The second option is traditionally what people mean by "monorepo" (multiple executables in a repo with a dependency tree). First one you'd call a "monolith" (single executable in a repo).

The second one you'd want to manage with a tool like Bazel, which will use whatever plugins are appropriate for the language (pip in Python's case).

It's a legitimate ambition to try and build a tool within a single language's ecosystem to manage the second option, but it's a really hard problem that Bazel (and others) have already solved well, so you might as well use them instead.