ToolUniverse Code Optimization

Always run Skill(skill="simplify") after writing or modifying code.

Pre-Commit Checklist

• ] return_schema has oneOf: [{data+metadata}, {error}]
• ] Test examples use real IDs (no DUMMY/PLACEHOLDER)
• ] try: has except: at exact same indentation level
• ] No trailing commas in JSON (python3 -c "import json; json.load(open('f.json'))")
• ] New tool class registered in _lazy_registry_static.py and default_config.py
• ] ruff check src/tooluniverse/<file>.py passes
• ] python -c "from tooluniverse.<module> import <Class>" passes
• ] python -m tooluniverse.cli run <Tool> '<real_args_json>' returns expected data
• ] Ran Skill(skill="simplify") on all modified files

Key Fix Categories

| Category | Signal | Reference | |---|---|---| | Silent param ignored | API accepts but drops filter | code-patterns.md — Client-Side Filter | | Wrong API field/endpoint | 0 results or 404 | api-fixes.md — Quick Lookup Table | | Schema invalid | null type, missing oneOf | code-patterns.md — Schema Patterns | | Undisclosed normalization | Auto-transform hidden from user | code-patterns.md — Normalization Disclosure | | try/except indent | SyntaxError at runtime | code-patterns.md — try/except section | | Truncation buried | Data count hidden in notes | code-patterns.md — Truncation | | Hosted model API (NIM) | async 404 on poll, JSON-wrapped output, 200+inner-failure, "not found for account" | code-patterns.md — Hosted Model-API Tools | | R subprocess tool | '\.' unrecognized escape from Rscript -e | code-patterns.md — R-subprocess Tools |

References

• references/api-fixes.md — Per-API bug fixes (GtoPdb, CIViC, GTEx, ENCODE, CPIC, etc.)
• references/code-patterns.md — Reusable Python patterns (schema, filtering, pagination, normalization)

Git & PR Workflow

bash
git fetch origin && git stash && git rebase origin/main && git stash pop
git push --force-with-lease origin fix/round-XX-bugs
gh pr view <N> --json mergeable  # must be MERGEABLE before done

• Never push to main directly
• Never have multiple open fix PRs
• Commit messages: "Feature" or "Fix" — never "Bug"
• No AI attribution in commits
• Repo: mims-harvard/ToolUniverse — verify with git remote -v