Build R Packages #8516
Workflow file for this run
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| name: Build R Packages | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - 'build/**' | |
| paths: | |
| - 'logs/dispatched-packages.txt' | |
| - 'logs/successful-packages.txt' | |
| concurrency: | |
| group: build-r-packages-${{ github.ref }} | |
| cancel-in-progress: false | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| persist-credentials: true | |
| - name: Update to latest | |
| run: | | |
| git pull origin ${GITHUB_REF#refs/heads/} | |
| git reset --hard origin/${GITHUB_REF#refs/heads/} | |
| - name: Save kubeconfig | |
| shell: bash | |
| run: mkdir -p ~/.kube && echo "${{ secrets.KUBECONFIG }}" > ~/.kube/config | |
| - name: Install Kubectl | |
| run: | | |
| curl -LO 'https://dl.k8s.io/release/v1.34.1/bin/linux/amd64/kubectl' && \ | |
| chmod +x ./kubectl && \ | |
| mv ./kubectl /usr/local/bin/kubectl && \ | |
| kubectl version | |
| - name: Check for completed cycle | |
| id: cycle_check | |
| run: | | |
| # Check if PACKAGES file exists (indicates completed cycle) | |
| if [[ -f "PACKAGES" ]]; then | |
| echo "Cycle already completed (PACKAGES file exists). Skipping." | |
| echo "skip=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "skip=false" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Manage build lifecycle | |
| if: steps.cycle_check.outputs.skip != 'true' | |
| env: | |
| RCLONE_CONF: ${{secrets.RCLONE_CONF}} | |
| id: build | |
| run: | | |
| set -euxo pipefail | |
| # Use branch name as the build identifier | |
| BRANCH_NAME=${GITHUB_REF#refs/heads/} | |
| BUILD_ID=$(echo "${BRANCH_NAME}" | sed 's|build/||' | tr '/' '-') | |
| echo "Build ID: ${BUILD_ID}" | |
| echo "Branch: ${BRANCH_NAME}" | |
| # Check if this is first run (no biocdeps.json yet) | |
| if [[ ! -s "biocdeps.json" ]]; then | |
| echo "First run - setting up Kubernetes resources..." | |
| CONTAINER=$(cat CONTAINER_BASE_IMAGE.bioc) | |
| # Setup Kubernetes resources - this handles running deps_json.R via init container | |
| bash ./.github/scripts/setup_k8s.sh "nfs-client" "500Gi" "${BUILD_ID}" | |
| else | |
| echo "Continuing existing build..." | |
| CONTAINER=$(cat CONTAINER_BASE_IMAGE.bioc) | |
| # Handle completed jobs | |
| bash ./.github/scripts/handle_k8s_jobs.sh \ | |
| "${BUILD_ID}" \ | |
| "logs/successful-packages.txt" \ | |
| "logs/failed-packages.txt" | |
| fi | |
| # Ensure log directory exists before any operations | |
| mkdir -p logs | |
| touch logs/dispatched-packages.txt | |
| # Find and dispatch packages | |
| python ./.github/scripts/find_ready_pkgs.py \ | |
| "biocdeps.json" \ | |
| "ready_packages.txt" \ | |
| "logs/dispatched-packages.txt" \ | |
| "logs/successful-packages.txt" \ | |
| "remaining-packages.json" | |
| # Calculate truncated build ID for PVC name | |
| BUILD_ID_CLEAN=$(echo "${BUILD_ID}" | tr '[:upper:]' '[:lower:]' | tr '.' '-' | tr -cd '[:alnum:]-') | |
| VERSION_SUFFIX="${BUILD_ID_CLEAN: -3}" | |
| DATE_PART=$(echo "$BUILD_ID_CLEAN" | cut -d'-' -f1-3 | tr -d '-') | |
| CONTAINER_HINT=$(echo "$BUILD_ID_CLEAN" | sed 's/^[0-9-]*-[0-9]*-//' | sed 's/-[^-]*$//' | cut -c1-4) | |
| BUILD_ID_SHORT="${DATE_PART}-${CONTAINER_HINT}-${VERSION_SUFFIX}" | |
| PVC_NAME="pvc-${BUILD_ID_SHORT}" | |
| # Dispatch jobs with xargs and delay | |
| cat "ready_packages.txt" | xargs -i bash -c "bash ./.github/scripts/dispatch_k8s_job.sh {} ${CONTAINER} ${PVC_NAME} ${BUILD_ID} && sleep 1" | |
| # Track if we had any new activity | |
| git add . | |
| ACTIVITY_CHECK=$(git diff --staged --name-status | grep -q "logs/.*packages.txt" && echo "true" || echo "false") | |
| echo "had_activity=${ACTIVITY_CHECK}" >> $GITHUB_OUTPUT | |
| # Get counter values | |
| NULL_PUSH_COUNT=$(cat "null_push_counter" 2>/dev/null || echo "0") | |
| RESET_ATTEMPTS=$(cat "reset_attempts_counter" 2>/dev/null || echo "0") | |
| # Note: Reset failed logic removed - handle failures manually or via separate workflow if needed | |
| # Backup changed files to temp directory | |
| mkdir -p /tmp/restore | |
| # Stage all changes to identify modified files | |
| git add . | |
