[REVIEW]: DearScholar: A mobile application to conduct qualitative and quantitative diary research

[whedon]

Submitting author: @pmkruyen (Peter Kruyen)
Repository: https://github.com/pmkruyen/dearscholar.git
Version: v1.0.49
Editor: @cMadan
Reviewer: @gcdeshpande, @kinow
Archive: 10.5281/zenodo.4267938

⚠️ 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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1896b88f26b987b9c7a07035751afd7b"><img src="https://joss.theoj.org/papers/1896b88f26b987b9c7a07035751afd7b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1896b88f26b987b9c7a07035751afd7b/status.svg)](https://joss.theoj.org/papers/1896b88f26b987b9c7a07035751afd7b)

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

@gcdeshpande & @kinow, 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 @cMadan know.

✨ 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 @gcdeshpande

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 (@pmkruyen) 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 @kinow

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 (@pmkruyen) 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. @gcdeshpande, @kinow 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]

Reference check summary:

OK DOIs

- 10.1111/puar.12388 is OK
- 10.1146/annurev.psych.54.101601.145030 is OK
- 10.5465/amj.2011.64869103 is OK
- 10.1108/13522750510592427 is OK
- 10.1080/10967494.2016.1169066 is OK
- 10.1037/13619-016 is OK
- 10.1177/104973200129118543 is OK
- 10.1111/j.2044-8325.2011.02047.x is OK
- 10.1080/01973533.2015.1049349 is OK
- 10.1027/1866-5888/a000009 is OK
- 10.1080/1359432X.2013.752247 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[pmkruyen]

Hi @cMadan thanks for starting the review; and @gcdeshpande and @kinow, thanks again for reviewing. I am looking forward to your feedback.

The repro contains two versions as you will see (two branches). It would be great if you could review the developer branch containing the last updates.

Also, I see that I filled out that we are at version 1.48 above -oops- that should be 1.048 (stable release) or 1.0.49 (developer release). Hope that does not cause any troubles.

[kinow]

Looking at this item now, under documentation

Installation: Does installation proceed as outlined in the documentation?

pmkruyen/dearscholar#18

[cMadan]

@pmkruyen, thanks for pointing out the version number issue. I'll update it to 1.048 for now, but usually the accepted version of the software is a later version number than the submitted one (e.g., changes in response to the reviewers' comments), so I will update it again when we're closer to acceptance.

[cMadan]

@whedon set 1.048 as version

[whedon]

OK. 1.048 is the version.

[kinow]

Hi @cMadan , thanks for assigning me as reviewer here. I will take up your offer, when you said I could ask if I had questions. I hope these are not too silly.

Q1/ The check list and the linked documentation are great! I can see the performance check box can be left unchecked if there are no claims of performance. What if the project doesn't have installation instructions, or tests? I asked the project maintainer to add those and he is working on that now. But what if the author decides those are not important? Then I just leave the checkbox unchecked and say that I have finished my review?

Q2/ When I was reviewing the readme.md file of the project, I found some markdown syntax issues. Normally I use GitHub UI to quickly send a PR whenever if find these in other projects. But since I am a reviewer of the project's paper, I wasn't sure if that would be alright? Would that be OK?

Q3/ After the review is done, should I avoid contributing to projects of papers I reviewed?

Thanks!
Bruno

[cMadan]

Hi @kinow,

Q1. For publication at JOSS, we would require install instructions and some form of testing. (E.g., automated tests are not required, but some minimal example of input/output would be.) As is the case here, then we would then wait for the author to work on those aspects of the project, and the review is 'on-going' until the project is suitable for publication. So, it's not just a 'one-pass and done' situation, but more of periodic back-and-forth as the authors attempt to address your comments.

Q2. Go ahead, that's perfectly fine! (And probably would help speed the process along.)

Q3. It's generally viewed that contributions you make as a reviewer do not count towards co-authorship on the project. But, should you continue to contribute to the project after the JOSS review process, then it may make sense for you to be a co-author on subsequent publications that come after the JOSS paper, and would involve a discussion with the project's authors accordingly.

I hope that helps clarify things!

[kinow]

Thanks a lot @cMadan !

[pmkruyen]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[pmkruyen]

Hi @gcdeshpande and @kinow,

To give a short update:

• Because the App Store approved version 1.0.48 of the app, I merged the developer and master branch in the GitHup repro to keep things manageable. The GitHub version is 1.0.49. Both versions are similar except that version 1.0.49 offers researchers the possibility to change the numbers of survey modules while version 1.0.48 does not offer this possibility. I am planning to upload version 1.0.49 soon to the stores because of requirements for my current research projects, taking your feedback into account.

• Over the weekend, I wrote down installation instructions (see 'Installation' section, in Readme.md. Hope these instructions are clear and work :)[also see issue 18 in the project repro].

• Will search for ways to include some (automatic) testing for the server and the app.

Best,
Peter

[cMadan]

@gcdeshpande, just thought I'd check in, how are things going?

[kinow]

Followed new build instructions written by @pmkruyen , successfully built and executed DearScholar locally. Other users should be able to reproduce it, given they follow the instructions and there are no packages removed from NPM/DockerHub. 👍 thanks @pmkruyen !

