Basic PySCF MCP tools

[JinchuLi2002]

This pull request adds support for PySCF workflows to the ChemGraph MCP tool suite, introduces schemas for PySCF molecule and crystal objects, and improves the CLI response formatting to handle complex content blocks. It also adds tests to ensure robust handling of new content shapes. The most important changes are grouped below:

PySCF Integration

• Added new MCP tools for creating and running PySCF molecule and crystal workflows, including create_pyscf_molecule, create_pyscf_crystal, run_pyscf_molecule, and run_pyscf_crystal, with robust stdout silencing to prevent library output from interfering with MCP communication. (src/chemgraph/mcp/mcp_tools.py) [1] [2]
• Added a new dependency group for PySCF in pyproject.toml.

Schema Additions

• Introduced src/chemgraph/schemas/pyscf_schema.py, defining Pydantic models and type aliases for PySCF molecule and crystal specifications, as well as shared enums for device, driver, unit, and reference types.

Testing

• Added tests for the new content extraction and atomic JSON detection logic in the CLI formatter. (tests/test_cli_formatting.py)