How about promoting the warnings to errors and catching them in the exact spots where you've seen these warnings popping up? This would be much more explicit, though I'm not sure how much work it would require to put this in place. See [this](http://stackoverflow.com/a/14822364) post for a context manager that can handle this (pretty elegant IMHO).

While ignoring the warnings using ```seterr``` won't change the computed values, it masks all "invalid" warnings from developers. This could lead to situations where a certain comparison/operation isn't correct or working as the dev expects, but it isn't noticed by the dev or users because it is suppressed. Also, if we change numpy versions and behavior changes from what it currently is, we won't be aware of (potentially useful) warnings that might arise from new/different parts of the code.