@Cadair - this is water under the bridge now, but you don't even need to commit, just need to build the docs locally without admitting to the crowd that looks at your travis that you brake something ;)
@bsipocz - in astropy/astropy-helpers#224 you mentioned “I tried to catch the warning there and ignore it, but it didn't work” - can you explain how you tried? (I have some ideas but want to make sure I don’t just try the same thing you did…)
and also tried to hack sphinx, by adding another option to the config, but that didn't work out either (I could only see the default config values in that method, etc), so I just opened an issue at their issue tracker.
Either way after spending a couple of hours trying to fix it, I gave up.