Ten years ago I posted a video on YouTube titled "org mode is awesome". This 18 minute video was a tour of features in org-mode that ranged included, outlining, task management, agendas, tables, code, exporting to different formats, and extendability. That video has been viewed 92.9K times!

A fair bit has changed since then, and a lot has stayed the same. org-mode is even more awesome! That video was made with what I called at the time jmax, and that has evolved into scimax today. I use scimax on a daily basis in my research, teaching and other work. It is as important in my work today as it was 10 years ago, and has survived watching other editors come and go.

I have had in mind to make an update of that video, but it has in my opinion really stood the test of time and is still highly relevant in its present form. The only thing that would really change is the background and font colors.

I have made over 200 other YouTube videos over that time, and many of them are on using Emacs and org-mode in a lot of different ways. These videos are organized in these playlists:

scimax-eln

Using scimax as an electronic lab notebook.

scimax

Videos on libraries I developed in scimax, including org-ref

org-mode

Videos exploring features in org-mode

pycse

Videos on using Python in Emacs to solve engineering and science problems

You can see how scimax has evolved, and continues to evolve over this time through these videos, and of course through the scimax repo at https://github.com/jkitchin/scimax. There are still great things coming for scimax, stay tuned!

Copyright (C) 2024 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 9.7.5

In this post we illustrated a simple export of org-ref citations to html. This was a simple export that simply replaced each citation with a hyperlink as defined in the export function for each type of link. Today we look at formatting in text citations with superscripted numbers, and having an unsorted (i.e. in order of citation) numbered bibliography. This will take one pass to get the citations and calculate replacements and the bibliography, and one pass to replace them and insert the bibliography.

This text is just some text with somewhat random citations in it for seeing it work. You might like my two data sharing articles ^1,2. We illustrate the use of org-mode in publishing computational work ^3,4,5, experimental ⁶and mixed computational and experimental work ^7,8. This example will correctly number multiple references to a citation, e.g. ¹and ².

This post is somewhat long, and the way I worked it out is at the end (Long appendix illustrating how we got the code to work). The short version is that we do some preprocessing to get the citations in the document, calculate replacement values for them and the bibliography, replace them in the org-buffer before the export in the backend (html) format we want, and then conclude with the export. This is proof of concept work.

The main issues you can see are:

1. Our formatting code is very rudimentary, and relies on reftex. It is not as good as bibtex, or presumably some citation processor. Major improvements would require abandoning the reftex approach to use something that builds up the bibliography entry, allows modification of author names, and accomodates missing information gracefully.
2. The bibliography contents reflect the contents of my bibtex file, which is LaTeX compatible. We could clean it up more, by either post-processing to remove some things like escaped &, or by breaking compatibility with LaTeX.
3. The intext citations could use some fine tuning on spaces, e.g. to remove trailing spaces after words, or to move superscripts to the right of punctuation, or to adjust spaces after some citations.
4. Changing the bibliography style for each entry amounts to changing a variable for the bibliography. We have to modify a function to change the intext citation style, e.g. to brackets, or (author year).
5. I stuck with only cite links here, and only articles and books. It would not get a citenum format correct, e.g. it should not be superscripted in this case, or a citeauthor format correct. That would require some code in the replacement section that knows how to replace different types of citations.

The org-ref-unsrt-html-processor function could be broken up more, and could take some parameters to fine-tune some of these things, and generalize some things like getting the citation elements for the buffer. Overall, I think this shows that citations in org-mode with org-ref are actually pretty flexible. It is not as good as bibtex/LaTeX, and won't be for an unforseeably long time unless someone really needs high quality citations in a format other than LaTeX. Note for LaTeX export, we don't have to do any preprocessing at all. If you wanted to try Word export, you might make a pandoc processor that replaces everything in pandoc citation syntax, and then use pandoc for the conversion. If you didn't care to use the bibtex database for anything else, you could just use backend specific markup to make it exactly right for your output. I did this in reference ⁸where you can see the chemical formulas are properly subscripted.

