Is this violation of academic integrity if I ask a question on Github public repository and post it as an issue?

Question

Recently, I asked a question on a public Github repository about a formula that is used in the code that is hosted on that public repository. Basically, if you are familiar with Github, you can create an issue on any public repositories to ask question, report an error, request new features, etc. I use the similar formula, that is embedded in that repository, in my research and based on my literature review that formula is implemented incorrectly in that repository and I have the reference as well. So, I opened an issue and said I think the formula implemented in this code is wrong and I think based on the literature it should be implemented differently, and asked if there is any plan to change or fix it.

Someone, that is responsible for the code to merge the pull requests or close the issues, posted a comment on the issue that I created, and said that probably nobody is aware of the problem in that formula cause there are really small community that use that code at all and that code is not used for a while, so he would be happy if I create a pull request based on correct formula and give the literature reference as well for the future people.

Long story short, I just created that pull request and I put my reference to the correct formula as well and I'm waiting for the opinion of the admin of that repository if it's possible to merge it into the original repository or not. So, nothing really strange happened here, I think.

I'm informed that my PhD adviser found that issue + pull request that I created and he thinks I'm wrong and the existing formula in the code is correct. OK, I'm fine with that. I know there is no one solution for a given problem and different people have different approaches.

But, the problem is that he is saying that: I violated the academic integrity by creating that issue and submitting that pull request, which I'm surprised and can't understand what exactly I violated here. I'm just really angry and confused and can't understand what's wrong here. I can understand he is not OK with formula and I don't care at all and I'm 100% OK to use the wrong formula, but I can't understand why I should be prosecuted with violation of academic integrity because I don't have same opinion about that formula or created that issue or pull request? Also, I read the graduate manual in our university for the 10th time and there is no such thing in it as violation of academic integrity if you don't have same opinion as your PhD adviser or if you create an issue to ask question or create pull request to fix something. Any suggestion or recommendation is appreciated.

Responses to comments: You raised some questions that I think it might help if I clarify them. One of the comments was:

Is your advisor pursuing a violation of academic integrity with your department and/or the school, or is this just a personal dispute?

My answer: No, but this personal conversation was kinda a threat and he said if he likes he would use it against me and students are always loser in front of professor, which I think is true.

Is it possible that your supervisor used the formula before and, without realising, you implicitely suggested that some of his research is wrong? I could see some people reacting badly to that, especially if they find out from a a public Github repository instead of directly from you...

My answer: No, my supervisor is new in my PhD research field and he had no experience/paper in this field before I started my PhD, and as a result of that he has a really vague and wrong idea about literature in this field and what's accepted or what's wrong in this area.

"I'm 100% OK to use the wrong formula" that sounds like poor academic integrity to me

My answer: I'm just saying that I'm OK to listen to him and use even the wrong formula and get my PhD as soon as possible and stay away from academia forever despite the fact that I always loved the academic environment and wanted to become a professor some day. But now, I have a really routine job offer in a company that has nothing to do with PhD or research and I'm aching to just get my PhD degree and start that job and maybe I could be happier in my miserable life.

Two of your statements are conflicting. First: "...based on my literature review that formula is implemented incorrectly in that repository and I have the reference as well.", but later: "I know there is no one solution for a given problem and different people have different approaches.". Could you clarify whether the original implementation is incorrect, or just different from your own? That seems to be the crux of the matter, really.

My answer: The reality is that people use the wrong formula because it's easier to understand and based on my experience wrong formula is OK within a range of 5 to 10 percent error in comparison to correct formula. It's not like nobody uses the correct formula and there are tons of literature out there that use the correct one. So, my intention was: If we have lots of other uncertainties in our model, why we induce another one when we could use the correct formula to make sure at least we are not creating another source of uncertainties when we could eliminate it without a price. Even, performance wise, correct formula is the same as wrong one.

To expand; if there are alternative methods that are also valid, and you go around flagging them as 'errors' and then promote your own method, then this would certainly be perceived as academic dishonesty.

