[REVIEW]: The Argo Online School: An e-learning tool to get started with Argo

whedon commented 1 year ago

Submitting author: !--author-handle-->@Alberto-GS@kls2177<!--end-editor-- Reviewers: @francispoulin, @djmallum Archive: Pending

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@francispoulin, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html. Any questions/concerns please let @kls2177 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 @francispoulin

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] 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 (1.0)?
[x] Authorship: Has the submitting author (@Alberto-GS) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] 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!)

[x] 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.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] 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)?

Reviewer instructions & questions

@djmallum, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

The reviewer guidelines are available here: https://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html. Any questions/concerns please let @kls2177 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 @djmallum

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] 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)
[x] Version: Does the release version given match the repository release (1.0)?
[x] Authorship: Has the submitting author (@Alberto-GS) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] 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!)

[x] 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.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] 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

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

whedon commented 1 year ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @francispoulin @djmallum it looks like you're currently assigned to review this paper :tada:.

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whedon commented 1 year ago

Wordcount for paper.md is 1382

whedon commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 1 year ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.52 s (83.2 files/s, 46540.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                30              0          21967            746
JSON                             3              0              0            635
Markdown                         5            163              0            244
YAML                             4             22             12            123
TeX                              1             16              4            116
-------------------------------------------------------------------------------
SUM:                            43            201          21983           1864
-------------------------------------------------------------------------------

Statistical information for the repository 'd2d0fabea262cbb9e09e0c6a' was
gathered on 2023/01/23.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Pedro Velez                     27         27542          28260           64.49
PedroVelez                      15         15719          15001           35.51

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments

whedon commented 1 year ago

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

OK DOIs

- 10.17882/42182 is OK
- 10.5281/zenodo.4539666 is OK
- 10.3389/fmars.2019.00439 is OK
- 10.1038/nclimate2872 is OK
- 10.1038/nclimate2872 is OK
- 10.1175/JTECH-D-19-0041.1 is OK
- 10.21105/joss.02425 is OK

MISSING DOIs

- None

INVALID DOIs

- None

PedroVelez commented 1 year ago

Dear @kls2177 on October 23rd we got from @labarba the following comments:

"hi @Alberto-GS and @PedroVelez 👋 Thank you for your patience. I did not receive a reply from the editor we initially assigned to this submission, despite several emails and DMs. (People have generally been much harder to reach in the past 2.5 years, and one can never know what is affecting them.) The good news is that JOSE had a campaign to recruit new editors, and we have 7 editors joining the board as we speak! (They need to be onboarded, though.)

In the meantime, I had a fresh look at the submission, in more depth, and let me anticipate a few things.

(1) About the videos: note that JOSE considers videos as supplementary material that we do not review. I did notice that you have the videos on Google Drive, and for me they did not play on JupyterBook, as you have embedded them. It needed a "pop-out" to Drive. Have you considered putting them in a YouTube channel? (Perhaps unlisted? Vimeo is also an option). Then using from IPython.display import YouTubeVideo they will be playable in the Jupyter notebook (and JupyterBook?).

(2) On your paper, a reader has to wonder what Argos is all the way to the "Statement of Need," so I think that first paragraph there should be moved to the top of the Introduction.

(3) Regarding the audience, you mention high-school students, which called my attention. Is there any experience involving high-school students in this topic? Do you have any experiences with different student populations that you could tell us about?

(*) We do not review videos, or slide presentations, or other forms of OCW, because they cannot be modified or easily reused. JOSE reviews open-source material that is reusable and allows derived works. Also, when you make an archive of the repository (source files for the JupyterBook), the videos will not be included."

we are working in these comments and shortly we will reply to them in this issue.

PedroVelez commented 1 year ago

Hi,

regarding the first topic (1), we have tested versions using YouTube (see here https://euroargodev.github.io/argo-online-school/Lessons/L01_TheArgoProgram/Chapter10_TheArgoProgram_intro.html ), however we do not like this option since YouTube will suggest new videos that distract the 'reader' from the school. And, as far as we know there is not way, either using IPython or an iframe within the markdown, to avoid this distraction. We have no tested Vimeo but probably is similar, since thew platform will promotes its own videos.

In general the Lesson1 and Lesson2 are meant to be seen in the main web page https://euroargodev.github.io/argoonlineschool/intro.html and Lesson 3 is the one to be downloaded to work with the Jupyter notebooks.

Please @kls2177 if you have another suggestion we will happy to test it. best Pedro

Alberto-GS commented 1 year ago

Hi all,

About (2), the "Statement of Need" has been placed where suggested.

