I commented on this line previously, but it must have been hidden (and only easily viewable via email) because the comment was on an outdated diff. Pasting my latest comment here so that this isn't forgotten:

Bonferroni is already very conservative, and I think we should be consistent in how we are calculating corrected p-values (e.g., compare_taxa_summaries.py and compare_alpha_diversity.py only take the successful tests into account when correcting for multiple comparisons). Given the number of forum posts that we get about these statistical tests returning None, it seems like this case is hit pretty often by our users. I think it's important to fix this.