drug-discovery-prompts/upstream/mims-harvard-ToolUniverse/skills/devtu-code-optimization/SKILL.md

lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, name, description

lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	name	description
import	https://github.com/mims-harvard/ToolUniverse/blob/3038dcbe/skills/devtu-code-optimization/SKILL.md	3038dcbe	2026-06-30	prompt	accepted	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.

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