feat: More domain examples

[jiriminarcik]

Description

Contains two new example domains:examples/molecules and examples/logic-circuit-domain.

Implementation strategy and design decisions

These examples exhibit higher complexity in both the number of degrees of freedom and objectives/constraints. Below is a comparison to most of the remaining examples (see caffeine, glutamine, full-adder and half-adder in the top right part of the diagram).

Note that it may take several resamples to obtain a nice local minimum, especially for the more intricate substance programs. Below is an example of an optimization run during which the current optimizer get stuck in undesirable local minima for many optimization steps.

Examples with steps to reproduce them

Molecules

Run: npx roger watch molecules/glutamine.sub molecules/molecules-basic.sty molecules/molecules.dsl

For more complicated example try molecules/caffeine.sub.

Alternative styles:
molecules/molecules.sty
molecules/molecules-elegant.sty

Logic gates

Run: npx roger watch logic-circuit-domain/half-adder.sub logic-circuit-domain/distinctive-shape.sty logic-circuit-domain/logic-gates.dsl

For more complicated example try logic-circuit-domain/full-adder.sub.

Checklist

• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• New and existing tests pass locally using yarn test
• I ran yarn docs and there were no errors when generating the HTML site
• My code follows the style guidelines of this project (e.g.: no ESLint warnings)

[codecov]

Codecov Report

Merging #635 (678dff7) into main (5cac9bc) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #635   +/-   ##
=======================================
  Coverage   65.03%   65.03%           
=======================================
  Files          41       41           
  Lines        6721     6721           
  Branches     1286     1286           
=======================================
  Hits         4371     4371           
  Misses       2342     2342           
  Partials        8        8           

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5cac9bc...678dff7. Read the comment docs.

[kai-qu]

LGTM! Awesome examples! I added them to this page: https://github.com/penrose/penrose/wiki/Example-diagrams

I do see that it takes quite a few resamples to reach a decent local minimum, as you reported. These could be good test examples for any improved solver. (e.g. This is the most # of pairwise repels I've seen in any example.)

I might also ask more questions about your Style programs later, for the domain expert study.