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

[editorialbot]

Submitting author: !--author-handle-->@ergoregion<!--end-author-handle-- (Neil Butcher) Repository: https://gitlab.com/djsmithbham/cnearest Branch with paper.md (empty if default branch): JOSS-paper Version: 0.0.1 Editor: !--editor-->@philipcardiff<!--end-editor-- Reviewers: Pending Managing EiC: Arfon Smith

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[editorialbot]

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]

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  n.a.butcher@bham.ac.uk
    52  Neil Butcher
    30  djsmithbham
     3  James Tyrrell (Advanced Research Computing)
     1  James Tyrrell

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2445

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

Stokesian Dynamics in Python Submitting author: @Pecnut Handling editor: @philipcardiff (Active) Reviewers: @rajeshrinet, @szwiep Similarity score: 0.7107

Swalbe.jl: A lattice Boltzmann solver for thin film hydrodynamics Submitting author: @Zitzeronion Handling editor: @arfon (Active) Reviewers: @mbernaschi, @lnacquaroli Similarity score: 0.6732

Ocellaris: a DG FEM solver for free-surface flows Submitting author: @TormodLandet Handling editor: @labarba (Retired) Reviewers: @inducer, @piyueh Similarity score: 0.6634

OpenCMP: An Open-Source Computational Multiphysics Package Submitting author: @nasserma Handling editor: @lucydot (Active) Reviewers: @bonh, @WilkAndy Similarity score: 0.6634

FlowSieve: A Coarse-Graining Utility for Geophysical Flows on the Sphere Submitting author: @bastorer Handling editor: @kthyng (Active) Reviewers: @NoraLoose, @ashwinvis Similarity score: 0.6605

⚠️ 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]

@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]

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

[ergoregion]

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

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

OpenCMP: An Open-Source Computational Multiphysics Package Submitting author: @nasserma 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

Stokesian Dynamics in Python Submitting author: @Pecnut Handling editor: @philipcardiff (Active) Reviewers: @rajeshrinet, @szwiep Similarity score: 0.6915

FEM_2D: A Rust Package for 2D Finite Element Method Computations with Extensive Support for hp-refinement Submitting author: @jeremiah-corrado Handling editor: @jedbrown (Active) Reviewers: @jeremylt, @YohannDudouit Similarity score: 0.6852

libCEED: Fast algebra for high-order element-based discretizations Submitting author: @jedbrown Handling editor: @diehlpk (Active) Reviewers: @thelfer, @FreddieWitherden, Similarity score: 0.6801

⚠️ 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]

@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]

@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

[ergoregion]

@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]

@editorialbot check references

[editorialbot]

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]

@editorialbot check references

[editorialbot]

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]

@editorialbot check references

[editorialbot]

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]

@editorialbot generate pdf

[ergoregion]

@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]

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

[editorialbot]

Five most similar historical JOSS papers:

OpenCMP: An Open-Source Computational Multiphysics Package Submitting author: @nasserma Handling editor: @lucydot (Active) Reviewers: @bonh, @WilkAndy Similarity score: 0.7132

BasicTools: a numerical simulation toolbox Submitting author: @fbordeu Handling editor: @diehlpk (Active) Reviewers: @hvonwah, @sthavishtha Similarity score: 0.7006

Stokesian Dynamics in Python Submitting author: @Pecnut Handling editor: @philipcardiff (Active) Reviewers: @rajeshrinet, @szwiep Similarity score: 0.6984

FEM_2D: A Rust Package for 2D Finite Element Method Computations with Extensive Support for hp-refinement Submitting author: @jeremiah-corrado Handling editor: @jedbrown (Active) Reviewers: @jeremylt, @YohannDudouit Similarity score: 0.6936

FeenoX: a cloud-first finite-element(ish) computational engineering tool Submitting author: @gtheler Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @vijaysm, @AnjaliSandip, @chennachaos Similarity score: 0.6849

⚠️ 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.