[REVIEW]: MODULO: a python toolbox for data-driven modal decomposition

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@mendezVKI@philipcardiff<!--end-editor-- Reviewers: @mengaldo, @AndreWeiner Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/c34edf50e0df8abe0eb03649813702ce/status.svg)](https://joss.theoj.org/papers/c34edf50e0df8abe0eb03649813702ce)

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

@mengaldo & @AndreWeiner, 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 @philipcardiff 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 @AndreWeiner

📝 Checklist for @mengaldo

editorialbot commented 3 months ago

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editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.20 s (768.7 files/s, 347709.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      26           4679           4647          17175
HTML                            61           2111            183          11399
Python                          28           1230           2281           3009
SVG                              3              0              0           2680
CSS                              8            383             90           1616
Jupyter Notebook                 5              0          17526            945
reStructuredText                17            266             71            327
TeX                              1             14              0             97
Markdown                         2             45              0             93
DOS Batch                        2             16              2             53
YAML                             2              9              4             28
make                             2              8             13             19
-------------------------------------------------------------------------------
SUM:                           157           8761          24817          37441
-------------------------------------------------------------------------------

Commit count by author:

   106  mendezVKI
    69  lorenzoschena
    55  davideninni
    47  Davide Ninni
    11  polettiRomain
     7  fratorhe
     2  Miguel Alfonso Mendez
     2  dependabot[bot]

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 842

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 months ago

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

OK DOIs

- 10.1002/nme.255 is OK
- 10.1017/jfm.2016.103 is OK
- 10.1007/s11340-014-9858-2 is OK
- 10.1016/j.softx.2020.100622 is OK
- 10.1017/jfm.2019.212 is OK
- 10.1017/S0022112010001217 is OK
- 10.1017/jfm.2018.283 is OK
- 10.1088/1361-6501/acaffe is OK
- 10.2514/1.J058462 is OK
- 10.21105/joss.02862 is OK

MISSING DOIs

- No DOI given, and none found for title: Proper Orthogonal Decomposition
- No DOI given, and none found for title: Spectral Proper Orthogonal Decomposition

INVALID DOIs

- https://doi.org/10.21105/joss.00530 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 3 months ago

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

AndreWeiner commented 3 months ago

Review checklist for @AndreWeiner

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/mendezVKI/MODULO?
[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 (@mendezVKI) 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?

philipcardiff commented 2 months ago

Hi @mengaldo, If anything about the review process is unclear, just let me know. You can generate your checklist by creating a comment with the command @editorialbot generate my checklist

mengaldo commented 2 months ago

Review checklist for @mengaldo

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/mendezVKI/MODULO?
[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 (@mendezVKI) 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

[ ] 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

[ ] 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?
[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?
[ ] 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?

mengaldo commented 2 months ago

Hi @philipcardiff, I have now completed the checklist, thank you. If comments are required about the unchecked boxes, let me know. I opened an issue with my review.

philipcardiff commented 2 months ago

Hi @philipcardiff, I have now completed the checklist, thank you. If comments are required about the unchecked boxes, let me know. I opened an issue with my review.

Thank you, @mengaldo.

@mendezVKI: please feel free to ask for clarification on any outstanding points.

Review breadcrumb: https://github.com/mendezVKI/MODULO/issues/28

mendezVKI commented 2 months ago

Hello,

Thank to you all. On it asap

mendezVKI commented 1 month ago

All comments have been addressed.

Thank to all of you for the time invested in the revision and handling the submission.

AndreWeiner commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

AndreWeiner commented 1 month ago

@mendezVKI In line 37 of the updated article, you write modes that can potentially vanish or decay. I assume you meant to write something like can decay or grow or can vanish or explode.

@philipcardiff Besides the minor remark above, I consider the review complete from my side. My remarks have been addressed by the authors.

Best, Andre

philipcardiff commented 1 month ago

@mendezVKI In line 37 of the updated article, you write modes that can potentially vanish or decay. I assume you meant to write something like can decay or grow or can vanish or explode.

@philipcardiff Besides the minor remark above, I consider the review complete from my side. My remarks have been addressed by the authors.

Best, Andre

Thanks, Andre!

mendezVKI commented 1 month ago

Indeed, thank you for spotting the typo Andre and for all the detailed comments!

mendezVKI commented 3 weeks ago

@philipcardiff May I kindly ask an update of the revision? Our last feedback is a greenlight from @AndreWeiner while @mengaldo still has the issue open, right? Please let us know what else is needed from our side.

philipcardiff commented 3 weeks ago

Hi @mendezVKI, yes, correct; that is my understanding.

@AndreWeiner recommends the submission for publication, while, from @mengaldo's comment above, he is happy to clarify any queries you have about his unchecked points.

mendezVKI commented 1 week ago

Hello,

All issues are closed now 🙂

philipcardiff commented 23 hours ago

Hi @mendezVKI, feel free to ask @mengaldo about any of the remaining unchecked boxes, as they requested.

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