My answer: No, the alternative method which is this wrong formula is just a really good approximation of the correct formula. Obviously, it just gives a close number to what correct formula gives you, but the wrong formula does not satisfy other properties of wrong formula, like the orthogonality of the correct formula, which is crucial in our research. So, my intention was to just use the correct thing in its mathematical sense when it is available, it doesn't have any additional cost, and it is well documented in the literature.

"I'm just really angry". Don't be. Confused is ok, but why angry?

My answer: These days I see myself as useless and miserable person that just works more than 12 hours per day and the other 12 hours that I suppose to rest or sleep still I'm thinking about my research but I'm not happy, I don't have any friends, I'm depressed, I'm nervous, I'm stressful, etc. So, yeah I'm angry that people hates me if even I tell them the truth.

at most this is ignorance. Has nothing to do with honesty. And reality is that either the adviser is an idiot (wouldn't be the first time) or OP misinterpreted the situation.

yeah, why the academic world makes people angry... that's the question. Maybe because you are punished for being proactive?

My answer: My question is ignorance of who? Me? That I want to find what's right and what's wrong? Yeah, I'm an ignorant, idiot, useless person that just devoted my whole life to something that doesn't worth.

I think you're reading that wrong. I took "I'm 100% OK to use the wrong formula" to mean that OP does not dispute the supervisor's claim that the formula is wrong; they're "100% okay" to be told that they're using the wrong formula. The question is how on earth being wrong is somehow a "violation of academic integrity".

My answer: Thank you!

Update:

Based on Wolfgang's answer, yesterday, I had a meeting with my PhD adviser and I did my best to be calm as possible and be really polite. I just asked what is wrong in his opinion about opening an issue in a public Github repository and express a valid concern based on a peer-reviewed reference (this reference is not mine nor my adviser's for those who think I shared research results without permission and this reference is more than 7 years old with so many citations) and if the owner of that Github repository is happy to accept a pull request, why it should be considered a violation of academic integrity? Also, I asked in which part of the graduate manual, this rule of approval and permission to post anything in World Wide Web is stated for my more information? Furthermore, I asked even if I'm totally misunderstood here, the repository owner could just point me to their documentation or any other reference that justifies the usage of current formula and just close the issue, and that's it.

My PhD adviser response was the pretty much the same as his initial reaction. He thinks even a single comment in World Wide Web from me should be approved by him before posting and it doesn't need to be stated explicitly in the graduate manual and graduate school gave him such an authority where he sees fit to consider this commenting as a violation of academic integrity. By the way, he thinks I'm wrong, he doesn't care about the references that I showed to him to support my idea and says he is going to send an email to the repository owner and ask him to block me cause I'm wasting the time of repository owners, despite the fact that I feel just repository owner is a welcoming person and is open to answer the questions!

I'm just shocked...!

Response to some of comments and answers:

One of the main assumptions, that I saw in the answers and comments, is that my PhD adviser is unfamiliar with Github. No, he claims that he is indeed an expert in Github, open source software, programming, etc. So, he is indeed pretty familiar with the concept of open source and Github, but his main area of expertise during his PhD and his post-docs was something else and not related to my PhD research. He just picked this topic for my PhD research, because his latest post-doc adviser developed an open source software specifically within my PhD research area many years ago and he wanted to maybe use that software and continue his collaboration with his post-doc adviser.

I can understand this behavior of my PhD adviser, when I compare his interaction with other people not just myself. Cause, logically if he is so nice and welcoming to other people, so certainly something is wrong probably with me. But, based on things that I saw, I could say: generally, my PhD adviser only respects people that are above him in hierarchical ranking or he doesn't have any authority over them. Even, with other junior professors or post-docs (my PhD adviser is also a fairly new assistant professor without tenure), he acts in a way that a few collaborators that we had during past four years just left us and some of them even doesn't reply to our emails at all now. Even, 2 or 3 years ago, I was reading his comments on Github to his colleagues for many years ago, and I was able to imagine how snarky and bad is the tone of his comments that nobody bothered to reply after 10 years or so.

Also, thank you all for your supportive comments and answers as well as your lots of useful suggestions.