[kinow]

We now have documentation on how to build DearScholar, scripts in-place that help others to build in their own environments, and also simple unit tests and some functional tests in BrowserStack (@pmkruyen is writing even more tests now 🎉 ).

I am done with the review, the DearScholar app passes all the items in the checklist. I've left performance unchecked as there are no claims about it in the paper, but I will say I didn't notice any performance issues using it locally 👍

@cMadan let me know if I have any other steps in the review process that I need to complete. Otherwise, I think I have finished reviewing my first JOSS paper? 😁

And thanks Peter for the help and patience with the review. And also for the fun and learning experience while working on the issues together.

Cheers
Bruno

[cMadan]

@kinow, that sounds great, yes, you're all done here. Thank you for the thorough review!

@pmkruyen, I have sent an email to @gcdeshpande to remind him about this review.

[kinow]

Thanks @cMadan !

[pmkruyen]

Hi @cMadan,

I really appreciated @kinow's constructive and pleasant input, questions, and help (he even constructed a docker file for the project to automate the installation). He helped me to push the project to another level! I learned a lot from him and hope we stay in touch and he stays connected to the project in some way. 👍

Peter

PS. And thanks for sending a reminder to @gcdeshpande, hope to hear from him soon.

[kthyng]

@cMadan Why is the performance checkbox unchecked for both reviewers?

[kthyng]

Looks like the zenodo doi wasn't copied correctly before, so I'll fix it

[kthyng]

@whedon set 10.5281/zenodo.4267938 as archive

[whedon]

OK. 10.5281/zenodo.4267938 is the archive.

[kthyng]

@pmkruyen Is it convention to have "prof dr" and "dr" not capitalized?

[kthyng]

Note to myself that the version is up to date, Zenodo archive looks good, and paper is good other than the question above. Waiting to hear back about the capitalization and the unchecked boxes.

[kinow]

@cMadan Why is the performance checkbox unchecked for both reviewers?

Ops, sorry @kthyng ! Checked it now. There are no claims about performance in the paper. Also, I tested it locally (and also briefly against the server with automated tests) and found no performance issues 👍

[pmkruyen]

Hi @kthyng,

Is it convention to have "prof dr" and "dr" not capitalized?

Good point. In the Netherlands, this is the convention I now see that in the English language, it is always Prof. Dr. I changed the text accordingly.

the unchecked boxes
As @kinow noted I have no specific performance claims.

Best,
Peter

[pmkruyen]

@whedon generate pdf

[whedon]

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

[pmkruyen]

@whedon generate pdf

[whedon]

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

[kthyng]

Good point. In the Netherlands, this is the convention I now see that in the English language, it is always Prof. Dr. I changed the text accordingly.

@pmkruyen At least in the U.S. we don't use "Dr Prof", just "Dr". But, you can specify however is appropriate for you, I think.

Thanks @kinow!

@gcdeshpande Can you verify that you are satisfied with this JOSS submission and check off the performance box in your review?

[cMadan]

@kthyng, I figured it's better to not 'enforce' US norms on titles, so had left that as-is. As for the performance checkbox, I was fine with it unchecked as no performance claims were made, though functionality was obviously assessed. @gcdeshpande signed off in comment #2506 (comment). (Part of why I'm responding like this is that @gcdeshpande doesn't always check Github regularly and I often had to follow up via email to prompt responses here.)

[danielskatz]

👋 @gcdeshpande - If there are no performance claims, the box should then be checked, as it says "If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)"

[gcdeshpande]

@danielskatz @kthyng @cMadan,
I just checked performance checkbox... I am satisfied with this JOSS submission.

[cMadan]

@gcdeshpande, great, thanks for following up with this last step!

[kthyng]

Ok looks good to go!

[kthyng]

@kthyng, I figured it's better to not 'enforce' US norms on titles, so had left that as-is. As for the performance checkbox, I was fine with it unchecked as no performance claims were made, though functionality was obviously assessed. @gcdeshpande signed off in comment #2506 (comment). (Part of why I'm responding like this is that @gcdeshpande doesn't always check Github regularly and I often had to follow up via email to prompt responses here.)

I agree either way is fine now that I know that was following some convention anyway. I'll assume the author doesn't care too much either way and finish this up now!

[kthyng]

@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.02506 joss-papers#1925
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02506
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...

[kthyng]

Congrats on your new publication @pmkruyen! Thanks to editor @cMadan and reviewers @gcdeshpande and @kinow for your time and expertise!! 🎉 🎉

[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.02506/status.svg)](https://doi.org/10.21105/joss.02506)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02506">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02506/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02506/status.svg
   :target: https://doi.org/10.21105/joss.02506

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[pmkruyen]

Thanks @cMadan, @kinow, @gcdeshpande, and @kthyng for your time, help and feedback. This review process was a super transparent and nice experience, I learned a lot too (though I missed some nights of sleep solving @kinow's issues 😂👍) . Hope now that other researchers will start using DearScholar in their own projects 😁. All the best! Peter