Using async code for tools. (#20)

* Rebase.

* image for mcp servers.

* tiny changes.

* edit gitignore file for a while.

* add changes.

* remove unnecessary import.

* tiny change.

* All the prsers are working well.

* clean a bit.

Author: RubelMozumder

README.md

@@ -44,6 +44,40 @@ To execute any script, use `uv run python <filepath>` (automatically calls `uv s
 To try out individual Python sessions open a new bash shell.
 Then activate the virtual environment via `. .venv/bin/activate`.You can now initiate your Python session (`python`).
 
+## Manual Testing setup
+MCP primitives developed for a single server can be tested using [MCP instructor](https://github.com/modelcontextprotocol/inspector). The problem with it can not handle multiple servers at once. So, it requires to test each server individually. (We did not find the way to inspect multiple servers at once using MCP inspector).
+```
+uv run mcp dev <path-to-server-file e.g., src/nomad/__main__.py>
+```
+Then click on the url link appeared on the terminal to open the MCP inspector in the browser or inspector will automatically open in browser.
+
+To run and test all the servers together in VS Code, as a client, list your servers in a `json` file e.g., `.vscode/mcp.json` and VSCode will be capable of detect the servers and can be run on the clicking button above the server (appeared in the VSCode UI).
+
+![mcp.json](images/mcp_json.png)
+
+Example of `mcp.json` listing all the servers:
+```Json
+{
+  "servers": {
+    "parse-patrol": {
+      "command": "uv",
+      "args": ["run", "python", "src/parse_patrol/__main__.py"],
+      "cwd": "${workspaceFolder}"
+    },
+    "cclib": {
+      "command": "uv",
+      "args": ["run", "python", "src/cclib/__main__.py"],
+      "cwd": "${workspaceFolder}"
+    },
+    "nomad": {
+      "command": "uv",
+      "args": ["run", "python", "src/nomad/__main__.py"],
+      "cwd": "${workspaceFolder}"
+    }
+  }
+}
+```
+
 ## Project Structure
 
 ```

images/mcp_json.png

@@ -10,6 +10,9 @@ dependencies = [
     "pydantic>=2.11.7",
     "qc-iodata>=1.0.0a8",
     "requests>=2.32.5",
+    "asyncio>=4.0.0",
+    "aiofiles>=24.1.0",
+    "aiohttp",
 ]
 
 

pyproject.toml

@@ -1,10 +1,16 @@
 import cclib
 from mcp.server.fastmcp import FastMCP # pyright: ignore[reportMissingImports]
+from mcp.server.fastmcp.utilities.logging import configure_logging, get_logger
+
 
 from typing import Optional, Dict, List, Any
 from pydantic import BaseModel, Field
 
 
+configure_logging("INFO")
+logger = get_logger(__name__)
+
+
 class CCDataModel(BaseModel):
     class Config:
         # Prevent model registration conflicts when imported multiple times
@@ -84,7 +90,7 @@ 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) -> CCDataModel: # type: ignore
+def ccdata_to_model(ccdata: cclib.parser.data.ccData) -> CCDataModel:  # type: ignore
     """Convert ccData object to CCDataModel (Pydantic) format.
     
     Args:
@@ -93,6 +99,7 @@ def ccdata_to_model(ccdata: cclib.parser.data.ccData) -> CCDataModel: # type: ig
     Returns:
         CCDataModel with converted data types for JSON serialization
     """
+    logger.info("Converting ccData to CCDataModel...")
     result = {}
     for field_name in CCDataModel.model_fields.keys():
         if hasattr(ccdata, field_name):
@@ -109,11 +116,12 @@ def ccdata_to_model(ccdata: cclib.parser.data.ccData) -> CCDataModel: # type: ig
                 result[field_name] = value
     return CCDataModel(**result)
 
+
 mcp = FastMCP("CCLib Chemistry Parser")
 
 
 @mcp.tool()
-def cclib_parse_file_to_model(filepath: str) -> CCDataModel:
+async def cclib_parse_file_to_model(filepath: str) -> CCDataModel:
     """Parse chemistry file and return as CCDataModel for JSON serialization.
     
     Args:
@@ -122,17 +130,18 @@ def cclib_parse_file_to_model(filepath: str) -> CCDataModel:
     Returns:
         CCDataModel with parsed data converted for JSON serialization
     """
-    filereader = cclib.io.ccopen(filepath) # type: ignore
+    logger.info("Parsing file: %s ...", filepath)
+    filereader = cclib.io.ccopen(filepath)  # type: ignore
     if filereader is None:
+        logger.error("File not found: %s", filepath)
         return CCDataModel()
     ccdata = filereader.parse()
     return ccdata_to_model(ccdata)
 
 
 @mcp.prompt()
-def cclib_test_prompt(
-    file_description: str,
-    output_format: str="a CCDataModel for JSON serialization"
+async def cclib_test_prompt(
+    file_description: str, output_format: str = "a CCDataModel for JSON serialization"
 ) -> str:
     """Generate a prompt for parsing chemistry files using cclib.
     

src/cclib/__main__.py

@@ -5,6 +5,11 @@
 from pydantic import BaseModel, Field
 import periodictable
 from mcp.server.fastmcp import FastMCP  # pyright: ignore[reportMissingImports]
+from mcp.server.fastmcp.utilities.logging import configure_logging, get_logger
+
+
+configure_logging("INFO")
+logger = get_logger(__name__)
 
 
 class CustomGaussianDataModel(BaseModel):
@@ -417,7 +422,7 @@ def read_block(start_idx: int) -> Tuple[int, List[str]]:
 
 
 @mcp.tool()
-def gauss_parse_file_to_model(filepath: str) -> CustomGaussianDataModel:
+async def gauss_parse_file_to_model(filepath: str) -> CustomGaussianDataModel:
     """
     Parse a Gaussian file (.log/.out, .gjf/.com, .fchk) and return a CustomGaussianDataModel.
 
@@ -432,8 +437,11 @@ def gauss_parse_file_to_model(filepath: str) -> CustomGaussianDataModel:
     Returns:
         CustomGaussianDataModel with parsed contents.
     """
+
+    logger.info("Parsing Gaussian file: %s ...", filepath)
     path = Path(filepath)
     if not path.exists():
+        logger.error("File not found: %s", filepath)
         return CustomGaussianDataModel(metadata={"error": f"File not found: {filepath}"})
 
     ext = path.suffix.lower()
@@ -459,9 +467,8 @@ def gauss_parse_file_to_model(filepath: str) -> CustomGaussianDataModel:
 
 
 @mcp.prompt()
-def custom_gaussian_test_prompt(
-    file_description: str,
-    analysis_type: str = "comprehensive analysis"
+async def custom_gaussian_test_prompt(
+    file_description: str, analysis_type: str = "comprehensive analysis"
 ) -> str:
     """Generate a prompt for parsing Gaussian files with custom analysis.
     

src/custom_gaussian/__main__.py

@@ -76,7 +76,7 @@ def iodata_to_model(ext_data: iodata_package.IOData) -> IODataModel:
     return IODataModel(**result)
 
 @mcp.tool()
-def iodata_parse_file_to_model(filepath: str) -> IODataModel:
+async def iodata_parse_file_to_model(filepath: str) -> IODataModel:
     """Parse chemistry file and return as IODataModel for JSON serialization.
     
     Args:
@@ -89,9 +89,8 @@ def iodata_parse_file_to_model(filepath: str) -> IODataModel:
     return iodata_to_model(data)
 
 @mcp.prompt()
-def iodata_test_prompt(
-    file_description: str,
-    output_format: str="a IOData for JSON serialization"
+async def iodata_test_prompt(
+    file_description: str, output_format: str = "a IOData for JSON serialization"
 ) -> str:
     """Generate a prompt for parsing chemistry files using IOData.
     
@@ -104,7 +103,7 @@ def iodata_test_prompt(
     """
 
     return (
-        f"Use `iodata_parse_file_to_model` to parse the file with description {file_description} "
+        f"Use `iodata_parse_file_to_model` to parse the file (with extension .fck) with description {file_description} "
         f"and return the data as {output_format}."
     )