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computer-aided-biotech / better-cb

A compendium of tools for (better) computational biology.
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Change in citation syntax in latest rootstock version #19

Closed dcsoto closed 3 years ago

dcsoto commented 3 years ago

@BenjaSanchez there was a change in how to write citations. For example, websites should be written as: @url:https://somewebsite.com, and PubMed IDs changed from "pubmed" to "pmid".

Check the changes here: https://github.com/manubot/rootstock/blob/b422130eb46ea5d188779910772192730d79b172/USAGE.md

BenjaSanchez commented 3 years ago

@dcsoto I get a 404 error when I open that link, but the usual style @https://somewebsite.com and @pubmed:26158728 works for me... I get the exact same output regardless of those options or @url:https://somewebsite.com and @pmid:26158728. Perhaps you are looking at an old version of the usage file? The current one proposes @https://somewebsite.com and @pubmed:26158728 as current formats:

https://github.com/manubot/rootstock/blob/master/USAGE.md#citations

dcsoto commented 3 years ago

Sorry, I fixed the link! Indeed, it's an older version. But the reason why I dived into this was because the "newest" syntax was not working with the most recent version of rootstock in my Mac 🤷‍♀️
But both syntax seem to pass the CI checks, so np!

BenjaSanchez commented 3 years ago

oh, did you eventually manage to make it work locally? If not, consider opening an issue at https://github.com/manubot/rootstock