Collate and SingleCells to accept less/different compartments

[fefossa]

Description

I'm proposing these changes to Collate and SingleCells for those to accept different numbers of cell compartments or even just one compartment.
Related to issue #272

This is still a work in progress.

So far, (1) I've added the option on collate.py to accept 3 flags, for no-cells, no-cytoplasm, or no-nuclei; (2) the checking on assert_linking_cols_complete only happens when there's more than one compartment.

Proposed changes/discussion

From some discussion with @bethac07, we saw two options:

1. The first option is just to add more documentation to SingleCells (which I did), and expect the user to build their dictionary and provide it as compartment_linking_cols. If that's how you'd like to do it, I think the changes I already did would be enough to merge.

2. OR build the dictionary for compartment_linking_cols based on the compartments given:

Now: the compartment_linking_cols is defined as the default_linking_cols if no dictionary is specified by the user. Also, for SingleCells to work right now with only one compartment, you must give a dictionary linking the compartment to itself, for example: { "cells": {"cells": "ObjectNumber"}}, which works, but I don't know if that's the right way to do it.

So, to build the dictionary:

• Have some sort of template dictionary like {"compA": {"parent":{"compB":"object_Parent_compB"}, "child":{"compA":"ObjectNumber"}}}, where it will take the user compartments and create this dictionary. I just don't know which is the best way to handle this, because how do we know which is the child-parent from objects other than nuclei, cell, and cytoplasm, if the user is not giving that info?
• To deal only with nuclei, cytoplasm, and cells objects combinations (if the user wants only one or two of those compartments), have a dictionary like par_child_dict = {"nuclei": {"cells", "cytoplasm"}, "cells":{"cytoplasm"}} from where the relationship can be inferred and the compartment_linking_cols is built based on par_child_dict.
• On merge_single_cells, something needs to change on where the dataframe sc_df is being merged to work with only one compartment without the need to provide a dictionary that links the compartment to itself.

What is the nature of your change?

• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

Checklist

• I have read the CONTRIBUTING.md guidelines.
• My code follows the style guidelines of this project.
• I have performed a self-review of my own code.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• New and existing unit tests pass locally with my changes.
• I have added tests that prove my fix is effective or that my feature works.
• I have deleted all non-relevant text in this pull request template.

[d33bs]

Hello, this is a courtesy notice that Pcytominer's master branch has been renamed to main as part of changes merged in #303. While changes here should be seamless, GitHub is unable to change your local git environment and offers the following guidance when it comes to this. Thank you for your understanding and please don't hesitate to reach out with any questions or concerns.