Documentation updates preceding 1.1.0 release

[timbernat]

Description

Update details and omissions in README and documentation prior to new release. Meant as a non-code follow-on to #58, as well as to address remaining TODOs in #60

Todos

Notable points that this PR has either accomplished or will accomplish.

• Advertise Python 3.12 compatibility
  • Update places where python=3.11 is specified to 3.12
• Include polymerization manuscript in docs
  • Add TOC graphic from that manuscript to cached, displayed graphics
• Update references to espaloma-charge from docs:
  • Remove for param toolkit install snippet In README
  • Point users to OpenFF NAGL/AshGC as the preferred GNN charge model docs/installation/paramtoolkits.rst
  • Remove the Espaloma install command and Espaloma section.
  • Update wording from “all 3” supplementary toolkits to whatever remains after deprecation.
  • Indicate OpenFF NAGL as recommended GNN charging option
• Remove references to outdated OpenFF boron example
• Create + link examples PR to ensure notebook changes there reflect what will change here (examples PR #2)

Questions

• Are packmol versions pins still necessary in examples? If not (test on examples), should be removed also

Status

• Verify docs build
  • Check correctness of content
  • Make sure all links in docs pages work
• Ensure quickstart instructions in README is accurate
• Ready to go