[REVIEW]: visualCaseGen: An SMT-based Experiment Configurator for Community Earth System Model

[editorialbot]

Submitting author: @alperaltuntas (Alper Altuntas)
Repository: https://github.com/ESMCI/visualCaseGen
Branch with paper.md (empty if default branch): paper
Version: 0.1.3
Editor: @mengqi-z
Reviewers: @brian-rose, @lars2015, @fzhao70
Archive: Pending

Status

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Reviewers and authors:

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Reviewer instructions & questions

@brian-rose & @lars2015, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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✨ 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 @lars2015

📝 Checklist for @fzhao70

📝 Checklist for @brian-rose

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

✅ OK DOIs

- 10.1007/978-3-540-78800-3_24 is OK
- 10.1029/2019MS001916 is OK
- 10.1029/2020MS002418 is OK
- 10.1029/2017EO079417 is OK
- 10.1029/2018RG000607 is OK
- 10.1145/1995376.1995394 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.17 s (600.0 files/s, 76559.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          75           2090           1943           7236
reStructuredText                11            372            248            677
Markdown                         9            100              0            382
YAML                             4             15             13            107
TeX                              1              5              0             63
TOML                             1              2              0             36
DOS Batch                        1              8              1             26
make                             1              4              7              9
Bourne Shell                     1              4              7              7
Jupyter Notebook                 1              0             34              1
-------------------------------------------------------------------------------
SUM:                           105           2600           2253           8544
-------------------------------------------------------------------------------

Commit count by author:

   435	alperaltuntas
    93	Alper Altuntas
    15	manishvenu
     3	Manish Venumuddula

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1250

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

[mengqi-z]

👋 @brian-rose @lars2015 @fzhao70 - This is the review thread for the paper. All of our communications will happen here from now on.

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@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

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[mengqi-z]

@editorialbot add @fzhao70 as reviewer

[editorialbot]

@fzhao70 added to the reviewers list!

[fzhao70]

Review checklist for @fzhao70

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/ESMCI/visualCaseGen?
• 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 (@alperaltuntas) 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?

[fzhao70]

I have tested this program on both the NCAR Derecho system and a local system. Overall, this is an excellent program that significantly enhances the user experience for working with Earth System Models and provides substantial value for beginners. This tool addresses a long-standing need identified by the community for improved user accessibility to complex model configurations. I recommend publication after the following minor revisions are addressed. The authors have made a commendable effort, and I hope this tool can be incorporated into future CESM tutorial workshops. Additionally, I hope the DOE to consider implementing a similar interface for their E3SM to provide comparable ease of use for that modeling framework.

Minor Revisions Required:

1. Reduce frontend documentation in the paper. The frontend figures can be removed from the manuscript, as this functionality is already well-illustrated in the accompanying documentation.

2. Improve standard compset selection guidance. Add links to relevant examples or reference resources such as https://docs.cesm.ucar.edu/models/cesm2/config/compsets.html to help users choose compset options more easily.

3. Fix error handling for custom component sets. When generating cases with custom component sets, the program occasionally throws the following error when generating the command for case building:

   int() argument must be a string, a bytes-like object or a real number, not 'NoneType'

For example, this error occurs when attempting to recreate the B1850MOM compset with the f09_t232 grid using the custom component set interface. The log file contains no entries related to this error. I encountered the same issue with the BMT1850 case and most other MOM-based configurations.

Notably, despite this error, the case is created successfully—the create_newcase command executes properly, and case.setup can be run manually. This suggests the error is related to error handling or status reporting rather than a fundamental failure in case generation.

4. Add documentation for non-bundled CESM versions. Include instructions in the documentation to guide users who are not using the bundled CESM version. Specifically, provide clear guidance on how to port this tool to other CESM versions that are not bundled with the software.

For example, we can add

git clone https://github.com/escomp/cesm.git my_cesm_sandbox

cd my_cesm_sandbox

git checkout [to user needed branch]

./bin/git-fleximod update

git clone https://github.com/ESMCI/visualCaseGen.git -b [user branch] visualCaseGen

Future Suggestions:

1. Add compilation command generation. Provide the ability to generate the appropriate compile command for each created case.

2. Support custom machine configuration files. Allow users to import their own machine configuration files for non-standard computing environments.

3. Add grid reuse functionality. Provide an option for users to reuse previously created custom grid files.

4. Allow run directory modification. Enable users to specify and modify the run directory location during case configuration.