Fixed a NumPy 2.x testing issue and added a NumPy 2.x build to the test workflow #1705
Workflow file for this run
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| # Run Tests | |
| # Matrix Options | |
| # DOCS: 2-Build and publish, 1-build only, 0-no docs | |
| name: Dymos Tests | |
| on: | |
| # Trigger on push, pull request | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master, develop ] | |
| # Allow running the workflow manually from the Actions tab | |
| # All jobs are excluded by default, desired jobs must be selected | |
| workflow_dispatch: | |
| inputs: | |
| run_name: | |
| type: string | |
| description: 'Name of workflow run as it will appear under Actions tab:' | |
| required: false | |
| default: "" | |
| baseline: | |
| type: boolean | |
| description: "Include 'baseline' in test matrix" | |
| required: false | |
| default: false | |
| no_pyoptsparse: | |
| type: boolean | |
| description: "Include 'no_pyoptsparse' in test matrix" | |
| required: false | |
| default: false | |
| numpy2_no_pyoptsparse: | |
| type: boolean | |
| description: "Include 'numpy2_no_pyoptsparse' in test matrix" | |
| required: false | |
| default: false | |
| no_snopt: | |
| type: boolean | |
| description: "Include 'no_snopt' in test matrix" | |
| required: false | |
| default: false | |
| no_mpi: | |
| type: boolean | |
| description: "Include 'no_mpi' Baseline in test matrix" | |
| required: false | |
| default: false | |
| latest: | |
| type: boolean | |
| description: "Include 'latest' in test matrix" | |
| required: false | |
| default: false | |
| oldest: | |
| type: boolean | |
| description: "Include 'oldest' in test matrix" | |
| required: false | |
| default: false | |
| run-name: ${{ inputs.run_name }} | |
| jobs: | |
| test_ubuntu: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # baseline versions | |
| - NAME: baseline | |
| PY: '3.12' | |
| NUMPY: 1.26 | |
| SCIPY: 1.13 | |
| PETSc: 3.21.0 | |
| PYOPTSPARSE: 'v2.11.0' | |
| SNOPT: 7.7 | |
| OPENMDAO: 'latest' | |
| PEP517: true | |
| OPTIONAL: '[all]' | |
| JAX: '0.4.28' | |
| EXCLUDE: ${{ github.event_name == 'workflow_dispatch' && ! inputs.baseline }} | |
| # baseline versions except no pyoptsparse or SNOPT | |
| - NAME: no_pyoptsparse | |
| PY: '3.12' | |
| NUMPY: 1.26 | |
| SCIPY: 1.13 | |
| PETSc: 3.21.0 | |
| OPENMDAO: 'latest' | |
| OPTIONAL: '[test]' | |
| EXCLUDE: ${{ github.event_name == 'workflow_dispatch' && ! inputs.no_pyoptsparse }} | |
| # numpy 2.x but no PETSc, pyoptsparse or SNOPT | |
| - NAME: numpy2_no_pyoptsparse | |
| PY: '3.12' | |
| NUMPY: 2 | |
| SCIPY: 1.14 | |
| OPENMDAO: 'latest' | |
| OPTIONAL: '[all]' | |
| EXCLUDE: ${{ github.event_name == 'workflow_dispatch' && ! inputs.numpy2_no_pyoptsparse }} | |
| # baseline versions except with pyoptsparse but no SNOPT | |
| - NAME: no_snopt | |
| PY: '3.12' | |
| NUMPY: 1.26 | |
| SCIPY: 1.13 | |
| PETSc: 3.21.0 | |
| PYOPTSPARSE: 'v2.11.0' | |
| OPENMDAO: 'latest' | |
| OPTIONAL: '[test]' | |
| EXCLUDE: ${{ github.event_name == 'workflow_dispatch' && ! inputs.no_snopt }} | |
| # baseline versions except no MPI/PETSc | |
| - NAME: no_mpi | |
| PY: '3.12' | |
| NUMPY: 1.26 | |
| SCIPY: 1.13 | |
| PYOPTSPARSE: 'v2.11.0' | |
| OPENMDAO: 'latest' | |
| OPTIONAL: '[test]' | |
| EXCLUDE: ${{ github.event_name == 'workflow_dispatch' && ! inputs.no_mpi }} | |
| # try latest versions | |
| - NAME: latest | |
| PY: 3 | |
| NUMPY: 1 | |
| SCIPY: 1 | |
| PETSc: 3.21.0 | |
| PYOPTSPARSE: 'latest' | |
| SNOPT: 7.7 | |
| OPENMDAO: 'dev' | |
| OPTIONAL: '[test]' | |
| JAX: 'latest' | |
| EXCLUDE: ${{ github.event_name == 'workflow_dispatch' && ! inputs.latest }} | |
| # oldest supported versions | |
