[PRE REVIEW]: CNearest: A C++ toolkit to use the nearest-neighbour method of regularised stokeslets algorithm to solve viscous flow problems #7191

editorialbot · 2024-09-07T12:29:06Z

Submitting author: @ergoregion (Neil Butcher)
Repository: https://gitlab.com/djsmithbham/cnearest
Branch with paper.md (empty if default branch): JOSS-paper
Version: 0.0.1
Editor: @philipcardiff
Reviewers: @fabienevrard, @Pecnut
Managing EiC: Arfon Smith

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2dedd709aa80938d14c38d8e9aabff79"><img src="https://joss.theoj.org/papers/2dedd709aa80938d14c38d8e9aabff79/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2dedd709aa80938d14c38d8e9aabff79/status.svg)](https://joss.theoj.org/papers/2dedd709aa80938d14c38d8e9aabff79)

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editorialbot · 2024-09-07T12:29:08Z

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editorialbot · 2024-09-07T12:29:38Z

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

✅ OK DOIs

- 10.1016/j.jcp.2017.12.008 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: 20 years of Regularized Stokeslets: Applications, ...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: NEAREST
- No DOI given, and none found for title: Boundary integral and singularity methods for line...
- No DOI given, and none found for title: A practical guide to boundary element methods with...

❌ MISSING DOIs

- 10.1016/j.jcp.2008.01.032 may be a valid DOI for title: The method of images for regularized Stokeslets
- 10.1137/s106482750038146x may be a valid DOI for title: The method of regularized Stokeslets
- 10.1063/1.1830486 may be a valid DOI for title: The method of regularized Stokeslets in three dime...
- 10.1016/j.jcp.2015.01.019 may be a valid DOI for title: A general system of images for regularized Stokesl...
- 10.1016/j.jcp.2018.08.055 may be a valid DOI for title: Regularized stokeslet segments
- 10.1103/physrevfluids.3.053101 may be a valid DOI for title: Meshfree and efficient modeling of swimming cells
- 10.1137/18m1191816 may be a valid DOI for title: Sharp quadrature error bounds for the nearest-neig...
- 10.1098/rsta.2019.0528 may be a valid DOI for title: Passively parallel regularized stokeslets
- 10.1098/rsos.210108 may be a valid DOI for title: The art of coarse Stokes: Richardson extrapolation...
- 10.1103/physrevfluids.4.113101 may be a valid DOI for title: Efficient implementation of elastohydrodynamics vi...
- 10.1140/epje/i2015-15139-7 may be a valid DOI for title: A regularised singularity approach to phoretic pro...
- 10.1103/physrevfluids.5.073101 may be a valid DOI for title: Doing more with less: the flagellar end piece enha...
- 10.1016/j.jfluidstructs.2016.07.006 may be a valid DOI for title: Kernel-independent fast multipole method within th...
- 10.1098/rspa.2009.0295 may be a valid DOI for title: A boundary element regularized Stokeslet method ap...
- 10.3390/fluids6110411 may be a valid DOI for title: The role of the double-layer potential in regulari...
- 10.1103/physrevfluids.4.063102 may be a valid DOI for title: Regularized Stokeslet rings: An efficient method f...
- 10.1103/physrevfluids.4.084104 may be a valid DOI for title: Method of regularized stokeslets: Flow analysis an...

❌ INVALID DOIs

- https://doi.org/10.1002/bip.1981.360200205 is INVALID because of 'https://doi.org/' prefix

editorialbot · 2024-09-07T12:29:44Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (2758.5 files/s, 208424.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             49           1122            143           3347
XML                              1              0              0            941
C/C++ Header                    32            184            375            623
Markdown                        12            219              0            366
TeX                              1             27              0            217
JSON                             1              0              0            103
CMake                            5             22              1             85
YAML                             2              6              9             47
Dockerfile                       1              8              1             12
-------------------------------------------------------------------------------
SUM:                           104           1588            529           5741
-------------------------------------------------------------------------------