If you would like to see the bibtex file used for this you can get it here: numbered.bib

Bibliography

1. Kitchin, Examples of Effective Data Sharing in Scientific Publishing, ACS Catalysis, 5(6), 3894-3899 (2015). link. doi.
2. John Kitchin, Data Sharing in Surface Science, Surface Science , (0), - (2015). link. doi.
3. Zhongnan Xu & John R Kitchin, Tuning Oxide Activity Through Modification of the Crystal and Electronic Structure: From Strain To Potential Polymorphs, Phys. Chem. Chem. Phys., 17(), 28943-28949 (2015). link. doi.
4. Prateek Mehta, Paul Salvador & John Kitchin, Identifying Potential BO2 Oxide Polymorphs for Epitaxial Growth Candidates, ACS Appl. Mater. Interfaces, 6(5), 3630-3639 (2014). link. doi.
5. Curnan & Kitchin, Effects of Concentration, Crystal Structure, Magnetism, and Electronic Structure Method on First-Principles Oxygen Vacancy Formation Energy Trends in Perovskites, The Journal of Physical Chemistry C, 118(49), 28776-28790 (2014). link. doi.
6. Hallenbeck & Kitchin, Effects of O2 and SO2 on the Capture Capacity of a Primary-Amine Based Polymeric CO2 Sorbent, Industrial & Engineering Chemistry Research, 52(31), 10788-10794 (2013). link. doi.
7. Spencer Miller, Vladimir Pushkarev, Andrew, Gellman & John Kitchin, Simulating Temperature Programmed Desorption of Oxygen on Pt(111) Using DFT Derived Coverage Dependent Desorption Barriers, Topics in Catalysis, 57(1-4), 106-117 (2014). link. doi.
8. Jacob Boes, Gamze Gumuslu, James Miller, Andrew, Gellman & John Kitchin, Estimating Bulk-Composition-Dependent H₂ Adsorption Energies on Cu_xPd_1-x Alloy (111) Surfaces, ACS Catalysis, 5(), 1020-1026 (2015). link. doi.

(setq org-ref-bibliography-entry-format
      '(("article" . "<li><a name=\"\%k\"></a>%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"https://doi.org/%D\">doi</a>.</li>")
        ("book" . "<li><a name=\"\%k\"></a>%a, %t, %u (%y).</li>")))

(defun org-ref-unsrt-latex-processor () nil)
(defun org-ref-unsrt-html-processor ()
  "Citation processor function for the unsrt style with html output."
  (let (links
        unique-keys numbered-keys
        replacements
        bibliography-link
        bibliographystyle-link
        bibliography)
    ;; step 1 - get the citation links
    (setq links (loop for link in (org-element-map
                                      (org-element-parse-buffer) 'link 'identity)
                      if (-contains?
                          org-ref-cite-types
                          (org-element-property :type link))
                      collect link))

    ;; list of unique numbered keys. '((key number))
    (setq unique-keys (loop for i from 1
                            for key in (org-ref-get-bibtex-keys)
                            collect (list key (number-to-string i))))


    ;; (start end replacement-text)
    (setq replacements
          (loop for link in links
                collect
                (let ((path (org-element-property :path link)))
                  (loop for (key number) in unique-keys
                        do
                        (setq
                         path
                         (replace-regexp-in-string
                          key (format "<a href=\"#%s\">%s</a>" key number)
                          path)))
                  (list (org-element-property :begin link)
                        (org-element-property :end link)
                        (format "@@html:<sup>%s</sup>@@" path)))))

    ;; construct the bibliography string
    (setq bibliography
          (concat "#+begin_html
<h1>Bibliography</h1><ol>"
                  (mapconcat
                   'identity
                   (loop for (key number) in unique-keys
                         collect
                         (let* ((result (org-ref-get-bibtex-key-and-file key))
                                (bibfile (cdr result))
                                (entry (save-excursion
                                         (with-temp-buffer
                                           (insert-file-contents bibfile)
                                           (bibtex-set-dialect
                                            (parsebib-find-bibtex-dialect) t)
                                           (bibtex-search-entry key)
                                           (bibtex-parse-entry t)))))
                           ;; remove escaped & in the strings
                           (replace-regexp-in-string "\\\\&" "&"
                                           (org-ref-reftex-format-citation
                                            entry
                                            (cdr (assoc (cdr (assoc "=type=" entry))
                                                        org-ref-bibliography-entry-format))))))
                   "")
                  "</ol>
#+end_html"))