About (3), we don't have previous experiences but this audience escope was proposed because here (at least in Spain) highschool students and first grade college students already have coding notions. We sadly don't have feedback with different student populations:( Do you find this scope audience too optimistic? Do you think it should be modified? @kls2177 @labarba

I just realized there is an error in our affilitaion (probably my bad) artice proof . It should be "Centro Oceanográfico de Canarias, Instituto Español de Oceanografía (IEO - CSIC)"

Thanks!

labarba commented 1 year ago

@whedon add @gaelforget as reviewer

whedon commented 1 year ago

OK, @gaelforget is now a reviewer

kls2177 commented 1 year ago

Hi @Alberto-GS and @PedroVelez,

Thank you for your patience. Reviewers have now been assigned.

Regarding the videos, I am able to view them and I think using Youtube is the easiest way to proceed. However, please keep in mind "We do not review videos, or slide presentations, or other forms of OCW, because they cannot be modified or easily reused. JOSE reviews open-source material that is reusable and allows derived works. Also, when you make an archive of the repository (source files for the JupyterBook), the videos will not be included."

Regarding your audience, I suggest that you focus on the audience that this material was originally intended for rather than speculating as to who it could potentially be for.

I hope this helps!

whedon commented 1 year ago

:wave: @bzemskova, please update us on how your review is going (this is an automated reminder).

kls2177 commented 1 year ago

Hello @bzemskova and @gaelforget, how is the review process going?

kls2177 commented 1 year ago

Hello @bzemskova and @gaelforget, since we have not hard from you in several weeks, we are now looking for new reviewers. Thank you for your original willingness to contribute a review.

kls2177 commented 1 year ago

@whedon remove @bzemskova as reviewer

whedon commented 1 year ago

OK, @bzemskova is no longer a reviewer

kls2177 commented 1 year ago

@whedon remove @gaelforget as reviewer

whedon commented 1 year ago

OK, @gaelforget is no longer a reviewer

kls2177 commented 1 year ago

@whedon add @francispoulin as reviewer

whedon commented 1 year ago

OK, @francispoulin is now a reviewer

kls2177 commented 1 year ago

@whedon add @djmallum as reviewer

whedon commented 1 year ago

OK, @djmallum is now a reviewer

francispoulin commented 1 year ago

I found a problem with one of the notebooks. I am going to post it here but if it's better to put it elsewhere, please let me know.

In L03-Chapter11_TheNetCDFFFormat, In [26], I get an error with the line ax.plot(dataOPsubsampled.sst)

francispoulin commented 1 year ago

In L03-Chapter22_ArgoDatabyFloat_Prof, in In [3]: the line should read as follows, otherwise the Data cannot be found and an error occurs,

prof = xr.open_dataset('../../Data/6901254/6901254_prof.nc').

francispoulin commented 1 year ago

In L03-Chapter31_ArgoDatabyData_Day, the following need to be changed.

In [3]: the first line should reference 2019, as that is what is found in the Data folder.

dayADS = xr.open_dataset('../../Data/atlantic_ocean/2019/11/20191111_prof.nc').

In [7]: again refer to 2019 data.

dayPDS = xr.open_dataset('../../Data/pacific_ocean/2019/11/20191111_prof.nc') dayIDS = xr.open_dataset('../../Data/indian_ocean/2019/11/20191111_prof.nc')

In [13]: 2019 not 2020.

for filein in ['../../Data/atlantic_ocean/2019/11/20191111_prof.nc', '../../Data/pacific_ocean/2019/11/20191111_prof.nc', '../../Data/indian_ocean/2019/11/20191111_prof.nc']:

More changes need to be made in this file I leave it to you to fix them.

francispoulin commented 1 year ago

In L03-Chapter32: there is problem with In [8], saying module 'argopy' has no attribute 'plotters'.

francispoulin commented 1 year ago

In L03-Chapter41:

In [4] should refer to 2019 not 2020.

In[ 13] has an error as another exception occured:.

francispoulin commented 1 year ago

Ln L03-Chapter42:

In [3]: has an error another exception occurred:.

francispoulin commented 1 year ago

This is an interesting contribution to the field that will be useful to many young researchers. I have pointed out a number of bugs that I found in the notebooks, but I presume these are easy to fix.

One general concern is that the first two lessons only involve watching videos and no actual python code. If that’s the case it’s nto clear the utility of including them in a notebook. I am okay with this but I feel like if there was some python in the first two lessons that might be better balanced.

Below are a few minor points that should be addressed.

