Documentation for the web

This section collects guidelines and examples for writing MolSysMT’s web documentation with MyST and Sphinx. It is aimed at contributors who edit the User Guide, Showcase, Cookbook, and developer documentation.

• Use myst.ipynb to see concrete examples of MyST admonitions and how to structure tutorial notebooks.

• Use references.md as the reference for cross-links between pages and API objects (labels, {ref}, {func}, {class}, etc.).

• MyST in MolSysMT documentation
  • Recommended admonitions in MolSysMT
  • Default MyST admonitions
• References and Cross-links in Documentation
  • Section labels and {ref} roles
  • Page-level labels for tutorials and recipes
  • API references: {func}, {class}, and friends
  • File-based links (when they are acceptable)
  • Cross-linking between major sections
  • Migration notes and legacy links