ci.yml

name: CI

on:
  push:
    branches: [ '**' ]
    tags: [ '**' ]
  pull_request:
    branches: [ '**' ]

jobs:
  ## Debug Build Job
  debug:
    name: Debug Build
    runs-on: ubuntu-latest
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - name: Install Prerequisites (Ubuntu)
        run: |
          export PATH="$HOME/.local/bin:$PATH"
          pip3 install --upgrade pip
          sudo pip3 install cpplint
          sudo apt-get update
          sudo apt-get install -y cppcheck doxygen liblzma-dev libzstd-dev libbz2-dev

      - name: Install HTSLib
        run: |
          git clone https://github.com/samtools/htslib.git
          cd htslib
          git checkout tags/1.21
          git submodule update --init --recursive
          autoreconf -i
          ./configure
          make -j
          sudo make install

      - name: Install LibBSC
        run: |
          git clone https://github.com/IlyaGrebnov/libbsc.git 
          cd libbsc 
          git checkout tags/v3.3.4
          sed -i 's/clang++/g++/g' makefile 
          make -j 
          sudo make install

      - name: Run Source Code Tests
        run: ./ci/src_test.sh

      - name: Build Documentation
        run: ./ci/build.sh doc

      - name: Build Genie (Debug)
        run: ./ci/build.sh debug

      - name: Upload Debug Binaries
        uses: actions/upload-artifact@v4
        with:
          name: genie-debug-ubuntu2404-${{ github.sha }}
          path: cmake-build-debug/bin

      - name: Upload Documentation
        uses: actions/upload-artifact@v4
        with:
          name: genie-documentation-${{ github.sha }}
          path: cmake-build-debug/documentation/html

  ## Release Build Job
  release:
    name: Release Build
    runs-on: ubuntu-latest
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - name: Install Prerequisites (Ubuntu)
        run: |
          export PATH="$HOME/.local/bin:$PATH"
          pip3 install --upgrade pip
          sudo pip3 install cpplint
          sudo apt-get update
          sudo apt-get install -y cppcheck doxygen liblzma-dev libzstd-dev libbz2-dev

      - name: Install HTSLib
        run: |
          git clone https://github.com/samtools/htslib.git
          cd htslib
          git checkout tags/1.21
          git submodule update --init --recursive
          autoreconf -i
          ./configure
          make -j
          sudo make install

      - name: Install LibBSC
        run: |
          git clone https://github.com/IlyaGrebnov/libbsc.git 
          cd libbsc 
          git checkout tags/v3.3.4
          sed -i 's/clang++/g++/g' makefile 
          make -j 
          sudo make install

      - name: Build Genie (Release)
        run: ./ci/build.sh release

      - name: Upload Release Binaries
        uses: actions/upload-artifact@v4
        with:
          name: genie-release-ubuntu2404-${{ github.sha }}
          path: cmake-build-release/bin

  ## Unit Tests Job
  unit:
    name: Unit Tests
    runs-on: ubuntu-latest
    needs: debug
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - name: Install Prerequisites (Ubuntu)
        run: |
          export PATH="$HOME/.local/bin:$PATH"
          pip3 install --upgrade pip
          sudo pip3 install cpplint
          sudo apt-get update
          sudo apt-get install -y cppcheck doxygen liblzma-dev libzstd-dev libbz2-dev

      - name: Install HTSLib
        run: |
          git clone https://github.com/samtools/htslib.git
          cd htslib
          git checkout tags/1.21
          git submodule update --init --recursive
          autoreconf -i
          ./configure
          make -j
          sudo make install

      - name: Download Debug Binaries
        uses: actions/download-artifact@v4
        with:
          name: genie-debug-ubuntu2404-${{ github.sha }}
          path: cmake-build-debug/bin

      - name: Make Debug Binaries Executable
        run: chmod +x cmake-build-debug/bin/*

