Suggested edits to address reviews of Chris' density branch

[jcass11]

Purpose

I took a stab at addressing the recommendations @chantelleleveille and I made in @cfrick13 's density branch PR. I am making a PR into his original branch with the hopes of having handled most of the edits needed to clear bandwidth for Chris. I completed this in a separate branch so that if I misinterpreted what Chris was trying to do or he doesn't like my edits is easy to change before affecting his branch.

Edits

• Removed references to old density and old filtering
• Added the new workflows for panels of Fig 3 and SFig S4 to be called within the figure_3_s4_workflow, so they are all one workflow
• Import updates (removing unused imports and fixing broken ones, which also fixes the mypy test that was failing on the original density branch)
• Removed commented code
• Used the example tracks dictionary

Testing

• ✅ Ran the new figure_3_s4_workflow first - which now includes all workflows related to these figures - which succeeded
• ✅ Ran run_all_manuscript_workflows

What didn't I address here that was part of the original density PR?

I didn't touch removing the actual old denisty features themselves, just the references to them. There were also a huge number of new features added in the density_fig_updates PR and I didn't feel prepared to decide how to pate that down. So @cfrick13 that will still need to be done with updates to your PR not covered here.

[chantelleleveille]

Nice :) Thanks for doing that!

[chantelleleveille]

@cfrick13 @jcass11 If it would be easier to address newly added columns in its own PR after adding the new workflows I would be okay with that!

[jcass11]

@cfrick13 @jcass11 If it would be easier to address newly added columns in its own PR after adding the new workflows I would be okay with that!

Fine with me!

[cfrick13]

I think we may want to keep the test_voronoi.py file. This was not added by me. I think it is one of the tests written to validate the voronoi tesslation distance measurment which is useful for the toymodel.