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[REVIEW]: DYCO: A Python package to dynamically detect and compensate for time lags in ecosystem time series #2575

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: @holukas (Lukas Hörtnagl) Repository: https://github.com/holukas/dyco Version: v1.1.2 Editor: @KristinaRiemer Reviewer: @mccabete, @r-barnes Archive: 10.5281/zenodo.4964068

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mccabete & @r-barnes, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @mccabete

Conflict of interest

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Software paper

Review checklist for @r-barnes

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whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mccabete, @r-barnes it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

holukas commented 4 years ago

Proof looks good!

mccabete commented 4 years ago

@KristinaRiemer I think the dyco repository aka target repository is being hosted through ETH Zurich. I seem to need an ETH Zurich log-in to add issues. How do you want me to proceed?

holukas commented 4 years ago

@mccabete @KristinaRiemer I will check with ETH Zurich how they handle this and if they can open the registration.

holukas commented 4 years ago

@mccabete @KristinaRiemer I just got feedback from ETH. While the code itself is open to everyone, issues can only be added after registering an account with an email address from the ETH domain. However, there is the possibility to create a guest account for the purpose of adding issues. Would this still be in line with JOSS requirements?

mccabete commented 4 years ago

I can't speak to JOSS requirements, but I am happy to create a guest account for the review. Also, I could just comment my reviews on this thread.

KristinaRiemer commented 4 years ago

@holukas if it's possible to use guest accounts to create issues in the repository, and the issues and their comments are able to be seen publicly, I think that would be the best route. Let me know if that ends up not being possible though!

mccabete commented 4 years ago

@holukas How should I request guest access?

holukas commented 4 years ago

@mccabete I am currently in contact with ETH to open a guest account and get back to you soon.

KristinaRiemer commented 4 years ago

Any progress on the guest accounts, @holukas?

holukas commented 4 years ago

@KristinaRiemer Sorry to keep you waiting, there were some surprising obstacles to overcome that should be solved now. @mccabete Can you get in contact with my via email (lukas.hoertnagl [at] usys.ethz.ch) so we can set up the guest account?

r-barnes commented 4 years ago

Just checking in to see if I should start on my review.

mccabete commented 4 years ago

Sent an email to you @holukas

holukas commented 4 years ago

Hi @r-barnes! Can you get in contact with me via email (lukas.hoertnagl [at] usys.ethz.ch) so we can set up the guest account for the review?

holukas commented 4 years ago

Sent credentials for guest account to @mccabete

KristinaRiemer commented 4 years ago

Hi @r-barnes & @mccabete. Have you been able to create and use your guest accounts? I only see issues from @holukas in the repository.

mccabete commented 4 years ago

Sorry about the delay!

I am still running into issues - @holukas convinced ETH to give me a guest account (thanks!). However, it seems like ETH gave me an account that may/might not include github.ethz.ch privileges. I sent out an email to ETH Zurich's service desk today.

mccabete commented 4 years ago

I am essentially sitting on the review. @KristinaRiemer if the ETH service desk doesn't get back to me soon, I am willing to just post issues/comments on this thread instead. Is that joss-acceptable?

KristinaRiemer commented 4 years ago

@mccabete (and @r-barnes), I agree with your assessment. I think you should not worry about creating issues in the repo and just post your review comments and discussion here in this thread, so as to not slow down the review any more.

r-barnes commented 4 years ago

I worry somewhat about issues getting lost, but can do. @holukas - will that work for you?

holukas commented 4 years ago

Dear @KristinaRiemer @r-barnes @mccabete, after some back-and-forth I decided to move the code over to GitHub to make collaborations and the review work easier. I agree with @r-barnes that submitting issues here might get lost and is not ideal. @KristinaRiemer I would therefore like to cancel this current submission. I will then re-submit the same code, but this time using the GitHub repo. I hope the reviewers are still on-board to review the new submission. I am sorry for the inconvenience and hope for a smooth GitHub workflow. I already uploaded the code to https://github.com/holukas/dyco and I will make an official re-submission after this current one is closed. Thanks!

KristinaRiemer commented 4 years ago

That seems like a good solution @holukas! There's no need to reopen a new submission, I just changed the repo URL in the first comment of this review issue so we can continue using this issue.

KristinaRiemer commented 3 years ago

@mccabete & @r-barnes just checking in to make sure that the new GitHub repo's issues are accessible to y'all now, and to see if there are any questions or issues currently?

KristinaRiemer commented 3 years ago

Hi all! Hopefully everyone had a good holiday season. @r-barnes & @mccabete I'm checking about progress on your reviews of this software. Now that the issues permission problem has been taken care of by migrating everything over to GitHub, is there anything blocking your work or anything I can do to help move this forward?

mccabete commented 3 years ago

Thanks @KristinaRiemer for the reminders. Sorry for not getting back to you both! @holukas, I added my comments as issues to the new repo.

