update paper #887
Comments
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In an attempt to avoid any debate (so we can focus on tackling other open issues), hopefully we can get an immediate decision: Reading the editor-in-chief's comments very carefully, in particular where and when others are To further prompt a decision:
I understand that is a big request with a lot of responsibility and research associated, especially considering the voluntary nature of the JOSS team's work. However I would very much appreciate if at least a suggestion if not a decision is provided. |
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Hi! Here I am! Arfon wrote: "all significant contributors should be included in the author list." I consider myself to be a significant contributor, by writing the initial working version. I acknowledge that a lot of significant work has been done since, probably with much more time spent than my initial effort. However, I still consider myself to be a significant contributor. Cheers, |
Apologies if this is how my comment was interpreted, this is not what I was trying to imply because...
I disagree. The journal's responsibility is to ensure that there has been ethical behaviour on the part of authors, reviewers, and editors. It it not the responsibility of the journal to decide who should be an author on a given paper. As I said in this comment authorship is a challenging subject and something that the authors/contributors of the package are best-placed to decide between themselves. To be absolutely clear here I think if @noamraph wants to be an author, he should be. Hopefully this is useful additional context. I am hoping this additional input from myself will be sufficient to guide you all in your decision. As I said over in openjournals/joss-reviews#1277 (comment), this is a conversation that needs to happen between you all, and really isn't something that I can/or should be steering. |
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Hi all, I'd like to introduce @gkthiruvathukal who is a member of the JOSS editorial team. @gkthiruvathukal has kindly volunteered to act as a neutral mediator/third party in these discussions. As past Editor in Chief of CiSE he has a wealth of experience with discussions such as these. |
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@arfon Thanks for the introduction. I've taken the time to look at tqdm. It's great to see all of the work that has gone into this effort. As the neutral mediator (and observer in general) I'd like to encourage us to start from the The Strong case for co-authorship: Strong case for acknowledgments and possible co-authorship: Again, I remind everyone that this is coming straight from the tqdm landing page. In Software Engineering, I teach that not all contributions can be measured by LOC or number of commits. There are multiple ways to make an impact, and sometimes an enormous amount of impact can be made without the singular focus on LOC (or commits). For example, there can be developers who write good tests, configuration scripts, and documentation. These all make for great projects, and tqdm seems to have most of the good things in SE going for itself. This project is lucky to have such a great group of contributors, and it is my hope that you all can work to understand the importance of your software being well-cited as opposed to individuals. @arfon and I have discussed this case, and we don't want to make decisions for you. We are both in agreement that this submission needs to recognize all co-authors in order for it to remain a JOSS submission, so if you are mentioned above, perhaps you can respond (concisely) with whether you agree with the above initial analysis. If you think you should be on a different list (co-authors or acknowledgments) than my initial triage, please make this clear in your follow up. I promise to hear everyone's input and help you to reach a conclusion that is good for the project and those who have made the most significant contributions to its success. This is a nice project and is the sort of contribution we really like to see submitted to JOSS. I'd like to see if we can bring the authorship issues to a resolution by Friday, 31 January, so JOSS can decide on the next steps, which will involve revising the submission one way or another. |
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@gkthiruvathukal, I have no concerns with your initial groupings for attribution. @lrq3000's comments about lack of attribution of changes had me a little worried as I remembered some funny feelings with some of my contributions. I think the primary missing part on my contributions was that two PRs showed as closed, not merged (#673, #622). The commits they were closed by do show me as author but for some reason have @casperdcl as committer. #674 (adding four words on one line...) was closed and a different solution committed without referencing me (no complaints here). #598 (my only significant contribution) was merged per normal GitHub methods. I closed #590 because I took a different approach in #598 that replaced it. I won't speak to @lrq300's issues but the only comment I would have related to mine is that it would probably be good practice to use the GitHub merge button so it shows up as merged in GitHub. It supports merge, squash-merge, and rebase so hopefully there's sufficient flexibility to satisfy personal git preferences. Based on the infamously