| - NAME: oldest | |
| PY: 3.9 | |
| NUMPY: 1.22 | |
| SCIPY: 1.7 | |
| OPENMPI: '4.0' | |
| MPI4PY: '3.0' | |
| PETSc: 3.13 | |
| PYOPTSPARSE: 'v2.9.0' | |
| SNOPT: 7.2 | |
| OPENMDAO: 3.28.0 | |
| MATPLOTLIB: 3.5 | |
| OPTIONAL: '[test]' | |
| EXCLUDE: ${{ github.event_name == 'workflow_dispatch' && ! inputs.oldest }} | |
| steps: | |
| - name: Display run details | |
| run: | | |
| echo "=============================================================" | |
| echo "Run #${GITHUB_RUN_NUMBER}" | |
| echo "Run ID: ${GITHUB_RUN_ID}" | |
| echo "Testing: ${GITHUB_REPOSITORY}" | |
| echo "Triggered by: ${GITHUB_EVENT_NAME}" | |
| echo "Initiated by: ${GITHUB_ACTOR}" | |
| echo "=============================================================" | |
| if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then | |
| if [[ "${{ matrix.EXCLUDE }}" == "false" ]]; then | |
| echo "Triggered by 'workflow_dispatch', '${{ matrix.NAME }}' build was selected and will run." | |
| else | |
| echo "Triggered by 'workflow_dispatch', '${{ matrix.NAME }}' build not selected and will not run." | |
| fi | |
| fi | |
| - name: Create SSH key | |
| if: ${{ ! matrix.EXCLUDE }} | |
| shell: bash | |
| env: | |
| SSH_PRIVATE_KEY: ${{secrets.SSH_PRIVATE_KEY}} | |
| SSH_KNOWN_HOSTS: ${{secrets.SSH_KNOWN_HOSTS}} | |
| run: | | |
| mkdir -p ~/.ssh/ | |
| echo "$SSH_PRIVATE_KEY" > ~/.ssh/id_rsa | |
| sudo chmod 600 ~/.ssh/id_rsa | |
| echo "$SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts | |
| - name: Checkout code | |
| if: ${{ ! matrix.EXCLUDE }} | |
| uses: actions/checkout@v4 | |
| - name: Setup conda | |
| if: ${{ ! matrix.EXCLUDE }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.PY }} | |
| channels: conda-forge | |
| - name: Install Numpy/Scipy | |
| if: ${{ ! matrix.EXCLUDE }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "Make sure we are not using anaconda packages" | |
| conda config --remove channels defaults | |
| echo "=============================================================" | |
| echo "Install Numpy/Scipy" | |
| echo "=============================================================" | |
| conda install numpy=${{ matrix.NUMPY }} scipy=${{ matrix.SCIPY }} -q -y | |
| - name: Install jax | |
| if: ${{ ! matrix.EXCLUDE && matrix.JAX }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install jax" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.JAX }}" == "latest" ]]; then | |
| python -m pip install jaxlib jax | |
| else | |
| python -m pip install jaxlib==${{ matrix.JAX }} jax==${{ matrix.JAX }} | |
| fi | |
| - name: Install PETSc | |
| if: ${{ ! matrix.EXCLUDE && matrix.PETSc }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install PETSc" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.OPENMPI }}" && "${{ matrix.MPI4PY }}" ]]; then | |
| conda install openmpi=${{ matrix.OPENMPI }} mpi4py=${{ matrix.MPI4PY }} petsc4py=${{ matrix.PETSc }} -q -y | |
| elif [[ "${{ matrix.MPI4PY }}" ]]; then | |
| conda install mpi4py=${{ matrix.MPI4PY }} petsc4py=${{ matrix.PETSc }} -q -y | |
| else | |
| conda install mpi4py petsc4py=${{ matrix.PETSc }} -q -y | |
| fi | |
| export OMPI_MCA_rmaps_base_oversubscribe=1 | |
| export OMPI_MCA_btl=^openib | |
| echo "OMPI_MCA_rmaps_base_oversubscribe=1" >> $GITHUB_ENV | |
| echo "OMPI_MCA_btl=^openib" >> $GITHUB_ENV | |
| echo "-----------------------" | |
| echo "Quick test of mpi4py:" | |
| mpirun -n 2 python -c "from mpi4py import MPI; print(f'Rank: {MPI.COMM_WORLD.rank}')" | |
| echo "-----------------------" | |
| echo "Quick test of petsc4py:" | |
| mpirun -n 2 python -c "import numpy; from mpi4py import MPI; comm = MPI.COMM_WORLD; import petsc4py; petsc4py.init(); x = petsc4py.PETSc.Vec().createWithArray(numpy.ones(5)*comm.rank, comm=comm); print(x.getArray())" | |