• The version should be 1.0 but the tag shows it to be v0.1.0.
• The name is sometimes abreviated as AOS and other times AoS.  Either is fine but be consistant.
• On the main documentation page, when I click on 1. The Argo Program, I get a 404 error.
• The paper.md file does not have any references, however I do see them in the PDF.  I presume this is okay then but wanted to confirm before I click the box.
• You should point out this is useful to high school, undergraduate and graduate students.

djmallum commented 1 year ago

First, I'd like to thank the authors for this very interesting module. I agree with Francis that this is a very good contribution to the field and should be considered for publication after resolving the issues I've raised. Below, I'll link to my comments which I organized in a manner which I hope is convenient. Please feel free to ask me questions about any of my comments.

kls2177 commented 1 year ago

@Alberto-GS and @PedroVelez, the reviewers have completed their reviews and have comments for your consideration. I recommend that these comments be addressed before publication.

Thanks @francispoulin and @djmallum for your helpful comments. @djmallum, quick question - I do not see an issue on the argoonlineschool repo entitled "General Comments". Not sure if this got included elsewhere.

@francispoulin and @djmallum, would you be willing to review the revised version when available?

Just a few of my own comments: I agree with @francispoulin, that it would be nice to integrate some python examples earlier in the course. Perhaps, just some simple plotting examples - rather that providing some static images, ask the students to generate the plots using python. This would allow students who are learning python for the first time to get some gradual exposure before Lesson 3.

You mention that this material is for high school or graduate students - what about undergraduate students?

I do not necessarily agree with your statement that no pre-requisite knowledge is required. There are certainly expectations about general science and mathematics knowledge. I suggest providing some information about pre-requisite knowledge on the landing page of the Argo Online School website. For example, what pre-requisite oceanography, maths, chemistry, geography knowledge is expected of students? This is likely more relevant for high school students than post-secondary students. At the beginning of Lesson 3, you provide students with a link to the Earth and Environmental Data Science course to learn python if they need to, but it would be nice to provide students with information about these pre-requisite coding skills and resources at the beginning of the course.

I really like the interactive quizzes! These look great and give timely feedback to students. I would recommend integrating a few more of these at regular intervals to keep the students engaged. Structurally, I would also suggest embedding the quizzes into each lesson, rather than having them as a separate section at the end. I feel that this would better reflect the sequencing of the material.

Thank you for your patience! Please let me know if you have any questions.

djmallum commented 1 year ago

@kls2177 I must not have saved that issue properly. I should be able to resolve that today. I'm also happy to review the revised version when available.

djmallum commented 1 year ago

@kls2177 @Alberto-GS @PedroVelez I have now fixed the links above and added a "General Comments" issue in the target repository. I will be away until the 29th of May and will not be able to respond to questions until then, but I will be available for the rest of the day if anything comes up.

francispoulin commented 1 year ago

@kls2177 I am happy to review a revised version of the manuscript.

Alberto-GS commented 1 year ago

Hello everyone, Thank you very much for the entire revision process, which will undoubtedly enrich the manuscript. We take up the baton from now on to revise all the comments made and include them. Thanks!

kls2177 commented 1 year ago

Hi @Alberto-GS, how are the revisions going?

Alberto-GS commented 1 year ago

Hello @kls2177. On hold to be honest. While we waited for a response at the time, we focused our efforts on finishing a paper that was published precisely last week. I will start this week and you will hear from us soon:) Thank you so much for asking!

kls2177 commented 3 months ago

Hello @Alberto-GS, I am following up on this thread. Let me know if you will have some time to proceed with the revisions in the coming months. Thanks!

Alberto-GS commented 3 months ago

Hello @Alberto-GS, I am following up on this thread. Let me know if you will have some time to proceed with the revisions in the coming months. Thanks!

Hello! We haven't forgotten about this thread:) We are overwhelmed with work and long sick leave. I hope to be able to make changes very soon and let you know in the next few months! Thank you very much, really appreciate it. @PedroVelez

Alberto-GS commented 2 months ago

Hi @kls2177 I'm trying to resolve some serious bugs but I'm having trouble pushing all the commits https://github.com/euroargodev/argoonlineschool/actions Could you shed some light on the problem? I'm familiar with GitHub but I'm not very skilled. I've installed all the dependencies, packages and updates on my local computer and it seems to work just fine. In fact, I can see the changes correctly. Once I push it to the repository, I get this GitHub report containing errors. I'm guessing something is going on with HDF5 but I still don't know how to solve it after several hours of searching (it's probably just a silly thing). Thanks.

kls2177 commented 2 months ago

@Alberto-GS, I am not an expert either, but I will take a look at your logs. I may not have a chance until Thursday.

