[REVIEW]: PySPOD: A Python package for Spectral Proper Orthogonal Decomposition (SPOD)

[whedon]

Submitting author: @mengaldo (Gianmarco Mengaldo)
Repository: https://github.com/mengaldo/PySPOD
Version: v0.3
Editor: @eloisabentivegna
Reviewer: @albertonogueira, @Joao-L-S-Almeida, @jdmoorman
Archive: 10.5281/zenodo.4680581

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Markdown: [![status](https://joss.theoj.org/papers/5586d8b99091bc9ee97ec74070f52711/status.svg)](https://joss.theoj.org/papers/5586d8b99091bc9ee97ec74070f52711)

Reviewers and authors:

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@albertonogueira & @Joao-L-S-Almeida & @jdmoorman, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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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 ✨

Review checklist for @albertonogueira and @Joao-L-S-Almeida

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 repository url?
• 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 (@mengaldo) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @jdmoorman

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 repository url?
• 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 (@mengaldo) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @albertonogueira, @Joao-L-S-Almeida, @jdmoorman it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2862 with the following error:

Can't find any papers to compile :-(

[eloisabentivegna]

@whedon generate pdf from branch paper/JOSS

[whedon]

Attempting PDF compilation from custom branch paper/JOSS. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #2862 with the following error:

Can't find any papers to compile :-(

[eloisabentivegna]

@whedon generate pdf from branch paper/JOSS

[whedon]

Attempting PDF compilation from custom branch paper/JOSS. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #2862 with the following error:

Can't find any papers to compile :-(

[eloisabentivegna]

@arfon, could you investigate why the paper is not found? I don't see any issues with the repository or the format. Thanks!

[mengaldo]

@eloisabentivegna I think that the branch is called papers/JOSS instead of paper/JOSS

[arfon]

@whedon generate pdf from branch papers/JOSS

[whedon]

Attempting PDF compilation from custom branch papers/JOSS. Reticulating splines etc...

[whedon]

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

[eloisabentivegna]

@eloisabentivegna I think that the branch is called papers/JOSS instead of paper/JOSS

🤦🏻‍♀️

Thanks!

[eloisabentivegna]

@whedon check references from branch papers/JOSS

[whedon]

Attempting to check references... from custom branch papers/JOSS

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1017/jfm.2018.283 may be a valid DOI for title: Spectral proper orthogonal decomposition and its relationship to dynamic mode decomposition and resolvent analysis
- 10.1175/mwr-d-18-0337.1 may be a valid DOI for title: Spectral empirical orthogonal function analysis of weather and climate data
- 10.1016/j.cpc.2018.11.009 may be a valid DOI for title: An efficient streaming algorithm for spectral proper orthogonal decomposition

INVALID DOIs

- None

[whedon]

👋 @albertonogueira, please update us on how your review is going.

[whedon]

👋 @jdmoorman, please update us on how your review is going.

[jdmoorman]

I have started my review.

Regarding scholarly effort, it is not clear whether the submission meets the scope eligibility described in the JOSS guidelines. The majority of the content was committed all at once initially with about 3 additional weeks of development since the initial commit, judging from the commit activity. As such, it is not clear whether the work represents at least three months of work for an individual. From a LOC perspective, the submission has around 3.2k LOC total with 0.8k in tests, 0.6k in tutorials, and 1.6k in the package. There is a large amount of code duplication between tests and tutorials, between the low RAM and low storage variants of the SPOD algorithm, and between the various post-processing/plotting functions. A refactor would cut the LOC by more than half.

[kyleniemeyer]

Hi @mengaldo, I am the AEIC on duty this week looking to help get this submission past the finish line.

There are a few remaining issues with your article that need addressing:

• In the author name list, the formatting we use is "Given Middle-initial Surname"; it looks like yours are reversed. Could you review and correct this? Normally we also use written-out names, with only an initial for middle name (if you have one).
• There are a handful of citations to software that do not use the appropriate bibtex fields; could you move the author names to the author field for the various SPOD code citations?
• It also looks like some citations throughout the paper do not use the appropriate syntax, in the third and fourth paragraphs. The options include:
  • @author:2001 -> "Author et al. (2001)"
  • [@author:2001] -> "(Author et al., 2001)"
  • [@author1:2001; @author2:2001] -> "(Author1 et al., 2001; Author2 et al., 2002)"

For example, the "(Lumley, 2007), (Towne et al. 2018)" should instead appear as "(Lumley, 2007; Towne et al., 2018)" with the appropriate command of [@lumley1970;@towne2017]. There are a few other cases to fix as well.

Could you make these edits, and let us know when you have?

[kyleniemeyer]

@whedon set 10.5281/zenodo.4680581 as archive

[whedon]

OK. 10.5281/zenodo.4680581 is the archive.

[mengaldo]

@whedon generate pdf from branch main

[whedon]

Attempting PDF compilation from custom branch main. Reticulating splines etc...

[whedon]

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

[mengaldo]

@kyleniemeyer Thank you for the help! These should be all fixed. The only issue seems to be related to the url of one of the references. Also, please use the main branch to compile the paper now, as I moved everything there, and papers/JOSS will be removed. Thank you for handling the publication process!

[eloisabentivegna]

Hi @mengaldo, I am the AEIC on duty this week looking to help get this submission past the finish line.

Thanks, @kyleniemeyer!

[kyleniemeyer]

Hi @mengaldo, I still saw some minor issues (or maybe I'm just very particular), which I fixed in MathEXLab/PySPOD#14 - can you merge this?

[mengaldo]

@kyleniemeyer Thank you, just did.

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1017/jfm.2018.283 is OK
- 10.1175/mwr-d-18-0337.1 is OK
- 10.1016/j.cpc.2018.11.009 is OK
- 10.2514/1.J058809 is OK
- 10.1038/s41561-017-0033-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2240

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2240, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.02862 joss-papers#2241
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02862
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...

[kyleniemeyer]

Congrats @mengaldo on your article's publication in JOSS!

Many thanks to @albertonogueira, @Joao-L-S-Almeida, and @jdmoorman for reviewing this, and @eloisabentivegna for editing.

[whedon]

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

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