    ;; now, we need to replace each citation. We do that in reverse order so the
    ;; positions do not change.
    (loop for (start end replacement) in (reverse replacements)
          do
          (setf (buffer-substring start end) replacement))

    ;; Eliminate bibliography style links
    (loop for link in (org-element-map
                          (org-element-parse-buffer) 'link 'identity)
          if (string= "bibliographystyle"
                      (org-element-property :type link))
          do
          (setf (buffer-substring (org-element-property :begin link)
                                  (org-element-property :end link))
                ""))

    ;; replace the bibliography link with the bibliography text
    (setq bibliography-link (loop for link in (org-element-map
                                                  (org-element-parse-buffer) 'link 'identity)
                                  if (string= "bibliography"
                                              (org-element-property :type link))
                                  collect link))
    (if (> (length bibliography-link) 1)
        (error "Only one bibliography link allowed"))

    (setq bibliography-link (car bibliography-link))
    (setf (buffer-substring (org-element-property :begin bibliography-link)
                            (org-element-property :end bibliography-link))
          bibliography)))


(defun org-ref-citation-processor (backend)
  "Figure out what to call and call it"
  (let (bibliographystyle)
    (setq
     bibliographystyle
     (org-element-property
      :path (car
             (loop for link in
                   (org-element-map
                       (org-element-parse-buffer) 'link 'identity)
                   if (string= "bibliographystyle"
                               (org-element-property :type link))
                   collect link))))
    (funcall (intern (format "org-ref-%s-%s-processor" bibliographystyle backend)))))

(add-hook 'org-export-before-parsing-hook 'org-ref-citation-processor)

(browse-url (org-html-export-to-html))

#<process open ./blog.html>

(mapcar
 (lambda (link) (org-element-property :path link))
 (loop for link in (org-element-map (org-element-parse-buffer) 'link 'identity)
       if (-contains? org-ref-cite-types (org-element-property :type link))
       collect link))

(loop for i from 1
      for key in (org-ref-get-bibtex-keys)
      collect (list key i))

(let ((links (loop for link in (org-element-map (org-element-parse-buffer) 'link 'identity)
                   if (-contains? org-ref-cite-types (org-element-property :type link))
                   collect link))
      (replacements (loop for i from 1
                          for key in (org-ref-get-bibtex-keys)
                          collect (list key (number-to-string i)))))
  (loop for link in links
        collect (let ((path (org-element-property :path link)))
                  (dolist (repl replacements)
                    (setq path (replace-regexp-in-string (car repl) (nth 1 repl) path)))
                  (list (org-element-property :begin link)
                        (org-element-property :end link)
                        (format "<sup>%s</sup>" path)))))

(setq org-ref-bibliography-entry-format
      '(("article" . "<li>%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"https://doi.org/%D\">doi</a>.</li>")
        ("book" . "<li>%a, %t, %u (%y).</li>")))

(concat "<h1>Bibliography</h1><br><ol>"
        (mapconcat
         'identity
         (loop for key in (org-ref-get-bibtex-keys)
               collect
               (let* ((result (org-ref-get-bibtex-key-and-file key))
                      (bibfile (cdr result))
                      (entry (save-excursion
                               (with-temp-buffer
                                 (insert-file-contents bibfile)
                                 (bibtex-set-dialect (parsebib-find-bibtex-dialect) t)
                                 (bibtex-search-entry key)
                                 (bibtex-parse-entry)))))
                 (org-ref-reftex-format-citation
                  entry
                  (cdr (assoc (cdr (assoc "=type=" entry))
                              org-ref-bibliography-entry-format)))))
         "")
        "</ol>")

Copyright (C) 2015 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 8.2.10

Some LaTeX citations look like \cite[pretext][post text]{key}. Here I explore parsing a link like (pre text)(post text)key. Note you cannot use [] inside the link, as it breaks the link syntax. Also, these links must be wrapped in [[]] because of the parentheses and spaces in the parentheses. This is a very different approach than used here which used the description of the link to define the pre and post text. The disadvantage of that approach is that the key is hidden, whereas in this approach it is not; you can see the key and pre/post text.

