tools-iuc.yml

# This is a basic workflow to help you get started with Actions
name: tools-iuc
# Controls when the action will run. 
on:
  schedule:
    - cron: "0 4 * * 1"
  push:
    branches: [ main ]
  
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # This workflow contains a single job called "build"
  build:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest
    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      # used for the skip lists
    - name: Checkout autoupdate
      uses: actions/checkout@v3
      with:
        token: ${{ secrets.PAT }}
        repository: planemo-autoupdate/autoupdate
        ref: main
        path: autoupdate

    - name: Checkout tools-iuc
      uses: actions/checkout@v3
      with:
        token: ${{ secrets.PAT }}
        repository: planemo-autoupdate/tools-iuc
        ref: main
        path: tools-iuc
        
    - uses: webfactory/ssh-agent@v0.7.0
      with:
        ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

    - name: Cache downloads
      uses: actions/cache@v3
      with:
        path: ~/.cache/pip
        key: cache-${{ matrix.python-version }}

    # Runs a set of commands using the runners shell
    - name: Run a multi-line script
      run: |
        echo "Installing planemo..."
        pip3 install https://github.com/galaxyproject/planemo/archive/refs/heads/master.zip

        # git credentials
        git config --global user.email "planemo-autoupdate@users.noreply.github.com"
        git config --global user.name "planemo-autoupdate"
        echo ${{ secrets.PAT }} > token.txt
        gh auth login --with-token < token.txt
        
        BASEDIR=`pwd`
        ls $BASEDIR/*
        cd tools-iuc
        echo "Adding upstream..."
        git remote add upstream https://github.com/galaxyproject/tools-iuc.git

        echo "Getting git remote..."
        git remote -v

        echo "Pulling latest from upstream..."
        git fetch --all
        git pull upstream main
        git push origin main
        
        REPOS=$(planemo ci_find_repos tools/)
        echo $REPOS
        for REPO in $REPOS; do
          echo $REPO

          # checkout branch, create if it doesn't exist
          if [[ $(gh pr list --limit 10000 | grep planemo-autoupdate:$REPO.\s*OPEN) ]]
          then
            echo "PR exists, we will checkout the branch and add to it"
            git checkout --track origin/$REPO
          else
            if [[ $(git branch -a --list origin/$REPO) ]]
            then
              echo "Branch exists without an open PR - deleting"
              git push origin --delete $REPO
            fi
            echo "Creating branch and checking out"
            git checkout -b $REPO upstream/main
          fi
          git branch
          echo "Running autoupdate command..."
          cd $REPO
          planemo autoupdate . --skiplist $BASEDIR/autoupdate/tools-iuc_skip_list > $BASEDIR/autoupdate.log
          rm -f tool_test_output.*
          cd $BASEDIR/tools-iuc

          if [[ $(git diff) ]]
          then
            TITLE=$(python3 $BASEDIR/autoupdate/pr_text.py --repo $REPO --log $BASEDIR/autoupdate.log --shed $REPO/.shed.yml --out $BASEDIR/body.txt)

            # first check if a closed PR exists with the same title - if so, we don't continue
            if [[ ! $(gh pr list -s closed --limit 1000 -A planemo-autoupdate | grep "$TITLE" | grep CLOSED) ]]
            then
              echo "Adding..."
              git add .

              echo "Committing..."
              git commit -m "$TITLE"

              echo "Push branch to remote..."
              git push --set-upstream origin $REPO

              OLD_TITLE=$(gh pr list --limit 1000 -A planemo-autoupdate | grep planemo-autoupdate:$REPO | cut -f 2)
              if [[ $OLD_TITLE ]] # just need to update PR title
              then
                if [[ $OLD_TITLE == *\) ]] # older PRs
                then
                  NEW_TITLE=$(echo $OLD_TITLE | cut --complement -f 4 -d ' ' && echo  " to " && echo $TITLE | cut -f 7 -d ' ')
                else # newer PRs
                  NEW_TITLE=$(echo $OLD_TITLE | cut --complement -f 7 -d ' ' && echo $TITLE | cut -f 7 -d ' ')
                fi
                PR_NUMBER=$(gh pr list --limit 1000 -A planemo-autoupdate | grep planemo-autoupdate:$REPO | cut -f 1)
                gh pr edit $PR_NUMBER -t "$NEW_TITLE"
              else # we need to create a PR
                echo "Creating a PR..."
                gh pr create --base main --head planemo-autoupdate:$REPO --title "$TITLE" --repo galaxyproject/tools-iuc --body-file $BASEDIR/body.txt
              fi
            fi
          fi
          # clean up for the next tool
          git checkout -- $REPO
        done