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In Drupal 7, in order to activate Honeypot for an individual form, you need to use the hook_form_alter() function From the Honeypot author:

in Drupal 7, I think my recommendation would be to use a custom module to add Honeypot to any of the forms you're interested in, or to do something like add a field to Webform nodes that's a 'Honeypot enabled' checkbox, then add the protections based on whether that checkbox is checked.

In Drupal 8, the integration is baked into the Webform module itself.