The basic strategy will be to use a regexp to parse the link path. The regexp below is pretty hairy, but basically it looks for optional text in () and uses numbered groups to store what is found. Then, we use what we found to construct the LaTeX syntax. We redefine the function in org-ref that gets the key for clicking, and we redefine the cite format function. The result is that we retain the click functionality that shows us what the key refers to.

(defun org-ref-parse-key (s)
  "return pretext, posttext and bibtex key from a string like \"(pre text)(post text)bibtexkey\""
  (string-match "\\(?1:(\\(?2:[^)]*\\))\\)?\\(?3:(\\(?4:[^]]*\\))\\)?\\(?5:.*\\)" s)
  ;; return pretext postext key
  (list (match-string 2 s) (match-string 4 s) (match-string 5 s)))

(defun org-ref-get-bibtex-key-and-file (&optional key)
  "returns the bibtex key and file that it is in. If no key is provided, get one under point"
 (interactive)
 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
       (file))
   (unless key
     ;; get the key
     (setq key (nth 2 (org-ref-parse-key (org-ref-get-bibtex-key-under-cursor)))))
   (setq file     (catch 'result
		    (loop for file in org-ref-bibliography-files do
			  (if (org-ref-key-in-file-p key (file-truename file)) 
			      (throw 'result file)))))
   (cons key file)))

(defun org-ref-format-cite (keyword desc format)
   (cond
    ((eq format 'latex)
     (let* ((results (org-ref-parse-key keyword))
	    (pretext (nth 0 results))
	    (posttext (nth 1 results))
	    (key (nth 2 results)))
       (concat "\\cite" 
	       (when pretext (format "[%s]" pretext))
	       (when posttext (format "[%s]" posttext))
	       (format "{%s}" key))))))

org-ref-format-cite

(org-ref-format-cite "(pre text)(post text)key" nil 'latex)

\cite[pre text][post text]{key}

(org-ref-format-cite "(pre text)key" nil 'latex)

\cite[pre text]{key}

(org-ref-format-cite "key" nil 'latex)

\cite{key}

It looks like they all work! Let us test the links: mehta-2014-ident-poten, (pre text)mehta-2014-ident-poten and (pre text)(post text)biskup-2014-insul-ferrom-films. a multiple citation mehta-2014-ident-poten,thompson-2014-co2-react,calle-vallejo-2013-number.

This seems to work from an export point of view. You can not mix multiple citations with this syntax, and I did not define the html export above. Otherwise, it looks like this might be a reasonable addition to org-ref.

Copyright (C) 2014 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 8.2.6

I wrote some emacs-lisp code in org-mode, and load them with org-babel-load-file. I thought it would be nice if there was load path for org-files, similar to the one for lisp files. Here I document what it might look like.

We need a load path to search for the org-file.

(setq org-load-path '("~/Dropbox/kitchingroup/jmax/"))

Next, we need the function to do the loading. We need to find the org-file, and then load it.

(defun org-require (orgfile)
  "orgfile is a symbol to be loaded"
  (let ((org-file (concat (symbol-name orgfile) ".org"))
	(path))

  ;; find the org-file
  (catch 'result
    (loop for dir in org-load-path do
	  (when (file-exists-p
		 (setq path
		       (concat
			(directory-file-name dir)
			"/"
			org-file)))
	    (throw 'result path))))
  (org-babel-load-file path)))


(org-require 'org-ref)

Loaded ~/Dropbox/kitchingroup/jmax/org-ref.el

That looks pretty simple. You do need write access to the location where the org-file is though. Let us look at a version that copies the file to a temporary directory. For some reason, I am not able to use org-babel-load-file with this. But, it does look like I can tangle the file, and assuming (big assumption) that the file tangles to a regularly named .el file, this seems to work too.

