[REVIEW]: feign: a Python package to estimate geometric efficiency in passive gamma spectroscopy measurements of nuclear fuel

[whedon]

Submitting author: @ezsolti (Zsolt Elter)
Repository: https://github.com/ezsolti/feign/
Version: v1.0.0
Editor: @katyhuff
Reviewer: @kellyrowland, @sskutnik
Archive: 10.5281/zenodo.3480082

Status

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Markdown: [![status](https://joss.theoj.org/papers/d6d0fa620abbd1777d73190b1038602a/status.svg)](https://joss.theoj.org/papers/d6d0fa620abbd1777d73190b1038602a)

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

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

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @katyhuff know.

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

Review checklist for @kellyrowland

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 (v1.0.0)?
• Authorship: Has the submitting author (@ezsolti) 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 @sskutnik

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 (v1.0.0)?
• Authorship: Has the submitting author (@ezsolti) 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. @kellyrowland, @sskutnik it looks like you're currently assigned to review 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:

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

2. 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]

👉 Check article proof 📄 👈

[ezsolti]

Hello @kellyrowland, @sskutnik. Thank you for taking on the review. Please consider that I have committed most of the work as "zsolt" and realized this only after like 70 commits, when it was too late to change. Next time I will be more careful:)

[kellyrowland]

Hi @ezsolti , it looks like JOSS requires a code release with a version number matching the one listed here, but there appear to be no releases on the source code repo.

[katyhuff]

@ezsolti : This issue regarding authorship can be helped with some rewriting of history, if you like... https://help.github.com/en/articles/changing-author-info

[katyhuff]

@kellyrowland @ezsolti : Since this will be the "v.1.0.0" release, it is not uncommon for authors to submit to JOSS before the release, and then, after making the edits requested by the reviewers (but not other major edits), make the v.1.0.0 release (since a release must be created for zenodo anyway, which is the last step of the JOSS publication.)

For now, let's assume this review process will end with a DOI that points to a v.1.0.0 release, but that all reviews are conducted at the most recent commit (at the time of submission: 61978385bd1b950ea66a9704572484dc20b93b34 ). @ezsolti This will require that, until acceptance and until after the release, you only make edits to your master branch that were requested by these two JOSS authors. Continuing development can happen in parallel of course, on an experimental branch -- but should not be included in the release, as it will not be included in the review.

[kellyrowland]

Thanks for the clarification @katyhuff !

[ezsolti]

Yes, thank you for the clarification @katyhuff. I am not supposed to change the code (which i havent done), or anything in the repo, like minor typos in the the readme (which i have done, but can go back to the original commit)?

[ezsolti]

Also, I have managed to rewrite the history, thanks for the help!

[katyhuff]

@ezsolti : very minor changes are fine, as are changes related to satisfying the recommendations of the reviewers. It's just that, for cleanliness of the meaning of the review process, major changes shouldn't be incorporated mid-review (unless called for by the review process itself). Don't worry, we try to keep it really quick, and you can always work in another branch to keep your master branch clean.

[kellyrowland]

Looks good to me, I think the proverbial ball is now in the court of @sskutnik .

[katyhuff]

Thanks @kellyrowland !

@sskutnik : I know it's a busy time. Please let us know if you expect this review to take more than a week or so to complete.

[sskutnik]

I've made a few minor comments re: the paper on ezsolti/feign/issues/7

In general, I'd recommend minor revisions, in part for clarity and also to clear up the theory of the efficiency calculation; also to update the references such that they render with fully-locatable citations. Otherwise, I think this looks fine.

[katyhuff]

Thanks @sskutnik ! Excellent first review!

@ezsolti : I agree with Prof. Skutnik regarding clarity. When you feel you've handled these comments (in ezsolti/feign/issues/7 mostly) please let me know (by @-mentioning me in this issue.) and we'll move forward.

[ezsolti]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[ezsolti]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[ezsolti]

@katyhuff : I have tried to address the comments of Prof. Skutnik, and as you see I have also tried to render a new paper based on some comments which did not require further "iterations" (I hope that this update was not against the rules). Unfortunately, one reference still renders strangely. Let's see whether @sskutnik would advise further changes based on the discussion in ezsolti/feign/issues/7 .