questionable metric of lines of code I would give @lrq3000 'author' level attribution. https://github.com/tqdm/tqdm/graphs/contributors (5220 lines compared to @casperdcl's 23,267 lines). It sounds like if I actually bothered to research it I would give 'author' level attribution for other reasons as well. Based on being the original author (I think there isn't contention on this 'fact'?) I would give @noamraph 'author' level attribution. Should I be an 'author'? Aside from the whole conflict of interest etc in me weighing in on credit due to me... I think it depends. Is an author someone that authored a block of code for tqdm? Or is an author someone that has contributed primary architecture or a large featureset? I certainly contributed one non-trivial bug-fix. I certainly did not design or author a significant portion of tqdm. I suspect that the sensible answer is to put me in the 'acknowledgements' group, not co-author. If I get co-author for my one bug-fix then we should look at everyone else that made non-trivial bug fixes and feature additions and include them as well. Oh, to be complete, I'd put @casperdcl in the 'author' group as well. |
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I would give @noamraph, @lrq3000 and @casperdcl 'author' level. As for me, I don't think I should choose for myself rather I will let others choose for me. That being said I am fine either way. The only thing I ask is to at least be cited in a 'history' paragraph. My contribution to the code is much more modest than the devs I've cited above but I would like to highlight that I am the one who originally forked Quickly after the creation of I don't know if the project would be different today without me forking it. I guess probably not, since someone would have done it anyway at some point. That was my modest contribution to the debate. I hope everyone will get their deserved acknowledgment/authorship without any more drama :-) |
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@hadim and @altendky, thanks for your quick follow-up. I am going to continue observing, but my initial reaction is that you probably deserve more than an acknowledgment for your contributions as significant contributors. I always take an inclusive approach to contributions, no matter how large or small. Hopefully, the lead contributors will chime in with whether we could live with the top contributors as minor co-authors. We can easily arrange the co-authors in any order. I don't think there is much doubt about @casperdcl, @lrq3000, and @noamraph but am at this point hoping the three of them could agree to be co-authors and invite any additional authors with a strong case for inclusion. |
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@gkthiruvathukal, agreed as far as tending towards more inclusivity. Is there something that restricts to co-authors and acknowledgments as opposed to adding a contributors group in between? I wouldn't feel slighted being 'merely' acknowledged but if there's any contention on the topic for others then perhaps more categories would help (I mean... three anyways, not 17). |
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Hello everyone! Thank you all (including Casper) so much for your feedbacks! Sorry for my delay, I tend to always spend more (too much?) time on research before doing anything :-) Thank you very very much @gkthiruvathukal and @arfon for accompanying us and your very valuable insights on this issue! About the main issue at hand, here are my suggestions:
Questions that need to be resolved:
For efficiency, I have created an etherpad (collaborative text editor) with a rough outline of my idea of the changes we could make, so that everyone here can contribute (if there is any vandalism, I can make it private and invite manually), and it's still of course meant to change depending what we agree on: https://board.net/p/tqdm-paper (Please enter your name in the upper right corner, language can be changed in the settings if it's not autodetected from your browser) |
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(For those who received the email notification, I have change the URL for the pad to be in English by default, please prefer to use this URL: https://board.net/p/tqdm-paper ) |
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Responding to @lrq3000's questions: Q: Arfon, you said the paper will be reviewed through a "fast-track", so @gkthiruvathukal do you know if this means we should stick with minimal modifications (ie, we shouldn't rewrite significant portions of the paper), right? Would a new History section (along with Acknowledgements) be ok? A: Yes, the modifications would be minimal, and a complete rewrite should not be necessary. Q: How do we organize the attributions? There are three possible places: In paper's authors list, In paper's body in context, In an Acknowledgements section. A: Speaking as an observer, I'd like to see as many authors as possible. I know tqdm is important, but let's remember that the paper with the record number of authors on LHC (Large Hadron Collider, a super important project, too) is more than 5,000 authors, https://www.nature.com/news/physics-paper-sets-record-with-more-than-5-000-authors-1.17567. Did everyone contribute equally to this paper? Did everyone even write it? Or do the actual research? We'll never know, but they're all co-authors. We have a much smaller number of potential authors