| echo "-----------------------" | |
| - name: Install pyOptSparse | |
| id: build_pyoptsparse | |
| if: ${{ ! matrix.EXCLUDE && matrix.PYOPTSPARSE }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install pyoptsparse" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.PYOPTSPARSE }}" == "conda-forge" ]]; then | |
| if [[ "${{ matrix.SNOPT }}" ]]; then | |
| echo "SNOPT ${{ matrix.SNOPT }} was requested but is not available on conda-forge" | |
| fi | |
| conda install -c conda-forge pyoptsparse | |
| else | |
| pip install git+https://github.com/OpenMDAO/build_pyoptsparse | |
| if [[ "${{ matrix.PYOPTSPARSE }}" == "latest" ]]; then | |
| LATEST_URL=`curl -fsSLI -o /dev/null -w %{url_effective} https://github.com/mdolab/pyoptsparse/releases/latest` | |
| LATEST_VER=`echo $LATEST_URL | awk '{split($0,a,"/tag/"); print a[2]}'` | |
| BRANCH="-b $LATEST_VER" | |
| else | |
| BRANCH="-b ${{ matrix.PYOPTSPARSE }}" | |
| fi | |
| if [[ "${{ matrix.PAROPT }}" ]]; then | |
| PAROPT="-a" | |
| fi | |
| if [[ "${{ matrix.SNOPT }}" == "7.7" && "${{ secrets.SNOPT_LOCATION_77 }}" ]]; then | |
| echo " > Secure copying SNOPT 7.7 over SSH" | |
| mkdir SNOPT | |
| scp -qr ${{ secrets.SNOPT_LOCATION_77 }} SNOPT | |
| SNOPT="-s SNOPT/src" | |
| elif [[ "${{ matrix.SNOPT }}" == "7.2" && "${{ secrets.SNOPT_LOCATION_72 }}" ]]; then | |
| echo " > Secure copying SNOPT 7.2 over SSH" | |
| mkdir SNOPT | |
| scp -qr ${{ secrets.SNOPT_LOCATION_72 }} SNOPT | |
| SNOPT="-s SNOPT/source" | |
| elif [[ "${{ matrix.SNOPT }}" ]]; then | |
| echo "SNOPT version ${{ matrix.SNOPT }} was requested but source is not available" | |
| fi | |
| build_pyoptsparse $BRANCH $PAROPT $SNOPT | |
| fi | |
| - name: Install OpenMDAO | |
| if: ${{ ! matrix.EXCLUDE && matrix.OPENMDAO }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install OpenMDAO" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.OPENMDAO }}" == "dev" ]]; then | |
| pip install git+https://github.com/OpenMDAO/OpenMDAO | |
| elif [[ "${{ matrix.OPENMDAO }}" == "latest" ]]; then | |
| echo "The latest version OpenMDAO will be installed from pypi per the Dymos dependency" | |
| else | |
| pip install openmdao==${{ matrix.OPENMDAO }} | |
| fi | |
| - name: Install Matplotlib | |
| if: ${{ ! matrix.EXCLUDE && matrix.MATPLOTLIB }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install requested version of Matpltlib" | |
| echo "=============================================================" | |
| python -m pip install matplotlib==${{ matrix.MATPLOTLIB }} | |
| - name: Install Dymos | |
| if: ${{ ! matrix.EXCLUDE }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install Dymos" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.PEP517 }}" == "true" ]]; then | |
| pip wheel --no-deps --use-pep517 . | |
| WHEEL=`find dymos-*.whl` | |
| echo "-----------------------------------------------------------" | |
| echo "Installing from wheel: $WHEEL" | |
| echo "-----------------------------------------------------------" | |
| python -m pip install $WHEEL${{ matrix.OPTIONAL }} | |
| else | |
| python -m pip install .${{ matrix.OPTIONAL }} | |
| fi | |
| - name: Install optional dependencies | |
| if: ${{ ! matrix.EXCLUDE && matrix.OPTIONAL == '[all]' }} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install additional packages for testing/coverage" | |
| echo "=============================================================" | |
| echo "Pre-install playwright dependencies to avoid 'Playwright Host validation warning'" | |
| pip install playwright | |
| playwright install --with-deps | |
| - name: Display environment info | |
