Don't report asan library in ygginfo since it is in the config file now #1412
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| # DO NOT MODIFY THIS FILE, IT IS GENERATED. | |
| # To make changes, modify '.git/../utils/test-install-base.yml' | |
| # and run 'ygggha' | |
| env: | |
| BUILDDOCS: 0 | |
| INSTALLC: 1 | |
| INSTALLEXCEL: 1 | |
| INSTALLFORTRAN: 1 | |
| INSTALLIMAGES: 1 | |
| INSTALLJULIA: 1 | |
| INSTALLLPY: 0 | |
| INSTALLMATLAB: 0 | |
| INSTALLMPI: 1 | |
| INSTALLOMP: 1 | |
| INSTALLPYGMENTS: 1 | |
| INSTALLPYTORCH: 1 | |
| INSTALLR: 1 | |
| INSTALLRMQ: 0 | |
| INSTALLSBML: 0 | |
| INSTALLSEQ: 1 | |
| INSTALLTRIMESH: 1 | |
| INSTALLZMQ: 1 | |
| NUMPY: numpy | |
| TMPDIR: /tmp/ | |
| USEVIRTUALENV: 0 | |
| YGG_GHA_JOB_ID_SUFFIX: null | |
| jobs: | |
| build_sdist: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| name: Build source distribution | |
| needs: | |
| - test_pip | |
| - test_conda | |
| - test_rmq_pip | |
| - test_rmq_conda | |
| - test_stripped | |
| - docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout sources | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Install build utilities | |
| run: 'python -m pip install build | |
| ' | |
| - name: Build sdist | |
| run: 'python -m build --sdist | |
| ' | |
| - name: Install sdist | |
| run: 'python -m pip install dist/*.gz | |
| python utils/setup_test_env.py deps pip | |
| ' | |
| - name: Test sdist | |
| run: 'ygginfo | |
| pytest -m subset_rapidjson tests | |
| ' | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sdist | |
| path: ./dist/* | |
| build_wheels: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| name: Build wheels on ${{ matrix.os }} | |
| needs: | |
| - test_pip | |
| - test_conda | |
| - test_rmq_pip | |
| - test_rmq_conda | |
| - test_stripped | |
| - docs | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout sources | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - if: runner.os == 'Linux' | |
| name: (LINUX) Set up QEMU | |
| uses: docker/setup-qemu-action@v1 | |
| with: | |
| platforms: all | |
| - if: ${{ matrix.windows_arch == 'x86' }} | |
| name: setup rtools for 32-bit | |
| run: 'echo "PLAT=i686" >> $env:GITHUB_ENV | |
| echo "PATH=$env:RTOOLS40_HOME\mingw32\bin;$env:PATH" >> $env:GITHUB_ENV | |
| gfortran --version | |
| ' | |
| - env: | |
| CIBW_ARCHS_LINUX: ${{ matrix.linux_arch }} | |
| CIBW_ARCHS_MACOS: ${{ matrix.mac_arch }} | |
| CIBW_ARCHS_WINDOWS: ${{ matrix.windows_arch }} | |
| name: Build wheels | |
| uses: pypa/cibuildwheel@v2.12.1 | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| path: ./wheelhouse/*.whl | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: windows-2019 | |
| windows_arch: x86 | |
| - linux_arch: aarch64 | |
| os: ubuntu-20.04 | |
| - linux_arch: ppc64le | |
| os: ubuntu-20.04 | |
| linux_arch: | |
| - auto | |
| mac_arch: | |
| - x86_64 arm64 | |
| os: | |
| - ubuntu-20.04 | |
| - macOS-11 | |
| - windows-2019 | |
| windows_arch: | |
| - AMD64 | |
| docker: | |
| if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event.schedule | |
| == '0 10 1 * *' | |
| name: Build and Publish Docker images | |
| needs: | |
| - test_pip | |
| - test_conda | |
| - test_rmq_pip | |
| - test_rmq_conda | |
| - test_stripped | |
| - docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v1 | |
| with: | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| - name: Build and push environment docker images for the new release | |
| run: python utils/build_docker.py --push | |
| - name: Build and push executable docker images for the new release | |
| run: python utils/build_docker.py --push executable | |
| docs: | |
| env: | |
| BUILDDOCS: 1 | |
| name: Build the Docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: python utils/setup_test_env.py install pip | |
| - name: Verify installation | |
| run: 'python -m pip install setuptools_scm | |
| python utils/setup_test_env.py verify | |
| ' | |
| - name: Build the docs | |
| run: 'cd docs | |
| make autodoc | |
| cd ../ | |
| ' | |
| - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| name: Publish docs to Github pages | |
| uses: JamesIves/github-pages-deploy-action@3.7.1 | |
| with: | |
| BRANCH: gh-pages | |
| FOLDER: docs/build/html/ | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| params: | |
| name: Prepare test parameters | |
| outputs: | |
| os-versions: ${{ steps.set-os-versions.outputs.versions }} | |
| test-flags: ${{ steps.set-test-flags.outputs.testflags }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: set-os-versions | |
| run: echo "versions={\"ubuntu\":\"latest\", \"macos\":\"latest\", \"windows\":\"latest\"}" | |
| >> $GITHUB_OUTPUT | |
| - id: set-test-flags | |
| run: echo "testflags={\"empty\":\"\", \"basic\":\"--long-running --suites timing | |
| demos top\", \"examples\":\"--suite=examples --extra-examples --mpi-script=run_mpi.sh | |
| --mpi-nproc=3\", \"types-no-c\":\"--suite=types --skip-languages c cpp\", | |
| \"types-c\":\"--suite=types --languages c cpp\", \"long\":\"--long-running\", | |
| \"long-mpi\":\"--long-running --mpi-script=run_mpi.sh\", \"examples-backwards\":\"--suite=examples | |
| --parametrize-example-name=backwards\", \"examples-sbml\":\"--suites examples | |
| --parametrize-language=sbml\", \"long-remote-service\":\"--long-running --remote-service\", | |
| \"examples-rpc-lesson3\":\"--suites examples top --parametrize-example-name=rpc_lesson3\", | |
| \"tools\":\"tests/test_tools.py\", \"long-interp\":\"--long-running --languages | |
| python R matlab\", \"services\":\"tests/test_services.py --nocapture\"}" >> | |
| $GITHUB_OUTPUT | |
| schema: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| name: Update the schema used by the model submission form | |
| needs: | |
| - test_pip | |
| - test_conda | |
| - test_rmq_pip | |
| - test_rmq_conda | |
| - test_stripped | |
| - docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: 'python -m pip install PyGithub | |
| python utils/setup_test_env.py install pip | |
| ' | |
| - name: Verify installation | |
| run: 'python -m pip install setuptools_scm | |
| python utils/setup_test_env.py verify | |
| ' | |
| - name: Update the form | |
| run: python utils/update_form_schema.py --token=${{ secrets.YGGDRASIL_UPDATE_TOKEN | |
| }} | |
| test_conda: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| name: Test (${{ matrix.python-version }}, ${{ matrix.os-base }}, ${{ matrix.install-method | |
| }}, ${{ matrix.test-flags1 }}, ${{ matrix.test-flags2 }}), Install C = ${{ matrix.install-c | |
| }} | |
| needs: params | |
| runs-on: ${{ matrix.os-base }}-${{ fromJSON(needs.params.outputs.os-versions)[matrix.os-base] | |
| }} | |
| steps: | |
| - env: | |
| TEST_FLAGS1: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags1]}} | |
| name: Set test-flags1 | |
| run: echo "TEST_FLAGS1=$TEST_FLAGS1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - env: | |
| TEST_FLAGS2: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags2]}} | |
| name: Set test-flags2 | |
