python-supply-chain

python-supply-chain

Installs layered supply-chain controls into a Python package repository on GitHub: dependency-update automation with a freshness delay, vulnerability and secret scanning, code scanning, ownership rules for the paths that define automation, and SBOM/provenance artifacts. The design premise, taken from the 2025–2026 incident wave (the Shai-Hulud npm worm, the malicious axios release spread by dependency bots, mutable-tag action compromises), is that the attack surface is now your automation and the first hours after a release — so no single control below is sufficient, and bot output is treated with the same suspicion as human PRs.

When NOT to use

• CI quality-gate workflows, branch rulesets, action SHA pinning, zizmor — the

python-ci skill, if installed, owns those. This skill only adds scanning and update workflows, and notes where a control depends on a ruleset.

• PyPI trusted publishing (OIDC) and the tag-triggered publish workflow — the

python-release skill. This skill stops at repo-side SBOM/provenance; the publish step that uploads to PyPI belongs there.

• Pre-commit hook wiring (including a local gitleaks hook) — the

python-precommit skill. Local hooks are advisory; this skill installs the enforcing server/CI layer.

• Packaging and lockfile setup (uv init, pyproject.toml) — python-packaging.
• Agent hooks / AGENTS.md rules — agent-guardrails. This skill only protects

agent-config paths via CODEOWNERS.

• Active incident response beyond credential rotation basics — escalate to a

human; do not attempt autonomous cleanup of a live compromise.

Workflow

Work through the steps in order; each is independently valuable, so stop where the user's scope ends. Steps that change GitHub settings need gh authenticated with admin rights on the repo — otherwise print the commands for the user to run.

1. Audit the current posture

Run the bundled read-only checker from the repo root before adding anything:

python3 "${CLAUDE_SKILL_DIR}/scripts/check_supply_chain.py" --root .           # file-level checks
python3 "${CLAUDE_SKILL_DIR}/scripts/check_supply_chain.py" --root . --github  # + GitHub-side settings via gh

(Invoke it from this skill's folder with an absolute path if cwd differs.) It prints one PASS|WARN|FAIL|NOTE check: detail line per control and exits non-zero on FAIL. Fix FAILs in the steps below; treat WARNs as the backlog. Never duplicate a control that already exists — tune it instead.

2. Baseline: a committed lockfile

Every control below assumes the dependency set is pinned and committed: uv.lock (preferred), poetry.lock/pdm.lock, or hash-pinned requirements (--generate-hashes with pip-tools). If there is no lockfile, that is a python-packaging problem — flag it and stop; auditing an unpinned dependency set audits a guess.

3. Dependency-update automation (Dependabot)

Write .github/dependabot.yml:

version: 2
updates:
  - package-ecosystem: "uv"        # uv.lock projects; use "pip" for requirements/pip-tools/poetry
    directory: "/"
    schedule:
      interval: "weekly"
    open-pull-requests-limit: 10
    cooldown:
      default-days: 7              # skip versions published < 7 days ago
    groups:
      python-minor-patch:
        update-types: ["minor", "patch"]   # majors stay individual PRs
  - package-ecosystem: "github-actions"    # keeps actions updated; pinning policy = python-ci
    directory: "/"
    schedule:
      interval: "weekly"
    cooldown:
      default-days: 7

Key decisions, with detail in references/dependabot.md:

• Cooldown is the supply-chain control, not the schedule: it delays adoption of

freshly published versions past the window in which malicious releases are usually caught, and it is auto-bypassed for security-advisory updates — the reason to prefer it over a package-manager-level freshness pin alone. Since 2026-07-14 github.com applies a 3-day default with no config; default-days: 7 is how you lengthen it deliberately (and keep it aligned with exclude-newer, step 5).

• Grouping minor+patch is the accepted fix for PR-noise complaints. Keep majors

ungrouped so breaking changes get individual review.

• Never blanket auto-merge bot PRs. In the April 2026 malicious-axios incident

bots opened 154 of 214 update PRs and ~60% of bot PRs merged without human review. Require CI plus a human review on Dependabot PRs like any other PR.

• Renovate is the alternative when the user needs config-as-code flexibility;

its cooldown equivalent is minimumReleaseAge. Trade-offs and its pinDigest footgun are in the reference. Pick one bot — running both doubles the noise.

• Cooldown (default-days, and semver-*-days for pip/uv) is supported for the

pip, uv, pre-commit and github-actions ecosystems; after enabling, confirm update PRs actually arrive on the next scheduled run.

