Sped up Smoldyn suface and panel lookup with new c-safe Hashtable

.github/workflows/build_wheels.yml

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+name: "Build Wheels"
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+  release:
+    types:
+      - published
+
+jobs:
+  build_wheels:
+    name: Build Python Wheels on ${{ matrix.os }} (for ${{ matrix.python_version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        #os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-13, macos-14]
+        os: [windows-latest]
+        python_version: ["cp39-*", "cp310-*", "cp311-*", "cp312-*", "cp313-*"]
+        exclude:
+          - os: windows-latest
+            python_version: "cp39-*"
+          - os: windows-latest
+            python_version: "cp313-*"
+
+    steps:
+      - name: Checkout repository (for non-windows)
+        if: matrix.os != 'windows-latest'
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+#      - name: Install Ubuntu Dependencies
+#        if: matrix.os == 'ubuntu-latest' || matrix.os == 'ubuntu-24.04-arm'
+#        run: |
+#          sudo apt update
+#          sudo apt install -y wget gfortran cmake ninja-build libboost-all-dev libzip-dev libhdf5-dev libbz2-dev libssl-dev liblzma-dev
+#
+#          # for some reason, there aren't headers included in libzip-dev???? so we're building from source!
+#          mkdir ../libzip-source
+#          wget https://libzip.org/download/libzip-1.11.3.tar.gz
+#          tar -xzvf libzip-1.11.3.tar.gz -C ../libzip-source
+#          cmake -S ../libzip-source/libzip-1.11.3 -B ../libzip-source/libzip-1.11.3/build -G Ninja
+#          cmake --build ../libzip-source/libzip-1.11.3/build
+#          sudo cmake --install ../libzip-source/libzip-1.11.3/build
+#          echo "Confirming header presence..."
+
+      - name: Install Intel MacOS Dependencies
+        if: matrix.os == 'macos-13'
+        shell: bash
+        run: |
+          brew install boost
+          brew install hdf5
+          brew install libzip
+          brew install ninja
+          brew install libaec
+
+          brew install llvm
+          echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
+          source /Users/runner/.bash_profile
+          ln -s $(which gfortran-14) /usr/local/bin/gfortran
+
+      - name: Install ARM MacOS dependencies
+        if: matrix.os == 'macos-14'
+        shell: bash
+        run: |
+          brew install boost
+          brew install hdf5
+          brew install libzip
+          brew install ninja
+          brew install libaec
+
+          brew install llvm
+          echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
+          ln -s /opt/homebrew/bin/gfortran-14 /usr/local/bin/gfortran
+
+# We're no longer using msys2, as it appears to not be able to give us native windows wheels.
+#      - name: Install Windows Dependencies
+#        if: matrix.os == 'windows-latest'
+#        run: |
+#          choco install msys2
+#          C:\tools\msys64\usr\bin\bash -lc "pacman -Sy --noconfirm \
+#            mingw-w64-clang-x86_64-cmake \
+#            mingw-w64-clang-x86_64-ninja \
+#            mingw-w64-clang-x86_64-toolchain \
+#            mingw-w64-clang-x86_64-boost \
+#            mingw-w64-clang-x86_64-hdf5 \
+#            mingw-w64-clang-x86_64-zlib \
+#            mingw-w64-clang-x86_64-libzip \
+#            mingw-w64-clang-x86_64-libaec"
+#            echo "C:\tools\msys64\clang64\bin" | Out-File -Append -Encoding ascii $env:GITHUB_PATH
+#            echo "C:\tools\msys64\clang64\lib" | Out-File -Append -Encoding ascii $env:GITHUB_PATH
+#            echo "C:\tools\msys64\clang64\include" | Out-File -Append -Encoding ascii $env:GITHUB_PATH
+
+      - name: Install Python for Windows (Python 3.9)
+        if: matrix.os == 'windows-latest' && matrix.python_version == 'cp39-*'
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      - name: Install Python for Windows (Python 3.10)
+        if: matrix.os == 'windows-latest' && matrix.python_version == 'cp310-*'
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install Python for Windows (Python 3.11)
+        if: matrix.os == 'windows-latest' && matrix.python_version == 'cp311-*'
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install Python for Windows (Python 3.12)
+        if: matrix.os == 'windows-latest' && matrix.python_version == 'cp312-*'
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install Python for Windows (Python 3.13)
+        if: matrix.os == 'windows-latest' && matrix.python_version == 'cp313-*'
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Clean Windows Workspace
+        if: ${{ matrix.os == 'windows-latest'}}
+        run: Remove-Item * -Recurse -Force
+
+      - name: Install Windows Dependencies (Part 0a - Setup Flang Source Code)
+        if: ${{ matrix.os == 'windows-latest'}}
+        run: |
+          git clone --depth 1 https://github.com/flang-compiler/flang.git ${{ github.workspace }}
+          mv ${{ github.workspace }}/* ${{ github.workspace }}/..
