[REVIEW]: DPFEHM: a differentiable subsurface physics simulator

[editorialbot]

Submitting author: @omalled (Daniel O'Malley) Repository: https://github.com/OrchardLANL/DPFEHM.jl Branch with paper.md (empty if default branch): Version: v0.1.0 Editor: @jedbrown Reviewers: @WilkAndy, @rtmills, @rezgarshakeri Archive: Pending

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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

@WilkAndy & @rtmills & @rezgarshakeri, 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 @jedbrown 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 @WilkAndy

📝 Checklist for @rezgarshakeri

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1270.2 files/s, 149223.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           36            295            347           2767
TOML                             2            205              1            911
Markdown                         3             51              0            367
Jupyter Notebook                 1              0             96            208
YAML                             3              1              5             92
TeX                              1              0              0             58
-------------------------------------------------------------------------------
SUM:                            46            552            449           4403
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 758

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.2172/1657092 may be a valid DOI for title: Amanzi–ATS: Modeling Environmental Systems across Scales [Brief]
- 10.1029/2021wr031188 may be a valid DOI for title: A Comparison of Linear Solvers for Resolving Flow in Three-Dimensional Discrete Fracture Networks
- 10.1615/jmachlearnmodelcomput.2022042093 may be a valid DOI for title: Inverse analysis with variational autoencoders: a comparison of shallow and deep networks
- 10.21203/rs.3.rs-1782030/v1 may be a valid DOI for title: Physics-informed machine learning with differentiable programming for heterogeneous underground reservoir pressure management
- 10.2172/1168703 may be a valid DOI for title: PFLOTRAN user manual: A massively parallel reactive flow and transport model for describing surface and subsurface processes

INVALID DOIs

- None

[editorialbot]

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

[jedbrown]

@WilkAndy @rezgarshakeri @rtmills :wave: Welcome to JOSS and thanks for agreeing to review! The comments from @editorialbot above outline the review process, which takes place in this thread (possibly with issues filed in the DPFEHM repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention this issue so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or two. Please let me know if you require some more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

[omalled]

BTW, I added a GitHub action to run the tests.

[WilkAndy]

Review checklist for @WilkAndy

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/OrchardLANL/DPFEHM.jl?
• [x] 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 (@omalled) 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?
• [ ] 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.
• [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

• [ ] 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?

[WilkAndy]

Cannot confirm contributions of Wu Hao and Dylan Harp

[WilkAndy]

@omalled - is it true that the code coverage is about 50%?

[omalled]

Regarding Wu Hao and Dylan Harp, I got the author list by including the people who made a commit. If I do git log | grep Ha, I see Dylan Harp and Wu Hao on there. I haven't checked the code coverage.

[rezgarshakeri]

Review checklist for @rezgarshakeri

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/OrchardLANL/DPFEHM.jl?
• [x] 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 (@omalled) 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?
• [ ] 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).
• [ ] 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

• [ ] 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?

[WilkAndy]

Hi @omalled - i'm not sure whether you think my open issues at DPFEHM are silly (no offense taken - they're just suggestions). Nothing has happened in that repo for the last month. Or maybe you're all on holiday?

[omalled]

@WilkAndy No, your suggestions are good. 😄 I've just been busy. I'm planning to get back to this next week.

[omalled]

@WilkAndy, I addressed the issues raised here, following the outline here. I also looked into all the issues raised in the repo and got the code coverage up over 85% (seems to not count code that is run at compile time, so the actual coverage is significantly higher, I believe). Got it done "next week" with a couple of hours to spare in my time zone. 😄 Thanks for looking into all this stuff - definitely helping me whip this code into shape!

[WilkAndy]

Hey everyone (viz @omalled ) - this seems to have gone off the boil. I'm quite keen for this article to be published, but have people lost interest?

[omalled]

I'm working on it.