(defun org-require (orgfile)
  "orgfile is a symbol to be loaded"
  (let ((org-file (concat (symbol-name orgfile) ".org"))
        (el-file (concat (symbol-name orgfile) ".el"))
	(path))

  ;; find the org-file
  (catch 'result
    (loop for dir in org-load-path do
	  (when (file-exists-p
		 (setq path
		       (concat
			(directory-file-name dir)
			"/"
			org-file)))
	    (throw 'result path))))
  (copy-file path temporary-file-directory t)

  (org-babel-tangle-file (concat temporary-file-directory (file-name-nondirectory path)))
  (load-file (concat temporary-file-directory el-file))
))

(org-require 'org-ref)

t

This actually seems pretty reasonable. I have not thought about complications but for simple cases, e.g. single org-file, it looks ok.

Copyright (C) 2014 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 8.2.6

I like to email org-mode headings and content to people. It would be nice to have some records of when a heading was sent, and to whom. We store this information in a heading. It is pretty easy to write a simple function that emails a selected region.

(defun email-region (start end)
  "Send region as the body of an email."
  (interactive "r")
  (let ((content (buffer-substring start end)))
    (compose-mail)
    (message-goto-body)
    (insert content)
    (message-goto-to)))

that function is not glamorous, and you still have to fill in the email fields, and unless you use gnus and org-contacts, the only record keeping is through the email provider.

What I would like is to send a whole heading in an email. The headline should be the subject, and if there are TO, CC or BCC properties, those should be used. If there is no TO, then I want to grab the TO from the email after you enter it and store it as a property. You should be able to set OTHER-HEADERS as a property (this is just for fun. There is no practical reason for this yet). After you send the email, it should record in the heading when it was sent.

It turned out that is a relatively tall order. While it is easy to setup the email if you have everything in place, it is tricky to get the information on TO and the time sent after the email is sent. Past lispers had a lot of ideas to make this possible, and a day of digging got me to the answer. You can specify some "action" functions that get called at various times, e.g. after sending, and a return action when the compose window is done. Unfortunately, I could not figure out any way to do things except to communicate through some global variables.

So here is the code that lets me send org-headings, with the TO, CC, BCC properties, and that records when I sent the email after it is sent.

(defvar *email-heading-point* nil
  "global variable to store point in for returning")

(defvar *email-to-addresses* nil
  "global variable to store to address in email")

(defun email-heading-return ()
  "after returning from compose do this"
  (switch-to-buffer (marker-buffer  *email-heading-point*))
  (goto-char (marker-position  *email-heading-point*))
  (setq *email-heading-point* nil)
  (org-set-property "SENT-ON" (current-time-string))
  ;; reset this incase you added new ones
  (org-set-property "TO" *email-to-addresses*)
  )

(defun email-send-action ()
  "send action for compose-mail"
  (setq *email-to-addresses* (mail-fetch-field "To")))

(defun email-heading ()
  "Send the current org-mode heading as the body of an email, with headline as the subject.

use these properties
TO
OTHER-HEADERS is an alist specifying additional
header fields.  Elements look like (HEADER . VALUE) where both
HEADER and VALUE are strings.

save when it was sent as s SENT property. this is overwritten on
subsequent sends. could save them all in a logbook?
"
  (interactive)
  ; store location.
  (setq *email-heading-point* (set-marker (make-marker) (point)))
  (org-mark-subtree)
  (let ((content (buffer-substring (point) (mark)))
	(TO (org-entry-get (point) "TO" t))
	(CC (org-entry-get (point) "CC" t))
	(BCC (org-entry-get (point) "BCC" t))
	(SUBJECT (nth 4 (org-heading-components)))
	(OTHER-HEADERS (eval (org-entry-get (point) "OTHER-HEADERS")))
	(continue nil)
	(switch-function nil)
	(yank-action nil)
	(send-actions '((email-send-action . nil)))
	(return-action '(email-heading-return)))
    
    (compose-mail TO SUBJECT OTHER-HEADERS continue switch-function yank-action send-actions return-action)
    (message-goto-body)
    (insert content)
    (when CC
      (message-goto-cc)
      (insert CC))
    (when BCC
      (message-goto-bcc)
      (insert BCC))
    (if TO
	(message-goto-body)
      (message-goto-to))       
    ))

This works pretty well for me. Since I normally use this to send tasks to people, it keeps the task organized where I want it, and I can embed an org-id in the email so if the person replies to it telling me the task is done, I can easily navigate to the task to mark it off. Pretty handy.

Copyright (C) 2014 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 8.2.6