+
+      - name: Install Windows Dependencies (Part 0b - Setup LLVM Build Env)
+        if: ${{ matrix.os == 'windows-latest'}}
+        uses: llvm/actions/setup-windows@main
+        with:
+          arch: amd64
+
+      - name: Install Windows Dependencies (Part 0c - Setup LLVM-style Ninja Build Env)
+        if: ${{ matrix.os == 'windows-latest'}}
+        uses: llvm/actions/setup-windows@main
+        with:
+          arch: amd64
+
+      - name: Install Windows Dependencies (Part 0d - Setup Graphviz for Doxygen)
+        if: ${{ matrix.os == 'windows-latest'}}
+        run: choco install graphviz wget
+
+      - name: Install Windows Dependencies (Part 0e - Setup Sphinx for Python)
+        if: ${{ matrix.os == 'windows-latest'}}
+        run: pip install sphinx
+
+      - name: Install Windows Dependencies (Part 0f - Download pre-built "cmade" LLVM)
+        run: |
+          cd ../..
+          # Search backwards in the workflow history for the specified branch
+          # for the first successful run that produced the desired artifact.
+          $build_name="llvm_build_win_amd64_clangcl_release_19x"
+          Invoke-WebRequest -Uri https://api.github.com/repos/flang-compiler/classic-flang-llvm-project/actions/workflows/pre-compile_llvm.yml/runs -OutFile llvm_runs.json
+          $urls = @($(jq -r --arg b release_19x '.workflow_runs[] | select(.head_branch == $b) | select (.conclusion == "success") | .artifacts_url?' llvm_runs.json))
+          Invoke-WebRequest "$(jq -r '.workflow_runs[0].artifacts_url?' llvm_runs.json)" -OutFile llvm_artifacts.json
+          for ($i = 0; $i -lt $urls.Count; $i++) {
+            $artifacts_url = $urls[$i]
+            Invoke-WebRequest -Uri "$artifacts_url" -OutFile llvm_artifacts.json
+            $archive_url = "$(jq -r --arg b $build_name '.artifacts[] | select(.name == $b) | .archive_download_url' llvm_artifacts.json)"
+            if (! $archive_url) {
+              Write-Output "$artifacts_url did not contain a $build_name archive; too old?"
+              continue
+            }
+            Write-Output "Downloading $archive_url."
+            $artifact_path = "$pwd\${build_name}.zip"
+            try {
+              $response = Invoke-WebRequest -Method Get -Uri $archive_url -OutFile $artifact_path -Headers @{ "Authorization" = "Bearer ${{ secrets.GITHUB_TOKEN }}" }
+              if ($response.StatusCode -lt 300) {
+                break
+              }
+            } catch {}
+          }
+          if (!(Test-Path "$artifact_path")) {
+            Write-Output "Could not download the correct prebuilt compiler; aborting."
+            exit 1
+          }
+          Expand-Archive -Force -Path "${build_name}.zip" -DestinationPath .
