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Was playing a bit with your package and denote, and noticed something that sometimes comes up in the org-roam world.

The reference property citekey: you may want to consider an embark "target-finder" (or similar for hydra/transient) for that, so that users can act on it at point.

If you conclude yes, you may want to consider a syntax with already-existing finder: @key?

Which actually raises another issue: by default, you don't put the properties in an org property drawer, so this function doesn't work with that change.

https://github.com/emacs-citar/citar/blob/d183ec20c407983c4ae22089ec481f1a6f5cbe69/citar-org.el#L312

I think you want to wrap them in :properties: and :end:?

Hi, I would like to discuss the addition of a new feature which I think would have its place in citar-denote (but might also require modification in denote?). I mostly use org-mode in my notes and am very fond of org-cite.

Imagine that I have a paper/reference that I cite in different notes (let's call them a.org, b.org, c.org). When I am in the note for this paper, I want to produce a backlinks buffer showing files that cite the paper (a.org, b.org, c.org) as well as the files linking directly to the current note (the default behaviour). Unfortunately, the backlinks are only registered for denote-type links but not citations.

I wrote the following function as a proof-of-concept of the functionality for org-cite :

(defun citar-denote-cite-backlinks ()
  "Construct a buffer of all the notes (in .org format) that cite
the current reference. This function must be called from a denote 
note.

TODO: add support for other citations provided by citar (latex,
markdown) ?
"
  (interactive)
   (let* ((file (buffer-file-name))
	  (key (citar-denote-retrieve-reference-key-value file 'org)))
     (if key
	 (xref--show-xrefs
	  (xref-matches-in-files (format "cite:@%s" key) (denote-directory-text-only-files))
	  nil)
       ;; check if current file is a reference note, add reference if needed and
       ;; rerun command
       (when (yes-or-no-p "Current buffer does not reference a bibliography item. Select a reference ?")
	 (citar-denote-add-citekey)
	 (citar-denote-cite-backlinks)))))

How can we extend the behaviour of denote-link-backlinks from within citar-denote to include the results of the above function ? Is it even possible in the current version of denote ?

I was unsure whether I should ask this question on the denote mailing list, but I feel that this is better suited for citar-denote.

when setting citar-denote-title-format to "author-year-title" I get the following error:

citar-denote-generate-title: Wrong number of arguments: (1 . 1), 3

which I don't get when setting it to "title"

I put my notes for denote in various subdirectories. It would be nice to add this as an option for citar-denote. You could do something like this for citar-denote-create-note

(defun citar-denote-create-note (key &optional _entry)
  "Create a bibliography note for `KEY' with properties `ENTRY'.
The file type for the note to be created is determined by user
option `denote-file-type'."
  (let ((denote-file-type citar-denote-file-type))
    (denote
     (read-string "Title: " (citar-get-value "title" key))
     (citar-denote-keywords-prompt))
    (citar-denote-add-reference key denote-file-type)
    (when denote-subdir (denote-subdirectory-prompt))))

I'm not sure if other functions would also need to be changed for note retrieval, etc.

Hi,

thanks for this code, I've been using and though it wanted to place citar notes in a specific directory (usually a subdirectory of denote-directory). I think this migh be useful, so you can define, say, a denote-citar-directory to be nil or a directory and pass it to the denote command:

(denote
     ;; Replace underscores in citation key
     (replace-regexp-in-string "_" "-" key)
     (denote-citar--keywords-prompt)
     nil
     denote-directory)

I'm providing a patch though it might not be the proper way to implement this (limited elisp knowledge here).

https://gist.github.com/gnava/b33eadb51e71abd9114904c04e7bbb72

best,

guille

Basically, is there an easy way to have two or more references/bibliographic entries use the same note file?

The practical use case for me is when I have the same work but from different translators. I'd like to have my notes for each translation in the same file.

Hi Peter

I've been exploring your package recently and think it's really useful. One thing I'm missing currently, is a way to call the user-facing functions (like citar-denote-find-citation) to be called programmatically by passing a key to it. This would make integration with Embark easier.

I've modified the citar-denote-find-citation as follows (the only change is the optional argument and the citekey in the if-let* form):

(defun citar-denote-find-citation (&optional key)
  "Find a Denote file that cites a bibliographic entry.

Provides a selection list of all bibliographic entries cited in Denote files."
  (interactive)
  (if-let* ((citations (citar-denote--extract-citations))
            (citekey (or key
                         (citar-select-ref
                           :filter (citar-denote--has-citekeys citations))))
            (files (citar-denote--retrieve-cite-files citekey)))
      (progn (find-file (denote-get-path-by-id
                         (denote-extract-id-from-string
                          (if (= (length files) 1)
                              (car files)
                            (denote-link--find-file-prompt files)))))
             (goto-char (point-min))
             (search-forward citekey))
    (message "Not citations found in Denote file")))

Is this something that makes sense? Or is there another way to achieve this?

The reason for doing so, is that now it is trivial to add something like:

(define-key citar-embark-citation-map "c" 'citar-denote-find-citation)

to include an embark action that works on a key.

Cheers
EFLS

PS: Thanks for including a manual in Emacs and explaining so in the readme, that's really useful.

Hi,
Thanks for your work on this, it's really great and I use it daily :)
I have this strange bug, the source of which I can't figure out:

This only happens with notes I create hrough citar (either citar-create-note, or throught citar-open, and then the "create denote" action).

Thanks for your assistance.

I'm trying to improve my usage of citar in a denote note-taking workflow. This packages seems like it could provide all the necessary elements but I'm not understanding how to create a regular denote file with the additional citekey included in the front matter. Is this supposed to be done in a two step process?

• create a regular denote note.
• use the citar-denote-add-citekey command.

If that where the case, could you provide some programmatic examples in the documentation of how to make use of the citar-denote template?. This would seem really useful for programmatically creating notes with the proper citekeys.

I ran into some problems after starting to use this package yesterday: when creating new notes, the reference wasn't inserted. I was able to determine that this due to two obsolete symbols in the function denote-citar-file--create-note (see https://protesilaos.com/emacs/denote-changelog).

I rewrote the function slightly to get it working again:

(defun denote-citar-file--create-note (key &optional entry)
  "Create a bibliography note through Citar."
  (let ((denote-file-type nil)) ; make sure it is Org
    (denote
     ;; Replace underscores in citation key
     (replace-regexp-in-string "_" "-" key)
     (denote-citar--keywords-prompt))
    ;; This sort of works now. It's not pretty, but hey.
    ;; denote-last-buffer was obsolete.
    ;; denote-retrieve--id-front-matter-key-regexp was obsolete.
    (with-current-buffer (current-buffer)
      (save-excursion
	(goto-char (point-min))
	(re-search-forward "^[^#]")
	(search-backward "#")
	(goto-char (point-at-eol))
        (newline)
        (insert (format "#+reference:  %s" key))))))

I'm quite bad with regex, so there's probably a nicer way of doing this. From what I can tell, though, this works.

Since I was already at it, I decided to see if I could get the integration with e.g. citar-open to work. I think I managed to get a basic implementation working; perhaps it's useful for future work.

Much of this work is writing our own citar-files--get-notes function (my function is largely based on citar-file--directory-files, which citar-files--get-notes relies on). The new function looks like this:

(defun denote-citar--get-notes (&optional keys)
   (let ((files (make-hash-table :test 'equal))
	;; For now, we only support one extension.
	(org-files-regexp ".*\.org$")
	(marker1 nil)
	(marker2 nil)
	(dirs citar-notes-paths))
    (prog1 files
      (dolist (dir dirs)
	(when (file-directory-p dir)
	  (dolist (file (directory-files dir t ".*\.org$"))
	    ;; There certainly is a more elegant way of doing this
	    (with-current-buffer (get-buffer (find-file-noselect file))
	      (save-excursion
		;; Not sure if this is needed
		(goto-char (point-min))
		;; This should put us at the beginnig of the reference
		;; name. If this search fails, we are not dealing with
		;; a notes file for a reference.
		(when (search-forward "#+reference: " nil t)
		  ;; Here we select the reference name
		  (forward-to-word 1)
		  (setq marker1 (point))
		  (end-of-line)
		  (setq marker2 (point))
		  (if keys
		      (dolist (key keys)
			(when (string= key
				       (buffer-substring-no-properties marker1 marker2))
			  (push file (gethash key files))))
		    (let ((key (buffer-substring-no-properties marker1 marker2)))
		      (push file (gethash key files))))))))))
      ;; Reverse file lists because push adds elements to the front
      (maphash (lambda (key filelist)
                 (puthash key (nreverse filelist) files))
	       files))))

(Note that this implementation takes into consideration citar-notes-path.)

We also need a new citar-file--has-notes. Our version will look more or less the same only, for some reason, I couldn't use let and instead had to use setq:

(defun denote-citar--has-notes ()
  (setq notes (denote-citar--get-notes))
    (unless (hash-table-empty-p notes)
      (lambda (citekey) (and (gethash citekey notes) t))))

Then we simply register a new note source with our new functions:

(citar-register-notes-source
 'denote-citar-source (list :name "Denote Notes"
			    :category 'file
			    :items 'denote-citar--get-notes
			    :hasitems 'denote-citar--has-notes
			    :open 'find-file
                            :create 'denote-citar-file--create-note))
(setq citar-notes-source 'denote-citar-source)

I haven't tested this extensively, but it seems to work so far.

Using the following citar-denote configuration

(add-directory-to-load-path "citar-denote")
(require 'citar-denote)
(setopt citar-denote-keyword "literature"
        citar-denote-subdir "literature"
        citar-denote-template t)
(citar-denote-mode)
(diminish 'citar-denote-mode)

Existing notes that were linked using citar-denote-add-citekey are not detected as existing. Have I missed some piece of configuration?

