I wrote my Bachelor’s Thesis with Google Docs and managed bibliography manually. Final formatting was done with Apple’s Pages. For Master’s Thesis I wanted more robust tooling: better control over changes, solid template and automated bibliography handling.

As a developer I’m a big fan of Git-based workflows. It gives you a full version history and I like how you must commit (save) changes with a comment, making it easy to avoid accidental edits. Also, when you’re doing commits it just feels more like you’re actually making some progress. So it was clear that my Master’s Thesis would consist of text files in a Git repository.

I also wanted to use LaTeX in order to have perfectly formatted documents. To make content files a bit more cleaner, I decided to use LaTeX with Markdown. I used Tom Pollard’s PhD thesis template as a basis and modified it to meet LUT University guidelines. This template uses Pandoc to make the conversion from Markdown to desired output format, such as PDF or HTML. You can find my template from GitHub.

While I still needed to use LaTeX inside Markdown files for some specific things, like referencing figures, I really enjoyed the separation between content and styles. I had my content in easy to read Markdown files and simple make pdf command generated formatted document. As I’m not an experienced LaTeX or Pandoc user, it did take me considerable amount of time to get the stylings right, but it was definitely worth the effort.

I used Zotero for managing references. With Chrome extension, it was really handy to be able to save articles via browser with full meta information for citations. Zotero would automatically update references.bib file in my project folder, keeping the list of references under version control as well.

I looked for different services for making it possible to share my thesis for other people for commenting and proof-reading purposes. GitHub alone would be enough for tech-savvy people, but I wanted something easier and more focused for textual content, like books. Penflip was the most promising service and I did subscribe to it. However, in the end the proof-reading was done by first printing out the thesis on paper and letting people to highlight typos with a pen – you know, the old fashioned way. But it was actually nice to hold the thesis physically in your hands a couple of times in the process, so I didn’t mind. Also, notes by the supervisor were just comments on a PDF document.