[sskutnik]

I think I'm happy with the proposed changes; I'd leave it to @ezsolti whether to include the figure provided in ezsolti/feign#7

Otherwise, I think all of my concerns have been addressed and I would happily recommend this to move forward for publication. (Edit: Forgot to nudge @katyhuff on this; I think I'm satisfied.)

[ezsolti]

@sskutnik : Thinking it over again, i might be on the opinion that the figure in ezsolti/feign#7 or a similar one for more pins should rather be included in the documentation when reasoning why using the random source case is superior to the center case in certain setups. Feels like it would overcomplicate the paper which has already reached the recommended upper limit for length.

[sskutnik]

@ezsolti This seems like a reasonable conclusion. I think the documentation is a reasonable alternative.

[katyhuff]

@ezsolti Thank you for working toward addressing my comments.

Please let me know when you are able to:

• Reduce the jargon in the 2nd paragraph (indeed, throughout the paper, which is already unusually long for a JOSS paper). The F5 tally mention is not the only item that I find problematic from a jargon perspective. Please aim to make clear the high-level functionality and purpose of the software for a diverse, non-specialist audience.
• Make clear, much earlier and more succinctly, a Statement of Need that illustrates the research purpose of the software. (e.g. what problems the software is designed to solve and who the target audience is).

Please note, these are not merely my suggestions, but are requirements at the core of our submission instructions, which can be found here:

https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

[ezsolti]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[ezsolti]

Hello @katyhuff , after reading through couple of more JOSS articles, I saw that some authors directly include a Statement of Need sections, so I tried to go with that. I also dropped the jargon. Please let me know what do you think of the text now?

[katyhuff]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.13182/NT11-135 is OK
- 10.1109/NSSMIC.2017.8533017 is OK
- 10.1016/j.nima.2016.07.032 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[katyhuff]

Thank you @kellyrowland and @sskutnik for your reviews -- we couldn't do this without you.
Thank you @ezsolti for your submission and for engaging actively in the review process! I have looked over the paper, double-checked all the DOI links, and have conducted a high-level review of the code itself. Everything looks ship-shape to me. At this point, please double-check the paper yourself, review any lingering details in your code/readme/etc., and then make an archive of the reviewed software in Zenodo/figshare/other service. Please be sure that the DOI metadata (title, authors, etc.) matches this JOSS submission. If you need to update the version, that's fine, please just let me know if the version in the DOI is different from the version named in the submission. Once that's complete, please update this thread with the DOI of the archive, and I'll move forward with accepting the submission. Until then, now is your moment for final touchups!

[ezsolti]

Thank you @katyhuff !

The DOI for the archive: 10.5281/zenodo.3480082
The version is the same as in this submission!

[katyhuff]

@whedon set 10.5281/zenodo.3480082 as archive

[whedon]

OK. 10.5281/zenodo.3480082 is the archive.

[katyhuff]

@openjournals/joss-eics I believe this is ready for acceptance. Over to you!

[labarba]

@ezsolti — I'm the Associate Editor-in-Chief on rotation this week. I made a few edits on the paper via PR. Unfortunately the diff is not too helpful, because long paragraphs were written on the same source line. The top fix I wanted to enter was an in-text citation that didn't use the right citation syntax. I also removed a few unnecessary "Then" and changed "analyze" to US spelling, plus little things.

[ezsolti]

@labarba Thank you! I have merged your commit.

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.13182/NT11-135 is OK
- 10.1109/NSSMIC.2017.8533017 is OK
- 10.1016/j.nima.2016.07.032 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1025

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1025, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[labarba]

@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.01650 joss-papers#1026
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01650
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...

[labarba]

Congratulations, @ezsolti, your JOSS paper is published! 🚀

Huge thanks to our editor: @katyhuff, and reviewers: @kellyrowland, @sskutnik — your contributions to JOSS are greatly appreciated 🙏

[whedon]

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

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