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harrispopgen / mushi

[mu]tation [s]pectrum [h]istory [i]nference
https://harrispopgen.github.io/mushi/
MIT License
24 stars 6 forks source link

alternatives to prox-tv dependency #59

Closed wsdewitt closed 2 years ago

wsdewitt commented 4 years ago

Prox-tv is great, but seems not to be under active development (albarji/proxTV#59), so it might be good to think about alternatives. As is, we're stuck at Python3.7 due to the lack of Python3.8 wheels for prox-tv albarji/proxTV#56.

kamdh commented 4 years ago

Could fork and regenerate py3.8 compatible I guess...

kamdh commented 4 years ago

Last I checked proxtv was the best option for this kind of package

wsdewitt commented 2 years ago

The 3.7 constraint is now creating friction in adoption of mushi.optimization in another project that requires 3.8. I plan to (at some point) write a JAX implementation of algorithm 1 from this paper (which is cited in the prox-tv docs), and compare performance to prox-tv.

wsdewitt commented 2 years ago

Reopening because, although this works for pip install from the GitHub package, a simple pip install mushi still doesn't work due to pypi disallowing direct git dependencies (the pypi deploy fails).