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

[editorialbot]

Submitting author: @mendezVKI (Miguel Alfonso Mendez)
Repository: https://github.com/mendezVKI/MODULO
Branch with paper.md (empty if default branch):
Version: v2.0
Editor: @philipcardiff
Reviewers: @mengaldo, @AndreWeiner
Managing EiC: Kyle Niemeyer

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c34edf50e0df8abe0eb03649813702ce"><img src="https://joss.theoj.org/papers/c34edf50e0df8abe0eb03649813702ce/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c34edf50e0df8abe0eb03649813702ce/status.svg)](https://joss.theoj.org/papers/c34edf50e0df8abe0eb03649813702ce)

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.20 s (568.7 files/s, 304131.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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JavaScript                      20           4548           4452          16359
HTML                            30           1160             90           5783
SVG                              3              0              0           2680
Python                          23           1008           1839           2566
Jupyter Notebook                 5              0          17460            944
CSS                              6            193             58            838
reStructuredText                18            217             57            309
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:                           114           7218          23975          29769
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 842

[editorialbot]

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

- None

INVALID DOIs

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

[editorialbot]

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

[editorialbot]

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[kyleniemeyer]

Hello @mendezVKI, thanks for your submission to JOSS. We'll use this pre-review issue to assign an editor and find reviewers; unfortunately, we don't have any editors available to handle your submission right now, so I need to put this on our waitlist until someone can edit it.

In the meantime, any reviewer recommendations you can make would be welcome.

[kyleniemeyer]

@faroit is this close to your areas of expertise?

[faroit]

@kyleniemeyer i am unfortunately not, but I can help providing reviewers once we have an editor

[kyleniemeyer]

@editorialbot invite @philipcardiff as editor

[editorialbot]

Invitation to edit this submission sent!

[philipcardiff]

@editorialbot assign me as editor

[editorialbot]

Assigned! @philipcardiff is now the editor

[arfon]

@kyleniemeyer i am unfortunately not, but I can help providing reviewers once we have an editor

@faroit – can you help @philipcardiff with finding some reviewers here?

[philipcardiff]

Hello (again!) @mendezVKI,

Would you mind clarifying the difference between this submission and the toolbox published at https://www.softxjournal.com/article/S2352-7110(20)30335-6/fulltext? This SoftwareX publication also refers to github.com/mendezVKI/MODULO.

Thanks

[mendezVKI]

Hello again Philip!

The toolbox published in https://www.softxjournal.com/article/S2352-7110(20)30335-6/fulltext was the first version of the toolbox in this submission. It was written in Matlab and equipped with a GUI and an executable. That version is no longer maintained and has been kept in one of the branches of the MODULO repository.

The version we have submitted to JOSS has been entirely rewritten in Python, updated with modern packages from scipy/numpy and considerably extended to have many more decompositions (the SPODs, the DMD, the Kernel POD) and features (non-uniform grids, more sophisticated memory saving, etc.).

The main novelties are listed on the doc page: https://modulo.readthedocs.io/en/latest/what_is_new.html .

The reason why I kept the original repo and did not move to a new one is that I have promoted it in various published materials (most notably in this chapter: https://www.cambridge.org/core/books/abs/datadriven-fluid-mechanics/generalized-and-multiscale-modal-analysis/F6C342E80A83D68756CEC1492848C6E1 ) and I would like to preserve that.

[philipcardiff]

Thanks, @mendezVKI, for the details.

To avoid any confusion, would it be possible to update the name in the paper to “MODULO v2” or “pyMODULO” or something similar?

[philipcardiff]

Hi @sichinaga, Would you be interested in reviewing the submission “MODULO: a python toolbox for data-driven modal decomposition ”, which we received at JOSS? The link for the submission is #6208, and the repository is at https://github.com/mendezVKI/MODULO.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

[philipcardiff]

Hi @modelflows, Would you be interested in reviewing the submission “MODULO: a python toolbox for data-driven modal decomposition ”, which we received at JOSS? The link for the submission is #6208, and the repository is at https://github.com/mendezVKI/MODULO.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

[mendezVKI]

Thanks, @mendezVKI, for the details.

To avoid any confusion, would it be possible to update the name in the paper to “MODULO v2” or “pyMODULO” or something similar?

Indeed, we could do that. We can change to pyMODULO. Our main constraint was keeping the same repository I constantly refer to in the book. I naively thought that having the different branches + readme + docs was enough, keeping in mind that (1) the Matlab version is no longer maintained, (2) there is only one module on PyPI (the Python version).

Would it be okay to change the name but keep it in the same repository? (in the master)

[philipcardiff]

Would it be okay to change the name but keep it in the same repository? (in the master)

Yes, that sounds fine.

[philipcardiff]

Hello @mengaldo, would you be interested in reviewing this submission?

[mengaldo]

@philipcardiff Yes, happy to review the submission

[philipcardiff]

@editorialbot add @mengaldo as reviewer

[editorialbot]

@mengaldo added to the reviewers list!

[philipcardiff]

Hi @mtezzele, Would you be interested in reviewing the submission “MODULO: a python toolbox for data-driven modal decomposition ”, which we received at JOSS? The link for the submission is #6208, and the repository is at https://github.com/mendezVKI/MODULO.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

[philipcardiff]

Hi @AndreWeiner, Would you be interested in reviewing the submission “MODULO: a python toolbox for data-driven modal decomposition ”, which we received at JOSS? The link for the submission is #6208, and the repository is at https://github.com/mendezVKI/MODULO.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

[mtezzele]

Hi @mtezzele, Would you be interested in reviewing the submission “MODULO: a python toolbox for data-driven modal decomposition ”, which we received at JOSS? The link for the submission is #6208, and the repository is at https://github.com/mendezVKI/MODULO.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

I'm sorry but I'm not available.

Best,
Marco

[philipcardiff]

Hi @mtezzele, Would you be interested in reviewing the submission “MODULO: a python toolbox for data-driven modal decomposition ”, which we received at JOSS? The link for the submission is #6208, and the repository is at https://github.com/mendezVKI/MODULO.
If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

I'm sorry but I'm not available.

Best, Marco

No problem, thanks, Marco, for your reply. Feel free to suggest a suitable reviewer.

[AndreWeiner]

@philipcardiff happy to review the submission.
Best, Andre

[philipcardiff]

@philipcardiff happy to review the submission. Best, Andre

Thanks, Andre.

[philipcardiff]

@editorialbot add @AndreWeiner as reviewer

[editorialbot]

@AndreWeiner added to the reviewers list!

[philipcardiff]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6753.

[philipcardiff]

Hi all, we can continue the review over on the review issue #6753.