[REVIEW]: ChooChoo the Checklist tool

[editorialbot]

Submitting author: @lucydot (Lucy Whalley)
Repository: https://github.com/lucydot/ChooChoo
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @ttimbers
Reviewers: @LittleAprilFool, @ggeorg02
Archive: Pending
Paper kind: software

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/e4199f0adb4eaf3e28d5976b25612fb5"><img src="https://jose.theoj.org/papers/e4199f0adb4eaf3e28d5976b25612fb5/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/e4199f0adb4eaf3e28d5976b25612fb5/status.svg)](https://jose.theoj.org/papers/e4199f0adb4eaf3e28d5976b25612fb5)

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

@LittleAprilFool & @ggeorg02, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html. Any questions/concerns please let @ttimbers 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 ✨

Checklists

📝 Checklist for @LittleAprilFool

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1145/3159450.3159548 is OK
- 10.1145/3159450.3159548 is OK
- 10.14786/FLR.V2I1.24 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1186/s12909-022-03632-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (780.5 files/s, 54778.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        24            465              0            886
Python                          12            249            162            676
YAML                             4             96              5            408
TeX                              1              4              0             55
JavaScript                       1              0              0              6
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            43            814            167           2037
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 968

[editorialbot]

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

[ggeorg02]

Review checklist for @ggeorg02

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source code for this software available at the target repository?
• 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?
• Authorship: Has the submitting author (@lucydot) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[arfon]

@xuanxu – looks like @editorialbot is failing to find the correct checklist when starting these reviews:

2023-08-13T07:05:47.372267+00:00 app[web.1]: W, [2023-08-13T07:05:47.372174 #8]  WARN -- : Error calling ReviewerChecklistCommentResponder: GET https://api.github.com/repos/openjournals/jose-reviews/contents/.buffy/templates/reviewer_checklist.md: 404 - Not Found // See: https://docs.github.com/rest/repos/contents#get-repository-content

It is looking for reviewer_checklist.md rather than a learning module or software checklist. I've gone ahead and edited the checklist for @ggeorg02 but this looks like a bug that needs fixing. Any chance you can take a look please?

[ttimbers]

@ggeorg02 - thank-you for your timely review! Did you have any comments to add in addition to what you indicated on the checklist? In particular with regards to the boxes you did not check?

[ttimbers]

@LittleAprilFool - thank-you again for agreeing to review this. Perhaps it got lost in all the information above, but for you to see your reviewer checklist we need to to type @editorialbot generate my checklist in a post in this issue thread. Can you please do this and complete your review? If you can no longer review this, please let us know. Thank-you!

[LittleAprilFool]

Hi Tiffany, sorry I forgot this task since my GitHub notification was not connected to my regular email account. I am working on the review now and will hopefully get it done by this weekends.

[ttimbers]

Many thanks @LittleAprilFool !

[LittleAprilFool]

Review checklist for @LittleAprilFool

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/lucydot/ChooChoo?
• 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?
• Authorship: Has the submitting author (@lucydot) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[ggeorg02]

I have noticed that the installation document lacks detail. I have identified a few minor issues with the instructions. Despite following all the steps, I was unable to get it to work and received an error message(check at the end of my notes). As a result, I was unable to test the tool's features.

---

—> Fork an existing choochoo repository and use or extend objectives/questions/tutorials from an existing ChooChoo project.

I see it to be something not readable, and a messed up site. Please update it.

—>"Click on Copy repository from template"

This was just “Create repository”

—> “ • You are advised to create one ChooChoo repository for each class group. This will allow you to track the progress of each individual class rather than all classes combined.
“

Is there anything that an instructor can do if they want to create 20 class groups? I was thinking about group project scenarios where 3 or 4 students in a class form a group. So, should I manually generate for all the student class groups with the current setup?

—> "Enable Issues"

Just wondering if it might makes sense to mention that it is enabled by default(at least, that was the case when I created it)

—> "Enable Workflows"

This was also enabled by default to me

—> "Enable Github Pages"
“3 Select gh-pages and /(root) in the drop-down menu below Branch.”

