Writing a scientific paper is hard. Doing your PhD is hard. Writing your thesis is hard. And to make me feel even more miserable I decided to measure my progress by counting the net change in words I achieve throughout each day. I am by no means a productivity guru and I don't know whether word count is a useful indicator for measuring the progress of a paper. That being said, it is a reality check to see how fast my work is progressing. So without further ado here's the Powershell command that outputs the wordcount for the last 25 days based on git commits. (For the bash command, see the bottom of this post)

for($i = 0; $i -lt 25; $i++){$j = $i + 1; Write-Host (get-date (get-date).addDays(-$i) -UFormat "%Y%m%d") ((git diff --word-diff=porcelain "@{$j days ago}" "@{$i days ago}"   -- "***.md"| Select-String -Pattern "^\+.*" | Measure-Object -word | select -ExpandProperty Words) - (git diff --word-diff=porcelain "@{$j days ago}" "@{$i days ago}"  -- "***.md"| Select-String -Pattern "^-.*" | Measure-Object -word | select -ExpandProperty Words)) }

While writing my papers I try not to get bogged down too much. So if a paragraph doens't flow right I just type TODO: rewrite on the line below it, and continue writing. When I think of something that I shouldn't forget, like an extra analysis to run I just write it down as a todo in the running text of my paper. I also write thoughts on my paper as a todo. Ideas on structure, whether I should maybe rearrange paragraphs or approach a subject differently, it all ends up as a todo in the running text.

When running the VSCode task for converting my paper to PDF (using Pandoc) it puts all the todos into the running text. That's fine by me, it helps as an extra reminder that stuff still needs to happen. But I wanted the todos to be visually different from the running text, so that it stands apart and doesn't confuse people who are reading my draft. That is where my Pandoc filter comes into play.

I found this super easy alternative way to animate your slides with reveal.js that works out of the box with Markdown and Pandoc. Here is how to do it.

Last week I had to give a progress presentation about the current state of my PhD, and I can whip those up in no time. I use Boilerplate Paper not only for writing my papers, but also for presentations like this.

I write the presentation in Markdown and then convert it to reveal.js. But sometimes you want something else than the default sliding transition that reveal.js provides.