[REVIEW]: SenSE: Community SAR ScattEring model

[editorialbot]

Submitting author: @McWhity (Thomas Weiß)
Repository: https://github.com/McWhity/sense
Branch with paper.md (empty if default branch): master
Version: v0.2
Editor: @mbobra
Reviewers: @scottstanie, @arthur-e
Archive: Pending

Status

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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

@scottstanie & @arthur-e, 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 @mbobra 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 @arthur-e

📝 Checklist for @scottstanie

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1109/36.917912 is OK
- 10.1109/36.406677 is OK
- 10.1109/TGRS.1985.289498 is OK
- 10.1163/156939302X01119 is OK
- 10.1109/36.134085 is OK
- 10.1109/36.134086 is OK
- 10.1109/TGRS.2003.821065 is OK
- 10.3390/rs12183037 is OK
- 10.3390/rs13122320 is OK
- 10.1029/RS013i002p00357 is OK
- 10.1109/TGRS.2002.800232 is OK
- 10.3998/0472119356 is OK
- 10.1109/JSTARS.2024.3448625 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.05 s (1805.1 files/s, 171105.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          51           1082           1131           2308
reStructuredText                18            381            240            973
TeX                              2             25              0            380
Jupyter Notebook                 4              0           1081            237
make                             1             33             11            151
Markdown                         2             45              3            141
YAML                             6             28             23            119
JSON                             1              5              0             31
TOML                             1             17             19             31
Text                             1              0              0             17
Dockerfile                       1              5              1              8
Bourne Shell                     1              1              0              2
DOS Batch                        1              0              0              2
-------------------------------------------------------------------------------
SUM:                            90           1622           2509           4400
-------------------------------------------------------------------------------

Commit count by author:

   112	Thomas Weiß
    98	Alex
    72	McWhity
     7	Ben
     6	PMarzahn
     3	loewalex
     2	BenMGeo
     1	P.Marzahn

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 720

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

[mbobra]

👋 @scottstanie @arthur-e Thank you so much for agreeing to review! You can find the article in the comment boxes above ⬆️ , the software repository linked in the first comment box on this issue. To generate your checklist, use the following command:

@editorialbot generate my checklist

I think you're good to go. Again, JOSS is an open review process and we encourage communication between the reviewers, the submitting author, and the editor. And please feel free to ask me questions, I'm always around.

Can you please respond here (or give a thumbs up) so I know you're in the right place and found all the materials?

[arthur-e]

Review checklist for @arthur-e

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/McWhity/sense?
• 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 (@McWhity) 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?

[arthur-e]

@McWhity, re: "Contribution and authorship," I am noting that this repository is a fork of another repository, which is unusual for a JOSS submission. Can you clarify:

1. What is the status of the upstream repository PMarzahn/sense? Could PMarzahn update the README to point to the new repository? (Would that be appropriate?)
2. Who is PMarzahn and should they be added to the list of authors? They have contributed a low number of commits but they are the owner of the upstream repository.
3. Should bulli92 be added to the authors list? They have contributed a large number of commits (101 to your 76 in the downstream repository).

[scottstanie]

Review checklist for @scottstanie

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/McWhity/sense?
• 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 (@McWhity) 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?

[scottstanie]

Hi @arthur-e , I think I saw the explanation for the forked repository in the Pre Review: #7354 (comment)

[arthur-e]

@scottstanie @McWhity thanks for the clarification! I think that just leaves the question of the user bulli92.

[arthur-e]

@McWhity I have verified the Jupyter Notebooks run as expected; thanks for providing those. However, I feel they can be substantially improved to help end-users. The sm_retrieval is particularly compelling but could use: 1) A better narrative throughout, i.e., more details as to each step in the process of simulating backscatter and retrieving soil moisture; 2) More code comments; 3) Brief, high-level descriptions of some alternative parameters or alternative inputs, to illustrate the range of options and to link to the documentation.

As a potential end-user but not a specialist, I'd love to bring, e.g., a Sentinel-1 backscatter image to this framework and retrieve soil moisture or vegetation optical depth. Can you include an additional notebook that shows how to work with real data? The purposes of the remaining three notebooks (i.e., other than sm_retrieval) are unclear and seem unconnected to potential applications. They, too, could use more detail and better narrative.

Similarly, I think the JOSS manuscript could use a brief statement (circa one paragraph) on the available SAR imaging platforms (air-borne or space-borne); not an exhaustive list, but perhaps mentioning some of the more prevalent options and how those data could (or could not) be used with this framework. What is required to use data from those platforms with this framework?

[McWhity]

First of all. Thank you @arthur-e and @scottstanie for your time and effort to help me improve the repository during the JOSS review process.

Regarding the authorship:

112 Thomas Weiß
98 Alex
72 McWhity
7 Ben
6 PMarzahn
3 loewalex
2 BenMGeo
1 P.Marzahn

• In retrospective it would have been better if I had directly forked the original repository pygeo/sense. However, as that was not the case and PMarzahn/Sense will no longer be updated I will ask PMarzahn to update the README to point to the repository currently under review.
• Alex, loewalex and bulli92 are actually the same person (Alexander Löw). He is listed as an author and he is again mentioned in the acknowledgements of the paper.
• Thomas Weiß and McWhity are the same person as well. I apologize for any confusion caused by the inconsistent use of names; back then, I was just beginning to use Python and Git.
• Additional commits were made by Ben (also associated with BenMGeo) and PMarzahn (also associated with P.Marzahn). These contributions were primarily focused on testing the repository's functionality shortly after the passing of bulli92.

Regarding the notebooks:

• @arthur-e: Thanks for testing
• I will incoperate your remarks in the new year