[REVIEW]: AgriFoodPy: a package for modelling food systems #6305

editorialbot · 2024-01-29T23:31:20Z

Submitting author: @jucordero (Juan P. Cordero)
Repository: https://github.com/FixOurFood/AgriFoodPy/
Branch with paper.md (empty if default branch): joss-paper
Version: v0.1.2
Editor: @crvernon
Reviewers: @kanishkan91, @jsun
Archive: 10.5281/zenodo.11236802

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271"><img src="https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271/status.svg)](https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271)

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

@kanishkan91 & @jsun, 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 @crvernon 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 @jsun

📝 Checklist for @kanishkan91

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-01-29T23:31:23Z

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

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:

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editorialbot · 2024-01-29T23:31:27Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (808.7 files/s, 74696.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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XML                              1              0              0            493
Python                          13            171            289            392
Markdown                         2             43              0            202
TeX                              1              9              0            116
YAML                             2              3              4             33
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SUM:                            19            226            293           1236
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gitinspector failed to run statistical information for the repository

editorialbot · 2024-01-29T23:31:29Z

Wordcount for paper.md is 1179

editorialbot · 2024-01-29T23:31:29Z

Failed to discover a valid open source license

editorialbot · 2024-01-29T23:31:41Z

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

OK DOIs

- 10.1126/science.aaq0216 is OK
- 10.5334/jors.148 is OK
- 10.5285/d6f8c045-521b-476e-b0d6-b3b97715c138 is OK
- 10.5281/zenodo.3946761 is OK
- 10.5194/gmd-14-3007-2021 is OK
- 10.1016/j.envsoft.2014.07.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-01-29T23:32:48Z

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

crvernon · 2024-01-29T23:32:51Z

👋 @jucordero , @kanishkan91 , and @jsun - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #6305 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

jsun · 2024-01-30T03:38:36Z

Review checklist for @jsun

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/FixOurFood/AgriFoodPy/?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@jucordero) 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?

jsun · 2024-02-28T03:23:20Z

Hi, @jucordero, @crvernon, I have not yet finished checking all the items; but I have written below with my comments on the parts I have checked so far.

Documentation

The documentation (probably README.md) gave several examples, however, I think more documentation is required for this package. For example, what kind of functions/methods are implemented in this package, what are the arguments of the function, ...

Software paper

It is recommended to write a more concise overview of the software in Summary section. Please consider writing about detailed features of the software and features to be implemented in the future in Features section.
The background was well-written, but more emphasis should be placed on what exactly this software can do and what it can do better than existing software.
The structure of the paper needs proofreading.

Additional comments

In the paper, the authors write a lot about future releases and implementations. This underlines that the development of the package is incomplete. I suggest that author implement these features during this review process.

jucordero · 2024-03-04T19:49:59Z

@jsun thanks for the comments. I'll provide a more comprehensive response soon.
@crvernon Regarding the last bullet point: In general, is it okay to push significant changes to the main branch while the review is in process?
We have been working on the features mentioned as the future work but haven't merged from my fork yet.

crvernon · 2024-03-04T19:53:32Z

@jucordero yes, no problem at all to update the main branch during review as long as those changes have been made known to reviewers in this thread. These changes should also not interfere with any current features that the reviewers are currently reviewing. So you may want to check with them directly as well. Anytime you link to this thread in your pull requests or issues it will show up here so all can track progress.

crvernon · 2024-03-22T13:45:56Z

👋 @jucordero , @kanishkan91 , and @jsun

Could you all provide a short few sentences/bullet points on how things are going with this review? Thanks and keep up the great work!

jucordero · 2024-03-27T12:44:21Z

Hi @crvernon

@jsun has made a few suggestions on the documentation and software paper which we have been addressing.
Simultaneously we have been working on one of the main functionalities which was missing in the first release, but haven't discussed with the reviewers yet on whether it is fine to merge this right now.

I haven't heard from @kanishkan91

Happy Easter!

crvernon · 2024-03-27T13:25:00Z

Thanks @jucordero, Happy Easter as well! I'll touch base with @kanishkan91, I know he had some other things he had to prioritize but should be back in the thread here soon.

kanishkan91 · 2024-03-27T13:59:09Z

@crvernon @jucordero - My apologies for the delay. Will get this review done by this weekend.

crvernon · 2024-03-27T14:00:51Z

No problem @kanishkan91 and thank you!

editorialbot · 2024-05-21T09:48:37Z

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

crvernon · 2024-05-21T11:41:56Z

@editorialbot check references

editorialbot · 2024-05-21T11:43:03Z

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

OK DOIs

- 10.1126/science.aaq0216 is OK
- 10.5334/jors.148 is OK
- 10.4060/cc8088en is OK
- 10.5285/d6f8c045-521b-476e-b0d6-b3b97715c138 is OK
- 10.5281/zenodo.3946761 is OK
- 10.5194/gmd-14-3007-2021 is OK
- 10.1016/j.envsoft.2014.07.009 is OK

MISSING DOIs

- No DOI given, and none found for title: United Nations, Department of Economic and Social ...
- No DOI given, and none found for title: Rasterio: geospatial raster I/O for Python program...

