Qiyun Zhu

@rgommers Thanks for the clarification! Is my understanding correct that if biom-format or scikit-bio is built against numpy>=2.0.0rc1, it will be compatible with both numpy 1.x and numpy 2.x. Therefore,...

@wasade @jakirkham We recently [removed hdmedians from](https://github.com/scikit-bio/scikit-bio/pull/2004) scikit-bio's dependencies. It won't be an issue in the next release.

@adswafford Perhaps there are multiple mapping files with conflicting hierarchies. For example, protein-to-gene and protein-to-enzrxn cannot be supplied simultaneously (at least not for now). Can you please provide the full...

@adswafford I figured out what was the problem. This ID `RXN-12373` is found both as a reaction and a pathway, which is confusing to the program, and it doesn't make...

@adswafford I have fixed the file `reaction2pathway.map`. I hope this is going to work now!

I also noticed and simply removed all these "RXN" values. Hope this time the file is good to go!

Hello @angelovaag thanks for your interest in our program. I think the issue is most likely due to the simultaneous use of taxonomy and phylogeny. Woltka allows combining heterogeneous classification...

@angelovaag This "phylogenetic profiling" is something we are still studying. The basic rationale is that we can use nodes instead of tips to represent components of a microbiome. Whether this...

Hello @ElDeveloper Thanks for reporting this issue. I check the data files and found that it is because some MetaCyc entries have conflicting rank assignments. For example, "RXN-12373" is defined...

@ElDeveloper That would be great. Thank you! I envision that Woltka's classification system needs an upgrade to make things more flexible (i.e., one classification unit identifier can be assigned to...