[REVIEW]: MITgcm.jl: a Julia Interface to the MITgcm
editorialbot opened this issue · comments
Submitting author: @gaelforget (Gael Forget)
Repository: https://github.com/gaelforget/MITgcm.jl
Branch with paper.md (empty if default branch): joss
Version: v0.3.2
Editor: @AnjaliSandip
Reviewers: @simone-silvestri, @christophernhill
Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/80a02d6e487533e9348fb4112a62dcbf"><img src="https://joss.theoj.org/papers/80a02d6e487533e9348fb4112a62dcbf/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/80a02d6e487533e9348fb4112a62dcbf)
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
@simone-silvestri & @christophernhill, 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
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:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Software report:
github.com/AlDanial/cloc v 1.90 T=0.08 s (475.1 files/s, 197776.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Julia 20 2684 9816 2074
TOML 6 77 0 1244
Markdown 10 145 0 328
TeX 1 19 0 161
YAML 3 5 0 98
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SUM: 40 2930 9816 3905
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Commit count by author:
395 gaelforget
12 Gael Forget
5 jbisits
4 CompatHelper Julia
1 Julia TagBot
Paper file info:
📄 Wordcount for paper.md is 828
✅ The paper includes a Statement of need section
License info:
✅ License found: MIT License (Valid open source OSI approved license)
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5194/bg-12-4447-2015 is OK
- 10.5281/zenodo.2653669 is OK
- 10.5281/zenodo.10903961 is OK
- 10.21105/joss.02813 is OK
- 10.21105/joss.04207 is OK
- 10.1101/2023.11.23.568480 is OK
- 10.11578/E3SM/dc.20240301.3 is OK
- 10.1126/sciadv.abf5478 is OK
- 10.1038/s41561-019-0333-7 is OK
- 10.21105/joss.02018 is OK
- 10.21105/joss.04207 is OK
- 10.21105/joss.02813 is OK
- 10.5194/gmd-8-3071-2015 is OK
MISSING DOIs
- 10.21203/rs.3.rs-3979671/v1 may be a valid DOI for title: Energy Imbalance in the Sunlit Ocean Layer
- 10.1029/96jc02775 may be a valid DOI for title: A finite-volume, incompressible Navier Stokes mode...
- 10.1016/s1463-5003(03)00009-x may be a valid DOI for title: Conservation of properties in a free surface model
- 10.1016/j.future.2004.11.010 may be a valid DOI for title: An efficient exact adjoint of the parallel MIT gen...
INVALID DOIs
- None
Review checklist for @simone-silvestri
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/gaelforget/MITgcm.jl?
- License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@gaelforget) 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?
@christophernhill, Do you still have the time to review this submission?
@simone-silvestri How close are you to completing the review?
@AnjaliSandip I am almost halfway through, I will finish it by next week.