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

[whedon]

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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Markdown: [![status](https://joss.theoj.org/papers/029f5d2be79462dd069e4541e7d16af2/status.svg)](https://joss.theoj.org/papers/029f5d2be79462dd069e4541e7d16af2)

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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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @mccabete

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@holukas) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @r-barnes

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@holukas) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

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 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[holukas]

Proof looks good!

[mccabete]

@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]

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

[holukas]

@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]

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]

@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]

@holukas How should I request guest access?

[holukas]

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

[KristinaRiemer]

Any progress on the guest accounts, @holukas?

[holukas]

@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]

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

[mccabete]

Sent an email to you @holukas

[holukas]

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]

Sent credentials for guest account to @mccabete

[KristinaRiemer]

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]

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]

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]

@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]

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

[holukas]

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]

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]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.2307/1941631 is OK
- 10.5194/amt-8-4197-2015 is OK
- 10.1016/S0022-1694(96)03194-0 is OK
- 10.1111/gcb.12518 is OK
- 10.1007/BF00128405 is OK
- 10.1515/intag-2017-0042 is OK
- 10.1111/gcb.14079 is OK
- 10.1007/978-94-007-2351-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2395

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2395, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@holukas - As part of a final proofread, I have suggested some changes in holukas/dyco#19 - please merge these or let me know what you disagree with, then we can proceed with the publishing.

[holukas]

@danielskatz There is only one small thing that needs to be changed, I commented directly in holukas/dyco#19

[danielskatz]

Sorry, I don't see any comment in holukas/dyco#19

[holukas]

@danielskatz Should be visible now (I forgot to hit the button it seems...).

[danielskatz]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[danielskatz]

@holukas - please confirm this looks good now, and I'll go ahead and publish it

[holukas]

@danielskatz There is only one small typo that I found. In the PDF L131 please change "compensated" to "compensates", rest looks good.

[danielskatz]

You can and should do that, since it's in your repo :) When you do it, run @whedon generate pdf again and then let me know that it's ready to publish

[holukas]

Yes you are right :)

[holukas]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[holukas]

Looks good and is ready to publish!

[danielskatz]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02575 joss-papers#2396
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02575
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @holukas (Lukas Hörtnagl)!!

And thanks to @mccabete and @r-barnes for reviewing, and @KristinaRiemer for editing!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[holukas]

Thanks a lot for your support @KristinaRiemer @mccabete @r-barnes @danielskatz (and whedon)!

[KristinaRiemer]

Congrats @holukas, and thanks for reviewing @mccabete and @r-barnes!