| run: echo "TEST_FLAGS2=$TEST_FLAGS2" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - if: matrix.install-c != true && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Set C installation based on matrix value | |
| run: echo "INSTALLC=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-mpi != true | |
| name: Set MPI installation based on matrix value | |
| run: echo "INSTALLMPI=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-sbml == true | |
| name: Set SBML installation based on matrix value | |
| run: echo "INSTALLSBML=1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-r != true | |
| name: Set R installation based on matrix value | |
| run: echo "INSTALLR=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-pytorch != true | |
| name: Set Pytorch installation based on matrix value | |
| run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - name: Store an ID string for the job | |
| run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{ | |
| matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{ | |
| env.YGG_GHA_JOB_ID_SUFFIX }}-${{ matrix.test-flags1 }}-${{ matrix.test-flags2 | |
| }}" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS) Patch TEMP/TMPDIR on Windows | |
| run: 'echo "TMPDIR=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, 'examples') | |
| name: (WINDOWS) Disable interpreted language example on Windows for speed | |
| run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLMPI | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSMPI | |
| uses: mpi4py/setup-mpi@v1 | |
| - if: startsWith(runner.os, 'Linux') && matrix.install-method == 'pip' | |
| name: (LINUX,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/.cache/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'macOS') && matrix.install-method == 'pip' | |
| name: (MACOS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/Library/Caches/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'Windows') && matrix.install-method == 'pip' | |
| name: (WINDOWS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~\AppData\Local\pip\Cache | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os | |
| != 'macOS') | |
| name: (PIP) Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os | |
| == 'macOS' | |
| name: (PIP) Set up Python 3.7 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.7.16 | |
| - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1 | |
| name: (PIP) Set up Julia | |
| uses: julia-actions/setup-julia@v1 | |
| - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows' | |
| name: Set up Matlab | |
| uses: matlab-actions/setup-matlab@v1 | |
| - if: env.USEVIRTUALENV == 1 && matrix.install-method == 'pip' | |
| name: (PIP) Set up Virtual Env | |
| run: 'python utils/setup_test_env.py env virtualenv ${{ matrix.python-version | |
| }} --env-name=test | |
| echo "source activate ygg" > ~/.bashrc | |
| source test/bin/activate | |
| echo "$VIRTUAL_ENV" | |
| echo "VIRTUAL_ENV=$VIRTUAL_ENV" >> $GITHUB_ENV | |
| echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV | |
| ' | |
| - if: matrix.install-method == 'pip' | |
| name: (PIP) Install dependencies & package | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set the vcpkg root config value | |
| run: yggconfig --vcpkg-dir=C:\\vcpkg | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLR | |
| == 1 | |
| name: (WINDOWS,PIP) Update R requirements | |
| run: ygginstall R --update-r-requirements | |
| - if: matrix.install-method == 'pip' && runner.os == 'macOS' | |
| name: (MACOS,PIP) Set C compiler to llvm clang | |
| run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++ | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS,CONDA) Prune the PATH variable | |
| run: 'echo "PATH=$(python utils/setup_test_env.py prune-path)" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') | |
| name: (CONDA) Set up miniconda base environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channel-priority: strict | |
| channels: conda-forge | |
| miniforge-variant: Mambaforge | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'Windows' && env.INSTALLC == 1 | |
| name: (WINDOWS,CONDA) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - continue-on-error: true | |
| id: conda_build | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Build package in base environment | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: ${{ steps.conda_build.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Build package in base environment (re-attempt) | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: runner.os == 'macOS' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: (MACOS,CONDA) Install old MacOSX SDK for compatibility with the conda | |
| llvm (7) | |
| run: ./utils/setup_old_mac_sdk.sh | |
| - if: runner.os == 'Linux' && matrix.install-sbml == true | |
| name: (LINUX) Install ncurses 5 for SBML runs with libroadrunner | |
| run: sudo apt-get install libncurses5 libncurses5-dev libncursesw5-dev | |
| - continue-on-error: true | |
| id: conda_install | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Install dependencies & package from existing build | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: ${{ steps.conda_install.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Install dependencies & package from existing build (re-attempt) | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'macOS' | |
| name: (MACOS,CONDA) Set allow_multiple_omp config | |
| run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib" | |
| "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib | |
| yggconfig --allow-multiple-omp | |
| ' | |
| - name: Verify installation | |
| run: 'python -m pip install setuptools_scm | |
| python utils/setup_test_env.py verify | |
| ' | |
| - name: Compile libraries | |
| run: yggcompile | |
| - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: Run cmake test in command prompt (CONDA) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Run cmake test in command prompt (PIP) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1 | |
| name: Run tests (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1.outcome == 'failure' }} | |
| name: Re-run test failures (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1_script | |
| if: ${{ contains(env.TEST_FLAGS1, '--mpi-script') }} | |
| name: Run generated test script (1st) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1_script.outcome == 'failure' }} | |
| name: Re-run test script failures (1st) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2 | |
| if: ${{ matrix.test-flags2 != 'empty' }} | |
| name: Run tests (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2.outcome == 'failure' }} | |
| name: Re-run test failures (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} --last-failed --last-failed-no-failures=all | |
| --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2_script | |
| if: ${{ matrix.test-flags2 != 'empty' && contains(env.TEST_FLAGS2, '--mpi-script') | |
| }} | |
| name: Run generated test script (2nd) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2_script.outcome == 'failure' }} | |