here? I'd like to see as many included as possible, provided their contributions can be justified in quantitative or qualitative terms. Q: In relation to the previous point, we also need to assess the contributions to the code. There are several tools for that (next I'll experiment with them). @gkthiruvathukal is there a tool (apart from git fame) you would advise to explore in more fine grained details the git history? We should also review issues since some were not properly merged in. A: I continue to research on this topic, but there are no really great tools, which is why I'm doing research on software metrics (hoping to change the state of affairs). One possible way is to look at other data that might show activity. You seem to have a fairly active issue tracker. Perhaps you can look at how many members of the team helped to raise and/or resolve issues. Did any contributors help, specifically, with user-facing aspects of the software (testing, docs, etc.?) In the end, however, this can't be left entirely to data. It comes down to team dynamics and people advocating for others who may have made significant contributions. It seems like we already have convergence on some key contributors. The question is, are there any other minor contributors who are worthy of co-authorship? I would like those in a strong position to speak for those who may not be willing to advocate for themselves. Once I see all of the responses, I will synthesize a list of co-authors. Again, I must stress that Arfon and I do not want to make the decisions for you. And similar to @lrq3000, I prefer to focus on research. Oddly, this project is helping to motivate the need for metrics, which is the subject of some of my current research. (Lest I digress.) I won't speak to the "end game" because @arfon and the board are still discussing how to handle papers where the DOI and its metadata may need to be changed. My goal is to help mediate the (ethics) issues that were raised and help everyone to bring the matter to a graceful (and civilized) conclusion. There seems to be a lot of goodwill here, and I am pleased with the responses I have seen thus far. I'm optimistic we can come together to get the co-author list right! |
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@gkthiruvathukal Thank you so much for your again very enlightening reply! And I hope you'll get all the funding needed to pursue your goal, it would really help to have better metrics indeed ;-) I get what you said, although I have I think a fairly good memory of what happened and all contributors (I tend to have a good memory of those things, as I am always grateful to anyone who freely spend time to help others such as in opensource projects), I don't know what happened after, so I'm now going to try to explore the history with tools and manually to get a more comprehensive view and then I'll offer suggestions :-) (this may take some time, any help is welcome, if anyone has some contributors in mind please feel free to cite them!) |
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Thanks for your support, @lrq3000. I had some funding for work on this topic, but it was only enough to prove some initial concepts. If interested to hear more, we can correspond sometime after getting tqdm's issues sorted out! It would be great if we can get a HISTORY.md document produced. This would go a long way to clarifying how the project came to be--and how it evolved. Although I suggested Friday as a deadline for gathering initial input, that doesn't mean we can't wait, especially if it means we will include everyone who deserves to be included. |
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@gkthiruvathukal Oh yes, I would be delighted to hear more! Yes great idea for HISTORY.md, I'll direct my effort towards drafting that then :-) |
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Actually, @casperdcl did a great job documenting changes and PRs in Releases, so maybe we can use that to build a HISTORY.md? |
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Here's a first attempt HISTORY.md generated by the wonderful github-changelog-generator. It neatly shows the contributor for PR that were merged in. I think this should be usable as a basis to refine :-) |
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Hi everyone, apart from my wish to be listed as an author, I would accept any decision that you take. I have no problem with the list of authors being inclusive. I'm grateful for all the hard work that you spent making my little project into something so awesome! Regarding history, I first wrote tqdm where I worked, at about 2006. Iterators where pretty new, and I really liked the possibility of showing a progress meter with only adding a few characters. I chose the name "tqdm" because I looked for a short and unique name, and I really like Arabic. (I'm a Jewish Israeli). "tqdm", which is Arabic "تَقَدُّم" in Latin letters, pronounced "taqaddum", simply means "progress". The small library turned out to be very popular in my work place, so I decided to open source it. |
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Hey! I think that any arrangement which includes @casperdcl, @noamraph and @lrq3000 as authors and mentions @hadim in some way is fine; their contributions were critical for having tqdm as it is now. It seems most proposals here suggest something similar anyways 👍 |
