Bug: Sorting imports reveals circular dependency

[kenibrewer]

Example code with output

After turrning on isort (in this branch), I received the following error:

(.venv) @kenibrewer ➜ /workspaces/pycytominer (fix/circular-imports) $ pytest
ImportError while loading conftest '/workspaces/pycytominer/tests/test_cyto_utils/conftest.py'.
tests/test_cyto_utils/conftest.py:12: in <module>
    from pycytominer.cyto_utils.cell_locations import CellLocation
pycytominer/__init__.py:3: in <module>
    from .aggregate import aggregate
pycytominer/aggregate.py:8: in <module>
    from pycytominer.cyto_utils import (
pycytominer/cyto_utils/__init__.py:7: in <module>
    from .DeepProfiler_processing import AggregateDeepProfiler
pycytominer/cyto_utils/DeepProfiler_processing.py:11: in <module>
    from pycytominer import aggregate, normalize
pycytominer/normalize.py:8: in <module>
    from pycytominer.cyto_utils import infer_cp_features, load_profiles, output
E   ImportError: cannot import name 'infer_cp_features' from partially initialized module 'pycytominer.cyto_utils' (most likely due to a circular import) (/workspaces/pycytominer/pycytominer/cyto_utils/__init__.py)

An attempt to resolve the error by moving cyto_utils.DeepProfiler_processing:AggregateDeepProfiler to deep_profiler.processing:AggregateDeepProfiler revealed additional circular dependencies within cyto_utils.

From a fresh codebase, a similar error also occurred when trying to switch the codebase from absolute imports (from pycytominer.cyto_utils import) to relative imports (from .cyto_utils import).

Issue description

The error message indicates an issue with circular dependencies. Resolving this issue will likely require a re-organization of cyto_utils into more granular submodules and moving anything that requires aggregate or other core functions out of cyto_utils into a new module.

Expected behavior

We should be able to sort our imports and use relative imports without impacting the ability to load modules.

Additional information

No response