[REVIEW]: Learning Machine Learning with Lorenz-96 #241

editorialbot · 2024-03-27T17:41:20Z

Submitting author: @dhruvbalwada (Dhruv Balwada)
Repository: https://github.com/m2lines/L96_demo
Branch with paper.md (empty if default branch):
Version: v1.0.3
Editor: @magsol
Reviewers: @Micky774, @AnonymousFool
Archive: 10.5281/zenodo.13921550
Paper kind: learning module

Status

Status badge code:

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Markdown: [![status](https://jose.theoj.org/papers/c644a0264f445698f212a051d8ace6e8/status.svg)](https://jose.theoj.org/papers/c644a0264f445698f212a051d8ace6e8)

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

@Micky774 & @AnonymousFool, 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 @magsol 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 @Micky774

📝 Checklist for @AnonymousFool

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-03-27T17:41:23Z

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editorialbot · 2024-03-27T17:41:41Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (584.4 files/s, 331163.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                28              0          16704           7734
Python                           6            405            581           1335
TeX                              2             37              1            388
Markdown                         6             71              0            290
YAML                             5             10             27            183
SVG                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                            49            523          17313           9932
-------------------------------------------------------------------------------

Commit count by author:

    58	Shubham Gupta
    57	Alistair Adcroft
    45	Ryan Abernathey
    29	Shantanu Acharya
    25	pre-commit-ci[bot]
    23	dhruvbalwada
    20	Dhruv Balwada
    17	Mohamed Aziz Bhouri
    16	Johanna Goldman
    14	Laure Zanna
     9	Brandon Reichl
     7	Feiyu Lu
     7	Yani Yoval
     5	Nora Loose
     5	Pierre Gentine
     4	lesommer
     3	Andrew Ross
     3	Arthur
     3	Lorenzo Zampieri
     3	Ziwei Li
     2	Mitch Bushuk
     2	Sara Shamekh
     1	Alex Connolly
     1	William-gregory
     1	chzhangudel

editorialbot · 2024-03-27T17:41:50Z

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

OK DOIs

- None

MISSING DOIs

- 10.1017/cbo9780511617652.004 may be a valid DOI for title: Predictability: a problem partly solved

INVALID DOIs

- None

editorialbot · 2024-03-27T17:42:23Z

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

editorialbot · 2024-03-27T17:42:42Z

Paper file info:

📄 Wordcount for paper.md is 1350

🔴 Failed to discover a Statement of need section in paper

editorialbot · 2024-03-27T17:42:44Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Micky774 · 2024-03-27T18:17:25Z

Review checklist for @Micky774

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 for this learning module available at the https://github.com/m2lines/L96_demo?
License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
Version: Does the release version given match the repository release?
Authorship: Has the submitting author (@dhruvbalwada) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

A statement of need: Do the authors clearly state the need for this module and who the target audience is?
Installation instructions: Is there a clearly stated list of dependencies?
Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Does the paper clearly state the need for this module and who the target audience is?
Description: Does the paper describe the learning materials and sequence?
Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
Could someone else teach with this module, given the right expertise?
Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

magsol · 2024-04-15T20:18:43Z

Hey @Micky774 @AnonymousFool 👋 Wanted to check in on the status of your reviews, see if you needed anything or if there are any roadblocks I can help troubleshoot. Thanks!

AnonymousFool · 2024-04-17T19:13:57Z

Oh my god, well this fell off my radar somehow. That was irresponsible of me. Mea culpa.

I've got too much scheduled today to work on it, so I'll start work in earnest tomorrow.

AnonymousFool · 2024-04-18T18:21:38Z

Review checklist for @AnonymousFool

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 for this learning module available at the https://github.com/m2lines/L96_demo?
License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
Version: Does the release version given match the repository release?
Authorship: Has the submitting author (@dhruvbalwada) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

A statement of need: Do the authors clearly state the need for this module and who the target audience is?
Installation instructions: Is there a clearly stated list of dependencies?
Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Does the paper clearly state the need for this module and who the target audience is?
Description: Does the paper describe the learning materials and sequence?
Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
Could someone else teach with this module, given the right expertise?
Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Micky774 · 2024-04-20T20:43:13Z

Sorry for the delay, and thank you for your patience. I will be performing the first part of my review today, and hope to complete a full round by tomorrow evening, circumstances permitting.