When calling citar-denote-find-cites on a bibliographic entry, the results don't include files only mention the bibtex key in the #+reference front-matter (and don't cite the bibtex key @-style in the body of the text).

The reason being that citar-denote--retrieve-cite-files includes a @ sign in the xref query.

Is this intended behaviour? If not, then this might be a bug. If this is intentional, I can prepare a PR that introduces a custom variable citar-denote-cite-includes-reference to make this customizable.

I encounter an error stating Buffer is not a Denote file every time I attempt to insert a citation using citar-denote, despite trying multiple configurations. Including the one here: https://github.com/pprevos/citar-denote/blob/6e236e9100d1401cd7c628c5f799badded77967d/test/init.el

I am on Windows and just did a fresh install, so I am sure there is nothing else interfering.

Would appreciate some help!

Thank you

It seems like citar-denote already has all the functionality to read an entry in a bibliography,
and write its data to a note in denote, e.g. the citation key in the note or the authors/years/title as the note's filename.
This is awesome, but right now it seems like this functionality can only be utilized in a very narrow way.
It would be great to use this functionality a bit more flexibly.

What a lot of people do with similar note-taking apps, is to create notes for an entry in their bibliography,
such that basic pre-definable information about the bibliographic entry is written into the note automatically.
For example, I choose an entry just like I do right now with citar-denote, and citar-denote creates a note,
just as it already does. But in addition to writing the citation key in the front matter, I'd like it to write something
like

author: NAME
date: DATE
publisher: PUBLISHER 
isbn: ISBN
pages: PAGES
arXiv: ARXIV

underneath or in the denote front matter (don't know if denote limits what can go in the FM),
where the uppercase variables are read from the bibliography, and the exact information to be displayed
is configurable via the citar-denote package. I hope it's clear what I'm asking.

Meaningful use cases:

• Adding the ISBN or arXiv identified makes rediscovery future-proof. Opposite to citation keys, it's not going to change or break. Even if citar-denote or denote itself should go away in the future, a literature note can be uniquely identified with a simple grep for its ISBN.

• One might want to create a note for every author one's reading in one's note-taking app (here denote), and link to them, such that visiting the author's note and displaying backlinks informs one about all previous times someone has read something by them. Having the author there takes away manual work.

Hi! I was thinking about an option of adding the reference key as the denote signature. This way, one could have the reference in the filename while still retaining the option of using descriptive titles like author-year etc.

Having the reference in the filename might also possibly make the lookup for reference notes easier, I suspect, but I don't know how that is solved currently.

What do you think? I could try do this myself and make a PR.

I'm in the process of rig-jigging my (academic) workflow, and am cleaning up my emacs.d configuration.

That's seen me adopt vertico (1.1), denote (1.2.0), and citar (20230227.2247). The citar-denote package (20230211.528) looks like it should be just the thing I need to join citar and denote.

I've installed it thus:

(use-package citar-denote
:after citar denote
:config
(citar-denote-mode)
(setq citar-open-always-create-notes t))

Alas ... there's a wee problem, when I create a new note (citar-create-note) a new buffer is created that with the right frontmatter (a title, date, filetags, and identifier), but without a reference.

E.g., a buffer called "20230305T155127--organizational-strategy-structure-and-process__bib_strategy.org" is created; this looks correct to me and has the following content.

#+title: Organizational Strategy, Structure, and Process
#+date: [2023-03-05 Sun 15:51]
#+filetags: :bib:strategy:
#+identifier: 20230305T155127

But I would expect to see a reference like "#+reference: miles_organizational_1978"

There is an error message that says, "citar-denote-add-reference: Buffer is not a Denote file".

Looking at the mode-line, it says Org citar-denote Ind Fly/en, which is exactly what it says when I open any other denote file.

I'm a little lost now ... any ideas

Hello @pprevos ,

Seems denote-link require at least 3 parameters here, but only 1 are offered here.

(denote-link FILE FILE-TYPE DESCRIPTION &optional ID-ONLY)

Zheng

Hi,
I appreciate the work you've put into this, and I think it's great.
I think it would be really useful to be able to quickly insert a link to the note attached to a given reference.
I imagine using the same interface as citar-denote-open-note, but inserting a denote link instead.

Hi,

is it possible to change the title of the note? In my field, we tend to talk about papers as "author (year)", with the consequence that we rarely know the titles of papers. However, citar-denote uses the title of the paper as the title of the note, and as far as I can tell there's no way to change this.

I think it would be really nice to have the option of customizing this. Can this be done? If not, are there any plans to add it?

For example, this is a note content.

#+title: test
#+date: [2023-03-22 Wed 11:43]
#+filetags: :bib:
#+identifier: 20230322T114151

This is a test[cite:@taerweluc2013].

If there is a dot at the end of citation, when I use citar-denote-find-citation to find denote files related to citation taerweluc2013, it do not exist in the completion minibuffer.

If I delete the dot, then use citar-denote-find-citation, the candidate appeared.

Above picture shows, one reference disappeared. Any char at the end of citation will cause this problem.