From org file with local bibtex to LaTeX and PDF

vxlabs-emacs-org-ref-pdf-example.png
Screenshot of orgmode source, PDF preview on the right, interactive citation selection in the minibuffer. Click for full resolution.

I have (co-)written a few LaTeX documents in my time.

However, as I have been writing my life and lab notes and many of my technical blog posts in Emacs orgmode for the past few years, I wanted to see how one would go about using BiBTeX references in orgmode files (using John Kitchin’s org-ref package) such that they would render correctly in orgmode’s export LaTeX and PDF.

My use case is of course slightly different than the norm: I maintain my master bibliography using the wonderful Zotero software, and I prefer exporting document-specific BiBTeX files from that main database.

This post shows you how to do it.

Pre-requisites

  • Make sure that latexmk is installed on your system. This is one of the easiest ways to make sure that pdflatex and bibtex are executed in the correct sequence, and a sufficient number of times.
  • With M-x package-install RET org-ref install the org-ref package. This will enable interactive selection and insertion of bibtex references from your local bib file.
  • You should also have the ox-latex Emacs package installed. This is what gives orgmode its LaTeX output powers.

Emacs setup

In your init.el somewhere, use the following code to ensure that the orgmode LaTeX exporter invokes latexmk in the correct way:

(setq org-latex-pdf-process
    '("latexmk -pdflatex='pdflatex -interaction nonstopmode' -pdf -bibtex -f %f"))

A minimal but complete orgmode example

The usual org-ref workflow is that you use it to manage a single main BiBTeX file, which is configured in your init.el. As mentioned above, I prefer using small document-specific BiBTeX files.

This is what the first three lines sets up using an Emacs file variable. Note that the local bib file is specified without quotes of any kind. Also, because there’s no path specified, it lives together with the orgmode document itself, which I prefer.

# Local Variables:
# org-ref-default-bibliography: local-bibtex-file.bib
# End:

After this, I have two LaTeX-specific lines ensuring that the output PDF looks prettier than default. You can thank me later.

The third LATEX_HEADER line imports the natbib package, which means I have extra cite commands to differentiate between for example textual citing (the first example) and parenthetical citing (the second example).

#+LATEX_CLASS_OPTIONS: [a4paper, 11pt, colorlinks=true, citecolor=., linkcolor=black, urlcolor=black]
#+LATEX_HEADER: \usepackage{fourier}
#+LATEX_HEADER: \usepackage{natbib}

#+TITLE: Example orgmode to LaTeX

* Introduction

  This is that really difficult intro spection, as was also
  demonstrated by cite:huang_identification_2016.

* Conclusions

  This is the even more difficult final section. We will now use a
  parenthetical citation citep:meyer_four-level_2012.

Finally, very importantly, I have the orgmode orgmode markup to select a suitable bibliography style, and again to specify the bib file. This will get automatically translated to the suitable LaTeX or even HTML versions.

Putting it all together

With something like the example above in your orgmode file, and a suitable bib-file, you can do C-c C-e l o to export to LaTeX, execute the latexmk command we specified above, and view the PDF.

In the screenshot at the start of this post, you can see what this looks like on my setup. I am using PDFTools for viewing the PDF inside of Emacs (this gets updated automatically whenever I rebuild the PDF).

You can also see the ivy-based completion as I’m in the process of interactively inserting a new citation into the document.

The default helm-based completion is more attractive, but it takes over the whole display, which is why I made use of ivy for instruction’s sake.

Sending emails with math and source code

Org mode is great for authoring rich documents with syntax highlighted source code, LaTeX math and images. It even supports evaluating live snippets of code embedded in the text. It does all of this whilst remaining a plain text format.

Imagine how useful it would be to author programming-related or technical emails using this functionality?

Imagine no more! org-mime, part of the org mode contrib, does this for a number of emacs-based mail clients. However, our preference is for mu4e, which is not part of that list.

Fortunately, it seems mu4e has orgmode support integrated. To get this working, configure the following in your ~/.emacs.d/init.el:

;; configure orgmode support in mu4e
(require 'org-mu4e)
;; when mail is sent, automatically convert org body to HTML
(setq org-mu4e-convert-to-html t)

When composing a new email, switch on the special mu4e / orgmode mode with M-x org~mu4e-mime-switch-headers-or-body (it will automatically switch between compose mode and orgmode depending on whether your cursor is on the headers or in the body).

You should add the following options to your org mode body. The first configures LaTeX (math) to be converted using imagemagick (instead of MathJax or dvipng), and the second removes the table of contents.

#+OPTIONS: tex:imagemagick
#+OPTIONS: toc:0

When you want to send the email, move to the headers, and then do C-c C-c. Because org-mu4e-convert-to-html is set to true, the orgmode body will automatically be converted to HTML before being sent.

Until my pull request is merged in, you will have to make the following change to function org~mu4e-mime-convert-to-html() in org-mu4e.el:

(insert (org~mu4e-mime-multipart
         body html (mapconcat 'identity html-images "\n")))

should be:

(insert (org~mu4e-mime-multipart
         raw-body html (mapconcat 'identity html-images "\n")))

In other words, body becomes raw-body, else your outgoing mails will have HTML in their text parts, instead of plain text.

In that same function, you might also want to change:

(org-export-preserve-breaks t)

to

(org-export-preserve-breaks nil)

So that the HTML email does not get hard linebreaks.

Following are examples of some of the elements you might include in such a rich text email. They should appear in your rich text capable email client as follows:

org-mu4e-example.png

Here are the originals:

A section with some math

We can easily include math using LaTeX:

\[ C(p,t) = \lbrace x_0(p,t), x_1(p,t), \cdots, x_{N-1}(p,t) \rbrace\tag{1} \]

Some syntax highlighted C++

Syntax highlighted source code, for all of the languages supported by emacs (a very long list):

int main() {
    // Recently discovered trick, local functions in C++!
    struct Kludge {
        static int doSomething(int x) {
            return x * 2;
        }
    };

    for (int i=0; i < 10; i++) {
        cout << Kludge::doSomething(i) << endl;
    }

    return 0;
}

Removing URLs from Zotero bibtex exports

When you export bibtex from zotero, it includes the URLs in the bibtex records. Some LaTeX bibliography styles include this information, and sometimes this is not what you want, for example because the URLs take up unnecessary space and are hard to wrap.

It’s quite easy to get zotero to export bibtex without the URLs.

  1. Go to Preferences | Advanced and click on the “Show Data Directory” button.
  2. Edit translators/BibTeX.js with your favourite text editor.
  3. In function doExport(), at around line 2040 in Zotero 3.0.7, change the “for (var field in fieldMap)” loop by adding a single line of code like this:
for(var field in fieldMap) {
    # only add the following line:
    if (field == "url") continue;
    if(item[fieldMap[field]]) {
        writeField(field, item[fieldMap[field]]);
    }
}

If your changes don’t seem to take, make sure that your text editor did not make a backup of the old BibTeX.js (vim does this, with an ~ appended), as Zotero could possible pick up the backed up version instead of your edited version.

Let me know in the comments if this helped!

Look! References without URLs!

Update on 2013-02-17: Added tip concerning editor backups of BibTeX.js (I ran into this problem myself).