Micky774 · 2024-04-20T22:09:42Z

Once again, sorry for the delay @dhruvbalwada. The good news is that the vast majority of the non-pedagogical components are already in a fantastic state, and there is no core content missing. If anything, most of these suggestions are to round out the existing content and offer some more concrete and explicit communication which future learners can benefit from. Below is my first-pass of the non-pedagogical sections.

If you have any questions about the feedback, please feel free to let me know! In particular, if there is something you'd like a more detailed discussion and dissection of, it would probably be best to open an issue in your repository corresponding to the specific piece of feedback that needs clarification. We can continue a more detailed discussion there and simply link back to it in this thread for brevity/clarity.

Non-pedagogical components review

General checks

Please create an initial release in the repository. For details, see the github docs. This should match the version provided in your application, i.e. v1.0

Documentation

Your README.md lacks a clear statement of need. The easiest resolution would be to add a small section describing a specific (but perhaps non-exhaustive) list of folks that may benefit from this content. You describe this a bit in your paper, albeit slightly scattered, so it should be fairly easy to add. In particular it would be beneficial to specify if there is any prior knowledge required for making full use of this module.
In a similar vein, while you provide instructions for building/serving the content, the readme lacks a discussion on the contextual use of the repository. Please add some words offering instructions or recommendations for using the repository as a teaching tool itself, e.g. a recommended pace/timeline, or potential adaptation of the content to suit specific needs (this is less obvious and may not be appropriate).
While your documentation includes instructions for contribution to the module, it does not provide instructions for reporting problems or obtaining support. This could be as simple as directing them to open an issue in the repository and perhaps including a code of conduct if appropriate. Optionally you may provide either individual or organizational contact information if there is a commitment to maintenance / support, but this is not strictly necessary.

JOSE paper

Your paper lacks a clear statement of need. Most of the content that would comprise the statement of need is present in the submission, however it is scattered and should instead be explicitly included in a separate section.
Please source any data or external models you may be using as a core part of the module (as opposed to transient or one-time use).
Please include some more context regarding the tooling your module covers, and its role in the field. Specifically, please explicitly mention and cite some other models/solutions that accomplish similar tasks to the L96 model your module focuses on. It is reasonable to expect future users to gain much value from a submission that includes relevant citations as they can use those citations as future reading.

AnonymousFool · 2024-05-06T20:19:55Z

Alright, I've done a run through of all the required material for the review. I agree with Meekail's feedback thus far, and I found one additional issue with respect to the non-pedagogical requirements that I've documented here.

With respect to the pedagogical content, I think that the structure, ordering, and pacing of ideas throughout the notebooks is impeccable. I think though that there are a lot of small edits I could make to various sentences and formulae to improve their precision and clarity.

I think the most productive and easiest way to deliver and discuss the feedback would be if I made a new branch of the repository in which I commit the edit ideas as changes to the notebooks. Then I can open a pull request, and we can use github's comment and suggestion infrastructure to organize discussion of the feedback. If you, on review, found the feedback valuable, then you can just merge the changes in.

I've also noticed a lot of small typos and grammatical errors throughout the notebooks, none of which affected my ability to understand the ideas the notebooks communicate. But as part of my editing feedback, I could include spelling and grammatical fixes. Or I could just ignore them if you prefer.

Thoughts @dhruvbalwada?

dhruvbalwada · 2024-05-06T20:26:16Z

@AnonymousFool - If you have the time to make the edits in a new branch, it would be great and very much appreciated.

IamShubhamGupto · 2024-05-20T15:08:33Z

@AnonymousFool let us know how the review is progressing.

If you face any further technical difficulties, reach out to me here / open an issue and I'll be addressing it

magsol · 2024-05-31T14:05:27Z

Hi @AnonymousFool and @Micky774, thanks so much for your help so far! I still see some items in your checklists that haven't been addressed. Are you waiting for feedback, or would you be able to continue your reviews?

Micky774 · 2024-05-31T15:47:44Z

@magsol I'll be updating my review this upcoming week, but afaik still waiting on changes in the repository to address the current given feedback as well.

magsol · 2024-06-05T14:29:11Z

Hi @dhruvbalwada, the reviewers are indicating that they're waiting on changes on your end. Can you provide an update on how that's going?

magsol · 2024-06-12T18:27:43Z

Hi @dhruvbalwada , @IamShubhamGupto: I saw you working on the feedback from @AnonymousFool, but I'm not clear on whether you have addressed the feedback from @Micky774 yet. I'd like to see if we can wrap this up soon; are you waiting on anything from the reviewers?

dhruvbalwada · 2024-06-21T20:43:14Z

Hi @magsol @Micky774 @AnonymousFool - we have made all the appropriate changes to the repo and the paper according to your suggestions. Please let us know what else to address and how to proceed.

