[REVIEW]: baseflow: a MATLAB and GNU Octave package for baseflow recession analysis

[editorialbot]

Submitting author: !--author-handle-->@mgcooper<!--end-author-handle-- (Matthew Cooper) Repository: https://github.com/mgcooper/baseflow Branch with paper.md (empty if default branch): joss Version: v1.0.0 Editor: !--editor-->@elbeejay<!--end-editor-- Reviewers: @alessandroamaranto, @tianydong Archive: 10.5281/zenodo.8401301

Status

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HTML: <a href="https://joss.theoj.org/papers/d0adcf9e526c841f7265c30844c576a3"><img src="https://joss.theoj.org/papers/d0adcf9e526c841f7265c30844c576a3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d0adcf9e526c841f7265c30844c576a3/status.svg)](https://joss.theoj.org/papers/d0adcf9e526c841f7265c30844c576a3)

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

@deboraydo & @aymnassar & @alessandroamaranto, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @alessandroamaranto

[mgcooper]

Hi @mgcooper - I need the title of the zenodo entry to match the title of the paper, if you could do that it'd be great.

Hi @elbeejay Are you referring the "title" field of the .zenodo.json file? If so, I updated it as requested.

Regarding the license file, I changed it to LICENSE as requested. I am not sure why it was COPYING but apparently that is the GNU standard. I find it off-putting so I am glad that you asked to change it.

Please let me know what else I can do. Thank you, Matt

[elbeejay]

Hi @mgcooper, I am referring to the title as shown in the sceenshot below:

JOSS asks that the title and authors (and ORCID information etc.) shown there in Zenodo match what's on the paper.

Hope that helps clarify.

Thanks

[mgcooper]

@elbeejay OK should be done.

[elbeejay]

@editorialbot set 10.5281/zenodo.8401301 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8401301

[elbeejay]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.cageo.2016.10.005 is OK
- 10.1029/WR013i003p00637 is OK
- 10.1029/97WR03068 is OK
- 10.1137/070710111 is OK
- 10.1029/2018WR022816 is OK
- 10.1029/2022WR033154 is OK
- 10.5194/hess-21-65-2017 is OK
- 10.1016/j.envsoft.2021.104983 is OK
- 10.1029/WR004i005p00973 is OK
- 10.1029/2008WR007392 is OK
- 10.5194/hess-24-1159-2020 is OK
- 10.1029/2008WR006912 is OK
- 10.1016/j.advwatres.2017.07.013 is OK
- 10.1029/2005WR004241 is OK
- 10.1016/j.advwatres.2005.03.019 is OK
- 10.1029/2006WR005080 is OK
- 10.1029/92WR02087 is OK
- 10.1002/wrcr.20407 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[elbeejay]

Thanks @mgcooper - next one of our associate editors will do one last review of the submission and finalize the publication. Big thank yous to @alessandroamaranto and @tianydong for reviewing this work!

[editorialbot]

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

No declaration for attribute displaystyle of element mfrac

[mgcooper]

@elbeejay is there something I need to do to resolve this error?

[elbeejay]

Good question @mgcooper - I haven't seen it before, and it isn't obvious to me how to fix it (or how to re-trigger the job), so I'd say hold off for now.. @kthyng please weigh in when you get a chance, thanks!

[mgcooper]

@elbeejay @kthyng Sounds good, thanks. I did want to flag the latex formatting in the .md file as a possible source for the error. Also, since the error is related to the paper.jats file, I just wanted to mention that this file is generated when I compile the paper locally using my compile.paper script. I assume an existing .jats file alongside the .md file is not problematic for the JOSS software, but maybe there is something about the way it's generated by compile.paper that is problematic? The script is just a slightly modified version of one that (I think) is posted on a JOSS-affiliated repo, but I can't recall right now where I found it. I think I just added the redirect to /dev/null/ but I might have modified it slightly in some other way.

[elbeejay]

Thanks for the description @mgcooper - I'll ping the wider group of JOSS editors to see if anyone has encountered this before.

[xuanxu]

I think the error comes from the use of dfrac in the paper.md file. Currently setting a fraction in displaystyle using \dfrac is not totally supported by the JOSS compilation tool. Changing it to \frac should fix the problem.

[mgcooper]

@elbeejay @xuanxu

I changed to \dfrac to \frac and pushed an update. Please let me know if it fixes the issue. Thanks!

[elbeejay]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.cageo.2016.10.005 is OK
- 10.1029/WR013i003p00637 is OK
- 10.1029/97WR03068 is OK
- 10.1137/070710111 is OK
- 10.1029/2018WR022816 is OK
- 10.1029/2022WR033154 is OK
- 10.5194/hess-21-65-2017 is OK
- 10.1016/j.envsoft.2021.104983 is OK
- 10.1029/WR004i005p00973 is OK
- 10.1029/2008WR007392 is OK
- 10.5194/hess-24-1159-2020 is OK
- 10.1029/2008WR006912 is OK
- 10.1016/j.advwatres.2017.07.013 is OK
- 10.1029/2005WR004241 is OK
- 10.1016/j.advwatres.2005.03.019 is OK
- 10.1029/2006WR005080 is OK
- 10.1029/92WR02087 is OK
- 10.1002/wrcr.20407 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4718, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[mgcooper]

@elbeejay

The proofs look good except one minor issue. If it is not too late, they recently updated the name of the division we are affiliated with at PNNL. I just pushed an update to the paper.md file to reflect this. If possible, please recompile the paper using that version. If not, no worries, it is not a big deal. Thanks! Matt

[kthyng]

@mgcooper That should be no problem.

[kthyng]

@editorialbot generate pdf

[kthyng]

My steps are:

• [x] Check that version was updated
• [x] Check that software archive exists, has been input to JOSS, and title and author list look good
• [x] Check paper

[editorialbot]

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

[kthyng]

@mgcooper Ok everything looks good from my perspective but I want to make sure your change came through. Can you let me know when you've checked?

[mgcooper]

@kthyng @elbeejay Looks ready to go on my end, thanks! Matt

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Cooper given-names: Matthew G. orcid: "https://orcid.org/0000-0002-0165-209X" - family-names: Zhou given-names: Tian orcid: "https://orcid.org/0000-0003-1582-4005" contact: - family-names: Cooper given-names: Matthew G. orcid: "https://orcid.org/0000-0002-0165-209X" doi: 10.5281/zenodo.8401301 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Cooper given-names: Matthew G. orcid: "https://orcid.org/0000-0002-0165-209X" - family-names: Zhou given-names: Tian orcid: "https://orcid.org/0000-0003-1582-4005" date-published: 2023-10-24 doi: 10.21105/joss.05492 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 5492 title: "baseflow: a MATLAB and GNU Octave package for baseflow recession analysis" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05492" volume: 8 title: "baseflow: a MATLAB and GNU Octave package for baseflow recession analysis" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/4722
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05492
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...

[kthyng]

Congrats on your new publication @mgcooper! Many thanks to editor @elbeejay and reviewers @alessandroamaranto and @tianydong for your time, hard work, and expertise!!

[editorialbot]

: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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05492/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05492/status.svg
   :target: https://doi.org/10.21105/joss.05492

This is how it will look in your documentation:

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