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Ok, I am synthesizing here. As you read this, please keep in mind that I do not know any of you personally and am focusing on the input you've given and what git tells us. I think there is strong consensus for @casperdcl, @lrq3000, @noamraph (probably in that order). Based on my earlier report, I think there is a strong case for @altendky as the 4th author, based on my earlier analysis and his follow up (where he took great care not to say whether he should be a co-author). In his case, however, he seems willing not to be a co-author but has made non-trivial contributions to the success of the project. For this reason alone, I take the view that he should be a co-author. I'm aware that number of commits and lines of code are not the only measures, but in looking at the actual commits, I am convinced his contributions are significant. As I mentioned, I am hoping to have any and all input by Friday of this week, after which I think @arfon can take the next editorial steps. Based on the information I have in git and on this issue thread, I feel comfortable moving toward these four as co-authors in the order mentioned but would certainly appreciate if all who have commented would react (an emoji will do) to this proposal. |
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There are two very distinct issues: ongoing maintenance of the library 1)
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A good point about authors of paper vs authors of the software. I can see how the whole situation could have arised from different expectations here. From https://joss.readthedocs.io/en/latest/submitting.html:
In the example below a "correct format" is used to define authors with affiliations, which is then shows as authors of the paper. From this I conclude that in JOSS it is expected to have authors of the software as authors of the paper. https://joss.readthedocs.io/en/latest/review_criteria.html#authorship asks for the list of authors to be reasonably complete. From this it follows that a list of paper authors should be a reasonably complete list of software authors. Then they ask community to decide what would be a reasonable list of authors. Wording may not be the most precise, but I think then intention is clear. So let's do it :) How to decide who's an author is subjective, and several approaches are possible. I don't think any legal stuff about authorship matters here. Rules are different in different countries, and we're not in the court. The whole thing is just about fairly acknowledging people for their contributions. Picking some top contributors, considering their code, discussion and historical contributions looks like a fair way to define an author list. Considering everyone who contributed an author also sounds fine to me. There is also an Acknowledgement section, which can be used to highlight contributions of people who're not in the author list. Alternatively, I think it can be used to highlight top contributors, if "all contributors are authors" approach is taken. It doesn't look that complicated, after all. Two concrete proposal on how to update the paper, which seems to be in line with the guidelines: Proposal A.
Proposal B.
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@casperdcl , you are shooting yourself in the foot. This situation is your fault, not JOSS's. This situation arose because you wrote the paper on your own without reaching to any other co-developers, with the exception of me when a JOSS editor requested it. This was evidently an unreasonable procedure. As you have worked in research, you know that the authors of a paper must include all those who contributed to the experiment. It would be foolish for any of the team member to quickly write a paper secretively, submit it as the sole author, and then claim they are right to do so because noone else contributed to the paper, that's an obvious circular reasoning. If you had reached to other developers to invite in the writing, and noone would have answered, then it would make for a far better case for you to be the sole paper author. But pre-emptively avoiding contacts barred any other contribution. So no need for legalese, just common ethical sense. I suggest we stop on this slippery path and come back to fixing the issue at hand. Although @gkthiruvathukal makes suggestions, which I am thankful for, we ultimately are the ones to decide, which is only logical (they only arbitrate). I agree the Zenodo list of authors can be a good basis, but maybe complemented? Also the order seems subjective, I would like to ensure some degree of objective fairness (if that is at all possible)... Side-note, about the legal status, if it comes to the worst, the whole project can probably be easily rebased on my minimalist implementation which I made from scratch. I don't know if it still lives here (in the PRs?) but we can certainly find it somewhere. |
Even if I did have anything in mind, I'll pass. I stated that you handled my contributions appropriately and what did you do? Rebutted that statement point by point. *boggle* I also commented that while I understand personal preference in workflow that your preference has the presumably unintended side effect of marking PRs as closed rather than merged which can be a bit confusing. Instead of understanding that point you... again, rebutted it. Please consider not responding to this at all and instead just thinking about the slight feedback on workflow.
