[REVIEW]: DIFFICE-jax: Differentiable neural-network solver for data assimilation of ice shelves in JAX

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@wangyji@AnjaliSandip<!--end-editor-- Reviewers: @daniel-cheng, @nmcardoso, @RahulSundar Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/4cf986d53809937f2352b5fc2b7a6120/status.svg)](https://joss.theoj.org/papers/4cf986d53809937f2352b5fc2b7a6120)

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

@daniel-cheng & @nmcardoso & @RahulSundar, 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 @AnjaliSandip 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 @nmcardoso

📝 Checklist for @daniel-cheng

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1153.2 files/s, 212526.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            491            777           1510
TeX                              2            247              0           1456
Jupyter Notebook                 5              0            960           1273
Markdown                        10            232              0            634
YAML                             2              8             10             45
TOML                             1              6              0             34
MATLAB                           1             12             13             32
-------------------------------------------------------------------------------
SUM:                            42            996           1760           4984
-------------------------------------------------------------------------------

Commit count by author:

   616  yjwang
   111  Yao Lai
     6  Yongi Wang

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.5194/tc-15-1975-2021 is OK
- 10.1002/2014JF003181 is OK
- 10.1029/2024JH000169 is OK
- 10.1017/jog.2020.112 is OK
- 10.1016/j.jcp.2023.112428 is OK
- 10.5194/gmd-16-6671-2023 is OK
- 10.1017/jog.2021.120 is OK
- 10.1017/jog.2022.41 is OK
- 10.1017/jog.2023.73 is OK
- 10.1016/j.jcp.2024.112865 is OK
- 10.21203/rs.3.rs-2135795/v1 is OK
- 10.1029/JB094iB04p04071 is OK
- 10.3189/S0022143000015744 is OK
- 10.1038/s43247-022-00385-x is OK
- 10.1073/pnas.2309788121 is OK
- 10.5194/tc-9-1427-2015 is OK
- 10.1002/jgrf.20125 is OK
- 10.5194/tc-5-315-2011 is OK
- 10.3189/172756403781816338 is OK
- 10.1137/19M1274067 is OK
- 10.48550/arXiv.2207.02338 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1029/2021MS002621 is OK
- 10.1017/jog.2023.8 is OK
- 10.1029/2010GL043853 is OK
- 10.1016/j.jcp.2023.112435 is OK
- 10.4208/cicp.oa-2020-0164 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Deep learning the flow law of Antarctic Ice Shelve...
- No DOI given, and none found for title: MEaSUREs Phase-Based Antarctica Ice Velocity Map, ...
- No DOI given, and none found for title: MEaSUREs BedMachine Antarctica, Version 2
- No DOI given, and none found for title: Euler operators for mis-specified physics-informed...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1315

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

nmcardoso commented 1 month ago

Review checklist for @nmcardoso

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 https://github.com/YaoGroup/DIFFICE_jax?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wangyji) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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

[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] 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).
[ ] 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?
[x] 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: 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?
[x] 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?

AnjaliSandip commented 1 month ago

@daniel-cheng & @RahulSundar, here's a friendly reminder to begin reviewing this software/paper.

AnjaliSandip commented 2 weeks ago

@nmcardoso How close are you to completing the review? @daniel-cheng & @RahulSundar, do you have time to review this submission in the next 2-3 weeks?

RahulSundar commented 2 weeks ago

Hi, I have been working on the review. Will be able to complete within next two weeks.

On Mon, 21 Oct, 2024, 9:45 pm Anjali Sandip, @.***> wrote:

@nmcardoso https://github.com/nmcardoso How close are you to completing the review? @daniel-cheng https://github.com/daniel-cheng & @RahulSundar https://github.com/RahulSundar, do you have time to review this submission in the next 2-3 weeks?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7254#issuecomment-2427128317, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFZGIWREY4XRKYSOGP36O6LZ4USCJAVCNFSM6AAAAABOSIVACGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRXGEZDQMZRG4 . You are receiving this because you were mentioned.Message ID: @.***>

daniel-cheng commented 2 weeks ago

Hi @AnjaliSandip, I will also target having the review done within the next two weeks. Thanks for your understanding!

daniel-cheng commented 2 weeks ago

Review checklist for @daniel-cheng

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 https://github.com/YaoGroup/DIFFICE_jax?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wangyji) 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
[x] 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.
[x] 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?

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