Commit count by author:

   107	[email protected]
    52	Neil Butcher
    30	djsmithbham
     3	James Tyrrell (Advanced Research Computing)
     1	James Tyrrell

editorialbot · 2024-09-07T12:29:48Z

Paper file info:

📄 Wordcount for paper.md is 2445

✅ The paper includes a Statement of need section

editorialbot · 2024-09-07T12:29:51Z

License info:

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

editorialbot · 2024-09-07T12:30:51Z

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

editorialbot · 2024-09-07T12:31:42Z

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⚠️ 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.

arfon · 2024-09-07T12:39:08Z

@ergoregion - 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.

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

Also, while we're waiting for an editor, could you please look at shortening your paper? We typically ask that JOSS papers are around 1000 words. Thanks!

kyleniemeyer · 2024-10-18T17:09:36Z

@ergoregion Have you shortened your paper yet, per @arfon's request?

ergoregion · 2024-10-18T17:40:11Z

@kyleniemeyer , yes my colleague, @djsmithbham, has reduced the word count.

kyleniemeyer · 2024-10-22T16:37:33Z

@editorialbot generate pdf

editorialbot · 2024-10-22T16:39:07Z

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

editorialbot · 2024-10-22T16:39:52Z

Five most similar historical JOSS papers:

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Handling editor: @lucydot (Active)
Reviewers: @bonh, @WilkAndy
Similarity score: 0.7039

BasicTools: a numerical simulation toolbox
Submitting author: @fbordeu
Handling editor: @diehlpk (Active)
Reviewers: @hvonwah, @sthavishtha
Similarity score: 0.6971

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Similarity score: 0.6915

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⚠️ 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 · 2024-10-22T16:44:56Z

@ergoregion great, thank you. It does look like the paper is missing DOIs for many/most articles, so please do add those. In addition, it appears that the Eigen reference is not formatted correctly, particularly the author names.

Regarding the software itself, I see that you have a test suite - do you have continuous integration set up? (If so, I can't see any indication of the status, though I do see the test coverage number.) Either way, please point to some documentation about running the test suite; this is a requirement for us but I cannot find it. Thanks!

@philipcardiff could you edit this, once the authors have addressed the above issues?

kyleniemeyer · 2024-10-22T16:45:01Z

@editorialbot invite @philipcardiff as editor

editorialbot · 2024-10-22T16:45:03Z

Invitation to edit this submission sent!

philipcardiff · 2024-10-22T16:47:55Z

@editorialbot assign me as editor

editorialbot · 2024-10-22T16:47:58Z

Assigned! @philipcardiff is now the editor

ergoregion · 2024-10-28T11:26:05Z

@kyleniemeyer @philipcardiff

Hi, yes the project has continuous integration set up. It is stored on gitlab, which uses a yml file to define CI pipelines.
The results are then displayed on the website, under build->pipelines, here.

The documentation for building and running tests yourself is on the docs page here

ergoregion · 2024-10-31T16:30:24Z

@editorialbot check references

editorialbot · 2024-10-31T16:31:09Z

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

✅ OK DOIs

- 10.1016/j.jcp.2017.12.008 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: 20 years of Regularized Stokeslets: Applications, ...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: NEAREST
- No DOI given, and none found for title: Boundary integral and singularity methods for line...
- No DOI given, and none found for title: A practical guide to boundary element methods with...

