update-deps

# Update Dependencies Automate the full dependency update lifecycle: discover what's outdated, apply updates grouped by ecosystem, fix breakage, get CI green, and hand off for human review. ## Repository context This is a Rust workspace containing utility crates published to crates.io. All dependency update PRs target the **`main`** branch. Dependabot is configured (`.github/dependabot.yaml`) to open PRs against `main` on the 2nd of each month. This skill gathers individual dependabot PRs, combines updates by ecosystem, fixes any breakage, gets CI green, and creates consolidated PRs for human review. ### Crates in this workspace | Crate | Description | |---|---| | **bpe** | Fast byte-pair encoding | | **bpe-openai** | OpenAI tokenizers built on bpe | | **geo_filters** | Probabilistic cardinality estimation | | **string-offsets** | UTF-8/UTF-16/Unicode position conversion (with WASM/JS bindings) | Supporting packages (not published): `bpe-tests`, `bpe-benchmarks`. ### Ecosystems in this repo | Ecosystem | Directories | Notes | |---|---|---| | **cargo** | `/` (workspace root) | Deps declared per-crate; `Cargo.lock` at workspace root pins versions | | **github-actions** | `.github/workflows/` | CI and publish workflows | | **npm** | `crates/string-offsets/js/` | JS bindings for string-offsets (WASM) | ### Build and validation commands ```bash make build # cargo build --all-targets --all-features make build-js # npm run compile in crates/string-offsets/js make lint # cargo fmt --check + cargo clippy (deny warnings, forbid unwrap_used) make test # cargo test + doc tests ``` CI runs on `ubuntu-latest` with the `mold` linker. The lint job depends on build. ## Workflow ### 1. Assess repo state Determine the repo identity and confirm the target branch. ```bash git remote get-url origin # extract owner/repo git fetch origin main git rev-parse --verify origin/main ``` Detect which ecosystems have pending updates: ```bash [ -f Cargo.toml ] && echo "cargo" ls .github/workflows/*.yml .github/workflows/*.yaml 2>/dev/null && echo "github-actions" [ -f crates/string-offsets/js/package.json ] && echo "npm" ``` Report discovered ecosystems to the user. ### 2. Gather dependency intelligence Fetch open dependabot PRs: ```bash gh pr list --author 'app/dependabot' --base main --state open --json number,title,headRefName,labels --limit 100 ``` Fetch open dependabot alerts: ```bash gh api --paginate /repos/{owner}/{repo}/dependabot/alerts --jq '[.[] | select(.state=="open") | {number: .number, package: .security_vulnerability.package.name, ecosystem: .security_vulnerability.package.ecosystem, severity: .security_advisory.severity, summary: .security_advisory.summary}]' ``` For ecosystems without dependabot coverage or when running ad-hoc, use native tooling: - **cargo:** `cargo update --dry-run` - **npm:** find directories containing `package.json`, then run `npm outdated --json || true` in each (npm exits non-zero when updates exist) Also fetch the advisory URLs for any security-related updates. Individual alert details are at `https://github.com/{owner}/{repo}/security/dependabot/{alert_number}`. Fetch alert numbers and GHSA IDs via: ```bash gh api --paginate /repos/{owner}/{repo}/dependabot/alerts --jq '[.[] | {number: .number, state, package: .security_vulnerability.package.name, ecosystem: .security_vulnerability.package.ecosystem, severity: .security_advisory.severity, ghsa_id: .security_advisory.ghsa_id, summary: .security_advisory.summary}]' ``` Include both open and auto_dismissed/dismissed alerts — the update may resolve alerts in any state. Cross-reference and group all updates by ecosystem. Present a summary to the user: - How many updates per ecosystem - Which have security alerts (with severity, GHSA IDs, and advisory links) - Which dependabot PRs already exist **Flag high-risk upgrades.** Before proceeding, explicitly call out upgrades that carry elevated risk: - **Major version bumps** — likely contain breaking API changes - **Packages with wide blast radius** — for this repo, pay special attention to: `serde`, `itertools`, `regex-automata`, `wasm-bindgen`, `criterion`, and the Rust toolchain itself - **Multiple major bumps in the same PR** — each major bump multiplies the risk; consider splitting them Present the risk assessment to the user and recommend which upgrades to include vs. defer. When in doubt, prefer a smaller, safe update over an ambitious one that might break. ### 3. Create branch and apply updates For each selected ecosystem, starting from `main`: ```bash git checkout main git pull origin main git checkout -b deps/{ecosystem}-updates-$(date +%Y-%m-%d) ``` Apply updates using ecosystem-appropriate tooling: **cargo:** ```bash cargo update # For major bumps, edit Cargo.toml version constraints then: cargo check ``` This is a Cargo workspace — always run from the repo root. All crate `Cargo.toml` files are in `crates/`. The `Cargo.lock` at the root is the single source of truth. **npm:** ```bash cd crates/string-offsets/js npm update npm install ``` **github-actions:** - Parse workflow YAML files in `.github/workflows/` for `uses:` directives - For each action with an outdated version (from dependabot PRs/alerts), update the SHA or version tag - Be careful to preserve comments and formatting ### 4. Build, lint, and test locally Always run: ```bash make lint # cargo fmt --check + clippy with deny warnings make test # cargo test with backtrace make build # full workspace build (all targets, all features) ``` If npm dependencies changed: ```bash make build-js # npm compile for string-offsets JS binding ``` **If the build/lint/test fails:** 1. Read the error output carefully 2. Analyze what broke — likely API changes, type errors, or deprecation removals 3. Make the necessary code changes to fix the breakage 4. Run the pipeline again 5. Repeat up to 3 times If still failing after 3 iterations, report the situation to the user and ask for guidance. Do not push broken code. ### 5. Commit and push Stage all changes and commit with a descriptive message: ```bash git add -A git commit -m "chore(deps): update {ecosystem} dependencies Updated packages: - package-a: 1.0.0 → 2.0.0 - package-b: 3.1.0 → 3.2.0 {If code changes were needed:} Fixed breaking changes: - Updated X API usage for package-a v2 Supersedes: #{dependabot_pr_1}, #{dependabot_pr_2} " ``` Push the branch: ```bash git push -u origin HEAD ``` ### 6. Create the PR **Title:** `chore(deps): update {ecosystem} dependencies` **Body should include:** - List of updated dependencies with version changes (old → new) - Any security alerts resolved — for each, link to the specific dependabot alert (`https://github.com/{owner}/{repo}/security/dependabot/{alert_number}`) and the GHSA advisory (`https://github.com/advisories/GHSA-xxxx-xxxx-xxxx`), along with severity and summary - **High-risk changes flagged for reviewer attention** (major version bumps, wide-blast-radius packages) - Code changes made to fix breakage (if any) - References to superseded dependabot PRs - Note that this was generated by the update-deps skill Write the body to a temp file and create the PR **targeting `main`**: ```bash gh pr create --title "chore(deps): update {ecosystem} dependencies" --body-file /tmp/deps-pr-body.md --base main rm /tmp/deps-pr-body.md ``` ### 7. Monitor CI and iterate on failures Watch the PR's checks: ```bash gh pr checks {pr_number} --watch --fail-fast ``` **If checks fail:** 1. Get the failed run details: ```bash gh run list --branch {branch} --status failure --json databaseId,name --limit 1 gh run view {run_id} --log-failed ``` 2. Analyze the failure — CI runs on `ubuntu-latest` with `mold` linker, which may differ from local builds. 3. Fix the issue locally, commit, and push: ```bash git add -A git commit -m "fix: resolve CI failure in {ecosystem} dep update {Brief description of what failed and why}" git push ``` 4. Monitor again. Repeat up to 3 iterations total. 5. If still failing after 3 pushes, report to the user with the failure details and ask for help. ### 8. Close superseded dependabot PRs For each dependabot PR that this update supersedes: ```bash gh pr close {dependabot_pr_number} --comment "Superseded by #{new_pr_number} which includes this update along with other {ecosystem} dependency updates." ``` ### 9. Assign for review Request review from CODEOWNERS or a user-provided reviewer (not the PR author): ```bash gh pr edit {pr_number} --add-reviewer {reviewer_login} ``` Report the final PR URL and a summary of what was done. ## Guidelines - **All PRs target `main`.** There is no separate dev branch. - **Never push to `main` directly.** Always work on a feature branch. - **Never push code that doesn't pass `make lint` and `make test`.** If you can't fix it in 3 tries, stop and ask. - **Be conservative with major version bumps.** If a major version update breaks things and the fix isn't obvious, skip that package and note it in the PR description. - **Regenerate lockfiles.** Always regenerate `Cargo.lock` and `package-lock.json` after updating — don't just edit manifests. - **One ecosystem at a time.** Complete the full cycle (update → build → push → PR → CI green) for one ecosystem before moving to the next. - **If no updates are needed** for an ecosystem, skip it and tell the user. - **Security alerts take priority.** Address security alerts first within each ecosystem. - **Clippy is strict.** This repo forbids `unwrap_used` outside tests and denies all warnings. New dependency versions may trigger new clippy lints — fix them. ## Edge cases - **Cargo workspace:** Dependencies are declared per-crate but share a single `Cargo.lock` at the workspace root. Always run `cargo update` and `cargo check` from the repo root. - **npm:** Look for `package.json` files to discover npm packages rather than hardcoding paths — the repo layout may change. - **WASM builds:** After updating `wasm-bindgen` or related deps, verify `make build-js` still works — WASM toolchain version mismatches are common. - **Rate limits:** If `gh api` hits rate limits, wait and retry. Report to user if persistent. - **Nothing to update:** Report cleanly and move to the next ecosystem (or exit). - **Merge conflicts on push:** Rebase on `main` and retry: `git fetch origin main && git rebase origin/main`. - **Branch already exists:** If `deps/{ecosystem}-updates-{date}` already exists, append a counter or ask user.