[REVIEW]: qgs: A flexible Python framework of reduced-order multiscale climate models

[whedon]

Submitting author: @jodemaey (Jonathan Demaeyer)
Repository: https://github.com/Climdyn/qgs
Version: v0.2.0
Editor: @harpolea
Reviewer: @eviatarbach, @sadielbartholomew
Archive: 10.5281/zenodo.4368844

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Markdown: [![status](https://joss.theoj.org/papers/3cf640133997e1394e3fd22963730391/status.svg)](https://joss.theoj.org/papers/3cf640133997e1394e3fd22963730391)

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Review checklist for @eviatarbach

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.

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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 (@jodemaey) 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 @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 (@jodemaey) 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. @eviatarbach, @sadielbartholomew it looks like you're currently assigned to review this paper 🎉.

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@whedon generate pdf

[whedon]

PDF failed to compile for issue #2597 with the following error:

Can't find any papers to compile :-(

[harpolea]

@whedon generate pdf from branch joss

[whedon]

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

[whedon]

👉 Check article proof 📄 👈

[eviatarbach]

qgs provides a modular implementation of a quasi-geostrophic atmospheric model. Having previously used the MAOOAM model in research, I was impressed with its ease-of-use, highly readable code, the elegance of the tensor-based implementation, and built-in tangent linear and adjoint models. qgs builds on this by adding two different land components, and making it easy to switch between ocean and land coupling. qgs is also written entirely in Python, as opposed to MAOOAM that had Fortran and Lua implementations also. I commend the authors for their excellent contribution and hope that qgs will become a widely used tool in the modelling hierarchy.

Suggested changes:

1. There are a few missing parts of the documentation, as per the review checklist. The statement of need is provided in the software paper, but it has to be in the documentation as well.

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

2. I would like to see the software paper mention the availability of the tangent linear and adjoint models, as this is a major advantage for data assimilation research, as well as for, e.g., computing the Lyapunov spectrum. Adding an example of the usage of the tangent linear or adjoint models to the documentation would be helpful.
3. This implementation is written in Python instead of Fortran, but uses Numba and sparse matrices to accelerate the computations. I would thus like to see a performance comparison to the Fortran version of MAOOAM, either in the documentation or the software paper (see the performance item on the checklist).

Minor issues:

• "Simpy" should be Sympy in the forthcoming developments section.
• The link to the notebooks folder works in the GitHub README, but is broken in the readthedocs documentation. Also, the link to the main folder just goes to the main page of the documentation.
• "montain" -> "mountain" in the Reinhold and Pierrehumbert (1982) example page

[kthyng]

Hi @jodemaey! I am the rotating associate editor in chief this week and am going through stale submissions. I see that one of your reviewers put forth some comments above but you haven't responded yet. Will you be able to get to this soon? If not, that is ok, but we should in that case pause this submission. I recommend that we pause this if we haven't heard back from the author within a week or so.

[sadielbartholomew]

Regarding your comment @kthyng, just to clarify that I was waiting on the submitting author's response to the first reviewer's comments, as in #2597 (comment), before starting my review, in case there were any significant changes made to the codebase or paper based on that feedback.

However, as you state it has been a while now, a good month, since that feedback without response. Would you recommend I start my review regardless, now? Or wait considering this could be considered 'stale'? I am just wary we are approaching six weeks since the review was opened and it is recommended I complete my review within that timeframe.

[jodemaey]

Hi @kthyng and @sadielbartholomew,

There was a misunderstanding here. I was waiting for the second review to address all the comments at once.

In any case I'm not able to work on this until the end of October. At that time I will work again fully on qgs and will address the comments and suggestions of @eviatarbach .

[sadielbartholomew]

Sorry that there was this misunderstanding, @jodemaey.

If you are unable to make changes until November it sounds like it would be best for me to complete my review by then so that you can know what else, if anything, might need to be addressed. I will ensure I have my review completed by then, and try to do it much sooner anyhow, now that I know about the situation. Thanks.

[kthyng]

@jodemaey, @sadielbartholomew I'm glad I commented then to clear this up!

@sadielbartholomew sounds good to me. I will not pause this submission then since we'll expect to hear from you in the next month with your review, and then subsequently from @jodemaey with responses.

Thanks all!

[jodemaey]

@sadielbartholomew , I am also sorry about this, I should have replied to Eviatar's review to clarify this. Thank you in advance for your review.

@kthyng Thank you.

[arfon]

👋 @sadielbartholomew - just checking you're planning on completing your review in the next week or so?

[sadielbartholomew]

Hi @arfon, yes, I will complete a first review over the weekend. Thanks for your patience.

[sadielbartholomew]

Really sorry for the further delay, I am having to co-manage an urgent operational infrastructure situation. I should have some time to review this later tonight and tomorrow so can complete my review by Saturday morning (UK time).

