 4 python pymultinest_demo.py | |
| - name: Long filename test | |
| run: | | |
| python tests/pymultinest_long_name_test.py; | |
| - name: Marginal scripts test | |
| run: | | |
| python multinest_marginals.py chains/3- | |
| python multinest_marginals_corner.py chains/3- | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@master | |
| if: ${{ matrix.MPI == 'no' }} | |
| with: | |
| path-to-lcov: lcov.info | |
| github-token: ${{ secrets.github_token }} | |
| flag-name: MPI-${{ matrix.MPI }} | |
| CondaTest: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 20 | |
| defaults: | |
| run: | |
| # this is needed, because otherwise conda env is not available | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| channels: conda-forge | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: conda-requirements.txt | |
| #mamba-version: "*" | |
| - name: Install mamba | |
| run: conda install -y -c conda-forge mamba | |
| - name: Install dependencies | |
| run: | | |
| mamba install --quiet multinest | |
| - name: Test imports | |
| run: | | |
| python -m pip install . | |
| python -c 'import pymultinest' | |
| - name: Tests | |
| run: | | |
| python pymultinest_demo_minimal.py |