[REVIEW]: pyradiosky: A Python package for Radio Sky Models

[editorialbot]

Submitting author: bhazelton (Bryna J. Hazelton) Repository: https://github.com/RadioAstronomySoftwareGroup/pyradiosky Branch with paper.md (empty if default branch): Version: 1.0 Editor: !--editor-->@xuanxu<!--end-editor-- Reviewers: @pritchardn, @0xCoto Archive: 10.5281/zenodo.11187469

Status

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Markdown: [![status](https://joss.theoj.org/papers/a0195a69e00cee9d3cca13937c793af7/status.svg)](https://joss.theoj.org/papers/a0195a69e00cee9d3cca13937c793af7)

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

@pritchardn & @0xCoto, 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 @xuanxu 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 @0xCoto

📝 Checklist for @pritchardn

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.21105/joss.00140 is OK
- 10.21105/joss.01234 is OK
- 10.1051/0004-6361/201322068 is OK

MISSING DOIs

- No DOI given, and none found for title: lunarsky: An astropy extension to describe observa...

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (575.4 files/s, 205713.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16           1607           1663           7824
XML                              3              0              6           3703
Markdown                        12            153              0            712
YAML                            11             60             22            484
TeX                              2             36              0            301
reStructuredText                 3            219            904            114
DOS Batch                        1              8              1             26
TOML                             1              3              0              9
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            50           2090           2603          13182
-------------------------------------------------------------------------------

Commit count by author:

   284  Bryna Hazelton
    62  Adam Lanman
    41  Matthew Kolopanis
    28  pre-commit-ci[bot]
    25  Ruby Byrne
    21  Steven Murray
    10  nicelmh
     3  aelanman
     2  Dara Storer
     1  Daniya
     1  James Aguirre
     1  Jonathan Pober
     1  daniel.d.quinter
     1  jburba

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 407

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 2-Clause "Simplified" License (Valid open source OSI approved license)

[editorialbot]

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

[0xCoto]

Review checklist for @0xCoto

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/RadioAstronomySoftwareGroup/pyradiosky?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (bhazelton) 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
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] 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).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[pritchardn]

Review checklist for @pritchardn

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/RadioAstronomySoftwareGroup/pyradiosky?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (bhazelton) 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
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] 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).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[pritchardn]

While the license file is valid, the code-files refer to the BSD-3 clause variant - this is a pretty easy to fix, but probably worth getting consistent. I've made an issue to address this.

[bhazelton]

While the license file is valid, the code-files refer to the BSD-3 clause variant - this is a pretty easy to fix, but probably worth getting consistent. I've made an issue to address this.

Thanks for pointing this out! We've fixed it now.

[xuanxu]

@pritchardn, @0xCoto :wave: can you update us on the progress of your review?

[0xCoto]

pytest runs with the following:

tests/test_skymodel.py: 618 warnings
  `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.

@bhazelton -- Minor thing if you wish to resolve; otherwise the tests runs fine.

[0xCoto]

Everything looks OK to me. The only thing I would request is a brief mention of how the software compares to other commonly-used packages, so that readers understand whether their needs are covered by pyradiosky vs a different module.

[bhazelton]

pytest runs with the following:

tests/test_skymodel.py: 618 warnings
  `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.

@bhazelton -- Minor thing if you wish to resolve; otherwise the tests runs fine.

@0xCoto I can’t seem to replicate these warnings. I made a fresh environment with all the dependencies and I don’t get them. I can’t find anywhere in pyradiosky or pyuvdata (a dependency that I help maintain) that calls np.prod, so I think these warnings must be coming from another dependency and I must have a different version of that dependency than you do.

[0xCoto]

I see. Feel free to dismiss this then; it is likely related to the way my own environment is configured.

[bhazelton]

Everything looks OK to me. The only thing I would request is a brief mention of how the software compares to other commonly-used packages, so that readers understand whether their needs are covered by pyradiosky vs a different module.

@0xCoto We have updated our paper with a paragraph addressing this.

[0xCoto]

@editorialbot generate pdf

[editorialbot]

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

[0xCoto]

Thank you for introducing the paragraph.

@xuanxu — From my side, all of my comments have been addressed.

[xuanxu]

@pritchardn I see there are some unchecked items in your list, is there any pending issue?

[xuanxu]

@0xCoto thanks, can you confirm you recommend the submission for publication?

[0xCoto]

@xuanxu I confirm my recommendation.

[pritchardn]

@xuanxu I confirm my recommendation too.

[xuanxu]

OK great, thanks! Let's move forward

[xuanxu]

@editorialbot check references

[xuanxu]

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.21105/joss.00140 is OK
- 10.21105/joss.01234 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1086/427976 is OK

MISSING DOIs

- No DOI given, and none found for title: lunarsky: An astropy extension to describe observa...
- No DOI given, and none found for title: TOPCAT & STIL: Starlink Table/VOTable Processing S...
- No DOI given, and none found for title: astropy healpix: BSD-licensed HEALPix for Astropy

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:

[xuanxu]

@bhazelton looks like we're close to being done here. Please give your own paper a final read to check for any potential typos etc. A small comment on one of your references: You cite astropy using their first paper from 2013, but the Astropy's guidelines recommend citing other papers or at least the more recent one, please consider updating the paper with that suggestion.

[xuanxu]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• [x] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [x] Recommend acceptance with @editorialbot recommend-accept

[xuanxu]

@bhazelton Please go through the "Author tasks" bullet list above (you can make a checklist for yourself if that helps) and let me know when you're finished with the actions.

[xuanxu]

@editorialbot generate pdf

[editorialbot]

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

[bhazelton]

@xuanxu I think we have now done all our tasks. Thanks!

[xuanxu]

@bhazelton can you post here the version number and the zenodo DOI?

[bhazelton]

Yes, sorry. The version is 1.0 (https://github.com/RadioAstronomySoftwareGroup/pyradiosky/releases/tag/v1.0.0) and the zenodo DOI is 10.5281/zenodo.11187469 (https://doi.org/10.5281/zenodo.11187469)

[xuanxu]

@editorialbot set 1.0 as version

[editorialbot]

Done! version is now 1.0

[xuanxu]

@editorialbot set 10.5281/zenodo.11187469 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11187469

[xuanxu]

@editorialbot generate pdf

[xuanxu]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.00140 is OK
- 10.21105/joss.01234 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1086/427976 is OK

MISSING DOIs

- No DOI given, and none found for title: lunarsky: An astropy extension to describe observa...
- No DOI given, and none found for title: TOPCAT & STIL: Starlink Table/VOTable Processing S...
- No DOI given, and none found for title: astropy healpix: BSD-licensed HEALPix for Astropy

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:

[xuanxu]

Looking good!

[xuanxu]

@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

- 10.21105/joss.00140 is OK
- 10.21105/joss.01234 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1086/427976 is OK

MISSING DOIs

- No DOI given, and none found for title: lunarsky: An astropy extension to describe observa...
- No DOI given, and none found for title: TOPCAT & STIL: Starlink Table/VOTable Processing S...
- No DOI given, and none found for title: astropy healpix: BSD-licensed HEALPix for Astropy

INVALID DOIs

- None

[editorialbot]

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5349, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[dfm]

I have opened a small PR with some edits to the manuscript. Once you've incorporated those, I'll run the final publication process. Thanks!