Clearly that is not an insulting statement. At the same time, there was certainly chance involved in venvs (was it mkenv at the time?) deciding to use tqdm before py2 went eol and capturing the output in the tests thus showing the bug and me being involved enough at that time that I decided to try to fix the issue rather than just dropping use of tqdm, etc. So, @casperdcl, is the summary of all that you wrote here that you are not clear as to what 'authors' are being discussed and whether they are supposed to be 'the people that wrote the paper' vs. 'the people that wrote the library'? That seems like something that @gkthiruvathukal could probably clear up if it's still in question. Though I haven't been involved in research so I may really be missing something. |
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ping @Separius, @RunOrVeith, @JoshKarpel, @JaviMerino, @EdwardBetts, @AbysmalBiscuit: Please see #887 (comment), looks like GitHub hit a limit with the long list, so you may not have got the mention. Cheers! |
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thank you for considering me! But with occasional whining and a single commit (c49021d) I do not consider myself yet deserving the honor! Thank you again and good luck! |
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My contribution was also trivial, and I have not reviewed the paper. Please do not add me. |
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Thanks for considering me. And yes, I agree to be a co-author. |
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Happy to be a co-author. |
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Thanks for the invite, but my contribution (so far) does not warrant authorship; please remove me from the list. |
In my case, IP rules of my university that I probably signed when I was hired state something to the effect of: if any university resources were used, the contribution I make is not my own. Even if I didn't explicitly sign a document to that effect, these rules are nonetheless in place and govern my ability to maintain employment - i.e. I can be fired if they "find out" that I'm using their resources but going around their back and claiming "ownership" over something. Ostensibly, these rules even apply to the use of e-mail from off-campus outside of normal working hours for non-university related things, but practically speaking they probably only enforceable when I'm sitting at my desk or otherwise "clocked in." In any case, I used tqdm as part of a script that I was writing at work, for work. The contributions I made stemmed from changes I made to do my job. Ergo, the university owns it. Ergo, my affiliation applies. This all being said, I'll be leaving the university next month and moving across the country, but there's no need to burn bridges and claim that the little bit of code I contributed is mine and mine alone. |
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yes, I agree to be a co-author |
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yes, I agree to be a co-author. Just in case if affiliations or email is needed, please use |
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yes, I agree to be a co-author |
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Thank you for considering me 👍 . My contribution was very small. In my opinion I should not be included as co-author. |
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Thank you for considering, but my contribution does not warrant authorship - please remove me from the list. |
However in your case legally the situation could be potentially far more complex. Given it's a minor contribution it's unlikely that any of this applies, but strictly speaking:
Sorry for going off on a tangent but I think I'm as interested in legal theory as you :) |
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Hi
thanks for asking, but I only did a one line change (more like a one
word change), so no need to add me as an author.
Arun
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Please don't include me, my contribution doesn't warrant co-authorship. |
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Don't include me, I don't consider my contribution to be substantial enough to be a co-author. |
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I agree, ORCID: 0000-0002-9300-0741 |
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My contribution was trivial, and I have not reviewed the paper. Please do not add me as a co-author. |
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Thanks for asking, but I don't think a typo fix qualifies. Please don't add me to the paper. |
Your take is probably correct. In my particular case, there's 0% chance they would find my open source software participation problematic, as the unit I work with is all about promoting the 'sister' to OSS: open data. They might have issue with the balance of time I spend on certain tasks, but they hired me for who I am. Edit: thank you also for clarifying your stance re: affiliation. I had noticed that my affiliation had been included as requested, but wasn't certain if that was just a temporary appeasement or not;) Your response clarifies your intent and I agree that your take on the topic seems appropriate. |
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Thanks, I'd be happy to be listed as an author. My contribution was small, but if you and the journal think it's enough, I'm pleased to be included. Name: David W.H. Swenson (That's really one affiliation, even though it looks like more. But it's what they tell me to put on papers.) Personal aside: I'm actually quite proud of my (tiny) contribution to tqdm. It was exciting to contribute to a project with such wide impact. And the existing code was clear enough that it was as easy for me to fix the problem as it would have been to write an issue explaining it. |
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I contributed support for explicitly known infinite iterators. Name: Veith Röthlingshöfer Is there a way to review/read the paper before publishing? |
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I decline co-authorship, but am grateful for this project and the thought you’ve put into this process. Godspeed! |
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Don't include me. |
@RunOrVeith, the source is here:
There's a proof here: |
and others
Discuss updating paper (archived at https://doi.org/10.21105/joss.01277) as per openjournals/joss-reviews#1277.
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