INVALID DOIs

- None

crvernon · 2024-05-21T11:48:29Z

👋 @jucordero - we are almost there! Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

Conduct a GitHub release of the current reviewed version of the software and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository). Please ensure that the software archive uses the same license as the license you have posted on GitHub.
Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list matches the people and order in your paper). You may also add the authors' ORCID.
Please respond with the 1) version and 2) DOI of the archived version here

I can then move forward with accepting the submission.

jucordero · 2024-05-21T16:59:48Z

@crvernon
I have just created Release v0.1.2 and its corresponding entry in Zenodo

crvernon · 2024-05-21T17:03:47Z

@editorialbot set v0.1.2 as version

editorialbot · 2024-05-21T17:03:50Z

Done! version is now v0.1.2

crvernon · 2024-05-21T17:07:40Z

@editorialbot set 10.5281/zenodo.11236802 as archive

editorialbot · 2024-05-21T17:07:43Z

Done! archive is now 10.5281/zenodo.11236802

crvernon · 2024-05-21T17:12:08Z

@editorialbot recommend-accept

👋 - @jucordero I am recommending that this submission be accepted for publication. The AEiC in this submission track will review shortly and if all goes well this will go live soon! Thanks to @kanishkan91 and @jsun for a timely and constructive review!

editorialbot · 2024-05-21T17:12:11Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-05-21T17:12:32Z

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

OK DOIs

- 10.1126/science.aaq0216 is OK
- 10.5334/jors.148 is OK
- 10.4060/cc8088en is OK
- 10.5285/d6f8c045-521b-476e-b0d6-b3b97715c138 is OK
- 10.5281/zenodo.3946761 is OK
- 10.5194/gmd-14-3007-2021 is OK
- 10.1016/j.envsoft.2014.07.009 is OK

MISSING DOIs

- No DOI given, and none found for title: United Nations, Department of Economic and Social ...
- No DOI given, and none found for title: Rasterio: geospatial raster I/O for Python program...

INVALID DOIs

- None

editorialbot · 2024-05-21T17:13:30Z

👋 @openjournals/bcm-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#5364, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-05-25T06:49:02Z

@jucordero as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, I only have the below point that require your attention:

In the affiliations, please spell out UK as United Kingdom

Kevin-Mattheus-Moerman · 2024-05-27T12:01:10Z

@jucordero 👋 please work on the above and let me know when you think we can proceed. Thanks.

jucordero · 2024-05-27T12:19:06Z

@editorialbot generate pdf

editorialbot · 2024-05-27T12:20:15Z

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

jucordero · 2024-05-27T12:22:51Z

Hi @Kevin-Mattheus-Moerman
Just made the changes you requested to the manuscript.

