Error installing on python 3.11 on Windows and running moduleEigengenes

[dmitriikamaevqia]

Hi, I cannot install the package on windows with python 3.11. There are some problems with installation old pandas version. Is there a reason you pinned pandas version?

Additionally, I tried to unpin pandas version and installed the package from source. Then I encountered an error running Quick Start.ipynb

I believe in wgcna.py inside moduleEigengenes function covEx[not np.isfinite(covEx)] = 0 should instead be covEx[~ np.isfinite(covEx)] = 0

Also to support new pandas version append on dataframe should be replaced with concat around line 1979

tmp = pd.concat([tmp, pd.DataFrame(v[0:min(n, p, nVarExplained), :],
                                              columns=tmp.columns.tolist())])

utils line 129: geneInfo = pd.concat([geneInfo, pd.DataFrame.from_records([dict])])

[nargesr]

Hi,

I haven’t had a chance to update the package to be compatible with newer pandas. It's on my to-do list but might take a while.

if you can downgrade your Python version, I think you should be fine with the older Pandas version. Meanwhile, I'll try to update it to a new version.

[zijunmeng]

Hi,

I haven’t had a chance to update the package to be compatible with newer pandas. It's on my to-do list but might take a while.

if you can downgrade your Python version, I think you should be fine with the older Pandas version. Meanwhile, I'll try to update it to a new version.

could u update PyWGNA as soon as possible, the installation of pywgcna was excruciating. Don't submit any more unimportant updates.

[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 get any error