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phylotastic / datelife

R package containing datelife's core functionality
http://phylotastic.org/datelife/
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add score to hard-coded Mus #83

Closed fmichonneau closed 1 year ago

fmichonneau commented 1 year ago

Hello,

I'm preparing a new release for rotl which includes a "breaking change". The output of the the tnrs_match_names now includes a new column called score. When there are multiple matches in OTL for a taxon, tnrs_match_names always returns the taxa with the highest score.

Given that the datelife code hardcodes the format of the tnrs_match_names output, I included this score for the Mus.

With this fix, the vignettes now build but I haven't tested if there are other side effects.

Thanks!

LunaSare commented 1 year ago

Thanks for the pull request @fmichonneau! the tests are failing now, but it's because the new rotl is not released yet, I'll be on the lookout.

I'll check if there are any other places that could be affected by the new score column. Also, we might not need to hard code Mus no more. I'll investigate.

fmichonneau commented 1 year ago

Thanks @LunaSare. I updated the PR slightly to accommodate older rotl versions. The alternative would be to add rotl >= 3.1.0 in your DESCRIPTION. I'm going to submit rotl 3.1.0 to CRAN today.

fmichonneau commented 1 year ago

rotl is now on CRAN so you can expect a message from them asking for a new datelife submission soon. Thanks!

LunaSare commented 1 year ago

Thanks @fmichonneau! This is a very clever fix. I'll pull your changes, we just need to change the version number to character in the comparison if (packageVersion("rotl") >= 3.1.0, because version numbers are not really numeric, so the "larger than or equals to" comparison fails. This will do if (packageVersion("rotl") >= "3.1.0" I received the message from CRAN, so I can do that!