Answer 1

It seems like you have to have a conversation with your adviser. There is certainly nothing wrong with your approach: You read through code on which you have knowledge and something to say; you then were proactive and wanted to fix the issue; all of these are commendable. If you happen to have been mistaken, well, that happens -- but then that's what patch review is there for.

So the stance of your adviser -- as you describe it -- doesn't make any sense to me or probably anyone here. That leaves two interpretations:

• Your adviser really has awkward ideas of what is appropriate or not on GitHub.
• You misunderstand what your adviser was trying to get at.

Option 1 seems unlikely, so option 2 seems like a distinct possibility to me. It's also one that can easily be addressed: Have a conversation about the issue in which you state that you are confused why the behavior was considered wrong, and ask your adviser to help you think it through.

---

Update: Following the addition to the original post about the conversation with the adviser, it does seem to me that option 1 above (that the adviser is a moron), however unlikely a priori, is in fact true. That's regrettable because in my fifteen years as a professor, I've never come across a situation where this kind of behavior by a professor would have been appropriate or, in fact, useful or warranted.

But, since I've been developing open-source software for more than 25 years now and have been leading open source communities for 20, I do think that it's worthwhile pointing out that the behavior of the maintainer of the GitHub repository is entirely reasonable and appropriate: We all value contributions from the general scientific community, and for all projects I know of (a substantial number), that includes cases where the person proposing a patch may in fact have been mistaken. So I continue to think that you did the right thing, and I do think that the response of the GitHub repository maintainer was reasonable and common. In other words, the behavior of the academic adviser really makes no sense to me. If I were to receive an email from someone's professor saying that their student had behaved inappropriately and suggesting that I block them from my repositories, I would certain (i) not do so, and (ii) be quite clear about the fact that I thought the student did the right thing and that the adviser is in the wrong and behaving in ways that make no sense to me. It is certainly no adviser's business to restrict what students post on the internet as long as it is in good faith and doesn't slander the adviser or university.

Given this adviser's stance, I am a bit at a loss as to what to suggest. Reasonable people are amenable to conversations, but apparently this person is not reasonable. Given that you have a job offer from elsewhere, the right choice may simply be to decide that it's not worth your mental energy to fight this fight. Or, you could talk to the department head or another trusted professor in the department -- what they will do is a separate matter, and it may not yield any outcomes that can still help you in the time before you graduate.

Answer 2

These days I see myself as useless and miserable person that just works more than 12 hours per day and the other 12 hours that I suppose to rest or sleep still I'm thinking about my research but I'm not happy, I don't have any friends, I'm depressed, I'm nervous, I'm stressful, etc. So, yeah I'm angry that people hates me if even I tell them the truth.

It sounds like you're going through a rough time. Grad school is stressful even in the best circumstances, and yours aren't the best right now. Seek professional help from a psychologist or similar professional ASAP. Your mental health is your first priority!

---

As of the original issue my two cents would be to make sure they mean what you think they do, as suggested in the other answers. If this is certainly their stance you need to find a new adviser. This person could be bullying you over nonsense for whatever reason. Get out.

Answer 3

I don't see any integrity issues. Your intentions seemed to be to correct an error. Unless your intention was to sabotage your competition, there is nothing wrong with this.

Possibily, your mentor believes you should have checked with others first, but acting rashly is not academic dishonesty.

Answer 4

Are you sure your adviser understood what you did? The concept of GitHub, PRs etc. may be alien to him and he could have understood that you publicly stated that his formula is incorrect, in a non-peer reviewed thing (I am making that up, just to show that interpretations can escalate quickly).

When you cool down, have a conversation with him clearly explaining the context of your update (less the "what" and more the "where" and "how")

Answer 5

There are a few things to consider and clarify:

1. GitHub is not an authoritative academic reference. Journal papers are expected to be thoroughly reviewed and free from most usual mistakes. They have their process for correcting mistakes, which is different from GitHub, where a single person and not necessarily a committee decides what is best for the code. Maybe your advisor does not understand this. In fact, you might quote publications that describe GitHub code, but citing GitHub is pretty much like citing Wikipedia.

