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

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@aurorarossi@fraukewiese<!--end-editor-- 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

editorialbot commented 1 year ago

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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 1 year ago

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 commented 1 year ago

Wordcount for paper.md is 1180

editorialbot commented 1 year ago

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 commented 1 year ago

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

fraukewiese commented 1 year ago

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

ranocha commented 1 year ago

Review checklist for @ranocha

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/worlddynamics/WorldDynamics.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[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?

ranocha commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fraukewiese commented 1 year ago

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

fraukewiese commented 12 months ago

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

fraukewiese commented 12 months ago

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

ranocha commented 11 months ago

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

👍

StanczakDominik commented 11 months ago

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

fraukewiese commented 11 months ago

@StanczakDominik : Thanks for the update.

ranocha commented 11 months ago

@editorialbot commands

editorialbot commented 11 months ago

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 commented 11 months ago

@editorialbot check repository

editorialbot commented 11 months ago

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 commented 11 months ago

Wordcount for paper.md is 1196

fraukewiese commented 11 months ago

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

aurorarossi commented 11 months ago

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

natema commented 10 months ago

@fraukewiese is there any update on the review process?

fraukewiese commented 10 months ago

@aurorarossi @natema : I am sorry that the review takes so long. I have contacted @StanczakDominik by mail to ask about his plans for the review.

natema commented 9 months ago

Hi @fraukewiese. Did @StanczakDominik update you since last month regarding his plans for the review?

fraukewiese commented 9 months ago

@natema : I am very sorry that this takes so long. I did not receive any answer. Thus I suggest to look for a different reviewer.

fraukewiese commented 9 months ago

@arbennett : – would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html One review has already been done, but the other reviewer cannot make it. Thus we are looking for a different person and I think that you would be a very suitable expert for that :)

arbennett commented 9 months ago

@fraukewiese - unfortunately I don't currently have the capacity to help out on this one. The paper/package does look super interesting though!

I'd be happy to recommend other potential reviewers if you'd like - feel free to send me an email: andrbenn@arizona.edu

natema commented 8 months ago

@fraukewiese : I'm sorry to ping you again about our submission, but on behalf of the authors I'd like to ask if there are any updates.

fraukewiese commented 8 months ago

I am currently contacting other potential reviewers by Mail. If you have any suggestions @natema for reviewers, please let me know, I would very much appreciate that. I am very sorry it takes so long

natema commented 8 months ago

@fraukewiese : I would like to suggest @TheCedarPrince or @miguelraz as potential reviewers (they have already kindly declared their availability).

miguelraz commented 8 months ago

I volunteer as tribute. I will try to get to it this week, otherwise I'll hand it off to CedarPrince. 👍🏾

TheCedarPrince commented 8 months ago

Oh! Is there anything else I have to do on my end? I thought we were just waiting from @fraukewiese for their approval :smiley:

natema commented 8 months ago

Yes, please let's wait for @fraukewiese's decision.

fraukewiese commented 8 months ago

Thank you very much @miguelraz @TheCedarPrince , this is great news :) Thus, I will make @miguelraz reviewer.

fraukewiese commented 8 months ago

@editorialbot add @miguelraz as reviewer

editorialbot commented 8 months ago

@miguelraz added to the reviewers list!

fraukewiese commented 8 months ago

At the beginning of this issue, you can find instructions how to create the checklist etc. Thank you very much for your willingness to review! :)

miguelraz commented 8 months ago

1 small detail: In the citations, the Fiddaman, T. [web.archive.org](http://web.archive.org/...) link is not accessible via the pdf link (and overruns the margin limit). The formatting is off, but technically not the citation itself AFAIK.

miguelraz commented 8 months ago

@editorialbot commands

editorialbot commented 8 months ago

Hello @miguelraz, 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

miguelraz commented 8 months ago

Review checklist for @miguelraz

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

miguelraz commented 8 months ago

@fraukewiese I've marked all the items on the checklist and pose no blockers. Do you need anything else from me?

aurorarossi commented 8 months ago

1 small detail: In the citations, the Fiddaman, T. [web.archive.org](http://web.archive.org/...) link is not accessible via the pdf link (and overruns the margin limit). The formatting is off, but technically not the citation itself AFAIK.

We have fixed the formatting, thank you for pointing this out.

fraukewiese commented 7 months ago

@miguelraz Thank you very much for your review. Do you have any further comments, suggestions for improvement?

miguelraz commented 7 months ago

Not at all, I'm quite pleased with the article.

fraukewiese commented 7 months ago

@aurorarossi : At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) 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 list the DOI of the archived version here.

aurorarossi commented 7 months ago

The release tag is v0.4.4 and the DOI of the archived version on Zenodo is .

natema commented 7 months ago

@fraukewiese is Aurora's reply fine or do we need to use the editorialbot in some way?

fraukewiese commented 7 months ago

@editorialbot generate pdf

openjournals / joss-reviews