search

Starlitnightly / omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
https://starlitnightly.github.io/omicverse/
GNU General Public License v3.0
479 stars 58 forks source link

pydeseq2 version conflicts with omicverse 1.6.8 #200

Open pandaqiuqiu opened 3 weeks ago

pandaqiuqiu commented 3 weeks ago

When running the following code in omicverse:

import omicverse as ov print(f"omiverse version: {ov.version}") ov.ov_plot_set()

I encounter a dependency error:

Version: 1.6.8, Tutorials: https://omicverse.readthedocs.io/ omiverse version: 1.6.8 Dependency error: (pydeseq2 0.4.12 (e:\software\miniforge3\envs\omicverse\lib\site-packages), Requirement.parse('pydeseq2<=0.4.0,>=0.3'))

Attempting to downgrade pydeseq2 to version 0.4.0 results in another error:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. omicverse 1.6.8 requires pydeseq2>=0.4.1, but you have pydeseq2 0.4.0 which is incompatible.

There seems to be a version conflict in omicverse's dependency on pydeseq2. omicverse version 1.6.8 specifies pydeseq2>=0.4.1 but simultaneously requires a version within 0.3 <= pydeseq2 <= 0.4.0.

Could you clarify which version of pydeseq2 is compatible with omicverse 1.6.8, or suggest a workaround for this dependency conflict?

Thank you!

Starlitnightly commented 3 weeks ago

The dependency error can be ignored: (pydeseq2 0.4.12 (e:\software\miniforge3\envs\omicverse\lib\site-packages), Requirement.parse('pydeseq2<=0.4.0,>=0.3'))