2. "Wrong" equations in code might still yield correct results. So it is important to clarify what exactly is the suggested change and impact of the concerned equation and its two versions. EDIT: From OP's clarification, it sounds like the "wrong" formula was actually an "approximate" expression. Never say an "approximate" equation is wrong, in many fields, accurate formulas and models are either unavailable or really hard to handle, people might discuss a lot on whether a given approximation is reasonable or not, but simply claiming it to be wrong is lacking maturity.

3. Science is not about discussing who is right or wrong on the basis of opinions, is about proving what's wrong and what resists (Popper's) falsification. Try to design tests or experiment which may assert what is right or wrong.

4. Not a breach of academic ethics to participate on GitHub, unless your pull request entailed some intelectual property issue. In some research environments, you are required to waive all the products of your work to whoever is paying you (and that makes perfect sense). So a code fix might be understood to be "intelectual property" which you might not be allowed to waive to the public without someone's authorization.

5. Also, it is not a breach of academic ethics to point out when things are wrong, I'd even say it's an academic obligation. However, how you do this might be a breach of social norms. I'd be very pissed at you if you publicly claimed my research to be wrong without even talking to me first, as doing so is common courtesy. It would be much worse if you were actually wrong, as people who are eager to point other's mistakes often dislike admitting mistakes of their own, let alone making reparations. Of course, if I post a repo on GitHub, I'm expecting people to raise issues on it, and do so publicly. But normally, you talk in private first if you think someone has made a mistake. I think that is how your advisor is framing these events. You might go to him and say "I maybe should have talked with you first". But prefer to do so after completing item 3.

Answer 6

The results of teamwork are not solely yours, and you have to be mindful how you share them.

As Mefitico mentioned in their answer, you may not have the rights to use the code you offered to that project. It's important to note that "open source" or "on GitHub" doesn't mean "do whatever" (though there is a license for that too). For example, the popular MIT license includes the provision:

Permission is hereby granted, free of charge, to any person obtaining a copy of this software … to deal in the Software without restriction, including without limitation to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software …

— The MIT License (via Open Source Initiative)

If you were the sole copyright holder, that would be fine — you could offer such a license to your code, and the project could include your code in their code. But it's very likely you're not the only copyright holder:

• If this is group research, you may share copyright with your advisor.
• If you are a paid researcher (e.g., supported by a grant or research assistantship), there is probably a clause in your contract that grants a license to the university or institution, which may be in conflict with the license you would grant to this project.
• Your contract may even grant sole copyright of any results of your research to your university or the institution that funds your grant.
• If you want to publish your results, you may have to transfer copyright of your published material to the journal.

So as you can see, the results of your research really aren't yours to share freely (even if that feels like the goal of research). This is a very common issue for people who write software professionally. It's important to talk with your advisor about what you can and can't do with the results.

---

All that said, it's probably not going to be a big deal. Likely no one will care that some niche open source project has a few lines of code based on this research. But the road to hell is paved with good intentions, and it's easy to get into trouble if you don't pay attention to your licenses.

Answer 7

No, posting an issue on GitHub is not an academic integrity violation

Based on the facts that you have laid out, there is nothing that remotely resembles an academic integrity violation. You say you have provided a reference to the "correct" formula. I understand you to mean that both the approximation and the exact methods are published and widely known. Providing a reference to published work is never unethical. (Willfully misrepresenting it is, but there is no indication that you are doing so, and that does not seem to be what is motivating your PhD advisor's accusation.)

As a suggestion, you should ease up on calling the old implementation the "wrong" formula, since you later clarify that it is a commonly used approximation that gives answers within 5-10% of the exact formula. (From your additional detail, there is no indication that this is what is motivating your PhD advisor's accusation either.)

Other Considerations

About GitHub and Academia

Many academics contribute to projects on GitHub. If you are working in a STEM field, it is almost beyond belief that your advisor would not be familiar with GitHub (at least know that it exists, how it works, and that colleagues are using it), or would not understand that posting code improvements, created by you, and based on properly on cited sources, is not an academic integrity violation. This accusation is completely unhinged. If your advisor is not familiar with GitHub, he has a moral obligation to educate himself before raising the very serious charge of an academic integrity violation.

