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Tests fail because Rhea SPARQL endpoint is temporarily down. The rest works fine. |
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Besides making tests parallel and running shared code once, here a benchmark against humann (uniref -> ko) and omixer (ko -> gmm) is added. For the latter, coverage matches (except for omixer bug for comma-separated entries) but abundance differs due to different estimation method (agglomerateByModule sums, while omixer maximises pathway abundance).
Also, some polishing done to weave functions.