[REVIEW]: ABSESpy: An agent-based modeling framework for social-ecological systems

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@SongshGeo@crvernon<!--end-editor-- Reviewers: @wang-boyu, @jamesdamillington Archive: 10.5281/zenodo.10935937

Status

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Markdown: [![status](https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52/status.svg)](https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52)

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

@wang-boyu & @jamesdamillington, 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 @wang-boyu

📝 Checklist for @jamesdamillington

editorialbot commented 10 months ago

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 commented 10 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=1.34 s (144.6 files/s, 159873.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      17           4989          20714         163824
JSON                            39              0              0           5131
Python                          53           1186           1644           3594
CSS                             15            460            543           3354
Markdown                        41            440              0            880
Jupyter Notebook                12              0           4662            834
TeX                              1             35              0            432
YAML                            11             48            100            393
TOML                             2             14              2            108
make                             1             10              8             41
INI                              1              1              0              7
-------------------------------------------------------------------------------
SUM:                           193           7183          27673         178598
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 10 months ago

Wordcount for paper.md is 1279

editorialbot commented 10 months ago

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

OK DOIs

- 10.1680/ensu.2011.164.2.129 is OK
- 10.4324/9781003021339 is OK
- 10.1016/j.envsoft.2015.08.018 is OK
- 10.1038/s41562-017-0181-7 is OK
- 10.1111/gwat.12569 is OK
- 10.1016/j.gloenvcha.2019.101972 is OK
- 10.1007/978-3-030-29443-4_9 is OK
- 10.1177/1745691614527464 is OK
- 10.21105/joss.03065 is OK
- 10.3389/fnins.2015.00332 is OK
- 10.1177/1464993413486544 is OK
- 10.5751/es-03610-150420 is OK
- 10.5751/ES-08748-210341 is OK
- 10.1038/s41562-022-01478-5 is OK
- 10.1201/9780429496639 is OK
- 10.1017/S1355770X12000460 is OK
- 10.1016/j.ecocom.2018.07.007 is OK
- 10.1146/annurev-environ-110615-085349 is OK
- 10.1016/j.ecolecon.2016.08.008 is OK
- 10.1007/978-3-319-67217-5_2 is OK
- 10.1007/978-3-030-61255-9_30 is OK

MISSING DOIs

- 10.18564/jasss.3423 may be a valid DOI for title: Agent-based modelling of social-ecological systems: achievements, challenges, and a way forward

INVALID DOIs

- None

editorialbot commented 10 months ago

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

crvernon commented 10 months ago

👋 @SongshGeo , @wang-boyu , and @jamesdamillington - 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 https://github.com/openjournals/joss-reviews/issues/6298 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.

wang-boyu commented 10 months ago

Review checklist for @wang-boyu

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ABSESpy/ABSESpy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@SongshGeo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

SongshGeo commented 10 months ago

@crvernon Thanks for your efforts on our project! We are glad to hear this update. I appreciate two reviewers, @wang-boyu and @jamesdamillington, for your time on reviewing our project. This is a long-term project, and we are still working to improve it. I want to make this project better through discussion with you. :)

jamesdamillington commented 10 months ago

Review checklist for @jamesdamillington

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ABSESpy/ABSESpy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@SongshGeo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

wang-boyu commented 9 months ago

Raised https://github.com/ABSESpy/ABSESpy/issues/36 for missing DOI and reference.

wang-boyu commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

wang-boyu commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

OK DOIs

- 10.1201/9780429496639 is OK
- 10.1680/ensu.2011.164.2.129 is OK
- 10.1038/s41562-022-01478-5 is OK
- 10.4324/9781003021339 is OK
- 10.1016/j.envsoft.2015.08.018 is OK
- 10.1038/s41562-017-0181-7 is OK
- 10.1111/gwat.12569 is OK
- 10.1016/j.gloenvcha.2019.101972 is OK
- 10.1007/978-3-030-29443-4_9 is OK
- 10.1177/1745691614527464 is OK
- 10.5751/es-03610-150420 is OK
- 10.5751/ES-08748-210341 is OK
- 10.21105/joss.03065 is OK
- 10.1016/j.ecocom.2018.07.007 is OK
- 10.1007/978-3-030-61255-9_30 is OK
- 10.1017/S1355770X12000460 is OK
- 10.1146/annurev-environ-110615-085349 is OK
- 10.1016/j.ecolecon.2016.08.008 is OK
- 10.18564/jasss.3423 is OK
- 10.1007/978-3-319-67217-5_2 is OK
- 10.3389/fnins.2015.00332 is OK
- 10.1145/3557989.3566157 is OK
- 10.1177/1464993413486544 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 9 months ago

👋 @SongshGeo , @wang-boyu , and @jamesdamillington

Just checking in to see how things are going. Could you provide a brief update here in this thread? Thanks!

jamesdamillington commented 9 months ago

@crvernon I've been struggling to get things running on my linux machine. Initially it was an issue at my end but now @SongshGeo thinks it might be an issue with python versioning and is investigating, so I'm waiting for the result of that. Have I got that right @SongshGeo ?

