bibentry does not correctly export to latex

[uliw]

the following statement in my org file

bibentry:&yao-2020-revis-seawat

results in this latex code:

bibentry:\&yao-2021-quant-pyrit

rather than

\bibentry{&yao-2021-quant-pyrit}

not sure how to go about this

[jkitchin]

I can't reproduce that error. It sounds like you don't have a bibentry link defined, but it should be defined here https://github.com/jkitchin/org-ref/blob/master/org-ref-citation-links.el#L796.

That suggests maybe org-ref is not getting fully loaded?

[uliw]

possibly, or the export function. is there a way to track this down?

[jkitchin]

You can check the export function like this

#+BEGIN_SRC emacs-lisp
(org-link-get-parameter "bibentry" :export)
#+END_SRC

#+RESULTS:
: #[128 "\302\300\303\301\"\"\207" [org-ref-cite-export ("bibentry") apply append] 6 "
: 
: (fn &rest ARGS2)"]

[uliw]

I added this to the org file, and exported the file to latex. But there is no output

[jkitchin]

this would just tell you what the export function is, it wouldn't change the export. If you get nil, it may mean there is no bibentry link defined.

you can see the links that are defined with

#+BEGIN_SRC emacs-lisp
(mapcar 'car org-link-parameters)
#+END_SRC

[uliw]

no bibentry in the output from this function. I tried to start with a minimal settings.el to exclude the possibility of a botched configuration, alas, the result is the same. I am running on emacs 28, but that should not really matter?

[jkitchin]

I guess this means that org-ref-citation-links is not getting loaded. I don't know why that would be the case though. if you open that file and eval it, presumably every thing works?

[uliw]

the file executes with no errors, and org-ref-cite-types shows the bibentry entry upon loading an org file. Could it be that this has to do with the export machinery?

[jkitchin]

after you run that (load the file), you can see bibentry in the output of (mapcar 'car org-link-parameters)?

You can run this block:

#+BEGIN_SRC emacs-lisp
(org-link-get-parameter "bibentry" :export)
#+END_SRC

and see that an export is defined,

and it still does not export?

[uliw]

1) go to org-ref-citation-links.el, load test.org, execute the above code: No bibentry in output 2) load test.org, go to org-ref-citation-links.el, execute the above code: No bibentry in output

[jkitchin]

can you check that bibentry is defined in your org-ref-citation-links.el? Maybe you have an older version.

[uliw]

indeed! There is no code for bibentry. The only mention is

(defcustom org-ref-cite-types
  (append
   org-ref-natbib-types
   org-ref-biblatex-types
   org-ref-biblatex-multitypes
   ;; for the bibentry package
   '("bibentry" "Insert the bibtex entry"))
  "List of citation types known in `org-ref'."
  :type '(repeat :tag "List of citation types (type description)" (list string string))
  :group 'org-ref)

I assume that org-ref is installed as part of the scimax install script, and as such does not appear as an installed package when calling package-list-packages. On the other hand, calling update-scimax, appears not to update org-ref. Probably best to install scimax as git clone?

[jkitchin]

That is mostly on me. I didn't realize you were using scimax as the update mechansim for org-ref. I just pushed a version bump commit on scimax for org-ref. that might do it for you.

[uliw]

the straightforward update did not work (some errors that branch is out of sync). Reinstallation did the trick though

[uliw]

As a follow-up. A fresh installation via git clone, complains about missing dash-functional, but dash functional now states that it is obsolete and absorbed in dash. After installing dash-functional, things work as expected

[jkitchin]

that seems to be something in ob-ipython. Probably this summer I will remove this from scimax, in favor of emacs-jupyter.

[uliw]

indeed! There is no code for bibentry. The only mention is

(defcustom org-ref-cite-types
  (append
   org-ref-natbib-types
   org-ref-biblatex-types
   org-ref-biblatex-multitypes
   ;; for the bibentry package
   '("bibentry" "Insert the bibtex entry"))
  "List of citation types known in `org-ref'."
  :type '(repeat :tag "List of citation types (type description)" (list
string string))
  :group 'org-ref)

I assume that org-ref is installed as part of the scimax install script, and as such does not appear as an installed package when calling package-list-packages. On the other hand, calling update-scimax, appears not to update org-ref. Probably best to install scimax as git clone?

On Mon, Mar 21, 2022 at 10:34 AM John Kitchin @.***> wrote:

can you check that bibentry is defined in your org-ref-citation-links.el? Maybe you have an older version.

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[jkitchin]

the version of org-ref is pinned in scimax, so it wouldn't change from update-scimax if it was already at the latest version. Maybe there is some funny git business that is making it not update.

You should see code here: https://github.com/jkitchin/org-ref/blob/ec449195438f815698241f0b01a5395221b3306e/org-ref-citation-links.el#L796 that defines the bibentry link.

I think you can delete the org-ref directory, and clone the current version (which is ahead of scimax) and then I guess it should work.

[uliw]

upps., not sure what happened here. I did not comment after closing this in March. Must be a github hickup