[REVIEW]: SPICY: A python toolbox for meshless assimilation from image velocimetry using radial basis functions

[editorialbot]

Submitting author: @mendezVKI (Miguel Alfonso Mendez)
Repository: https://github.com/mendezVKI/SPICY_VKI
Branch with paper.md (empty if default branch):
Version: 1.0.5
Editor: @philipcardiff
Reviewers: @nolankucd, @MatthewFlamm, @ctdegroot
Archive: 10.5281/zenodo.10473329

Status

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Markdown: [![status](https://joss.theoj.org/papers/ca453152e765cab3bab8a8b57f6aa400/status.svg)](https://joss.theoj.org/papers/ca453152e765cab3bab8a8b57f6aa400)

Reviewers and authors:

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Reviewer instructions & questions

@nolankucd & @MatthewFlamm & @ctdegroot, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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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 ✨

Checklists

📝 Checklist for @nolankucd

📝 Checklist for @MatthewFlamm

📝 Checklist for @ctdegroot

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.42 s (55.6 files/s, 96208.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      24          10477          24993          76426
HTML                            15            911             38           6885
Python                           5            811           2072           3048
SVG                              1              0              0           2671
CSS                              9            341            300           2503
Jupyter Notebook                 8              0           3411           1127
YAML                             2             26             43            205
reStructuredText                10             59             34             98
TeX                              1              8              0             81
Markdown                         2             35              0             59
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            79          12680          30899          93138
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 748

[editorialbot]

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

OK DOIs

- 10.1088/1361-6501/ac70a9 is OK
- 10.1017/s0962492914000130 is OK
- 10.1007/s00348-016-2133-9 is OK
- 10.1007/s00348-021-03172-0 is OK

MISSING DOIs

- 10.18409/ispiv.v1i1.198 may be a valid DOI for title: Main results of the first Data Assimilation Challenge
- 10.55037/lxlaser.20th.115 may be a valid DOI for title: A RANS approach to the Meshless Computation of Pressure Fields From Image Velocimetry

INVALID DOIs

- https://doi.org/10.1016/j.taml.2020.01.039 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[philipcardiff]

Hi @mendezVKI, please address the missing and invalid DOIs above; thanks!

[philipcardiff]

Also, please look at the pull request I created (philipcardiff/SPICY_VKI#1, fix: mendezVKI/SPICY_VKI#7), which aims to fix an issue with the first reference.

[MatthewFlamm]

Review checklist for @MatthewFlamm

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/mendezVKI/SPICY_VKI?
• 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 (@mendezVKI) 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?

[philipcardiff]

Hi @nolankucd and @ctdegroot, a reminder that you can generate your reviewer checklist by running this command in a separate comment:

@editorialbot generate my checklist

[MatthewFlamm]

Installation requires:
mendezVKI/SPICY_VKI#4

The dependencies of the package are also a little messy, and this results in unneeded packages being installed, not as critical:
mendezVKI/SPICY_VKI#3

Edit: I now think both are important as some dependencies might be required to run tutorials for verifying functionality.

[MatthewFlamm]

I could not find any community guidance in the repo/documentation. Tracked in mendezVKI/SPICY_VKI#8

[MatthewFlamm]

I have gone through the checklist and consider my review complete, pending needed changes to the paper and repository. High level is that I believe this submission solves a useful scientific need. The tutorials are of generally good quality, although I was not able to run the 3D case on my machine due to memory constraint. In the future, I would suggest to the authors to think about how the package could become easier to use for users as the workflow seems to have many common elements in each case. Today, the code does provide useful tools for researchers in this area. However, the repository is currently messily organized (see mendezVKI/SPICY_VKI#2) and missing several key items for acceptance today. See below on specifics.

Other than what I have already commented above, these are my comments relating to the last items:
Major comments:

• First reference is not handled correctly. There is a PR that hopefully will address this, already linked above.
• Statement of need: is lacking a clear description of who the software is intended to be used by.
• State of the field: there is some discussion of recent applications, but PIV techniques have been used for many years. The solution that this paper provides is at least adjacent to PIV techniques. All the references are to scholarly publications, but I think the intent is to also discuss available software packages for these techniques. There are several PIV software packages that are openly available, and I'm not sure if there are similar packages available more similar to SPCIY. A discussion of the larger landscape including the available software packages would strengthen this paper greatly.

Minor comments:

• Automated tests: I have checked this box as there are tutorials which definitely increase the confidence in the functionality and accuracy of the code. Within there are some hints to the user on how to verify the functionality, although some are qualitative. A more dedicated test procedure would increase confidence in the package especially against regressions.

[mendezVKI]

Thank you so much for your feedback and wonderful work, Matthew.

I will address all points early next week.

All the best,

[philipcardiff]

I have gone through the checklist and consider my review complete, pending needed changes to the paper and repository. ...

Thanks for your comprehensive review, @MatthewFlamm!

[mendezVKI]

Dears, thank you so much for your detailed review.

I have addressed all points in the issues. Concerning the ones open in this check list:

1. References: I modified a bit them, removing the one that was creating problem and added others concerning open-software for PIV/PTV. There are still a couple of references that do not have a DOI; this is because these are conf papers. I considered for a moment removing these, but I feel that there is very useful information there so I prefer to keep them.

2. A statement of need: I add a sentence mentioning open-source software and about positioning SPICY in the larger landscape. Although some authors (e.g. the cited Rao 2020) shared a github ref with their implementation of the assimilation using PINNs, we have not found any software package similar to SPICY. We state this clearly. Concerning the lack of "a clear description of who the software is intended to be used by", we added a clear statement in the readme but can't fit it in the 2 page format of the article without removing important references. The section reports the main context (data assimilation for velocimetry) that the SPICY package targets, so it is implicit that it targets anyone interested in this topic.