SongshGeo commented 9 months ago

@jamesdamillington was right. A new release with compatible improvements (and some other useful changes) is coming soon. I've been working on that in the past few days. Thanks for the patience @wang-boyu @crvernon

crvernon commented 8 months ago

👋 @SongshGeo , @wang-boyu , and @jamesdamillington

Could you provide a brief update to how things are going in this thread? Thanks!

jamesdamillington commented 8 months ago

I have completed my review of the software and checked off all items in my checklist satisfactorily.

Before I can check off items regarding the paper, I have comments for @SongshGeo and colleagues to address as follows:

[ ] Line 24: 'research' not 'researches'
[x] Line 44: rather than 'et al.' maybe use actual words (e.g. 'and others') so as not to confuse against the file suffixes which are similar abbreviations
[ ] Line 55: What do you mean by 'practicing' here? This doesn't seem right. Please edit to clarify
[x] Lines 57-65: I'm surprised these three points (Perceptions, Decision-making, Response) don't match the words used in Fig 2 (Options, Evaluate, Behaviour). Or are the latter three (in the Fig) all part of the 'decision-making' step? Aligning the steps in the list with the figure would be useful, I think
[ ] Line 76: I think 'vary' should be 'varying'
[ ] Line 93: 'more accurate' - this is a relative statement, so please clarify 'more accurate' than what?
[x] Line 99: ( wang2022h? )) is not included in the reference list
[x] Line 100: it's good that you recognise the similarity here to AgentPy but you don't then clearly explain how absespy is beneficial for SES researchers - maybe you could highlight the explicit functionality for representing the 'nature' side of CHANS (AgentPy really focuses on the 'human' side).
[x] Line 108: 'merely heuristic' - I think this is a little over-critical of NetLogo, which can incorporate 'real-world' (I think you mean 'empirical'?) data although not at the scale absespy could. I suggest you edit here to focus on the value of absespy for working with large-scale, empirical data so that models can run more efficiently than would be possible for the same data in NetLogo. You might also highlight your TimeDriver module which is a benefit over NetLogo's more simple 'ticks'

SongshGeo commented 8 months ago

👋 @crvernon

Hi, Thanks to the comments of the two reviewers, our software has been significantly improved. I am glad that the software review was satisfactory, and I will carefully revise it following the comments listed here as soon as possible. @jamesdamillington

wang-boyu commented 8 months ago

Just found two small issues regarding test cases but I'm overall ok with the software. Will start checking the software paper.

SongshGeo commented 8 months ago

@jamesdamillington Thanks for the valuable comments! I followed your checklist of comments one by one. Besides the corrections, here are three responses:

...

[x] Regarding the misalignment of three points with the figure. I'm sorry about the previous misleading figure. I have now updated Figure 2. Perception, decision-making, and response are three steps in the workflow, different from the "options, evaluate, action" (three points for decision-making). ...
[x] Your suggestion regarding comparing AgentPy and NetLogo was insightful. I updated the whole paper to explain better ABSESpy's advantages. I hope the new version makes our contributions more clear:

"The design focuses on two core improvements: (1) handling actors and their interactions and (2) enhancing reality and manageability of ABMs."

@wang-boyu I also followed your suggestions and corrected the names. So, I closed the issue. Did I miss anything?

@crvernon, I sincerely thank you and the two reviewers for your time, and I hope you are satisfied with my responses and the latest significant revisions. I look forward to publishing the paper on JOSS.

@editorialbot generate pdf

SongshGeo commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

SongshGeo commented 8 months ago

Sorry, I forgot to merge a PR before generating pdf. I will do it again. The newest version of my paper in HTML is always available here.

SongshGeo commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

wang-boyu commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

wang-boyu commented 8 months ago

Hi @crvernon I have checked all the items in the checklist. There's an open issue about two failing test cases but I don't think that will block the paper.

Thanks for letting me review the paper!

crvernon commented 8 months ago

Thanks for reviewing @wang-boyu! It is people like yourself that make this journal possible!

SongshGeo commented 8 months ago

👋 Hi, @wang-boyu. Thank you for your time for reviewing ABSESpy!

wang-boyu commented 8 months ago

You're welcome! Great work @SongshGeo

jamesdamillington commented 8 months ago

@crvernon This version looks good to me and I have checked off all items in my checklist.

Nice work @SongshGeo and colleagues!

