[REVIEW]: Utopia: A Comprehensive and Collaborative Modeling Framework for Complex and Evolving Systems

[whedon]

Submitting author: @peanutfun (Lukas Riedel)
Repository: https://gitlab.com/utopia-project/utopia
Branch with paper.md (empty if default branch):
Version: latest
Editor: @arfon
Reviewers: @platipodium, @Shibabrat, @szhorvat
Archive: 10.5281/zenodo.4011979

Status

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Markdown: [![status](https://joss.theoj.org/papers/8ce6d2bc26c0c6553c5ce5aff38d83c3/status.svg)](https://joss.theoj.org/papers/8ce6d2bc26c0c6553c5ce5aff38d83c3)

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

@platipodium, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @platipodium

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 repository url?
• 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 (@peanutfun) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @Shibabrat

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 repository url?
• 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 (@peanutfun) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @szhorvat

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 repository url?
• 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 (@peanutfun) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @platipodium it looks like you're currently assigned to review this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[arfon]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

@platipodium - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

[arfon]

@whedon add @Shibabrat as reviewer

[whedon]

OK, @Shibabrat is now a reviewer

[arfon]

@Shibabrat - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

[arfon]

@whedon add @szhorvat as reviewer

[whedon]

OK, @szhorvat is now a reviewer

[arfon]

@szhorvat - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

[szhorvat]

It seems I needed to install netcdf as well before it worked (apparently as a dependency of dantro). netcdf was not listed in the instructions. (I'm on macOS, using MacPorts.)

[peanutfun]

Hi @szhorvat and thanks for reviewing Utopia!

I assume that netcdf is a requirement of the Python xarray package which in turn is required by dantro, a main dependency of Utopia. However, it seems to me like pip should take care of the dependencies automatically when installing xarray. I assume this is an issue related to MacPorts and xarray. Could you open an issue in the dantro repo including an explanation how exactly you resolved it on your machine? Unfortunately, nobody of the Utopia devs or users currently uses MacPorts, so we are quite happy about any feedback on the installation procedure with this package manager.

[platipodium]

netcdf is notorious for causing downstream issues with dependent software. I am also using macports, so stumbling across the same issues. The port variant concept of macports also allows different compilers and MPI implementations, all resulting in a rather long dependency list for xarray and the like.

[blsqr]

(Another one of the Utopia and dantro devs here. Hi everyone 👋 )

netcdf is notorious for causing downstream issues with dependent software

Agree. We removed it as a dependency of dantro v0.12, the next release, due for release sometime this week. The dependency in utopya will be updated accordingly in the next couple of days.

[platipodium]

Opened a new authorship issue at https://ts-gitlab.iup.uni-heidelberg.de/utopia/utopia/issues/170

[platipodium]

New copyright issue at https://ts-gitlab.iup.uni-heidelberg.de/utopia/utopia/issues/171

[platipodium]

Opened new issues for macports on https://ts-gitlab.iup.uni-heidelberg.de/utopia/utopia/issues/172 https://ts-gitlab.iup.uni-heidelberg.de/utopia/utopia/issues/173 https://ts-gitlab.iup.uni-heidelberg.de/utopia/utopia/issues/174

[peanutfun]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

@whedon set 10.5281/zenodo.4011979 as archive

[whedon]

OK. 10.5281/zenodo.4011979 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #2165 with the following error:

Can't find any papers to compile :-(

[arfon]

@whedon accept from branch joss-paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1007/s11424-006-0001-z is OK
- 10.1103/RevModPhys.55.601 is OK
- 10.1057/jos.2016.7 is OK
- 10.1103/RevModPhys.74.47 is OK
- 10.1016/j.physrep.2005.10.009 is OK
- 10.1142/S0219525902000602 is OK
- 10.1145/3084225 is OK
- 10.1090/S0273-0979-02-00965-5 is OK
- 10.21105/joss.02316 is OK
- 10.1007/978-3-030-50436-6_32 is OK
- 10.1016/j.infsof.2014.05.006 is OK
- 10.21105/joss.01611 is OK
- 10.1016/j.softx.2019.02.009 is OK
- 10.25080/Majora-7b98e3ed-009 is OK
- 10.1103/PhysRevLett.69.1629 is OK
- 10.21105/joss.00026 is OK
- 10.1007/978-3-319-96418-8_50 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1695

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1695, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-paper 

[arfon]

@whedon accept deposit=true from branch joss-paper

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02165 joss-papers#1696
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02165
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@platipodium, @Shibabrat, @szhorvat - many thanks for your reviews here ✨

@peanutfun - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02165/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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[peanutfun]

@platipodium, @Shibabrat, @szhorvat, thank you very much for your reviews and for endorsing our publication! @arfon, thank you for your work! 🎊

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#3470