Closed editorialbot closed 5 months ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=1.34 s (144.6 files/s, 159873.2 lines/s)
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Language files blank comment code
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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
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SUM: 193 7183 27673 178598
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1279
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
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👋 @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.
@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. :)
Raised https://github.com/ABSESpy/ABSESpy/issues/36 for missing DOI and reference.
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@editorialbot check references
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
👋 @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!
@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 ?
@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
👋 @SongshGeo , @wang-boyu , and @jamesdamillington
Could you provide a brief update to how things are going in this thread? Thanks!
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:
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). 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'👋 @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
Just found two small issues regarding test cases but I'm overall ok with the software. Will start checking the software paper.
@jamesdamillington Thanks for the valuable comments! I followed your checklist of comments one by one. Besides the corrections, here are three responses:
...
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.
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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.
@editorialbot generate pdf
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@editorialbot generate pdf
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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!
Thanks for reviewing @wang-boyu! It is people like yourself that make this journal possible!
👋 Hi, @wang-boyu. Thank you for your time for reviewing ABSESpy
!
You're welcome! Great work @SongshGeo
@crvernon This version looks good to me and I have checked off all items in my checklist.
Nice work @SongshGeo and colleagues!
@jamesdamillington 👋 I appreciate your time in reviewing ABSESpy
! I wish you all the best.
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@editorialbot check references
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
:wave: @SongshGeo great job on this submission!
Here are some comments I have on the paper:
{"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.time
module..." where backticks are used.Let me know after you have addressed the above and we can move to the next steps. Thanks!
Hi @crvernon were you trying to tag @SongshGeo instead of me? 😄
Hi @crvernon were you trying to tag @SongshGeo instead of me? 😄
Yes! Sorry about that!
No worries! : )
@crvernon Hi! No problem. I will fix the issues in a day. 😉
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@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?
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👋 @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.
Submitting author: !--author-handle-->@SongshGeo<!--end-author-handle-- (Shuang Song) Repository: https://github.com/ABSESpy/ABSESpy Branch with paper.md (empty if default branch): dev Version: 0.5.6 Editor: !--editor-->@crvernon<!--end-editor-- Reviewers: @wang-boyu, @jamesdamillington Archive: 10.5281/zenodo.10935937
Status
Status badge code:
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:
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