kxc42 | 2 years ago | on: The Notetaking Cold War (2020)
kxc42's comments
kxc42 | 3 years ago | on: We're wasting money by only supporting gzip for raw DNA files
That can be a challenge, but you can also build an "artificial" reference genome. You just use it for compression, not for any real analyses. This would allow you to still use alignment-based compression.
But I agree with you: it really depends on the type of the data.
kxc42 | 3 years ago | on: We're wasting money by only supporting gzip for raw DNA files
I'm not sure why gzip still pops up for FASTQ data, as it is quite easy to bin the quality scores, align it against a reference genome and compress it as e.g. CRAM [1,2].
With 8 bins, the variant calling accuraccy seems to be preserved, while drastically reducing the file size.
[1]: https://en.wikipedia.org/wiki/CRAM_%28file_format%29
[2]: https://lh3.github.io/2020/05/25/format-quality-binning-and-...
kxc42 | 3 years ago | on: Goodbye, data science
That answer somehow reminds me of an article in logicmag: An Interview with an Anonymous Data Scientist [1].
[1]: https://logicmag.io/intelligence/interview-with-an-anonymous...
kxc42 | 3 years ago | on: Why Domain Driven Design?
Funny coincidence: just one week ago I and a colleague of mine started with "pytest-arch" [1], a pytest plugin to test for architectural constraints. On purpose we kept it very simple. It is already usable and works well, at least for our use cases.
You can use it to check e.g. if your domain model is importing stuff that it should not import.
We are planning to publish it soon on pypi.
kxc42 | 3 years ago | on: Why Lisp?
Difficult to say, as I did not measure anything. From the code I've written I get the "feeling" that it is more compact compared to plain lua, reducing (my) cognitive load.
Fennel transpiles to lua, it doesn't give more capabilities, I would say. The concept of productivity (and capability) is anyway confounded by so many factors, making the choice of programming language negligible (unless you pick one of the extremes, such as Brainfuck, of course).
kxc42 | 3 years ago | on: Why Lisp?
In terms of practical application, I saw (e.g. leap[1]) and enjoyed using fennel[2] for writing neovim plugins.
[1]: https://github.com/ggandor/leap.nvim [2]: https://fennel-lang.org/
kxc42 | 4 years ago | on: Sorry everybody, I failed with you
I was surprised that nobody mentioned the Collective Code Construction Contract of zeromq/Pieter Hintjens [1]. It tries to minimise the friction created by maintaining & contributing to open source projects.
It is not perfect of course, but at least it is a good start. Especially the "value-" & opinion-based discussions can be reduced considerably.
kxc42 | 4 years ago | on: Technical documentation that just works
Basically you have three approaches to tackle code samples in markdown files:
1. run the code with some kind of plugin as part of your doc pipeline
2. generate documentation from your code
3. take some kind of hybrid approach
I went for 3., annotate snippet "areas" in the source code of a project (mainly in tests) and extract the snippets to a folder, e.g. into the mkdocs folder. I commit them to the (docs) repo. If the project changes, usually I fix the tests and update the snippets in mkdocs. This way I can be sure that the code in the documentation is actually working and people can copy&paste it. To scratch my own itch, I (surprise, surprise) created a script and even packaged it[1].
page 1
To take clothes as analogy: when you buy a shirt off-the-shelf, you can (usually) choose between XXS to XXL. Let's assume you want to wear the shirt for the rest of your life, wouldn't the natural conclusion be: a tailor-made shirt?
The real solution is to take one note taking system as starting point and adapt it to your needs. There is no shortcut, it will take a while till you've figured out what your needs are and how you can adapt the system you chose.