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Make _commutes_ consistent (quantumlib#5217)
- Requires atol to be a named parameter. - Also changes atol to be uniformly float around the codebase. (not sure why it would be int, are people using an atol=1?) - Technically a breaking change, but it's unlikely people are using this widely as most commutes do not even use atol. Fixes: quantumlib#3695
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