Autosummary: autosummary_ignore_module_all does not work as documented

[ClementPinard]

Describe the bug

As per documentation :

Note that if an imported member is listed in __all__, it will be documented regardless of the value of autosummary_imported_members.

So the way I understand it is that if I have a small package like this :

my_package/
    __init__.py
    my_class.py
    my_module/
        my_submodule.py

with the following files :

my_class.py

class myClass:
    """" my Class docstring """"
    def my_class_method(self, a):
        """ method docstring """
        return

my_submodule.py

def f():
    """ f docstring """
    return

__init__.py

from .my_class import myClass
from . import my_module

__all__ = ["myClass", "my_module"]

and a rst file like this:

An example of recursive module documentation
====================================

.. autosummary::
    :toctree: generated
    :recursive:

    my_package

assume the option autosummary_ignore_module_all is set to False in conf.py, the autosummary should only consider myClass and my_module to be part of the package my_package. The generated folder should normally look like this:

generated
    my_package.myClass
    my_packge.my_module

But actually, it looks like this :

generated
    my_package.my_class

Meaning it ignored the imported elements, even though they were in the __all__ and it did take the my_module package even though it was not in the __all__

How to Reproduce

$ git clone git@github.com:ClementPinard/sphinx_autosummary_bug_example.git
$ cd sphinx_autosummary_bug_example.gt
$ pip install sphinx
$ sphinx-build -b html docs docs/_build
$ # see docs/generated/ folder

Expected behavior

generated folder should have the files

my_package.rst
my_package.my_module.rst
my_patckage.my_module.my_submodule.rst
my_package.myClass.rst

Your project

https://github.com/ClementPinard/sphinx_autosummary_bug_example

Screenshots

No response

OS

Ubuntu 20.04

Python version

3.9

Sphinx version

5.1

Sphinx extensions

sphinx.ext.autodoc, sphinx.ext.autosummary

Additional context

[ClementPinard]

After some investigation in the code, I do believe that there is a problem in the generate.py file, when populating the ns dictionnary

https://github.com/sphinx-doc/sphinx/blob/5.x/sphinx/ext/autosummary/generate.py#L313

Problem with myClass

ns["members"] has the right dict, i.e. myClass and my_module, but when trying to populate ns["classes"] , myClass gets dismissed, because imported_member is not True, and the function get_members does not check if the imported memeber is in __all__ or not as seen here :

sphinx/sphinx/ext/autosummary/generate.py

Line 259 in 7473b05

if imported or getattr(value, '__module__', None) == obj.__name__:

See how if skips the block if either the imported is not evaluated to True or the __module__ of considered object is not the root, i.e. the element is imported.

As a consequence, ns["classes"] is empty

Problem with my_module

The code only seem to care about modules found by the function get_modules and otherwise are simply ignored.

sphinx/sphinx/ext/autosummary/generate.py

Line 320 in 7473b05

ns['modules'], ns['all_modules'] = get_modules(obj)

It explains why we find my_package.my_class even though it's not in my_package.__all__. Not sure how to explain the lack of my_package.my_module though, it seems that the fact that it has a submodule and no __init__.py is the problem.

[ClementPinard]

See a proposition for how to fix it here : #10811