SongshGeo commented 8 months ago

@jamesdamillington 👋 I appreciate your time in reviewing ABSESpy! I wish you all the best.

crvernon commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

crvernon commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.1201/9780429496639 is OK
- 10.1680/ensu.2011.164.2.129 is OK
- 10.1038/s41562-022-01478-5 is OK
- 10.4324/9781003021339 is OK
- 10.1016/j.envsoft.2015.08.018 is OK
- 10.1038/s41562-017-0181-7 is OK
- 10.1111/gwat.12569 is OK
- 10.1016/j.gloenvcha.2019.101972 is OK
- 10.1007/978-3-030-29443-4_9 is OK
- 10.1177/1745691614527464 is OK
- 10.5751/es-03610-150420 is OK
- 10.5751/ES-08748-210341 is OK
- 10.21105/joss.03065 is OK
- 10.1016/j.ecocom.2018.07.007 is OK
- 10.1007/978-3-030-61255-9_30 is OK
- 10.1017/S1355770X12000460 is OK
- 10.1146/annurev-environ-110615-085349 is OK
- 10.1016/j.ecolecon.2016.08.008 is OK
- 10.18564/jasss.3423 is OK
- 10.1007/978-3-319-67217-5_2 is OK
- 10.3389/fnins.2015.00332 is OK
- 10.1145/3557989.3566157 is OK
- 10.1177/1464993413486544 is OK
- 10.1073/pnas.2215674121 is OK
- 10.1073/pnas.2215676120 is OK
- 10.5334/jors.148 is OK

MISSING DOIs

- No DOI given, and none found for title: Applying Plural Rationality to Some Wicked Problem...
- No DOI given, and none found for title: Plural Rationality and Interactive Decision Proces...
- No DOI given, and none found for title: Towards a community framework for agent-based mode...
- No DOI given, and none found for title: MODFLOW 6 modular hydrologic model version 6.2. 1:...
- No DOI given, and none found for title: Complexity: A guided tour
- No DOI given, and none found for title: Understanding Institutional Diversity
- No DOI given, and none found for title: NetLogo: A simple environment for modeling complex...

INVALID DOIs

- None

crvernon commented 8 months ago

:wave: @SongshGeo great job on this submission!

Here are some comments I have on the paper:

[x] LINE 30: Missing space between "...tools (Schlüter et al., 2023)" and "to implement...". Should appear as "...tools (Schlüter et al., 2023) to implement..."
[x] LINE 42: The figure reference "(Figure 1)" should not be bold but instead use formatting that enables linking to the actual figure. You can see how this is done in other JOSS publications such as https://joss.theoj.org/papers/10.21105/joss.06294. I'll only mention this for This figure, but note that this should be done for all figure references in your paper.
[x] LINE 48: The statement "...but somehow enhanced." should be changed here. Perhaps use "...but with enhanced functionality." or the something similar.
[x] LINE 49: Since YAML is a data serialization language, it should be referenced by its name here instead of the extension which sometimes varies. So instead of "...through .yaml files." you could use "...through the use of YAML configuration files." or something similar. You can read more about YAML here if you like. Note that there are several of these usages throughout the paper that you may need to correct.
[x] LINE 53: Wording is off here. Instead of "...(2) enhancing reality and manageability of ABMs." something like the following would be more clear "...(2) enhancing the reality and manageability of ABMs." This is phrased several times like this throughout the paper, so please let me know if it should be written as stated. I'll not mention the other occurrences, but address those if needed.
[x] LINE 56: "...and can be..." should be "...which can be..."
[x] LINE 63: "(Schlüter et al., 2017), (Beckage et al., 2022)" should appear as "(Schlüter et al., 2017; Beckage et al., 2022)"
[x] LINE 87-88: You use the formatting {"start: '2022-12-31', "end": 2024-01-01, year: 1} please add in what I believe should be the correct, consistent formatting as following: {"start: "2022-12-31", "end": "2024-01-01", "year": 1}. Please correct me if I am wrong. I am also assuming "year" requires an integer as you have written.
[x] LINE 88: "...to the 'time' module..." should be formatted as "...to the time module..." where backticks are used.
[x] LINE 102: You use "input/output" though earlier in the paper you use "Input/Ouput" please choose one method to be consistent.
[x] LINE 131: Your reference for the Janssen et al. paper is not formatted correctly. See https://www.jasss.org/11/2/6/citation.html
[x] LINE 135: Should have a colon after "In". See https://link.springer.com/chapter/10.1007/978-3-030-61255-9_30#citeas
[x] LINE 159: Missing colon after "In" see https://link.springer.com/chapter/10.1007/978-3-319-67217-5_2#citeas

Let me know after you have addressed the above and we can move to the next steps. Thanks!

wang-boyu commented 8 months ago

Hi @crvernon were you trying to tag @SongshGeo instead of me? 😄

crvernon commented 8 months ago

Hi @crvernon were you trying to tag @SongshGeo instead of me? 😄

Yes! Sorry about that!

wang-boyu commented 8 months ago

No worries! : )

SongshGeo commented 8 months ago

@crvernon Hi! No problem. I will fix the issues in a day. 😉

SongshGeo commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

SongshGeo commented 8 months ago

@crvernon 👋 Hi, I followed all the comments. Please check the newest version throughout.

I just wanted to let you know about the last two comments on citation formats. I confirmed that I used the .bib provided by the sources. However, their default category was @InProceedding. When I used this category, the colon didn't appear. I suppose this category is not available in JOSS's document. Therefore, I changed the categories to '@book'. Does it work?

crvernon commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

crvernon commented 8 months ago

👋 @SongshGeo - Thanks for making the requested changes to the paper! 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 is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please respond with the DOI of the archived version here

I can then move forward with accepting the submission.

openjournals / joss-reviews