❌ MISSING DOIs

- 10.1016/j.jcp.2008.01.032 may be a valid DOI for title: The method of images for regularized Stokeslets
- 10.1137/s106482750038146x may be a valid DOI for title: The method of regularized Stokeslets
- 10.1063/1.1830486 may be a valid DOI for title: The method of regularized Stokeslets in three dime...
- 10.1016/j.jcp.2015.01.019 may be a valid DOI for title: A general system of images for regularized Stokesl...
- 10.1016/j.jcp.2018.08.055 may be a valid DOI for title: Regularized stokeslet segments
- 10.1103/physrevfluids.3.053101 may be a valid DOI for title: Meshfree and efficient modeling of swimming cells
- 10.1137/18m1191816 may be a valid DOI for title: Sharp quadrature error bounds for the nearest-neig...
- 10.1098/rsta.2019.0528 may be a valid DOI for title: Passively parallel regularized stokeslets
- 10.1098/rsos.210108 may be a valid DOI for title: The art of coarse Stokes: Richardson extrapolation...
- 10.1103/physrevfluids.4.113101 may be a valid DOI for title: Efficient implementation of elastohydrodynamics vi...
- 10.1140/epje/i2015-15139-7 may be a valid DOI for title: A regularised singularity approach to phoretic pro...
- 10.1103/physrevfluids.5.073101 may be a valid DOI for title: Doing more with less: the flagellar end piece enha...
- 10.1016/j.jfluidstructs.2016.07.006 may be a valid DOI for title: Kernel-independent fast multipole method within th...
- 10.1098/rspa.2009.0295 may be a valid DOI for title: A boundary element regularized Stokeslet method ap...
- 10.3390/fluids6110411 may be a valid DOI for title: The role of the double-layer potential in regulari...
- 10.1103/physrevfluids.4.063102 may be a valid DOI for title: Regularized Stokeslet rings: An efficient method f...
- 10.1002/bip.1981.360200205 may be a valid DOI for title: Diffusion coefficients for rigid macromolecules wi...
- 10.1103/physrevfluids.4.084104 may be a valid DOI for title: Method of regularized stokeslets: Flow analysis an...

❌ INVALID DOIs

- None

ergoregion · 2024-11-01T10:39:43Z

@editorialbot check references

editorialbot · 2024-11-01T10:40:14Z

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

✅ OK DOIs

- 10.1016/j.jcp.2008.01.032 is OK
- 10.1137/S106482750038146X is OK
- 10.1063/1.1830486 is OK
- 10.1016/j.jcp.2015.01.019 is OK
- 10.1016/j.jcp.2018.08.055 is OK
- 10.1103/PhysRevFluids.3.053101 is OK
- 10.1137/18M1191816 is OK
- 10.1098/rsta.2019.0528 is OK
- 10.1098/rsos.210108 is OK
- 10.1103/PhysRevFluids.4.113101 is OK
- 10.1140/epje/i2015-15139-7 is OK
- 10.1103/PhysRevFluids.5.073101 is OK
- 10.1016/j.jfluidstructs.2016.07.006 is OK
- 10.1098/rspa.2009.0295 is OK
- 10.1016/j.jcp.2017.12.008 is OK
- 10.1098/rspa.2009.0295 is OK
- 10.1103/PhysRevFluids.4.063102 is OK
- 10.1002/bip.1981.360200205 is OK
- 10.1103/PhysRevFluids.4.084104 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: 20 years of Regularized Stokeslets: Applications, ...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: NEAREST
- No DOI given, and none found for title: Boundary integral and singularity methods for line...
- No DOI given, and none found for title: A practical guide to boundary element methods with...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

ergoregion · 2024-11-01T11:02:10Z

@editorialbot check references

editorialbot · 2024-11-01T11:02:30Z

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

✅ OK DOIs

- 10.1016/j.jcp.2008.01.032 is OK
- 10.1137/S106482750038146X is OK
- 10.1063/1.1830486 is OK
- 10.1016/j.jcp.2015.01.019 is OK
- 10.1016/j.jcp.2018.08.055 is OK
- 10.1103/PhysRevFluids.3.053101 is OK
- 10.1137/18M1191816 is OK
- 10.1098/rsta.2019.0528 is OK
- 10.1098/rsos.210108 is OK
- 10.1103/PhysRevFluids.4.113101 is OK
- 10.1140/epje/i2015-15139-7 is OK
- 10.1103/PhysRevFluids.5.073101 is OK
- 10.1017/CBO9780511624124 is OK
- 10.1017/S0022112004008201 is OK
- 10.1016/j.jfluidstructs.2016.07.006 is OK
- 10.1098/rspa.2009.0295 is OK
- 10.1016/j.jcp.2017.12.008 is OK
- 10.1098/rspa.2009.0295 is OK
- 10.1103/PhysRevFluids.4.063102 is OK
- 10.1002/bip.1981.360200205 is OK
- 10.1103/PhysRevFluids.4.084104 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: 20 years of Regularized Stokeslets: Applications, ...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: NEAREST

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

ergoregion · 2024-11-01T11:04:40Z

@editorialbot generate pdf

ergoregion · 2024-11-01T11:05:51Z

@kyleniemeyer @philipcardiff

I don't think the remaining citations have any DOI numbers.
Could you let me know if these changes and descriptions solve all the concerns you raised earlier?

editorialbot · 2024-11-01T11:06:37Z

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

editorialbot · 2024-11-01T11:07:29Z

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Submitting author: @fbordeu
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Submitting author: @Pecnut
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⚠️ 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.

ergoregion · 2024-12-05T09:45:54Z

@philipcardiff If you're still looking for reviewers, @djsmithbham has suggested these names:

Eric Keaveny ([email protected]),
Sarah Olson ([email protected]),
Adam Townsend ([email protected])
Becca Thomases ([email protected])

philipcardiff · 2024-12-06T09:49:23Z

Hi @fabienevrard, Would you be interested in reviewing the submission “CNearest: A C++ toolkit to use the nearest-neighbour method of regularised stokeslets algorithm to solve viscous flow problems”, which we received at JOSS? The link for the submission is #7191 , and the repository is at https://gitlab.com/djsmithbham/cnearest.

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 · 2024-12-06T09:55:13Z

FYI, I emailed two other potential reviewers.

fabienevrard · 2024-12-08T23:22:23Z

Hi @philipcardiff, yes I am happy to review this submission. This is my first time reviewing for JOSS so bear with me! I will go through the review checklist and report back here shortly.

philipcardiff · 2024-12-09T15:04:00Z

Hi @philipcardiff, yes I am happy to review this submission. This is my first time reviewing for JOSS so bear with me! I will go through the review checklist and report back here shortly.

Thanks, @fabienevrard.

philipcardiff · 2024-12-09T15:04:44Z

@editorialbot add @fabienevrard as reviewer

editorialbot · 2024-12-09T15:04:47Z

@fabienevrard added to the reviewers list!

philipcardiff · 2024-12-09T15:08:04Z

Hi @Pecnut, would you be interested in acting as a reviewer for this submission?

Pecnut · 2024-12-18T09:07:22Z

Hi @philipcardiff! Yes, I am happy to review this submission, but I won't be able to do this until after Christmas. Is that OK?

philipcardiff · 2024-12-19T09:55:19Z

@editorialbot add @Pecnut as reviewer

editorialbot · 2024-12-19T09:55:22Z

@Pecnut added to the reviewers list!

philipcardiff · 2024-12-19T09:55:55Z

@editorialbot start review

editorialbot · 2024-12-19T09:55:59Z

OK, I've started the review over in #7605.

philipcardiff · 2024-12-19T09:56:20Z

Hi all, we can continue the review over on the review issue #7605.

editorialbot added pre-review Track: 3 (PE) Physics and Engineering labels Sep 7, 2024

editorialbot added C++ TeX CMake labels Sep 7, 2024

arfon added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Sep 7, 2024

editorialbot assigned philipcardiff Oct 22, 2024

editorialbot assigned fabienevrard Dec 9, 2024

editorialbot assigned Pecnut Dec 19, 2024

editorialbot closed this as completed Dec 19, 2024

[PRE REVIEW]: CNearest: A C++ toolkit to use the nearest-neighbour method of regularised stokeslets algorithm to solve viscous flow problems #7191

[PRE REVIEW]: CNearest: A C++ toolkit to use the nearest-neighbour method of regularised stokeslets algorithm to solve viscous flow problems #7191

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