IamShubhamGupto · 2024-06-21T21:19:10Z

@magsol @Micky774 thank you for reviewing our work so far and waiting for the new changes. I believe as of today all the remaining requested changes have been published except for releasing version v1.0. Since we would have to recreate the release to incorporate newer commits, I would keep this as the last step.

Let me know if the current version of the repository is ready and the release will be created subsequently

AnonymousFool · 2024-07-16T16:38:45Z

Alright, yeah, I think the latest round of edits has covered the whole checklist without problems.

I hope at some point to get around to those edit suggestions I want to do, but I seem to have bogged myself down in other problems, and I see no reason to prevent publishing what I already believe is a well-functioning educational resource.

IamShubhamGupto · 2024-10-11T20:02:47Z

@labarba @dhruvbalwada

Let me know if this preview is good for the website:

Its replicated across all pages, if all is good, ill make a PR

labarba · 2024-10-11T20:18:00Z

Your could list the copyright owners as well as the year, and then the license. Like:

IamShubhamGupto · 2024-10-11T20:35:30Z

@labarba

labarba · 2024-10-11T20:39:25Z

Doubly licensed Jupyter notebooks are the norm nowadays, but are not handled gracefully by hosting services. You could leave the CC-BY license in Zenodo (I think it admits only one, but haven't checked in a while.) In the GitHub repo, you could add a License notice in the README.

IamShubhamGupto · 2024-10-11T20:49:42Z

Once merged, we will have to update the version one more time on GitHub if im not wrong

labarba · 2024-10-11T20:57:46Z

We don't require a new version tag for minor tweaks like this, but up to you.

dhruvbalwada · 2024-10-13T01:26:13Z

@labarba - I believe we have made all the changes you requested.

dhruvbalwada · 2024-10-31T11:23:42Z

@labarba - just a gentle nudge about this issue. I believe we have passed all the requirements now for a few weeks.

dhruvbalwada · 2024-11-19T21:27:28Z

@labarba - apologies for pinging again. Could you please take the next steps to help us get through.

labarba · 2024-12-24T18:42:49Z

Hi @dhruvbalwada — thank you for your patience!

It doesn't look like this comment was addressed:

The title and author list on the Zenodo archive do not match the paper title and authors. Please check. (On Zenodo you can just update the metadata, there's no need for a new archive version. Note that you may not want Zenodo to do automatic updates of versions with each release, and that Zenodo pulls from committers into the author list.)

Can you update the title of the Zenodo archive so it matches the paper? Please also double check the author list: it looks like Johanna Goldman is listed on Zenodo but not the paper. The author list should match.

dhruvbalwada · 2024-12-25T02:58:23Z

@labarba - Now the latest version should have all these things fixed.
Apologies for this, I think I got confused since there are multiple versions on zenodo, which don't automatically get updated metadata from previous version. Everything is fixed in latest version now.

labarba · 2024-12-25T12:40:39Z

If I follow the archive DOI https://zenodo.org/records/13357587 I don't see the changes applied — are we on different archives?

dhruvbalwada · 2024-12-25T12:53:19Z

Could you try now?
https://zenodo.org/records/13921550

Hopefully you can see this:

dhruvbalwada · 2024-12-25T13:01:11Z

Also when I go to the link that you posted, which is taking me to version 3 instead of 4, I see something different:

Both version 3 and 4 are essentially the same, and have complete and correct metadata as far I can tell (with version 4 being even more correct).

labarba · 2024-12-25T13:59:20Z

At the very top of this thread, you see that the archive for this paper has been set as:

Archive: 10.5281/zenodo.13357587

Can you confirm then that we should change the archive DOI to 10.5281/zenodo.13921550, Dec 25, 2024 ?

dhruvbalwada · 2024-12-25T14:11:20Z

Yes, please let us change the archive if that helps. I am not sure and don't remember how the DOI link got set at the top. But please let us use the link that works for this submission process to be completed.