| name: Re-run test script failures (2nd) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| name: Combine coverage reports | |
| run: '# ls .* | |
| coverage combine --append | |
| ' | |
| - if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Generate XML version of coverage report | |
| run: '# ls .* | |
| coverage xml -i | |
| ' | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{ env.YGG_GHA_JOB_ID }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - continue-on-error: true | |
| if: ${{ always() }} | |
| name: Download the last successful workflow environment log | |
| uses: dawidd6/action-download-artifact@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: . | |
| workflow: test-install.yml | |
| - if: ${{ always() }} | |
| name: Create a log of Python package versions | |
| run: python utils/setup_test_env.py log | |
| - if: ${{ success() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: new_environment_log.txt | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - install-c: true | |
| install-method: conda | |
| install-mpi: false | |
| install-pytorch: false | |
| install-r: false | |
| install-sbml: false | |
| os-base: ubuntu | |
| python-version: 3.7 | |
| test-flags1: long | |
| test-flags2: empty | |
| - install-c: true | |
| install-method: conda | |
| install-mpi: false | |
| install-pytorch: true | |
| install-r: true | |
| install-sbml: true | |
| os-base: ubuntu | |
| python-version: 3.9 | |
| test-flags1: long-remote-service | |
| test-flags2: examples-sbml | |
| - install-c: true | |
| install-method: conda | |
| install-mpi: false | |
| install-pytorch: true | |
| install-r: true | |
| install-sbml: false | |
| os-base: ubuntu | |
| python-version: '3.10' | |
| test-flags1: long | |
| test-flags2: empty | |
| - install-c: true | |
| install-method: conda | |
| install-mpi: false | |
| install-pytorch: true | |
| install-r: true | |
| install-sbml: false | |
| os-base: ubuntu | |
| python-version: '3.11' | |
| test-flags1: long | |
| test-flags2: empty | |
| - install-c: true | |
| install-method: conda | |
| install-mpi: false | |
| install-pytorch: true | |
| install-r: true | |
| install-sbml: false | |
| os-base: macos | |
| python-version: 3.8 | |
| test-flags1: examples-rpc-lesson3 | |
| test-flags2: tools | |
| install-c: | |
| - true | |
| install-method: | |
| - conda | |
| install-mpi: | |
| - true | |
| install-pytorch: | |
| - true | |
| install-r: | |
| - true | |
| install-sbml: | |
| - false | |
| os-base: | |
| - ubuntu | |
| - macos | |
| - windows | |
| python-version: | |
| - 3.8 | |
| test-flags1: | |
| - long-mpi | |
| test-flags2: | |
| - examples-backwards | |
| max-parallel: 20 | |
| test_pip: | |
| name: Test (${{ matrix.python-version }}, ${{ matrix.os-base }}, ${{ matrix.install-method | |
| }}, ${{ matrix.test-flags1 }}, ${{ matrix.test-flags2 }}), Install C = ${{ matrix.install-c | |
| }} | |
| needs: params | |
| runs-on: ${{ matrix.os-base }}-${{ fromJSON(needs.params.outputs.os-versions)[matrix.os-base] | |
| }} | |
| steps: | |
| - env: | |
| TEST_FLAGS1: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags1]}} | |
| name: Set test-flags1 | |
| run: echo "TEST_FLAGS1=$TEST_FLAGS1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - env: | |
| TEST_FLAGS2: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags2]}} | |
| name: Set test-flags2 | |
| run: echo "TEST_FLAGS2=$TEST_FLAGS2" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - if: matrix.install-c != true && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Set C installation based on matrix value | |
| run: echo "INSTALLC=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-mpi != true | |
| name: Set MPI installation based on matrix value | |
| run: echo "INSTALLMPI=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-sbml == true | |
| name: Set SBML installation based on matrix value | |
| run: echo "INSTALLSBML=1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-r != true | |
| name: Set R installation based on matrix value | |
| run: echo "INSTALLR=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-pytorch != true | |
| name: Set Pytorch installation based on matrix value | |
| run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - name: Store an ID string for the job | |
| run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{ | |
| matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{ | |
| env.YGG_GHA_JOB_ID_SUFFIX }}-${{ matrix.test-flags1 }}-${{ matrix.test-flags2 | |
| }}" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS) Patch TEMP/TMPDIR on Windows | |
| run: 'echo "TMPDIR=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, 'examples') | |
| name: (WINDOWS) Disable interpreted language example on Windows for speed | |
| run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLMPI | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSMPI | |
| uses: mpi4py/setup-mpi@v1 | |
| - if: startsWith(runner.os, 'Linux') && matrix.install-method == 'pip' | |
| name: (LINUX,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/.cache/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'macOS') && matrix.install-method == 'pip' | |
| name: (MACOS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/Library/Caches/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'Windows') && matrix.install-method == 'pip' | |
| name: (WINDOWS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~\AppData\Local\pip\Cache | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os | |
| != 'macOS') | |
| name: (PIP) Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os | |
| == 'macOS' | |
| name: (PIP) Set up Python 3.7 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.7.16 | |
| - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1 | |
| name: (PIP) Set up Julia | |
| uses: julia-actions/setup-julia@v1 | |
| - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows' | |
| name: Set up Matlab | |
| uses: matlab-actions/setup-matlab@v1 | |
| - if: env.USEVIRTUALENV == 1 && matrix.install-method == 'pip' | |
| name: (PIP) Set up Virtual Env | |
| run: 'python utils/setup_test_env.py env virtualenv ${{ matrix.python-version | |
| }} --env-name=test | |
| echo "source activate ygg" > ~/.bashrc | |
| source test/bin/activate | |
| echo "$VIRTUAL_ENV" | |
| echo "VIRTUAL_ENV=$VIRTUAL_ENV" >> $GITHUB_ENV | |
| echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV | |
| ' | |
| - if: matrix.install-method == 'pip' | |
| name: (PIP) Install dependencies & package | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set the vcpkg root config value | |
| run: yggconfig --vcpkg-dir=C:\\vcpkg | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLR | |
| == 1 | |
| name: (WINDOWS,PIP) Update R requirements | |
| run: ygginstall R --update-r-requirements | |
| - if: matrix.install-method == 'pip' && runner.os == 'macOS' | |
| name: (MACOS,PIP) Set C compiler to llvm clang | |
| run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++ | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS,CONDA) Prune the PATH variable | |
