numpy 2 breaks the int-encoding representation of the BP tree #562
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fedarko
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Ideally we would test this on numpy v2, but I can't seem to get empress running with numpy v2 on my system (get a cython error from iow). in any case this should address the problem
fedarko
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As documented in #561.
As far as I can tell, there are two possible solutions:
numpy < 2empress.tools.shifting()to convert all bits in the inputbitlisttointobjects, rather thannp.uint8objectsFor the time being, the first option is easier. But I imagine QIIME 2 will eventually move to using numpy 2, which will mean we'll have to go with the second option. (For reference: the latest release of Q2, 2024.5, uses
numpy=1.26.4-- which is literally the latest numpy version before the 2.x versions.)Option 2 isn't really that bad -- I think just adding
bitlist = [int(x) for x in bitlist]to line 3 ofshifting()would fix the problem.The text was updated successfully, but these errors were encountered: