Merge branch 'master' into psc_arrays #430
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
| # This file is based on examples in | |
| # https://docs.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions | |
| # Note that all the "sudo" commands here appear to cause a warning message | |
| # "sudo: setrlimit(RLIMIT_CORE): operation not permitted" | |
| # This appears to be a known harmless annoyance: | |
| # https://gitlab.alpinelinux.org/alpine/aports/-/issues/11122 | |
| name: Tests | |
| on: | |
| push: | |
| branches-ignore: [master] | |
| tags-ignore: [v*] | |
| pull_request: | |
| branches-ignore: [master] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| env: | |
| OMPI_ALLOW_RUN_AS_ROOT: 1 | |
| OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.9] | |
| test-type: [unit, integrated] | |
| steps: | |
| # First print out lots of information. We do this in separate | |
| # "name" blocks because otherwise the output gets mixed together | |
| # in the github actions log. | |
| - name: Print user and group id | |
| run: | | |
| set -ex | |
| id | |
| - name: PWD | |
| run: | | |
| set -ex | |
| pwd | |
| - name: ls -l | |
| run: | | |
| set -ex | |
| ls -l | |
| - name: Print python location | |
| run: | | |
| set -ex | |
| which python | |
| - name: apt-get stuff needed for libstell and vmec | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential gfortran openmpi-bin libopenmpi-dev libnetcdf-dev libnetcdff-dev liblapack-dev libscalapack-mpi-dev libhdf5-dev libhdf5-serial-dev git m4 libfftw3-dev libboost-all-dev libopenblas-dev | |
| - uses: actions/checkout@v4 | |
| - name: Fetch all history for all tags | |
| run: git fetch --all --tags --prune --unshallow | |
| # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. | |
| - name: Download the VMEC2000 standalone repository | |
| run: git clone --depth=1 https://github.com/hiddensymmetries/VMEC2000.git | |
| - name: ls -l again | |
| run: | | |
| set -ex | |
| ls -l | |
| pwd | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: which python3 after python setup | |
| run: which python3 | |
| - name: which pip after python setup | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip --version | |
| - name: env after adding python | |
| run: env | |
| - name: Install python dependencies | |
| run: | | |
| sudo apt-get install graphviz graphviz-dev | |
| pip install "numpy<2.0.0" cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann | |
| - name: Install booz_xform | |
| run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform | |
| - name: Install virtual_casing | |
| run: pip install -v git+https://github.com/hiddenSymmetries/virtual-casing | |
| # See https://github.community/t/best-way-to-clone-a-private-repo-during-script-run-of-private-github-action/16116/7 | |
| # https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions | |
| # https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token | |
| - name: Check out SPEC | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: PrincetonUniversity/SPEC | |
| path: SPEC | |
| - name: ls -l again | |
| run: | | |
| ls -l | |
| pwd | |
| - name: ls -l inside SPEC | |
| run: | | |
| cd SPEC | |
| pwd | |
| ls -l | |
| # For some reason, installing py_spec does not install the dependencies f90nml and h5py. Therefore I installed these manually above. | |
| - name: Install py_spec | |
| run: | | |
| pip install -r SPEC/Utilities/pythontools/requirements.txt | |
| pip install -e SPEC/Utilities/pythontools | |
| python -c "import py_spec; print('success')" | |
| - name: Install f90wrap | |
| run: pip install -U git+https://github.com/zhucaoxiang/f90wrap | |
| - name: Build SPEC python wrapper. | |
| run: | | |
| cd SPEC | |
| pip install . | |
| - name: Try import spec | |
| run: python -c "import spec.spec_f90wrapped as spec; print(spec.constants.version)" | |
| - name: ls in /usr/lib/x86_64-linux-gnu | |
| run: ls -l /usr/lib/x86_64-linux-gnu | |
| - name: Add to LD_LIBRARY_PATH so scalapack etc can be found | |
| run: echo "LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu" >> $GITHUB_ENV | |
| - name: env after adding to LD_LIBRARY_PATH | |
| run: env | |
| - name: ls in VMEC2000/python 1 | |
| run: ls -l VMEC2000/python | |
| - name: Configure and install VMEC2000 module | |
| run: | | |
| cd VMEC2000 | |
| cp cmake/machines/ubuntu.json cmake_config_file.json | |
| cat cmake_config_file.json | |
| pip install . | |
| - name: Try importing vmec module | |
| run: python -c "print(dir()); import vmec; print(dir()); print(dir(vmec)); print('package:', vmec.__package__); print('spec:', vmec.__spec__); print('doc:', vmec.__doc__); print('file:', vmec.__file__); print('path:', vmec.__path__)" | |
| - name: Install simsopt package | |
| # run: env CMAKE_BUILD_TYPE=Debug pip install -v .[MPI,SPEC] | |
| run: pip install -v ".[MPI,SPEC,VIS]" | |
| - name: Verify that importing simsopt does not automatically initialize MPI | |
| run: ./tests/verify_MPI_not_initialized.py | |
| - name: Run examples as part of integrated tests | |
| if: contains(matrix.test-type, 'integrated') | |
| run: | | |
| cd examples | |
| ./run_serial_examples | |
| ./run_parallel_examples | |
| ./run_vmec_examples | |
| ./run_spec_examples | |
| ./run_spec_vmec_examples | |
| - name: Install coverage dependencies | |
| if: contains(matrix.test-type, 'unit') | |
| run: pip install coverage | |
| - name: Run tests on 1 process using coverage | |
| if: contains(matrix.test-type, 'unit') | |
| run: | | |
| coverage run --source=simsopt -m unittest discover -t tests -v -s tests/core | |
| coverage run --source=simsopt -m unittest discover -t tests -v -s tests/field | |
| coverage run --source=simsopt -m unittest discover -t tests -v -s tests/geo | |
| coverage run --source=simsopt -m unittest discover -t tests -v -s tests/mhd | |
| coverage run --source=simsopt -m unittest discover -t tests -v -s tests/objectives | |
| coverage run --source=simsopt -m unittest discover -t tests -v -s tests/solve | |
| coverage run --source=simsopt -m unittest discover -t tests -v -s tests/util | |
| - name: Run MPI tests using coverage | |
| if: contains(matrix.test-type, 'unit') | |
| run: | | |
| mpiexec -n 1 coverage run -m unittest discover -k "mpi" -s tests -v | |
| mpiexec -n 2 coverage run -m unittest discover -k "mpi" -s tests -v | |
| mpiexec -n 3 --oversubscribe coverage run -m unittest discover -k "mpi" -s tests -v | |
| - name: Combine coverage reports | |
| if: contains(matrix.test-type, 'unit') | |
| run: | | |
| coverage combine | |
| coverage report | |
| coverage xml | |
| - name: Upload coverage to github | |
| if: contains(matrix.test-type, 'unit') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: tox-gh-actions-coverage | |
| path: coverage.xml | |
| if-no-files-found: error | |
| - name: Upload coverage to Codecov | |
| # The last conditional on the next line prevents github from trying to upload to Codecov on forks of the repository, avoiding a permissions error | |
| if: contains(matrix.test-type, 'unit') && github.repository_owner == 'hiddenSymmetries' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| #files: ./coverage1.xml,./coverage2.xml | |
| #directory: ./coverage/reports/ | |
| flags: unittests | |
| env_vars: PYTHON | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| #path_to_write_report: ./coverage/codecov_report.gz | |
| verbose: true |