An important project in my field (I am not a contributor) is PySAL. If someone were to find that a particular formula or algorithm in that library were generating a result that was incorrect, approximate (where an exact solution was available), or just slow and could be improved, that contribution would be welcomed by the maintainers (as it was by the maintainer of the repo that you contributed to). An example that might parallel yours is Improvements to distance functions?, which discusses different methods for measuring Earth distance. Whether that person's PhD advisor valued this contribution--many would, some would not, particularly if it was outside of their field and/or they thought it was interfering with RA responsibilities or your own progress to completion--there is no world in which they would consider a GitHub PR with a properly cited source to be an academic integrity violation.

My own experience: I have been doing redistricting research for a couple of years, and have created or contribute to a number of repos in this field. I often post code related to other topics of interest as well, and post and make use of educational material posted by others in my area of teaching, Geographic Information Systems.

About Protecting Yourself

A number of the responses seem to be trying to consider ways in which your advisor could have misunderstood, or ways in which you might have stepped over a line. You have provided a number of clarifications. However, the facts as you have presented them seem so clear cut, and his accusation so unfounded, that you need to consider how to protect yourself, and how (or whether) to complete your PhD with your current advisor.

Unfortunately, many academics behave in very shitty ways. I'm not certain that we are worse than other industries--finance, law, Hollywood, and many others have a lot to answer for--but it is far too common for graduate students to have to put up with abusive PhD advisors, who often are also work supervisors (if you are a Research Assistant), and who can utterly sabotage your PhD if they choose to. Furthermore, since the emphasis is often on education rather than employment, grad students do not typically get training on workplace harassment and how to report it.

You say that you are depressed, overworked, have no friends, and want to leave academia after completing your PhD. You need to consider your options and make use of available resources.

Things to do immediately

• Seek help from counseling services on campus.
• If you are a member of a union, e.g. graduate students union, or if you are an RA or TA and are a member of a bargaining unit, report your interaction now, and ask them if you should be concerned and what your options are.
• If you are an RA or TA you should report your interaction to HR, perhaps to an office that deals with workplace harassment. If you are not part of a union, reporting to HR will be a first step. If you are part of a union, I would talk to the union first and see how they recommend proceeding.
• Talk to your department chair. You may not be able to get them to do anything, but it should at least give you an idea of what you're up against. Present the facts as neutrally as possible, and ask if there is anything you should do. If the chair does not know what GitHub is and/or seems uninterested in your concern, and closes with "You should talk to your advisor about it," there probably isn't much more to accomplish with them. If the chair seems concerned (and knows what GitHub is), they might offer to talk directly to the advisor, or seek to facilitate a discussion.
• Do not tell your advisor about any outside projects, going to the gym, going on a date, seeing a counselor, or anything related to anything outside your thesis research and job responsibilities (if any).

Things to consider working toward

• Can you switch advisors? This is often difficult, but plenty of graduate students do it. Sometimes grad students put up with awful advisors because of their reputation in the field, but you say that your field was new to your advisor when you started your PhD. Is there anyone else in your department who is working in this field, or a related field, who would be willing to step up? Is there someone else on your committee who could take over as advisor? It may even be possible to change programs, as disciplines are often represented in multiple departments.
• Can you apply to a new PhD program? This sucks, but if there is really no one else at your university that would be a suitable advisor, it is worth exploring. Do you know faculty at other institutions from conferences? It might be worth reaching out to one or two that you have met to discuss options. You do not have to say why you are looking to leave your university at first, though if you decide to pursue this option, it will doubtless come up later.

In the end, you may have no choice but to try to see it through with this advisor. In which case minimize your interactions with him, make use of mental health resources, and start reviewing Academia.SE questions related to bad advisors:

• Advisor's Negativity
• What to do when phd advisor wants me to work on side projects but i'm starting a post-doc?
• Help! Professor/Advisor Refuses to Publish Any of His Students' Research

Answer 8

There may be a few situations in which, from what you describe, your advisor considers an issue of academic integrity. It is not clear what the exact situation of 'your reference' is referring to though. These are pretty speculative until your question is more refined.

