Joss-reviews: [REVIEW]: Gramm: grammar of graphics plotting in Matlab

[whedon]

Submitting author: @piermorel (Pierre Morel)
Repository: https://github.com/piermorel/gramm
Version: v2.23
Editor: @cMadan
Reviewer: @trallard
Archive: 10.5281/zenodo.1188423

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

@trallard, 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 @cMadan know.

### 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 (v2.23)?
• [x] Authorship: Has the submitting author (@piermorel) 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. @trallard it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00568/joss.00568/10.21105.joss.00568.pdf

[trallard]

Currently doing the review of gramm and have a couple of things to raise @piermorel:

Documentation

• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally, these should be handled with an automated package management solution.

Even though the instructions allow for correct installation they might be a bit dry? cryptic? for those that have never added 3rd party code to their MATLAB path (issue here)

• [ ] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?

I could not find any tests in the repository so I was wondering if you'd considered adding any
(issue here)

• [ ] 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

It would be good to add some contributing guidelines to the repository, this encourages people a lot to get involved in the improvement of packages they use / love (issue here)

Software paper

• [ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Just found out that Wilkinson's _'The Grammar of Graphics'_ has a DOI http://dx.doi.org/10.1007/978-1-4757-3100-2.

[trallard]

Documentation

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

I think the summary of the software paper makes an excellent point on why gramm is needed and how it offers a better visualization environment for MATLAB users. This could probably be incorporated to the gramm repository (issue here)

[piermorel]

Thank you for these suggestions @trallard. I just adressed all these comments in commit https://github.com/piermorel/gramm/commit/f74c06deb4944d41509667a102f7cf9b162351eb and closed the corresponding issues. Do not hesitate to reopen them if not satisfactory. The latest commit https://github.com/piermorel/gramm/commit/efaa6f7b4a8b397532b909a581b3641ce05cd196 also adds the doi for "grammar of graphics".

[trallard]

@piermorel great! I think these edits are great and they help users understand why they'd want to use gramm and how to contribute to it

I also created a PR. It is mainly around re-structuring the Readme a bit. Feel free to merge it or not shall you feel it makes sense.

[trallard]

@cMadan would it be possible to re-generate the pdf with the newly added DOI?

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[trallard]

@cMadan I think we can consider the revision of the package completed for the JOSS submission. @piermorel has sorted out the issues identified and I am sure this package will continue to evolve since it seems to be already well accepted by the MATLAB community.

What are the next steps to be followed?

[cMadan]

@trallard, great, thank you for your thorough review!

@brian-lau, have you had a chance to test the submission?

[cMadan]

@brian-lau, thank you for your interest, but I think I'll go ahead and accept the submission as-is now.

@trallard, thank you again for your review!

@piermorel, can you provide the DOI for an archived version of the project's code? (I.e., archive the current codebase on Zenodo or FigShare). After that we'll be all set to accept!

[trallard]

You are very welcome @cMadan it has been an absolute pleasure to review this package

[piermorel]

Thank you @cMadan, and thank you @trallard for the useful comments.

Gramm is already on Zenodo since several releases. I think Zenodo provides this DOI that allows to track new releases automatically: https://doi.org/10.5281/zenodo.594625 . If there is the need to provide the doi from the reviewed version, the latest release on zenodo corresponds to that https://doi.org/10.5281/zenodo.1188423 .

[cMadan]

@whedon set 10.5281/zenodo.1188423 as archive

[whedon]

OK. 10.5281/zenodo.1188423 is the archive.

[cMadan]

@piermorel, perfect, we're all set then!

@arfon, can you do the honors?

[arfon]

@trallard - many thanks for your review here and to @cMadan for editing this submission ✨

@piermorel - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00568 ⚡️ 🚀 💥

[whedon]

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

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