+          & 7z x "$pwd\llvm_build.7z" -o"$pwd\classic-flang-llvm-project\" -y
+          Write-Output "$(Get-ChildItem)"
+
+
+      - name: Install Windows Dependencies (Part 1a - Build Flang)
+        if: matrix.os == 'windows-latest'
+        shell: powershell
+        run: |
+          $pcount = $($(Get-WmiObject -class Win32_ComputerSystem).numberoflogicalprocessors)
+          python ..\scripts\build_flang.py -b "Release" -d build -t X86 -p "$(pwd)\..\..\classic-flang-llvm-project\classic-flang-llvm-project\build\" -j $pcount -v
+          $resolved = Resolve-Path "$(pwd)\..\..\classic-flang-llvm-project\classic-flang-llvm-project\build\bin\"
+          $resolved_path = $resolved.Path
+          $new_path = $resolved_path + ";" + [Environment]::GetEnvironmentVariable("GITHUB_PATH", "Machine")
+          $env:PATH = "$resolved_path;$env:PATH"
+          $resolved_path | Set-Content -Path $env:GITHUB_PATH
+          Write-Output "New GITHUB_PATH: "
+          Write-Output "$new_path"
+          [Environment]::SetEnvironmentVariable("GITHUB_PATH", "$new_path", "Machine")
+          flang --version
+
+      - name: Install Windows Dependencies (Part 2a - Reclean Windows Workspace)
+        if: ${{ matrix.os == 'windows-latest'}}
+        run: Remove-Item * -Recurse -Force
+
+      - name: Install Windows Dependencies (Part 2b - Setup Flang Source Code)
+        if: ${{ matrix.os == 'windows-latest'}}
+        uses: actions/checkout@v4
+
+      - name: Install Windows Dependencies (Part 2c - Configure Conan)
+        if: matrix.os == 'windows-latest'
+        shell: powershell
+        run: |
+          choco install conan -y
+          $conanDir = "C:\Program Files\Conan\conan"
+          $env:PATH = "$conanDir;$env:PATH"
+          $conanDir | Set-Content -Path $env:GITHUB_PATH
+          $env:CONAN_HOME = "C:\.conan"
+          "CONAN_HOME=C:\.conan" | Out-File -FilePath $env:GITHUB_ENV -Append
+          conan --version
+
+
+      - name: Install Windows Dependencies (Part 2d - Get Remaining Dependencies through Conan)
+        if: matrix.os == 'windows-latest'
+        run:
+          conan profile detect --force
+
+          conan install . --output-folder=build --build=missing -s compiler.cppstd=17 -s compiler=clang
+
+      - name: Build Wheels (Windows)
+        uses: pypa/[email protected]
+        if: matrix.os == 'windows-latest'
+        env:
+          CC: "clang"
+          CXX: "clang++"
+          FC: "flang"
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_ARCHS_WINDOWS: "native"
+          CIBW_BEFORE_BUILD: "pip install cmake ninja"
+          CIBW_PYTHON_BIN: ${{ env.CUSTOM_PYTHON_BIN }}
+          CIBW_ENVIRONMENT: >
+            CC=clang
+            CXX=clang++
+            FC=flang
+            CMAKE_GENERATOR=Ninja
+            CMAKE_TOOLCHAIN_FILE=D:\\a\\vcell-fvsolver\\vcell-fvsolver\\build\\conan_toolchain.cmake
+
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Build Wheels (MacOS<x86_64>)
+        uses: pypa/[email protected]
+        if: matrix.os == 'macos-13'
+        env:
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_ARCHES: "native"
+          CIBW_ENVIRONMENT: >
+            FC=/usr/local/bin/gfortran
+            MACOSX_DEPLOYMENT_TARGET="10.13"
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Build Wheels (MacOS<ARM>)
+        uses: pypa/[email protected]
+        if: matrix.os == 'macos-14'
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 14.0
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_ARCHES: "native"
+          CIBW_ENVIRONMENT: >
+            FC=/opt/homebrew/bin/gfortran-14
