Autoupdate #67
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Autoupdate | |
| on: | |
| schedule: | |
| - cron: "0 4 * * 1" | |
| push: | |
| branches: [main] | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| env: | |
| python-version: '3.11' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - upstream_repo_owner: bgruening | |
| upstream_repo_name: galaxytools | |
| upstream_repo_branch: master | |
| upstream_repo_dir: . | |
| - upstream_repo_owner: galaxycomputationalchemistry | |
| upstream_repo_name: galaxy-tools-compchem | |
| upstream_repo_branch: master | |
| upstream_repo_dir: . | |
| - upstream_repo_owner: galaxyproject | |
| upstream_repo_name: iwc | |
| upstream_repo_branch: main | |
| upstream_repo_dir: workflows/ | |
| - upstream_repo_owner: galaxyproject | |
| upstream_repo_name: tools-iuc | |
| upstream_repo_branch: main | |
| upstream_repo_dir: tools/ | |
| - upstream_repo_owner: lldelisle | |
| upstream_repo_name: tools-lldelisle | |
| upstream_repo_branch: master | |
| upstream_repo_dir: tools/ | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout this repo | |
| uses: actions/checkout@v4 | |
| with: | |
| path: autoupdate | |
| - name: Checkout our fork of ${{ matrix.upstream_repo_name }} | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: planemo-autoupdate/${{ matrix.upstream_repo_name }} | |
| token: ${{ secrets.PAT }} # So we can push to it | |
| path: tools_repo | |
| fetch-depth: 0 # So we can checkout other branches | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| - name: Cache pip dir | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: cache-${{ env.python-version }} | |
| - name: Install planemo | |
| run: | | |
| # pip3 install https://github.com/galaxyproject/planemo/archive/refs/heads/master.zip | |
| pip3 install planemo | |
| - name: Set git credentials | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "planemo-autoupdate" | |
| - name: Pull from upstream tool repo and push to our fork | |
| run: | | |
| git remote add upstream "https://github.com/${{ matrix.upstream_repo_owner }}/${{ matrix.upstream_repo_name }}" | |
| git pull upstream "${{ matrix.upstream_repo_branch}}" | |
| git push origin "${{ matrix.upstream_repo_branch}}" | |
| working-directory: ./tools_repo | |
| - name: Ensure skip_list file exists | |
| run: touch "${{ matrix.upstream_repo_owner }}_${{ matrix.upstream_repo_name }}_skip_list" | |
| working-directory: ./autoupdate | |
| - name: Run a multi-line script | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.PAT }} | |
| run: | | |
| errors="" | |
| REPOS=$(planemo ci_find_repos "${{ matrix.upstream_repo_dir }}") | |
| for REPO in $REPOS; do | |
| echo $REPO | |
| # First try to update | |
| echo "Running autoupdate command..." | |
| cd "$REPO" | |
| # This may fail | |
| planemo autoupdate . --skiplist "${{ github.workspace }}/autoupdate/${{ matrix.upstream_repo_owner }}_${{ matrix.upstream_repo_name }}_skip_list" 2>&1 1> "${{ github.workspace }}/autoupdate.log" | tee "${{ github.workspace }}/autoupdate.err" || errors="${errors}\nCannot autoupdate $REPO, last line of stderr is\n$(tail -n 1 "${{ github.workspace }}/autoupdate.err")" | |
| rm -f tool_test_output.* tools.yml | |
| cd - | |
| # Check if it changed something | |
| if git diff --quiet; then | |
| echo "nothing has been updated" | |
| continue | |
| fi | |
| # Get the PR title and change the CHANGELOG.md for workflows | |
| git status | |
| case $REPO in | |
| workflows/*) | |
| TITLE=$(python3 "${{ github.workspace }}/autoupdate/pr_text_iwc.py" --repo "$REPO" --log "${{ github.workspace }}/autoupdate.log" --out "${{ github.workspace }}/body.txt" --changelog "$REPO/CHANGELOG.md") | |
| FILE_TO_CHECK=${REPO}/CHANGELOG.md | |
| ;; | |
| *) | |
| TITLE=$(python3 "${{ github.workspace }}/autoupdate/pr_text.py" --repo "$REPO" --log "${{ github.workspace }}/autoupdate.log" --shed "$REPO/.shed.yml" --out "${{ github.workspace }}/body.txt") | |
| FILE_TO_CHECK= | |
| ;; | |
| esac | |
| # Check if there is a branch/PR that already exists | |
| # We cannot use the -A option of `gh pr list` because the PR author changes with the Personal Access Token used, | |
| # so we filter on the 3rd output field (headRefName, i.e. remote_repository:branch). | |
| if gh_pr_list_out=$(gh pr list --search "head:$REPO" | grep -P "^\d+\t[^\t]+\tplanemo-autoupdate:$REPO\t"); then | |
| OLD_TITLE=$(echo "$gh_pr_list_out" | cut -f 2) | |
| PR_EXISTS=1 | |
| PR_NUMBER=$(echo "$gh_pr_list_out" | cut -f 1) | |
| PR_STATUS="OPENED" | |
