Reorganize Python API for Garden Lattice book materials and add understanding book section

[d33bs]

Description

This PR reorganizes some of the Python API for alignment with the Garden Lattice book materials. It also adds an understanding book section to begin explaining relevant best practices we have measured within the Python package. Initially I had planned to make the updates all together - adding the connectedness and practicality sections alongside the understanding section. However, the changes grew more than I expected, and as a result I'm opting to get feedback on what I have so far.

References #25

What is the nature of your change?

• Content additions or updates (adds or updates content)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• 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 contributions.
• I have commented my content, particularly in hard-to-understand areas.
• I have made corresponding changes to related documentation (outside of book content).
• My changes generate no new warnings.
• New and existing tests pass locally with my changes.
• I have added tests that prove my additions are effective or that my feature works.
• I have deleted all non-relevant text in this pull request template.

[gwaybio]

Thanks for deciding to break off this pull request and file now rather than later! It is much easier this way and will generate a better product. Mostly minor suggestions, feel free to merge when you're happy!

[d33bs]

Thank you @gwaybio and @MattsonCam (for the discussion)! After addressing your comments I'll now merge this in.