      - name: Run Unit Tests
        run: ci/unit_test.sh

      - name: Upload Utils Test Results
        uses: actions/upload-artifact@v4
        with:
          name: utils-ubuntu2404-${{ github.sha }}
          path: cmake-build-debug/bin/utils_test.xml

      - name: Upload Coding Test Results
        uses: actions/upload-artifact@v4
        with:
          name: coding-ubuntu2404-${{ github.sha }}
          path: cmake-build-debug/bin/coding_test.xml

      - name: Upload Gabac Test Results
        uses: actions/upload-artifact@v4
        with:
          name: gabac-ubuntu2404-${{ github.sha }}
          path: cmake-build-debug/bin/gabac_test.xml

  ## Conformance Roundtrip Tests Job
  conformance_roundtrip:
    name: Conformance Roundtrip Tests
    runs-on: ubuntu-latest
    needs: release
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - name: Install Prerequisites (Ubuntu)
        run: |
          export PATH="$HOME/.local/bin:$PATH"
          pip3 install --upgrade pip
          sudo pip3 install cpplint
          sudo apt-get update
          sudo apt-get install -y cppcheck doxygen liblzma-dev libzstd-dev libbz2-dev

      - name: Install HTSLib
        run: |
          git clone https://github.com/samtools/htslib.git
          cd htslib
          git checkout tags/1.21
          git submodule update --init --recursive
          autoreconf -i
          ./configure
          make -j
          sudo make install

      - name: Checkout Reference Decoder
        run: |
          mkdir ref-decoder
          cd ref-decoder
          git config --global init.defaultBranch master
          git config --global pull.ff only
          git init
          git config user.email "mitogen-group@gmail.com"
          git config user.name "Azure test script"
          git pull https://${{ secrets.EPFL_SCI_STI_MM_GITLAB_USERNAME }}:${{ secrets.EPFL_SCI_STI_MM_GITLAB_PASSWORD }}@git.mpeg.expert/MPEG/Genomic_Information_Representation/mpegg-reference-sw.git Fix_LA

      - name: Configure Reference Decoder (CMake)
        run: |
          cd ref-decoder
          sed -i '/set (CMAKE_C_FLAGS "-Wall -Werror ${CMAKE_C_FLAGS}")/s/^/#/' CMakeLists.txt
          cmake .

      - name: Build Reference Decoder
        run: |
          cd ref-decoder
          make --jobs

      - name: Download Release Binaries
        uses: actions/download-artifact@v4
        with:
          name: genie-release-ubuntu2404-${{ github.sha }}
          path: cmake-build-release/bin

      - name: Make Release Binaries Executable
        run: chmod +x cmake-build-release/bin/*


      - name: Run Conformance Tests
        run: MPEGG_REF_DECODER=$PWD/ref-decoder/bin/decoder/mpegg-decoder-p2 ci/conformance_test.sh

  ## Docker Build and Push Job
  docker:
    name: Docker Build and Push
    runs-on: ubuntu-latest
    needs: [ unit, conformance_roundtrip ]
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - name: Docker Login
        uses: docker/login-action@v2
        with:
          username: ${{ secrets.DOCKERHUB_USERNAME }}
          password: ${{ secrets.DOCKERHUB_PASSWORD }}

      - name: Build and Push Docker Image (develop branch)
        if: github.ref == 'refs/heads/develop'
        uses: docker/build-push-action@v3
        with:
          context: .
          file: '**/Dockerfile'
          push: true
          tags: muefab/genie:develop

      - name: Build and Push Docker Image (main branch)
        if: github.ref == 'refs/heads/main'
        uses: docker/build-push-action@v3
        with:
          context: .
          file: '**/Dockerfile'
          push: true
          tags: muefab/genie:latest

      - name: Build and Push Docker Image (Git tag)
        if: startsWith(github.ref, 'refs/tags/')
        uses: docker/build-push-action@v3
        with:
          context: .
          file: '**/Dockerfile'
          push: true
          tags: muefab/genie:${{ github.ref_name }}