[REVIEW]: amisrsynthdata: A Python package for generating synthetic data for the Advanced Modular Incoherent Scatter Radars

[editorialbot]

Submitting author: @ljlamarche (Leslie Lamarche)
Repository: https://github.com/amisr/amisrsynthdata
Branch with paper.md (empty if default branch): joss
Version: v1.1.8
Editor: @mbobra
Reviewers: @rweigel, @peijin94
Archive: 10.5281/zenodo.14174414

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/bff6c9a069307dd62bebd57e476352b8/status.svg)](https://joss.theoj.org/papers/bff6c9a069307dd62bebd57e476352b8)

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

@rweigel & @peijin94, 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 @peijin94

📝 Checklist for @rweigel

[editorialbot]

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:

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.jastp.2009.01.009 is OK
- 10.1029/2007RS003805 is OK
- 10.1029/2019JA027112 is OK
- 10.1002/2014RS005519 is OK
- 10.17226/13060 is OK
- 10.1029/2004RS003042 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.6575970 is OK
- 10.21105/joss.00580 is OK
- 10.1109/MCSE.2007.55 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Cartopy: a cartographic python library with a Matp...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1283.4 files/s, 144189.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            444            759           1468
reStructuredText                11            216            127            364
YAML                             8             89             72            310
TeX                              1             13              0            138
TOML                             1              7              0             49
Markdown                         1             15              0             31
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            37            796            966           2395
-------------------------------------------------------------------------------

Commit count by author:

   198	Leslie Lamarche

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 896

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[mbobra]

@rweigel @peijin94 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?

[peijin94]

Review checklist for @peijin94

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/amisr/amisrsynthdata?
• 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 (@ljlamarche) 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?

[peijin94]

amisr/amisrsynthdata#13
amisr/amisrsynthdata#14
amisr/amisrsynthdata#15
amisr/amisrsynthdata#16

[ljlamarche]

@peijin94 @mbobra I have addressed all four comments but left them open for more feedback if you'd like anything else modified! Thank you for the useful suggestions!

[mbobra]

@peijin94 I see the performance box unchecked on the reviewer checklist -- do you have any specific issue related to that performance?

@rweigel Do you need any help with the review? If so, please let me know!

[peijin94]

Previously no benchmark and performance is provided, now it is completed, I have no more questions

[rweigel]

Review checklist for @rweigel

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/amisr/amisrsynthdata?
• 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 (@ljlamarche) 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?
• [n/a] 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?

[mbobra]

@rweigel Just checking in again. Please let me know if you need help with the review or if you'd like the submitting author to address any particular issues.

[rweigel]

@mbobra - I have been active at amisr/amisrsynthdata#17 over the past month.

It is close to satisfying the checklist requirements. I expect to look at this tomorrow.

[mbobra]

Thank you @rweigel!

[rweigel]

I have completed my review and concluded the manuscript is acceptable for publication.

The manuscript is well-written and clear, and the software provides a significant algorithm that is justified in the manuscript. I expect this software to be useful for validating and learning about ASMIR measurements.

[mbobra]

Thank you both so very much for your thorough reviews, @rweigel and @peijin94! I know you put a lot of effort into this. Your volunteer time keeps JOSS running and we sincerely appreciate your time and effort.

[mbobra]

@editorialbot generate pdf

[editorialbot]

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

[mbobra]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.jastp.2009.01.009 is OK
- 10.1029/2007RS003805 is OK
- 10.1029/2019JA027112 is OK
- 10.1002/2014RS005519 is OK
- 10.1002/2015JA021116 is OK
- 10.17226/13060 is OK
- 10.1029/2004RS003042 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.6575970 is OK
- 10.21105/joss.00580 is OK
- 10.1109/MCSE.2007.55 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Cartopy: a cartographic python library with a Matp...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[mbobra]

Congratulations, @ljlamarche -- we're almost ready to publish the paper! Could you please make sure that the title on the Zenodo deposit matches the title on the JOSS paper? Then I can move forward with accepting the paper.

[ljlamarche]

Thank you @mbobra! I'm a bit confused. I believe that zenodo deposit is the automatic archiving of the source code. Would you like me to make a separate zenodo repo for the paper itself?

[mbobra]

@ljlamarche Ah sorry, not at all. Right now, the title of your Zenodo deposit is amisr/amisrsynthdata: v1.1.8. I'm requesting you change the title, by manually editing this page, to amisrsynthdata: A Python package for generating synthetic data for the Advanced Modular Incoherent Scatter Radars. This way the title of the JOSS paper and Zenodo deposit match exactly, and people can easily tell which version of the software matches up with the description of the package in the JOSS paper.

[ljlamarche]

Ah, thank you for explaining! Is this suitable?

[mbobra]

@editorialbot set 10.5281/zenodo.14174414 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.14174414

[mbobra]

@editorialbot set v1.1.8 as version

[editorialbot]

Done! version is now v1.1.8

[mbobra]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.jastp.2009.01.009 is OK
- 10.1029/2007RS003805 is OK
- 10.1029/2019JA027112 is OK
- 10.1002/2014RS005519 is OK
- 10.1002/2015JA021116 is OK
- 10.17226/13060 is OK
- 10.1029/2004RS003042 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.6575970 is OK
- 10.21105/joss.00580 is OK
- 10.1109/MCSE.2007.55 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Cartopy: a cartographic python library with a Matp...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6178, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[warrickball]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1268.7 files/s, 156533.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            448            769           1491
reStructuredText                11            224            126            376
YAML                             8             89             72            310
TeX                              1             16              0            148
Jupyter Notebook                 1              0            516             66
TOML                             1              7              0             49
Markdown                         1             17              0             33
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            39            813           1491           2508
-------------------------------------------------------------------------------

Commit count by author:

   211	Leslie Lamarche

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 977

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[ljlamarche]

@mbobra , the proof looks good to me! Do I need to enter the accept command or you?

[warrickball]

Hi @ljlamarche — I'm the assistant editor in chief for this subject area and am working on some editorial changes. One thing that needs addressing is that the software licence in the Zenodo archive (currently CC-BY-4.0) should be changed to match the software repo (GPLv3).

I also noticed you've cited a particular version of h5py via this Zenodo archive. If you wish, you could use the DOI for all versions of that repository, which will always resolve to the latest version on Zenodo. I won't change this but you may want to.

You should see a PR with my editorial tweaks in the next few minutes.

[warrickball]

I've opened a PR with some tweaks. With those implemented and the archive licence updated, I'll do another test run of our publication pipeline.

[warrickball]

As an aside, I noticed that your CI reports failures on one set of tests. To me, this simply looks like small variation from differences in floating point numbers. If you call numpy.testing.assert_allclose with a small absolute tolerance (atol, 1e-12 should do) then I think your tests will pass in Python 3.7–3.11 (assuming that's a reasonable choice given the specific problem being tested).