cd.yml

name: CD

on: [push, workflow_dispatch]

env:
  REGISTRY: ghcr.io
  IMAGE_NAME: ${{ github.repository }}

jobs:
  build-and-push-image:
    runs-on: ubuntu-latest
    permissions:
      contents: read
      packages: write

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Log in to the Container registry
        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Extract metadata (tags, labels) for Docker
        id: meta
        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
        with:
          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}

      - name: Build and push Docker image
        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
        with:
          context: .
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}

  native-build:
    name:
      native-build-${{ matrix.platform }}
    strategy:
      fail-fast: false
      matrix:
        platform: [macos-latest, windows-latest, ubuntu-latest]


    runs-on: ${{ matrix.platform }}

    steps:
      - name: checkout vcell-solvers repo
        uses: actions/checkout@v3

      - name: Install MacOS dependencies
        if: matrix.platform == 'macos-latest'
        shell: bash
        run: |
          brew install boost
          brew install hdf5
          brew install ninja

          brew install llvm
          echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
          ln -s /usr/local/bin/gfortran-12 /usr/local/bin/gfortran
          
          gcc --version
          gfortran --version
          cmake --version
          brew info boost
          brew info hdf5

      - name: Build Macos
        if: matrix.platform == 'macos-latest'
        run: |
          platform=macos
          echo "working dir is $PWD"

          mkdir build
          cd build

          export PATH="/usr/local/opt/llvm/bin:$PATH"

          cmake \
          -G Ninja \
          -DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \
          -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \
          -DOPTION_MINGW=ON \
          -DOPTION_TARGET_MESSAGING=OFF \
          -DOPTION_TARGET_PARALLEL=OFF \
          -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
          -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
          -DOPTION_TARGET_FV_SOLVER=ON \
          -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
          -DOPTION_TARGET_NFSIM_SOLVER=ON \
          -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
          -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
          -DOPTION_TARGET_HY3S_SOLVERS=OFF \
          -B . -S ..

          ninja

      - name: Test Macos
        if: matrix.platform == 'macos-latest'
        run: |
          platform=macos
          echo "working dir is $PWD"

          cd build

          ctest -VV
          
          echo "------ running FiniteVolume_x64 ------"
          ./bin/FiniteVolume_x64 || true
          echo
          echo "------ running NFsim_x64 ------"
          ./bin/NFsim_x64 || true
          echo "------ running SundialsSolverStandalone_x64 ------"
          ./bin/SundialsSolverStandalone_x64 || true
          echo "------ running VCellStoch_x64 ------"
          ./bin/VCellStoch_x64 || true
          echo "------ running smoldyn_x64 ------"
          ./bin/smoldyn_x64 || true
          echo "------ running testzip ------"
          ./bin/testzip || true
          echo "------ running ziptool ------"
          ./bin/ziptool || true

#      - name: Setup tmate session
#        uses: mxschmitt/action-tmate@v3
#        with:
#          limit-access-to-actor: false


      - 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-netcdf
            mingw-w64-clang-x86_64-zlib
            mingw-w64-clang-x86_64-libaec

#      - name: Setup tmate session
#        uses: mxschmitt/action-tmate@v3
#        with:
#          limit-access-to-actor: false

      - name: Build Windows
        if: matrix.platform == 'windows-latest'
        shell: msys2 {0}
        run: |
          platform=windows
          echo "working dir is $PWD"

          mkdir build
          cd build

          PATH="/c/Program\ Files/LLVM/bin:$PATH"

          cmake \
          -G Ninja \
          -DCMAKE_C_COMPILER="clang.exe" \
          -DCMAKE_CXX_COMPILER="clang++.exe" \
          -DOPTION_TARGET_MESSAGING=OFF \
          -DOPTION_TARGET_PARALLEL=OFF \
          -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
          -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
          -DOPTION_TARGET_FV_SOLVER=ON \
          -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
          -DOPTION_TARGET_NFSIM_SOLVER=ON \
          -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
          -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
          -DOPTION_TARGET_HY3S_SOLVERS=OFF \
          -B . -S ..

          ninja -j 1

      - name: Test Windows
        if: matrix.platform == 'windows-latest'
        shell: msys2 {0}
        run: |
          platform=windows
          echo "working dir is $PWD"

          cd build

          ctest -VV

          echo "------ running FiniteVolume_x64 ------"
          ./bin/FiniteVolume_x64 || true
          echo
          echo "------ running NFsim_x64 ------"
          ./bin/NFsim_x64 || true
          echo "------ running SundialsSolverStandalone_x64 ------"
          ./bin/SundialsSolverStandalone_x64 || true
          echo "------ running VCellStoch_x64 ------"
          ./bin/VCellStoch_x64 || true
          echo "------ running smoldyn_x64 ------"
          ./bin/smoldyn_x64 || true
          echo "------ running testzip ------"
          ./bin/testzip || true
          echo "------ running ziptool ------"
          ./bin/ziptool || true

