[REVIEW]: OpenSCM Two Layer Model: A Python implementation of the two-layer climate model

[whedon]

Submitting author: @znicholls (Zebedee Nicholls)
Repository: https://github.com/openscm/openscm-twolayermodel
Version: v0.2.3
Editor: @leouieda
Reviewer: @sadielbartholomew, @ashiklom
Archive: 10.5281/zenodo.4950772

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/94a3759c9ea117499b90c56421ef4857"><img src="https://joss.theoj.org/papers/94a3759c9ea117499b90c56421ef4857/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/94a3759c9ea117499b90c56421ef4857/status.svg)](https://joss.theoj.org/papers/94a3759c9ea117499b90c56421ef4857)

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

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

1. Make sure you're logged in to your GitHub account
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✨ 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 ✨

Review checklist for @sadielbartholomew

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 (@znicholls) 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

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 @ashiklom

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 (@znicholls) 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

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. @sadielbartholomew, @ashiklom it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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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:

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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

[whedon]

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

OK DOIs

- 10.1175/JCLI-D-12-00195.1 is OK
- 10.1175/JCLI-D-12-00196.1 is OK
- 10.1175/2009JCLI3466.1 is OK
- 10.1002/2015GL064240 is OK
- 10.5194/gmd-11-2273-2018 is OK
- 10.5194/gmd-2019-375 is OK

MISSING DOIs

- 10.1007/s10584-011-0156-z may be a valid DOI for title: The RCP greenhouse gas concentrations and their extensions from 1765 to 2300
- 10.1007/s00382-019-04686-4 may be a valid DOI for title: On simple representations of the climate response to external radiative forcing

INVALID DOIs

- None

[whedon]

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

[leouieda]

👋 @sadielbartholomew, @ashiklom, @znicholls this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread 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 openjournals/joss-reviews#2766 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 reviews to be completed within about 4 weeks. Please let me know if any of you require some more time. We can also use @whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me here (@leouieda) or email me privately if you have any questions/concerns.

[ashiklom]

General checks

• Repository: Link is valid; code is well-organized according to typical standards of a Python module.
• License: BSD 3-caluse, present in full in LICENSE file in the repository
• Contribution and authorship: Submission author @znicholls is the largest contributor by far. No obvious issues with the author list.
• Substantial scholarly effort:
  • Oldest commit is April 15, 2020.
  • This model is a new addition to the growing list of reduced-complexity climate models. It serves as an interesting alternative to similar efforts, such as Hector, MAGICC, and FAIR, and in this context, is a member of the Reduced Complexity Model Intercomparison Project (RCMIP), phase 1.

Functionality

• Installation: I successfully installed the module and its dependencies via pip from the Python Package Index (PyPI) and from source, as described in the instructions.
• Functionality: I ran all of the notebooks without errors, and ran a few simple experiments of my own, tweaking parameters of the model to explore the response. Everything worked as expected.
• Performance: There are no performance claims. However, the notebooks run almost instantaneously on my 2019 Macbook Pro -- this is a fast model!

Documentation

• Statement of need: Missing from documentation. I suggest adding a brief (1-3 sentences) note about this to the documentation home page. See Add statement of need to documentation home page openscm/openscm-twolayermodel#18.
• Installation instructions: Described in the README, and are very straightforward (see above).
• Example usage: Four Jupyter notebooks distributed with the repository provide useful examples of general usage and a few interesting specific cases.
• Functionality documentation: All methods and their arguments are well documented using ReadTheDocs.
• Automated tests: The installation process and Jupyter notebooks (examples of typical usage) are automatically tested using GitHub Actions.
• Community guidelines: The authors provide a thorough and detailed contributing guide in the "Development" section of their documentation.

Software paper

• Summary: Summary provides a brief overview of the role of simple climate models, a concise theoretical description of the two-layer model, and a description of the implementation here.
• Statement of need: Present, and provides a compelling case for the extensible nature of this implementation. Also makes a useful comparison with another similar model (FaIR). One minor suggestion: It may be worth advertising the fact that this implementation is in Python, a language that is open source, easy to use, and popular in the atmospheric sciences (and Earth and computational sciences more generally). For instance, were previous implementation of the two-layer model in something less user-friendly like Fortran or less open like Matlab?
• State of the field: Generally present in the Summary, but could be fleshed out a bit. Specifically, it might be worth (briefly) giving a few other simple climate model examples (that can be pulled directly from the RCMIP paper). Even more useful might be a short table stating the model, a brief description of its scientific basis (in a few words; <1 full sentence), and its programming language and paradigm. This would also provide useful context for this model.
• Quality of writing: Writing is solid; no major concerns.
• References: References are used appropriately and formatted correctly.

