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[PRE REVIEW]: MODULO: a python toolbox for data-driven modal decomposition #6208

Closed editorialbot closed 6 months ago

editorialbot commented 10 months ago

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

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

Author instructions

Thanks for submitting your paper to JOSS @mendezVKI. Currently, there isn't a JOSS editor assigned to your paper.

@mendezVKI if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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editorialbot commented 10 months ago

Hello human, 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:

@editorialbot commands

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

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editorialbot commented 10 months ago 
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
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 842

editorialbot commented 10 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

- None

INVALID DOIs

- https://doi.org/10.21105/joss.00530 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 10 months ago

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

editorialbot commented 10 months ago

Five most similar historical JOSS papers:

PySPOD: A Python package for Spectral Proper Orthogonal Decomposition (SPOD) Submitting author: @mengaldo Handling editor: @eloisabentivegna (Active) Reviewers: @albertonogueira, @joao-l-s-almeida, @jdmoorman Similarity score: 0.8899

Moead-framework: a modular MOEA/D Python framework Submitting author: @geoffreyp Handling editor: @melissawm (Retired) Reviewers: @sjvrijn, @chkoar Similarity score: 0.8336

EMD: Empirical Mode Decomposition and Hilbert-Huang Spectral Analyses in Python Submitting author: @ajquinn Handling editor: @dpsanders (Retired) Reviewers: @JanCBrammer, @EtienneCmb, @neurofractal Similarity score: 0.8278

WrightTools: a Python package for multidimensional spectroscopy Submitting author: @untzag Handling editor: @yochannah (Retired) Reviewers: @daissi, @ivergara Similarity score: 0.8244

TLViz: Visualising and analysing tensor decomposition models with Python Submitting author: @marieroald Handling editor: @faroit (Active) Reviewers: @sara-02, @yiitozer Similarity score: 0.8227

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kyleniemeyer commented 10 months ago

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 commented 10 months ago

@faroit is this close to your areas of expertise?

faroit commented 10 months ago

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

kyleniemeyer commented 8 months ago

@editorialbot invite @philipcardiff as editor

editorialbot commented 8 months ago

Invitation to edit this submission sent!

philipcardiff commented 8 months ago

@editorialbot assign me as editor

editorialbot commented 8 months ago

Assigned! @philipcardiff is now the editor

arfon commented 7 months ago

@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 commented 7 months ago

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 commented 7 months ago

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 commented 7 months ago

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 commented 7 months ago

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 https://github.com/openjournals/joss-reviews/issues/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 commented 7 months ago

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 https://github.com/openjournals/joss-reviews/issues/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 commented 7 months ago

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 commented 7 months ago

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

Yes, that sounds fine.

philipcardiff commented 7 months ago

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

mengaldo commented 7 months ago

@philipcardiff Yes, happy to review the submission

philipcardiff commented 7 months ago

@editorialbot add @mengaldo as reviewer

editorialbot commented 7 months ago

@mengaldo added to the reviewers list!

philipcardiff commented 6 months ago

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 https://github.com/openjournals/joss-reviews/issues/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 commented 6 months ago

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 https://github.com/openjournals/joss-reviews/issues/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 commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

@philipcardiff happy to review the submission. Best, Andre

philipcardiff commented 6 months ago

@philipcardiff happy to review the submission. Best, Andre

Thanks, Andre.

philipcardiff commented 6 months ago

@editorialbot add @AndreWeiner as reviewer

editorialbot commented 6 months ago

@AndreWeiner added to the reviewers list!

philipcardiff commented 6 months ago

@editorialbot start review

editorialbot commented 6 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6753.

philipcardiff commented 6 months ago

Hi all, we can continue the review over on the review issue https://github.com/openjournals/joss-reviews/issues/6753.