      - name: Install Linux Dependencies
        if: matrix.platform == 'ubuntu-latest'
        run: |
          sudo apt-get update
          sudo apt-get install -y libboost-all-dev
          sudo apt-get install -y libhdf5-dev
          sudo apt-get install -y ninja-build

          gcc --version
          gfortran --version
          cmake --version
          dpkg -s libboost-all-dev
          dpkg -s libhdf5-dev

      - name: Build Linux
        if: matrix.platform == 'ubuntu-latest'
        run: |
          platform=linux
          echo "working dir is $PWD"

          mkdir build
          cd build

          cmake \
          -G Ninja \
          -DOPTION_TARGET_MESSAGING=OFF \
          -DOPTION_TARGET_PARALLEL=OFF \
          -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
          -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
          -DOPTION_TARGET_FV_SOLVER=ON \
          -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
          -DOPTION_TARGET_NFSIM_SOLVER=ON \
          -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
          -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
          -DOPTION_TARGET_HY3S_SOLVERS=OFF \
          -B . -S ..

          ninja

      - name: Test Linux
        if: matrix.platform == 'ubuntu-latest'
        run: |
          platform=linux
          echo "working dir is $PWD"

          cd build

          ctest -VV

          echo "------ running FiniteVolume_x64 ------"
          ./bin/FiniteVolume_x64 || true
          echo
          echo "------ running NFsim_x64 ------"
          ./bin/NFsim_x64 || true
          echo "------ running SundialsSolverStandalone_x64 ------"
          ./bin/SundialsSolverStandalone_x64 || true
          echo "------ running VCellStoch_x64 ------"
          ./bin/VCellStoch_x64 || true
          echo "------ running smoldyn_x64 ------"
          ./bin/smoldyn_x64 || true
          echo "------ running testzip ------"
          ./bin/testzip || true
          echo "------ running ziptool ------"
          ./bin/ziptool || true

      - name: Setup tmate session
        uses: mxschmitt/action-tmate@v3
        with:
          limit-access-to-actor: false


      - name: fix Macos shared object paths
        if: matrix.platform == 'macos-latest'
        shell: bash
        run: |
          mkdir build/upload
          cd build/bin
          rm hello_test TestVCellStoch testzip ziptool || true
          ls *_x64   | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
          ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
          ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
          chmod u+w,+x *
          tar czvf ../upload/mac64_bad_paths.tgz .
          ../../.github/scripts/install_name_tool_macos.sh
          tar czvf ../upload/mac64.tgz --dereference .

      - name: handle shared object paths for Windows native build
        if: matrix.platform == 'windows-latest'
        shell: msys2 {0}
        run: |
          mkdir build/upload
          cd build/bin
          rm hello_test TestVCellStoch testzip ziptool || true
          ls *.exe | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
          ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
          ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
          chmod u+w,+x *
          zip ../upload/win64.zip ./*
          cd ../..
          # fi

      - name: handle shared object paths for Linux native build
        if: matrix.platform == 'ubuntu-latest'
        shell: bash
        run: |
          mkdir build/upload
          cd build/bin
          rm hello_test TestVCellStoch testzip ziptool || true
          ls *_x64   | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
          ls *.so    | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
          ls *.so    | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
          chmod u+w,+x *
          tar czvf ../upload/linux64.tgz --dereference .
          cd ../..

      - name: Upload Macos binaries
        if: matrix.platform == 'macos-latest'
        uses: actions/upload-artifact@v3
        with:
          name: mac64.tgz
          path: build/upload/mac64.tgz

      - name: Upload Windows binaries
        if: matrix.platform == 'windows-latest'
        uses: actions/upload-artifact@v3
        with:
          name: win64.zip
          path: build/upload/win64.zip

      - name: Upload Linux binaries
        if: matrix.platform == 'ubuntu-latest'
        uses: actions/upload-artifact@v3
        with:
          name: linux64.tgz
          path: build/upload/linux64.tgz

      - name: Setup tmate session
        if: ${{ failure() }}
        uses: mxschmitt/action-tmate@v3
        with:
          limit-access-to-actor: false