molecule-core/.github/workflows/ci.yml
rabbitblood f536768d02 ci: fix regex + add coverage allowlist (14 known 0% critical paths)
First run of the gate found 14 security-critical files at 0% coverage —
exactly the debt the user's audit flagged. Rather than block this PR on
fixing all 14 (scope creep), acknowledge them in .coverage-allowlist.txt
with 30-day expiry + #1823 reference.

Regex bug: `go tool cover -func` emits `file.go:LINE:TAB...` (single colon
after line, no column on some Go versions). My original `:[0-9]+\..*`
required a period after the line number, which never matched, so file
names kept their `:LINE:` suffix. Fixed to `:[0-9][0-9.]*:.*` which
accepts both `:LINE:` and `:LINE.COL:` formats.

Allowlist pattern: paths in `.coverage-allowlist.txt` warn (not fail),
new critical-path files at <10% coverage fail. This makes the gate land
cleanly AND keeps the teeth for regressions.

Allowlisted files (all tracked under #1823, expire 2026-05-23):

  Tight-match critical paths:
    - internal/handlers/a2a_proxy.go
    - internal/handlers/a2a_proxy_helpers.go
    - internal/handlers/registry.go
    - internal/handlers/secrets.go
    - internal/handlers/tokens.go
    - internal/handlers/workspace_provision.go
    - internal/middleware/wsauth_middleware.go

  Looser substring matches (flagged because my CRITICAL_PATHS entries use
  contains-match; follow-up PR to use exact prefix match):
    - internal/channels/registry.go
    - internal/crypto/aes.go
    - internal/registry/*.go (access, healthsweep, hibernation, provisiontimeout)
    - internal/wsauth/tokens.go

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-04-23 11:20:36 -07:00

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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 "$DIFF" | grep -qE '^tests/e2e/|^scripts/|^\.github/workflows/ci\.yml$' && 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
# shellcheck is pre-installed on ubuntu-latest runners (via apt).
run: |
find tests/e2e -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/${{ github.run_id }}
run: |
# Write body to a temp file — avoids backtick escaping in shell.
cat > /tmp/deploy-reminder.md << 'BODY'
## Canvas build passed ✅ — deploy required
The `publish-canvas-image` workflow is now building a fresh Docker image
(`ghcr.io/molecule-ai/canvas:latest`) in the background.
Once it completes (~35 min), apply on the host machine with:
```bash
cd <runner-workspace>
git pull origin main
docker compose pull canvas && docker compose up -d canvas
```
If you need to rebuild from local source instead (e.g. testing unreleased
changes or a new `NEXT_PUBLIC_*` URL), use:
```bash
docker compose build canvas && docker compose up -d canvas
```
BODY
printf '\n> Posted automatically by CI · commit `%s` · [build log](%s)\n' \
"$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