Comments (20)
@xuanxu β 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?
from jose-reviews.
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
from jose-reviews.
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
from jose-reviews.
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
from jose-reviews.
Wordcount for paper.md
is 968
from jose-reviews.
ππ Download article proof π View article proof on GitHub π π
from jose-reviews.
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)?
from jose-reviews.
@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?
from jose-reviews.
@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!
from jose-reviews.
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.
from jose-reviews.
Many thanks @LittleAprilFool !
from jose-reviews.
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)?
from jose-reviews.
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.
β> 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.
β>"Click on Copy repository from template"
This was just βCreate repositoryβ
β> β β’ 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.
β
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?
β> "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)
β> "Enable Workflows"
This was also enabled by default to me
β> "Enable Github Pages"
β3 Select gh-pages and /(root) in the drop-down menu below Branch.β
I didnβt see gh-pages branch. Should the user create a branch? Provide details please.
β> I went with using secrets.GITHUB_TOKEN
β> When running choochoo build checklists
I get error and nothing is printing
[ggeorg02/testachoo] Fat Controller workflow run
from jose-reviews.
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.
from jose-reviews.
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.
β> 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
from jose-reviews.
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.
from jose-reviews.
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 toubuntu-22.04
so that the specified python version was no longer supported. I've now updated topython-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 π€ . 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
from jose-reviews.
Hi @ttimbers, just checking in on the review; is there anything I can do to help move along?
from jose-reviews.
Hello, @ttimbers - perhaps @ppxasjsm is free to review this? In the pre-review they indicated they might be available for this.
from jose-reviews.
@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?
from jose-reviews.
Related Issues (20)
- [PRE REVIEW]: Good Enough Practices in Scientific Computing: A Learning Module for Researchers HOT 18
- [PRE REVIEW]: CodeBuddy: A programming assignment management system for short-form exercises HOT 10
- [PRE REVIEW]: Learning Machine Learning with Lorenz-96 HOT 22
- [PRE REVIEW]: Can you predict the future? A tutorial for the National Ecological Observatory Network Ecological Forecasting Challenge HOT 31
- [PRE REVIEW]: Self-Guided Decision Support Groundwater Modelling with Python HOT 20
- [PRE REVIEW]: The University of Toronto Climate Downscaling Workflow: Tools and Resources for Climate Change Impact Analysis HOT 47
- [PRE REVIEW]: Practical machine learning with PyTorch HOT 25
- [PRE REVIEW]: An R reproducibility toolkit for the practical researcher HOT 19
- [PRE REVIEW]: Course Materials for an Introduction to Bayesian Modeling in Spanish HOT 5
- [PRE REVIEW]: Static Equilibrium in Remote Alaska HOT 13
- [REVIEW]: Practical machine learning with PyTorch HOT 79
- [REVIEW]: Self-Guided Decision Support Groundwater Modelling with Python HOT 15
- [REVIEW]: Learning Machine Learning with Lorenz-96 HOT 22
- [REVIEW]: Scientific programming in Julia - An introductory course HOT 10
- [REVIEW]: The University of Toronto Climate Downscaling Workflow: Tools and Resources for Climate Change Impact Analysis HOT 67
- JOSE Review - comments on "Self-Guided Decision Support Groundwater Modelling with Python " [Documentation section] HOT 2
- JOSE Review - comments on "Self-Guided Decision Support Groundwater Modelling with Python " [Pedagogy / Instructional design ] HOT 2
- JOSE Review - comments on "Self-Guided Decision Support Groundwater Modelling with Python " [JOSE paper] HOT 2
- [PRE REVIEW]: An open-sourced comprehensive Monte-Carlo-aided educational toolkit for statistics HOT 6
- [PRE REVIEW]: ARC4CFD: Learning how to leverage High-Performance Computing with Computational Fluid Dynamics HOT 15
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from jose-reviews.