Pandas versions should be pinned to be below v1

biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis

BSD 3-Clause "New" or "Revised" License

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Pandas versions should be pinned to be below v1 #117

Open fedarko opened 4 years ago

fedarko commented 4 years ago

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.

ElDeveloper commented 4 years ago

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.

mortonjt commented 4 years ago

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.

fedarko commented 4 years ago

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