molecule-core/.github/workflows/ci.yml

name: CI

on:
  push:
    branches: [main, staging]
  pull_request:
    branches: [main, staging]

# Cancel in-progress CI runs when a new commit arrives on the same ref.
# This prevents stale runs from queuing behind each other.
concurrency:
  group: ci-${{ github.ref }}
  cancel-in-progress: true

jobs:
  # Detect which paths changed so downstream jobs can skip when only
  # docs/markdown files were modified.
  changes:
    name: Detect changes
    runs-on: ubuntu-latest
    outputs:
      platform: ${{ steps.check.outputs.platform }}
      canvas: ${{ steps.check.outputs.canvas }}
      python: ${{ steps.check.outputs.python }}
      scripts: ${{ steps.check.outputs.scripts }}
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - id: check
        run: |
          # For PR events: diff against the base branch (not HEAD~1 of the branch,
          # which may be unrelated after force-pushes). When a push updates a PR,
          # both pull_request and push events fire — prefer the PR base so that
          # the diff is always computed against the actual merge base, not the
          # previous SHA on the branch which may be on a different history line.
          BASE="${GITHUB_BASE_REF:-${{ github.event.before }}}"
          # GITHUB_BASE_REF is set by GitHub for PR events (the base branch name).
          # For pull_request events we use the stored base.sha; for push events
          # (or when base.sha is unavailable) fall back to github.event.before.
          if [ "${{ github.event_name }}" = "pull_request" ] && [ -n "${{ github.event.pull_request.base.sha }}" ]; then
            BASE="${{ github.event.pull_request.base.sha }}"
          fi
          # Fallback: if BASE is empty or all zeros (new branch), run everything
          if [ -z "$BASE" ] || echo "$BASE" | grep -qE '^0+$'; then
            echo "platform=true" >> "$GITHUB_OUTPUT"
            echo "canvas=true" >> "$GITHUB_OUTPUT"
            echo "python=true" >> "$GITHUB_OUTPUT"
            echo "scripts=true" >> "$GITHUB_OUTPUT"
            exit 0
          fi
          DIFF=$(git diff --name-only "$BASE" HEAD 2>/dev/null || echo ".github/workflows/ci.yml")
          echo "platform=$(echo "$DIFF" | grep -qE '^workspace-server/|^\.github/workflows/ci\.yml$' && echo true || echo false)" >> "$GITHUB_OUTPUT"
          echo "canvas=$(echo "$DIFF" | grep -qE '^canvas/|^\.github/workflows/ci\.yml$' && echo true || echo false)" >> "$GITHUB_OUTPUT"
          echo "python=$(echo "$DIFF" | grep -qE '^workspace/|^\.github/workflows/ci\.yml$' && echo true || echo false)" >> "$GITHUB_OUTPUT"
          echo "scripts=$(echo "$DIFF" | grep -qE '^tests/e2e/|^scripts/|^infra/scripts/|^\.github/workflows/ci\.yml$' && echo true || echo false)" >> "$GITHUB_OUTPUT"          

  platform-build:
    name: Platform (Go)
    needs: changes
    if: needs.changes.outputs.platform == 'true'
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: workspace-server
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-go@v5
        with:
          go-version: 'stable'
      - run: go mod download
      - run: go build ./cmd/server
      # CLI (molecli) moved to standalone repo: github.com/Molecule-AI/molecule-cli
      - run: go vet ./...
      - name: Run golangci-lint
        uses: golangci/golangci-lint-action@v9
        with:
          version: latest
          working-directory: workspace-server
          args: --timeout 3m
        continue-on-error: true  # Warn but don't block until codebase is clean
      - name: Run tests with race detection and coverage
        run: go test -race -coverprofile=coverage.out ./...

