Implement toehold-mediated strand exchange (TMSE) circuits as a "companion module"

[murrayrm]

This is a tracking issue to discuss the implementation of toehold-mediated strand exchange (TMSE) circuits in BioCRNpyler. Rather than incorporate this directly into the library, we are going to try to use this capability to figure out the right way to implement "companion modueles" where there is separately retained repository that has components, mechanisms, and mixtures, but it is easily integrate with BioCRNpyler.

[zjuradoq]

As a next step, we are moving forward with the "companion module" architecture to keep the core BioCRNpyler library lightweight while allowing for domain-specific scale.

The toehold-mediated strand exchange (TMSE) circuits repo is now available at:
https://github.com/usnistgov/TMSE_BioCRNpyler_Library

This repository will act as our blueprint for how companion modules should interact with the core codebase. To track the progress of this integration, I've broken down the remaining work into the following action items:

1. Repository Setup & CI/CD

• Initialize standalone repository for the TMSE companion module.
• Configure pyproject.toml with biocrnpyler and bioscrape (for simulation) as strict dependencies.
• Set up GitHub Actions to run tests against BioCRNpyler's main branch to catch breaking API changes early.

2. Interoperability & Validation

• Documentation: Draft a "Companion Module Guide" in the Developer Notes so future developers can replicate this architecture.
• Documentation: Add a section to the ReadtheDocs listing available companion modules.