Basic PySCF MCP tools

.gitignore

@@ -29,13 +29,16 @@ eggs/
 
 # Jupyter Notebook checkpoints and modified notebooks
 .ipynb_checkpoints/
+05*_*.ipynb
 
 # env
 chemgraph-env/
 # env
 .env
 # Log files
 *run_logs/
+cg_logs/
+runs/
 *vib/
 plots/
 initial_evaluations/
@@ -60,5 +63,12 @@ nwchem.nwo
 
 vib*.traj
 
+# Local calculation artifacts
+pyscf_output*/
+pyscf_h2*/
+
+# Local persistent working memory
+current_status.md
+
 # Kubernetes secrets (keep secrets.yaml.template, ignore actual secrets)
 k8s/secrets.yaml

pyproject.toml

@@ -64,6 +64,9 @@ ui = [
 parsl = [
     "parsl",
 ]
+pyscf = [
+    "pyscf",
+]
 xanes = [
     "mp-api; python_version >= '3.11'",
     "parsl"

src/chemgraph/cli/formatting.py

@@ -27,6 +27,7 @@
 # Banner
 # ---------------------------------------------------------------------------
 
+
 def create_banner() -> Panel:
     """Create a welcome banner for ChemGraph CLI."""
     banner_text = """
@@ -45,6 +46,7 @@ def create_banner() -> Panel:
 # Model listing
 # ---------------------------------------------------------------------------
 
+
 def list_models() -> None:
     """Display available models in a formatted table."""
     console.print(Panel("Available Models", style="bold cyan"))
@@ -89,6 +91,7 @@ def list_models() -> None:
 # API-key status
 # ---------------------------------------------------------------------------
 
+
 def check_api_keys_status() -> None:
     """Display API key availability status."""
     console.print(Panel("API Key Status", style="bold cyan"))
@@ -162,12 +165,38 @@ def check_api_keys_status() -> None:
 # Response formatting
 # ---------------------------------------------------------------------------
 
-def _is_atomic_json(content: str) -> bool:
+
+def _content_to_text(content: Any) -> str:
+    """Extract displayable text from common LangChain/MCP content shapes."""
+    if isinstance(content, str):
+        return content
+
+    if isinstance(content, list):
+        parts: list[str] = []
+        for block in content:
+            if isinstance(block, dict):
+                text = block.get("text")
+                if isinstance(text, str):
+                    parts.append(text)
+            else:
+                text = getattr(block, "text", None)
+                if isinstance(text, str):
+                    parts.append(text)
+        return "\n".join(parts)
+
+    return ""
+
+
+def _is_atomic_json(content: Any) -> bool:
     """Return True if *content* is a JSON string with atomic-structure keys.
 
     This replaces the old fragile substring check (Bug 10) with a
     proper parse attempt.
     """
+    content = _content_to_text(content)
+    if not content:
+        return False
+
     try:
         data = json.loads(content.strip())
     except (json.JSONDecodeError, ValueError):
@@ -197,14 +226,14 @@ def format_response(result: Any, verbose: bool = False) -> None:
     final_answer = ""
     for message in reversed(messages):
         if hasattr(message, "content") and hasattr(message, "type"):
-            if message.type == "ai" and message.content.strip():
-                content = message.content.strip()
+            content = _content_to_text(message.content).strip()
+            if message.type == "ai" and content:
                 if not _is_atomic_json(content):
                     final_answer = content
                     break
         elif isinstance(message, dict):
-            if message.get("type") == "ai" and message.get("content", "").strip():
-                content = message["content"].strip()
+            content = _content_to_text(message.get("content", "")).strip()
+            if message.get("type") == "ai" and content:
                 if not _is_atomic_json(content):
                     final_answer = content
                     break
@@ -223,9 +252,9 @@ def format_response(result: Any, verbose: bool = False) -> None:
     for message in messages:
         content = ""
         if hasattr(message, "content"):
-            content = message.content
+            content = _content_to_text(message.content)
         elif isinstance(message, dict):
-            content = message.get("content", "")
+            content = _content_to_text(message.get("content", ""))
 
         if content and _is_atomic_json(content):
             console.print(
@@ -239,7 +268,5 @@ def format_response(result: Any, verbose: bool = False) -> None:
     # Verbose output
     if verbose:
         console.print(
-            Panel(
-                f"Messages: {len(messages)}", title="Debug Information", style="dim"
-            )
+            Panel(f"Messages: {len(messages)}", title="Debug Information", style="dim")
         )