Joss-reviews: [REVIEW]: CoralP: Flexible visualization of the human phosphatome

[whedon]

Submitting author: @dphansti (Douglas Phanstiel)
Repository: https://github.com/PhanstielLab/coralp
Version: v1.0.1
Editor: @majensen
Reviewer: @daissi, @stulacy
Archive: 10.5281/zenodo.3560845

Status

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Markdown: [![status](https://joss.theoj.org/papers/3fd2226fa440647b187de756beb21c65/status.svg)](https://joss.theoj.org/papers/3fd2226fa440647b187de756beb21c65)

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

@daissi & @stulacy, 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 @majensen know.

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

Review checklist for @daissi

Conflict of interest

• [x] 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

• [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] Contribution and authorship: Has the submitting author (@dphansti) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @stulacy

Conflict of interest

• [x] 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

• [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] Contribution and authorship: Has the submitting author (@dphansti) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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. @daissi, @stulacy it looks like you're currently assigned to review 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:

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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]

:point_right: Check article proof :page_facing_up: :point_left:

[stulacy]

Hi!

Could you please clean up some of the typos in the paper, such as: 'inlcuding', the odd symbol in the first sentence of Methods, and capitalising 'JavaScript'.
Also, the first two sentences in Methods are somewhat duplicated.

[dphansti]

@stulacy Thanks for finding these issues. We have corrected those typos and made several other tiny edits to improve clarity and accuracy.

[daissi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[majensen]

@daissi, @stulacy - how are the checks coming? Can I ask you to check off or create issues for @dphansti for these over the next week? Let me know a timeline that works for you.

[daissi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[daissi]

@daissi, @stulacy - how are the checks coming? Can I ask you to check off or create issues for @dphansti for these over the next week? Let me know a timeline that works for you.

Everything is fine from my side! :thumbsup:

[stulacy]

The only thing left I need to do is try and run the package locally which I
will try and complete tonight.

The only thing I'm unsure about is how to assess the "Automated Tests"
point, since this is a web-app rather than a package interfaced with via an
API. Is this criteria not valid for web-apps or should they still have some
sort of testing procedure?

On Wed, 13 Nov 2019 at 09:33, Dylan Aïssi [e-mail] wrote:

@daissi https://github.com/daissi, @stulacy https://github.com/stulacy

• how are the checks coming? Can I ask you to check off or create issues
  for @dphansti https://github.com/dphansti for these over the next week?
  Let me know a timeline that works for you.

Everything is fine from my side! 👍

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[stulacy]

I've gone through the remaining points and am happy that the submission meets them all, although I still am unsure how to handle the Automated Tests criteria as mentioned above. Any thoughts @majensen ?

[majensen]

Thanks @stulacy - I will have a look and make a rec within a couple days. (Sorry I have been slow to respond for a couple weeks)

[majensen]

@dphansti - per @stulacy comments: I agree that there should be some tests associated with the R code (the JS is less critical IMO). I wish I had time to help you stub these out, but for now let me suggest you look at https://testthat.r-lib.org/ - this looks really easy to use, and is a common testing system in other R-based pubs in JOSS. Here's an example : https://github.com/junbinzhao/FluxCalR/tree/master/tests
I can provide more advice if needed - but I wanted to get you looking at this.
thanks!

[dphansti]

@daissi, @stulacy, @majensen We have added unit tests using the testthat package for key functions, as well as an application-level test using the shinytest package that emulates simple tasks in the user interface and compares with pre-validated results. We also configured Travis CI to automatically run these tests with every change and report failures.

[stulacy]

Great, thanks @dphansti . I've completed my review.

[majensen]

@dphansti thanks very much for that additional work. Thanks @stulacy and @daissi for the review!
Next step is to create a public archive of the software with a DOI. @dphansti, you can use Zenodo for this purpose, or other service you prefer. If you're unfamiliar with this process, have a look at https://github.com/openjournals/joss-reviews/issues/1839#issuecomment-560048729 for a brief tutorial. Once this is done, please report the DOI back here.
thanks again

[dphansti]

@majensen Done. Here is the doi 10.5281/zenodo.3560845

[majensen]

@whedon set 10.5281/zenodo.3560845 as archive

[whedon]

OK. 10.5281/zenodo.3560845 is the archive.

[majensen]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.

[majensen]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[majensen]

@openjournals/joss-eics this paper is recommended for publication. Please initiate final checks- thanks!

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.febslet.2012.05.008 is OK
• 10.1109/TVCG.2011.185 is OK
• 10.1038/nrd773 is OK
• 10.7717/peerj.126 is OK
• 10.1042/BJ20061548 is OK
• 10.1086/422827 is OK
• 10.1126/scisignal.aag1796 is OK
• 10.1038/msb.2010.52 is OK
• 10.1111/febs.12000 is OK
• 10.1074/jbc.M505159200 is OK
• 10.1016/j.cels.2018.07.001 is OK
• 10.1111/j.1742-4658.2008.06250.x is OK
• 10.1096/fj.02-1212rev is OK
• 10.1038/nrc1837 is OK
• 10.1186/s12859-016-1433-7 is OK
• 10.1126/science.1075762 is OK
• 10.1038/nrm2039 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1148

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1148, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1149
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01837
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[danielskatz]

Thanks to @daissi & @stulacy for reviewing, and @majensen for editing, and congratulations to @dphansti and co-authors!

[whedon]

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

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