Dependencies requiring updates (pandas and pyvis)

[GentlemanOfFate]

Hi, PyWGCNA developers,

Thanks for creating and maintaining this package, it's really a relief to finally see the pythonic implementation of WGCNA. However, I've found a couple of drawbacks when running it, which I'll split into a couple of issues.

First of all, the pandas used in the package (v1.4.4) is very outdated, I'd really recommend you update it to >2.0.0, there are a lot of great features that can't be accessed in the same environment where PyWGCNA is.

Secondly, the pyvis module appears to be installed in a wrong way: pip automatically reaches for the latest version (0.3.2), but this version seems malfunctioning, because running the WGCNA.CoexpressionModulePlot() function results in the error that comes not from PyWGCNA, but from the pyvis itself (it occurs at the net.show(f"{self.outputPath}figures/network/{file_name}.html") step). If I manually do pip install pyvis==0.3.1, the error is gone, and the rest works as it should. So I'd really recommend setting it like that in the dependencies.

Hope these suggestions will make it an ever better package!

[nargesr]

Hi,

I just released a new version(2.0.0) which is compatible with Pandas > 2.0.0

Please feel free to reopen this issue if you face any error

[tanush84]

After installing the new version, PyWGCA Version 2.0; The issue with pandas is still indicated. I tried to install both Pandas 1.5.3 as well as 2.1.2, but in both cases it displays error as below:

ModuleNotFoundError: No module named 'pandas' Kindly assist.

[nargesr]

@tanush84 please answer questions in #79