Autoupdate #71
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| 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 | |
| # To get an exit code of 1 even with tee: | |
| set -o pipefail | |
| 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 "${{ github.workspace }}/autoupdate.err")" | |
| # Restore | |
| set +o pipefail | |
| # Waiting for https://github.com/galaxyproject/planemo/issues/1478 to be solved | |
| if [[ "$(tail -n 1 "${{ github.workspace }}/autoupdate.log")" = "Could not update"* ]]; then | |
| errors="${errors}\n$(tail -n 1 "${{ github.workspace }}/autoupdate.log")\n$(tail -n 1 "${{ github.workspace }}/autoupdate.err")" | |
| fi | |
| 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=${REPO} | |
| ;; | |
| esac | |
| # Check if there is a branch/PR that already exists | |
| # We cannot use the -A option of `gh pr list` because the PR author changes with the Personal Access Token used, | |
| # so we filter on the 3rd output field (headRefName, i.e. remote_repository:branch). | |
| if gh_pr_list_out=$(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 $FILE_TO_CHECK | cut -f 1) = "1" ]; then | |
| echo "A single line was added, probably the date, nothing is changed" | |
| # clean up for the next repo | |
| git checkout -- . | |
| continue | |
| fi | |
| fi | |
| echo "There are changes" | |
| if [ "$DIFF_BRANCH" = "origin/$REPO" ] ; then | |
| # Check if the last commit of the existing branch was manual | |
| LAST_AUTHOR=$(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 "gxydevbot" | 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 |