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Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

👋 @pankajkmishra @Kevin-Mattheus-Moerman @vijaysm the actual review takes place in this issue. Please note the two separate review checklists above.

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@whedon check references

@kyleniemeyer: Is there anything required from my side at this point?

@pankajkmishra not at the moment—the reviewers will report any issues requiring your attention here or in the software repository as appropriate.

I should be able to complete the full review by next Monday. It has been a busy couple of weeks. @pankajkmishra @kyleniemeyer

@@kyleniemeyer: Is it allowed to update the repository while it is under review?

I'll finalize the review by next Monday. Apologies for the delay.

@pankajkmishra Yes, but please let us know here when you update it and what changes were made; it sounds like the reviewers may not have started with the current version, so should be fine.

@kyleniemeyer Should I upload a list of my suggestions separately or just continue discussion with the author here as part of the comment thread ?

@pankajkmishra I also noticed that there is no official release for NodeLab yet. So it may be appropriate to update the versioning info first and then tag the commit as a checkpoint for the review. Thoughts @kyleniemeyer ?

@vijaysm feel free to continue the discussion here; you can submit a list of suggestions as a single comment and we can go from there.

Regarding the official release, I'm fine if @pankajkmishra waits until after making any changes as part of this review process, and then makes an official release associated with the version accepted here.

Thanks @vijaysm! I'll look forward to your suggestions. @kyleniemeyer - That would be convenient! Thanks.

@pankajkmishra Here are some comments on the paper:

• Add "be" in the following: "....(Persson & Strang, 2004), which can [be] computed based on a..."

• Remove plural in: "As a results, NodeLab can take the following..."

• Rephrase "some discrete set of point cloud on the boundary, which need not to be uniformly
  sampled." e.g. to: "some discrete set of point cloud on the boundary, which need not to be uniformly
  sampled."

• Can you work to rephrase/clarify this awkward sounding sentence: "The boundary can be smoothed through curve-interpolation according to the fill-distance near the boundary, which provides the flexibility to create the domain by manually digitizing of the geometry from a hand-drawing, digital-drawing, or a downloaded image."

• Can you add a References heading?

@whedon check references

Attempting to check references...

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/j.camwa.2015.01.009 may be missing for title: Fast generation of 2-D node distributions for mesh-free PDE discretizations
- https://doi.org/10.1137/s0036144503429121 may be missing for title: A simple mesh generator in MATLAB

INVALID DOIs

- None

I've created a pull request (pankajkmishra/NodeLab#2) to enhance the demos/documentation. I recommend clarifying the required input arguments and perhaps to visualize them as I suggest.
I also recommend making use of the MATLAB documentation generation tools. I give an example in that demo. You can publish it to create HTML documentation which can be integrated in MATLAB.

Thanks @Kevin-Mattheus-Moerman! I'll get back to you after implementing your suggestions.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

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@pankajkmishra great. Can you also work on adding those DOI's? Let me know if you have questions.

@whedon check references

Attempting to check references...

@kyleniemeyer I have updated the paper showing better a clarity for the value addition.
Added the statistics toolbox dependency as @vijaysm had suggested. However, I couldn't make a similar 3D extension of it at the moment and it continues to be in the future work section. If the present form of the repository does not qualify to be listed in JOSS, I would be happy to withdraw the submission :)
P.S. I have a paper under review where I need to cite this work, which was the original purpose of submitting this to the JOSS.

Thanks @pankajkmishra.

@vijaysm, do you recommend acceptance based on the changes made?

@pankajkmishra Thanks for the description update.

@kyleniemeyer While the updated paper makes the application space clearer than before, I would like to reiterate that the work on NodeLab still remains incremental. Node generation support for 3-D volumes or surfaces would certainly compel me to accept the paper. Also, other open-source Matlab packages by Per-Olof Persson (Distmesh [1]) and by Darren Engwirda (Mesh2D [2]), already do provide adaptive node generation and delaunay triangulation based on user-defined distance functions as well for 2-D domains. Additionally, I think some NodeLab examples showing adaptive refinement with integration to a mesh-free solver would have added value to this contribution with a practical use-case.

As it stands, I am taking the decision to reject the paper submission. @pankajkmishra, please consider updating examples and adding support for 3-D domains to differentiate this work from other existing open-source alternatives. I would be happy to discuss my comments further if you have any questions.

[1] http://persson.berkeley.edu/distmesh/
[2] https://github.com/dengwirda/mesh2d

Hi @vijaysm, thanks for your input.

I should point out that JOSS does not reject submissions for novelty, originality, or impact; instead, we only reject when the authors are unwilling to improve the software to meet our standards. Since both you and @Kevin-Mattheus-Moerman have checked off all the review items, and it doesn't seem like there are any remaining items of that nature, I am going to move this into the final acceptance stages.

@pankajkmishra at this point please archive the software repository (e.g., in Zenodo) and provide the DOI here. I'm going to do a final review/edit of the paper itself.

@kyleniemeyer Fair enough. In that case, the description update from @pankajkmishra was all that was needed to make the submission complete for me.

Hey @kyleniemeyer , thanks! I'll do it ASAP.
Thank you @vijaysm @Kevin-Mattheus-Moerman for your valuable inputs.

@kyleniemeyer following is the Zenodo DOI
10.5281/zenodo.3361734

@whedon set 10.5281/zenodo.3361734 as archive

OK. 10.5281/zenodo.3361734 is the archive.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

Hi @pankajkmishra , just a few final edits needed on the paper:

• can you provide more-complete affiliation info, like what you'd typically see in a journal article? (i.e., city, country)
• Please merge my PR for fixes to the bib file: pankajkmishra/NodeLab#4
• I did some copy editing to the paper in pankajkmishra/NodeLab#5, please merge that.

There are a few more places in the paper that should be edited:

The literature in this context is up-and-coming, which focus on different aspects of node-generation based on typical requirements. The node-placing approach by @Fornberg:2015 is similar to advancing front methods and has been reported to have advantages like computational speed, simple algorithms, and good quality of distribution.

• The first sentence here doesn't make sense to me—I'm not sure what it's actually saying.
• Anytime you reference "literature", it should be followed by multiple citations. Also, what are the "typical requirements"?
• You mention "advancing front methods", but provide no definition or citation. Why is the fact that the node-placing approach is similar to these methods meaningful?

Aside from that, the first paragraph should start with a statement of need, meant for a general reader. I think you could move your sentence about the applications here, and do some revision to make it work.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

@pankajkmishra 👍

@openjournals/joss-eics ok, this is ready for acceptance from my point of view

Thanks @kyleniemeyer , and everyone :)

@whedon accept

Attempting dry run of processing paper acceptance...

Check final proof 👉 openjournals/joss-papers#903

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#903, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Thanks to @Kevin-Mattheus-Moerman and @vijaysm for reviewing and @kyleniemeyer for editing

@whedon accept deposit=true

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