The Wiki link is now behind an ETH login, so there was some content I had access to that I no longer have access to. That said, I had already gone through the wiki content before the migration, so I was able to post my comments. Likely 98% of my review is now posted, and once the link is fixed I can verify the final remaining check marks.

Thank you for being helpful and patient @KristinaRiemer and @holukas

r-barnes commented 3 years ago

@KristinaRiemer : I can't seem to mark things off in my designated reviewer checklist above. Is there anything I can do about that? If not, I can keep track manually.

KristinaRiemer commented 3 years ago

@r-barnes let's see if this fixes that.

KristinaRiemer commented 3 years ago

@whedon re-invite @r-barnes as reviewer

whedon commented 3 years ago

The reviewer already has a pending invite.

@r-barnes please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

KristinaRiemer commented 3 years ago

Ah, @r-barnes try going to that link and accepting the invite to see if that makes a difference?

r-barnes commented 3 years ago

I'm sorry, the link expired. Can we try again? I have my JOSS reviews at the top of the queue now, so I'll be ready for it.

holukas commented 3 years ago

@mccabete Thanks for the feedback. Unfortunately the Wiki got lost during the migration from GitLab to GitHub. I will add an updated Wiki directly to GitHub in the next days.

KristinaRiemer commented 3 years ago

@whedon re-invite @r-barnes as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@r-barnes please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

r-barnes commented 3 years ago

I've finished my review, per the above.

I think the biggest issue is that I'm left confused about whether Dyco is a tool I use kind of from the command-line or a library I use from within Python.

It looks as though Dyco produces a number of output directories and files, even if it's run from within Python. I think that's weird. Running commands from within a programming language should (mostly) give me products I can work with from within that language.

Conversely, the example I saw shows Dyco being run as a single, very large command from within Python to produce all of those outputs. So it's almost as though I have to open Python to run what's effectively a command-line command. If this is what's happening, then the authors should embrace the command-line nature of the work and modify their setup.py to add CLI commands.

Other than that, things look pretty good. The code appears clean and decently structured, though there is some missing documentation and dead code. Cleaning that up shouldn't be too difficult, though.

KristinaRiemer commented 3 years ago

Thank you @mccabete and @r-barnes for adding specific comments as issues to the software's repo, hopefully @holukas will have a chance to address all of them soon.

holukas commented 3 years ago

Thanks @mccabete and @r-barnes for the helpful comments! I will address the issues over the next days.

KristinaRiemer commented 3 years ago

Hi @holukas, just checking in to see how working on these issues is going for you?

holukas commented 3 years ago

Hi @KristinaRiemer, I am nearly finished with the Issues. I was not sure if I should close the issues if I think they are done, or if it is up to the reviewers to confirm that an issue was solved and then I can close them. What would be the correct procedure?

KristinaRiemer commented 3 years ago

@holukas I think we should do the latter. When you're done addressing all of the issues, let the reviewers know here. They can then review the work you've done and you can close the issues once they indicate they're satisfied with it. Hopefully that's the easiest way for @r-barnes and @mccabete to keep track of everything!

holukas commented 3 years ago

Dear @KristinaRiemer @r-barnes @mccabete,

thank you all for your input and feedback, highly appreciated! I have now addressed all issues and followed up on your suggestions. The script and documentation underwent quite some changes and I hope DYCO now meets the criteria for publication. Please let me know in case there are further changes you would like to see.

Cheers Lukas

KristinaRiemer commented 3 years ago

Hi @r-barnes and @mccabete, have you had a chance yet to review the addressing of your issues in the DYCO repo yet? Please let me know if you need any help.

KristinaRiemer commented 3 years ago

Hi @r-barnes and @mccabete, this is just a reminder to look over your issues in the repo. If @holukas has sufficiently addressed them, feel free to comment and close. Hopefully this can be taken care of in the next week?

r-barnes commented 3 years ago

Sorry for going MIA. I've noticed github's notification system has improved, so hopefully I can make better use of that in the future. I'll take another look and see if we can get this wrapped up.

KristinaRiemer commented 3 years ago

Thanks for the update @r-barnes. I've struggled some with GitHub notifications, including accidentally turning off notifications for this entire repository (and therefore notifications for all submissions I'm editor for!), so I definitely understand that pain point.

KristinaRiemer commented 3 years ago

Hi @r-barnes and @mccabete, have you had a chance to look through the issues that @holukas has addressed?

r-barnes commented 3 years ago

I hope to have time this weekend or late Friday night :-(

r-barnes commented 3 years ago

@mccabete : I accidentally clicked some of your check boxes :-( There's not an undo button, so I tried to reverse as best I could, but may have made a couple of mistakes.

r-barnes commented 3 years ago

I feel like my concerns have been reasonably addressed and that the remaining issues I've left open shouldn't preclude moving this toward publication. My ability to really deep-dive into the results/processing of the package is hampered by my lack of domain knowledge here, but I think there's sufficient explanatory information that a user with this knowledge would be able to figure out what's going on and derive value from this software. I'm happy to approve this.