Over the years, I have been using various approaches to note taking on my Mac, especially to annotate articles or books I read, or just quickly write some reminders or archive snippets of code. None has definitely been satisfactory — the last iteration was a combination of a standard BibTeX file and hundreds of ebooks managed by Papers app, and I definitely need a more robust workflow.

So, I decided to start again from scratch. Since I use (Space)macs¹ for almost everything serious in my work, I set up a solution entirely based on two dedicated directories and a set of Markdown and Org files. I took inspiration from a very instructive Reddit thread in which one of the poster describes his setup to manage bibliographic entries using a combination of Helm-bibtex and org-ref, and by another great blog post by Piotr Limanowski: Reading for Programmers.

I followed the instructions to initialize Helm-bibtex and org-ref, which basically amounts to define a few variables in my .emacs, as described on the Github links referenced above. For whatever reason we have to define the PDF directory and the BibTeX file twice, but this is something that I can live with. However, at some point I should really setq a constant filename to define the BibTeX file, since I only have once now. (Previously, I was exporting a separate bib file from Papers app to help differentiate entries coming from Papers and Emacs.)

The BibTeX keys are automagically generated (C-c C-c when editing an entry) and formatted thanks to additional work from org-ref-clean-bibtex-entry. Sometimes, the Bibtex mode does not do a good job at generating a proper key and I found that the combination of the two commands yields best results. Each key basically consists in the name of the first author, the year, and the abbreviated title–all separated with hyphen to avoid messing the PDF filename with colon all over. Using this scheme, “cormen-2009-introd-algor” will stand for the following entry:

Cormen, Thomas H and Leiserson, Charles E and Rivest, Ronald L and Stein, Clifford
Introduction to Algorithms
2009
The MIT Press

Then, Helm-bibtex comes to the rescue, and it really is a killer package! It can be insinuated in $\TeX$, Org, Markdown and Text mode, and it is bound to M-m m i c (major mode > insert > org-ref) in Markdown, or you can just M-x helm-bibtex just about anywhere. For instance, in a Markdown file like the one I am currently editing, it will bring up a window where I can locate or search all my references, like in Deft mode, and insert a reference that pandoc-citeproc will take care of formatting in the final bibliography for me. Moreover, I can annotate or update any entry on the fly, and of course if there is an associated PDF file I can read it right away. I do not use Interleave that much, nor org-noter. In fact, I am fine with reading articles or books using Preview, Skim, or Highlights app which offers a nice UI for visualizing annotations and highlighted paragraphs. But i know that I could potentially use Emacs as a PDF reader, thanks to the pdf-tools package. Likewise, I still use the great Marked app to visualize the final output of my Markdown files even if Emacs already has a live preview mode.

Finally, I added a few templates for org-capture, which are heavily inspired from the documentation itself and a few links I found on the internet, nothing really original: TODO item and Journal entry. But I also have a quick template for capturing web link I am currently visiting on Safari app, thanks to a little gem found on Irreal’s blog.