1) You are referring to work that is yet to be published or reviewed by your advisor and are publicly releasing it.

2) Your advisor does not think you are clear on the github issue that the reference is to your own work and not the original literature, and it seems unethical to them that you are claiming it is your algorithm when it originally came from your literature review

3) After reading and finding the issue, your advisor noticed that the original code is correct, and that your implementation is incorrect. If you had published this before, your advisor may be making a jump to a conclusion that you were unethical in how you explained your results or your paper to them, which they did not realize until seeing a correct implementation.

Answer 9

I am sorry for what happened to you, even if I don't know wether wrong formula is actually wrong or not.

A country/cultural tag could be interested there, since I think your last edit presents a very rude reaction from you supervisor.

I would recommend something that is often said in company world, but is actually a matter of fact and should be thought about everywhere: Write a mail with feedback of your meeting. You could do it right now with what you described in your edit during second meeting:

• First, explain the facts. Don't use what you said in this post, because it could be misintepretated. Give link rather than explanation. And be overpolite: for example: "I had a comment [link to the comment] on the GitHub [GitHub]. Thank you for the meeting today about this issue".
• Second, state your case: You want to improve the GitHub repository. You want to use a good formula (not correct or wrong, but the best fit) for your PHD
• Third, ask questions: You need to force your Administrator to explain himself in the mail: "Do I need to delete my comment?" "Do I need to ask you before posting in the future?"
• Fourth, trace back what he said: Your supervisor is going to burn you in front of the GitHub Administrator: Trace it by giving the contact (pseudo, mail) of the Administrator in the mail with something along the lines: "You said during the meeting you want to speak with the Administrator: here is the contact"

Besides this advice, I have another subject to raise. I am not familiar with GitHub, but I feel from your text that your supervisor is not familiar with Web and GitHub? Maybe he thinks GitHub is something like a research paper? Then it would explain his behaviour.

But if you think your had passed this step with your supervisor, and that he is of bad faith, you could find a pretext to put in copy another one of the Academia, maybe a superior to both of you.

Anyway don't be too offensive for now. Keep your calm, stay polite, ask question, write done as much as possible.

Answer 10

The advisor is silly but you shouldn’t have contacted them about it in the first place. There was no point, they aren’t your personal censor. I think you could have confused your advisor by contacting them in the first place, and they misunderstood what’s going on or simply had a bad day and decided to be nasty to you.

In other words: there’s nothing to it. Remember it, keep the emails, print them to a PDF and add the PDF “prinout” of the GitHub issue you submitted as well. In case the project were to somehow vanish, your advisor won’t be able to get silly ideas and blackmail you just because they get another case of a bad day or a bad week.

Otherwise treat it as if your advisor had a brain fart. And don’t tell your advisor anymore every time you go to the restroom, or next they’ll accuse you of wasting University water on purpose :/ Sadly, such people exist: they have a tendency to be unpredictable and you reach out to them with the best of intentions and they just turn it into a nightmare. I’m really sorry you got such an unreasonable experience. It was through no fault of your own.

A reasonable response from your advisor would have been to inform you that it’s fine and that there’s no reason to ask for such things.

Answer 11

Let put it this way. You are a very good, devoted employee, and your adviser is a Project Manager. Due to the lack of communication in the beginning that your PM didn't explain the Contract for you or make sure you understand it fully. Any on-progress work you have been working on is subject to your institution under the management of your Manager. He was angry which was not very professional, you accidentally shared your idea stemming from your research to an opensource project was wrong too. So no one is right here. Your PM couldn't use your correct formula anymore since it was merged to that open source so he decided to use another formula. Dont be angry with how complicated in terms the academia created. You can choose to finish your project in your current institution under the management of other PM/advisor or still the same advisor, which depends on you if the PhD is important in your career plan. Otherwise, you can switch to the industrial field and find a suitable position to pursue what you like/love to do. Dont think too much since I have been there. Best of luck to you!!!