| id: env_info | |
| if: ${{ ! matrix.EXCLUDE }} | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda env export --name test --file ${{ matrix.NAME }}_environment.yml | |
| echo "=============================================================" | |
| echo "Check installed versions of Python, Numpy and Scipy" | |
| echo "=============================================================" | |
| python -c "ver='${{ matrix.PY }}'; import sys; assert str(sys.version).startswith(ver), \ | |
| f'Python version {sys.version} is not the requested version ({ver})'" | |
| python -c "ver='${{ matrix.NUMPY }}'; import numpy; assert str(numpy.__version__).startswith(ver), \ | |
| f'Numpy version {numpy.__version__} is not the requested version ({ver})'" | |
| python -c "ver='${{ matrix.SCIPY }}'; import scipy; assert str(scipy.__version__).startswith(ver), \ | |
| f'Scipy version {scipy.__version__} is not the requested version ({ver})'" | |
| - name: Display dependency tree | |
| if: failure() && steps.env_info.outcome == 'failure' | |
| run: | | |
| pip install pipdeptree | |
| pipdeptree | |
| - name: Upload environment artifact | |
| if: ${{ ! matrix.EXCLUDE }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.NAME }}_environment | |
| path: ${{ matrix.NAME }}_environment.yml | |
| retention-days: 5 | |
| - name: Check NumPy 2.0 Compatibility | |
| if: ${{ ! matrix.EXCLUDE }} | |
| run: | | |
| echo "=============================================================" | |
| echo "Check Dymos code for NumPy 2.0 compatibility" | |
| echo "See: https://numpy.org/devdocs/numpy_2_0_migration_guide.html" | |
| echo "=============================================================" | |
| python -m pip install ruff | |
| ruff check . --select NPY201 | |
| - name: Perform linting with Ruff | |
| if: ${{ ! matrix.EXCLUDE && matrix.NAME == 'baseline' }} | |
| run: | | |
| echo "=============================================================" | |
| echo "Lint Dymos code per settings in pyproject.toml" | |
| echo "=============================================================" | |
| python -m pip install ruff | |
| ruff check . --config pyproject.toml | |
| - name: Run tests | |
| if: ${{ ! matrix.EXCLUDE }} | |
| env: | |
| DYMOS_CHECK_PARTIALS: True | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Run Tests" | |
| echo "Environment:" | |
| echo " DYMOS_CHECK_PARTIALS: $DYMOS_CHECK_PARTIALS" | |
| echo "=============================================================" | |
| testflo -n 1 docs/dymos_book/test --pre_announce | |
| testflo -n 1 joss/test --pre_announce | |
| testflo -b benchmark --pre_announce | |
| cd $HOME | |
| if [[ "${{ matrix.NAME }}" != "latest" ]]; then | |
| testflo dymos -n 2 --pre_announce --show_skipped --durations 20 --coverage --coverpkg dymos | |
| else | |
| testflo dymos -n 2 --pre_announce --show_skipped --durations 20 | |
| fi | |
| - name: Submit coverage | |
| if: github.event_name != 'workflow_dispatch' | |
| continue-on-error: true | |
| shell: bash -l {0} | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_SERVICE_NAME: "github" | |
| COVERALLS_PARALLEL: True | |
| run: | | |
| echo "=============================================================" | |
| echo "Submit coverage" | |
| echo "=============================================================" | |
| cp $HOME/.coverage . | |
| pip install coveralls | |
| SITE_DIR=`python -c 'import site; print(site.getsitepackages()[-1])'` | |
| coveralls --basedir $SITE_DIR | |
| coveralls: | |
| name: Finish coveralls | |
| if: github.event_name != 'workflow_dispatch' | |
| continue-on-error: true | |
| needs: test_ubuntu | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel-finished: true |