| run: 'echo "PATH=$(python utils/setup_test_env.py prune-path)" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') | |
| name: (CONDA) Set up miniconda base environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channel-priority: strict | |
| channels: conda-forge | |
| miniforge-variant: Mambaforge | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'Windows' && env.INSTALLC == 1 | |
| name: (WINDOWS,CONDA) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - continue-on-error: true | |
| id: conda_build | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Build package in base environment | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: ${{ steps.conda_build.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Build package in base environment (re-attempt) | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: runner.os == 'macOS' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: (MACOS,CONDA) Install old MacOSX SDK for compatibility with the conda | |
| llvm (7) | |
| run: ./utils/setup_old_mac_sdk.sh | |
| - if: runner.os == 'Linux' && matrix.install-sbml == true | |
| name: (LINUX) Install ncurses 5 for SBML runs with libroadrunner | |
| run: sudo apt-get install libncurses5 libncurses5-dev libncursesw5-dev | |
| - continue-on-error: true | |
| id: conda_install | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Install dependencies & package from existing build | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: ${{ steps.conda_install.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Install dependencies & package from existing build (re-attempt) | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'macOS' | |
| name: (MACOS,CONDA) Set allow_multiple_omp config | |
| run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib" | |
| "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib | |
| yggconfig --allow-multiple-omp | |
| ' | |
| - name: Verify installation | |
| run: 'python -m pip install setuptools_scm | |
| python utils/setup_test_env.py verify | |
| ' | |
| - name: Compile libraries | |
| run: yggcompile | |
| - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: Run cmake test in command prompt (CONDA) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Run cmake test in command prompt (PIP) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1 | |
| name: Run tests (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1.outcome == 'failure' }} | |
| name: Re-run test failures (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1_script | |
| if: ${{ contains(env.TEST_FLAGS1, '--mpi-script') }} | |
| name: Run generated test script (1st) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1_script.outcome == 'failure' }} | |
| name: Re-run test script failures (1st) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2 | |
| if: ${{ matrix.test-flags2 != 'empty' }} | |
| name: Run tests (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2.outcome == 'failure' }} | |
| name: Re-run test failures (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} --last-failed --last-failed-no-failures=all | |
| --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2_script | |
| if: ${{ matrix.test-flags2 != 'empty' && contains(env.TEST_FLAGS2, '--mpi-script') | |
| }} | |
| name: Run generated test script (2nd) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2_script.outcome == 'failure' }} | |
| name: Re-run test script failures (2nd) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| name: Combine coverage reports | |
| run: '# ls .* | |
| coverage combine --append | |
| ' | |
| - if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Generate XML version of coverage report | |
| run: '# ls .* | |
| coverage xml -i | |
| ' | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{ env.YGG_GHA_JOB_ID }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - continue-on-error: true | |
| if: ${{ always() }} | |
| name: Download the last successful workflow environment log | |
| uses: dawidd6/action-download-artifact@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: . | |
| workflow: test-install.yml | |
| - if: ${{ always() }} | |
| name: Create a log of Python package versions | |
| run: python utils/setup_test_env.py log | |
| - if: ${{ success() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: new_environment_log.txt | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - install-c: false | |
| install-method: pip | |
| install-mpi: false | |
| install-pytorch: true | |
| install-r: false | |
| install-sbml: false | |
| os-base: windows | |
| python-version: 3.8 | |
| test-flags1: long | |
| test-flags2: empty | |
| install-c: | |
| - true | |
| install-method: | |
| - pip | |
| install-mpi: | |
| - true | |
| install-pytorch: | |
| - true | |
| install-r: | |
| - true | |
| install-sbml: | |
| - false | |
| os-base: | |
| - ubuntu | |
| - macos | |
| - windows | |
| python-version: | |
| - 3.8 | |
| test-flags1: | |
| - basic | |
| - examples | |
| - types-no-c | |
| - types-c | |
| test-flags2: | |
| - empty | |
| max-parallel: 20 | |
| test_rmq_conda: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| INSTALLAPY: 1 | |
| INSTALLRMQ: 1 | |
| USEVIRTUALENV: 1 | |
| name: Test RMQ (${{ matrix.python-version }}, ${{ matrix.os-base }}, ${{ matrix.install-method | |
| }}) | |
| needs: params | |
| runs-on: ${{ matrix.os-base }}-${{ fromJSON(needs.params.outputs.os-versions)[matrix.os-base] | |
| }} | |
| services: | |
| rabbitmq: | |
| image: rabbitmq:latest | |
| options: --health-cmd "rabbitmqctl node_health_check" --health-interval 10s | |
| --health-timeout 5s --health-retries 5 | |
| ports: | |
| - 5672:5672 | |
| steps: | |
| - env: | |
| TEST_FLAGS1: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags1]}} | |
| name: Set test-flags1 | |
| run: echo "TEST_FLAGS1=$TEST_FLAGS1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - env: | |
| TEST_FLAGS2: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags2]}} | |
| name: Set test-flags2 | |
| run: echo "TEST_FLAGS2=$TEST_FLAGS2" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - if: matrix.install-c != true && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Set C installation based on matrix value | |
| run: echo "INSTALLC=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-mpi != true | |
| name: Set MPI installation based on matrix value | |
| run: echo "INSTALLMPI=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-sbml == true | |
| name: Set SBML installation based on matrix value | |
| run: echo "INSTALLSBML=1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-r != true | |
| name: Set R installation based on matrix value | |
| run: echo "INSTALLR=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-pytorch != true | |
| name: Set Pytorch installation based on matrix value | |
| run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - name: Store an ID string for the job | |
| run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{ | |
| matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{ | |
