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berntpoppberntpopp/stringdb-link/.claude/skills/dependency-cve-sweep/SKILL.md

dependency-cve-sweep

Skill1 starsChanged 4 months agoMITView on GitHub

Use when handling Dependabot PRs, CodeQL/Trivy alerts, or doing a routine dependency/CVE sweep for this repo.

We split this skill into the rules it gives an agent

3 rules. About 0 are common, 1 is distinctive, and 2 are very specific to this project.

  • ≈0

    Common · estimate

    Many files like this have a rule of this kind.

  • ≈1

    Distinctive · estimate

    This author's own choices. Worth a look.

  • 2

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Distinctive:

    Follow AGENTS.md first. Consolidate a repo's open Dependabot PRs into one clean PR rather than merging many.

    line 8
  2. Very specific:

    Keep the Trivy gate in the ratified 2-step form (severity: CRITICAL,HIGH + ignore-unfixed: true + exit-code: "1") and retain the SBOM …

    line 15
  3. Very specific:

    When bumping FastMCP, verify validation-error wrapping: some 3.4.x releases re-raise argument-validation errors as …

    line 20

≈ “Common” is an estimate: at least 1 in 5 of the 308,232 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
SKILL.md

Dependency & CVE Sweep

Follow AGENTS.md first. Consolidate a repo's open Dependabot PRs into one clean PR rather than merging many.

Workflow

  1. Bump Python deps with uv lock --upgrade-package <name> (targeted) or uv lock --upgrade (full); keep uv.lock committed and --frozen in the build.
  2. SHA-pin GitHub Actions (uses: owner/action@<40-char-sha> # vX.Y.Z), never floating tags.
  3. Fix CodeQL findings at the cause; for the common py/incomplete-url-substring-sanitization test-assertion false positive, switch to exact-match assertions.
  4. Keep the Trivy gate in the ratified 2-step form (severity: CRITICAL,HIGH + ignore-unfixed: true + exit-code: "1") and retain the SBOM (../genefoundry-router/docs/CONTAINER-HARDENING-STANDARD-v1.md).
  5. Gate on make ci-local; patch-bump the app version; squash-merge only on green.

Gotcha (FastMCP bumps)

When bumping FastMCP, verify validation-error wrapping: some 3.4.x releases re-raise argument-validation errors as fastmcp.exceptions.ValidationError, so a test asserting on a Pydantic ValidationError must walk __cause__. A version/catalog guard test may also need regenerating.

Common mistakes

  • Merging Dependabot PRs one-by-one instead of one consolidated PR.
  • Floating action tags instead of SHA pins.
  • Flipping Trivy exit-code: "1" without ignore-unfixed: true — gates on unfixable base-image CVEs → self-inflicted outage.

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