pprcode-refresh-readme.yml

name: PPRCODE_Guideline Workflow - for README refreshing

on:
  push:
    paths:
      - 'README.md'  # Monitor the 'README.md' file
      - '.github/workflows/pprcode-refresh-readme.yml'  # Monitor the 'README.md' ci script file
      - '.biolib/config.yml'  # Monitor the Biolib config file

    branches:
      - main
    
jobs:
  refresh-and-push:
    runs-on: ubuntu-latest
    
    steps:
    - name: Checkout code
      uses: actions/checkout@v3
      
    - name: Set environment variable with current date
      run: |
        echo "DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
        echo "DATE: ${{ env.DATE }}"
    
    - name: Set environment variable with current repo dir
      run: |
        echo "REPO=$PWD" >> $GITHUB_ENV
        echo "REPO: ${{ env.REPO }}"
      
    # - name: Build Docker image
    #   run: docker build -f docker/Dockerfile -t pprcode .

    # - name: Tag Docker image with date and latest
    #   run: |
    #     docker tag pprcode yaoyinying/pprcode:${{ env.DATE }}
    #     docker tag pprcode yaoyinying/pprcode:latest

    - name: Log in to Docker Hub
      run: echo "${{ secrets.DOCKER_GITHUB_REPO_SECRET }}" | docker login -u yaoyinying --password-stdin

    # - name: Create Testing and Run it
    #   run: |
    #     python -m venv pprcode_test
    #     source pprcode_test/bin/activate
    #     pip install -r docker/requirements.txt
    #     python ${{ env.REPO }}/docker/run_docker.py --fasta ${{ env.REPO }}/PPR_example.fasta --save_dir ./save-psscan --plot_item=bar,score,edge,ppr,rna
    #     python ${{ env.REPO }}/docker/run_docker.py --fasta ${{ env.REPO }}/PPR_example.fasta --save_dir ./save-pprfinder --plot_item=bar,score,edge,ppr,rna --program=pprfinder
    #     deactivate 
        
    # - name: Push Docker image
    #   run: |
    #     cd ${{ env.REPO }}
    #     docker push yaoyinying/pprcode:${{ env.DATE }}
    #     docker push yaoyinying/pprcode:latest

    - name: Update Readme file for CI actions
      run: |
        awk '{if ($0 !~ "https://img.shields.io" && $0 !~ "https://tinyurl.com/pprcode-badge" && $0 !~ "badge.svg" ){print }}' README.md >README.ci.md
        cat README.ci.md

    - name: Refresh Docker Hub Description
      uses: peter-evans/dockerhub-description@v3
      with:
        username: yaoyinying
        password: ${{ secrets.DOCKER_GITHUB_REPO_SECRET }}
        repository: yaoyinying/pprcode
        readme-filepath: ./README.md
        enable-url-completion: true
        
    - name: Install pybiolib package
      run: pip3 install -U pybiolib
      
    - name: Build and push biolib application
      run: BIOLIB_TOKEN=${{ secrets.BIOLIB_TOKEN }}  biolib push YaoYinYing/pprcode

    - name: Delete temp Readme
      run: rm -f README.ci.md