| # Copy changed files to restore directory | |
| git diff --staged --name-only | xargs -r -I{} bash -c 'mkdir -p "/tmp/restore/$(dirname "{}")" && cp "{}" "/tmp/restore/{}"' | |
| echo "Backup complete - copied changed files" | |
| - name: Commit and push results | |
| if: steps.cycle_check.outputs.skip != 'true' | |
| id: repo_changes | |
| run: | | |
| BRANCH_NAME=${GITHUB_REF#refs/heads/} | |
| git pull origin ${BRANCH_NAME} && git reset --hard origin/${BRANCH_NAME} || git reset --hard origin/${BRANCH_NAME} | |
| cp -r /tmp/restore/* ./ || true | |
| git config --global user.name 'GitHub Actions' | |
| git config --global user.email 'actions@github.com' | |
| git add . || true | |
| # Check if there are actual changes to commit | |
| if git diff --staged --quiet; then | |
| echo "No changes to commit" | |
| # If no changes, increment the null push counter | |
| NULL_PUSH_COUNT=$(cat "null_push_counter" 2>/dev/null || echo "0") | |
| NEW_COUNT=$((NULL_PUSH_COUNT + 1)) | |
| echo "${NEW_COUNT}" > "null_push_counter" | |
| # Commit just the counter change | |
| git add "null_push_counter" | |
| git commit -m "Increment null push counter to ${NEW_COUNT}" | |
| git push || (git pull --rebase && git push) | |
| echo "pushed=false" >> $GITHUB_OUTPUT | |
| else | |
| # Check for new successful packages | |
| NEW_SUCCESS=$(git diff --staged -- "logs/successful-packages.txt" | grep -c "^\+" | grep -v "^\+\+\+" || echo "0") | |
| # Always reset null push counter on meaningful changes | |
| echo "0" > "null_push_counter" | |
| git add "null_push_counter" | |
| # Only reset attempts counter if we have new successful packages | |
| if [ "${NEW_SUCCESS}" -gt 0 ]; then | |
| echo "New successful packages detected (${NEW_SUCCESS}), resetting attempts counter" | |
| echo "0" > "reset_attempts_counter" | |
| git add "reset_attempts_counter" | |
| fi | |
| # Commit all changes | |
| git commit -m "Build state update: ${{ github.run_id }}" | |
| git push || (git pull --rebase && git push) | |
| echo "pushed=true" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Check if cycle is ready to finish | |
| if: steps.cycle_check.outputs.skip != 'true' | |
| id: check_complete | |
| run: | | |
| if bash ./.github/scripts/check_cycle_complete.sh > /tmp/cycle-check-output.txt 2>&1; then | |
| echo "notify=yes" >> $GITHUB_OUTPUT | |
| # Get container name for notification | |
| CONTAINER=$(cat CONTAINER_BASE_IMAGE.bioc) | |
| # Get stats for notification | |
| SUCCESSFUL=$(wc -l < logs/successful-packages.txt 2>/dev/null || echo 0) | |
| FAILED=$(wc -l < logs/failed-packages.txt 2>/dev/null || echo 0) | |
| # Count only blocked packages (remaining packages that are not failed) | |
| REMAINING=$(python3 -c "import json; remaining = json.load(open('remaining-packages.json')); failed = set(line.strip() for line in open('logs/failed-packages.txt') if line.strip()); blocked = [pkg for pkg in remaining if pkg not in failed]; print(len(blocked))" 2>/dev/null || echo 0) | |
| # Create simple single-line notification message (avoid quotes to prevent JSON escaping issues) | |
| MSG="Build cycle ready for ${CONTAINER}: ${SUCCESSFUL} successful, ${FAILED} failed, ${REMAINING} blocked. Run finish_cycle: https://github.com/${{ github.repository }}/actions/workflows/finish_cycle.yaml" | |
| # Replace any double quotes with single quotes to avoid JSON issues | |
| MSG="${MSG//\"/\'}" | |
| echo "SLACK_MESSAGE=${MSG}" >> "$GITHUB_ENV" | |
| else | |
| echo "notify=no" >> $GITHUB_OUTPUT | |
| cat /tmp/cycle-check-output.txt || true | |
| fi | |
| - name: Notify slack channel | |
| uses: slackapi/slack-github-action@v2.1.1 | |
| with: | |
| method: chat.postMessage | |
| token: ${{ secrets.SLACK_BOT_TOKEN }} | |
| payload: | | |
| { | |
| "channel": "${{ secrets.SLACK_CHANNEL_ID }}", | |
| "text": "${{ env.SLACK_MESSAGE }}" | |
| } | |
| env: | |
| SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }} | |
| SLACK_CHANNEL_ID: ${{ secrets.SLACK_CHANNEL_ID }} | |
| if: env.SLACK_BOT_TOKEN != null && env.SLACK_CHANNEL_ID != null && steps.check_complete.outputs.notify == 'yes' | |
| continue-on-error: true |