What do you think about org-ref V3?

Hi all!

Today, the new org-ref version 3 was released (GitHub - jkitchin/org-ref: org-mode modules for citations, cross-references, bibliographies in org-mode and useful bibtex tools to go with it.).

Besides some changes in the configurations, the most prominent is the use of & instead of @ (used by org-cite) to cite references.

Here it is a comparative of the formats

  • org-ref => [[cite:&my-key]]
  • org-cite => [cite:@my-key].

My daily work is based in org-roam and org-roam-bibtex thus I’m a little confused if I should use org-ref or change to org-cite.

For the moment, I pinned org-ref to version 2, to avoid breaking something with ORB.

What do you think about those changes?
What do you think org-roam and org-roam-bibtex should use in the long term?

Thanks.

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OR3 basically reimplements the (better) org-cite citation model in a new and non-standard syntax, and adds it as a preferred option alongside the earlier org-ref link citation syntax.

You can see his explanation for why he did this, and my reply, here:

I think it will lead to years of needless confusion and fragmentation for users and developers.

So, for example, the OR devs will now have to figure out if they want to support three different citation syntaxes, and which to prioritize.

My strong preference is org-cite, since it’s very well-designed, is highly-modular, and is built-in.

But I’ve never really used org-ref much. If you have a ton of legacy org-ref documents, and you rely heavily on its features beyond citations (cross-references and such), then you might as well continue to use it, and maybe experiment with org-cite?

I’m personally hoping to see a more flexible and modular ecosytem of org-cite libraries develop over the next year or two.

Thanks @bruce for your response.

I read the discussion in the org-ref issue tracker, and I agree with you that it will be a lot of confusion between the 3 formats.

I’m the regular Joe Doe user, and in terms of usability and stability, I prefer something consistent across the time.

At least for me, I think that I will keep using org-ref V2 for a while and try to convert all my references to org-cite (I hope your biblio module in doom gets merged soon).

Just one last question. In what cases, org-ref is superior to the built-in tools in org-mode for cross-references?

Thanks.

You can play with the built-in tools yourself; for example [[tab-1]] is a cross-reference, that will export to latex, etc.

But unlike org-ref, there’s no easy insertion (for example nothing like M-x org-crossref-insert), or other functionality attached to those links.

This new package does allow one to just use the org-ref cross-reference features without loading the rest. Just wish it were distributed as a separate melpa package.

Thanks again @bruce. Your reply was very informative.

If I understood correctly, the only missing piece to make ORB completely functional with org-cite is to solve this issue Add org-cite support · Issue #191 · org-roam/org-roam-bibtex · GitHub, isn’t ?

Depends what you mean by “completely functional”.

OR supports OC now.

If you use oc-bibtex-actions you get pretty robust functionality in org, and so also in OR.

That works out-of-box with OR notes without need for ORB. Or, per that post, you can use the ORB note function instead.

I’m not really sure what is missing at this point actually. What else do you need?

For example, with org-ref if I have a citation, by just pressing “ENTER” I get a prompt to select “Add notes” and it triggers the org-roam capture template for this reference

For org-cite if I press “ENTER” over the cite, I got an error in the minibuffer

Following your PR in doom, I copied this in my config:

(after! org
  (require 'oc)
  (setq org-cite-global-bibliography '("~/Dropbox/home/documents/org/roam/_library.bib"))
  (map! :map org-mode-map
        :localleader
        :desc "Insert citation" "@" #'org-cite-insert)

  (setq org-cite-export-processors
        '((latex biblatex)
          (t csl))))


(use-package! oc-bibtex-actions
  :when (featurep! :completion vertico)
  :after oc
  :demand t
  :config
  (setq org-cite-insert-processor 'oc-bibtex-actions
        org-cite-follow-processor 'oc-bibtex-actions
        org-cite-activate-processor 'oc-bibtex-actions
        ;; The activate processor relies on shift-select, so we set to t.
        org-support-shift-select t))

And now with SPC a I can trigger embark-act and get this menu

But if I select “open notes” another error appears

For the moment, I can’t figure it out how to trigger the org-roam's template system to create a note with my citation. The idea is this new note has the property :ROAM_REFS: @Hastie1990.

For sure, I am missing something in my config, but I don’t know.

Thanks.

Did you do set bibtex-actions-file-open-note-function, or leave it default?

By default, it should (does on my system) open the new or existing note; here’s what a new one looks like:

image

It doesn’t include :ROAM_REFS: line ATM, though I’ll figure that out (probably add a dedicate OR function).

If you want to use ORB there instead, you need to do:

(setq bibtex-actions-file-open-note-function 'orb-bibtex-actions-edit-note)

If this doesn’t help, you might post an issue on the bibtex-actions tracker?

I tried bibtex-actions-file-open-note-function with the default value bibtex-actions-file-open-notes-default-org and with orb-bibtex-actions-edit-note and nothing works for me.

