.github/workflows/main.yml

name: gw

on:
  push:
  pull_request:

env:
  version: 1.1.0

jobs:
  mingw:
   strategy:
     fail-fast: false
     matrix:
       sys: [ucrt64]  # clang64,
   name: ${{ matrix.sys }}
   runs-on: windows-latest
   defaults:
     run:
       shell: msys2 {0}
   steps:
     - uses: actions/checkout@v3
     - uses: msys2/setup-msys2@v2
       with:
         msystem: ${{ matrix.sys }}
         update: true
         install: make
         pacboy: toolchain:p glfw:p skia:p htslib:p freeglut:p glew:p ncurses:p fontconfig:p dlfcn:p libpng:p
     - name: build
       run: |
         make
     - name: upload
       uses: actions/upload-artifact@v3
       with:
         name: mingw-${{ matrix.sys }}
         path: ${{ github.workspace }}/*.exe

  macos-package:

    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ macos-14 ]  # macos-12,
        include:
          - os: macos-12
            arch: intel
          - os: macos-14
            arch: m1

    steps:
      - uses: actions/checkout@v3

      - name: Install dependencies
        run: |
          brew install imagemagick graphicsmagick dylibbundler glfw fontconfig
          # npm broken for python3.12 so use this as work around
          brew list | grep python@
          # brew unlink python@3.12
          shopt -s expand_aliases
          alias python=$(brew --prefix)/bin/python3.11
          alias python3=$(brew --prefix)/bin/python3.11
          
          sudo rm -rf /Library/Frameworks/Python.framework/Versions/3.12
          sudo rm -f /usr/local/bin/python3
          sudo rm -f /Library/Frameworks/Python.framework/Versions/Current/bin/python
          
          which python && python --version
          which python3 && python --version
          python -m pip install packaging
          python3 -m pip install packaging
          
          npm install --global create-dmg

      - name: Build and install htslib with libdeflate
        run: |
          
          wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
          tar -xvf htslib.tar.bz2 && mv htslib-* htslib && rm htslib.tar.bz2
          
          git clone --depth 1 https://github.com/ebiggers/libdeflate.git
          cd libdeflate && CFLAGS+=' -fPIC -O3 ' cmake -B build && CFLAGS+=' -fPIC -O3 ' cmake --build build
          cp build/libdeflate.a ../htslib
          cp libdeflate.h ../htslib
          ls ../htslib

          cd ../htslib
          LDFLAGS="$LDFLAGS -L./" CPPFLAGS="$CPPFLAGS -I./" ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate
          make
          sudo make install

      - name: Make Prep
        run: |
          make prep

      - name: package
        run: |
          
          osacompile -o gw.app deps/gw_applescript_prog.txt
          cp deps/gw_droplet.icns gw.app/Contents/Resources/droplet.icns
          
          echo "BUILDING GW"
          
          brew_lib=$(brew --prefix)/lib
          brew_include=$(brew --prefix)/include
          brew_bin=$(brew --prefix)/bin
          
          LDFLAGS="${LDFLAGS} -L${brew_lib}" CPPFLAGS="${CPPFLAGS} -I${brew_include}" make
          
          mv gw ./gw.app/Contents/MacOS
          rm -rf include lib src Makefile
          
          PATH="$PATH:$brew_bin" dylibbundler -od -b -x ./gw.app/Contents/MacOS/gw -d ./gw.app/Contents/libs/ -p @executable_path/../libs/
          
          echo "VALIDATION"
          otool -L gw.app/Contents/MacOS/gw
          echo ""
          
          echo "CODE SIGNING"
          ls -l
          sudo chown -R $(whoami) ./gw.app
          chmod -R a+rw ./gw.app
          sudo codesign --remove-signature ./gw.app
          sudo codesign --force --deep -s - gw.app -v
          sudo codesign --verify -vvvv gw.app
          
          PATH="$PATH:$brew_bin" create-dmg 'gw.app' || true
          ls
          mv gw\ undefined.dmg gw_macos_${{ matrix.arch }}.dmg
          ls
          pwd

