Fix transport configuration not working with PyPI entry point

[aditya-atlan]

Bug Description

When the atlan-mcp-server package was installed via PyPI and executed using uvx atlan-mcp-server, the transport configuration was not being applied. The server would always start in stdio mode, ignoring both environment variables (MCP_TRANSPORT, MCP_HOST, etc.) and command-line arguments.

Root Cause

The argument parsing logic was only executed in the if __name__ == "__main__": block, which runs when the script is executed directly (python server.py) but not when called via the PyPI entry point (uvx atlan-mcp-server). The PyPI entry point calls the main() function directly, bypassing the argument parsing.

Solution

Moved the argument parsing logic from the if __name__ == "__main__": block into the main() function itself. This ensures that:

• Environment variables are properly read (MCP_TRANSPORT, MCP_HOST, MCP_PORT, MCP_PATH)
• Command-line arguments work as expected
• Transport configuration works regardless of execution method (direct Python execution or PyPI entry point)
• Backward compatibility is maintained

This also updates the uv lock which was not in sync with latest fastmcp version

[firecast]

We also use dotenv for env variables. Lets use the setting.py for these configurations

[aditya-atlan]

stale , closing