AI4S-agent-tools

Tool annotations

No tools have read-only/destructive annotations

Add readOnlyHint or destructiveHint annotations to every tool so hosts can warn users before invoking.

All four hints declared on every tool

114/114 tools missing one or more hints — retrosynthesis_planning (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint); reaction_prediction (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint); single_step_retrosynthesis (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint), +111 more. OpenAI's directory rejects tools where any of the four hints are missing or non-boolean.

For every tool, set all four hints (readOnlyHint, destructiveHint, idempotentHint, openWorldHint) to explicit true/false values that match the handler’s actual behaviour.

Destructive tools are labelled

5 tools perform destructive updates without destructiveHint — optimize_structure deletes at line 177 (Path(traj_file).unlink()); HEA_predictor deletes at line 67 (os.remove(folds_file)); generate_crystalformer_structures deletes at line 1380 (shutil.rmtree(output_path))

Add destructiveHint:true to any tool whose handler calls .delete(), .upsert(), .update(), unlink, rm, DELETE, DROP, REPLACE INTO, or any operation that overwrites existing data.

Descriptions match behaviour

6 tools describe read intent but their handlers mutate — search_paper (line 93: with open(file_path, "wb") as f:); fetch_structures_with_filter (line 142: (out_folder / "summary.json").write_text(json.dumps(manifest, indent=2))); fetch_structures_with_spg (line 269: (out_folder / "summary.json").write_text(json.dumps(manifest, indent=2)))

Rename the tool, rewrite the description, or move the side-effect into a separate clearly-named tool.

Tool inputs are validated

109/111 tool handlers declare input schemas (98%)

Declare an inputSchema with zod/joi/yup on every tool definition.

Tool handlers catch errors

85/111 tool handlers wrap calls in try/catch (77%)

Wrap each tool handler body in try/catch and return a structured error response.

Tests exist

No test files found

Add tests that exercise each declared tool.

Shell command execution

8 child_process calls — runs shell commands

Prefer library functions over shell-outs. If you must shell out, ensure all inputs are properly escaped.

Tool description accuracy

6 tools have description/behavior mismatches: search_paper: description implies read-only but handler writes/deletes/executes; fetch_structures_with_filter: description implies read-only but handler writes/deletes/executes; fetch_structures_with_spg: description implies read-only but handler writes/deletes/executes

Update tool descriptions to accurately reflect all capabilities — especially write, delete, or execute operations.