[REVIEW]: ROSS - Rotordynamic Open Source Software

[whedon]

Submitting author: @raphaeltimbo (Raphael Silva)
Repository: https://github.com/ross-rotordynamics/ross
Version: v0.3.2
Editor: @meg-simula
Reviewer: @srmnitc, @nnadeau
Archive: 10.5281/zenodo.3746582

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7006399ebbe19bfb187a194789c862d7"><img src="https://joss.theoj.org/papers/7006399ebbe19bfb187a194789c862d7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7006399ebbe19bfb187a194789c862d7/status.svg)](https://joss.theoj.org/papers/7006399ebbe19bfb187a194789c862d7)

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

@srmnitc & @nnadeau, 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 @meg-simula know.

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

Review checklist for @srmnitc

Conflict of interest

• 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

• 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 (@raphaeltimbo) 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 @nnadeau

Conflict of interest

• 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

• 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 (@raphaeltimbo) 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. @srmnitc, @nnadeau 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]

Reference check summary:

OK DOIs

- 10.1017/CBO9780511780509 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1002/9780470903704 is OK
- 10.1002/9783527651894 is OK
- 10.1007/978-3-662-09786-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[meg-simula]

@nnadeau @srmnitc Thanks again for agreeing to review. Reviewer checklists have been generated for each you above - please feel free to dig in at will!

[meg-simula]

@srmnitc @nnadeau @raphaeltimbo 👋 Just checking in - how are matters progressing?

[srmnitc]

@meg-simula I took a first look, everything seems to be well documented and easy to review. I hope to finish my first round of review in 2-3 days !

[srmnitc]

@meg-simula @raphaeltimbo I have completed my first round of review. I think the submission already meets most of the review checkpoints and is quite nicely documented with a lot of examples. I only have three main issues - with installation, tests and citations in the paper. I have raised these issues on the repository. The jupyter notebooks are quite helpful, I will also go a bit more into detail in the next one or two days.

[meg-simula]

/ooo March 12 until March 27

[ooo]

👍 Marked @meg-simula as OOO from Thursday, March 12th 2020 to Friday, March 27th 2020. 📆

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[whedon]

Reference check summary:

OK DOIs

- 10.1017/CBO9780511780509 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1115/1.1349417 is OK
- 10.1007/s40430-019-1652-8 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1038/s41592-019-0686-2 is INVALID because of 'https://doi.org/' prefix

[engnadeau]

@arfon @meg-simula @raphaeltimbo we're good to go! good work!

@raphaeltimbo i patched the DOI issue here: petrobras/ross#518

[arfon]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1017/CBO9780511780509 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1115/1.1349417 is OK
- 10.1007/s40430-019-1652-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[raphaeltimbo]

Submitting author: @raphaeltimbo (Raphael Silva)
Repository: https://github.com/ross-rotordynamics/ross
Version: v0.2.0
Editor: @meg-simula
Reviewer: @srmnitc, @nnadeau
Archive: Pending

@meg-simula, with the review process we had to make some modifications to the package and the final version now is v0.3.2. Can we update that information?

[arfon]

👋 @raphaeltimbo - I'll take over this paper from here as I'm not sure about @meg-simula's availability given the COVID-19 stuff going on.

I've read your paper and have a few suggested changes to improve the readability in petrobras/ross#519 .

[arfon]

@whedon set v0.3.2 as version

[whedon]

OK. v0.3.2 is the version.

[arfon]

@raphaeltimbo - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[raphaeltimbo]

@raphaeltimbo - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

@arfon, I have added the software to zenodo: http://doi.org/10.5281/zenodo.3746582

[arfon]

@whedon set 10.5281/zenodo.3746582 as archive

[whedon]

OK. 10.5281/zenodo.3746582 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1017/CBO9780511780509 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1115/1.1349417 is OK
- 10.1007/s40430-019-1652-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1412

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1412, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@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.02120 joss-papers#1413
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02120
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...

[arfon]

@srmnitc, @nnadeau - many thanks for your reviews here and to @meg-simula for editing this submission ✨

@raphaeltimbo - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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.02120/status.svg)](https://doi.org/10.21105/joss.02120)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02120/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02120/status.svg
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This is how it will look in your documentation:

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[raphaeltimbo]

Thanks @arfon and @meg-simula!
And thank you @srmnitc and @nnadeau for the review. It really helped us to improve the paper and the software!