Can't check only submodules (except if installed with `pip install -e .`)

Bug Report

Checking a submodule only of a project seems impossible, when not installed using pip install -e .

Usecase:
I have project that contains auto-generated API code which is not correctly typed.
I only want to check the controllers that are located in a submodule.

To Reproduce

1. Create a example project with the following structure

.
├── setup.py
└──src
    └── example_project
        ├── __init__.py
        ├── calc.py
        ├── py.typed
        └── sub
            ├── __init__.py
            └── foo.py

src/example_project/calc.py :

def int_add(a: int, b: int) -> int:
    """
    Simply add two numbers
    """
    return a + b


def float_diff(a: float, b: float) -> float:
    """
    Diff two numbers
    """
    return a / b


if __name__ == "__main__":
    int_add("a", "b")

src/ems_example_project/sub/foo.py:

import example_project.calc

example_project.calc.int_add("foo", "bar")

a: int = 1
a = "2"

2. Install the package with pip install . OR do not install it at all.

3. Run mypy for the given submodule

mypy src/example_project/sub

Expected Behavior

Only type errors for the submodule are found:

src/example_project/sub/foo.py:3: error: Argument 1 to "int_add" has incompatible type "str"; expected "int"  [arg-type]
src/example_project/sub/foo.py:3: error: Argument 2 to "int_add" has incompatible type "str"; expected "int"  [arg-type]
src/example_project/sub/foo.py:6: error: Incompatible types in assignment (expression has type "str", variable has type "int")  [assignment]
Found 3 errors in 1 file (checked 2 source files)

This actually works, if I install the package with pip install -e ..
But I expect this to work no matter if I install the package normally or not installing it at all.

Actual Behavior

The type errors for the top level modules are also listed.

src/example_project/calc.py:21: error: Argument 1 to "int_add" has incompatible type "str"; expected "int"  [arg-type]
src/example_project/calc.py:21: error: Argument 2 to "int_add" has incompatible type "str"; expected "int"  [arg-type]
src/example_project/sub/foo.py:3: error: Argument 1 to "int_add" has incompatible type "str"; expected "int"  [arg-type]
src/example_project/sub/foo.py:3: error: Argument 2 to "int_add" has incompatible type "str"; expected "int"  [arg-type]
src/example_project/sub/foo.py:6: error: Incompatible types in assignment (expression has type "str", variable has type "int")  [assignment]
Found 5 errors in 2 files (checked 2 source files)

If I use the option -p example_project.sub instead of the path it works as expected. But in my environment I am only able to add specific files (think pre-commit or similar).
It also works if I install the package using pip install -e.
Still I would not expect a such a difference just depending on how I installed the package.

Your Environment

• Mypy version used: 1.4.1
• Mypy command-line flags: none besides the path to the file
• Mypy configuration options from mypy.ini (and other config files): none
• Python version used: 3.9.16

This might be related to:

• #10956
• #10260
• #6861
• #10428

Start with the reported setup.py layout and reproduce the difference between mypy src/example_project/sub, -p example_project.sub, and an editable versus normal install. Compare diagnostics from calc.py and sub/foo.py, then trace the path-based module discovery behavior. Done means checking only the requested submodule produces the three expected errors without also checking calc.py.