Reorganize Configuration Processing

[gwaybio]

As I was progressing the recipe to the aggregate profiling step, I recognized that it is very difficult to follow all the directories and locations of necessary files.

We need to strike a balance between modularity and overburdening our users. Since we are working towards a unified file structure in regular Cell Painting experiments (see cytomining/profiling-handbook#54 (comment)) it makes sense to expect certain files and directory structure to never change. This removes unnecessary options from our users.

If in the rare event that CellProfiler output files change save locations after a Pooled Cell Painting image analysis pipeline, then we will have to revisit this structure and decision. For now, it makes development easier.

[ErinWeisbart]

I understand that the convention for paths going forward will be pathlib.Path. The goal is to remove unnecessary f-strings? What about situations where the .csv name has a variable in it?Would the format be something like: pathlib.Path(output_folder, f"metadata_{site}.tsv.gz")

[gwaybio]

The goal is to remove unnecessary f-strings?

Anything unnecessary should be removed 😄

Would the format be something like: pathlib.Path(output_folder, f"metadata_{site}.tsv.gz")

Yep, this is exactly right