Sped up Smoldyn suface and panel lookup with new c-safe Hashtable; Upgrade to CI/CD, all LLVM tooling now

.github/workflows/build_wheels.yml

@@ -0,0 +1,244 @@
+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-15-intel, macos-15]
+        python_version: ["cp310-*", "cp311-*", "cp312-*", "cp313-*"]
+        exclude:
+          - os: windows-latest
+            python_version: "cp313-*"
+
+    steps:
+      - name: Checkout repository (for non-windows)
+        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 MacOS Dependencies
+        if: matrix.os == 'macos-15' || matrix.os == 'macos-15-intel'
+        shell: bash
+        run: |
+          brew install boost
+          brew install hdf5
+          brew install libzip
+          brew install ninja
+          brew install libaec
+          brew uninstall llvm@18
+          brew install flang
+
+          clang --version
+          flang --version
+          cmake --version
+          brew info boost
+          brew info hdf5
+
+      - 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: Install Windows Dependencies (Part 1 - Configure Conan ...and all other dependencies)
+        if: matrix.os == 'windows-latest'
+        shell: powershell
+        run: |
+          choco install graphviz wget llvm zip gtk-runtime -y
+          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
+          conan profile detect --force  
+
+      - name: Install Windows Dependencies (Part 2 - Setup Sphinx for Python)
+        if: matrix.os == 'windows-latest'
+        run: pip install sphinx cmake ninja
+
+      - name: Install Windows Dependencies (Part 2 - Reconfigure Conan)
+        if: matrix.os == 'windows-latest'
+        shell: bash
+        run: |
+          cp conan-profiles/CI-CD/Windows-AMD64_profile.txt $CONAN_HOME/profiles/default
+
+      - name: Install Windows Dependencies (Part 3b - Get Remaining Dependencies through Conan)
+        if: matrix.os == 'windows-latest'
+        run:
+          conan install . --output-folder=build --build=missing
+
+      - name: Build Wheels (Windows)
+        uses: pypa/cibuildwheel@v2.23.2
+        if: matrix.os == 'windows-latest'
+        env:
+          CC: "clang"
+          CXX: "clang++"
+          FC: "flang"
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_ARCHS_WINDOWS: "native"
+          CIBW_BEFORE_BUILD: "./conanbuild.ps1"
+          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
+            OPTION_EXTRA_CONFIG_INFO=ON
+
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Build Wheels (MacOS<x86_64>)
+        uses: pypa/cibuildwheel@v2.23.2
+        if: matrix.os == 'macos-15-intel'
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 15.0
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_ARCHES: "native"
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Build Wheels (MacOS<ARM>)
+        uses: pypa/cibuildwheel@v2.23.2
+        if: matrix.os == 'macos-15'
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 15.0
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_ARCHES: "native"
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - name: Build Wheels (Linux<ARM>)
+        uses: pypa/cibuildwheel@v2.23.2
+        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/cibuildwheel@v2.23.2
+        if: matrix.os == 'ubuntu-latest'
+        env:
+          CIBW_BUILD: ${{ matrix.python_version }}
+          CIBW_SKIP: "*musllinux*"
+          CIBW_ARCHS_LINUX: "native"
+          CIBW_MANYLINUX_X86_64_IMAGE: 'quay.io/pypa/manylinux_2_34_x86_64'
+          CIBW_REPAIR_WHEEL_COMMAND: 'auditwheel repair --disable-isa-ext-check {wheel} -w {dest_dir}'
+          CIBW_BEFORE_BUILD:  "yum install -y curl boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel \
+            && pip install h5py \
+            "
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+#  && mkdir /libzip_source \
+#  && curl -O https://libzip.org/download/libzip-1.11.3.tar.gz \
+#  && tar -xzvf libzip-1.11.3.tar.gz -C /libzip_source \
+#  && cmake -S ../libzip-source/libzip-1.11.3 -B ../libzip-source/libzip-1.11.3/build -G Ninja \
+#  && cmake --build ../libzip-source/libzip-1.11.3/build \
+#  && cmake --install ../libzip-source/libzip-1.11.3/build \
+#  && export LIBZIP_INCLUDE_DIR=/usr/local/include \
+#  && export LIBZIP_LIBRARY=/usr/local/lib/libzip.so
+
+      - name: Upload Artifact (Python 3.10)
+        uses: actions/upload-artifact@v4
+        if: matrix.python_version == 'cp310-*'
+        with:
+          name: pyvcell-fv-${{ 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