Joss-reviews: [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: Pending

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Reviewer instructions & questions

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

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Review checklist for @eviatarbach

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 repository url?
• [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 (@jodemaey) 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

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] 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?
• [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?
• [ ] 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [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?

Review checklist for @sadielbartholomew

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 repository url?
• [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 (@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 :tada:.

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[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]

:point_right: Check article proof :page_facing_up: :point_left:

[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
• 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.
• 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 https://github.com/openjournals/joss-reviews/issues/2597#issuecomment-683972381, 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]

:wave: @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]

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# List Whedon's capabilities
@whedon commands

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EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

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@whedon generate pdf from branch custom-branch-name

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

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[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.