get rid of the nonsense accidentally introduced by claude

Author: antonkulaga

README.md

@@ -180,7 +180,7 @@ Use this configuration for most AI clients. Create or update your MCP configurat
   "mcpServers": {
     "gget-mcp": {
       "command": "uvx",
-      "args": ["gget-mcp", "server-stdio"]
+      "args": ["--from", "gget-mcp", "stdio"]
     }
   }
 }
@@ -195,7 +195,7 @@ For HTTP mode:
   "mcpServers": {
     "gget-mcp": {
       "command": "uvx",
-      "args": ["gget-mcp", "server-http"]
+      "args": ["--from", "gget-mcp", "server"]
     }
   }
 }
@@ -210,37 +210,12 @@ Use this mode when you want to save large output files (sequences, structures, a
   "mcpServers": {
     "gget-mcp": {
       "command": "uvx",
-      "args": ["gget-mcp", "server-local", "--output-dir", "./gget_output"]
+      "args": ["--from", "gget-mcp", "stdio", "--output-dir", "./gget_output"]
     }
   }
 }
 ```
 
-### Local Development Configuration
-
-For local development when you've cloned the repository:
-
-```json
-{
-  "mcpServers": {
-    "gget-mcp": {
-      "command": "uv",
-      "args": ["run", "server-stdio"],
-      "env": {
-        "MCP_PORT": "3002",
-        "MCP_HOST": "0.0.0.0",
-        "MCP_TRANSPORT": "stdio"
-      }
-    }
-  }
-}
-```
-
-**Files Available:**
-- **STDIO mode:** `mcp-config-stdio.json`
-- **HTTP mode:** `mcp-config.json` 
-- **STDIO-Local mode:** `mcp-config-stdio-local.json`
-- **Local development:** `mcp-config-stdio-debug.json`
 
 ### Configuration Video Tutorial
 
@@ -255,25 +230,15 @@ If you want to inspect the methods provided by the MCP server, use npx (you may
 
 For STDIO mode with uvx:
 ```bash
-npx @modelcontextprotocol/inspector --config mcp-config-stdio.json --server gget-mcp
-```
-
-For HTTP mode (ensure server is running first):
-```bash
 npx @modelcontextprotocol/inspector --config mcp-config.json --server gget-mcp
 ```
 
-For local development:
-```bash
-npx @modelcontextprotocol/inspector --config mcp-config-stdio-debug.json --server gget-mcp
-```
-
 You can also run the inspector manually and configure it through the interface:
 ```bash
 npx @modelcontextprotocol/inspector
 ```
 
-After that you can explore the tools and resources with MCP Inspector at http://127.0.0.1:6274 (note, if you run inspector several times it can change port)
+After that you can explore the tools and resources with MCP Inspector at which is usually at 6274 port (note, if you run inspector several times it can change port)
 
 </details>
 
@@ -299,13 +264,10 @@ If you already cloned the repo you can run the server with uv:
 
 ```bash
 # Start the MCP server locally (HTTP mode)
-uv run server-http
+uv run server
 
 # Or start in STDIO mode  
-uv run server-stdio
-
-# Or start in STDIO-local mode (saves files locally)
-uv run server-local
+uv run stdio
 
 # Or start in SSE mode
 uv run server-sse

mcp-config-stdio.json mcp-config-server.jsonmcp-config-stdio.json renamed to mcp-config-server.json

@@ -2,7 +2,7 @@
   "mcpServers": {
     "gget-mcp": {
       "command": "uvx",
-      "args": ["gget-mcp", "server-stdio"]
+      "args": ["--from", "gget-mcp", "server"]
     }
   }
 } 

mcp-config-stdio-debug.json

@@ -2,7 +2,7 @@
   "mcpServers": {
     "gget-mcp": {
       "command": "uvx",
-      "args": ["gget-mcp", "server-http"]
+      "args": ["--from", "gget-mcp", "stdio", "--output-dir", "./gget_output"]
     }
   }
 } 

mcp-config-stdio-local.json

@@ -1,6 +1,6 @@
 [project]
 name = "gget-mcp"
-version = "0.2.4"
+version = "0.2.5"
 description = "MCP server for gget bioinformatics library"
 readme = "README.md"
 authors = [
@@ -23,6 +23,9 @@ dependencies = [
 
 [project.scripts]
 gget-mcp = "gget_mcp.server:cli_app"
+stdio = "gget_mcp.server:stdio"
+server = "gget_mcp.server:server"
+sse = "gget_mcp.server:sse"
 
 [build-system]
 requires = ["hatchling"]

mcp-config.json

@@ -14,7 +14,6 @@
 
 class TransportType(str, Enum):
     STDIO = "stdio"
-    STDIO_LOCAL = "stdio-local"
     STREAMABLE_HTTP = "streamable-http"
     SSE = "sse"
 
@@ -59,8 +58,7 @@ def _register_gget_tools(self):
             self.tool(name=f"{self.prefix}search_genes")(self.search_genes_simple)
             self.tool(name=f"{self.prefix}info")(self.get_gene_info_simple)
 
-            # Sequence tools - use local wrapper if in local mode
-            if self.transport_mode == "stdio-local":
+            if self.transport_mode == "stdio":
                 self.tool(name=f"{self.prefix}seq")(self.get_sequences_local_simple)
             else:
                 self.tool(name=f"{self.prefix}seq")(self.get_sequences_simple)
@@ -73,7 +71,7 @@ def _register_gget_tools(self):
             self.tool(name=f"{self.prefix}blat")(self.blat_sequence_simple)
 
