Supply-chain hardening for the CI pipeline. 23 workflow files
modified, 59 mutable-tag refs replaced with commit SHAs.
The risk
Every `uses:` reference in .github/workflows/*.yml was pinned to a
mutable tag (e.g., `actions/checkout@v4`). A maintainer of an
action — or a compromised maintainer account — can repoint that
tag to malicious code, and our pipelines silently pull it on the
next run. The tj-actions/changed-files compromise of March 2025 is
the canonical example: maintainer credential leak, attacker
repointed several `@v<N>` tags to a payload that exfiltrated
repository secrets. Repos that pinned to SHAs were unaffected.
The fix
Replace each `@v<N>` with `@<commit-sha> # v<N>`. The trailing
comment preserves human readability ("ah, this is v4"); the SHA
makes the reference immutable.
Actions covered (10 distinct):
actions/{checkout,setup-go,setup-python,setup-node,upload-artifact,github-script}
docker/{login-action,setup-buildx-action,build-push-action}
github/codeql-action/{init,autobuild,analyze}
dorny/paths-filter
imjasonh/setup-crane
pnpm/action-setup (already pinned in molecule-app, listed here for completeness)
Excluded:
Molecule-AI/molecule-ci/.github/workflows/disable-auto-merge-on-push.yml@main
— internal org reusable workflow; we control its repo, threat model
is different from third-party actions. Conventional to pin to @main
rather than SHA for internal reusables.
The maintenance cost
SHA pinning means upstream fixes require manual SHA bumps. Without
automation, pinned SHAs go stale. So this PR also enables Dependabot
across four ecosystems:
- github-actions (workflows)
- gomod (workspace-server)
- npm (canvas)
- pip (workspace runtime requirements)
Weekly cadence — the supply-chain attack window is "minutes between
repoint and pull"; weekly auto-bumps don't help with zero-days
regardless. The point is to pull in non-zero-day fixes without
operator effort.
Aligns with user-stated principle: "long-term, robust, fully-
automated, eliminate human error."
Companion PR: Molecule-AI/molecule-controlplane#308 (same pattern,
smaller surface).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Two related workflow hygiene changes:
## (1) canary-verify: graceful-skip when canary secrets absent
Before: canary-verify hit `scripts/canary-smoke.sh` which exited
non-zero when CANARY_TENANT_URLS was empty. Every main publish
ran → canary-verify failed → red check on main CI signal (7/7 in
past 24h). Noise, no value.
After: smoke step detects the missing-secrets case, writes a
warning to the step summary, sets an output `smoke_ran=false`,
and exits 0. The workflow completes green without pretending to
have tested anything.
Gated downstream: `promote-to-latest` now requires BOTH
`needs.canary-smoke.result == success` AND
`needs.canary-smoke.outputs.smoke_ran == true`. A skip does NOT
auto-promote — manual `promote-latest.yml` remains the release
gate while Phase 2 canary is absent (see
molecule-controlplane/docs/canary-tenants.md for the fleet
stand-up plan + decision framework).
When the canary fleet is stood up and secrets populated: delete
the early-exit branch + the smoke_ran gate. The workflow goes back
to its original "smoke gates promotion" semantics.
## (2) auto-promote-staging.yml — draft
New workflow that fires after CI / E2E Staging Canvas / E2E API /
CodeQL complete on the staging branch, checks that ALL four are
green on the same SHA, and fast-forwards `main` to that SHA.
Shipped disabled: the promote step is gated behind repo variable
`AUTO_PROMOTE_ENABLED=true`. Until that's set, the workflow
dry-runs and logs what it would have done. Toggle via Settings →
Variables when staging CI has been reliably green for a few days.
Safety:
- workflow_run events only fire on push to staging (PRs into
staging don't promote).
- Every required gate must be `completed/success` on the same
head_sha. Pending / failed / skipped / cancelled → abort.
- `--ff-only` push. Refuses to advance main if it has diverged
from staging history (someone landed a direct-to-main commit
that's not on staging). Human resolves the fork.
- `workflow_dispatch` with `force=true` lets us test the flow
end-to-end before flipping the variable on.
Motivation: molecule-core#1496 has been open with 1172 commits
divergence between staging and main. Today that trapped PR #1526
(dynamic canvas runtime dropdown) on staging while prod users
hit the hardcoded-dropdown bug. Auto-promote retires the bulk
staging→main PR pattern once the staging CI it depends on is
reliable.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
molecule-core is a public repo — GHA-hosted minutes are free. The
self-hosted Mac mini was only in play to dodge GHA rate limits
(memory feedback_selfhosted_runner), but for these specific
workflows it came with real costs:
- Docker-push workflows emulated linux/amd64 from arm64 via QEMU —
every canvas + platform image build ran ~2-3x slower than native.
- Six PRs worth of keychain-avoidance hacks in publish-* because
`docker login` on macOS writes to osxkeychain unconditionally,
and the Mac mini's launchd user-agent keychain is locked.
- Homebrew pin-down environment variables (HOMEBREW_NO_*) sprinkled
everywhere to work around the shared /opt/homebrew symlink mess
on the runner.
