edit_distance_align() in distance.py gives wrong alignment path when substitution_cost is greater than 2

[yzhaoinuw]

When setting substitution_cost in edit_distance_align() to a value greater than 2, it still gives a alignment path that includes substitutions. This is incorrect because with a substitution cost greater than the sum of a deletion followed by an insertion, substitutions are essentially inhibited and thus shouldn't be included.

This issue is brought up by @yzhangcs in this comment as a follow-up to #3017. I submitted a pull request #3180, but it failed two checks although it seemed to have passed the checks when I ran pre-commit.

@tomaarsen and @stevenbird, you approved my earlier pull request #3017. Could you provide some insights on this issue? If #3180 addresses the issue, could you please provide pointers on how I can get it to pass all the checks?