Post merge hotfixes

README.md

@@ -204,6 +204,65 @@ Once the servers passes the checks, register the new MCP server:
 
 For running or adding tests, as well as contributing to the official repository, see `./tests/README.md`.
 
+### Warning Suppression for Dependencies
+
+Some third-party dependencies (like cclib) may emit warnings during compilation or runtime. Here's how to suppress them:
+
+#### For MCP Server Usage (Compile-time warnings)
+
+Warnings like `SyntaxWarning` occur when Python compiles source files. To suppress them, set the `PYTHONWARNINGS` environment variable in your MCP configuration:
+
+```json
+{
+  "servers": {
+    "parse-patrol": {
+      "command": "uv",
+      "args": ["run", "python", "-m", "parse_patrol"],
+      "env": {
+        "PYTHONWARNINGS": "ignore::SyntaxWarning"
+      }
+    }
+  }
+}
+```
+
+This is already configured in all template files under `templates/`.
+
+#### For Direct Python Usage (Runtime warnings)
+
+For runtime warnings when using parsers as direct dependencies, parse-patrol includes specialized `__init__.py` files in parser modules (e.g., `src/parse_patrol/parsers/cclib/__init__.py`) that automatically suppress known dependency warnings before imports.
+
+If you need additional suppression in your own scripts, use Python's warnings module:
+
+```python
+import warnings
+warnings.filterwarnings("ignore", category=SyntaxWarning)
+
+from parse_patrol import cclib_parse
+```
+
+Alternatively, set the environment variable before running your script:
+
+```bash
+export PYTHONWARNINGS="ignore::SyntaxWarning"
+python your_script.py
+```
+
+#### For pytest (Test suite)
+
+Warning filters are configured in `pyproject.toml`:
+
+```toml
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore::DeprecationWarning",
+    "ignore::PendingDeprecationWarning",
+    "ignore::SyntaxWarning",
+]
+```
+
+This ensures tests run cleanly without noise from dependency warnings.
+
 ## Online Resources
 
 The following links explain the basics of MCP, including the distinction between *tools*, *resources*, and *prompts*. **Make sure to respect these distinctions!**

pyproject.toml

@@ -77,6 +77,7 @@ addopts = [
 filterwarnings = [
     "ignore::DeprecationWarning",
     "ignore::PendingDeprecationWarning",
+    "ignore::SyntaxWarning",
 ]
 
 [build-system]

src/parse_patrol/__main__.py

@@ -54,17 +54,17 @@ def register_parsers():
             module = import_module(config["module"], package=__package__)
 
             # Register tools
-            for tool_name in getattr(config, "tools", []):
+            for tool_name in config.get("tools", []):
                 tool_func = getattr(module, tool_name)
                 mcp.tool()(tool_func)
 
             # Register resources
-            for resource_name in getattr(config, "resources", []):
+            for resource_name in config.get("resources", []):
                 resource_func = getattr(module, resource_name)
                 mcp.resource(f"{RESOURCE_PREFIX}{resource_name.replace('_', '/')}")(resource_func)
 
             # Register prompts
-            for prompt_name in getattr(config, "prompts", []):
+            for prompt_name in config.get("prompts", []):
                 prompt_func = getattr(module, prompt_name)
                 mcp.prompt()(prompt_func)
 

src/parse_patrol/parsers/cclib/__init__.py

@@ -0,0 +1,15 @@
+"""
+CCLib parser module initialization.
+Suppresses SyntaxWarning from cclib before module imports.
+"""
+
+import warnings
+import importlib
+
+# Suppress SyntaxWarning from cclib's invalid escape sequences
+warnings.filterwarnings("ignore", category=SyntaxWarning, module="cclib")
+
+# Explicitly import the external cclib package to avoid self-import
+external_cclib = importlib.import_module("cclib")
+
+__all__ = ["external_cclib"]

src/parse_patrol/parsers/cclib/utils.py

@@ -3,7 +3,7 @@
 This module provides sync functions that can be imported and used directly.
 """
 
-import cclib
+from . import external_cclib
 from typing import Optional, Dict, List, Any
 from pydantic import BaseModel, Field # pyright: ignore[reportMissingImports]
 
@@ -93,7 +93,7 @@ class Config:
     zpve: Optional[float] = Field(None, description="Zero-point vibrational energy correction (hartree/particle, float)")
 
 
-def ccdata_to_model(ccdata: cclib.parser.data.ccData, filepath: str = None) -> CCDataModel:  # type: ignore
+def ccdata_to_model(ccdata: external_cclib.parser.data.ccData, filepath: str = None) -> CCDataModel:  # type: ignore
     """Convert ccData object to CCDataModel (Pydantic) format.
 
     Args:
@@ -151,7 +151,7 @@ def cclib_parse(filepath: str) -> CCDataModel:
         FileNotFoundError: If file cannot be opened
         ValueError: If file cannot be parsed
     """
-    filereader = cclib.io.ccopen(filepath)  # type: ignore
+    filereader = external_cclib.io.ccopen(filepath)  # type: ignore
     if filereader is None:
         raise FileNotFoundError(f"File not found or unsupported format: {filepath}")
 

templates/claude-desktop-mcp.json

@@ -5,7 +5,8 @@
       "args": ["run", "python", "-m", "parse_patrol"],
       "cwd": "/path/to/parse-patrol",
       "env": {
-        "PYTHONPATH": "/path/to/parse-patrol/src"
+        "PYTHONPATH": "/path/to/parse-patrol/src",
+        "PYTHONWARNINGS": "ignore::SyntaxWarning"
       }
     }
   }

templates/neovim-mcp.json

@@ -5,7 +5,8 @@
       "args": ["run", "python", "-m", "parse_patrol"],
       "cwd": "/path/to/parse-patrol",
       "env": {
-        "PYTHONPATH": "/path/to/parse-patrol/src"
+        "PYTHONPATH": "/path/to/parse-patrol/src",
+        "PYTHONWARNINGS": "ignore::SyntaxWarning"
       }
     }
   }

templates/vscode-mcp.json

@@ -5,7 +5,8 @@
       "args": ["run", "python", "-m", "parse_patrol"],
       "cwd": "${workspaceFolder}",
       "env": {
-        "PYTHONPATH": "${workspaceFolder}/src"
+        "PYTHONPATH": "${workspaceFolder}/src",
+        "PYTHONWARNINGS": "ignore::SyntaxWarning"
       }
     }
   }