241–250 of 487 posts
I mean, Python 2->3 alone is gonna kill this challenge for most people.
You can always run old Python2 stuff in a Docker container, so long as the dependencies haven't disappeared.
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I am all for open science, but you understand that the links in your post are the exact worry people have when it comes to releasing code: people claiming that their non-software engineering grade code invalidates the results of their study. I'm an accelerator physicist and I wouldn't want my code to end up on acceleratorskeptics.com with people that don't understand the material making low effort critiques of minor…
> I wouldn't want my code to end up on acceleratorskeptics.com with people that don't understand the material making low effort critiques of minor technical points. I'm here to turn out science, not production ready code. In what way do idiots making idiotic comments about your correct code invalidate your scientific production? You can still turn out science and let people read and comment freely on it. > As an exam…
How would a layperson identify a faulty critique? It would be picked up by the media who would do their usual “both sides” thing.
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Controlling randomness can be extremely difficult to get right, especially when there's anything asynchronous about the code (e.g. multiple worker threads populating a queue to load data). In machine learning, some of the most popular frameworks (e.g. TensorFlow [0]) don't offer this as a feature, and in other frameworks that do (PyTorch [1]) it will cripple the speed you get as a result as GPU accelerators rely on n…
> But a much stronger and more relevant form of reproducibility for actually advancing science is running the same study e.g. on different groups of participants (or in computer science / applied math/stats / etc., with different codebases, with different model variants/hyperparameters, on different datasets) and the overall conclusions hold > Plenty of good science got done before modern devops came to be This isn't…
Code written in Oak still works in Java 14. You can still write `public abstract interface BlaBla{}` and it still works. If it doesn't work (due to reflection safety changes in Java9), it sill surely compile with newer compiler. Another thing, are tools used to compile still available? I tried to compile my BCS Android+native OpenCV project and failed quickly. Gradle removed some plugin for native code integration, a…
Strangely, they were running (some of ) the code on old hardware. That's hardly a useful case, and much easier than 'resurrecting' the code for modern reuse.
This is a challenge with many types of code. Earlier this year it took me a weekend to get a 7 year old Rails project running again. It's a simple project but the packages it used had old system dependencies that were no longer available. I ended up having to upgrade a lot of things, including code, just to get it running again.
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> protested when version control was suggested Academics are strange like this. The root reason is fear: fear that you're complicating their process, that you're going to interrupt their productivity or flow state, that you're introducing complication that has no benefit. They then build up a massive case in their minds for why they shouldn't do this; good luck fighting it. Doubly so if you're IT staff and don't have…
> The root reason is fear: fear that you're complicating their process, that you're going to interrupt their productivity or flow state, that you're introducing complication that has no benefit. Yes, but how does it compare to all the complicated processes that exist in academic institutions currently? Almost all of which originated from academics themselves, mind you.
This means it makes most sense to pick up processes that are portable and have longevity. Learning Git is a pretty solid example.
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> Doesn't it concern you that it would be possible for critics to look at your scientific software and find mistakes (some of which the OP mentioned are not "minor") so easily? A non-native English speaker may make grammatical mistakes when communicating their research in English—it does not in any way invalidate their results or hint that there is anything amiss. It is simply what happens when you are a non-native s…
Journals employ copy editors to address just those sorts of mistakes, why should we not hold software to the same standard as academic language? But more importantly, these software best practices aren't mere "grammatical mistakes," they exist because well-organized, well-tested code has fewer bugs and is easier for third parties to verify. Third-parties validating that the code underlying an academic paper executes…
First, it's not no different--it's completely different. Third parties have always constructed their own apparatus to reproduce an experiment. They don't go to the original author's lab to perform the experiment!
Second, a lot of scientific code won't run at all outside the environment it was developed in.
If it's HPC code, it's very likely that the code makes assumptions about the HPC cluster that will cause it to break on a different cluster. If it's experiment control / data-acquisition code, you'll almost certainly need the exact same peripherals for the program to do anything at all sensible.
I see a lot of people here on HN vastly over-estimating the value of bit-for-bit reproducibility of one implementation, and vastly underestimating the value of having a diversity of implementations to test an idea.
This article brings up scientific code from 10 years ago, but how about code from .. right now? Scientists really need to publish their code artifacts, and we can no longer just say "Well they're scientists or mathematicians" and allow that as an excuse for terrible code with no testing specs. Take this for example: https://github.com/mrc-ide/covid-sim/blob/e8f7864ad150f40022... This was used by the Imperial College…
Short answer: Yes, my 30 year old Fortran code runs (with a few minor edits between f77 and modern fortran), as did my ancient Perl codes. Watching the density functional theory based molecular dynamics zip along at ~2 seconds per time step on my 2 year old laptop, versus the roughly 6k seconds per time step on an old Sun machine back in 1991. I remember the same code getting down to 60 seconds per time step on my de…
Yes, I know a couple of Fortran 77 apps and libraries which were developed more than 25 years ago and which are still in use today. My C++ Qt GUI application for NMR spectrum analysis ( https://github.com/rochus-keller/CARA ) runs since 20 years now with continuing high download and citation rates. So obviously C++/Qt or Fortran 77 are very well suited to outlast time.