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Build Wheels (Linux<ARM>)
+        uses: pypa/[email protected]
+        if: matrix.os == 'ubuntu-24.04-arm'
+        env:
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_SKIP: "*musllinux*"
+          CIBW_ARCHS_LINUX: "native"
+          CIBW_MANYLINUX_AARCH64_IMAGE: 'quay.io/pypa/manylinux_2_34_aarch64'
+          CIBW_REPAIR_WHEEL_COMMAND: 'auditwheel repair --disable-isa-ext-check {wheel} -w {dest_dir}'
+          CIBW_BEFORE_BUILD: "yum install -y wget boost-devel hdf5-devel zlib-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel \ 
+            && mkdir /xz_source \
+            && wget https://github.com/tukaani-project/xz/releases/download/v5.8.1/xz-5.8.1.tar.gz \
+            && tar -xzvf xz-5.8.1.tar.gz -C /xz_source \
+            && cmake -S /xz_source/xz-5.8.1 -B /xz_source/xz-5.8.1/build \
+            && cmake --build /xz_source/xz-5.8.1/build \
+            && cmake --install /xz_source/xz-5.8.1/build \
+            && pip install h5py"
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Build Wheels (Linux<x86_64>)
+        uses: pypa/[email protected]
+        if: matrix.os == 'ubuntu-latest'
+        env:
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_SKIP: "*musllinux*"
+          CIBW_ARCHS_LINUX: "native"
+          CIBW_MANYLINUX_X86_64_IMAGE: 'quay.io/pypa/manylinux_2_34_x86_64'
+          CIBW_REPAIR_WHEEL_COMMAND: 'auditwheel repair --disable-isa-ext-check {wheel} -w {dest_dir}'
+          CIBW_BEFORE_BUILD:  "yum install -y curl boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel \
+            && pip install h5py \
+            "
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+#  && mkdir /libzip_source \
+#  && curl -O https://libzip.org/download/libzip-1.11.3.tar.gz \
+#  && tar -xzvf libzip-1.11.3.tar.gz -C /libzip_source \
+#  && cmake -S ../libzip-source/libzip-1.11.3 -B ../libzip-source/libzip-1.11.3/build -G Ninja \
+#  && cmake --build ../libzip-source/libzip-1.11.3/build \
+#  && cmake --install ../libzip-source/libzip-1.11.3/build \
+#  && export LIBZIP_INCLUDE_DIR=/usr/local/include \
+#  && export LIBZIP_LIBRARY=/usr/local/lib/libzip.so
+
+      - name: Upload Artifact (Python 3.9)
+        uses: actions/upload-artifact@v4
+        if: matrix.python_version == 'cp39-*'
+        with:
+          name: pyvcell-fv-${{ matrix.os }}-cp39-cibw-wheels
+          path: ./wheelhouse/*.whl
+
+      - name: Upload Artifact (Python 3.10)
+        uses: actions/upload-artifact@v4
+        if: matrix.python_version == 'cp310-*'
+        with:
+          name: pyvcell-fv-${{ matrix.os }}-cp310-cibw-wheels
+          path: ./wheelhouse/*.whl
+
+      - name: Upload Artifact (Python 3.11)
+        uses: actions/upload-artifact@v4
+        if: matrix.python_version == 'cp311-*'
+        with:
+          name: pyvcell-fv-${{ matrix.os }}-cp311-cibw-wheels
+          path: ./wheelhouse/*.whl
+
+      - name: Upload Artifact (Python 3.12)
+        uses: actions/upload-artifact@v4
+        if: matrix.python_version == 'cp312-*'
+        with:
+          name: pyvcell-fv-${{ matrix.os }}-cp312-cibw-wheels
+          path: ./wheelhouse/*.whl
+
+      - name: Upload Artifact (Python 3.13)
+        uses: actions/upload-artifact@v4
+        if: matrix.python_version == 'cp313-*'
+        with:
+          name: pyvcell-fv-${{ matrix.os }}-cp313-cibw-wheels
+          path: ./wheelhouse/*.whl
+
+      - name: Setup tmate session on failure
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ failure() }}
+        with:
+          limit-access-to-actor: true