Best way to structure article and issue relationship for CPT

I think the easiest way would be like this:

  • Custom Taxonomy Issue
  • Custom Post Type Article

You can add custom fields to Taxonomies like described here:
https://pippinsplugins.com/adding-custom-meta-fields-to-taxonomies/

This way, you get the relation between articles and issues, you can add information about the issue by the custom taxonomy fields, and you can use the taxonomy archive for displaying one issue.

Happy Coding,

Kuchenundkakao

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