| echo "PR exists and is opened" | |
| DIFF_BRANCH="origin/$REPO" | |
| else | |
| # Check if a closed PR exists with the same title | |
| if gh_pr_list_out=$(gh pr list --search "is:closed is:unmerged '$TITLE' in:title" | grep -P "^\d+\t[^\t]+\tplanemo-autoupdate:"); then | |
| # Only take the first one | |
| gh_pr_list_out=$(echo "$gh_pr_list_out" | head -n 1) | |
| echo "Found a closed PR with title: $TITLE" | |
| OLD_TITLE=$(echo "$gh_pr_list_out" | cut -f 2) | |
| PR_EXISTS=1 | |
| PR_NUMBER=$(echo "$gh_pr_list_out" | cut -f 1) | |
| PR_STATUS="CLOSED" | |
| if [ "$(git branch -a --list "origin/$REPO")" != "" ]; then | |
| # The branch still exists and the PR should be reopened only if there is a new change | |
| DIFF_BRANCH="origin/$REPO" | |
| else | |
| # The branch does not exists anymore so any change should reopen the PR | |
| DIFF_BRANCH="upstream/${{ matrix.upstream_repo_branch }}" | |
| fi | |
| else | |
| OLD_TITLE= | |
| PR_EXISTS=0 | |
| PR_NUMBER= | |
| PR_STATUS= | |
| if [ "$(git branch -a --list "origin/$REPO")" != "" ]; then | |
| echo "Branch exists without an open PR - deleting" | |
| git push origin --delete "$REPO" | |
| fi | |
| DIFF_BRANCH="upstream/${{ matrix.upstream_repo_branch }}" | |
| fi | |
| fi | |
| if ! git diff $DIFF_BRANCH --quiet $FILE_TO_CHECK; then | |
| # Check if it is only the date in workflows | |
| if [[ "$REPO" = "workflows/"* ]]; then | |
| if [ $(git diff --numstat $DIFF_BRANCH $FILE_TO_CHECK | cut -f 1) = "1" ]; then | |
| echo "A single line was added, probably the date, nothing is changed" | |
| # clean up for the next repo | |
| git checkout -- . | |
| continue | |
| fi | |
| fi | |
| echo "There are changes" | |
| if [ "$PR_EXISTS" -eq 1 ]; then | |
| # Check if the last commit of the existing branch was manual | |
| LAST_AUTHOR=$(git log -1 --pretty=format:'%an' $DIFF_BRANCH) | |
| if [ "$LAST_AUTHOR" != "planemo-autoupdate" ]; then | |
| # There were manual commits we do not do anything | |
| gh pr comment "$PR_NUMBER" --body "There are new updates, if you want to integrate them, close the PR and delete branch." | |
| # clean up for the next repo | |
| git checkout -- . | |
| continue | |
| fi | |
| fi | |
| echo "Creating branch and checking out" | |
| git checkout -b "$REPO" "upstream/${{ matrix.upstream_repo_branch }}" | |
| echo "Adding..." | |
| git add . | |
| echo "Committing..." | |
| git commit -m "$TITLE" | |
| echo "Push branch to our fork" | |
| git push --force --set-upstream origin "$REPO" | |
| if [ "$PR_EXISTS" -eq 1 ]; then | |
| # just need to update PR title | |
| if [[ $OLD_TITLE == *\) ]]; then | |
| # older PRs | |
| NEW_TITLE="$OLD_TITLE $(echo "$TITLE" | cut -f 6,7 -d ' ')" | |
| else # newer PRs | |
| NEW_TITLE="$(echo "$OLD_TITLE" | cut --complement -f 7 -d ' ') $(echo "$TITLE" | cut -f 7 -d ' ')" | |
| fi | |
| if [ "$NEW_TITLE" != "$OLD_TITLE" ]; then | |
| # This may fail if for example the PR was opened by someone else like | |
| # https://github.com/bgruening/galaxytools/pull/1353 | |
| gh pr edit "$PR_NUMBER" -t "$NEW_TITLE" || errors="${errors}\nCannot change title of PR $PR_NUMBER for $REPO" | |
| fi | |
| # If the PR is closed, we need to reopen it. | |
| if [ "$PR_STATUS" = "CLOSED" ]; then | |
| # This may fail | |
| gh pr reopen "$PR_NUMBER" || errors="${errors}\nCannot reopen PR $PR_NUMBER for $REPO" | |
| fi | |
| # Comment on the PR | |
| gh pr comment "$PR_NUMBER" --body "There are new updates, they have been integrated to the PR, check the file diff." | |
| else # we need to create a PR | |
| echo "Creating a PR..." | |
| gh pr create --base "${{ matrix.upstream_repo_branch }}" --head "planemo-autoupdate:$REPO" --title "$TITLE" --repo "${{ matrix.upstream_repo_owner}}/${{ matrix.upstream_repo_name }}" --body-file "${{ github.workspace }}/body.txt" | |
| fi | |
| else | |
| echo "No changes compared to $DIFF_BRANCH" | |
| # clean up for the next repo | |
| git checkout -- . | |
| fi | |
| done | |
| if [ ! -z "$errors" ]; then | |
| echo "ERRORS OCCURED DURING AUTOUPDATE:" | |
| echo -e $errors | |
| # Write these errors to an issue | |
| body="$(date), there were errors when running autoupdate\n\n$errors" | |
| echo -e $body > body.txt | |
| if gh_issue_list=$(gh issue list --author "planemo-autoupdate" | grep -P "^\d+\t[^\t]+\tAutoupdate errors\t"); then | |
| gh issue comment $(echo "$gh_issue_list" | cut -f 1 | head -n 1) -F body.txt | |
| else | |
| gh issue create -t "Autoupdate errors" -F body.txt | |
| fi | |
| rm body.txt | |
| exit 1 | |
| fi | |
| working-directory: ./tools_repo |