Sonny Software

My Bookends Tools for Alfred includes a couple of actions that almost do what you want. For example I have an action that can take a selected Bookends unique id from a temp ref and search for it in Bookends with one key binding, using this fairly simple applescript underneath which copies selection ...

Thanks Jon; interestingly I still see the jats tags with the DOI I sent, some sort of regional server difference or something...

Hi Jon, <jats> tags are sometimes present when I use Quick add... which uses Crossref , for example for this DOI [10.1126/sciadv.abm2219] Bookends calls crossref and you can see from the API you use the abstract is wrapped in <jats:p> tags (I use the jq command to show just the JSON abstract field):...

Crossref does have some delay for new articles. This drives me crazy, and I end up with just adding these shiny baby DOIs to a temporary note and every so often importing them after a week or two.

I also would like a regex replace. As an example, jats XML litters my abstracts and while Zotero seems to be able to strip this XML out, Bookends doesn't so I have a bunch of <jats:p> / </jats:p / <jats:title> etc. in abstracts. I could go through each tag and manually find/replace, but regex's supe...

is it just me, in my madness? Madness? I concur! :P If you are using markdown, why are you not using Pandoc's CSL citeproc engine instead of the [clunky] document scanning? Bookends can output [@citekey] Pandoc citations, and Bookends + Markdown + Pandoc yields a robust and fully automated output w...

Having made my own CSL and Bookends styles, I much prefer Bookends format manager! The CSL editors I tried are less intuitive, and the CSL XML spec, while comprehensive, takes more time to understand. Writing a converter is a non-trivial task, each system represents the underlying data in different ...

The braces make the bib file look dirty. Furthermore, it will mess up bibliographies that want a specific type of case on the references. Bibliography styles are made for this purpose. One can have all in caps, all in small, or in title case outputs in the Latex from the same bibliography file usin...

My personal preference would be for CamelCase without hyphens, semicolons or underscores, I'm not quite sure what advantage making citekeys longer (even if just by 1 character) has?

A related API that will be invaluable is for Pubpeer; Zotero already has support but a more general API is apprently available: https://pubpeer.com/static/faq#33

Endnote has just added a tool to check for whether a paper has been retracted when you are citing it (in their CWYW tool). Zotero, Papers and a few others have already supported checking for retractions for some time. There are several sources of this data. Zotero, Papers, Endnote etc. are apparentl...

Do you and any others reading this think it would be useful if Bookends surrounded any words in this list that begin with a capital letter in curly brackets? In such as case, if Shaddai and Abram were entered in preferences you'd get {The Names {{Shaddai}} and {{Abram}}}. In my script to do this po...

I personally don't have any requirement or preference (I prefer to use a single library and authoryear works well for me). But I thought I would at least add some comments about other attempts for cite key generation for context. Papers (I think before they were assimilated by the Borg, um I mean ac...

What you want is not possible within Bookends AFAIK, and Jon would hopefully be able to say if this would be possible. However, shouldn't it be the job of the system that creates the bibliography to respect your title case? For my use (biology) where terms must be enforced wether the rest of the tit...

Just delete the file; Bookends appears smart enough that if the file disappears then the menu changes and you can create the sync file again...