Joss-reviews: [REVIEW]: libRL: A Python library for the characterization of microwave absorption

[whedon]

Submitting author: @1mikegrn (Michael Green)
Repository: https://github.com/1mikegrn/libRL-package
Version: v1.1.0
Editor: @dfm
Reviewer: @kjappelbaum, @mdoucet
Archive: 10.5281/zenodo.3555457

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/61a4e825e28a34037d0ba03f335a7537"><img src="https://joss.theoj.org/papers/61a4e825e28a34037d0ba03f335a7537/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/61a4e825e28a34037d0ba03f335a7537/status.svg)](https://joss.theoj.org/papers/61a4e825e28a34037d0ba03f335a7537)

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) by leaving comments 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

@kjappelbaum & @mdoucet, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dfm know.

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

Review checklist for @kjappelbaum

Conflict of interest

• [X] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@1mikegrn) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [X] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [X] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @mdoucet

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@1mikegrn) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @kjappelbaum, @mdoucet it looks like you're currently assigned to review 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[1mikegrn]

Hey @matthewturk, just hoping to get an update on some sort of timetable we can expect for conducting the peer-review. I'm getting ready to submit a set of high-impact research manuscripts and I'd like to be able to reference this manuscript therein for more coverage of the software. Thanks :)

[matthewturk]

@1mikegrn I think I might have been autocompleted by mistake - or I hope so! This paper is news to me, I'm afraid. :)

[dfm]

I think you mean @mdoucet!

@mdoucet: Can you let us know what sort of time frame you need to finish going through the checklist? Thanks!

[1mikegrn]

@matthewturk haha ya, oops. Sorry about that!

[mdoucet]

@dfm Sorry for the delay. It's on my to-do list for this week.

[1mikegrn]

@mdoucet no worries, appreciate the update :)

[dfm]

@mdoucet: Any updates on this? Please let me know if you have any questions!

[mdoucet]

I'm just done with my review. Sorry for the delay.

[dfm]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[dfm]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.jmat.2019.07.003 is OK
• 10.1016/j.nanoms.2019.02.001 is OK
• 10.1016/j.jmat.2018.12.005 is OK
• 10.1109/TMTT.1971.1127446 is OK
• 10.1016/j.matdes.2010.02.019 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[dfm]

@kjappelbaum, @mdoucet: I see that you have completed the checklist - thanks!! Do you have anything else you would like to add or any final recommendations?

@1mikegrn: Looking good! I can't seem to track down that Naito (1969) reference. Is it available online anywhere? Either way, can you now generate a new Zenodo release where the title and author list match this submission. Once you do that, can you post the new DOI and version number to this thread?

[dfm]

Also: can you all take a last quick look at the paper to make sure that the current version looks good?

[1mikegrn]

Ya it took me about a month to track it down myself, ended up finding it though a university in Tel Aviv who sent me a pdf of their copy; it's the original paper the mathematics is legible, but the text is in Japanese.

About the thickness of the ferrite absorption wall - Naito.pdf

Also, what exactly needs to go in the Zenodo release? is it the entire package or just the .md file which points to the repository?

[dfm]

Thanks! The archive should be a snapshot of the full source. The easiest way to do it is following this guide: https://guides.github.com/activities/citable-code/

[1mikegrn]

Thanks, that really helped :)

Here's the DOI:

10.5281/zenodo.3555457

[dfm]

@whedon set 10.5281/zenodo.3555457 as archive

[whedon]

OK. 10.5281/zenodo.3555457 is the archive.

[dfm]

@whedon set v1.1.0 as version

[whedon]

OK. v1.1.0 is the version.

[1mikegrn]

Just a follow-up, but is there anything else that needs to be done before pushing this to production?

[danielskatz]

Once @dfm tells @openjournals/jose-eics that this is ready to publish, one of us (this week, me) will perform the final steps.

[dfm]

@kjappelbaum, @mdoucet: Can you please confirm that you are satisfied with the changes and recommend this submission for acceptance? Thanks!

[mdoucet]

@dfm all good!

[kjappelbaum]

@dfm I'm also fine with it.

[dfm]

@kjappelbaum, @mdoucet: Great. Thank you for your contributions to this review!!

[dfm]

Pinging @openjournals/joss-eics to say that this is ready for the final processing.

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.jmat.2019.07.003 is OK
• 10.1016/j.nanoms.2019.02.001 is OK
• 10.1016/j.jmat.2018.12.005 is OK
• 10.1109/TMTT.1971.1127446 is OK
• 10.1016/j.matdes.2010.02.019 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1150

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1150, 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]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1151
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01868
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[danielskatz]

Thanks to @kjappelbaum & @mdoucet for reviewing, and to @dfm for editing!

And congratulations to @1mikegrn and co-author!

[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 snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01868/status.svg)](https://doi.org/10.21105/joss.01868)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01868">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01868/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01868/status.svg
   :target: https://doi.org/10.21105/joss.01868

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: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss