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

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

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

devtu-code-optimization

ToolUniverse Code Optimization

Pre-Commit Checklist

Key Fix Categories

References

Git & PR Workflow