Sped up Smoldyn suface and panel lookup with new c-safe Hashtable
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| name: "Pip" | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| push: | |
| branches: | |
| - master | |
| release: | |
| types: | |
| - published | |
| jobs: | |
| build: | |
| name: Build with Pip | |
| runs-on: ${{ matrix.platform }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: [ windows-latest, macos-13, macos-14, ubuntu-latest ] | |
| #platform: [ macos-13, macos-14, ubuntu-latest ] | |
| python-version: ["3.9","3.10","3.11","3.12"] | |
| exclude: | |
| - platform: windows-latest | |
| python-version: "3.9" | |
| # - platform: windows-latest | |
| # python-version: "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install Intel MacOS dependencies | |
| if: matrix.platform == 'macos-13' | |
| shell: bash | |
| run: | | |
| brew install boost | |
| brew install hdf5 | |
| brew install libzip | |
| brew install ninja | |
| brew install libaec | |
| brew install llvm | |
| echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile | |
| source /Users/runner/.bash_profile | |
| ln -s $(which gfortran-14) /usr/local/bin/gfortran | |
| gcc --version | |
| gfortran --version | |
| cmake --version | |
| brew info boost | |
| brew info hdf5 | |
| - name: Install ARM MacOS dependencies | |
| if: matrix.platform == 'macos-14' | |
| shell: bash | |
| run: | | |
| brew install boost | |
| brew install hdf5 | |
| brew install libzip | |
| brew install ninja | |
| brew install libaec | |
| brew install llvm | |
| echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile | |
| ln -s /opt/homebrew/bin/gfortran-14 /usr/local/bin/gfortran | |
| gcc --version | |
| gfortran --version | |
| cmake --version | |
| brew info boost | |
| brew info hdf5 | |
| - name: Install Windows Dependencies | |
| if: matrix.platform == 'windows-latest' | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: CLANG64 | |
| update: true | |
| install: > | |
| zip | |
| git | |
| mingw-w64-clang-x86_64-curl | |
| mingw-w64-clang-x86_64-toolchain | |
| mingw-w64-clang-x86_64-flang | |
| mingw-w64-clang-x86_64-cmake | |
| mingw-w64-clang-x86_64-boost | |
| mingw-w64-clang-x86_64-hdf5 | |
| mingw-w64-clang-x86_64-libzip | |
| mingw-w64-clang-x86_64-zlib | |
| mingw-w64-clang-x86_64-libaec | |
| mingw-w64-clang-x86_64-python-pip-tools | |
| - name: Fix windows python version for python3.10 | |
| if: matrix.platform == 'windows-latest' && matrix.python-version == '3.10' | |
| shell: msys2 {0} | |
| run: | | |
| echo "Preparing files for installation" | |
| pacman -Sy --noconfirm mingw-w64-clang-x86_64-python-pip | |
| echo "Downloading old archives" | |
| curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python3.10-3.10.5-1-any.pkg.tar.zst | |
| curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python-pip-23.1.2-1-any.pkg.tar.zst | |
| echo "Installing Python 3.10" | |
| pacman -U --noconfirm mingw-w64-clang-x86_64-python3.10-3.10.5-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python3.10 | grep bin/python | |
| echo "Installing Corresponding Pip" | |
| pacman -U --noconfirm mingw-w64-clang-x86_64-python-pip-23.1.2-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python-pip | grep bin/pip | |
| echo "Attempting to create python symlink" | |
| ln -sf /clang64/bin/python3.10.exe /clang64/bin/python3 | |
| /clang64/bin/python3 --version | |
| - name: Fix windows python version for python3.11 | |
| if: matrix.platform == 'windows-latest' && matrix.python-version == '3.11' | |
| shell: msys2 {0} | |
| run: | | |
| echo "Preparing files for installation" | |
| pacman -Sy --noconfirm mingw-w64-x86_64-python-pip | |
| echo "Downloading old archives" | |
| curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python3.11-3.11.4-1-any.pkg.tar.zst | |
| curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python-pip-23.3.2-1-any.pkg.tar.zst | |
