editorialbot commented 10 months ago

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

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52"><img src="https://joss.theoj.org/papers/b6f6440bc05648fa7945bec1ae901e52/status.svg"></a>
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

SongshGeo commented 8 months ago

@crvernon 👋 Please check the following repo:

10.5281/zenodo.10934351

crvernon commented 8 months ago

:wave: @SongshGeo - Please change your declared license in the Zenodo archive (currently creative commons attribution 4.0 international) to match what you use for your software (Apache License 2.0).

Also, your Zenodo archive name has to match the name of your paper. Please adjust accordingly.

Let me know when you have this done and I'll move forward. Thanks!

crvernon commented 8 months ago

@editorialbot set 0.5.5 as version

editorialbot commented 8 months ago

Done! version is now 0.5.5

crvernon commented 8 months ago

@editorialbot set 10.5281/zenodo.10934351 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10934351

SongshGeo commented 8 months ago

@crvernon Hi, thanks for reminding me. I've changed the information. However, when I double-checked the paper, I found that the funding information needs to be slightly modified. Thus, I created a new release, v0.5.6. There are also some format improvements without changing features in this latest version. Please set 0.5.6 as the version and archive. Sorry about this change.

v0.5.6: 10.5281/zenodo.10935937

crvernon commented 8 months ago

@editorialbot set 0.5.6 as version

editorialbot commented 8 months ago

Done! version is now 0.5.6

crvernon commented 8 months ago

@editorialbot set 10.5281/zenodo.10935937 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10935937

crvernon commented 8 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

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 it looks like one of your co-authors names appear differently between what is in the paper (Elías José Mantilla) versus what is in the Zenodo archive (Elías José Mantilla Ibarra).

Also, you have ORCIDs for some authors in archive that do not have the ORCID listed in the paper.

Please make these consistent.

No need to conduct another release. Thanks!

SongshGeo commented 8 months ago

@crvernon Hi, Sorry. I sometimes struggle with Western names 😂. Now, I updated the ORCIDs in the paper and the name in the Zenodo archive.

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 I am recommending that this submission be accepted for publication. An EiC will review shortly and if all goes well this will go live soon! Thanks to @wang-boyu and @jamesdamillington for a timely and constructive review!

crvernon commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

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
- 10.1017/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
- 10.3389/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: Utilizing Python for agent-based modeling: The Mes...
- 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
- 10.1007/978-3-319-67217-5_2 may be a valid DOI for title: ABCE: A Python library for economic agent-based mo...
- No DOI given, and none found for title: NetLogo: A simple environment for modeling complex...

INVALID DOIs

- None

editorialbot commented 8 months ago

: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/5228, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

SongshGeo commented 7 months ago

@crvernon Hi, I cannot download the proof article from the above link. When I tried to check the PDF file from JOSS's GitHub repo, I got the following error:

Error rendering embedded code Invalid PDF

kthyng commented 7 months ago

Hi I can take over from here. 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

kthyng commented 7 months ago

@SongshGeo Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. I think "earth" and "anthropocene" should be capitalized right?

SongshGeo commented 7 months ago

@kthyng Hi, sure! Now they are up-in-date in this PR.

kthyng commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

kthyng commented 7 months ago

@editorialbot accept

editorialbot commented 7 months ago

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

editorialbot commented 7 months ago

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: Song given-names: Shuang orcid: "https://orcid.org/0000-0002-8112-8780" - family-names: Wang given-names: Shuai orcid: "https://orcid.org/0000-0003-1595-9858" - family-names: Jiao given-names: Chentai orcid: "https://orcid.org/0000-0003-1737-9814" - family-names: Ibarra given-names: Elías José Mantilla contact: - family-names: Wang given-names: Shuai orcid: "https://orcid.org/0000-0003-1595-9858" doi: 10.5281/zenodo.10935937 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Song given-names: Shuang orcid: "https://orcid.org/0000-0002-8112-8780" - family-names: Wang given-names: Shuai orcid: "https://orcid.org/0000-0003-1595-9858" - family-names: Jiao given-names: Chentai orcid: "https://orcid.org/0000-0003-1737-9814" - family-names: Ibarra given-names: Elías José Mantilla date-published: 2024-04-10 doi: 10.21105/joss.06298 issn: 2475-9066 issue: 96 journal: Journal of Open Source Software publisher: name: Open Journals start: 6298 title: "ABSESpy: An agent-based modeling framework for social-ecological systems" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06298" volume: 9 title: "ABSESpy: An agent-based modeling framework for social-ecological 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 commented 7 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 7 months ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/5234
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06298
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 7 months ago

Congrats on your new publication @SongshGeo! Many thanks to editor @crvernon and reviewers @wang-boyu and @jamesdamillington for your time, hard work, and expertise!!

editorialbot commented 7 months 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.06298/status.svg)](https://doi.org/10.21105/joss.06298)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06298">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06298/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06298/status.svg
   :target: https://doi.org/10.21105/joss.06298

This is how it will look in your documentation:

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kthyng commented 7 months ago

@SongshGeo if you're interested in reviewing for JOSS in the future, please sign up here: https://reviewers.joss.theoj.org/

SongshGeo commented 7 months ago

@kthyng @crvernon @jamesdamillington @wang-boyu

Thanks for the efforts from you all. The comments helped us improve our package. Sure! I'm delighted to help with potential reviews in the future. I signed up just now.

By the way, does anyone know how to change JOSS's badge style? It seems not supported by Shields. I cannot add ?style= to make it consistent with my other badges.

kthyng commented 7 months ago

@SongshGeo I got an answer for you: We (JOSS) make them badges ourselves and they can't be re-styled. Sorry!

SongshGeo commented 7 months ago

@kthyng OK! It's such a pity!

openjournals / joss-reviews

[REVIEW]: ABSESpy: An agent-based modeling framework for social-ecological systems #6298

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance