Yes, it is all pasted into my thesis, comments and all, like all code should.
Challenge to scientists: does your ten-year-old code still run?
371–380 of 487 posts
Re: Challenge to scientists: does your ten-year-old code still run?
#372Earlier quoted context omitted.
The findings really should be independent of the code. Reproduction should occur by taking the methodology and re-implementing the software and running new experiments.
That's exactly the philosophy we follow e.g. in particle physics and its a common excuse to dismiss all guidelines made in the article. However, this kind of validation/falsification is often done between different research groups (maybe using different but formally equivalent approaches) while people within the same group have to deal with the 10 years old code base. I myself had very bad experience with extending t…
> If it's a one-man-show I would not give too much on code quality
This makes me a little uneasy, as I'm not too worried about code quality can easily translate into Yes I know my code is full of undefined behaviour, and I don't care.
> PS: quite excited about my first post here
Welcome to HN! reddit has more cats, Slashdot has more jokes about sharks and laserbeams, but somehow we get by.
Re: Challenge to scientists: does your ten-year-old code still run?
#373Earlier quoted context omitted.
One of the things I come across is scientists who believe they're capable of learning code quickly because they're capable in another field. After they embark on solving problems, it does become an eyeopening experience, and one that becomes now about keeping things running. For those who have a STEM discipline in addition to a software development background >5Y, would you agree with seeing the above? I would have t…
> I would have thought the scientists among us would approach someone with familiarity with software development expertise. Is there a pool of skilled software architects willing to provide consultations at well-below market wages? Or a Q&A forum full of people interested in giving this kind of advice? (StackOverflow isn't useful for this; the allowed question scope is too narrow.) I guess one incentive to publish on…
I'll state the obvious and answer with No. There are not enough skilled software architects to go around and many who consider themselves skilled are not actually producing good code themselves, probably including many confident posters here in this forum.
The idiosyncrasies and tastes of many 'senior' software engineers would likely make the code unreadable and unmaintainable for the average scientist and possibly discourage them from programming altogether.
Software architecture is an unsolved problem as evident in the frequent fundamental discussions about even trivial things, highlighted by a cambrian explosion of frameworks who try to help herding cats, and made obvious in senior programmers struggling to get a handle on moderately complex code.
I propose scientists keep their code base as simple as possible, review the code along with the ideas with their peers, maybe use Jupyter notebooks to show the iterations and keep intermediate steps, and, as others state, show the code as appropriate and try to keep it running. There is no silver bullet and very few programmers could walk into your lab or office and really clean things up the way you'd hope.
Re: Challenge to scientists: does your ten-year-old code still run?
#374Earlier quoted context omitted.
> Spack/Guix/nix are the best solution in theory, but they come with a host of other problems that made them less desirable. I would be quite interested to learn more what these problems are, in your experience. I've only tried Guix (on top of Debian and Arch) and while it is definitively more resource-hungry (especially in terms of disk space), I don't percive it as impractical.
As someone coming from the computing side of things, I found nix to be quite difficult to grok enough to write a package spec, and guix was pretty close, at least in part because of the whole "packages are just side-effects of a functional programming language" idea. At least nix also suffers from a lot of "magic"; if you're trying to package, say, an autotools package then the work's done for you - and that's great,…
> guix was pretty close, at least in part because of the whole "packages are just side-effects of a functional programming language" idea
This must be a misunderstanding. One of the big visible differences of Guix compared to Nix is that packages are first-class values.
Re: Challenge to scientists: does your ten-year-old code still run?
#375The Fossil documentation has this gem:
> "The global state of a fossil repository is kept simple so that it can endure in useful form for decades or centuries. A fossil repository is intended to be readable, searchable, and extensible by people not yet born."
I always liked that they planned for the long-term. Keeping that in mind helps you build systems that will work in 10 years, or in 100, if it happens to last that long. When you are building a foundation, like a language or database, it is nice to plan for long term support since so much depends on it. C has stayed mostly recognizable over the years, much more so than C++ or other high level languages. When your design is simple, you can have a "feature complete" end.
Re: Challenge to scientists: does your ten-year-old code still run?
#376"Python 2.7 puts “at our disposal an advanced programming language that is guaranteed not to evolve anymore”, Rougier writes1." Oh no. That's not at all what was intended. Regarding my own research: I'm doing theoretical biophysics. Often I do simulations. If conda stays stable enough, my code should be reproducible. There's however some external binaries(like lammps) I did not turn into a conda package yet. There's…
I added different variants of lammps to a Guix channel we maintain at our institute:
https://github.com/BIMSBbioinfo/guix-bimsb/blob/master/bimsb...
Thankfully, Guix makes it easy to take an existing package definition and create an altered variant of it.
Re: Challenge to scientists: does your ten-year-old code still run?
#377Earlier quoted context omitted.
That's not how the game is played. If you cannot the release the code because the code is too ugly or untested or has bugs, how do you expect anyone with the right expertise to assess your findings? It reminds me of Kerckhoffs's principle in cryptography, which states: A cryptosystem should be secure even if everything about the system, except the key, is public knowledge.
> If you cannot the release the code because the code is too ugly or untested or has bugs, how do you expect anyone with the right expertise to assess your findings? Yes, that should be this way. Also all cases where some company research team goes to a scientific conference and presents a nifty solution for problem X without telling how it was purportedly done, it should be absolutely required to publish code and da…
With the caveat that while in some cases, like computational science, numerical analysis, machine learning algorithms, computer-assisted proofs, and so on, details of the code could be crucial, in other cases, they should not matter that much. I too have the impression that the HN public tends to over-value the importance of code in these cases when it is mostly a tool for evaluating a scientific result.
Re: Challenge to scientists: does your ten-year-old code still run?
#378Glad to see many mentions of Nix in this thread! I wonder if Nix and Guix should standardize the derivation format both share to kick that off as the agreed-upon "thin waste" other projects and the the academy can standardize around.
The derivation format is little more than a compilation artifact (a low-level representation of a build), and I think standardizing on it would not be as useful as it may seem.
Re: Challenge to scientists: does your ten-year-old code still run?
#379Earlier quoted context omitted.
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…
> 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. If code is what is substantiating a scientific claim, then code needs to stand up to scientific scrutiny. This is how science is done. I came from physics, but systems and computer engineering was always an interest of mine, even before physics, I thought it…
The history of physics is full of complex, one-off custom hardware. Reviewers have not been expected to take the full technical specs and actually build and run the exact same hardware, just to verify correctness for publication.
I doubt any physicist believes we need to get the Tevatron running again just to check decade-old measurements of the top quark. I don't understand why decade-old scientific software code must meet that bar.
Re: Challenge to scientists: does your ten-year-old code still run?
#380"Visual Basic," Maggi writes in his report, "is a dead language and long since has been replaced..."
In fact I still have the VB6 IDE installed on my primary workstation and use it for quick and dirty projects from time to time.