[REVIEW]: EnsembleKalmanProcesses.jl: Derivative-free ensemble-based model calibration

[editorialbot]

Submitting author: @odunbar (Oliver Dunbar)
Repository: https://github.com/CliMA/EnsembleKalmanProcesses.jl
Branch with paper.md (empty if default branch):
Version: v0.14.1
Editor: @jbytecode
Reviewers: @odow, @ziyiyin97
Archive: 10.5281/zenodo.7407193

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5cb2d4c6af8840af61b44071ae1e672a"><img src="https://joss.theoj.org/papers/5cb2d4c6af8840af61b44071ae1e672a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5cb2d4c6af8840af61b44071ae1e672a/status.svg)](https://joss.theoj.org/papers/5cb2d4c6af8840af61b44071ae1e672a)

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

@odow & @ziyiyin97, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ 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 ✨

Checklists

📝 Checklist for @ziyiyin97

📝 Checklist for @odow

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (1168.2 files/s, 151224.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Julia                            43           1570           1141           6553
Markdown                         28            622              0           1743
YAML                              8             14              5            213
TeX                               1             26              0            194
TOML                             11             22             12            157
SVG                               1              0              0             71
Bourne Again Shell                4             18             26             40
--------------------------------------------------------------------------------
SUM:                             96           2272           1184           8971
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1415

[editorialbot]

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

OK DOIs

- 10.1029/2022MS003105 is OK
- 10.1016/j.jcp.2022.111262 is OK
- 10.48550/arXiv.2204.04386 is OK
- 10.1175/1520-0493(1998)126<0796:DAUAEK>2.0.CO;2 is OK
- 10.1029/94JC00572 is OK
- 10.1175/1520-0493(2001)129<0123:ASEKFF>2.0.CO;2 is OK
- 10.1137/19M1251655 is OK
- 10.1088/0266-5611/29/4/045001 is OK
- 10.1137/19M1304891 is OK
- 10.1016/j.jcp.2022.111559 is OK
- 10.1111/1467-9868.00294 is OK
- 10.1029/2022MS002997 is OK
- 10.1029/2020MS002454 is OK
- 10.1029/2021MS002735 is OK
- 10.1371/journal.pcbi.1010171 is OK
- 10.48550/arxiv.2105.11341 is OK
- 10.48550/arXiv.2201.10821 is OK
- 10.1029/2022MS002994 is OK
- 10.1016/j.jcp.2020.109716 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jbytecode]

Dear @odow and @ziyiyin97,

Thank you again, for accepting our invitation to review.

This is the review thread. Please, firstly type

@editorialbot generate my checklist

to generate your own checklist. In that checklist, there are 21 check items. Whenever you complete the corresponding task, you can check off them.

Please write your comments as separate posts and do not modify your checklist descriptions.

The review process is interactive so you can always interact with the authors, reviewers, and the editor. You can also create issues and pull requests in the target repo. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.

Please do not hesitate to ask me about anything, anytime.

Thank you in advance!

[ziyiyin97]

Review checklist for @ziyiyin97

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 https://github.com/CliMA/EnsembleKalmanProcesses.jl?
• 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 (@odunbar) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[odow]

Review checklist for @odow

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 https://github.com/CliMA/EnsembleKalmanProcesses.jl?
• 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 (@odunbar) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[jbytecode]

Dear @odunbar

Our reviewer has opened a new issue in the target repository. Please read the entries carefully and take an action.

Thank you in advance.

[jbytecode]

@odunbar - Could you please update your status and inform us about the progress? Thank you in advance.

[ziyiyin97]

Sorry I was a bit swamped these days. I've been running some example scripts from the package and I'll finish my review by the end of this weekend.

[jbytecode]

@odunbar - could you please update your status?

[odunbar]

Hi @jbytecode , Sorry I did not catch these requests for an update. In short we are "working on it".
We have addressed the first reviewers comments,
We are currently working on the second reviewers comments.

We are listing PRs on the reviewer's individual issues in our repository to track this progress.

[jbytecode]

@odunbar - thank you for the update. Please mention this thread's URL in your PR's and issues so we can keep tracking on them.

