This week was time for the Annual Conference of the Microbiology Society. This was my second time at this meeting, and I enjoyed it once again. There’s a committed core of attendees which gives a good community spirit, and the society is openly very keen on supporting PhD students attending.

Favourite session – plasmids

There was a great block of talks in the Genetics and Genomics session on plasmids that I thought fit together really nicely. I only have a bit of knowledge about them, and I think the talks covered a good range of questions on these charismatic genome elements:

About a year ago I had my first foray into rust, which I used to do advent of code. I wrote up my thoughts at the time, but in summary although there were some immediately nice features such as the build and dependency system, I wasn’t immediately convinced and decided to stick with C++. I also said I’d give it a go for my next WASM project.

That time arrived at the end of last year, and what I intended to be a web implementation has turned into a full CLI tool where I used rust over C++. If you’re interested, the code is here and documentation at https://docs.rs/ska.

I think the last post I made on video games has been one of the most popular I’ve written on this blog, so thought I’d update you with some more recent favourites.

I didn’t play as many video games in 2022 as the past couple of years, but there were still a fair few I enjoyed.

Though, looking back, there weren’t any games that really knocked my socks off like the previous list I made, and in general I haven’t felt like there were as many games coming out that I wanted to play. Maybe it’s a COVID-effect? Fingers crossed for at least one that blows my mind in 2023!

Last week I attended ‘100 days and 100 lines of code’, which was organised by the Epiverse team at LSHTM. The overall idea was to think about when the next pandemic happens, what the first 100 lines of code written would be (I think more as a cute reference to similar thoughts about vaccine development, rather than a totally serious concept).

The format was over three days:

1. Talks from academics, public health and field epidemiologists on their thoughts and experiences with epidemiology software.
2. Exercise: starting with data simulated from an outbreak, create problems in the data and a list of questions to answer. Then swap with another group and try and answer their questions. (You can find our exercise response on github)
3. Summarise common experiences and problems with software from the second day.

The only couple of reservations about the event I had was that no software developers or research software engineers spoke – which I found odd considering it was ostensibly an event about writing code – and I think we missed their perspective, and whether problems with epidemiology software are similar to other scientific fields. There was also more of a focus on outbreak response and field epi, rather than pandemic response, but maybe that’s reasonable.

We moved from Azure to github actions to run the continuous integration tests in PopPUNK about a year ago. It’s been working pretty well and wasn’t too bad to set up, and integrates nicely into the pull requests.

However, in the past month two things happened:

• joblib v1.2 introduced a breaking security change which meant that hdbscan errored. Solving a conda environment pinning joblib to 1.1 takes about 12 hours (😱) to solve (longer than the 4 hour github limit).
• Even without the pin, environment resolution increased from about an hour to 3-4hrs, so the CI would only sometimes run.

Fixing conda on the CI

About 4/5 years ago I’d tried using mamba as a replacement for conda. It worked really well and was much faster, but I’d since read that some of its techniques were being merged into conda, and in general I stopped having hugely long times while solving the environment. But times seemed to be getting longer again (especially on the CI, not sure why), and I think mamba actually remains fundamentally different to the conda solver.

I originally set up a free wordpress (https://leesjohn.wordpress.com) in 2013, which I updated slightly when I moved it to some cheap hosting on www.johnlees.me in 2019. The hosting was fairly unreliable and every year’s renewal I thought about moving. Maintaining a wordpress also takes a bit of effort and I also worried about eventually allowing it to lapse. Finally, I’d grown increasingly frustrated with the wordpress style of editing, which had made it difficult to write code and embed HTML, and really wanted to move to something more like text to write posts.