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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:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @KristinaRiemer know.

✨ 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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @r-barnes

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

KristinaRiemer commented 3 years ago

Thanks for the review @r-barnes! @mccabete, it looks like you have a few items left on the review checklist and have two issues open in the software repo, so let me know if you need any help addressing those!

arfon commented 3 years ago

👋 folks, what's the status of this submission? It looks like we might be waiting on @mccabete to do a final check on the modifications by the author here?

mccabete commented 3 years ago

Thank you for the kind reminders @arfon and @KristinaRiemer. Sorry, my github notifications we not reaching me. Thanks for your patience, @holukas. I just checked everything off!

KristinaRiemer commented 3 years ago

@arfon thank you for checking in on this! @mccabete it looks like the "functionality" and "summary" items in the check list are currently unchecked, do you have further comments about those areas?

mccabete commented 3 years ago

Nope! Sorry, just missed those

From: Kristina Riemer @.> Sent: Wednesday, June 2, 2021 11:18 AM To: openjournals/joss-reviews @.> Cc: Mccabe, Tempest @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: DYCO: A Python package to dynamically detect and compensate for time lags in ecosystem time series (#2575)

@arfonhttps://github.com/arfon thank you for checking in on this! @mccabetehttps://github.com/mccabete it looks like the "functionality" and "summary" items in the check list are currently unchecked, do you have further comments about those areas?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/2575#issuecomment-853116751, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFCH6F6KMJDQ5GQLOO3A4L3TQZDUZANCNFSM4P73JFRA.

KristinaRiemer commented 3 years ago

Okay, thanks @mccabete. I checked those off just for the sake of completion.

@holukas there are a few more steps to go before publication. I'm going to check over the paper for typos and such, and it's suggested that you do also. Once that's done, I'll ask for archive links.

KristinaRiemer commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

KristinaRiemer commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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
KristinaRiemer commented 3 years ago

Okay, I found only a few small errors for you to fix in the paper @holukas:

It also looks like the subscripts on CO2 and N20 aren't rendering. You put them correctly in the markdown, so I'm not sure what's going on and someone is looking into why that's happening.

KristinaRiemer commented 3 years ago

Hi @holukas, it looks like the syntax for the subscripts should be with ~ instead of <sub> for some reason. So CO<sub>2</sub> should instead be CO~2~. If you can modify those in the paper, we'll see if that works!

holukas commented 3 years ago

Thanks @KristinaRiemer for checking the PDF. I made the corrections and adjustments, except regarding the reference International Agrophysics. It seems like that the ellipsis was added when the PDF was generated and I am not sure I can change this from my side. In the .bib file all authors are included with their full name. Regarding the double captions for the figures, I now left the captions empty when importing the images, I hope that works.

KristinaRiemer commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

KristinaRiemer commented 3 years ago

Okay, I can't figure out why it truncated the author list for that reference, but I guess it's a default for a reason, so we can leave it. Thanks for making all those changes to the paper!

The next steps for you to do @holukas are: 1) Create a tagged release of the GitHub repo (instructions here) and post the version number here, and 2) generate a DOI by archiving the code on Zenodo, figshare, an institutional repository, etc. and provide that DOI. Make sure the archive has the same title as the paper title, and the same authors.

danielskatz commented 3 years ago

👋 @holukas - note that this is basically ready to accept and publish, and is waiting on you to do the 2 items above

holukas commented 3 years ago

@KristinaRiemer 1) I have created a new release on GitHub, the version number is v1.1.2: https://github.com/holukas/dyco/releases/tag/v1.1.2 2) I have archived the this version 1.1.2 on Zenodo, DOI: 10.5281/zenodo.4964068 https://zenodo.org/record/4964068

holukas commented 3 years ago

With the submission coming to a close, I wanted to thank @mccabete @r-barnes for reviewing the code. I highly appreciate your helpful comments and suggestions!

Thank you @KristinaRiemer for guiding me through the publication process!

KristinaRiemer commented 3 years ago

@whedon set v1.1.2 as version

whedon commented 3 years ago

OK. v1.1.2 is the version.

KristinaRiemer commented 3 years ago

@holukas thanks for getting these together!

For the Zenodo archive, could you change the name of the archive to the name of the paper ("DYCO: A Python package to dynamically detect and1compensate for time lags in ecosystem time series")? Additionally, could you make the author name your name as in the paper?

holukas commented 3 years ago

@KristinaRiemer I have updated the Zenodo record accordingly: https://zenodo.org/record/4964068

KristinaRiemer commented 3 years ago

@whedon set 10.5281/zenodo.4964068 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4964068 is the archive.

KristinaRiemer commented 3 years ago

Excellent! That looks perfect.

I'm now turning this over to the EiCs for final acceptance and publication.

KristinaRiemer commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
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 commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2395

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

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

holukas commented 3 years ago

@danielskatz There is only one small thing that needs to be changed, I commented directly in https://github.com/holukas/dyco/pull/19

danielskatz commented 3 years ago

Sorry, I don't see any comment in https://github.com/holukas/dyco/pull/19

holukas commented 3 years ago

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

danielskatz commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 3 years ago

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

holukas commented 3 years ago

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

danielskatz commented 3 years ago

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 commented 3 years ago

Yes you are right :)

holukas commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

holukas commented 3 years ago

Looks good and is ready to publish!

danielskatz commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2396
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02575
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

Congratulations to @holukas (Lukas Hörtnagl)!!

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

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02575/status.svg)](https://doi.org/10.21105/joss.02575)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02575">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02575/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02575/status.svg
   :target: https://doi.org/10.21105/joss.02575

This is how it will look in your documentation:

DOI

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holukas commented 3 years ago

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