magsol · 2024-12-25T19:43:33Z

@editorialbot set 10.5281/zenodo.13921550 as archive

editorialbot · 2024-12-25T19:43:35Z

Done! archive is now 10.5281/zenodo.13921550

labarba · 2024-12-26T11:01:14Z

@editorialbot accept

editorialbot · 2024-12-26T11:01:17Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-12-26T11:02:44Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
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message: If you use this software, please cite our article in the
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  - family-names: Sommer
    given-names: Julien Le
    orcid: "https://orcid.org/0000-0002-6882-2938"
  - family-names: Li
    given-names: Ziwei
  - family-names: Loose
    given-names: Nora
    orcid: "https://orcid.org/0000-0002-3684-9634"
  - family-names: Lu
    given-names: Feiyu
    orcid: "https://orcid.org/0000-0001-6532-0740"
  - family-names: O'Gorman
    given-names: Paul
    orcid: "https://orcid.org/0000-0001-6532-0740"
  - family-names: Perezhogin
    given-names: Pavel
    orcid: "https://orcid.org/0000-0003-2098-3457"
  - family-names: Reichl
    given-names: Brandon
    orcid: "https://orcid.org/0000-0001-9047-0767"
  - family-names: Ross
    given-names: Andrew
    orcid: "https://orcid.org/0000-0002-2368-6979"
  - family-names: Sane
    given-names: Aakash
    orcid: "https://orcid.org/0000-0002-9642-008X"
  - family-names: Shamekh
    given-names: Sara
    orcid: "https://orcid.org/0000-0001-7441-4116"
  - family-names: Verma
    given-names: Tarun
    orcid: "https://orcid.org/0000-0001-7730-1483"
  - family-names: Yuval
    given-names: Janni
    orcid: "https://orcid.org/0000-0001-7519-0118"
  - family-names: Zampieri
    given-names: Lorenzo
    orcid: "https://orcid.org/0000-0003-1703-4162"
  - family-names: Zhang
    given-names: Cheng
    orcid: "https://orcid.org/0000-0003-4278-9786"
  - family-names: Zanna
    given-names: Laure
    orcid: "https://orcid.org/0000-0002-8472-4828"
  date-published: 2024-12-26
  doi: 10.21105/jose.00241
  issn: 2577-3569
  issue: 82
  journal: Journal of Open Source Education
  publisher:
    name: Open Journals
  start: 241
  title: Learning Machine Learning with Lorenz-96
  type: article
  url: "https://jose.theoj.org/papers/10.21105/jose.00241"
  volume: 7
title: Learning Machine Learning with Lorenz-96

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editorialbot · 2024-12-26T11:02:48Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2024-12-26T11:02:48Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSE! 🚨🚨🚨

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Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00241 jose-papers#165
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labarba · 2024-12-26T11:08:40Z

Congratulations @dhruvbalwada – your JOSE paper is published! 🚀

And thank you to our Editor: @magsol Reviewers: @Micky774, @AnonymousFool – ya'll make this possible! 🙏

editorialbot · 2024-12-26T11:08:42Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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dhruvbalwada · 2024-12-26T12:22:31Z

Thank you @labarba and @magsol the reviewers: @Micky774 @AnonymousFool !

editorialbot added Jupyter Notebook Python review TeX labels Mar 27, 2024

editorialbot assigned magsol Mar 27, 2024

editorialbot mentioned this issue Mar 27, 2024

[PRE REVIEW]: Learning Machine Learning with Lorenz-96 #231

Closed

This was referenced Jun 17, 2024

Creating initial release m2lines/L96_demo#155

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Update README.md m2lines/L96_demo#154

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IamShubhamGupto mentioned this issue Oct 11, 2024

Footer license fix m2lines/L96_demo#160

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editorialbot added accepted published Papers published in JOSE labels Dec 26, 2024

labarba closed this as completed Dec 26, 2024

[REVIEW]: Learning Machine Learning with Lorenz-96 #241

[REVIEW]: Learning Machine Learning with Lorenz-96 #241

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editorialbot commented Mar 27, 2024 • edited Loading

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Micky774 commented Mar 27, 2024 • edited Loading

Review checklist for @Micky774

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

magsol commented Apr 15, 2024

AnonymousFool commented Apr 17, 2024

AnonymousFool commented Apr 18, 2024 • edited Loading

Review checklist for @AnonymousFool

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

Micky774 commented Apr 20, 2024 • edited Loading

Micky774 commented Apr 20, 2024

Non-pedagogical components review

General checks

Documentation

JOSE paper

AnonymousFool commented May 6, 2024 • edited Loading

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IamShubhamGupto commented May 20, 2024

magsol commented May 31, 2024

Micky774 commented May 31, 2024

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