fix for failing workflows on github actions #91
Workflow file for this run
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| # 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: Extensive CI | |
| on: | |
| push: | |
| branches: [master] | |
| tags: [v*] | |
| pull_request: | |
| branches: [master] | |
| workflow_dispatch: | |
| 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: | |
| test-type: [unit, integrated] | |
| packages: [all, vmec, spec, none] | |
| python-version: [3.8, 3.9, "3.10"] | |
| include: | |
| - python-version: 3.9 | |
| test-type: unit | |
| packages: none | |
| - python-version: 3.9 | |
| test-type: integrated | |
| packages: none | |
| 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: 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 libopenblas-dev libboost-all-dev | |
| - uses: actions/checkout@v4 | |
| # If we want submodules downloaded, uncomment the next 2 lines: | |
| #with: | |
| # submodules: true | |
| # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. | |
| - name: Download the VMEC2000 standalone repository | |
| if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') | |
| run: git clone 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 wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann | |
| - name: Install booz_xform | |
| if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') | |
| 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 | |
| if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: PrincetonUniversity/SPEC | |
| path: SPEC | |
| # For some reason, installing py_spec does not install the dependencies f90nml and h5py. Therefore I installed these manually above. | |
| - name: Install py_spec | |
| if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') | |
| 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. | |
| if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') | |
| run: | | |
| cd SPEC | |
| pip install . | |
| - name: Try import spec | |
| if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') | |
| 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 | |
| if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') | |
| run: ls -l VMEC2000/python | |
| - name: Configure VMEC2000 module | |
| if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') | |
| run: | | |
| cd VMEC2000 | |
| cp cmake/machines/ubuntu.json cmake_config_file.json | |
| cat cmake_config_file.json | |
| pip install . | |
| - name: Try importing vmec module | |
| if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') | |
| 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 | |
| if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') | |
| run: | | |
| pip install -v . | |
| pip install mpi4py py_spec pyoculus h5py | |
| - name: Install simsopt package | |
| if: contains(matrix.packages, 'none') | |
| run: pip install -v . | |
| - name: Install simsopt package | |
| if: contains(matrix.packages, 'vmec') | |
| run: | | |
| pip install -v . | |
| pip install mpi4py | |
| - name: Run serial examples as part of integrated tests | |
| if: contains(matrix.test-type, 'integrated') && (contains(matrix.packages, 'none') || contains(matrix.packages, 'all')) | |
| run: | | |
| cd examples | |
| ./run_serial_examples | |
| - name: Run simple parallel examples as part of integrated tests | |
| if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'all') | |
| run: | | |
| cd examples | |
| ./run_parallel_examples | |
| - name: Run spec examples as part of integrated tests | |
| if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'spec') | |
| run: | | |
| cd examples | |
| ./run_spec_examples | |
| - name: Run vmec examples as part of integrated tests | |
| if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'vmec') | |
| run: | | |
| cd examples | |
| ./run_vmec_examples | |
| - name: Run vmec and spec examples as part of integrated tests | |
| if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'all') | |
| run: | | |
| cd examples | |
| ./run_spec_vmec_examples | |
| - name: Install coverage dependencies | |
| if: contains(matrix.test-type, 'unit') | |
| run: pip install coverage | |
| - name: Run expensive tests on 1 MPI process using coverage | |
| if: contains(matrix.test-type, 'unit') && (contains(matrix.packages, 'none') || contains(matrix.packages, 'all')) | |
| run: | | |
| 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/field | |
| - name: Run remaining tests on 1 MPI 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/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') && (contains(matrix.packages, 'all') || contains(matrix.packages, 'vmec') || contains(matrix.packages, 'spec')) | |
| 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: Upload uncombined coverage to github | |
| if: contains(matrix.test-type, 'unit') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: gh-actions-parallel-coverage | |
| path: .coverage.* | |
| if-no-files-found: error | |
| coverage: | |
| runs-on: ubuntu-latest | |
| needs: [ test ] | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Install coverage | |
| run: pip install coverage | |
| - name: Checkout simsopt | |
| uses: actions/checkout@v4 | |
| - name: Install simsopt before running coverage | |
| run: pip install . | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: gh-actions-parallel-coverage | |
| path: ./ | |
| - name: Display coverage files before combine | |
| run: ls -a | |
| - name: Combine coverage reports | |
| run: | | |
| coverage combine | |
| coverage report | |
| coverage xml | |
| - name: Upload coverage to github | |
| 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 next line prevents github from trying to upload to Codecov on forks of the repository, avoiding a permissions error | |
| if: github.repository_owner == 'hiddenSymmetries' | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| env_vars: PYTHON | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| verbose: true |