3. Automated tests: We will consider this for the next release; thank you very much for the suggestion. As beginners in software developments we limited ourselves to tutorials designed to test all the key functions. In our experience, it seems that users learn how to use the code quite quickly while having a good grasp of the underlying numerics from the videos we provided on youtube (https://www.youtube.com/@spicyVKI).

4. Community guidelines. Indeed, these were missing. We added an .md file with instructions (as per solved issue)

5. Installation instructions and related documentation. Indeed, several dependencies were unclear. We fixed this as suggested in the issue. We now include an installation with optional dependencies for the tutorials.

The folder should now be clean. I twine upload everything in a few hours.

Once again, thank you so much for the very detailed review and suggestions :)

[philipcardiff]

Hi, again, @nolankucd and @ctdegroot, another reminder about this review. Let us know if you have a timeline in mind. Thanks.

[philipcardiff]

Hi @nolankucd and @ctdegroot, another reminder about this review. Thanks.

[philipcardiff]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1088/1361-6501/ac70a9 is OK
- 10.1016/j.cageo.2019.03.007 is OK
- 10.5334/jors.101 is OK
- 10.6084/M9.FIGSHARE.12330608 is OK
- 10.5334/jors.334 is OK
- 10.1017/s0962492914000130 is OK
- 10.1007/s00348-016-2133-9 is OK
- 10.1007/s00348-021-03172-0 is OK

MISSING DOIs

- 10.18409/ispiv.v1i1.198 may be a valid DOI for title: Main results of the first Data Assimilation Challenge
- 10.55037/lxlaser.20th.115 may be a valid DOI for title: A RANS approach to the Meshless Computation of Pressure Fields From Image Velocimetry

INVALID DOIs

- https://doi.org/10.1016/j.taml.2020.01.039 is INVALID because of 'https://doi.org/' prefix

[philipcardiff]

Hi @nolankucd and @ctdegroot, no doubt you are both very busy; if possible, can you indicate an expected timeline for the start of your review? Thanks!

@MatthewFlamm, as your review is complete, please tick all remaining unticked boxes in your checklist, assuming you agree they are complete.

[MatthewFlamm]

I was waiting for other reviews based on the previous comments. I will re check based on the recent changes.

[philipcardiff]

@editorialbot generate pdf

[editorialbot]

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

[philipcardiff]

FYI, I proposed some minor English edits to the paper at mendezVKI/SPICY_VKI#10

[mendezVKI]

English edits and version tag applied.

[philipcardiff]

@editorialbot generate pdf

[philipcardiff]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1088/1361-6501/ac70a9 is OK
- 10.1016/j.cageo.2019.03.007 is OK
- 10.5334/jors.101 is OK
- 10.6084/M9.FIGSHARE.12330608 is OK
- 10.5334/jors.334 is OK
- 10.1017/s0962492914000130 is OK
- 10.1016/j.taml.2020.01.039 is OK
- 10.1007/s00348-016-2133-9 is OK
- 10.1007/s00348-021-03172-0 is OK

MISSING DOIs

- 10.18409/ispiv.v1i1.198 may be a valid DOI for title: Main results of the first Data Assimilation Challenge
- 10.55037/lxlaser.20th.115 may be a valid DOI for title: A RANS approach to the Meshless Computation of Pressure Fields From Image Velocimetry

INVALID DOIs

- None

[editorialbot]

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

\mathsemicolon
              ^
unexpected control sequence \mathsemicolon
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

[editorialbot]

👋 @openjournals/pe-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#4908, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[philipcardiff]

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

\mathsemicolon
              ^
unexpected control sequence \mathsemicolon
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

@mendezVKI , can you check if you can resolve this error? Thanks.

[kyleniemeyer]

@mendezVKI the issue looks to be in your paper.bib file, specifically the Heyman2019 reference. Please change the journal field to be just Computers \& Geosciences.

[mendezVKI]

Sorry guys for the late response and thank you for all your help. It should be fixed

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

Hi @mendezVKI, I made a few more changes in this PR: mendezVKI/SPICY_VKI#11

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Sperotto
  given-names: Pietro
  orcid: "https://orcid.org/0000-0001-9412-0828"
- family-names: Ratz
  given-names: M.
  orcid: "https://orcid.org/0009-0008-8491-8367"
- family-names: Mendez
  given-names: M. A.
  orcid: "https://orcid.org/0000-0002-1115-2187"
contact:
- family-names: Mendez
  given-names: M. A.
  orcid: "https://orcid.org/0000-0002-1115-2187"
doi: 10.5281/zenodo.10473329
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sperotto
    given-names: Pietro
    orcid: "https://orcid.org/0000-0001-9412-0828"
  - family-names: Ratz
    given-names: M.
    orcid: "https://orcid.org/0009-0008-8491-8367"
  - family-names: Mendez
    given-names: M. A.
    orcid: "https://orcid.org/0000-0002-1115-2187"
  date-published: 2024-01-16
  doi: 10.21105/joss.05749
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5749
  title: "SPICY: a Python toolbox for meshless assimilation from image
    velocimetry using radial basis functions"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05749"
  volume: 9
title: "SPICY: a Python toolbox for meshless assimilation from image
  velocimetry using radial basis functions"

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.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.05749 joss-papers#4916
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05749
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]

Congratulations @mendezVKI on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @nolankucd, @MatthewFlamm, and @ctdegroot for reviewing this, and @philipcardiff for editing.

[editorialbot]

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

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