| env.YGG_GHA_JOB_ID_SUFFIX }}-${{ matrix.test-flags1 }}-${{ matrix.test-flags2 | |
| }}" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS) Patch TEMP/TMPDIR on Windows | |
| run: 'echo "TMPDIR=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, 'examples') | |
| name: (WINDOWS) Disable interpreted language example on Windows for speed | |
| run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLMPI | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSMPI | |
| uses: mpi4py/setup-mpi@v1 | |
| - if: startsWith(runner.os, 'Linux') && matrix.install-method == 'pip' | |
| name: (LINUX,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/.cache/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'macOS') && matrix.install-method == 'pip' | |
| name: (MACOS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/Library/Caches/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'Windows') && matrix.install-method == 'pip' | |
| name: (WINDOWS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~\AppData\Local\pip\Cache | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os | |
| != 'macOS') | |
| name: (PIP) Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os | |
| == 'macOS' | |
| name: (PIP) Set up Python 3.7 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.7.16 | |
| - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1 | |
| name: (PIP) Set up Julia | |
| uses: julia-actions/setup-julia@v1 | |
| - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows' | |
| name: Set up Matlab | |
| uses: matlab-actions/setup-matlab@v1 | |
| - if: env.USEVIRTUALENV == 1 && matrix.install-method == 'pip' | |
| name: (PIP) Set up Virtual Env | |
| run: 'python utils/setup_test_env.py env virtualenv ${{ matrix.python-version | |
| }} --env-name=test | |
| echo "source activate ygg" > ~/.bashrc | |
| source test/bin/activate | |
| echo "$VIRTUAL_ENV" | |
| echo "VIRTUAL_ENV=$VIRTUAL_ENV" >> $GITHUB_ENV | |
| echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV | |
| ' | |
| - if: matrix.install-method == 'pip' | |
| name: (PIP) Install dependencies & package | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set the vcpkg root config value | |
| run: yggconfig --vcpkg-dir=C:\\vcpkg | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLR | |
| == 1 | |
| name: (WINDOWS,PIP) Update R requirements | |
| run: ygginstall R --update-r-requirements | |
| - if: matrix.install-method == 'pip' && runner.os == 'macOS' | |
| name: (MACOS,PIP) Set C compiler to llvm clang | |
| run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++ | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS,CONDA) Prune the PATH variable | |
| run: 'echo "PATH=$(python utils/setup_test_env.py prune-path)" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') | |
| name: (CONDA) Set up miniconda base environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channel-priority: strict | |
| channels: conda-forge | |
| miniforge-variant: Mambaforge | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'Windows' && env.INSTALLC == 1 | |
| name: (WINDOWS,CONDA) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - continue-on-error: true | |
| id: conda_build | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Build package in base environment | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: ${{ steps.conda_build.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Build package in base environment (re-attempt) | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: runner.os == 'macOS' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: (MACOS,CONDA) Install old MacOSX SDK for compatibility with the conda | |
| llvm (7) | |
| run: ./utils/setup_old_mac_sdk.sh | |
| - if: runner.os == 'Linux' && matrix.install-sbml == true | |
| name: (LINUX) Install ncurses 5 for SBML runs with libroadrunner | |
| run: sudo apt-get install libncurses5 libncurses5-dev libncursesw5-dev | |
| - continue-on-error: true | |
| id: conda_install | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Install dependencies & package from existing build | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: ${{ steps.conda_install.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Install dependencies & package from existing build (re-attempt) | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'macOS' | |
| name: (MACOS,CONDA) Set allow_multiple_omp config | |
| run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib" | |
| "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib | |
| yggconfig --allow-multiple-omp | |
| ' | |
| - name: Verify installation | |
| run: 'python -m pip install setuptools_scm | |
| python utils/setup_test_env.py verify | |
| ' | |
| - name: Compile libraries | |
| run: yggcompile | |
| - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: Run cmake test in command prompt (CONDA) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Run cmake test in command prompt (PIP) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1 | |
| name: Run tests (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1.outcome == 'failure' }} | |
| name: Re-run test failures (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1_script | |
| if: ${{ contains(env.TEST_FLAGS1, '--mpi-script') }} | |
| name: Run generated test script (1st) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1_script.outcome == 'failure' }} | |
| name: Re-run test script failures (1st) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2 | |
| if: ${{ matrix.test-flags2 != 'empty' }} | |
| name: Run tests (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2.outcome == 'failure' }} | |
| name: Re-run test failures (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} --last-failed --last-failed-no-failures=all | |
| --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2_script | |
| if: ${{ matrix.test-flags2 != 'empty' && contains(env.TEST_FLAGS2, '--mpi-script') | |
| }} | |
| name: Run generated test script (2nd) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2_script.outcome == 'failure' }} | |
| name: Re-run test script failures (2nd) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| name: Combine coverage reports | |
| run: '# ls .* | |
| coverage combine --append | |
| ' | |
| - if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Generate XML version of coverage report | |
| run: '# ls .* | |
| coverage xml -i | |
| ' | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{ env.YGG_GHA_JOB_ID }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - continue-on-error: true | |
| if: ${{ always() }} | |
| name: Download the last successful workflow environment log | |
| uses: dawidd6/action-download-artifact@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: . | |
| workflow: test-install.yml | |
| - if: ${{ always() }} | |
| name: Create a log of Python package versions | |
| run: python utils/setup_test_env.py log | |
| - if: ${{ success() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: new_environment_log.txt | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| install-c: | |