[leouieda]

@ashiklom thank you for your thorough review (and issues on the software repository)!

@znicholls please do you best to address some of the points raised, in particular:

1. Adding suggested context to the statement of need. Including it in the docs is a good idea and helps define the scope of the project.
2. Fleshing out the "State of the field" in the JOSS paper.

Please keep us posted on your progress 🙂

[znicholls]

@znicholls please do you best to address some of the points raised, in particular

Will do. I've started in a couple of PRs, will work on point 2 this week. Thanks to both for the great review and co-ordination!

[znicholls]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[znicholls]

I've updated the missing DOIs (openscm/openscm-twolayermodel#24) so will recompile

[znicholls]

@whedon check references

[whedon]

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

OK DOIs

- 10.1175/JCLI-D-12-00195.1 is OK
- 10.1175/JCLI-D-12-00196.1 is OK
- 10.1175/2009JCLI3466.1 is OK
- 10.1002/2015GL064240 is OK
- 10.1007/s10584-011-0156-z is OK
- 10.1007/s00382-019-04686-4 is OK
- 10.5194/gmd-11-2273-2018 is OK
- 10.5194/gmd-2019-375 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[znicholls]

@whedon generate pdf

[whedon]

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

[znicholls]

• For instance, were previous implementation of the two-layer model in something less user-friendly like Fortran or less open like Matlab?

On this one I'm not sure. There's FaIR, but it is missing some of the conversion functionality and modularisation we've implemented here (as mentioned in the draft). I haven't been able to find any other public implementations so couldn't comment on other languages unfortunately.

[leouieda]

@whedon set 10.5281/zenodo.4950772 as archive

[whedon]

OK. 10.5281/zenodo.4950772 is the archive.

[leouieda]

@whedon set v0.2.3 as version

[whedon]

OK. v0.2.3 is the version.

[leouieda]

@whedon check references

[whedon]

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

OK DOIs

- 10.1175/JCLI-D-12-00195.1 is OK
- 10.1175/JCLI-D-12-00196.1 is OK
- 10.1175/2009JCLI3466.1 is OK
- 10.1002/2015GL064240 is OK
- 10.1007/s10584-011-0156-z is OK
- 10.1007/s00382-019-04686-4 is OK
- 10.5194/gmd-11-2273-2018 is OK
- 10.5194/gmd-13-5175-2020 is OK
- 10.1007/s00382-011-1026-0 is OK
- 10.5194/gmd-8-939-2015 is OK
- 10.5194/acp-11-1417-2011 is OK
- 10.21105/joss.00516 is OK
- 10.5194/bg-17-4075-2020 is OK
- 10.1029/2019gl082887 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[leouieda]

@whedon generate pdf

[whedon]

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

[leouieda]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1175/JCLI-D-12-00195.1 is OK
- 10.1175/JCLI-D-12-00196.1 is OK
- 10.1175/2009JCLI3466.1 is OK
- 10.1002/2015GL064240 is OK
- 10.1007/s10584-011-0156-z is OK
- 10.1007/s00382-019-04686-4 is OK
- 10.5194/gmd-11-2273-2018 is OK
- 10.5194/gmd-13-5175-2020 is OK
- 10.1007/s00382-011-1026-0 is OK
- 10.5194/gmd-8-939-2015 is OK
- 10.5194/acp-11-1417-2011 is OK
- 10.21105/joss.00516 is OK
- 10.5194/bg-17-4075-2020 is OK
- 10.1029/2019gl082887 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#2389

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2389, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[leouieda]

@znicholls I'm happy to recommend acceptance of this paper for publication in JOSS! 🎉 🎊

Thank you to our reviewers @sadielbartholomew and @ashiklom for your thorough and helpful comments! I'm particularly grateful for all of your patience and understanding with the big delay in this review.

[znicholls]

Awesome thanks @leouieda @sadielbartholomew and @ashiklom ! Much appreciated

[danielskatz]

Thanks @znicholls - this basically looks good to me to finalize, though I've suggested some small changes in the paper in openscm/openscm-twolayermodel#37 Please merge this, or let me know what you disagree with, then we can proceed to publishing.

[znicholls]

Changes look good, all merged

[danielskatz]

@whedon generate pdf

[whedon]

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

[danielskatz]

@whedon accept deposit=true

[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.02766 joss-papers#2390
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02766
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...

[danielskatz]

Congratulations to @znicholls (Zebedee Nicholls) and co-author!!

And thanks to @sadielbartholomew and @ashiklom for reviewing, and @leouieda for editing!

[whedon]

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

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.02766/status.svg)](https://doi.org/10.21105/joss.02766)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02766">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02766/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02766/status.svg
   :target: https://doi.org/10.21105/joss.02766

This is how it will look in your documentation:

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