[REVIEW]: RHEOS - A Julia package for Rheology Data Analysis.

[whedon]

Submitting author: @akabla (Alexandre Kabla)
Repository: https://github.com/JuliaRheology/RHEOS.jl
Version: v0.9.1
Editor: @jedbrown
Reviewer: @adambeall, @gbruer15, @HaoZeke
Archive: 10.5281/zenodo.3458310

Status

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Markdown: [![status](https://joss.theoj.org/papers/553250d815e1990db1b89c742854c71a/status.svg)](https://joss.theoj.org/papers/553250d815e1990db1b89c742854c71a)

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

@adambeall & @gbruer15 & @HaoZeke, 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 @jedbrown know.

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

Review checklist for @adambeall

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?
• Contribution and authorship: Has the submitting author (@akabla) 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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 @gbruer15

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?
• Contribution and authorship: Has the submitting author (@akabla) 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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 @HaoZeke

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?
• Contribution and authorship: Has the submitting author (@akabla) 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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. @adambeall, @gbruer15, @HaoZeke 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 😿

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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 📄 👈

[jedbrown]

@adambeall, @gbruer15, @HaoZeke 👋 Welcome and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the RHEOS.jl repository). I'll be watching this thread if you have any questions.

[akabla]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[akabla]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[moustachio-belvedere]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[adambeall]

Thank you for the opportunity to review. I have enjoyed trying out RHEOS and think that it is accessible, the examples hosted in the repository nicely demonstrate its functionality and the documentation is thorough. RHEOS should be useful for researchers from a range of disciplines teaching and forward modelling a variety of linear viscoelastic rheologies, as well as fitting experimental data (the Bonfanti et al., 2019 demonstration is impressive).

Thanks to the authors for making the minor recommended changes. While issue 43 is still open, I will be unavailable for the next week and don’t want to hold up the review, so I have completed the checklist and recommend acceptance after the issue is closed.

[akabla]

Thank you so much Adam for your support and all your input and comments throughout. We will address issue 43 very soon - you made a good point indeed, and it should be straight-forward to address.

[HaoZeke]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1137/141000671 is OK
- 10.1101/543330 is OK
- 10.1016/j.mechmat.2013.09.017 is OK
- 10.1101/565614 is OK
- 10.1017/CBO9780511626722 is OK
- 10.1122/1.5025622 is OK
- 10.1122/1.5018715 is OK

MISSING DOIs

- https://doi.org/10.1115/1.3424077 may be missing for title: Creep and Relaxation of Nonlinear Viscoelastic Materials: With an Introduction to Linear Viscoelasticity

INVALID DOIs

- None

[gbruer15]

I've finished my review and recommend accepting this submission, pending issue #43. Other than that issue, the software's documentation is in a good, user-friendly state, and I believe this package is a very useful contribution to rheology.

[HaoZeke]

I have completed my review @jedbrown, and as soon as JuliaRheology/RHEOS.jl#43 is closed satisfactorily, I recommend this for publication. RHEOS is very well documented and easily extensible, it's really well structured and addresses an existing gap in the rheology community. Glad to have been introduced to it, and thanks for addressing all minor changes promptly, @akabla.

[alebonfanti]

Many thanks @adambeall @gbruer15 @HaoZeke for all your comments. They have improved the quality of our work. Just to let you know that we have just closed the final issue JuliaRheology/RHEOS.jl#43. Thank you again for your work.

[moustachio-belvedere]

Many thanks from me too @adambeall @gbruer15 @HaoZeke for all your valuable feedback and being so efficient in working through everything. We are very grateful.

[akabla]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[akabla]

Dear Jed @jedbrown,

here is the submission doi:
10.5281/zenodo.3458310

Many thanks for your help editing this paper!

[jedbrown]

@akabla Please edit the author info on Zenodo to match the paper. (Kyle and myself should not be authors.) Looks good otherwise and we're ready to accept.

[jedbrown]

@whedon set v0.9.1 as version

[whedon]

OK. v0.9.1 is the version.

[akabla]

Thanks @jedbrown for spotting this. It should be fixed now.
https://doi.org/10.5281/zenodo.3458310

[jedbrown]

@whedon set 10.5281/zenodo.3458310 as archive

[whedon]

OK. 10.5281/zenodo.3458310 is the archive.

[jedbrown]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#976

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#976, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[jedbrown]

@openjournals/joss-eics This paper is now accepted; over to you.

[danielskatz]

Thanks @jedbrown - will process shortly

(and a minor point on the terminology - it's not accepted yet, but will be once the final processing is done)

[danielskatz]

Thanks to @adambeall & @gbruer15 & @HaoZeke for reviewing and to @jedbrown 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.01700 joss-papers#977
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01700
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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[moustachio-belvedere]

Thanks very much for editing @jedbrown .

And thankyou @danielskatz for finalizing the process.

The entire review process has been very valuable to us.