Conversation
Update dev from main
Add RAG Agent to ChemGraph
Add session memory persistence with CLI session management.
Add evaluation & benchmarking module with LLM-as-judge and documentation
Add OpenCode MCP configuration for using ChemGraph tools directly
Add missing evaluation documentations and update config.toml
…anes workflow XANES tools refactoring (xanes_tools.py): - Separate original monolithic workflow into core and ensemble functions - Add run_xanes_core() for single-structure FDMNES calculations via subprocess - Refactor fetch_materials_project_data() to accept Pydantic schema input with runtime MP_API_KEY validation (removed hardcoded API key) - Replace inline Parsl config with clean subprocess-based FDMNES execution - Extract create_fdmnes_inputs(), expand_database_results(), plot_xanes_results() as standalone reusable functions - Add proper docstrings, structured logging, and error handling throughout New schemas (xanes_schema.py): - xanes_input_schema: single FDMNES calculation parameters - xanes_input_schema_ensemble: batch Parsl-based calculation parameters - mp_query_schema: Materials Project queries with optional API key and energy_above_hull filter New MCP server (xanes_mcp_parsl.py): - Expose run_xanes_single, run_xanes_ensemble, fetch_mp_structures, and plot_xanes tools via FastMCP - Parsl integration for HPC ensemble FDMNES execution (Polaris/Aurora) - Async gather for parallel result collection with JSONL summary logging New single_agent_xanes workflow: - Dedicated LangGraph graph with XANES-specific tools (run_xanes, fetch_xanes_data, molecule_name_to_smiles, smiles_to_coordinate_file) - XANES-focused system and formatter prompts (xanes_prompt.py) - MP_API_KEY and FDMNES_EXE env var warnings at graph construction time - Repeated tool-call cycle detection to prevent infinite loops - Register single_agent_xanes in ChemGraph agent dispatcher and write_state Cleanup: - Remove all XANES tools from single_agent and multi_agent default tool lists - Update test_graph_constructors.py with single_agent_xanes parametrization
Add XANES support
Add structured output evaluation with checkpointing and FormatterAgent retry
Collaborator
Author
|
@keceli I will keep this PR open for now so I can track the major changes before asking you to review it. |
tdpham2
changed the title
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Major improvements for ChemGraph: