[REVIEW]: SLEPLET: Slepian scale-discretised wavelets in Python about joss-reviews HOT 91 CLOSED

@vissarion:
I have completed my review and after @paddyroddy has added the missing years to the references in the paper, I recommend the paper for acceptance.

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I currently have issues installing the required packages pyssht and pys2let on my machine. I have opened a bug report in their projects.

After I am able to resolve these issues, I will continue my review of the submitted sleplet package.

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Thanks for your hard work @danielskatz, @vissarion, @Saran-nns and @klb2!

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I've added argument/function level description of the API https://astro-informatics.github.io/sleplet/index.html

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Have addressed the community guidelines

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Years added!

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@paddyroddy I started my review and created an issue in the repo with few suggestions and requests

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Years added!

Thank you @paddyroddy

That completes my review @vissarion

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@vissarion @paddyroddy Couple of steps to go. Will be happy to flag accept then

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@paddyroddy thank you, great work @vissarion my checklist is complete and I am happy to recommend accept

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Many thanks to both reviewers @Saran-nns and @klb2 !

@paddyroddy could you please create a tagged release and an archive with the code (e.g. in zenodo) and share the link and the release version here? Please use the same title and authors while creating the zenodo archive.

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@vissarion - please set the archive to the DOI - note that link above from editorialbot isn't one that works

I'll proofread the paper later and continue the process

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I've made the changes @danielskatz

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Congratulations to @paddyroddy (Patrick James Roddy) on your work's publication!!

And thanks to @Saran-nns and @klb2 for reviewing, and to @vissarion for editing!
We couldn't do this without your voluntary efforts

(note that the DOI is not yet resolving, so I'll leave this open until it does)

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The DOI now resolves!

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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:

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (918.4 files/s, 65529.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         140           1613           1363           7221
Markdown                         3            134              0            571
TOML                             8             10              0            265
YAML                             5             21              0            158
TeX                              1              0              0            120
Unity-Prefab                     4              0              0             12
-------------------------------------------------------------------------------
SUM:                           161           1778           1363           8347
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 968

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

OK DOIs

- 10.1002/j.1538-7305.1961.tb03977.x is OK
- 10.1002/j.1538-7305.1962.tb03279.x is OK
- 10.1051/0004-6361/201220729 is OK
- 10.1145/3134472.3134497 is OK
- 10.1109/TSP.2011.2166394 is OK
- 10.5281/zenodo.7268074 is OK
- 10.1109/LSP.2021.3050961 is OK
- 10.1109/TSP.2022.3233309 is OK
- 10.5281/zenodo.4085210 is OK
- 10.1002/j.1538-7305.1961.tb03976.x is OK
- 10.1111/j.1365-2966.2008.13448.x is OK
- 10.1029/2018GC007529 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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Review checklist for @klb2

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/astro-informatics/sleplet?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@paddyroddy) 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?

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Review checklist for @Saran-nns

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/astro-informatics/sleplet?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@paddyroddy) 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?

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The developers of the pyssht and pys2let packages fixed the issue and I was now able to install the sleplet package.

I will continue my review this week.

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From the JOSS guidelines (https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain):

As this short list shows, JOSS papers are only expected to contain a limited set of metadata (see example below), a Statement of need, Summary, Acknowledgements, and References sections. You can look at an example accepted paper. Given this format, a “full length” paper is not permitted, and software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation.

Based on this, I think that the "Demonstration" section should be completely removed from the paper and the "Conclusions" section should be merged into the "Summary" and "Statement of Needs" sections.

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From the JOSS guidelines (https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain):

As this short list shows, JOSS papers are only expected to contain a limited set of metadata (see example below), a Statement of need, Summary, Acknowledgements, and References sections. You can look at an example accepted paper. Given this format, a “full length” paper is not permitted, and software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation.

Based on this, I think that the "Demonstration" section should be completely removed from the paper and the "Conclusions" section should be merged into the "Summary" and "Statement of Needs" sections.

Have done

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@editorialbot generate pdf

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

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Is there any documentation besides the examples in the README? I could not find an API documentation that documents all of the individual functions of the package.

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In the paper, it is stated that

To the author’s knowledge, there is no public software which allows one to compute Slepian wavelets (or similar approach) on the sphere or general manifolds/meshes.
SHTools (Wieczorek & Meschede, 2018) and slepian_alpha (Simons et al., n.d.) are examples of codes which allow one to compute Slepian functions on the sphere. In conjunction with SSHT (McEwen & Wiaux, 2011), S2LET (Leistedt, B. et al., 2013) may be used to develop scale-discretised wavelets on the whole sphere.

and later

Whilst Slepian wavelets may be trivially computed from a set of Slepian functions, the computation of the spherical Slepian functions themselves are computationally complex

Based on this, it is unclear for me what the advantages of the sleplet package are over the existing ones like SHTools and slepian_alpha. It is said in the paper that these two packages allow computing the Slepian functions and that it is trivial to compute the Slepian wavelets from the Slepian functions.

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Good point @klb2. @paddyroddy could you please clarify?

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On closer inspection ShTools only computes the Slepian functions of a polar cap https://shtools.github.io/SHTOOLS/pysphericalcapcoef.html which is much easier to compute. Whereas SLEPLET handles any arbitrary mask. Further, it works for mesh data rather than just the sphere.

slepian_alpha is a huge set of MATLAB code with no documentation or anything. I believe it's largely used to create the various plots on this paper, https://arxiv.org/pdf/math/0408424.pdf. Again, it is defined only for the sphere.

In an ideal world, SLEPLET would have relied on another library to generate the Slepian functions and the build the wavelets from them. However, this proved non-trivial to use and, as such, it was necessary to compute them myself. My wording should have been clearer.

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Is there any documentation besides the examples in the README? I could not find an API documentation that documents all of the individual functions of the package.

I hadn't realised full API documentation was required. I can look into this.

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Is there any documentation besides the examples in the README? I could not find an API documentation that documents all of the individual functions of the package.

I hadn't realised full API documentation was required. I can look into this.

I've made some: https://astro-informatics.github.io/sleplet/

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On closer inspection ShTools only computes the Slepian functions of a polar cap https://shtools.github.io/SHTOOLS/pysphericalcapcoef.html which is much easier to compute. Whereas SLEPLET handles any arbitrary mask. Further, it works for mesh data rather than just the sphere.

slepian_alpha is a huge set of MATLAB code with no documentation or anything. I believe it's largely used to create the various plots on this paper, https://arxiv.org/pdf/math/0408424.pdf. Again, it is defined only for the sphere.

In an ideal world, SLEPLET would have relied on another library to generate the Slepian functions and the build the wavelets from them. However, this proved non-trivial to use and, as such, it was necessary to compute them myself. My wording should have been clearer.

Thank you for clarifying. I guess it would be good, if some of these details could also be added to the paper in order to make the differences to the sleplet package clear.

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With the latest version of the software, I was able to run all provided examples without any errors. The unit tests also all pass on my machine.
Thank you for adding pooch for the data management/downloads @paddyroddy.

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From my side as a reviewer, only the following points are open:

• Community guidelines (CONTRIBUTING.md and issue templates)
• Argument/function documentation. I appreciate the API documentation, however, it does not contain any explanations of the individual functions and their arguments.

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On closer inspection ShTools only computes the Slepian functions of a polar cap https://shtools.github.io/SHTOOLS/pysphericalcapcoef.html which is much easier to compute. Whereas SLEPLET handles any arbitrary mask. Further, it works for mesh data rather than just the sphere.
slepian_alpha is a huge set of MATLAB code with no documentation or anything. I believe it's largely used to create the various plots on this paper, https://arxiv.org/pdf/math/0408424.pdf. Again, it is defined only for the sphere.
In an ideal world, SLEPLET would have relied on another library to generate the Slepian functions and the build the wavelets from them. However, this proved non-trivial to use and, as such, it was necessary to compute them myself. My wording should have been clearer.

Thank you for clarifying. I guess it would be good, if some of these details could also be added to the paper in order to make the differences to the sleplet package clear.

I've added some comments to explain this.

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@editorialbot generate pdf

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

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On closer inspection ShTools only computes the Slepian functions of a polar cap https://shtools.github.io/SHTOOLS/pysphericalcapcoef.html which is much easier to compute. Whereas SLEPLET handles any arbitrary mask. Further, it works for mesh data rather than just the sphere.
slepian_alpha is a huge set of MATLAB code with no documentation or anything. I believe it's largely used to create the various plots on this paper, https://arxiv.org/pdf/math/0408424.pdf. Again, it is defined only for the sphere.
In an ideal world, SLEPLET would have relied on another library to generate the Slepian functions and the build the wavelets from them. However, this proved non-trivial to use and, as such, it was necessary to compute them myself. My wording should have been clearer.

Thank you for clarifying. I guess it would be good, if some of these details could also be added to the paper in order to make the differences to the sleplet package clear.

I've added some comments to explain this.

Thank you @paddyroddy for adding this part to the paper. It all looks good for me now.
The only minor comment: The dates/years for two references are missing in the paper, for the SLEPLET package on Zenodo (2023) and for the slepian_alpha package on Zenodo (2020).

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@editorialbot generate preprint

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📄 Preprint file created: Find it here in the Artifacts list 📄

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@editorialbot generate preprint

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Thank you, @klb2 and @Saran-nns for your guidance.

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📄 Preprint file created: Find it here in the Artifacts list 📄

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Sorry just have just capitalised the title

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@editorialbot generate preprint

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@vissarion here is the archive link https://zenodo.org/record/7802428, current version v1.3.4

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Thanks! Please use the full title in the archive i.e. "SLEPLET: Slepian scale-discretised wavelets in Python" which is the same as the paper.

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@editorialbot generate pdf

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@editorialbot check references

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Couldn't check the bibtex because branch name is incorrect: joss-paper

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⚠️ An error happened when generating the pdf.

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@editorialbot generate pdf

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⚠️ An error happened when generating the pdf.

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@editorialbot set main as branch

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Done! branch is now main

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@editorialbot generate pdf

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

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@editorialbot check references

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

OK DOIs

- 10.1109/TSP.2016.2646668 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1002/j.1538-7305.1961.tb03977.x is OK
- 10.1002/j.1538-7305.1962.tb03279.x is OK
- 10.1051/0004-6361/201220729 is OK
- 10.1145/3134472.3134497 is OK
- 10.1109/TSP.2011.2166394 is OK
- 10.1109/LSP.2021.3050961 is OK
- 10.1109/TSP.2022.3233309 is OK
- 10.5281/zenodo.7268074 is OK
- 10.1137/S0036144504445765 is OK
- 10.5281/zenodo.4085210 is OK
- 10.1002/j.1538-7305.1961.tb03976.x is OK
- 10.1111/j.1365-2966.2008.13448.x is OK
- 10.1029/2018GC007529 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Thanks! Please use the full title in the archive i.e. "SLEPLET: Slepian scale-discretised wavelets in Python" which is the same as the paper.

Sorry do you mean in the paper.bib in the archive or do you mean the archive name should be that?

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Thanks! Please use the full title in the archive i.e. "SLEPLET: Slepian scale-discretised wavelets in Python" which is the same as the paper.

Sorry do you mean in the paper.bib in the archive or do you mean the archive name should be that?

I mean the zenodo archive name, thanks.

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Apologies, I was on holiday and hadn't understood what you meant previously. I've made a release v1.3.5 with the name in the archive https://zenodo.org/record/7825341.

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@paddyroddy I think @vissarion asks for the zenodo archive title to be same as the title of the paper SLEPLET: Slepian Scale-Discretised Wavelets in Python. But the archive title is still SLEPLET.

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Ah, thanks @Saran-nns, I get it now. All updated!

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Realised I forgot to update the Zenodo citation in the paper. Have fixed in v1.3.6 https://zenodo.org/record/7835860.

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@editorialbot set https://zenodo.org/record/7835860 as archive

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Done! Archive is now [ https://zenodo.org/record/7835860](https://doi.org/ https://zenodo.org/record/7835860)

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@editorialbot set v1.3.6 as version

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Done! version is now v1.3.6

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1109/TSP.2016.2646668 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1002/j.1538-7305.1961.tb03977.x is OK
- 10.1002/j.1538-7305.1962.tb03279.x is OK
- 10.1051/0004-6361/201220729 is OK
- 10.1145/3134472.3134497 is OK
- 10.1109/TSP.2011.2166394 is OK
- 10.1109/LSP.2021.3050961 is OK
- 10.1109/TSP.2022.3233309 is OK
- 10.5281/zenodo.7268074 is OK
- 10.1137/S0036144504445765 is OK
- 10.5281/zenodo.4085210 is OK
- 10.1002/j.1538-7305.1961.tb03976.x is OK
- 10.1111/j.1365-2966.2008.13448.x is OK
- 10.1029/2018GC007529 is OK

MISSING DOIs

- Errored finding suggestions for "Slepian Wavelets for the Analysis of Incomplete Da...", please try later

INVALID DOIs

- None

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👋 @openjournals/csism-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#4151, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@editorialbot set 10.5281/zenodo.7835860 as archive

@vissarion - nvm, I'll just do this while I'm proofreading...

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Done! Archive is now 10.5281/zenodo.7835860

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@paddyroddy - I'm suggesting some changes in astro-informatics/sleplet#142 Please merge this, or let me know what you disagree with.

In addition, I have a suggestion: In the paper, lines 29-31 seem redundant with the previous part of that section. Can these lines be removed (29) and/or merged (30-31)?

Once you've decided on and made changes, please let me know, and we can continue the acceptance and publication process.

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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👋 @openjournals/csism-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#4155, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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

OK DOIs

- 10.1109/TSP.2016.2646668 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1002/j.1538-7305.1961.tb03977.x is OK
- 10.1002/j.1538-7305.1962.tb03279.x is OK
- 10.1051/0004-6361/201220729 is OK
- 10.1145/3134472.3134497 is OK
- 10.1109/TSP.2011.2166394 is OK
- 10.1109/LSP.2021.3050961 is OK
- 10.1109/TSP.2022.3233309 is OK
- 10.5281/zenodo.7268074 is OK
- 10.1137/S0036144504445765 is OK
- 10.5281/zenodo.4085210 is OK
- 10.1002/j.1538-7305.1961.tb03976.x is OK
- 10.1111/j.1365-2966.2008.13448.x is OK
- 10.1029/2018GC007529 is OK

MISSING DOIs

- Errored finding suggestions for "Slepian Scale-Discretised Wavelets on Manifolds", please try later

INVALID DOIs

- None

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@editorialbot accept

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

cff-version: "1.2.0"
authors:
- family-names: Roddy
  given-names: Patrick J.
  orcid: "https://orcid.org/0000-0002-6271-1700"
doi: 10.5281/zenodo.7835860
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Roddy
    given-names: Patrick J.
    orcid: "https://orcid.org/0000-0002-6271-1700"
  date-published: 2023-04-20
  doi: 10.21105/joss.05221
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5221
  title: "SLEPLET: Slepian Scale-Discretised Wavelets in Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05221"
  volume: 8
title: "SLEPLET: Slepian Scale-Discretised Wavelets in Python"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#4156
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05221
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

from joss-reviews.

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05221/status.svg)](https://doi.org/10.21105/joss.05221)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05221">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05221/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05221/status.svg
   :target: https://doi.org/10.21105/joss.05221

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

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@editorialbot generate preprint

from joss-reviews.

📄 Preprint file created: Find it here in the Artifacts list 📄

from joss-reviews.