A. Murat Eren (Meren)

You are the best, Florian! Thank you for providing an example here and helping Mete with this :)

Thank you very much for looking into this, @Ge0rges. I'll take a look and see if I can come up with a workaround for this. The current version of sklearn...

Since you were able to do the downgrade, it means the environment is stable. If this version breaks something, you will certainly notice that :) I think you're good.

This is weird. Under no circumstance a change in scikit version number should cause an error in the threads module of Python. Probably these two things are independent :( But...

I agree. Since we are no longer doing a lot of genome binning in the lab, those parts of the code and documentation is at the mercy of those who...

Thank you @Ge0rges. I updated the installation instructions. Now there is a little note that looks like this: 

I'm afraid there is a problem with the internal genomes system. While we hope to address this soon, you can continue your analysis by using the program `anvi-split` to get...

We used to solve similar situations with migration scripts that add new keys with None values. Perhaps that would be a better way to do it to ensure it is...

Oh! Sorry for missing that! I wonder if there was a manual update of versions in the SQlite database :p

For posterity, I see it here that it is indeed required to be a part of any contigs-db that is *upgraded* to `v21`: https://github.com/merenlab/anvio/blob/master/anvio/migrations/contigs/v20_to_v21.py But is the variable also set...