Joss-reviews: [REVIEW]: sigmajs: An R htmlwidget interface to the sigma.js visualization library

[whedon]

Submitting author: @JohnCoene (Jean-Philippe Coene)
Repository: https://github.com/JohnCoene/sigmajs
Version: v0.1.1
Editor: @arfon
Reviewer: @strengejacke, @jankatins
Archive: 10.5281/zenodo.1342765

Status

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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) 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

@strengejacke & @jankatins, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Review checklist for @strengejacke

Conflict of interest

• [x] 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

• [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] Version: Does the release version given match the GitHub release (v0.1.0)?
• [x] Authorship: Has the submitting author (@JohnCoene) 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

• [ ] 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jankatins

Conflict of interest

• [x] 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

• [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?
• [ ] Version: Does the release version given match the GitHub release (v0.1.0)?
• [x] Authorship: Has the submitting author (@JohnCoene) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @strengejacke, it looks like you're currently assigned as the reviewer for 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[strengejacke]

The GitHub release is already version 0.1.1, while the submitted version for review is 0.1.0 - @arfon how to deal this? Should John resubmit or edit the submission, or should we just proceed with our review?

[arfon]

The GitHub release is already version 0.1.1, while the submitted version for review is 0.1.0 - @arfon how to deal this? Should John resubmit or edit the submission, or should we just proceed with our review?

If it's OK with @JohnCoene, it probably makes sense to review the latest code and just update the JOSS submission (I can do that here).

[JohnCoene]

@arfon, @strengejacke Sure, can do.

[strengejacke]

I hope to finish the last parts of my review today, as I'm on holiday tomorrow and be back after 29th of July.

[strengejacke]

Ok, I have finished my review so far. @JohnCoene please look at the issues I raised. If you have any questions, don't hesitate to ask. I'm out of office now until July 29th, so will, if at all, only sporadically read and response to mails until then.

[jankatins]

I currently can't get output in neither jupyter notebook nor in Rstudio. I opened https://github.com/JohnCoene/sigmajs/issues/6 to track the issue.

[strengejacke]

From my perspective, just a minor issue left (statement of need in readme-file, see https://github.com/JohnCoene/sigmajs/issues/3).

[jankatins]

From my perspective, all points are checked in master (the statement of need is added to the readme). I assume the version requirement in this issue can be fixed somehow, but it needs a new release of sigmajs first?

Functions can be piped, referring to the magrittr package [@magrittr] pipe operator (%>%), to build the desired graph.

This sounds a bit strange (to my german-english ears, so take it with bit of care): "Functions can be piped (with %>% from the magrittr package [@magrittr]) to build the desired graph" or "Functions can be piped with the standard tidyverse pipe operator %>% [@magrittr] to build the desired graph"?

[strengejacke]

All my raised issues have been addressed adequately, too. I recommend to accept the paper.

[arfon]

@JohnCoene - do you want to make a final release based on the changes from this review?

[JohnCoene]

@arfon yes I do. Thank you very much!

[JohnCoene]

@arfon Updated version https://github.com/JohnCoene/sigmajs/commit/7aa86886df65e58a82d7cb983c3db29e10fd1565, I believe the dev (.9000) did not meet the requirements: sigmajs is now on 0.1.1.

[arfon]

@JohnCoene - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[JohnCoene]

@arfon I hope I got this right, it's the first time I do this.

[arfon]

@whedon set 10.5281/zenodo.1342765 as archive

[whedon]

OK. 10.5281/zenodo.1342765 is the archive.

[arfon]

@strengejacke, @jankatins - many thanks for your reviews here!

@JohnCoene - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00814 :zap: :rocket: :boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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[JohnCoene]

Thank you for your time @arfon, @strengejacke, and @jankatins!