[odow]

I'm happy with the changes that have been made: CliMA/EnsembleKalmanProcesses.jl#222 (comment)

The paper is a little long (> 6 pages), but a large part are references, so the content is ~5 pages.

[odunbar]

Thanks very much! We are conscious of the length and will review it after addressing the other reviewer's comments.

The link provided above contains all the work toward the 1st review, I will create a similar comment and link for the 2nd review that lists the PRs too

[odunbar]

An update:

The 3 PRs in this comment are addressing the second reviewers comments.

The PRs are undergoing the final internal review, then I shall ask the second reviewer to take a look.

[jbytecode]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.04723 is OK
- 10.21105/joss.00615 is OK
- 10.1137/141000671 is OK
- 10.1029/2022MS003105 is OK
- 10.1016/j.jcp.2022.111262 is OK
- 10.1088/1361-6420/ac99fa is OK
- 10.1175/1520-0493(1998)126<0796:DAUAEK>2.0.CO;2 is OK
- 10.1029/94JC00572 is OK
- 10.1175/1520-0493(2001)129<0123:ASEKFF>2.0.CO;2 is OK
- 10.1137/19M1251655 is OK
- 10.1088/0266-5611/29/4/045001 is OK
- 10.1137/19M1304891 is OK
- 10.1016/j.jcp.2022.111559 is OK
- 10.1111/1467-9868.00294 is OK
- 10.1029/2022MS002997 is OK
- 10.1029/2020MS002454 is OK
- 10.1029/2021MS002735 is OK
- 10.1371/journal.pcbi.1010171 is OK
- 10.48550/arxiv.2105.11341 is OK
- 10.48550/arXiv.2201.10821 is OK
- 10.1029/2022MS002994 is OK
- 10.1016/j.jcp.2020.109716 is OK
- 10.1137/16M105959X is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

@editorialbot set 10.5281/zenodo.7407193 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7407193

[jbytecode]

Thank you @odunbar, the things seem okay to me. I am now recommending an accept. The final decision will be made by our associate eic.

[jbytecode]

@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

- 10.21105/joss.04723 is OK
- 10.21105/joss.00615 is OK
- 10.1137/141000671 is OK
- 10.1029/2022MS003105 is OK
- 10.1016/j.jcp.2022.111262 is OK
- 10.1088/1361-6420/ac99fa is OK
- 10.1175/1520-0493(1998)126<0796:DAUAEK>2.0.CO;2 is OK
- 10.1029/94JC00572 is OK
- 10.1175/1520-0493(2001)129<0123:ASEKFF>2.0.CO;2 is OK
- 10.1137/19M1251655 is OK
- 10.1088/0266-5611/29/4/045001 is OK
- 10.1137/19M1304891 is OK
- 10.1016/j.jcp.2022.111559 is OK
- 10.1111/1467-9868.00294 is OK
- 10.1029/2022MS002997 is OK
- 10.1029/2020MS002454 is OK
- 10.1029/2021MS002735 is OK
- 10.1371/journal.pcbi.1010171 is OK
- 10.48550/arxiv.2105.11341 is OK
- 10.48550/arXiv.2201.10821 is OK
- 10.1029/2022MS002994 is OK
- 10.1016/j.jcp.2020.109716 is OK
- 10.1137/16M105959X is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#3779, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[odunbar]

Hi @jbytecode, do you know how long this stage typically takes?

[gkthiruvathukal]

Hi, I'm the track EIC. After going through some final checks, it will be accepted. Usually just a few days but I am home sick with an eye infection. Thank you for understanding!

[arfon]

👋 @gkthiruvathukal I can help wrap this one up for you.

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot 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.04869 joss-papers#3817
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04869
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]

@odow, @ziyiyin97 – many thanks for your reviews here and to @jbytecode for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@odunbar – your paper is now accepted and published in JOSS ⚡🚀💥

[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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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04869/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04869/status.svg
   :target: https://doi.org/10.21105/joss.04869

This is how it will look in your documentation:

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[odunbar]

Thank you all! This was a very smooth and open experience.