build.yml

# Name of the GitHub Action
name: Build scipion-em-xmipp on Pull Request

# Specify when the Action should be triggered: when a pull request is opened against the 'devel' or 'master' branch
on:
  pull_request:
    branches: [devel, master]

# Define the job that should be run
jobs:
  build:
    # Specify the machine to run the job on
    runs-on: ubuntu-22.04

    # Define the steps to be taken in the job
    steps:    
    # Installing dependencies
    - name: Install dependencies 
      run: |
        sudo apt-get update
        sudo apt-get install -y libfftw3-dev libopenmpi-dev openmpi-bin libhdf5-dev python3-numpy python3-dev libtiff5-dev unzip libsqlite3-dev default-jdk git cmake libopencv-dev libopenmpi-dev make cmake
    
    # Installing CUDA
    - name: Install CUDA
      uses: Jimver/cuda-toolkit@v0.2.11
      id: cuda-toolkit
      with:
        cuda: '11.8.0'
        linux-local-args: '[ "--toolkit" ]'

    # Installing Miniconda
    - name: Install Miniconda
      working-directory: ${{ github.workspace }}/../
      run: |
        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
        bash Miniconda3-latest-Linux-x86_64.sh -b -p ${{ github.workspace }}/../miniconda/
        source ./miniconda/etc/profile.d/conda.sh
        conda update -n base -c defaults conda -y
        
    # Installing Scipion
    - name: Install Scipion with dependencies
      working-directory: ${{ github.workspace }}/../
      run: |
        eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)"
        pip3 install --user scipion-installer
        python3 -m scipioninstaller -conda -noXmipp -noAsk scipion
    
    # Installing Xmipp's Python dependencies in scipion conda enviroment
    - name: Install scons in scipion enviroment
      run: |
        eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)"
        conda activate scipion3
        pip install scons
        
    # Cloning Xmipp 
    - name: Cloning Xmipp
      working-directory: ${{ github.workspace }}/../
      run: git clone https://github.com/I2PC/xmipp.git
    
    # Checkout Xmipp to Pull Request branch if exists, by default stays in devel
    - name: Conditionally checkout Xmipp to ${{ github.head_ref }}
      working-directory: ${{ github.workspace }}/../xmipp
      env:
        BRANCH_NAME: ${{ github.head_ref }}
      run: |
        if [ $(git ls-remote --heads https://github.com/I2PC/xmipp.git $BRANCH_NAME | wc -l) -eq 1 ]; then
          git checkout $BRANCH_NAME
        fi
      
    # Installing Xmipp
    - name: Compile Xmipp and show log
      working-directory: ${{ github.workspace }}/../xmipp
      env:
        BUILD_TESTS: True
      run: |
        ../scipion/scipion3 run ./xmipp
        cat compileLOG.txt
    
    # Check out the repository in the pull request
    - name: Checkout repository
      uses: actions/checkout@v3
      with:
        ref: ${{ github.head_ref }}
            
    # Install plugin from the pull request using the Scipion3 installp command
    - name: Install plugin from pull request
      working-directory: ${{ github.workspace }}
      run: ../scipion/scipion3 installp -p . --devel --noBin