[REVIEW]: WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models #5772

editorialbot · 2023-08-21T08:03:04Z

Submitting author: @aurorarossi (Aurora Rossi)
Repository: https://github.com/worlddynamics/WorldDynamics.jl
Branch with paper.md (empty if default branch): JOSS-paper
Version: v0.4.4
Editor: @fraukewiese
Reviewers: @ranocha, @StanczakDominik, @miguelraz
Archive: 10.5281/zenodo.10684579

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/08cccf50f6c78d89128b2eb3c6c68a05/status.svg)](https://joss.theoj.org/papers/08cccf50f6c78d89128b2eb3c6c68a05)

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

@ranocha & @StanczakDominik, 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 @fraukewiese 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 @ranocha

📝 Checklist for @miguelraz

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

editorialbot · 2023-08-21T08:03:06Z

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 · 2023-08-21T08:03:08Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (1469.6 files/s, 103297.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          135           1868             15           7200
Markdown                         7            134              0            927
TeX                              1             26              0            178
YAML                             3              3              4             55
TOML                             2              3              0             31
SVG                              1              0              4             25
-------------------------------------------------------------------------------
SUM:                           149           2034             23           8416
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-08-21T08:03:09Z

Wordcount for paper.md is 1180

editorialbot · 2023-08-21T08:03:29Z

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

OK DOIs

- 10.21203/rs.3.rs-55125/v1 is OK
- 10.1088/1748-9326/ac243e is OK
- 10.31223/X50W8D is OK
- 10.1007/s10584-018-2218-y is OK
- 10.1038/sdata.2018.187 is OK
- 10.48550/arXiv.2206.03866 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.5083412 is OK
- 10.21105/joss.04561 is OK
- 10.1016/S1364-8152(01)00059-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-08-21T08:04:39Z

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

fraukewiese · 2023-09-06T13:33:35Z

@ranocha, @StanczakDominik : How is the review going? Do not hesitate to ask in case of questions :)

ranocha · 2023-09-08T09:28:09Z

Review checklist for @ranocha

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/worlddynamics/WorldDynamics.jl?
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 (@aurorarossi) 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?

ranocha · 2023-09-18T15:46:45Z

@editorialbot generate pdf

editorialbot · 2023-09-18T15:48:05Z

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

fraukewiese · 2023-09-25T12:08:41Z

@StanczakDominik : How is the review going? Do not hesitate to ask in case of questions :)

fraukewiese · 2023-10-06T11:11:23Z

@ranocha : Are you satisfied with the answers and updated documented here worlddynamics/WorldDynamics.jl#197 ?

fraukewiese · 2023-10-06T11:12:36Z

@StanczakDominik : Do you have an estimate for us when you could get into the review? Thank you very much :)

ranocha · 2023-10-14T03:55:45Z

@ranocha : Are you satisfied with the answers and updated documented here worlddynamics/WorldDynamics.jl#197 ?

👍

StanczakDominik · 2023-10-14T10:23:46Z

Apologies for the delay. I will get to it by tomorrow.

fraukewiese · 2023-10-19T13:41:54Z

@StanczakDominik : Thanks for the update.

ranocha · 2023-10-24T06:01:27Z

@editorialbot commands

editorialbot · 2023-10-24T06:01:29Z

Hello @ranocha, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

ranocha · 2023-10-24T06:01:54Z

@editorialbot check repository

editorialbot · 2023-10-24T06:01:57Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (2053.5 files/s, 144930.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          135           1868             15           7200
Markdown                         7            134              0            927
TeX                              1             28              0            219
YAML                             3              3              4             55
TOML                             2              3              0             31
SVG                              1              0              4             25
-------------------------------------------------------------------------------
SUM:                           149           2036             23           8457
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-10-24T06:01:58Z

Wordcount for paper.md is 1196

fraukewiese · 2023-10-25T11:19:13Z

@StanczakDominik : Are there any updates from your side regarding the review? Thank you very much for your willingness to review this submission.

aurorarossi · 2023-11-06T10:04:53Z

We would like to know if there are any updates on the review process. Thank you in advance.

natema · 2023-11-14T18:42:22Z

@fraukewiese is there any update on the review process?

fraukewiese · 2024-03-04T08:54:41Z

@editorialbot generate pdf

fraukewiese · 2024-03-04T08:55:03Z

@editorialbot check references

fraukewiese · 2024-03-04T08:55:32Z

@editorialbot set v0.4.4 as version

editorialbot · 2024-03-04T08:55:35Z

Done! version is now v0.4.4

editorialbot · 2024-03-04T08:55:39Z

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

OK DOIs

- 10.21203/rs.3.rs-55125/v1 is OK
- 10.1088/1748-9326/ac243e is OK
- 10.31223/X50W8D is OK
- 10.1007/s10584-018-2218-y is OK
- 10.1038/sdata.2018.187 is OK
- 10.48550/arXiv.2206.03866 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.5083412 is OK
- 10.21105/joss.04561 is OK
- 10.1016/S1364-8152(01)00059-7 is OK
- 10.1137/141000671 is OK
- 10.3182/20140824-6-ZA-1003.01654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-03-04T08:55:53Z

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

fraukewiese · 2024-03-04T08:58:43Z

@editorialbot set 10.5281/zenodo.10684579 as archive

editorialbot · 2024-03-04T08:58:45Z

Done! archive is now 10.5281/zenodo.10684579

fraukewiese · 2024-03-04T10:12:55Z

@editorialbot recommend-accept

editorialbot · 2024-03-04T10:12:57Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-04T10:13:29Z