4. Vulnerability audit of the lockfile (pip-audit)

Audit the project's pinned set, exported from the lockfile:

uv export --format requirements-txt --no-emit-project -o /tmp/audit-req.txt
uvx --from pip-audit==2.10.1 pip-audit -r /tmp/audit-req.txt --no-deps

(==2.10.1 is an example pin — check PyPI for the current release and pin that. Unpinned uvx executes whatever was published minutes ago: the exact attack this skill exists to prevent.) Plain-pip fallback, run inside the project environment: python -m pip install pip-audit==2.10.1 && pip-audit.

• Do NOT run bare uvx pip-audit with no -r: it audits pip-audit's own ephemeral

environment, not your project, and reports a clean bill for the wrong thing.

• --no-deps skips re-resolution and is correct because the export is fully pinned.
• Report findings with the fix version per package; do not blind-upgrade everything,

and avoid pip-audit --fix in automation (it mutates the environment, not the lockfile).

• Alternatives: osv-scanner (Go binary) reads uv.lock directly; uv audit

(preview since June 2026, OSV-backed, lockfile-aware) is the zero-install option once it stabilizes — pin the uv version you verified it with.

• Recurrence: Dependabot security updates cover the alerting side; add a scheduled

scan workflow only if the user wants audit output in CI (workflow shape in references/scanning-and-provenance.md).

5. Resolution freshness window (uv projects)

For uv projects, add a resolver-level buffer against just-published packages:

[tool.uv]
exclude-newer = "2026-06-27T00:00:00Z"   # resolver ignores anything published after this

uv also accepts a relative window — exclude-newer = "7 days" (or ISO 8601 P7D) — and exclude-newer-package scopes the cutoff per package; run uv lock after setting it. The cutoff compares each artifact's upload time, not the release date, so a wheel uploaded late is filtered on its own. Two gotchas: a fixed timestamp freezes resolution in the past until someone bumps it (add it to the release checklist), and unlike Dependabot's cooldown it delays security fixes too — which is why you run both: exclude-newer guards uv lock runs on laptops and CI, cooldown guards the bot, security advisories bypass the bot's cooldown. Reference: <https://docs.astral.sh/uv/reference/settings/#exclude-newer>.

6. Secret scanning, push protection, and a CI backstop

GitHub-side scanning is free and on by default for public repos; private repos need GitHub Secret Protection licensing. Enable/verify both toggles:

gh api -X PATCH "repos/{owner}/{repo}" --input - <<'EOF'
{ "security_and_analysis": {
    "secret_scanning": { "status": "enabled" },
    "secret_scanning_push_protection": { "status": "enabled" } } }
EOF

Push protection blocks a detected secret before it enters history — strictly stronger than any after-the-fact scan — but GitHub documents that it only blocks a subset of high-confidence patterns. Add a CI gitleaks scan as the backstop that also catches --no-verify bypasses of local hooks (workflow YAML, plus the gitleaks-action org-license gotcha, in the reference). If a secret is ever found: rotate the credential first; history rewriting does not un-leak anything already cloned, forked, or cached.

7. Code scanning (CodeQL)

Default setup is enough for pure-Python repos (no build step needed):

gh api -X PATCH "repos/{owner}/{repo}/code-scanning/default-setup" -f state=configured

Free for public repos; private repos need GitHub Code Security licensing. Use the advanced workflow (in the reference) only when the user needs query-pack control or language: actions coverage of workflow files. Making code-scanning results block merges is a ruleset — hand that to python-ci.

8. CODEOWNERS for the paths that define automation

# .github/CODEOWNERS — LAST matching rule wins (not first)
*                      @OWNER/maintainers
/.github/              @OWNER/platform-security
/.github/CODEOWNERS    @OWNER/platform-security
/AGENTS.md             @OWNER/platform-security
/CLAUDE.md             @OWNER/platform-security
/.claude/              @OWNER/platform-security

Rationale: whoever can edit workflows, dependabot.yml, or agent instruction files can bypass every other control, so those paths need a stricter owner than the code. Two silent failures: CODEOWNERS enforces nothing until "require review from code owners" is enabled in branch protection/rulesets (python-ci's territory — say so in the handoff), and an owner without write access is ignored without error — check the file's rendered view on GitHub for syntax/owner errors.

9. Posture dashboard (OpenSSF Scorecard, optional)

Add the ossf/scorecard-action weekly workflow (YAML in the reference) to get a 0–10 score across ~a dozen heuristics with SARIF results in the Security tab. Treat it as a triage dashboard, not a gate: its own maintainers call the checks heuristic, and chasing the number (e.g. pinning SHAs no one audited) is documented security theater. Public repos can check their existing score at <https://scorecard.dev/viewer/?uri=github.com/OWNER/REPO> before adding anything.

10. SBOM and release provenance

Two SBOM paths — pick per audience:

# Repo-level SPDX from GitHub's dependency graph (compliance requests):
gh api "repos/{owner}/{repo}/dependency-graph/sbom" --jq .sbom > sbom.spdx.json

# Build-time CycloneDX from the lockfile (ship next to the wheel):
uv export --format requirements-txt --no-emit-project -o /tmp/sbom-req.txt
uvx --from cyclonedx-bom==7.3.1 cyclonedx-py requirements /tmp/sbom-req.txt -o sbom.cdx.json

For releases, attest the built artifacts with actions/attest-build-provenance (and actions/attest-sbom for the SBOM) inside the release workflow — snippet and required permissions in the reference. The publish workflow itself, and PyPI-side attestations via trusted publishing, belong to the python-release skill. Tell the user the honest limit: an attestation proves where and how an artifact was built, not that it is safe — real campaigns have shipped validly-signed malicious builds — and it only matters if consumers verify (gh attestation verify dist/pkg.whl --repo OWNER/REPO).

11. Re-audit and hand off

Re-run step 1; the script should report no FAILs. List remaining WARN/NOTE items with a one-line reason each (deliberate skip vs. needs licensing vs. sibling-skill territory).

Output spec — what done looks like

• .github/dependabot.yml with a pip or uv ecosystem entry, weekly schedule,

cooldown, grouped minor/patch updates, and a github-actions entry.

• Committed lockfile; a documented, pinned pip-audit invocation (or scheduled scan).
• Secret scanning + push protection enabled (or exact commands handed to the user

when permissions/licensing block it), plus a CI gitleaks backstop.

• CodeQL enabled (default setup or committed workflow).
• CODEOWNERS covering /.github/ and agent-config paths, with the

branch-protection dependency stated in the handoff.

• Optional per scope: Scorecard workflow, SBOM artifact, attestation step wired into

the release workflow (or delegated to python-release).

• scripts/check_supply_chain.py --root . exits 0.

Failure modes and gotchas

• `uvx pip-audit` without `-r` audits the wrong environment (the tool's own

ephemeral venv) and happily reports zero findings.

• Dependabot cooldown can wedge frequently-released dependencies: the filter has

evaluated only the latest release, so a dep that ships weekly may never propose an update (dependabot-core #14234/#14579; partially fixed — verify current behavior). Symptom: a dependency silently months stale despite Dependabot running green.

• Cooldown at the package-manager level blocks security fixes; Dependabot's

cooldown does not (advisory updates bypass it). Don't replace one with the other.

• Cooldown is not proven for transitive dependencies (confirmed gap for npm in

dependabot-core #14683; unverified for pip/uv) — the lockfile audit in step 4 is the control that actually covers transitives.

• Bot-authored PRs carry unearned trust: attackers mimic Dependabot branding,

and auto-merge-on-green shipped malware in the axios incident. Review like any PR.

• Dependabot does not alert on SHA-pinned actions (only semver tags) — a known

gap between this skill's alerting and python-ci's pinning policy; the dependabot github-actions entry still proposes pin bumps, so keep it.

• gitleaks-action requires a license key for organization repos

(GITLEAKS_LICENSE secret; free for personal accounts) — a silent-failure setup step people miss.

• CODEOWNERS is last-match-wins — a trailing * rule overrides every protection

above it. Put the catch-all first, specific security paths after.

• Push protection is a subset filter, not a guarantee — keep the CI backstop.
• Scorecard is gameable and heuristic — never wire it as a merge gate; its

public weekly scan omits several checks (CI-Tests, Contributors, Dependency-Update-Tool) for API-cost reasons, so scores differ from local runs.

• Installing a Python package executes code — at install time (build backends,

setup.py) and import time. Never install a package to inspect it; read it on <https://inspector.pypi.io> first. Watch for typosquats (request vs requests) and for hallucinated package names in LLM suggestions (slopsquatting) — verify the exact name, repo link, and release history on pypi.org before uv add.

• Free-tier boundary: dependency graph, Dependabot alerts and security updates

are free everywhere; secret scanning and CodeQL are free for public repos only — on private repos, hand the user the licensing decision instead of a broken toggle.

Files

• references/dependabot.md — full annotated

dependabot.yml, cooldown semantics and bug detail, Renovate comparison, noise-tuning, auto-merge policy evidence.

• references/scanning-and-provenance.md —

gitleaks/TruffleHog CI workflows, advanced CodeQL workflow, Scorecard workflow, SBOM/attestation snippets with permissions, verification commands.

• scripts/check_supply_chain.py — read-only posture

audit; --github adds GitHub-settings checks via gh; exits non-zero on FAIL.