      - name: upload
        uses: actions/upload-artifact@v3
        with:
          name: gw_macos_${{ matrix.arch }}
          path: ./*.dmg

  deb-package:
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v3
      - name: Install dependencies
        run: |
          sudo apt update
          sudo apt-get install dh-make build-essential debhelper dh-virtualenv
          sudo apt-get install debugedit devscripts fakeroot debootstrap pbuilder autotools-dev
          sudo apt install zlib1g-dev libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev libssl-dev
          sudo apt install libgl1-mesa-dev libfontconfig-dev libcurl4-openssl-dev libglfw3 libglfw3-dev
      - name: build
        run: |

          BUILD_DIR=$(pwd)

          mkdir -p usr/bin
          mkdir -p usr/lib/x86_64-linux-gnu
          mkdir -p usr/lib/gwhts
          mkdir -p usr/include/gwhts
          mkdir -p usr/share/icons
          mkdir -p usr/share/icons/hicolor/512x512/apps/
          mkdir -p usr/share/applications

          sudo mkdir -p /usr/lib/gwhts
          sudo mkdir -p /usr/include/gwhts/htslib
          sudo cp /usr/lib/x86_64-linux-gnu/libglfw* usr/lib/x86_64-linux-gnu/.

          git clone --depth 1 https://github.com/ebiggers/libdeflate.git
          cd libdeflate && CFLAGS+=' -fPIC -O3 ' cmake -B build && CFLAGS+=' -fPIC -O3 ' cmake --build build
          sudo cp build/libdeflate.a /usr/local/lib && sudo cp libdeflate.h /usr/local/include
          echo "LIBDEFLATE BUILT" && pwd
          cd ${BUILD_DIR}

          wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
          tar -xvf htslib.tar.bz2
          mv htslib-1.20 htslib && rm htslib.tar.bz2 && cd htslib
          sed -i 's/ -g -Wall/ -Wall/' Makefile  # strip debug information
          ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate
          make -j3
          echo "HTSLIB BUILT" && pwd
          cp -rf htslib ../include
          sudo cp libhts.* /usr/lib/gwhts
          sudo cp htslib/*.h /usr/include/gwhts/htslib
          cp libhts.* ${BUILD_DIR}/usr/lib/gwhts

          cd ${BUILD_DIR}

          sed -i '133 i \\t-mv gw usr/bin' Makefile
          sed -i 's@-L/usr/local/lib@-L/usr/local/lib -L/usr/lib/gwhts@g' Makefile

          make prep

          cp include/gw_icon.png usr/share/icons/
          cp include/gw_icon.png usr/share/icons/hicolor/512x512/apps/
          cp deps/gw.desktop usr/share/applications/

      - name: package
        run: |
          dh_make --single --createorig --packagename gw_${version} --email clealk@cardiff.ac.uk --yes --native

          printf "usr/bin/gw\nusr/share/icons/gw_icon.png\nusr/share/applications/gw.desktop\nusr/lib/gwhts/\nusr/lib/x86_64-linux-gnu/libglfw.so.3\nusr/lib/x86_64-linux-gnu/libglfw.so.3.3" > debian/install

          export LDFLAGS="$LDFLAGS -L./lib/skia/out/Release-x64 -L/usr/local/lib -L/usr/lib -L./usr/lib/gwhts -Wl,-rpath,'$ORIGIN/../lib/gwhts'"

          sed -i '/^Section/c\Section: Bioinformatics' debian/control
          sed -i '/^Homepage/c\Homepage: https://github.com/kcleal/gw' debian/control
          sed -i '/^Description/c\Description: Genome browser and variant annotation' debian/control
          sed -i '/<insert long/d' debian/control
          printf "Conflicts: libglfw3 (<< 3.3)\nReplaces: libglfw3\n" >> debian/control

          # Override dh_shlibdeps to include /usr/lib/gwhts
          printf '#!/usr/bin/make -f\n%%:\n\tdh $@\n\nclean:\n\tdh_clean\n\noverride_dh_shlibdeps:\n\tdh_shlibdeps -l/usr/lib/gwhts\n' > debian/rules
          chmod +x debian/rules

          dpkg-buildpackage -us -uc

      - name: upload
        uses: actions/upload-artifact@v3
        with:
          name: debian-package
          path: /home/runner/work/gw/*.deb