Joss-reviews: [REVIEW]: ParticleScattering: Solving and optimizing multiple-scattering problems in Julia

[whedon]

Submitting author: @bblankrot (Boaz Blankrot)
Repository: https://github.com/bblankrot/ParticleScattering.jl
Version: v0.0.2
Editor: @Kevin-Mattheus-Moerman
Reviewer: @ziotom78, @ysimillides
Archive: 10.5281/zenodo.1241368

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f8edc7ef1fb130748b125861a26b9232"><img src="http://joss.theoj.org/papers/f8edc7ef1fb130748b125861a26b9232/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f8edc7ef1fb130748b125861a26b9232/status.svg)](http://joss.theoj.org/papers/f8edc7ef1fb130748b125861a26b9232)

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

@ziotom78 & @ysimillides, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Review checklist for @ziotom78

Conflict of interest

• [x] 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

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v0.0.2)?
• [x] Authorship: Has the submitting author (@bblankrot) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

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

Review checklist for @ysimillides

Conflict of interest

• [x] 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

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v0.0.2)?
• [x] Authorship: Has the submitting author (@bblankrot) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

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

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @ziotom78, it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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 :page_facing_up: <--

[ziotom78]

Everything looks fine to me, I created two PRs (#18 and #19) to improve the documentation and make the plots actually appear.

I have checked the claim in the paper that the optimization example takes 35 seconds to complete: on my (quite old) laptop the two calls to optimize_φ take 27 s and 18 s, so this point is ok as well.

[bblankrot]

Thanks for reviewing this so quickly, @ziotom78 , as well as fixing the issues! I merged both PRs.

[Kevin-Mattheus-Moerman]

Thanks @ziotom78 for the fast review :zap: !

[Kevin-Mattheus-Moerman]

@bblankrot the citation in your paper:

Blankrot, Boaz, and Clemens Heitzinger. 2018. “Efficient Computational Design and
Optimization of Dielectric Metamaterial Devices.” _Submitted for Publication_.

Would you be able to upload a pre-print e.g. via engrxiv.org/, and to add the pre-print DOI to the JOSS paper?

[Kevin-Mattheus-Moerman]

At @ysimillides thanks for acting as reviewer here. I think you mentioned being able to review near the end of April. I look forward to your review. Let me know if you have any questions.

[bblankrot]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[bblankrot]

@Kevin-Mattheus-Moerman thanks for the comment, I uploaded the preprint to arxiv. Is the citation OK as is or are any changes necessary?

[Kevin-Mattheus-Moerman]

:clap: @bblankrot Looks good thanks.

[ysimillides]

Looks good! Two very minor thing's i'd suggest adding are JLD to the Require file (as you use it in the majority of the examples), and citing the Julia paper as a reference .

[bblankrot]

Thank you, @ysimillides! Both good ideas, I'm merging your PR and adding a reference to the 2017 Julia paper in SIAM Review.

@whedon generate pdf

[bblankrot]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[bblankrot]

@ysimillides, @Kevin-Mattheus-Moerman – anything else I should take care of on my end?

[Kevin-Mattheus-Moerman]

@ysimillides if you are happy with these edits and there are no more points, are you able to tick the last boxes? Thanks!

[ysimillides]

Done.

[Kevin-Mattheus-Moerman]

Great! Thanks for reviewing @ysimillides and @ziotom78 :rocket:

[Kevin-Mattheus-Moerman]

@bblankrot at this point, can you please make an archive of the final reviewed software in Zenodo, or figshare, or another service, and update this thread with the DOI of the archive? Once we have that available we can process acceptance.

[bblankrot]

Is this OK, @Kevin-Mattheus-Moerman ?

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1241368.svg)](https://doi.org/10.5281/zenodo.1241368)
Thanks @ziotom78 @ysimillides @Kevin-Mattheus-Moerman @arfon for the quick and smooth review!

[bblankrot]

@arfon @Kevin-Mattheus-Moerman - anything else I need to do? The release with the incorporated changes is v0.0.3, archived at https://doi.org/10.5281/zenodo.1241368 .

[Kevin-Mattheus-Moerman]

@bblankrot apologies for the delay. @arfon we are all good to accept here.

[arfon]

@whedon set 10.5281/zenodo.1241368 as archive

[whedon]

OK. 10.5281/zenodo.1241368 is the archive.

[arfon]

@ziotom78, @ysimillides - many thanks for your reviews here and to @Kevin-Mattheus-Moerman for editing this submission ✨

@bblankrot - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00691 :zap: :rocket: :boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00691/status.svg)](https://doi.org/10.21105/joss.00691)

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=

[bblankrot]

no worries @Kevin-Mattheus-Moerman . Thanks everybody!