[feat] Pubchempy

[tdadela]

• Added PubChemPy library for accessing PubChem chemical data.
• Registered new tools in main_agent.py for chemical name/SMILES conversion and info retrieval using PubChemPy.
• Updated instructions.txt to document these new functionalities and their usage.
• The agent can now convert between chemical names and SMILES, and fetch detailed compound info, all using authoritative PubChem data.

[Copilot]

Pull Request Overview

This PR integrates PubChemPy into ReAgentAI to enable chemical name/SMILES conversions and detailed compound information retrieval via the PubChem database.

• Adds pubchempy dependency and implements three new tools (get_smiles_from_name, get_compound_info, get_name_from_smiles) in tools/pubchem.py.
• Registers these tools in the main agent and updates UI, examples, and constants to surface the new functionality.
• Updates documentation (instructions.txt, README.md) to describe usage of the PubChem-based features.

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/reagentai/ui/app.py	Removed duplicate gr.Examples block and reordered imports
src/reagentai/tools/pubchem.py	New PubChem integration functions for SMILES/name conversions and info retrieval
src/reagentai/constants.py	Extended example prompts to showcase name/SMILES conversion and compound info
src/reagentai/agents/main/main_agent.py	Registered the three new PubChem tools in the agent’s tool list
src/reagentai/agents/main/instructions.txt	Documented how to use each new PubChem tool
pyproject.toml	Added pubchempy>=1.0.4 dependency
README.md	Updated feature list and setup notes for PubChem integration

Comments suppressed due to low confidence (3)

src/reagentai/tools/pubchem.py:142

• Consider returning molecular_weight as a numeric value instead of a string to maintain consistent data types and simplify downstream processing. If string format is required, document this clearly in the signature and return-type annotation.

"molecular_weight": str(getattr(compound, \"molecular_weight\", None))

src/reagentai/tools/pubchem.py:91

• The return type annotation uses a bare list for synonyms; consider specifying list[str] for clarity. Also, use Optional[...] from typing for readability, e.g., dict[str, Optional[Union[str, List[str]]]].

def get_compound_info(compound_name: str) -> dict[str, str | list | None]:

src/reagentai/tools/pubchem.py:1

• The new PubChem integration functions currently lack unit tests. Add tests for get_smiles_from_name, get_compound_info, and get_name_from_smiles to verify correct outputs, error handling for invalid inputs, and network-failure scenarios.

import logging