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Ask HN: Should I publish my research code?

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Re: Ask HN: Should I publish my research code?

#291

Post by rubyist5eva »

del82 wrote: post #25

> it's substantially more work to clean and organize the code for publishing, it will increase the surface for nitpicking and criticism (e.g. coding style, etc). Matt Might has a solution for this that I love: Don't clean & organize! Release it under the CRAPL[0], making explicit what everyone understands, viz.: "Generally, academic software is stapled together on a tight deadline; an expert user has to coerce it int…

You don't need an esoteric license, just use a standard license like MIT>

relevant section from MIT license:

"THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE."

Re: Ask HN: Should I publish my research code?

#292

Post by rubyist5eva »

There is a reason most free-software licenses have the following clauses:

"THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE."

So just pick one that is compatible with the 3rd party code you used to write your software (mostly pertaining to copyleft licenses like the GPL) - MIT and BSD licenses are generally "fine" - and just publish it. Just because your code is not "clean" or whatever doesn't preclude it from being free.

Re: Ask HN: Should I publish my research code?

#294

Post by f6v »

1. It might seem like the paper is enough to reproduce to you, but in my field, it’s not more often than it is. Hell, even a software version change produces different result with the same params and seed. So don’t exclude a possibility you’re biased.

2. Code IS a competitive advantage. Some times you’ll reach out to the author to ask for clarification. And after some back and forth they’ll just suggest you send them the data and put them on the paper because they don’t really want to disclose the details or the method they’ve previously published.

3. I don’t think you’ll have issues if you share less than perfect code. Most reviewers are as bad at production code as you are.

All in all, I think sharing code advances science. Yes, there’s gatekeeping, tricks to keep the knowledge inside the lab. But didn’t you choose the field because you want to advance the knowledge, help humankind? Making your research more reproducible by sharing the source code is a step in that direction.

Re: Ask HN: Should I publish my research code?

#296

Post by actually_a_dog »

TremendousJudge wrote: post #244
actually_a_dog wrote: post #238

Earlier quoted context omitted.

Maybe a little OT, but, I'd rather it be called "comput ing science." Computers are just the tool. I believe it was Dijkstra who famously objected to it being called "computer science," because they don't call astronomy "telescope science," or something to that effect.

I never thought about this, but it's right. However, to get more nitpicky, most of the uses of "Comput[er|ing] Science" should be replaced with "Computer Engineering" anyway. If you are building something for a company, you are doing engineering, not science research

I agree. I can't find it right now, but there was an article on HN within the past few days talking about how software engineering is often more like writing and editing a book than engineering. That makes perfect sense to me. Code should be meant primarily to communicate with people, and only incidentally to give instructions to computers. It seems to be lost to the sands of time who said this first, but it is certainly true that code is read by humans many more times than it is written. Therefore, ceteris paribus, we should optimize for readability.

Readable code is often simple code, as well. This also has practical benefits. Kernighan's law[0] states:

> Debugging is twice as hard as writing the code in the first place. Therefore, if you write the code as cleverly as possible, you are, by definition, not smart enough to debug it.

Dijkstra says it this way:

> The competent programmer is fully aware of the strictly limited size of his own skull; therefore he approaches the programming task in full humility, and among other things he avoids clever tricks like the plague.[1]

Knuth has a well-documented preference for "re-editable" code over reusable code. Being "re-editable" implies that the code must be readable and understandable (i.e. communicate its intention well to any future editors), if not simple.

I know that I have sometimes had difficulty debugging overly clever code. I am not inclined to disagree with the giants on this one.

---

[0]: https://www.defprogramming.com/q/188353f216dd/

[1]: https://www.cs.utexas.edu/users/EWD/transcriptions/EWD03xx/E...

Re: Ask HN: Should I publish my research code?

#297

Post by caconym_ »

vngzs wrote: post #200
del82 wrote: post #25

> it's substantially more work to clean and organize the code for publishing, it will increase the surface for nitpicking and criticism (e.g. coding style, etc). Matt Might has a solution for this that I love: Don't clean & organize! Release it under the CRAPL[0], making explicit what everyone understands, viz.: "Generally, academic software is stapled together on a tight deadline; an expert user has to coerce it int…

Please don't use this license. Copy the language from the preamble and put it in your README if you'd like, but the permissions granted are so severely restricted as to make this license essentially useless for anything besides "validation of scientific claims." It's not an open-source license - if someone wished to include code from CRAPL in their MIT-licensed program, the license does not grant them the permission…

Yeah, this seems a bit verbose and overbearing to me. The open-source licenses I've used myself include something like this, which seems quite sufficient:

> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

From a non-academic's point of view I might include a brief disclaimer in the README too, explaining the context for the code and why it's in the state it's in, but there's no obligation to hold the user's hand. To be frank, anybody nitpicking or criticizing code released under these circumstances with the expectation that the author do something about it can go fuck themselves.

Competitive advantage, on the other hand, is a perfectly valid reason to hold code back. There may also be some cost in academia to opening an attack surface for any sort of criticism, even irrelevant criticism made in obvious bad faith. Based on what I've heard about academia, this wouldn't surprise me.

Re: Ask HN: Should I publish my research code?

#298

Post by Frost1x »

peoplefromibiza wrote: post #271
paulluuk wrote: post #137

Earlier quoted context omitted.

They don't call it "Computer Science" for nothing ;)

notoriously Philip Wadler says that computer science has two problems: computer and science. It's not about computers and "You don't put science on your name if you're a real science" He prefers the name informatics. source: https://youtube.com/watch?v=IOiZatlZtGU

"Information science" is basically long form of "informatics" so that breaks it I'd say. Also, "information" tends to imply a focus on state and places computational aspects (operations performed on information) as second hand.

I've yet to find a classification I really like but this is an interesting take. I still tend to like CIS (Computing and Information Sciences). The problem with CS is it focuses on computation and puts state as second class. The problem with IS is it focuses on state and puts computing as second class. To me, both are equally important.

Re: Ask HN: Should I publish my research code?

#299

Post by cycomanic »

bmitc wrote: post #262
cycomanic wrote: post #247

Earlier quoted context omitted.

I think you don't understand the realities of work in scientific/academic organisations. Unless you work in computer science you likely never received any formal education on programming except for some numerical methods in c/matlab/fortran course during your studies (which often also focus more on the numerical methods and not the programming). So pretty much every person, just learned by doing. Moreover you are not…

I understand it fine. Like I said, it’s really not that hard to write pretty good code for prototypes. I'm not saying the code needs to be architected for scale or performance or whatever else needless expectation. I don't have a formal education in programming or computer science and write clean code just fine, as do some other non-computer science people I've worked with in advanced R&D contexts. And then some (man…

I'm not making excuses I'm just talking about the realities. For the significant majority of researchers I know about version control is still program_v1.py, program_v1.py, program_final.py, program_final2.py (and this is the good version, at least they are using python), so talking about clean code is still quite a bit away. I'm teaching PhD students and it's even hard to convince them, because they just look at how to get the next publishable result. For academics it becomes even more unrealistic, most don't even have time to go to a lab, they are just writing grants typically.

I'm actually a strong supporter of open science, release my code OSS (and actually clean it up) and data (when possible). But just saying it's easy and there is no cost, is just setting the wrong expectations. Generally unless you enjoy it, spending significant time on your code is not smart for your career. Hopefully things are changing, but it is a slow process.

Funny that you talk about optics I know some of the most productive people in my field and their optical tables are an absolute mess (as is their code btw). They don't work at universities though.

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