[REVIEW]: NodeLab: A MATLAB package for meshfree node-generation and adaptive refinement

[whedon]

Submitting author: @pankajkmishra (Pankaj K Mishra)
Repository: https://github.com/pankajkmishra/NodeLab
Version: v1.0
Editor: @kyleniemeyer
Reviewer: @Kevin-Mattheus-Moerman, @vijaysm
Archive: 10.5281/zenodo.3361734

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@Kevin-Mattheus-Moerman & @vijaysm, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @Kevin-Mattheus-Moerman

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v1.0)?
• Authorship: Has the submitting author (@pankajkmishra) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @vijaysm

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v1.0)?
• Authorship: Has the submitting author (@pankajkmishra) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Kevin-Mattheus-Moerman, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kyleniemeyer]

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

[pankajkmishra]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Ask Whedon to check the references for missing DOIs
@whedon check references

[pankajkmishra]

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

[kyleniemeyer]

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

[vijaysm]

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

[pankajkmishra]

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

[Kevin-Mattheus-Moerman]

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

[kyleniemeyer]

@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.

[vijaysm]

@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 ?

[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.

[pankajkmishra]

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

[Kevin-Mattheus-Moerman]

@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?

[Kevin-Mattheus-Moerman]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

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

[Kevin-Mattheus-Moerman]

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.

[pankajkmishra]

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

[pankajkmishra]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[Kevin-Mattheus-Moerman]

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

[pankajkmishra]

@whedon check references

[whedon]

Attempting to check references...

[kyleniemeyer]

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.

[vijaysm]

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

[pankajkmishra]

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

[pankajkmishra]

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

[kyleniemeyer]

@whedon set 10.5281/zenodo.3361734 as archive

[whedon]

OK. 10.5281/zenodo.3361734 is the archive.

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kyleniemeyer]

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: Update paper.bib pankajkmishra/NodeLab#4
• I did some copy editing to the paper in Update paper.md 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.

[pankajkmishra]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kyleniemeyer]

@pankajkmishra 👍

[kyleniemeyer]

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

[pankajkmishra]

Thanks @kyleniemeyer , and everyone :)

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

[danielskatz]

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

[danielskatz]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01173 joss-papers#904
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01173
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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