[sadielbartholomew]

@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

[sadielbartholomew]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.36 s (159.6 files/s, 37541.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              4              4           2937
Python                          17           1058           1792           2480
reStructuredText                20            373            387            454
Jupyter Notebook                 8              0           3037            439
TeX                              1             34              0            385
Markdown                         1             46              0             97
DOS Batch                        1              8              1             26
YAML                             2              5              4             23
Bourne Shell                     3              8              0             15
make                             1              4              9              9
-------------------------------------------------------------------------------
SUM:                            58           1540           5234           6865
-------------------------------------------------------------------------------


Statistical information for the repository 'ce242648c96bcd1558042443' was
gathered on 2020/11/06.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jonathan Demaeyer               18          6983           1653          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Jonathan Demaeyer          5330           76.3          4.0                6.45

[jodemaey]

Hi @sadielbartholomew ,

I have seen that you raised two issues in the qgs repo. Does that mean that your review is complete?

Thank you in advance,

Jonathan

[sadielbartholomew]

Hi @jodemaey, no I only got part way through my review in the time I could devote last week. I will try to finish the review tonight and tomorrow. Sorry for the delay and thanks for your patience.

[jodemaey]

And the DOI for the Lorenz paper (Predictability: A problem partly solved) actually point to a re-edition but I want to cite the original one here. There is no DOI for the original one.

Maybe I could cite the original article but then join to it the citation the DOI of the re-edition so that people still get a link to an electronic version.

[arfon]

Maybe I could cite the original article but then join to it the citation the DOI of the re-edition so that people still get a link to an electronic version.

Yes, that sounds like a reasonable solution.

[jodemaey]

Hi @arfon ,

Sorry but after discussing with my co-authors, we don't think it is a good idea to put the DOI of one citation corresponding to another one.
Again we prefer to cite the original Lorenz 96 article since it is the one that gave its name to the model being referred to. It is also the seminal reference that is usually cited in our field (1163 times according to google).
It's a seminar proceeding that was never officially published and thus never got a DOI, however it is quite easy to find it on many place on the web with a quick google search.

If you agree with this, I will proceed and make the release.

Jonathan

[arfon]

If you agree with this, I will proceed and make the release.

OK, this sounds reasonable. Please proceed.

[jodemaey]

Ok thanks, I will proceed as soon as possible.

[jodemaey]

@whedon generate pdf from branch joss

[whedon]

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

[whedon]

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

[jodemaey]

Hi @arfon ,

I've just merged the JOSS branch in master and released a new version v0.2.1 containing the paper and the modifications. Zenodi has automatically generated a new DOI: 10.5281/zenodo.4368844 that is already linked on the main page. Do I need to generate a specific archive for the article as you mentioned?

Also, please note that the online doc is currently not updated due to a bug .

[arfon]

@whedon set 10.5281/zenodo.4368844 as archive

[whedon]

OK. 10.5281/zenodo.4368844 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/j.physd.2015.07.006 is OK
- 10.5194/gmd-9-2793-2016 is OK
- 10.1007/s13351-018-8012-y is OK
- 10.1145/2833157.2833162 is OK
- 10.5194/npg-27-307-2020 is OK
- 10.1175/1520-0469(1963)020<0130:DNF>2.0.CO;2 is OK
- 10.1017/CBO9780511617652.004 is OK
- 10.1111/j.1600-0870.1984.tb00230.x is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.5334/jors.151 is OK
- 10.1029/2019MS001652 is OK
- 10.1007/s10955-020-02525-z is OK
- 10.1002/qj.3594 is OK
- 10.1007/s00382-020-05313-3 is OK
- 10.5194/gmd-11-843-2018 is OK
- 10.3402/tellusa.v41i4.11842 is OK
- 10.1504/IJCSE.2009.029165 is OK

MISSING DOIs

- 10.2142/biophys.48.324 may be a valid DOI for title: Isca
- 10.1017/cbo9780511617652.004 may be a valid DOI for title: Predictability: A problem partly solved

INVALID DOIs

- 10.1175/1520-0469(1987)044%3C3282:TOMEAW%3E2.0.CO;2 is INVALID
- 10.1175/1520-0493(1982)110%3C1105:DOWRQS%3E2.0.CO;2 is INVALID
- 10.1002/(SICI)1097-024X(199606)26:6%3C635::AID-SPE26%3E3.0.CO;2-P is INVALID

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2004

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2004, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@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.02597 joss-papers#2005
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02597
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]

@eviatarbach, @sadielbartholomew - many thanks for your reviews here. JOSS simply wouldn't work without the volunteer effort of folks like yourselves ✨

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

[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:

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HTML:
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</a>

reStructuredText:
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