[REVIEW]: Reorient: A Web tool for reorienting and cropping MRI data.

[whedon]

Submitting author: @katjaq (Katja Heuer)
Repository: https://github.com/neuroanatomy/reorient
Version: v1.0.0
Editor: @oliviaguest
Reviewer: @sneakers-the-rat, @pauldmccarthy
Archive: 10.5281/zenodo.4165153

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Markdown: [![status](https://joss.theoj.org/papers/bb072e58308a3fa006d424ca23851dbd/status.svg)](https://joss.theoj.org/papers/bb072e58308a3fa006d424ca23851dbd)

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

@sneakers-the-rat & @pauldmccarthy, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @sneakers-the-rat

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 (@katjaq) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 @pauldmccarthy

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 (@katjaq) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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. @sneakers-the-rat, @pauldmccarthy it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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]

PDF failed to compile for issue #2670 with the following error:

Can't find any papers to compile :-(

[oliviaguest]

Hi all! 👋 Thank you so much, @sneakers-the-rat, @pauldmccarthy for accepting to review this. Please read the instructions above. Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread so we can all keep track of them. 🌸

For an example of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

[oliviaguest]

@whedon generate pdf from branch joss-paper-branch

[whedon]

Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[oliviaguest]

@whedon generate pdf from branch joss-paper-branch

[whedon]

Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[oliviaguest]

Hey @sneakers-the-rat, @pauldmccarthy — could you please let us know when your reviews might be ready by?

[pauldmccarthy]

Hi @oliviaguest, I'm aiming to complete my review in the next 7 days.

[oliviaguest]

@whedon remind @pauldmccarthy in 2 weeks

[whedon]

Reminder set for @pauldmccarthy in 2 weeks

[sneakers-the-rat]

yes give me the same - setting reminder for 10/7

[oliviaguest]

@whedon remind @sneakers-the-rat in 2 weeks

[whedon]

Reminder set for @sneakers-the-rat in 2 weeks

[oliviaguest]

@sneakers-the-rat you got it! ✨

[sneakers-the-rat]

may need an extra day or two but i am with ya

[sneakers-the-rat]

nvm just finished <3

loved it! very straightforward to review, tool worked as expected and was quite intuitive. I made a few suggestions (wasn't sure where to put them) and raised a few issues but nothing that would prevent me from accepting the paper according to the checklist & claims in the paper.

Olivia let me know if i've messed anything up/need to do anything further. Katja & Roberto, thanks for this tool!

[oliviaguest]

@sneakers-the-rat Amazing! Can you do me a favour and move what you wrote into a comment in the issue as opposed to into the OP? I'd prefer it if everything to-be-addressed was a comment here to make it easier to keep track of. ☺️

[oliviaguest]

PS: @sneakers-the-rat if you need examples/inspiration, check: #2285 and #2348. 🌼

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[oliviaguest]

@katjaq @r03ert0 can you deposit the code on zenodo or similar and post the DOI here, please?

[oliviaguest]

@katjaq @r03ert0 Has neuroanatomy/reorient/issues/9 been addressed? Can you close if so.

[katjaq]

Hello,
issue #9 has bee addressed and is now closed. Thanks.

The code is deposited on Zenodo under DOI 010.5281/zenodo.4165153

Thank you!

[oliviaguest]

@whedon set 010.5281/zenodo.4165153 as archive

[whedon]

010.5281/zenodo.4165153 doesn't look like an archive DOI.

[oliviaguest]

@whedon set 10.5281/zenodo.4165153 as archive

[whedon]

OK. 10.5281/zenodo.4165153 is the archive.

[oliviaguest]

@katjaq @r03ert0 great! can you also change the title of the zenodo repo to the same as the JOSS paper, please? ☺️

Oh, and is the version number at the top correct? If not, what's the current version?

[r03ert0]

Done! I updated the title to match that of the paper.
The DOI which appears in the Zenodo badge in reorient's repo is automatically set to the one of the latest version (10.5281/zenodo.4165154).
The DOI Katja sent is the umbrella DOI for all versions (10.5281/zenodo.4165153). It's better to use that one, no?

[oliviaguest]

@katjaq @r03ert0 I mean this version here in the OP, get me?

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #2670 with the following error:

Can't find any papers to compile :-(

[oliviaguest]

@whedon accept from branch joss-paper-branch

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.cortex.2019.04.011 is OK
- 10.1016/j.neuron.2019.12.023 is OK
- 10.5281/ZENODO.3402456 is OK
- 10.5281/ZENODO.3937147 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#1887

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1887, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-paper-branch 

[arfon]

@whedon accept deposit=true from branch joss-paper-branch

[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.02670 joss-papers#1888
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02670
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]

@sneakers-the-rat, @pauldmccarthy - many thanks for your reviews here and to @oliviaguest for editing this submission ✨

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

[whedon]

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

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