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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Repository: mims-harvard/ToolUniverse
Last source activity: June 30, 2026 at 14:49
Detected SKILL.md language: English
Stars: 1,624
Forks: 246

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npx skills add https://github.com/mims-harvard/ToolUniverse --skill devtu-code-optimization

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tooluniverse-drug-research

Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory work.

2026-08-11

tooluniverse-gene-enrichment

Gene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, ORA, GSEA. Use for interpreting DEG lists, screen hit lists, or any gene-list-to-pathways query. Includes simplify-cutoff handling and union-vs-total denominator conventions for percent-DE questions.

2026-08-11

tooluniverse-multiomic-disease-characterization

Comprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level understanding. Identifies therapeutic opportunities and biomarker candidates by integrating multi-layer molecular data. Use for full-omics disease deep-dive reports, mechanism mapping, and biomarker-and-target identification from multi-omics data.

2026-08-11

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name

devtu-code-optimization

description

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

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

devtu-code-optimization

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Review the source files

ToolUniverse Code Optimization

Pre-Commit Checklist

ToolUniverse Code Optimization

Pre-Commit Checklist

Key Fix Categories

References

Git & PR Workflow

devtu-code-optimization

Source facts

Install options

Review the source files

More from this repository

More from this repository

ToolUniverse Code Optimization

Pre-Commit Checklist

ToolUniverse Code Optimization

Pre-Commit Checklist

Key Fix Categories

References

Git & PR Workflow