docs: update CLI to use --dep instead of --deps

- Update README.md examples to use --dep (repeatable) instead of --deps
- Hide --deps from CLI help (argparse.SUPPRESS)
- Add DeprecationWarning when --deps is used
- Keep --deps working for backwards compatibility

Author: juan-abia

README.md

@@ -34,7 +34,7 @@ To use this server, you must have both Python and [Deno](https://deno.com/) inst
 The server can be run with `deno` installed using `uvx`:
 
 ```bash
-uvx mcp-run-python [-h] [--version] [--port PORT] [--deps DEPS] [--index-url URL] {stdio,streamable-http,streamable-http-stateless,example}
+uvx mcp-run-python [-h] [--version] [--port PORT] [--dep PKG]... [--index-url URL]... {stdio,streamable-http,streamable-http-stateless,example}
 ```
 
 where:
@@ -49,7 +49,7 @@ where:
 - `streamable-http-stateless` runs the server with [Streamable HTTP MCP transport](https://modelcontextprotocol.io/specification/2025-06-18/basic/transports#streamable-http) in stateless mode and does not
   support server-to-client notifications
 - `example` will run a minimal Python script using `numpy`, useful for checking that the package is working, for the code
-  to run successfully, you'll need to install `numpy` using `uvx mcp-run-python --deps numpy example`
+  to run successfully, you'll need to install `numpy` using `uvx mcp-run-python --dep numpy example`
 
 ## Usage with Pydantic AI
 
@@ -172,7 +172,7 @@ Dependencies must be provided when initializing the server so they can be instal
 Use `--index-url` to install dependencies from private registries (can be repeated, tried in order before PyPI):
 
 ```bash
-uvx mcp-run-python --index-url https://private.repo.com/simple --deps mypackage stdio
+uvx mcp-run-python --index-url https://private.repo.com/simple --dep mypackage stdio
 ```
 
 The Python API accepts `index_urls` in `code_sandbox`, `prepare_deno_env`, and `run_mcp_server`. See [micropip documentation](https://micropip.pyodide.org/en/stable/project/api.html#micropip.install) for index URL requirements.

mcp_run_python/_cli.py

@@ -3,6 +3,7 @@
 import argparse
 import logging
 import sys
+import warnings
 from collections.abc import Sequence
 
 from . import __version__
@@ -25,7 +26,7 @@ def cli_logic(args_list: Sequence[str] | None = None) -> int:
     parser.add_argument(
         '--dep', action='append', dest='dep_list', metavar='PKG', help='Dependency to install (can be repeated)'
     )
-    parser.add_argument('--deps', '--dependencies', help='(Deprecated) Comma separated list of dependencies to install')
+    parser.add_argument('--deps', '--dependencies', help=argparse.SUPPRESS)
     parser.add_argument(
         '--index-url',
         action='append',
@@ -58,6 +59,11 @@ def cli_logic(args_list: Sequence[str] | None = None) -> int:
 
         deps: list[str] = args.dep_list or []
         if args.deps:
+            warnings.warn(
+                '--deps is deprecated, use --dep instead (can be repeated)',
+                DeprecationWarning,
+                stacklevel=2,
+            )
             deps.extend(args.deps.split(','))
         index_urls: list[str] = args.index_urls or []
         return_code = run_mcp_server(