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

[editorialbot]

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

Status

Status badge code:

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

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (1264.4 files/s, 199617.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            86           1914           1208          16788
MATLAB                         167           3142           8204           9454
JSON                             4              4              0            768
PHP                              1             14             26            289
Markdown                         5             92              0            251
TeX                              1             17              0            236
XML                              4             12             82             98
CSS                              1             13              0             77
YAML                             2             11             41             43
-------------------------------------------------------------------------------
SUM:                           271           5219           9561          28004
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[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
- 10.1029/2006WR005080 is OK
- 10.1002/wrcr.20407 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1212

[editorialbot]

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

[elbeejay]

Hi @deboraydo, @aymnassar, and @alessandroamaranto,

This is the official "review" issue. @mgcooper has asked that you review the content in the joss branch of the baseflow repository, so please make your comments accordingly. Instructions for creating your reviewer checklist and conducting the review should be in the top comment of this issue, but please do not hesitate to reach out to me with any questions or to ask for any clarification.

Ideally we'd like to ask that you complete your reviews within 6 weeks, and I will set up reminder so the bot prods us all in 3 weeks.

Thanks,
Jay

[elbeejay]

@editorialbot remind @deboraydo in three weeks

[editorialbot]

Reminder set for @deboraydo in three weeks

[elbeejay]

@editorialbot remind @aymnassar in three weeks

[editorialbot]

Reminder set for @aymnassar in three weeks

[elbeejay]

@editorialbot remind @alessandroamaranto in three weeks

[editorialbot]

Reminder set for @alessandroamaranto in three weeks

[mgcooper]

@deboraydo @aymnassar @alessandroamaranto @elbeejay
I aim to push the Octave-compatibility fixes tomorrow afternoon. If anyone is reviewing the toolbox exclusively in Octave, please let me know if this is an inconvenience and I will push the update asap. Thank you,
Matt

[alessandroamaranto]

Review checklist for @alessandroamaranto

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 https://github.com/mgcooper/baseflow?
• 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 (@mgcooper) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[editorialbot]

👋 @deboraydo, please update us on how your review is going (this is an automated reminder).

[editorialbot]

👋 @aymnassar, please update us on how your review is going (this is an automated reminder).

[editorialbot]

👋 @alessandroamaranto, please update us on how your review is going (this is an automated reminder).

[elbeejay]

Hi @deboraydo, @aymnassar, @alessandroamaranto,

I just wanted to check in here to remind you all about this review. Feel free to reach out if you have any questions about the JOSS process.

Jay

[elbeejay]

@deboraydo and @aymnassar,

Just checking in here, please let me know if you still anticipate being able to complete your review in the next two weeks or so or if you'll need an extension.

@alessandroamaranto,

It looks like you've checked off all of the items on your review checklist. Can you please summarize your review briefly here and let us know if you have any suggestions or recommendations for the authors? Thanks!

[alessandroamaranto]

I was going to do it this morning but got caught up in some meetings. I will submit a brief summary soon (perhaps tomorrow). Thanks

…

On Wed, Jun 21, 2023, 14:31 J. Hariharan ***@***.***> wrote: @deboraydo <https://github.com/deboraydo> and @aymnassar <https://github.com/aymnassar>, Just checking in here, please let me know if you still anticipate being able to complete your review in the next two weeks or so or if you'll need an extension. @alessandroamaranto <https://github.com/alessandroamaranto>, It looks like you've checked off all of the items on your review checklist. Can you please summarize your review briefly here and let us know if you have any suggestions or recommendations for the authors? Thanks! — Reply to this email directly, view it on GitHub <#5492 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJOC4MHCABYW4U3AMJTWRDXMLSR5ANCNFSM6AAAAAAYMG7F4Y> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[elbeejay]

@deboraydo and @aymnassar,

Just trying to follow up here and make sure this review doesn't get lost - please check in with us here when you get a chance, thanks!

[alessandroamaranto]

The package is easy to install, use and understand. It is well-documented and comes with a set of workflows to ease the users through the functionalities. Much appreciated, thanks.

[elbeejay]

@deboraydo and @aymnassar, I'm checking in here, would be great to get an update from you both on when you might be able to review this package. Please let us know and do not hesitate to reach out if you've got any questions, thanks

[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]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#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:

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

[editorialbot]

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

[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 👉 Creating pull request for 10.21105.joss.05492 joss-papers#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]

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

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.05492/status.svg)](https://doi.org/10.21105/joss.05492)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05492">
  <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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