devtu-code-optimization

Code quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring tool Python code in the ToolUniverse project. Encodes lessons from 80+ debug rounds. Use alongside devtu-fix-tool and devtu-self-evolve. Triggers: implementing tool fixes, writing new tool classes, reviewing tool code quality, checking schema correctness, looking up API-specific bug fixes.

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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

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

Repository: mims-harvard/ToolUniverse
Path: skills/devtu-code-optimization/SKILL.md
Commit: 089eb8e

Last updated: about 6 hours ago
First committed: about 1 month ago

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