Greetings, wanderer.
We are Vedran and Matea, two academics who are enthusiastic about scientific research, especially in the field of computational chemistry, and open-source software, especially Linux, Python, FreeBSD, LaTeX, and Markdown. We sometimes write about these and related topics on this blog.
Enjoy your stay.
Photo source: Lemon Pepper Pictures (@lemonpepperpictures) | Unsplash
FreeBSD Ports provide editors/vscode with the latest stable version of Visual Studio Code and the FreeBSD Foundation provides an excellent guide how to install and use it. Unfortunately, the latest stable version of Visual Studio Code Remote - SSH still does not officially support FreeBSD, but only Linux, Windows, and macOS.
Photo source: Lautaro Andreani (@lautaroandreani) | Unsplash
As many readers of this blog are already aware, we make great use of GitHub Pages for hosting this website and several others. In particular, after FIDIT's inf2 server was finally decomissioned, Pages was the obvious choice for replacing the remaining services it offered.
Since the number and variety of applications and services hosted on inf2 server grew and diminished organically over time, what remained afterward was a collection of complex, but unrelated link hierarchies that had to be redirected to new locations (remember that Cool URIs don't change).
/homePhoto source: Julian Hochgesang (@julianhochgesang) | Unsplash
FreeBSD 14.0-RELEASE annoucement is immiment. Due to faster (re)boot and related improvements by Colin Percival, this version made headlines in tech media even before it got released, which got me interested in trying it out on some of our machines. I installed the first beta on one of our servers and shortly afterward reported an upgrade bug, which got fixed during the beta cycle and was shipped as an errata in 13.2-RELEASE-p4 and 12.4-RELEASE-p6.
I was following the subsequent pre-releases with great interest as well. The final FreeBSD 14.0-RELEASE brings Clang/LLVM 16.0 (which we use in scientific software development and course teaching), OpenSSL 3.0, OpenZFS 2.2, Lua configuration support in the boot loader, upgraded WireGuard in the kernel wg driver, and plenty of other changes that are relevant to our usage. I found it well worth the time it took to go through these changes and learn what to expect from the release.
Photo source: Darran Shen (@darranshen) | Unsplash
My employment as a research and teaching assistant at Faculty of Informatics and Digital Technologies (FIDIT for short), University of Rijeka (UniRi) ended last month with the expiration of the time-limited contract I had. This moment has marked almost two full years I spent in this institution and I think this is a good time to take a look back at everything that happened during that time. Inspired by the recent posts by the PI of my group, I decided to write my perspective on the time that I hope is just the beginning of my academic career.
Photo source: Jahanzeb Ahsan (@jahan_photobox) | Unsplash
This month we had Alumni Meeting 2023 at the Heidelberg Institute for Theoretical Studies, or HITS for short. I was very glad to attend this whole-day event and reconnect with my former colleagues as well as researchers currently working in the area of computational biochemistry at HITS. After all, this is the place and the institution where I worked for more than half of my time as a postdoc, where I started regularly contributing code to GROMACS molecular dynamics simulator, and published some of my best papers.
Photo source: Patrik Kernstock (@pkernstock) | Unsplash
Our everyday scientific and educational work relies heavily on hardware, software, and, in modern times, cloud services. The equipment that we will mention below is specific to our group; common services used by university and/or faculty employees will not be specifically mentioned here.
Photo source: Santeri Liukkonen (@iamsanteri) | Unsplash
Tough question, and the one that has been asked and answered over and over. The simplest answer is, of course, it depends on many factors.
As I started blogging at the end of my journey as a doctoral student, the topic of how I selected the field and ultimately decided to enroll in the postgraduate studies never really came up. In the following paragraphs, I will give a personal perspective on my Ph.D. endeavor. Just like other perspectives from doctors of not that kind, it is specific to the person in the situation, but parts of it might apply more broadly.
Photo source: Roman Synkevych (@synkevych) | Unsplash
As you can probably see, this website is built using the Material theme for MkDocs, which we have been happily using for over one year after using Sphinx for many years prior to that. GitHub Pages offers built-in support for Jekyll, but not for MkDocs and therefore it requires the manual building and deployment of our website. However, it automates many other things, including HTTPS certificate provisioning on our domain via Let's Encrypt.
There are several somewhat related approaches using GitHub Actions for automating the deployment of MkDocs-generated sites, usually with the Material theme, to GitHub Pages. These guides are not only found on blogs written by enthusiasts; the official Getting started section of the Material for MkDocs documentation describes the usage of GitHub Actions for deployment and provides a generic YAML file for that purpose.
Photo source: Tim Mossholder (@ctimmossholder) | Unsplash
I sometimes joke with my TA Milan Petrović that his usage of RAR does not imply that he will be driving a rari. After all, he is not Devito rapping^Wsinging Uh 😤. Jokes aside, if you search for "should I use RAR" or a similar phrase on your favorite search engine, you'll see articles like 2007 Don't Use ZIP, Use RAR and 2011 Why RAR Is Better Than ZIP & The Best RAR Software Available.
Photo source: Eugenio Mazzone (@eugi1492) | Unsplash
Back in summer 2017. I wrote an article explaining why we used Sphinx and reStructuredText to produce teaching materials and not a wiki. In addition to recommending Sphinx as the solution to use, it was general praise for generating static HTML files from Markdown or reStructuredText.
This summer I made the conversion of teaching materials from reStructuredText to Markdown. Unfortunately, the automated conversion using Pandoc didn't quite produce the result I wanted so I ended up cooking my own Python script that converted the specific dialect of reStructuredText that was used for writing the contents of the group website and fixing a myriad of inconsistencies in the writing style that accumulated over the years.
