tools-iuc #196
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| # 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/[email protected] | |
| 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 "[email protected]" | |
| 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 |