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pepkit / pipestat

Pipeline results reporting package
https://pep.databio.org/pipestat/
BSD 2-Clause "Simplified" License
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Pypiper + pipestat: minimal dependencies set #143

Closed vreuter closed 8 months ago

vreuter commented 8 months ago

Hello @donaldcampbelljr it seems like there's been optionality added to SQL-related (and perhaps other dependencies). Can you advise now on the versions and installation syntax to get the bare minimal set of dependencies needed to use pypiper? This would allow me to update from pypiper 0.12.3 to 0.14.0. In particular, I guess pypiper 0.14.0 --> pipestat >= 0.6. Looking at the setup.py, it seems like this will avoid pulling the SQL-related dependencies, using only requirements-all.txt.

My questions are...

  1. Is the above description/assessment right?
  2. If so, is it stable to use pypiper (not calling anything from pipestat directly), without the SQL dependencies? Asking b/c of #116

Thanks in advance!

donaldcampbelljr commented 8 months ago

Hey @vreuter, Yes, your assessment is correct. Pypiper should only install the base pipestat package without SQL dependencies. And it should be stable to use as Pypiper is using pipestat to report to a file backend.

vreuter commented 8 months ago

Cool, thanks @donaldcampbelljr !