refactor: simplify indexUrls passing and add --dep flag for consistency

- Always pass indexUrls to prepare_env (even if empty), matching how dependencies are handled
- Add repeatable --dep flag alongside existing --deps for CLI consistency with --index-url
- Mark --deps as deprecated but keep it working for backwards compatibility

Author: juan-abia

mcp_run_python/_cli.py

@@ -22,7 +22,10 @@ def cli_logic(args_list: Sequence[str] | None = None) -> int:
     )
 
     parser.add_argument('--port', type=int, help='Port to run the server on, default 3001.')
-    parser.add_argument('--deps', '--dependencies', help='Comma separated list of dependencies to install')
+    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(
         '--index-url',
         action='append',
@@ -53,7 +56,9 @@ def cli_logic(args_list: Sequence[str] | None = None) -> int:
             format='%(message)s',
         )
 
-        deps: list[str] = args.deps.split(',') if args.deps else []
+        deps: list[str] = args.dep_list or []
+        if args.deps:
+            deps.extend(args.deps.split(','))
         index_urls: list[str] = args.index_urls or []
         return_code = run_mcp_server(
             args.mode.replace('-', '_'),

mcp_run_python/deno/src/runCode.ts

@@ -124,9 +124,10 @@ export class RunCode {
 
     const preparePyEnv: PreparePyEnv = pyodide.pyimport(moduleName)
 
-    const prepareStatus = indexUrls.length > 0
-      ? await preparePyEnv.prepare_env(pyodide.toPy(dependencies), pyodide.toPy(indexUrls))
-      : await preparePyEnv.prepare_env(pyodide.toPy(dependencies))
+    const prepareStatus = await preparePyEnv.prepare_env(
+      pyodide.toPy(dependencies),
+      pyodide.toPy(indexUrls),
+    )
     return {
       pyodide,
       preparePyEnv,
@@ -218,6 +219,6 @@ interface PrepareError {
   message: string
 }
 interface PreparePyEnv {
-  prepare_env: (dependencies: any, index_urls?: any) => Promise<PrepareSuccess | PrepareError>
+  prepare_env: (dependencies: any, index_urls: any) => Promise<PrepareSuccess | PrepareError>
   dump_json: (value: any, always_return_json: boolean) => string | null
 }