- Setup-python@v5 couldn't write to /Users/runner, so ci.yml
python-lint resorted to a hand-rolled Homebrew python3.11 dance.
- Single runner → fan-out contention; CodeQL's 45-min analysis
fought the canvas publish for the one slot.
Changes across the 7 workflows:
- runs-on: [self-hosted, macos, arm64] → ubuntu-latest (every job)
- publish-canvas-image + publish-workspace-server-image:
drop the hand-rolled auths-map step + QEMU setup + buildx v4
→ docker/login-action@v3 + setup-buildx@v3. Linux + amd64
target = native build.
- canary-verify + promote-latest: replace `brew install crane` +
HOMEBREW_NO_* incantations with imjasonh/setup-crane@v0.4.
- codeql.yml: drop `brew install jq` — jq is preinstalled on
ubuntu-latest.
- ci.yml shellcheck: drop the self-hosted existence check —
shellcheck is preinstalled via apt.
- ci.yml python-lint: replace the Homebrew python3.11 path dance
with actions/setup-python@v5 (which works fine on GHA-hosted),
add requirements.txt caching while we're there.
- Remove stale comments referencing "the self-hosted runner",
"Mac mini", keychain, osxkeychain etc.
The self-hosted Mac mini remains in service for private-repo
workflows only. Memory feedback_selfhosted_runner updated to
reflect the public-repo scope carve-out.
Net -96 lines across the 7 files.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The canary-verify workflow blocked the self-hosted runner for a fixed
6 minutes regardless of whether canaries had already updated. This
wastes the runner slot when canaries update in 2-3 minutes.
Fix: poll each canary's /health endpoint every 30s for up to 7 min.
Exit early when all canaries report the expected SHA. Falls back to
proceeding after timeout — the smoke suite validates regardless.
Typical time saving: ~3-4 minutes per canary verify run.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
GitHub-hosted ubuntu-latest runs on this repo hit "recent account
payments have failed or your spending limit needs to be increased"
— same root cause as the publish + CodeQL + molecule-app workflow
moves earlier this quarter. canary-verify was the last one still on
ubuntu-latest.
Switches both jobs to [self-hosted, macos, arm64]. crane install
switched from Linux tarball to brew (matches promote-latest.yml's
install pattern + avoids /usr/local/bin write perms on the shared
mac mini).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Completes the canary release train. Before this, publish-workspace-
server-image.yml pushed both :staging-<sha> and :latest on every
main merge — meaning the prod tenant fleet auto-pulled every image
immediately, before any post-deploy smoke test. A broken image
(think: this morning's E2E current_task drift, but shipped at 3am
instead of caught in CI) would have fanned out to every running
tenant within 5 min.
Now:
- publish workflow pushes :staging-<sha> ONLY
- canary tenants are configured to track :staging-<sha>; they pick
up the new image on their next auto-update cycle
- canary-verify.yml runs the smoke suite (Phase 2) after the sleep
- on green: a new promote-to-latest job uses crane to remotely
retag :staging-<sha> → :latest for both platform and tenant images
- prod tenants auto-update to the newly-retagged :latest within
their usual 5-min window
- on red: :latest stays frozen on prior good digest; prod is untouched
crane is pulled onto the runner (~4 MB, GitHub release) rather than
docker-daemon retag so the workflow doesn't need a privileged runner.
Rollback: if canary passed but something surfaces post-promotion,
operator runs "crane tag ghcr.io/molecule-ai/platform:<prior-good-sha>
latest" manually. A follow-up can wrap that in a Phase 4 admin
endpoint / script.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Post-deploy verification for staging tenant images. Runs against the
canary fleet after each publish-workspace-server-image build — catches
auto-update breakage (a la today's E2E current_task drift) before it
propagates to the prod tenant fleet that auto-pulls :latest every 5 min.
scripts/canary-smoke.sh iterates a space-sep list of canary base URLs
(paired with their ADMIN_TOKENs) and checks:
- /admin/liveness reachable with admin bearer (tenant boot OK)
- /workspaces list responds (wsAuth + DB path OK)
- /memories/commit + /memories/search round-trip (encryption + scrubber)
- /events admin read (AdminAuth C4 path)
- /admin/liveness without bearer returns 401 (C4 fail-closed regression)
.github/workflows/canary-verify.yml runs after publish succeeds:
- 6-min sleep (tenant auto-updater pulls every 5 min)
- bash scripts/canary-smoke.sh with secrets pulled from repo settings
- on failure: writes a Step Summary flagging that :latest should be
rolled back to prior known-good digest
Phase 3 follow-up will split the publish workflow so only
:staging-<sha> ships initially, and canary-verify's green gate is
what promotes :staging-<sha> → :latest. This commit lays the test
gate alone so we have something running against tenants immediately.
Secrets to set in GitHub repo settings before this workflow can run:
- CANARY_TENANT_URLS (space-sep list)
- CANARY_ADMIN_TOKENS (same order as URLs)
- CANARY_CP_SHARED_SECRET (matches staging CP PROVISION_SHARED_SECRET)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
