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biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis
BSD 3-Clause "New" or "Revised" License
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qiime2-2020.8 and songbird-1.0.3 unsatisfiable #144

Closed AbhishakeL closed 3 years ago

AbhishakeL commented 3 years ago

It seems songbird-1.0.3 needs numpy<1.19.0,>=1.16.0 but qiime2-2020.8 needs numpy=1.19.1 and thus version conflict is not letting installation. Is there a way around here?

mortonjt commented 3 years ago

Hi @AbhishakeL , thank you for reporting. This is a known problem as highlighted below https://github.com/biocore/songbird/issues/126

The problem isn't with numpy, its with Tensorflow. The full error message you would get if you tried to install tensorflow 1.15.4 in qiime2 is tensorflow 1.15.4 requires numpy<1.19.0,>=1.16.0, but you'll have numpy 1.19.1 which is incompatible.

Unfortunately, there is not much we can do without a rewriting the entire package -- tensorflow 2.0 is incompatible with our current code base. We will be ditching tensorflow in the next version of songbird, but in the meantime the solution is to install songbird in a qiime2 environment with qiime2-2020.6 or earlier.