| - true | |
| install-method: | |
| - conda | |
| install-mpi: | |
| - false | |
| install-pytorch: | |
| - true | |
| install-r: | |
| - true | |
| install-sbml: | |
| - false | |
| os-base: | |
| - ubuntu | |
| python-version: | |
| - 3.8 | |
| test-flags1: | |
| - long-interp | |
| test-flags2: | |
| - services | |
| test_rmq_pip: | |
| env: | |
| INSTALLAPY: 1 | |
| INSTALLRMQ: 1 | |
| USEVIRTUALENV: 1 | |
| YGG_DEFAULT_COMM: IPCComm | |
| name: Test RMQ (${{ matrix.python-version }}, ${{ matrix.os-base }}, ${{ matrix.install-method | |
| }}) | |
| needs: params | |
| runs-on: ${{ matrix.os-base }}-${{ fromJSON(needs.params.outputs.os-versions)[matrix.os-base] | |
| }} | |
| services: | |
| rabbitmq: | |
| image: rabbitmq:latest | |
| options: --health-cmd "rabbitmqctl node_health_check" --health-interval 10s | |
| --health-timeout 5s --health-retries 5 | |
| ports: | |
| - 5672:5672 | |
| steps: | |
| - env: | |
| TEST_FLAGS1: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags1]}} | |
| name: Set test-flags1 | |
| run: echo "TEST_FLAGS1=$TEST_FLAGS1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - env: | |
| TEST_FLAGS2: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags2]}} | |
| name: Set test-flags2 | |
| run: echo "TEST_FLAGS2=$TEST_FLAGS2" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - if: matrix.install-c != true && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Set C installation based on matrix value | |
| run: echo "INSTALLC=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-mpi != true | |
| name: Set MPI installation based on matrix value | |
| run: echo "INSTALLMPI=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-sbml == true | |
| name: Set SBML installation based on matrix value | |
| run: echo "INSTALLSBML=1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-r != true | |
| name: Set R installation based on matrix value | |
| run: echo "INSTALLR=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-pytorch != true | |
| name: Set Pytorch installation based on matrix value | |
| run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - name: Store an ID string for the job | |
| run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{ | |
| matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{ | |
| env.YGG_GHA_JOB_ID_SUFFIX }}-${{ matrix.test-flags1 }}-${{ matrix.test-flags2 | |
| }}" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS) Patch TEMP/TMPDIR on Windows | |
| run: 'echo "TMPDIR=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, 'examples') | |
| name: (WINDOWS) Disable interpreted language example on Windows for speed | |
| run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLMPI | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSMPI | |
| uses: mpi4py/setup-mpi@v1 | |
| - if: startsWith(runner.os, 'Linux') && matrix.install-method == 'pip' | |
| name: (LINUX,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/.cache/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'macOS') && matrix.install-method == 'pip' | |
| name: (MACOS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/Library/Caches/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'Windows') && matrix.install-method == 'pip' | |
| name: (WINDOWS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~\AppData\Local\pip\Cache | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os | |
| != 'macOS') | |
| name: (PIP) Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os | |
| == 'macOS' | |
| name: (PIP) Set up Python 3.7 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.7.16 | |
| - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1 | |
| name: (PIP) Set up Julia | |
| uses: julia-actions/setup-julia@v1 | |
| - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows' | |
| name: Set up Matlab | |
| uses: matlab-actions/setup-matlab@v1 | |
| - if: env.USEVIRTUALENV == 1 && matrix.install-method == 'pip' | |
| name: (PIP) Set up Virtual Env | |
| run: 'python utils/setup_test_env.py env virtualenv ${{ matrix.python-version | |
| }} --env-name=test | |
| echo "source activate ygg" > ~/.bashrc | |
| source test/bin/activate | |
| echo "$VIRTUAL_ENV" | |
| echo "VIRTUAL_ENV=$VIRTUAL_ENV" >> $GITHUB_ENV | |
| echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV | |
| ' | |
| - if: matrix.install-method == 'pip' | |
| name: (PIP) Install dependencies & package | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set the vcpkg root config value | |
| run: yggconfig --vcpkg-dir=C:\\vcpkg | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLR | |
| == 1 | |
| name: (WINDOWS,PIP) Update R requirements | |
| run: ygginstall R --update-r-requirements | |
| - if: matrix.install-method == 'pip' && runner.os == 'macOS' | |
| name: (MACOS,PIP) Set C compiler to llvm clang | |
| run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++ | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS,CONDA) Prune the PATH variable | |
| run: 'echo "PATH=$(python utils/setup_test_env.py prune-path)" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') | |
| name: (CONDA) Set up miniconda base environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channel-priority: strict | |
| channels: conda-forge | |
| miniforge-variant: Mambaforge | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'Windows' && env.INSTALLC == 1 | |
| name: (WINDOWS,CONDA) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - continue-on-error: true | |
| id: conda_build | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Build package in base environment | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: ${{ steps.conda_build.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Build package in base environment (re-attempt) | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: runner.os == 'macOS' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: (MACOS,CONDA) Install old MacOSX SDK for compatibility with the conda | |
| llvm (7) | |
| run: ./utils/setup_old_mac_sdk.sh | |
| - if: runner.os == 'Linux' && matrix.install-sbml == true | |
| name: (LINUX) Install ncurses 5 for SBML runs with libroadrunner | |
| run: sudo apt-get install libncurses5 libncurses5-dev libncursesw5-dev | |
| - continue-on-error: true | |
| id: conda_install | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Install dependencies & package from existing build | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: ${{ steps.conda_install.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Install dependencies & package from existing build (re-attempt) | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'macOS' | |
| name: (MACOS,CONDA) Set allow_multiple_omp config | |
| run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib" | |
| "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib | |
| yggconfig --allow-multiple-omp | |
| ' | |
| - name: Verify installation | |
| run: 'python -m pip install setuptools_scm | |
| python utils/setup_test_env.py verify | |
| ' | |
| - name: Compile libraries | |
| run: yggcompile | |
| - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: Run cmake test in command prompt (CONDA) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Run cmake test in command prompt (PIP) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1 | |
| name: Run tests (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1.outcome == 'failure' }} | |
| name: Re-run test failures (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1_script | |
| if: ${{ contains(env.TEST_FLAGS1, '--mpi-script') }} | |
| name: Run generated test script (1st) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1_script.outcome == 'failure' }} | |
| name: Re-run test script failures (1st) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2 | |
| if: ${{ matrix.test-flags2 != 'empty' }} | |
| name: Run tests (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2.outcome == 'failure' }} | |
| name: Re-run test failures (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} --last-failed --last-failed-no-failures=all | |
| --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2_script | |
| if: ${{ matrix.test-flags2 != 'empty' && contains(env.TEST_FLAGS2, '--mpi-script') | |
| }} | |
| name: Run generated test script (2nd) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2_script.outcome == 'failure' }} | |
| name: Re-run test script failures (2nd) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| name: Combine coverage reports | |
| run: '# ls .* | |
| coverage combine --append | |
| ' | |
| - if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Generate XML version of coverage report | |
| run: '# ls .* | |
| coverage xml -i | |
| ' | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{ env.YGG_GHA_JOB_ID }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - continue-on-error: true | |
| if: ${{ always() }} | |
| name: Download the last successful workflow environment log | |
| uses: dawidd6/action-download-artifact@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: . | |
| workflow: test-install.yml | |
| - if: ${{ always() }} | |
| name: Create a log of Python package versions | |
| run: python utils/setup_test_env.py log | |
| - if: ${{ success() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: new_environment_log.txt | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| install-c: | |
| - true | |
| install-method: | |
| - pip | |
| install-mpi: | |
| - false | |
| install-pytorch: | |
| - true | |
| install-r: | |
| - true | |
| install-sbml: | |
| - false | |
| os-base: | |
| - ubuntu | |
| python-version: | |
| - 3.8 | |
| test-flags1: | |
| - long-interp | |
| test-flags2: | |
| - empty | |
| test_stripped: | |
| env: | |
| INSTALLC: 0 | |
| INSTALLFORTRAN: 0 | |
| INSTALLLPY: 0 | |
| INSTALLMPI: 0 | |
| INSTALLPYGMENTS: 0 | |
| INSTALLR: 0 | |
| INSTALLRMQ: 0 | |
| INSTALLTRIMESH: 0 | |
| INSTALLZMQ: 0 | |
| YGG_GHA_JOB_ID_SUFFIX: -stripped | |
| name: Test stripped install (${{ matrix.python-version }}, ${{ matrix.os-base | |
| }}, ${{ matrix.install-method }}) | |
| needs: params | |
| runs-on: ${{ matrix.os-base }}-${{ fromJSON(needs.params.outputs.os-versions)[matrix.os-base] | |
| }} | |
| steps: | |
| - env: | |
| TEST_FLAGS1: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags1]}} | |
| name: Set test-flags1 | |
| run: echo "TEST_FLAGS1=$TEST_FLAGS1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - env: | |
| TEST_FLAGS2: ${{fromJSON(needs.params.outputs.test-flags)[matrix.test-flags2]}} | |
| name: Set test-flags2 | |
| run: echo "TEST_FLAGS2=$TEST_FLAGS2" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Get tags required by setuptools_scm to generate version | |
| run: 'git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| ' | |
| - if: matrix.install-c != true && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Set C installation based on matrix value | |
| run: echo "INSTALLC=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-mpi != true | |
| name: Set MPI installation based on matrix value | |
| run: echo "INSTALLMPI=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-sbml == true | |
| name: Set SBML installation based on matrix value | |
| run: echo "INSTALLSBML=1" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-r != true | |
| name: Set R installation based on matrix value | |
| run: echo "INSTALLR=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: matrix.install-pytorch != true | |
| name: Set Pytorch installation based on matrix value | |
| run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - name: Store an ID string for the job | |
| run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{ | |
| matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{ | |
| env.YGG_GHA_JOB_ID_SUFFIX }}-${{ matrix.test-flags1 }}-${{ matrix.test-flags2 | |
| }}" >> $GITHUB_ENV | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS) Patch TEMP/TMPDIR on Windows | |
| run: 'echo "TMPDIR=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, 'examples') | |
| name: (WINDOWS) Disable interpreted language example on Windows for speed | |
| run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLMPI | |
| == 1 | |
| name: (WINDOWS,PIP) Set up MSMPI | |
| uses: mpi4py/setup-mpi@v1 | |
| - if: startsWith(runner.os, 'Linux') && matrix.install-method == 'pip' | |
| name: (LINUX,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/.cache/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'macOS') && matrix.install-method == 'pip' | |
| name: (MACOS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~/Library/Caches/pip | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: startsWith(runner.os, 'Windows') && matrix.install-method == 'pip' | |
| name: (WINDOWS,PIP) Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| path: ~\AppData\Local\pip\Cache | |
| restore-keys: '${{ runner.os }}-pip- | |
| ' | |
| - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os | |
| != 'macOS') | |
| name: (PIP) Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os | |
| == 'macOS' | |
| name: (PIP) Set up Python 3.7 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.7.16 | |
| - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1 | |
| name: (PIP) Set up Julia | |
| uses: julia-actions/setup-julia@v1 | |
| - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows' | |
| name: Set up Matlab | |
| uses: matlab-actions/setup-matlab@v1 | |
| - if: env.USEVIRTUALENV == 1 && matrix.install-method == 'pip' | |
| name: (PIP) Set up Virtual Env | |
| run: 'python utils/setup_test_env.py env virtualenv ${{ matrix.python-version | |
| }} --env-name=test | |
| echo "source activate ygg" > ~/.bashrc | |
| source test/bin/activate | |
| echo "$VIRTUAL_ENV" | |
| echo "VIRTUAL_ENV=$VIRTUAL_ENV" >> $GITHUB_ENV | |
| echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV | |
| ' | |
| - if: matrix.install-method == 'pip' | |
| name: (PIP) Install dependencies & package | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC | |
| == 1 | |
| name: (WINDOWS,PIP) Set the vcpkg root config value | |
| run: yggconfig --vcpkg-dir=C:\\vcpkg | |
| - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLR | |
| == 1 | |
| name: (WINDOWS,PIP) Update R requirements | |
| run: ygginstall R --update-r-requirements | |
| - if: matrix.install-method == 'pip' && runner.os == 'macOS' | |
| name: (MACOS,PIP) Set C compiler to llvm clang | |
| run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++ | |
| - if: runner.os == 'Windows' | |
| name: (WINDOWS,CONDA) Prune the PATH variable | |
| run: 'echo "PATH=$(python utils/setup_test_env.py prune-path)" >> $GITHUB_ENV | |
| ' | |
| shell: bash -l {0} | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') | |
| name: (CONDA) Set up miniconda base environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channel-priority: strict | |
| channels: conda-forge | |
| miniforge-variant: Mambaforge | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'Windows' && env.INSTALLC == 1 | |
| name: (WINDOWS,CONDA) Set up MSVC Compiler | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| toolset: 14.0 | |
| - continue-on-error: true | |
| id: conda_build | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Build package in base environment | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: ${{ steps.conda_build.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Build package in base environment (re-attempt) | |
| run: 'conda deactivate | |
| conda activate base | |
| python utils/setup_test_env.py build ${{ matrix.install-method }} --python | |
| ${{ matrix.python-version }} --use-mamba | |
| ' | |
| - if: runner.os == 'macOS' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: (MACOS,CONDA) Install old MacOSX SDK for compatibility with the conda | |
| llvm (7) | |
| run: ./utils/setup_old_mac_sdk.sh | |
| - if: runner.os == 'Linux' && matrix.install-sbml == true | |
| name: (LINUX) Install ncurses 5 for SBML runs with libroadrunner | |
| run: sudo apt-get install libncurses5 libncurses5-dev libncursesw5-dev | |
| - continue-on-error: true | |
| id: conda_install | |
| if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Install dependencies & package from existing build | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: ${{ steps.conda_install.outcome == 'failure' && (matrix.install-method == | |
| 'conda' || matrix.install-method == 'mamba')}} | |
| name: (CONDA) Install dependencies & package from existing build (re-attempt) | |
| run: python utils/setup_test_env.py install ${{ matrix.install-method }} --without-build | |
| --use-mamba | |
| - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') && | |
| runner.os == 'macOS' | |
| name: (MACOS,CONDA) Set allow_multiple_omp config | |
| run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib" | |
| "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib | |
| yggconfig --allow-multiple-omp | |
| ' | |
| - name: Verify installation | |
| run: 'python -m pip install setuptools_scm | |
| python utils/setup_test_env.py verify | |
| ' | |
| - name: Compile libraries | |
| run: yggcompile | |
| - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method | |
| == 'mamba') | |
| name: Run cmake test in command prompt (CONDA) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method | |
| != 'mamba' | |
| name: Run cmake test in command prompt (PIP) | |
| run: pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py | |
| shell: cmd /C CALL {0} | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1 | |
| name: Run tests (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1.outcome == 'failure' }} | |
| name: Re-run test failures (1st) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS1 }} ${{ env.TEST_FLAGS1_SUFFIX | |
| }} --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test1_script | |
| if: ${{ contains(env.TEST_FLAGS1, '--mpi-script') }} | |
| name: Run generated test script (1st) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test1_script.outcome == 'failure' }} | |
| name: Re-run test script failures (1st) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2 | |
| if: ${{ matrix.test-flags2 != 'empty' }} | |
| name: Run tests (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2.outcome == 'failure' }} | |
| name: Re-run test failures (2nd) | |
| run: pytest --ci --cov-append ${{ env.TEST_FLAGS2 }} --last-failed --last-failed-no-failures=all | |
| --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| id: test2_script | |
| if: ${{ matrix.test-flags2 != 'empty' && contains(env.TEST_FLAGS2, '--mpi-script') | |
| }} | |
| name: Run generated test script (2nd) | |
| run: ./run_mpi.sh | |
| timeout-minutes: 180 | |
| - if: ${{ steps.test2_script.outcome == 'failure' }} | |
| name: Re-run test script failures (2nd) | |
| run: ./run_mpi.sh --last-failed --last-failed-no-failures=all --second-attempt | |
| timeout-minutes: 180 | |
| - continue-on-error: true | |
| name: Combine coverage reports | |
| run: '# ls .* | |
| coverage combine --append | |
| ' | |
| - if: matrix.install-method == 'conda' || matrix.install-method == 'mamba' | |
| name: (CONDA) Generate XML version of coverage report | |
| run: '# ls .* | |
| coverage xml -i | |
| ' | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{ env.YGG_GHA_JOB_ID }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - continue-on-error: true | |
| if: ${{ always() }} | |
| name: Download the last successful workflow environment log | |
| uses: dawidd6/action-download-artifact@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: . | |
| workflow: test-install.yml | |
| - if: ${{ always() }} | |
| name: Create a log of Python package versions | |
| run: python utils/setup_test_env.py log | |
| - if: ${{ success() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: environment-log-${{ env.YGG_GHA_JOB_ID }} | |
| path: new_environment_log.txt | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| install-c: | |
| - false | |
| install-method: | |
| - pip | |
| install-mpi: | |
| - false | |
| install-pytorch: | |
| - true | |
| install-r: | |
| - true | |
| install-sbml: | |
| - false | |
| os-base: | |
| - ubuntu | |
| - macos | |
| - windows | |
| python-version: | |
| - 3.8 | |
| test-flags1: | |
| - long | |
| test-flags2: | |
| - empty | |
| upload_sdist: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| name: Upload sdist | |
| needs: | |
| - build_sdist | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: sdist | |
| path: dist | |
| - name: Publish package to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.pypi }} | |
| skip_existing: true | |
| user: __token__ | |
| upload_wheels: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| name: Upload wheels | |
| needs: | |
| - build_wheels | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: artifact | |
| path: dist | |
| - name: Publish package to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.pypi }} | |
| skip_existing: true | |
| user: __token__ | |
| name: Test of package installation & execution | |
| 'on': | |
| push: | |
| branches-ignore: | |
| - gh-pages | |
| tags: | |
| - '*' | |
| schedule: | |
| - cron: 0 10 * * 1 | |
| - cron: 0 10 1 * * |