      - name: Per-file coverage report
        # Advisory — lists every source file with its coverage so reviewers
        # can see at-a-glance where gaps are. Sorted ascending so the worst
        # offenders float to the top. Does NOT fail the build; the hard
        # gate is the threshold check below. (#1823)
        run: |
          echo "=== Per-file coverage (worst first) ==="
          go tool cover -func=coverage.out \
            | grep -v '^total:' \
            | awk '{file=$1; sub(/:[0-9][0-9.]*:.*/, "", file); pct=$NF; gsub(/%/,"",pct); s[file]+=pct; c[file]++}
                   END {for (f in s) printf "%6.1f%%  %s\n", s[f]/c[f], f}' \
            | sort -n          

      - name: Check coverage thresholds
        # Enforces two gates from #1823 Layer 1:
        #   1. Total floor (25% — ratchet plan in COVERAGE_FLOOR.md).
        #   2. Per-file floor — non-test .go files in security-critical
        #      paths with coverage <10% fail the build, UNLESS the file
        #      path is listed in .coverage-allowlist.txt (acknowledged
        #      historical debt with a tracking issue + expiry).
        run: |
          set -e
          TOTAL_FLOOR=25
          # Security-critical paths where a 0%-coverage file is a real risk.
          CRITICAL_PATHS=(
            "internal/handlers/tokens"
            "internal/handlers/workspace_provision"
            "internal/handlers/a2a_proxy"
            "internal/handlers/registry"
            "internal/handlers/secrets"
            "internal/middleware/wsauth"
            "internal/crypto"
          )

          TOTAL=$(go tool cover -func=coverage.out | grep '^total:' | awk '{print $3}' | sed 's/%//')
          echo "Total coverage: ${TOTAL}%"
          if awk "BEGIN{exit !($TOTAL < $TOTAL_FLOOR)}"; then
            echo "::error::Total coverage ${TOTAL}% is below the ${TOTAL_FLOOR}% floor. See COVERAGE_FLOOR.md for ratchet plan."
            exit 1
          fi

          # Aggregate per-file coverage → /tmp/perfile.txt: "<fullpath> <pct>"
          go tool cover -func=coverage.out \
            | grep -v '^total:' \
            | awk '{file=$1; sub(/:[0-9][0-9.]*:.*/, "", file); pct=$NF; gsub(/%/,"",pct); s[file]+=pct; c[file]++}
                   END {for (f in s) printf "%s %.1f\n", f, s[f]/c[f]}' \
            > /tmp/perfile.txt

          # Build allowlist — paths relative to workspace-server, one per line.
          # Lines starting with # are comments.
          ALLOWLIST=""
          if [ -f ../.coverage-allowlist.txt ]; then
            ALLOWLIST=$(grep -vE '^(#|[[:space:]]*$)' ../.coverage-allowlist.txt || true)
          fi

          FAILED=0
          WARNED=0
          for path in "${CRITICAL_PATHS[@]}"; do
            while read -r file pct; do
              [[ "$file" == *_test.go ]] && continue
              [[ "$file" == *"$path"* ]] || continue
              awk "BEGIN{exit !($pct < 10)}" || continue

              # Strip the package-import prefix so we can match .coverage-allowlist.txt
              # entries written as paths relative to workspace-server/.
              rel=$(echo "$file" | sed 's|^github.com/Molecule-AI/molecule-monorepo/platform/||')

              if echo "$ALLOWLIST" | grep -qxF "$rel"; then
                echo "::warning file=workspace-server/$rel::Critical file at ${pct}% coverage (allowlisted, #1823) — fix before expiry."
                WARNED=$((WARNED+1))
              else
                echo "::error file=workspace-server/$rel::Critical file at ${pct}% coverage — must be >=10% (target 80%). See #1823. To acknowledge as known debt, add this path to .coverage-allowlist.txt."
                FAILED=$((FAILED+1))
              fi
            done < /tmp/perfile.txt
          done

          echo ""
          echo "Critical-path check: $FAILED new failures, $WARNED allowlisted warnings."

