[REVIEW]: DataAssimilationBenchmarks.jl: a data assimilation research framework

[whedon]

Submitting author: @cgrudz (Colin Grudzien)
Repository: https://github.com/cgrudz/DataAssimilationBenchmarks.jl
Branch with paper.md (empty if default branch):
Version: v0.3.4
Editor: @diehlpk
Reviewers: @peanutfun, @tmigot
Archive: 10.5281/zenodo.7311847

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Markdown: [![status](https://joss.theoj.org/papers/478dcc0b1608d2a4d8c930edebb58736/status.svg)](https://joss.theoj.org/papers/478dcc0b1608d2a4d8c930edebb58736)

Reviewers and authors:

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Review checklist for @peanutfun

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@cgrudz) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @tmigot

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@cgrudz) 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?
• 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?
• 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 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)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @peanutfun, @tmigot 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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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1301

[whedon]

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

OK DOIs

- 10.5281/zenodo.2029296 is OK

MISSING DOIs

- 10.1175/2009bams2618.1 may be a valid DOI for title: The data assimilation research testbed: A community facility
- 10.5194/gmd-2021-306 may be a valid DOI for title: A fast, single-iteration ensemble Kalman smoother for sequential data assimilation
- 10.1080/16000870.2018.1445364 may be a valid DOI for title: State-of-the-art stochastic data assimilation methods for high-dimensional non-Gaussian problems
- 10.5194/gmd-13-1903-2020 may be a valid DOI for title: On the numerical integration of the Lorenz-96 model, with scalar additive noise, for benchmark twin experiments
- 10.1002/wcc.535 may be a valid DOI for title: Data assimilation in the geosciences: An overview of methods, issues, and perspectives
- 10.5194/gmd-13-1903-2020 may be a valid DOI for title: On the numerical integration of the Lorenz-96 model, with scalar additive noise, for benchmark twin experiments

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.24 s (261.9 files/s, 74008.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           24           1353           3628           6036
Python                          27            971            120           3984
Markdown                         3            119              0            583
TOML                             2            108              1            451
TeX                              2             11              0            107
YAML                             3              3              4             39
Bourne Shell                     1              1              0              2
-------------------------------------------------------------------------------
SUM:                            62           2566           3753          11202
-------------------------------------------------------------------------------


Statistical information for the repository '01771c2f9ef55a9d0f8f5c70' was
gathered on 2022/02/03.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Colin Grudzien                  18          1572            312           26.23
Colin J Grudzien                 4            32            124            2.17
cgrudz                           7          2460            448           40.48
plinx                           17          2065            170           31.12

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
Colin J Grudzien              7           21.9          8.4                0.00
plinx                      5068          245.4          4.4                2.35

[whedon]

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

[peanutfun]

Hi @cgrudz 👋 I'll review your software in the next couple of days, and open up issues in the repository as I go along. Some of them might only be suggestions and not crucial to the review. Once I'm finished, I'll report back here and summarize the issues with respect to the review criteria and the checklist above.

Happy coding! 🚀

[cgrudz]

Hi @peanutfun, thanks so much, I'll be looking forward to hearing your recommendations for improvement.

Cheers,
Colin

[cgrudz]

@peanutfun, thanks so much for these useful and detailed suggestions for improvement. I'll start working through them slowly as I'm also in a somewhat reduced service mode with this project, as I just started a new position. Cheers!

[peanutfun]

@cgrudz, no worries, take your time. Then I can also take a more relaxed pace with the review 😇

[whedon]

👋 @tmigot, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @peanutfun, please update us on how your review is going (this is an automated reminder).

[peanutfun]

@cgrudz, I finished my review. Let me summarize:

DataAssimilationBenchmarks.jl is a well-working framework for researching data assimilation techniques. Installation is easy and I experienced no issues when executing functions of this package. The automated tests are working well and help understanding the inner workings of the module, although code coverage is still a bit low. The README.md gives a good overview of the framework and extensively documents the public API. Finally, the paper is well written and does an especially good job in motivating the development of the framework.

My main issue with the current state of the package is that I, as a person unfamiliar with the source code, see no clear way of extending the framework with new models and DA methods. In that regard, I feel that DataAssimilationBenchmarks.jl fails its own premise because it is intended to compare DA methods against each other and include more filters and smoothers in the future. As an open-source project, it should encourage contributions by others, and therefore needs instructions on how to add such new methods to the framework.

