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[PRE REVIEW]: NMRInversions.jl, a julia package for time-domain Nuclear Magnetic Resonance #7496

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editorialbot opened this issue Nov 18, 2024 · 48 comments
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editorialbot commented Nov 18, 2024

Submitting author: @aris-mav (Aristarchos Mavridis)
Repository: https://github.com/aris-mav/NMRInversions.jl
Branch with paper.md (empty if default branch): master
Version: v0.9.2
Editor: @zhubonan
Reviewers: @cfarm6, @hessammehr
Managing EiC: Kyle Niemeyer

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HTML: <a href="https://joss.theoj.org/papers/ad59c8b34ac785bfdff155d4e579a086"><img src="https://joss.theoj.org/papers/ad59c8b34ac785bfdff155d4e579a086/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ad59c8b34ac785bfdff155d4e579a086/status.svg)](https://joss.theoj.org/papers/ad59c8b34ac785bfdff155d4e579a086)

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

@aris-mav 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 3 (PE) Physics and Engineering labels Nov 18, 2024
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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:

@editorialbot generate pdf

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@editorialbot set paper as branch

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Done! branch is now paper

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@editorialbot generate pdf

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@editorialbot set master as branch

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Done! branch is now master

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@editorialbot generate pdf

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

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Five most similar historical JOSS papers:

NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals
Submitting author: @nluetts
Handling editor: @jbytecode (Active)
Reviewers: @myousefi2016, @mseri
Similarity score: 0.7261

ModeCouplingTheory.jl: A solver for mode-coupling-theory-like integro-differential equations
Submitting author: @IlianPihlajamaa
Handling editor: @mstimberg (Active)
Reviewers: @epspebble, @dawbarton
Similarity score: 0.7203

SyntheticEddyMethod.jl: A Julia package for the creation of inlet flow conditions for LES
Submitting author: @carlodev
Handling editor: @philipcardiff (Active)
Reviewers: @atzberg, @akshaysridhar
Similarity score: 0.7154

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.7125

OpenGeoSysUncertaintyQuantification.jl: a Julia library implementing an uncertainty quantification toolbox for OpenGeoSys
Submitting author: @baxmittens
Handling editor: @kanishkan91 (Active)
Reviewers: @ziyiyin97, @dannys4
Similarity score: 0.7093

⚠️ 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.

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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (932.2 files/s, 166213.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0              0           2660
Julia                           16            667            589           1295
Markdown                         7            144              0            419
YAML                             6              3              7            142
TeX                              1              6              0             49
TOML                             2              6              0             43
CSV                              1              0              0             32
-------------------------------------------------------------------------------
SUM:                            34            826            596           4640
-------------------------------------------------------------------------------

Commit count by author:

    67	aris
    40	Aris bpHPC
    12	CompatHelper Julia

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Paper file info:

📄 Wordcount for paper.md is 740

✅ The paper includes a Statement of need section

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License info:

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

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@editorialbot check references

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

✅ OK DOIs

- 10.62721/diffusion-fundamentals.29.952 is OK
- 10.1016/j.pnmrs.2011.07.002 is OK
- 10.1103/PhysRev.73.679 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Discrete inverse problems: Insight and algorithms

❌ MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing

❌ INVALID DOIs

- None

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Hello @aris-mav thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

While we are waiting, could you please:

  • Fix the DOIs (noting that @editorialbot's suggestions are not always right), you can, then use the following commands (one at a time, as the first line of a new comment) to regenerate the PDF and check the references:
    @editorialbot generate pdf
    @editorialbot check references

  • Recommend some potential reviewers from the database, though please do not tag them with @ directly.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

@kyleniemeyer kyleniemeyer added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Nov 18, 2024
@aris-mav
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Hello Kyle,
Thank you very much for the information.

As for the reviewers, should I only look at the current list, or should I also ask people in the field who might be willing to review?
From the list, the only person into magnetic resonance seems to be nicksisco1932 (based on a quick keyword search).