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

OK DOIs

- 10.21203/rs.3.rs-55125/v1 is OK
- 10.1088/1748-9326/ac243e is OK
- 10.31223/X50W8D is OK
- 10.1007/s10584-018-2218-y is OK
- 10.1038/sdata.2018.187 is OK
- 10.48550/arXiv.2206.03866 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.5083412 is OK
- 10.21105/joss.04561 is OK
- 10.1016/S1364-8152(01)00059-7 is OK
- 10.1137/141000671 is OK
- 10.3182/20140824-6-ZA-1003.01654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-03-04T10:14:18Z

👋 @openjournals/csism-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#5087, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-03-04T10:27:50Z

Thanks. I'll work on the next steps later today or tomorrow.

danielskatz · 2024-03-04T17:56:47Z

@aurorarossi - I've suggested a few minor changes in the paper/bib in worlddynamics/WorldDynamics.jl#207 - please merge this, or let me know what you disagree with

aurorarossi · 2024-03-05T09:37:06Z

Merged! Thank you!

danielskatz · 2024-03-05T10:05:15Z

@editorialbot recommend-accept

editorialbot · 2024-03-05T10:05:17Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-05T10:05:56Z

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

OK DOIs

- 10.21203/rs.3.rs-55125/v1 is OK
- 10.1088/1748-9326/ac243e is OK
- 10.31223/X50W8D is OK
- 10.1007/s10584-018-2218-y is OK
- 10.1038/sdata.2018.187 is OK
- 10.48550/arXiv.2206.03866 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.5083412 is OK
- 10.21105/joss.04561 is OK
- 10.1016/S1364-8152(01)00059-7 is OK
- 10.1137/141000671 is OK
- 10.3182/20140824-6-ZA-1003.01654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-03-05T10:07:06Z

👋 @openjournals/csism-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#5091, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-03-05T10:07:49Z

@editorialbot accept

editorialbot · 2024-03-05T10:07:51Z

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

editorialbot · 2024-03-05T10:15:27Z

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: Crescenzi
  given-names: Pierluigi
  orcid: "https://orcid.org/0000-0001-8789-3195"
- family-names: Natale
  given-names: Emanuele
  orcid: "https://orcid.org/0000-0002-8755-3892"
- family-names: Rossi
  given-names: Aurora
  orcid: "https://orcid.org/0009-0001-3302-0468"
- family-names: Serafim
  given-names: Paulo Bruno
  orcid: "https://orcid.org/0000-0002-5980-8149"
contact:
- family-names: Rossi
  given-names: Aurora
  orcid: "https://orcid.org/0009-0001-3302-0468"
doi: 10.5281/zenodo.10684579
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Crescenzi
    given-names: Pierluigi
    orcid: "https://orcid.org/0000-0001-8789-3195"
  - family-names: Natale
    given-names: Emanuele
    orcid: "https://orcid.org/0000-0002-8755-3892"
  - family-names: Rossi
    given-names: Aurora
    orcid: "https://orcid.org/0009-0001-3302-0468"
  - family-names: Serafim
    given-names: Paulo Bruno
    orcid: "https://orcid.org/0000-0002-5980-8149"
  date-published: 2024-03-05
  doi: 10.21105/joss.05772
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5772
  title: "WorldDynamics.jl: A Julia Package for Developing and
    Simulating Integrated Assessment Models"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05772"
  volume: 9
title: "WorldDynamics.jl: A Julia Package for Developing and Simulating
  Integrated Assessment Models"

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 · 2024-03-05T10:15:30Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-03-05T10:15:30Z

🚨🚨🚨 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.05772 joss-papers#5092
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05772
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2024-03-05T10:22:22Z

Congratulations to @aurorarossi (Aurora Rossi) and co-authors on your publication!!

And thanks to @ranocha, @StanczakDominik, and @miguelraz for reviewing, and to @fraukewiese for editing!
JOSS depends on volunteers and we couldn't do this without you

editorialbot · 2024-03-05T10:22:24Z

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

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05772/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05772/status.svg
   :target: https://doi.org/10.21105/joss.05772

This is how it will look in your documentation:

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editorialbot added Julia review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Aug 21, 2023

editorialbot assigned fraukewiese Aug 21, 2023

editorialbot mentioned this issue Aug 21, 2023

[PRE REVIEW]: WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models #5365

Closed

ranocha mentioned this issue Sep 8, 2023

JOSS Review worlddynamics/WorldDynamics.jl#197

Closed

7 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 4, 2024

editorialbot added accepted published Papers published in JOSS labels Mar 5, 2024

danielskatz closed this as completed Mar 5, 2024

[REVIEW]: WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models #5772

[REVIEW]: WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models #5772

Comments

editorialbot commented Aug 21, 2023 • edited

Status

Reviewer instructions & questions

Checklists

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fraukewiese commented Sep 6, 2023

ranocha commented Sep 8, 2023 • edited

Review checklist for @ranocha

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ranocha commented Sep 18, 2023

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ranocha commented Oct 14, 2023

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ranocha commented Oct 24, 2023

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editorialbot commented Aug 21, 2023 •

edited

ranocha commented Sep 8, 2023 •

edited