             # Alignment tools - use local wrappers if in local mode
-            if self.transport_mode == "stdio-local":
+            if self.transport_mode == "stdio":
                 self.tool(name=f"{self.prefix}muscle")(self.muscle_align_local_simple)
                 self.tool(name=f"{self.prefix}diamond")(self.diamond_align_local_simple)
             else:
@@ -86,7 +84,7 @@ def _register_gget_tools(self):
             self.tool(name=f"{self.prefix}bgee")(self.bgee_orthologs_simple)
 
             # Protein structure and function - use local wrappers if in local mode
-            if self.transport_mode == "stdio-local":
+            if self.transport_mode == "stdio":
                 self.tool(name=f"{self.prefix}pdb")(self.get_pdb_structure_local_simple)
                 self.tool(name=f"{self.prefix}alphafold")(self.alphafold_predict_local_simple)
             else:
@@ -700,7 +698,7 @@ async def get_sequences_local_simple(
         output_path: Optional[str] = None,
         format: Literal["fasta"] = "fasta"
     ) -> LocalFileResult:
-        """Fetch sequences and save to local file in stdio-local mode.
+        """Fetch sequences and save to local file in stdio mode.
         
         PREREQUISITE: Use search_genes first to get Ensembl IDs from gene names/symbols.
         
@@ -728,7 +726,7 @@ async def get_pdb_structure_local_simple(
         output_path: Optional[str] = None,
         format: Literal["pdb"] = "pdb"
     ) -> LocalFileResult:
-        """Fetch PDB structure and save to local file in stdio-local mode.
+        """Fetch PDB structure and save to local file in stdio mode.
         
         Args:
             pdb_id: PDB ID to query (e.g., '7S7U', '2GS6')
@@ -831,43 +829,35 @@ def create_app(transport_mode: str = "stdio", output_dir: Optional[str] = None,
 def server(
     host: Annotated[str, typer.Option(help="Host to run the server on.")] = DEFAULT_HOST,
     port: Annotated[int, typer.Option(help="Port to run the server on.")] = DEFAULT_PORT,
-    transport: Annotated[str, typer.Option(help="Transport type: stdio, stdio-local, streamable-http, or sse")] = DEFAULT_TRANSPORT,
-    output_dir: Annotated[Optional[str], typer.Option(help="Output directory for local files (stdio-local mode)")] = None,
+    transport: Annotated[str, typer.Option(help="Transport type: stdio, streamable-http, or sse")] = DEFAULT_TRANSPORT,
+    output_dir: Annotated[Optional[str], typer.Option(help="Output directory for local files (stdio mode)")] = None,
     extended: Annotated[bool, typer.Option(help="Use extended mode with all parameters (fallback to full API)")] = False
 ):
     """Runs the gget MCP server."""
     # Validate transport value
-    if transport not in ["stdio", "stdio-local", "streamable-http", "sse"]:
-        typer.echo(f"Invalid transport: {transport}. Must be one of: stdio, stdio-local, streamable-http, sse")
+    if transport not in ["stdio","streamable-http", "sse"]:
+        typer.echo(f"Invalid transport: {transport}. Must be one of: stdio, streamable-http, sse")
         raise typer.Exit(1)
 
     app = create_app(transport_mode=transport, output_dir=output_dir, extended_mode=extended)
 
     # Different transports need different arguments
-    if transport in ["stdio", "stdio-local"]:
+    if transport in ["stdio"]:
         app.run(transport="stdio")  # Both stdio modes use stdio transport
     else:
         app.run(transport=transport, host=host, port=port)
 
-@cli_app.command(name="server-stdio")
-def server_stdio(
+@cli_app.command(name="stdio")
+def stdio(
     extended: Annotated[bool, typer.Option(help="Use extended mode with all parameters (fallback to full API)")] = False
 ):
     """Runs the gget MCP server in stdio mode (standard input/output)."""
     app = create_app(transport_mode="stdio", extended_mode=extended)
     app.run(transport="stdio")
 
-@cli_app.command(name="server-local")
-def server_local(
-    output_dir: Annotated[Optional[str], typer.Option(help="Output directory for local files")] = None,
-    extended: Annotated[bool, typer.Option(help="Use extended mode with all parameters (fallback to full API)")] = False
-):
-    """Runs the gget MCP server in stdio-local mode (saves large files locally)."""
-    app = create_app(transport_mode="stdio-local", output_dir=output_dir, extended_mode=extended)
-    app.run(transport="stdio")
 
-@cli_app.command(name="server-http")
-def server_http(
+@cli_app.command(name="http")
+def server(
     host: Annotated[str, typer.Option(help="Host to run the server on.")] = DEFAULT_HOST,
     port: Annotated[int, typer.Option(help="Port to run the server on.")] = DEFAULT_PORT,
     output_dir: Annotated[Optional[str], typer.Option(help="Output directory for local files")] = None,
@@ -877,14 +867,14 @@ def server_http(
     app = create_app(transport_mode="streamable-http", output_dir=output_dir, extended_mode=extended)
     app.run(transport="streamable-http", host=host, port=port)
 
-@cli_app.command(name="server-sse")
-def server_sse(
+@cli_app.command(name="sse")
+def sse(
     host: Annotated[str, typer.Option(help="Host to run the server on.")] = DEFAULT_HOST,
     port: Annotated[int, typer.Option(help="Port to run the server on.")] = DEFAULT_PORT,
     output_dir: Annotated[Optional[str], typer.Option(help="Output directory for local files")] = None,
     extended: Annotated[bool, typer.Option(help="Use extended mode with all parameters (fallback to full API)")] = False
 ):
-    """Runs the gget MCP server in Server-Sent Events (SSE) mode."""
+    """Runs the gget MCP server in Sent Events (SSE) mode."""
     app = create_app(transport_mode="sse", output_dir=output_dir, extended_mode=extended)
     app.run(transport="sse", host=host, port=port)