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OpenTreeOfLife / germinator

miscellaneous scripts and data for concerns that span more than one of the Open Tree code repositories: integration tests, system statistics, etc.
BSD 2-Clause "Simplified" License
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remove annelids from monophyly tests #112

Closed mtholder closed 7 years ago

mtholder commented 7 years ago

The contesting of annelids by an input to synth 7.0 later appears to be legit. I think we decided that we'd move to a "warnings.csv" for taxa to warn about. I can't recall. w/o this change, propinquity reports an error in the assessments run.

jar398 commented 7 years ago

I think I removed the test because it is not clear what an annelid is, and depending on what you think the circumscription is, the group might actually be monophyletic or not, with evidence both ways. That makes it interesting, but not a very good test of anything.

The issue title suggests that someone thinks that it is a bug (so to speak) that there is no annelid monophyly test. If you think there should be one, can you tell me whether myzostomida is in annelida?

mtholder commented 7 years ago

sorry for the title confusing you. No, I removed annelids from the test so that the propinquity build would pass. I'm requesting that we merge this to master (for the reasons that you mention about myzostomids)

jar398 commented 7 years ago

Ah. Was reading in gmail and didn't realize this was a PR. I have many updates to inclusions.tsv, made during preparation of OTT 2.10, which include removing the annelid test. I will make a PR for those changes.