Since updating to the newest version

Do you happen to recall what version(-ish) you upgraded from?

Any suggestions on what might be causing this?

Hmm, I'm not having any luck reproducing this (Emacs 25.3, GNU/Linux).
Starting with point in front of "message", TAB indents it four spaces.

You could try debugging snakemake--calculate-indentation,
particularly

That should return the value of snakemake-indent-field-offset (4 by
default).

I did upgrade a bunch of things at once, of course, so the cause might be somewhere else.

You could also try testing with emacs -Q, and then just loading
snakemake-mode and its dependencies (dash, magit-popup).

If you have a local clone of the repo, running make test would tell
you if the indentation tests (ran with emacs -Q) are passing for you.

What version of Emacs are you using?

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