| echo "Installing Python 3.11" | |
| pacman -U --noconfirm mingw-w64-clang-x86_64-python3.11-3.11.4-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python3.11 | grep bin/python | |
| echo "Installing Corresponding Pip" | |
| pacman -U --noconfirm mingw-w64-clang-x86_64-python-pip-23.3.2-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python-pip | grep bin/pip | |
| echo "Attempting to create python symlink..." | |
| ln -sf /clang64/bin/python3.11.exe /clang64/bin/python3 | |
| /clang64/bin/python3 --version | |
| - name: Fix windows python version for python3.12 | |
| if: matrix.platform == 'windows-latest' && matrix.python-version == '3.12' | |
| shell: msys2 {0} | |
| run: | | |
| echo "Preparing files for installation" | |
| pacman -Sy --noconfirm mingw-w64-x86_64-python-pip | |
| echo "Downloading old archives" | |
| curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python3.12-3.12.7-1-any.pkg.tar.zst | |
| curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python-pip-25.0.1-1-any.pkg.tar.zst | |
| echo "Installing Python 3.12" | |
| pacman -U --noconfirm mingw-w64-clang-x86_64-python3.12-3.12.7-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python3.12 | grep bin/python | |
| echo "Installing Corresponding Pip" | |
| pacman -U --noconfirm mingw-w64-clang-x86_64-python-pip-25.0.1-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python-pip | grep bin/pip | |
| echo "Attempting to create python symlink" | |
| ln -sf /clang64/bin/python3.12.exe /clang64/bin/python3 | |
| /clang64/bin/python3 --version | |
| - uses: actions/setup-python@v5 | |
| if: matrix.platform != 'windows-latest' | |
| with: | |
| python-version: "${{ matrix.python-version }}" | |
| - name: Build and install macos-13 | |
| run: | | |
| export MACOSX_DEPLOYMENT_TARGET=13.0 | |
| PATH="/usr/local/opt/llvm/bin:$PATH" | |
| pip wheel . -w dist | |
| ls -al dist | |
| pip install delocate | |
| delocate-listdeps dist/*.whl | |
| delocate-wheel -v dist/*.whl | |
| pip install dist/*.whl | |
| if: matrix.platform == 'macos-13' | |
| - name: Build and install macos-14 | |
| run: | | |
| PATH="/opt/homebrew/opt/llvm/bin:$PATH" | |
| pip wheel . -w dist | |
| ls -al dist | |
| pip install delocate | |
| delocate-listdeps dist/*.whl | |
| delocate-wheel -v dist/*.whl | |
| pip install dist/*.whl | |
| if: matrix.platform == 'macos-14' | |
| - name: Build and install windows-latest | |
| shell: msys2 {0} | |
| run: | | |
| which python3 | |
| python3 --version | |
| python3 -m pip wheel --verbose -Ccmake.define.CMAKE_C_COMPILER="clang.exe" -Ccmake.define.CMAKE_CXX_COMPILER="clang++.exe" . -w dist | |
| python3 -m pip install delvewheel | |
| for wheel_file in dist/*.whl; do | |
| echo "not inspecting $wheel_file" | |
| echo "delvewheel needed -v $wheel_file" | |
| echo "not repairing $wheel_file" | |
| echo "delvewheel repair -v $wheel_file" | |
| done | |
| python3 -m pip install dist/*.whl | |
| if: matrix.platform == 'windows-latest' | |
| - name: Build and install manylinux for python 3.9 | |
| run: | | |
| docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \ | |
| /bin/bash -c \ | |
| "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \ | |
| /opt/python/cp39-cp39/bin/pip wheel /io/ -w /io/dist && \ | |
| auditwheel repair --disable-isa-ext-check /io/dist/*.whl -w /io/dist/" | |
| echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name" | |
| sudo rm -rf dist/*-linux_x86_64.whl | |
| pip install dist/*.whl | |
| if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.9' | |
| - name: Build and install manylinux for python 3.10 | |
| run: | | |
| docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \ | |
| /bin/bash -c \ | |
| "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \ | |
| /opt/python/cp310-cp310/bin/pip wheel /io/ -w /io/dist && \ | |