I didn’t see gh-pages branch. Should the user create a branch? Provide details please.

—> I went with using secrets.GITHUB_TOKEN
—> When running choochoo build checklists
I get error and nothing is printing
[ggeorg02/testachoo] Fat Controller workflow run

[LittleAprilFool]

Same, I have tried multiple approaches to use this tool, including testing it under the author's example repository: lucydot/ChooChoo-template#37, as well as testing it under my own build: LittleAprilFool/choochoo#1. None of the approaches works as the documentation described.

[lucydot]

Hi @LittleAprilFool and @ggeorg02,

Thanks for agreeing to review and test ChooChoo. I suspect that Github has updated its interface and default settings since I submitted this for review 6 months ago which is why some instructions are out of date (also the wrong link, see below, would not have helped!). I will run through the steps myself and update as necessary, and will confirm here once that is done. Thank you for your patience!

This is actually very good timing for me as will be using it again for my own induction week teaching in a fortnight :)

Please note that you ChooChoo does not allow you to run under someone elses repository unless you are added as a student or instructor (this allows repository admin to control who can participate). Of course, you should be able to run under your own so that is what I will look into.

—> Fork an [existing choochoo repository](https://lucydot.github.io/ChooChoo/instructors/setup/existing.md) and use or extend objectives/questions/tutorials from an existing ChooChoo project.

I see it to be something not readable, and a messed up site. Please update it.

This is a link to the wrong page! Will fix.

Thanks,

Lucy

[lucydot]

Hi @LittleAprilFool and @ggeorg02,

As suspected the problems were related to update of the Github defaults, including permissions (https://github.blog/changelog/2023-02-02-github-actions-updating-the-default-github_token-permissions-to-read-only/). I've made a few commits to the choochoo-template repository which should fix the problems you were having (and to update the docs) but I've not yet had a chance to do a full test of the choochoo functionality to make sure that other aspects are working as expected after gh changes, so could I ask you to hold off until next week when I will have a chance to test myself?

I was a little confused why the automatic testing happening at this repo didn't flag something up via my github notifications, but then realised that these had been disabled after 60 days of inactivity on that repo (as all workflows to update the fork with any choochoo changes and test are scheduled to run daily, so I don't manually change anything there). I'll set myself a reminder to enable the workflows every two months so as to avoid this in future, as a workaround (there may be a neater solution I'm not aware of).

UPDATE: It wasn't the 60 day timeout that caused the problem, it is that the changes to permissions were only applied to new repositories.

[lucydot]

Hello @LittleAprilFool, @ggeorg02 and @ttimbers,

Apologies for my testing to take longer than expected - I have been struggling to balance this with the start of a new academic year and lecturing. Thanks for bearing with me.

I have just completed a thorough run-through and located the issues you found.

• as mentioned above, part of the problem was a change in github_token permissions which was only applied to new repositories (which was why it wasn't caught in automated testing).
• another problem was related to the ubuntu-default used for running github actions. This was recently updated to ubuntu-22.04 so that the specified python version was no longer supported. I've now updated to python-3.11 and tested against this.

I have just run through the functionality outlined in the documentation (starting with instructor setup) - https://lucydot.github.io/ChooChoo/instructors/setup/ - and can confirm it ran as expected.

So hopefully you should not have any problems running through now 🤞 . I also used it during induction week with my second year undergraduate class without hiccups (though they did not use full functionality due to lack of time in schedule - they used checklist tool but did not generate their own question sets).

You may note some changes to documentation - I have adjusted some wording to improve readability.

All the best,

Lucy

[lucydot]

Hi @ttimbers, just checking in on the review; is there anything I can do to help move along?

[lucydot]

Hello, @ttimbers - perhaps @ppxasjsm is free to review this? In the pre-review they indicated they might be available for this.

[ttimbers]

@LittleAprilFool and @ggeorg02 - any chance you could revisit this and take a look at @lucydot 's changes. In particular the issues related to Github defaults, including permissions, and the resulting inability to get it to work?