I will fill the issue in the ORB github.

Thanks for all the help.

Sorry; I meant the bibtex-actions repo.

@maikol I haven’t had a chance to start using new org-cite citations yet but I just tried it and it works well with Bibtex-actions and ORB. Both opening the existing notes and creating new ones works as expected with ORB properly expanding Org-roam templates. Note that :ROAM_REFS: will still use the old Org-ref cite:link syntax though.

This error looks to me as what we discussed with @bruce some time ago when the internal data structures used in Bibtex-actions had changed their signatures. ORB has introduced the dedicated function orb-bibtex-actions-edit-note to be used with bibtex-actions-file-open-note-function to play nice with Bibtex-actions. Typically you don’t have to do anything, just enable org-roam-bibtex-mode as usual. I believe you just have to upgrade either Bibtex-actions or ORB or both to the latest state, otherwise the mismatching versions will cause this error.

@bruce I noticed that bibtex-actions-open-notes would refuse to open a note if bibtex-actions-notes-paths is set to nil throwing the following warning:

bibtex-actions-open-notes: You must set ’bibtex-actions-notes-paths’ to open notes

Conceptually, I would expect bibtex-actions-open-notes to be less strict. Since an external function for note processing such as orb-bibtex-actions-edit-note may take care of locating the note and would not necessarily rely on bibtex-actions-notes-paths. But this is a minor nuance hardly relevant here.

Yes, that makes sense. I’ll take a look at it.

Thanks.

Thanks, @mshevchuk. The problem was that I had an old version of bibtex-actions.

This config works and SPC a work for me,

(use-package! oc-bibtex-actions
  :when (featurep! :completion vertico)
  :after oc
  :demand t
  :config

  (setq org-cite-global-bibliography '("~/Dropbox/home/documents/org/roam/_library.bib"))
  (setq bibtex-actions-bibliography org-cite-global-bibliography)
  (setq bibtex-completion-bibliography org-cite-global-bibliography)
  (setq bibtex-actions-notes-paths '("~/Dropbox/home/documents/org/roam/literature"))
  (setq org-cite-insert-processor 'oc-bibtex-actions
        org-cite-follow-processor 'oc-bibtex-actions
        org-cite-activate-processor 'oc-bibtex-actions
        ;; The activate processor relies on shift-select, so we set to t.
        org-support-shift-select t))

For me is ok to leave it like cite:my-cite for the ROAM_REFS: as a standard way to access the citations. The users can choose whatever they like to insert them in their documents.

Just curious about the future, do you plan to add @my-cite or &my-cite formats for this property, or leave it like now?

Best.

2 Likes

Org itself doesn’t allow citations in the property drawer (I asked).

Edit: I just merged a commit to fix the too aggressive error, and also better support org-roam with the default function.

1 Like

Awesome! Thanks for all.

This is exactly how I view it.

As far as I know, Org-roam recognizes Org-cite’s @my-cite citations as a :ROAM_REFS: keys and treats them identically to Org-ref’s cite:links. If you have a note with such a key, it should be indexed into the database and would pop up in the backlinks section of the Org-roam buffer. It may also partially work with ORB in that you would be able to open such a note from Helm-bibtex, Bibtex-actions or Org-ref but I haven’t checked it. What definitely does not work is creating a new note with ORB - you’ll always get an Org-ref cite:link in the properties drawer.

So the Github issue you mentioned earlier is about bringing a user option to allow them to choose which format they prefer.

I however have little incentive currently to address this due to a lack of time and because there is no added value to Org-cite @citations in :ROAM_REFS. As @bruce has already mentioned, this type of structures in property drawers is not recognized by Org and is simply a non-functional piece of plain text. Unlike with Org-ref cite:links, you won’t be able to interact with Org-cite @citations in property drawers, e.g. open a PDF file or the BibTeX entry, as some users find it useful with cite:links.

The issue is there though so I’ll address it sooner or later but it’s not on the top of the priority list.

I agree; it’s really not a significant practical problem.

If a user wants access to additional actions from an org citation, they can just include the citation(s) in the body of the note, which is what they should be doing anyway for serious academic writing (Ahrens talks about this in his discussion of the topic, and I emphasize it to my students).

Right, also the ORB’s orb-note-actions functionality was actually designed for such additional actions based on the citation key. It acts on the note level so the point does not have to be on the :ROAM_REFS: citation key. It’s also easily extensible.

1 Like

Thanks @bruce and @mshevchuk for this enlightening conversation.

I agree with you two, and I think the way org-roam, org-roam-bibtex and org-cite interact is stable enough to make any changes.

As a side note, today I finally could adjust org-cite and bibtex-actions to behave similar to the old org-ref. I’ll keep using org-ref V3 only for the cross-references. Best of the two worlds.

Best.

@maikol can I get your .doom.d configuration so that I can also setup the same in my doom emacs.