| auditwheel repair --disable-isa-ext-check /io/dist/*.whl -w /io/dist/" | |
| echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name" | |
| sudo rm -rf dist/*-linux_x86_64.whl | |
| pip install dist/*.whl | |
| if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.10' | |
| - name: Build and install manylinux for python 3.11 | |
| run: | | |
| docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \ | |
| /bin/bash -c \ | |
| "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \ | |
| /opt/python/cp311-cp311/bin/pip wheel /io/ -w /io/dist && \ | |
| auditwheel repair --disable-isa-ext-check /io/dist/*.whl -w /io/dist/" | |
| echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name" | |
| sudo rm -rf dist/*-linux_x86_64.whl | |
| pip install dist/*.whl | |
| if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.11' | |
| - name: Build and install manylinux for python 3.12 | |
| run: | | |
| docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \ | |
| /bin/bash -c \ | |
| "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \ | |
| /opt/python/cp312-cp312/bin/pip wheel /io/ -w /io/dist && \ | |
| auditwheel repair --disable-isa-ext-check /io/dist/*.whl -w /io/dist/" | |
| echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name" | |
| sudo rm -rf dist/*-linux_x86_64.whl | |
| pip install dist/*.whl | |
| if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' | |
| - name: Test not windows | |
| run: | | |
| pip install pytest | |
| pytest | |
| if: matrix.platform != 'windows-latest' | |
| - name: Test on windows | |
| shell: msys2 {0} | |
| run: | | |
| which python3 | |
| python3 --version | |
| python3 -m pip install pytest | |
| python3 -m pytest | |
| if: matrix.platform == 'windows-latest' | |
| - name: set wheel_file and artifact_name environment vars (non-windows) | |
| if: matrix.platform != 'windows-latest' | |
| run: | | |
| for wheel_file in dist/*.whl; do | |
| echo "Uploading $wheel_file" | |
| echo "wheel_file=$wheel_file" >> $GITHUB_ENV | |
| echo "artifact_name=$(basename $wheel_file)" >> $GITHUB_ENV | |
| done | |
| - name: set wheel_file and artifact_name environment vars (windows) | |
| if: matrix.platform == 'windows-latest' | |
| shell: pwsh | |
| run: | | |
| foreach ($wheel_file in Get-ChildItem -Path dist -Filter *.whl) { | |
| Write-Output "Uploading $wheel_file" | |
| echo "wheel_file=$wheel_file" | Out-File -Append -FilePath $env:GITHUB_ENV -Encoding utf8 | |
| echo "artifact_name=$(Split-Path $wheel_file -Leaf)" | Out-File -Append -FilePath $env:GITHUB_ENV -Encoding utf8 | |
| } | |
| - name: Upload wheel file | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ env.artifact_name }} | |
| path: ${{ env.wheel_file }} | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} | |
| with: | |
| limit-access-to-actor: true | |
| publish-to-pypi: | |
| name: Publish to PyPI | |
| needs: build | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| environment: pypi | |
| permissions: | |
| id-token: write | |
| steps: | |
| - name: download all artifacts (wheels and executables) | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: dist_temp/ | |
| - name: Install Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.12' | |
| - name: Publish wheels to PyPI | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | |
| run: | | |
| pip install twine | |
| mkdir dist | |
| echo "current directory is $(pwd)" | |
| ls -al dist* | |
| echo "absolute paths of wheels:" | |
| find dist_temp -type f -name '*.whl' -exec sh -c 'echo "$(realpath {})"/' \; | |
| echo "moving wheels to dist directory" | |
| find dist_temp -type f -name '*.whl' -exec sh -c 'mv "$(realpath {})" dist/' \; | |
| twine upload --repository pypi dist/*.whl | |
| - name: Setup tmate session for PyPI upload failure | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} | |
| with: | |
| limit-access-to-actor: true | |