Kevin-Mattheus-Moerman · 2024-05-27T12:24:28Z

@editorialbot accept

editorialbot · 2024-05-27T12:24:31Z

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

editorialbot · 2024-05-27T12:31:06Z

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: Cordero
  given-names: Juan P.
  orcid: "https://orcid.org/0000-0002-6625-7656"
- family-names: Donkers
  given-names: Kevin
  orcid: "https://orcid.org/0000-0003-0160-8467"
- family-names: Harrison
  given-names: Ian
  orcid: "https://orcid.org/0000-0002-4437-0770"
- family-names: Bridle
  given-names: Sarah L.
  orcid: "https://orcid.org/0000-0002-0128-1006"
- family-names: Frankowska
  given-names: Angelina
  orcid: "https://orcid.org/0000-0003-1483-114X"
- family-names: Cain
  given-names: Michelle
  orcid: "https://orcid.org/0000-0003-2062-6556"
- family-names: Ward
  given-names: Neil
  orcid: "https://orcid.org/0000-0002-0732-2278"
- family-names: Frendenburgh
  given-names: Jez
- family-names: Pope
  given-names: Edward
  orcid: "https://orcid.org/0000-0002-8295-2667"
- family-names: Kluczkovski
  given-names: Alana
  orcid: "https://orcid.org/0000-0001-6462-6801"
- family-names: Schmidt
  given-names: Ximena
  orcid: "https://orcid.org/0000-0003-0157-2679"
- family-names: Silva
  given-names: Jacqueline
  orcid: "https://orcid.org/0000-0002-6082-8905"
- family-names: Reynolds
  given-names: Christian
  orcid: "https://orcid.org/0000-0002-1073-7394"
- family-names: Denby
  given-names: Katherine
  orcid: "https://orcid.org/0000-0002-7857-6814"
- family-names: Doherty
  given-names: Bob
  orcid: "https://orcid.org/0000-0001-6724-7065"
- family-names: Jones
  given-names: Aled
  orcid: "https://orcid.org/0000-0001-7823-9116"
contact:
- family-names: Cordero
  given-names: Juan P.
  orcid: "https://orcid.org/0000-0002-6625-7656"
doi: 10.5281/zenodo.11236802
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Cordero
    given-names: Juan P.
    orcid: "https://orcid.org/0000-0002-6625-7656"
  - family-names: Donkers
    given-names: Kevin
    orcid: "https://orcid.org/0000-0003-0160-8467"
  - family-names: Harrison
    given-names: Ian
    orcid: "https://orcid.org/0000-0002-4437-0770"
  - family-names: Bridle
    given-names: Sarah L.
    orcid: "https://orcid.org/0000-0002-0128-1006"
  - family-names: Frankowska
    given-names: Angelina
    orcid: "https://orcid.org/0000-0003-1483-114X"
  - family-names: Cain
    given-names: Michelle
    orcid: "https://orcid.org/0000-0003-2062-6556"
  - family-names: Ward
    given-names: Neil
    orcid: "https://orcid.org/0000-0002-0732-2278"
  - family-names: Frendenburgh
    given-names: Jez
  - family-names: Pope
    given-names: Edward
    orcid: "https://orcid.org/0000-0002-8295-2667"
  - family-names: Kluczkovski
    given-names: Alana
    orcid: "https://orcid.org/0000-0001-6462-6801"
  - family-names: Schmidt
    given-names: Ximena
    orcid: "https://orcid.org/0000-0003-0157-2679"
  - family-names: Silva
    given-names: Jacqueline
    orcid: "https://orcid.org/0000-0002-6082-8905"
  - family-names: Reynolds
    given-names: Christian
    orcid: "https://orcid.org/0000-0002-1073-7394"
  - family-names: Denby
    given-names: Katherine
    orcid: "https://orcid.org/0000-0002-7857-6814"
  - family-names: Doherty
    given-names: Bob
    orcid: "https://orcid.org/0000-0001-6724-7065"
  - family-names: Jones
    given-names: Aled
    orcid: "https://orcid.org/0000-0001-7823-9116"
  date-published: 2024-05-27
  doi: 10.21105/joss.06305
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6305
  title: "AgriFoodPy: a package for modelling food systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06305"
  volume: 9
title: "AgriFoodPy: a package for modelling food systems"

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 · 2024-05-27T12:31:09Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-05-27T12:31:10Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06305 joss-papers#5394
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06305
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2024-05-27T13:10:43Z

@jucordero congratulations on this JOSS publication!

Thanks for editing @crvernon

And a special thank you to the reviewers: @kanishkan91, @jsun !!

editorialbot · 2024-05-27T13:10:45Z

🎉🎉🎉 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.06305/status.svg)](https://doi.org/10.21105/joss.06305)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06305">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06305/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06305/status.svg
   :target: https://doi.org/10.21105/joss.06305

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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jucordero · 2024-05-27T17:19:36Z

Thanks @Kevin-Mattheus-Moerman !

And special thanks to @crvernon , @jsun, @kanishkan91 for your comments and suggestions!

editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Jan 29, 2024

editorialbot assigned crvernon Jan 29, 2024

editorialbot mentioned this issue Jan 29, 2024

[PRE REVIEW]: AgriFoodPy: a package for modelling food systems #6080

Closed

crvernon removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 29, 2024

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 21, 2024

editorialbot added accepted published Papers published in JOSS labels May 27, 2024

Kevin-Mattheus-Moerman closed this as completed May 27, 2024

[REVIEW]: AgriFoodPy: a package for modelling food systems #6305

[REVIEW]: AgriFoodPy: a package for modelling food systems #6305

Comments

editorialbot commented Jan 29, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

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crvernon commented Jan 29, 2024

jsun commented Jan 30, 2024 • edited Loading

Review checklist for @jsun

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jsun commented Feb 28, 2024

jucordero commented Mar 4, 2024

crvernon commented Mar 4, 2024

crvernon commented Mar 22, 2024

jucordero commented Mar 27, 2024

crvernon commented Mar 27, 2024

kanishkan91 commented Mar 27, 2024

crvernon commented Mar 27, 2024

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