Primer 4.0 TODO List

[tfenne]

• Make sure everything works on python 3.11 and re-enable in all github action workflows
• Make sure docs build and look good
• Add parameters to PrimerAndAmpliconParameters and ProbeParameters that allow for setting all the parameters that affect thermodynamic computations (e.g. concentrations of various things)
• Add builder functions to Thermo that can construct an instance from PrimerAndAmpliconParameters or ProbeParameters with matching parameters
• Remove all deprecated classes
• Make tm and salt correction methods into enums (rather than string constants) (see this discussion) in the Thermo class
• Remove as many of the checked in FASTAs, VCFs, and related files as possible
• Update prymer.yml
• Ensure all major classes/modules have good docs and examples