centos.yaml

name: BLOOM CentOS

on:
  push:
    branches:
      - 'main'
    tags:
      - '*'
  pull_request:
    branches:
      - '**'

jobs:
  centos9-job:
    runs-on: ubuntu-latest  # We use the default GitHub runner to start a Docker container

    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Set up Docker
        uses: docker/setup-buildx-action@v2

      - name: Build and run CentOS 9 compatible container
        run: |
          docker run --name rocky9-container -d rockylinux:9 sleep infinity
          docker exec rocky9-container yum install -y python3 python3-pip wget
          docker exec rocky9-container python3 -m pip install --upgrade pip
          
          # Create a user named 'bloom' and switch to this user
          docker exec rocky9-container useradd -m bloom
          
          # Install Miniconda for user 'bloom'
          docker exec rocky9-container su - bloom -c "wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh"
          docker exec rocky9-container su - bloom -c "bash /tmp/miniconda.sh -b -p /home/bloom/miniconda"
          docker exec rocky9-container su - bloom -c "echo 'export PATH=/home/bloom/miniconda/bin:$PATH' >> /home/bloom/.bashrc"
          docker exec rocky9-container su - bloom -c "/home/bloom/miniconda/bin/conda init"
          
          # Source the conda script and create conda environment
          docker exec rocky9-container su - bloom -c "source /home/bloom/.bashrc && conda create -n BLOOM2 python=3.12.0 pip -y"

          # Copy repository content to container
          docker cp . rocky9-container:/home/bloom/workspace
          docker exec rocky9-container chown -R bloom:bloom /home/bloom/workspace

          # Run the setup script and tests
          docker exec rocky9-container su - bloom -c "cd /home/bloom/workspace && source /home/bloom/.bashrc && source bloom_lims/env/install_postgres.sh && pytest"
          
      - name: Clean up Docker container
        run: docker rm -f rocky9-container