The other points I want to address mostly concern documentation. The README.md should include an Example Usage section, that illustrates the capabilities of the framework and the intended workflow, and supplies a useful set of default function arguments. As the module functions do not return data structures but write all data into files, the structure and content of these files should be documented as well. Additionally, the repository lacks community guidelines, which is more of a technicality. And finally, I think the paper can be shortened, and some of its references can be improved.

I suggested a lot more in the issues I created during my review, which is mainly due to the fact that I see a lot of potential in DataAssimilationBenchmarks.jl. But most of them are well beyond the scope of this review. Two things I still would like to point out: First, you already documented the API extensively in the README.md. Moving this documentation over to docstrings in the code would yield a documentation that is formatted in a standardized and expected way, and should not be much work. And second, I think that reworking the analysis scripts to work on any system would be a huge selling point. Ideally, the framework would then cover everything from running a model, over benchmarking DA methods in parallel, to evaluating and analyzing their performance.

Issues for meeting review criteria

• Add usage examples and workflow to README.md cgrudz/DataAssimilationBenchmarks.jl#7
• Document output file structure cgrudz/DataAssimilationBenchmarks.jl#10
• Add community guidelines cgrudz/DataAssimilationBenchmarks.jl#14
• Add instructions on how to add new DA schemes and models cgrudz/DataAssimilationBenchmarks.jl#15
• Incorporate suggestions to JOSS paper (or conclusively reject them) Suggestions for improving JOSS paper cgrudz/DataAssimilationBenchmarks.jl#16

Possible improvements I strongly recommend

(These are personal suggestions to improve the package, and they are not required to meet the review criteria for publication in JOSS)

• Use docstrings to document API Consider adding docstrings to exported functions cgrudz/DataAssimilationBenchmarks.jl#8
• Rework analysis scripts to be used with every experiment/benchmark Rework analysis scripts to take path to data file as argument cgrudz/DataAssimilationBenchmarks.jl#11

[cgrudz]

@peanutfun thank you for your excellent suggestions and detailed review, I really appreciate the effort you took to go through the code as you did. I just wanted to write a quick message to let you know that I am intending to start on revisions and reading through the posted issues in about a month or two -- I am waiting in part to see if I can fund an undergraduate research assistant to help resolve the issues, as I think these will make good exercises for an RA again. However, if this funding does not go through, I do intend to resolve these issues myself. I'll keep the review process updated with my status shortly.

Cheers!
Colin

[diehlpk]

@editorialbot set v0.3.4 as version

[editorialbot]

Done! version is now v0.3.4

[diehlpk]

@editorialbot set 10.5281/zenodo.7311847 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7311847

[diehlpk]

@cgrudz The title of the Zenodo archive reads as cgrudz/DataAssimilationBenchmarks.jl: JOSS Paper Version, but it should read as DataAssimilationBenchmarks.jl: a data assimilation research framework to match the paper. Please edit the title. There is no need for a new verison.

[diehlpk]

@editorialbot check references

[diehlpk]

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1175/2009BAMS2618.1 is OK
- 10.5194/gmd-15-7641-2022 is OK
- 10.1080/16000870.2018.1445364 is OK
- 10.5281/zenodo.7036069 is OK
- 10.5194/gmd-13-1903-2020 is OK
- 10.1137/1.9781611974546 is OK
- 10.1002/wcc.535 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1600-0870.2007.00261.x is OK
- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[diehlpk]

@cgrudz After that change, I can recommend the paper for acceptance.

[cgrudz]

Great! I think I just got this fixed, let me know if there is anything else to do.

[diehlpk]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1175/2009BAMS2618.1 is OK
- 10.5194/gmd-15-7641-2022 is OK
- 10.1080/16000870.2018.1445364 is OK
- 10.5281/zenodo.7036069 is OK
- 10.5194/gmd-13-1903-2020 is OK
- 10.1137/1.9781611974546 is OK
- 10.1002/wcc.535 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1600-0870.2007.00261.x is OK
- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[diehlpk]

@cgrudz Thanks, I can now recommend the paper for acceptance.

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3718, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kthyng]

Everything looks good!

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.04129 joss-papers#3719
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04129
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...

[kthyng]

Congratulations on your new publication @cgrudz!! Many thanks to editor @diehlpk and reviewers @peanutfun and @tmigot for your time, hard work, and expertise!!

[editorialbot]

🎉🎉🎉 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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[![DOI](https://joss.theoj.org/papers/10.21105/joss.04129/status.svg)](https://doi.org/10.21105/joss.04129)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04129/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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