          if [ "$FAILED" -gt 0 ]; then
            echo ""
            echo "$FAILED security-critical file(s) have <10% test coverage and are"
            echo "NOT in the allowlist. These paths handle auth, tokens, secrets, or"
            echo "workspace provisioning — a 0% file here is the exact gap that let"
            echo "CWE-22, CWE-78, KI-005 slip through in past incidents. Either:"
            echo "  (a) add tests to raise coverage above 10%, or"
            echo "  (b) add the path to .coverage-allowlist.txt with an expiry date"
            echo "      and a tracking issue reference."
            exit 1
          fi          

  canvas-build:
    name: Canvas (Next.js)
    needs: changes
    if: needs.changes.outputs.canvas == 'true'
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: canvas
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: '22'
      - run: rm -f package-lock.json && npm install
      - run: npm run build
      - name: Run tests
        run: npx vitest run

  # MCP Server + SDK removed from CI — now in standalone repos:
  # - github.com/Molecule-AI/molecule-mcp-server (npm CI)
  # - github.com/Molecule-AI/molecule-sdk-python (PyPI CI)

  # e2e-api job moved to .github/workflows/e2e-api.yml (issue #458).
  # It now has workflow-level concurrency (cancel-in-progress: false) so
  # new pushes queue the E2E run rather than cancelling it at the run level.

  shellcheck:
    name: Shellcheck (E2E scripts)
    needs: changes
    if: needs.changes.outputs.scripts == 'true'
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Run shellcheck on tests/e2e/*.sh and infra/scripts/*.sh
        # shellcheck is pre-installed on ubuntu-latest runners (via apt).
        # infra/scripts/ is included because setup.sh + nuke.sh gate the
        # README quickstart — a shellcheck regression there silently breaks
        # new-user onboarding. scripts/ is intentionally excluded until its
        # pre-existing SC3040/SC3043 warnings are cleaned up.
        run: |
          find tests/e2e infra/scripts -type f -name '*.sh' -print0 \
            | xargs -0 shellcheck --severity=warning          

  canvas-deploy-reminder:
    name: Canvas Deploy Reminder
    runs-on: ubuntu-latest
    needs: [changes, canvas-build]
    # Only fires on direct pushes to main (i.e. after staging→main promotion).
    if: needs.changes.outputs.canvas == 'true' && github.event_name == 'push' && github.ref == 'refs/heads/main'
    permissions:
      # Required to post commit comments via the GitHub API.
      contents: write
    steps:
      - name: Post deploy reminder as commit comment
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          COMMIT_SHA: ${{ github.sha }}
          RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
        run: |
          # Write body to a temp file — avoids backtick escaping in shell.
          cat > /tmp/deploy-reminder.md << 'BODY'
          ## Canvas build passed ✅ — deploy required

          The `publish-canvas-image` workflow is now building a fresh Docker image
          (`ghcr.io/molecule-ai/canvas:latest`) in the background.

          Once it completes (~3–5 min), apply on the host machine with:
          ```bash
          cd <runner-workspace>
          git pull origin main
          docker compose pull canvas && docker compose up -d canvas
          ```

          If you need to rebuild from local source instead (e.g. testing unreleased
          changes or a new `NEXT_PUBLIC_*` URL), use:
          ```bash
          docker compose build canvas && docker compose up -d canvas
          ```
          BODY
          printf '\n> Posted automatically by CI · commit `%s` · [build log](%s)\n' \
            "$COMMIT_SHA" "$RUN_URL" >> /tmp/deploy-reminder.md

          gh api \
            --method POST \
            "repos/${{ github.repository }}/commits/${{ github.sha }}/comments" \
            --field "body=@/tmp/deploy-reminder.md"          

  python-lint:
    name: Python Lint & Test
    needs: changes
    if: needs.changes.outputs.python == 'true'
    runs-on: ubuntu-latest
    env:
      WORKSPACE_ID: test
    defaults:
      run:
        working-directory: workspace
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.11'
          cache: pip
          cache-dependency-path: workspace/requirements.txt
      - run: pip install -r requirements.txt pytest pytest-asyncio pytest-cov
      - run: python -m pytest --tb=short -q --cov=. --cov-report=term-missing

      # SDK + plugin validation moved to standalone repo:
      # github.com/Molecule-AI/molecule-sdk-python