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@aris-mav we'd welcome any suggestions here, but please don't ask them directly - that is the editor's job

@aris-mav
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Understood!
I'll ask around and I'll let you know.
Should I post any suggestions in this thread, or should I send a mail instead?

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You can just list some suggestions here

@aris-mav
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Thanks a lot Kyle.
For now, I'd like to recommend Viliam Bortolotti and nicksisco1932.

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@editorialbot invite @zhubonan as editor

Hi @zhubonan, could you edit this submission?

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Invitation to edit this submission sent!

@zhubonan
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Sure I am happy to edit this one

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@editorialbot assign @zhubonan as editor

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Assigned! @zhubonan is now the editor

@kyleniemeyer kyleniemeyer removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Dec 12, 2024
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zhubonan commented Jan 2, 2025

@editorialbot generate pdf

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

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Five most similar historical JOSS papers:

NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals
Submitting author: @nluetts
Handling editor: @jbytecode (Active)
Reviewers: @myousefi2016, @mseri
Similarity score: 0.7256

ModeCouplingTheory.jl: A solver for mode-coupling-theory-like integro-differential equations
Submitting author: @IlianPihlajamaa
Handling editor: @mstimberg (Active)
Reviewers: @epspebble, @dawbarton
Similarity score: 0.7193

SyntheticEddyMethod.jl: A Julia package for the creation of inlet flow conditions for LES
Submitting author: @carlodev
Handling editor: @philipcardiff (Active)
Reviewers: @atzberg, @akshaysridhar
Similarity score: 0.7147

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.7137

MPIFiles.jl: A Julia Package for Magnetic Particle Imaging Files
Submitting author: @tknopp
Handling editor: @brainstorm (Retired)
Reviewers: @IgorBaratta
Similarity score: 0.7135

⚠️ 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.

@zhubonan
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zhubonan commented Jan 2, 2025

Hi @Luthaf and @nicksisco1932, and @nluetts - Happy New Year! Would you be happy to review this submission for JOSS?

JOSS is unique and takes place on GitHub. This involves reviewing the manuscript and installing/testing/reading the underlying code. You can learn more about it here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#reviewing-for-joss

Please let me know if you are able/unable to review. Your response is greatly appreciated. Thanks in advance.

@nluetts
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nluetts commented Jan 6, 2025

@zhubonan Thank you for the invitation and a late "Happy New Year" to you too! Unfortunately, I am too busy to do this review in good time in the moment.

@Luthaf
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Luthaf commented Jan 7, 2025

Hi! Unfortunately, I will have to decline as well. This is too far from my programming expertise and area of research for me to be able to review it effectively.

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zhubonan commented Jan 13, 2025

@nluetts @Luthaf Okay no worries, and thanks for letting me know!

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Hi @hessammehr, @cfarm6 and @tknopp Would you be happy to review this submission for JOSS?

JOSS is unique and takes place on GitHub. This involves reviewing the manuscript and installing/testing/reading the underlying code. You can learn more about it here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#reviewing-for-joss

Please let me know if you are able/unable to review. Your response is greatly appreciated. Thanks in advance.

@hessammehr
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@zhubonan Thank you for reaching out. Yes, pleased to review this submission.

@hessammehr
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@editorialbot generate my checklist

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Checklists can only be created once the review has started in the review issue

@cfarm6
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cfarm6 commented Jan 31, 2025

@zhubonan I am available to review. Apologies for the delay getting back to you.

@aris-mav
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aris-mav commented Feb 3, 2025

Hello all,

Thank you @cfarm6 and @hessammehr for offering your time to review this!

@zhubonan , shall we begin the review process?

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zhubonan commented Feb 4, 2025

@editorialbot add @cfarm6 as reviewer

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@cfarm6 added to the reviewers list!

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zhubonan commented Feb 4, 2025

@editorialbot add @hessammehr as reviewer

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@hessammehr added to the reviewers list!

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zhubonan commented Feb 4, 2025

Hi @cfarm6 and @hessammehr thanks for agreeing to review this submission. We will do the review process in a dedicated review issue.

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zhubonan commented Feb 4, 2025

@editorialbot start review

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OK, I've started the review over in #7745.

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