Thanks to this post by @anthonyfok, I can now override the theme specified in the config file by setting the environment variable HUGO_THEME
in netlify.toml
[build]
publish = "exampleSite/public"
command = "cd exampleSite && hugo --gc --themesDir ../.."
[build.environment]
HUGO_VERSION = "0.53"
HUGO_THEME = "repo"
HUGO_BASEURL = "https://vanilla-bootstrap-hugo-theme.netlify.com/"
Edit: use HUGO_BASEURL
env var per tip from @kaushalmodi