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Published 20 hours ago • verified publisher icon biocore

Pandas versions should be pinned to be below v1

Open fedarko opened this issue 5 years ago • 3 comments

This is causing problems with the standalone songbird installation instructions. Easiest solution is just modifying this part of the README to specify the pandas version, ideal solution is modifying the setup.py/conda requirements/conda-forge dependencies to enforce this.

fedarko avatar Feb 21 '20 22:02 fedarko

This might not work well with newer versions of QIIME2 since the move to 1.0 is happening (as far as I can tell) as of the next version.

ElDeveloper avatar Feb 21 '20 22:02 ElDeveloper

Agree @ElDeveloper , we will need a better solution for that.

Not clear to me where the dep issue arise from (other than the one spotted in biom). Will need to dig into this.

mortonjt avatar Feb 21 '20 22:02 mortonjt

Oh dang, in the February 2020 release? I think that might break a few third-party plugins -- I know Qurro at least will also explode.

@mortonjt I think the problem is due to the use of SparseDataFrame / SparseSeries rather than the new-style pandas sparse data structures -- this is why Qurro will explode on pandas 1, and an error about SparseSeries was what broke Songbird on barnacle for @vjcantu and I today

fedarko avatar Feb 21 '20 23:02 fedarko