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[BUG] DeseqDataSet.deseq2() still prints when quiet=True is set

Open yihming opened this issue 8 months ago • 4 comments

Describe the bug

My following code

from pydeseq2.dds import DeseqDataSet
from pydeseq2.default_inference import DefaultInference

inference = DefaultInference(n_cpus=1)

dds = DeseqDataSet(counts=..., metadata=..., design_factors=..., inference=inference, quiet=True)
dds.deseq2()

still prints the following 3 sentences when quiet=True, while from the source code they should be controlled by quiet parameter:

Fitting dispersions...
... done in 0.20 seconds.

Fitting MAP dispersions...
... done in 0.22 seconds.

Fitting LFCs...
... done in 0.17 seconds.

To Reproduce

This case happens for some data, not all. However, my case uses internal data, so I may have to do some anonymization work before sharing it with you.

Expected behavior

These sentences should not be printed if quiet=True is set.

Screenshots

Already shown above.

Desktop (please complete the following information):

  • OS: Ubuntu 22.04.4 LTS
  • Version: pydeseq2 v0.4.9

Additional context Add any other context about the problem here.

yihming avatar Jun 09 '24 23:06 yihming