devtu-code-optimization

# 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](references/code-patterns.md) — Client-Side Filter | | Wrong API field/endpoint | 0 results or 404 | [api-fixes.md](references/api-fixes.md) — Quick Lookup Table | | Schema invalid | null type, missing oneOf | [code-patterns.md](references/code-patterns.md) — Schema Patterns | | Undisclosed normalization | Auto-transform hidden from user | [code-patterns.md](references/code-patterns.md) — Normalization Disclosure | | try/except indent | SyntaxError at runtime | [code-patterns.md](references/code-patterns.md) — try/except section | | Truncation buried | Data count hidden in notes | [code-patterns.md](references/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](references/code-patterns.md) — Hosted Model-API Tools | | R subprocess tool | `'\.' unrecognized escape` from `Rscript -e` | [code-patterns.md](references/code-patterns.md) — R-subprocess Tools | ## References - **[references/api-fixes.md](references/api-fixes.md)** — Per-API bug fixes (GtoPdb, CIViC, GTEx, ENCODE, CPIC, etc.) - **[references/code-patterns.md](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`