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Rework dependency updates: Dependabot for CVEs, Renovate for everything else #400

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Description

@coretl

Rework dependency updates: Renovate only, no automerge, 3-day cooldown, weekly unlocked tests

Problem

  • We use an uncomfortable mix of Renovate and Dependabot, with no clear split of responsibilities.
  • Renovate's lockFileMaintenance automerges, which people dislike, and it fills git history with lockfile commits.
  • Nothing tells us when an upstream release will break downstream users who install unlocked.
  • There's no cooldown on new releases, which leaves us exposed to supply-chain attacks via freshly published packages.
  • Until recently, Renovate only fixed CVEs in direct dependencies, so CVEs in transitive dependencies in uv.lock sat unfixed (see python-zocalo#319 for an example of the manual catch-up).

Goals

  1. CI runs against the lockfile, so upstream releases don't break unrelated PRs.
  2. A periodic unlocked run tells us what upstream changes would break downstream users.
  3. Nothing resolves releases newer than 3 days: not lock refreshes, not local upgrades, not unlocked runs.
  4. CVEs are patched as soon as the fix release is 3 days old, including in transitive dependencies. Urgent fixes can bypass the cooldown per package.

Proposal

Area Current Proposed
CI Runs locked (uv run --locked) Unchanged
Release cooldown None exclude-newer = "3 days" in pyproject.toml, matched by Renovate minimumReleaseAge: "3 days". Applies to every resolution: lock refreshes, local uv lock --upgrade, and the unlocked job
CVE alerts Dependabot alerts (enabled in settings) Unchanged. Used only as the alert source; no Dependabot PRs, no settings changes
CVE fixes Renovate vulnerabilityAlerts (via config:recommended), direct dependencies only Unchanged config, and now covers transitive deps in uv.lock (Renovate ≥ 44.221.0, renovatebot/renovate#47482). Security PRs open immediately, ignoring schedule and grouping. If the fix is under 3 days old, the PR fails to lock until the window passes; for urgent cases, add exclude-newer-package to bypass
Lockfile refresh Renovate lockFileMaintenance, automerged On demand only: a Dependency Dashboard checkbox, never automerged. Obeys the cooldown via pyproject.toml
Upstream breakage Nothing Weekly unlocked test job in periodic.yml; opens/updates an issue on failure
Actions / pre-commit bumps Renovate, minor/patch grouped Renovate, all grouped into a weekly PR, no automerge
Template-managed deps downstream Ignored in template/renovate.json.jinja Unchanged
Copier updates Renovate copier manager Unchanged
Automerge On for lock maintenance, via the renovate-approve app Off everywhere; renovate-approve no longer needed

Renovate is the only bot. Dependabot is used only as the source of alerts on GitHub. On internal GitLab, Renovate's osvVulnerabilityAlerts plays the same role, and also covers uv transitive deps. So the setup is consistent across both.

Renovate doesn't apply minimumReleaseAge to lockFileMaintenance; it just runs uv lock --upgrade. That's why the cooldown has to live in pyproject.toml rather than only in Renovate config.

Implementation (outline)

  • template/pyproject.toml.jinja (and the template's own pyproject.toml): add exclude-newer = "3 days" under [tool.uv].
  • renovate.json / template/renovate.json.jinja:
    • set automerge: false
    • add a weekly schedule
    • set minimumReleaseAge: "3 days"
    • set lockFileMaintenance.dependencyDashboardApproval: true
    • group actions/pre-commit updates
    • keep the existing template-managed ignores and the default vulnerabilityAlerts
  • periodic.yml:
    • add a weekly job that runs tests with --upgrade instead of --locked, across the supported Python matrix (the cooldown comes from pyproject.toml)
    • open or update a single issue on failure
    • render periodic.yml unconditionally, since it's currently gated on sphinx, and make the linkcheck job conditional instead
  • Docs:
    • rewrite renovate.md to remove automerge and the renovate-approve app, and to describe the dashboard lock refresh and security PRs
    • document the cooldown in lock-requirements.md, including how to bypass it for an urgent fix with exclude-newer-package = { <pkg> = false }, to be removed after merge

Open questions

  • Is the Mend-hosted Renovate app on ≥ 44.221.0, and does it have read access to Dependabot alerts? Both are needed for transitive CVE fixes.
  • Verify on a test repo that Renovate opens a fix PR for a transitive-only vulnerable package in uv.lock, and that a fix under 3 days old succeeds on a later run once the window passes. The transitive feature only landed on 2026-11-05.
  • Should the weekly periodic job also run pip-audit against the locked environment, as a safety net while the transitive support beds in?
  • Does dependencyDashboardApproval behave as expected for lockFileMaintenance on our Renovate version?
  • Should repos that build and deploy images from the lock keep a scheduled (e.g. monthly) lock refresh in their own Renovate config?
  • Align the cooldown window with python-zocalo, which uses the same pattern with 7 days.

Activity

  1. gilesknap commented on Nov 6, 2026

    @gilesknap
    Contributor

    This looks good to me, and matches what I found going through Dependabot alerts across DLS repos this week. A few gaps worth covering:

    1. "No Dependabot PRs" needs a settings change. Dependabot security-update PRs come from a repo/org setting, with no dependabot.yml needed: e.g. aioca Select more ruff checks and fix the errors it finds #85, Fix packaging issues #86, merge main into branch to overcome downgrades aren't supported error #89, Import version from setuptools_scm generated file #90 and fastcs-odin Make template .gitignore a file #103 are all open against uv.lock today. Unless that setting is turned off (per repo or org-wide), both bots keep editing the lock.
    2. Stale dependabot.yml downstream. Repos that adopted the template before 5.0 can still carry one: dls-bba's 2022 file is still active alongside Renovate and produces duplicate PRs (Select more ruff checks and fix the errors it finds #85 vs added adopting template docs #99/Add link to template how-to guides in contributing.md #100/Change wording for ADRs and add template #102 for PyQt6, Fix packaging issues #86 vs Make template .gitignore a file #103 for actions). A release note or upgrade checklist item to delete it would close that off.
    3. Alerts disabled on many repos. Dependabot alerts are switched off on a large number of DiamondLightSource repos (287 of the ~590 non-archived ones when I scanned), so Renovate gets no alert data there. Enabling osvVulnerabilityAlerts on GitHub as well, as proposed for GitLab, would give those repos CVE PRs too.

    Smaller points:

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