Alberto-GS commented 1 month ago

Hello @kls2177, after some checks @PedroVelez solved the bug. Apparently there was some issue between the workflow and the netCDF package. Now we're on the road again.

PedroVelez commented 1 month ago

Hi, thanks a lot for the patience @kls2177 we have all most ended including all the suggestions , we have replied to each of of them in the issues opened for the repository:

Typos Lesson 1 Lesson 2 Lesson 3 Checklist Comments (See above) General Comments

and we would like to know what do we have to do for re-submission.

thanks pedro

PedroVelez commented 1 month ago

@Alberto-GS and @PedroVelez, the reviewers have completed their reviews and have comments for your consideration. I recommend that these comments be addressed before publication.

Thanks @francispoulin and @djmallum for your helpful comments. @djmallum, quick question - I do not see an issue on the argoonlineschool repo entitled "General Comments". Not sure if this got included elsewhere.

@francispoulin and @djmallum, would you be willing to review the revised version when available?

Just a few of my own comments: I agree with @francispoulin, that it would be nice to integrate some python examples earlier in the course. Perhaps, just some simple plotting examples - rather that providing some static images, ask the students to generate the plots using python. This would allow students who are learning python for the first time to get some gradual exposure before Lesson 3.

[x] Thanks for the comment, but the way the AoS has been designed the lessons 1 and 2 are a module by itself, that do not have any requirements for high school students , and we want to keep in that way. using some python code, for instance to plot the active floats shown in the first lesson may scare student without programming background. We have eliminated the 'with no prerequisites' statements
[x] on the other hand we have modified the Lesson 3, and we think is more gradual, and we point the students to basic python courses.

You mention that this material is for high school or graduate students - what about undergraduate students?

[x] Yes, it is also for undergrads, we now mention it on the paper and the AoS.

I do not necessarily agree with your statement that no pre-requisite knowledge is required. There are certainly expectations about general science and mathematics knowledge. I suggest providing some information about pre-requisite knowledge on the landing page of the Argo Online School website. For example, what pre-requisite oceanography, maths, chemistry, geography knowledge is expected of students?
[X] Thanks, we have removed the statement about no pre-requisit, in the paper and the landing page, and modified the text to show what it is necessary, basically the knowledge obtained in middle school.
This is likely more relevant for high school students than post-secondary students. At the beginning of Lesson 3, you provide students with a link to the Earth and Environmental Data Science course to learn python if they need to, but it would be nice to provide students with information about these pre-requisite coding skills and resources at the beginning of the course.
[X] Thanks, we warn the students in the landing page and also in the JOSE paper, that lesson 3 requieres basic knownledge of python. We do not ask for xarray or numpy, since once you understand python, either from the AoS or the Earth and Environmental Data Science course yoy can learn the basics of xarray and numpy.

I really like the interactive quizzes! These look great and give timely feedback to students. I would recommend integrating a few more of these at regular intervals to keep the students engaged. Structurally, I would also suggest embedding the quizzes into each lesson, rather than having them as a separate section at the end. I feel that this would better reflect the sequencing of the material.

[X] Thanks!, we have moved each quizz to the end of each lesson.

PedroVelez commented 1 month ago

Hi @francispoulin @kls2177 @djmallum we haver finished to do the review, including all the suggestions, typos and errors. Please could you let us now what is the next step? best pedro

labarba commented 1 month ago

Hi @PedroVelez — thank you for your patience, as everyone here is a volunteer, and doing their best! In my case, for example, the semester started and it is a hectic time. My response times are going to be delayed.

PedroVelez commented 1 month ago

Hi @labarba, of course, no rush. Thanks

kls2177 commented 3 weeks ago

Hello @PedroVelez and @Alberto-GS, I apologize for the delay. I was on vacation when the updates were coming in.

Thank you for responding to the reviewers comments. @francispoulin and @djmallum, I would now ask that you please take a look at the revisions and let me know whether you are satisfied and whether or not you would recommend the materials for publication.

Thanks to everyone for their patience!

francispoulin commented 3 weeks ago

I did a git pull of the repo and see that there is a problem in Chapter32.

When I execute the second cell I get a KeyError.

Can the authors please check if this works for them in the freshly pulled repo?

PedroVelez commented 3 weeks ago

Thanks for reviewing it!

There was a problem with the numpy version and xarray, therefore the numpy version has to be 1.26.4 until xarray fix the problem.

We have updated the environment.yml and verified that a clean installation of the enviroment, using

conda env create -n AOS -f environment.yml 
conda activate AOS

works. I know is very inconvenient, but in my experience this is often the case of python.

By the way, following some suggestion we have just added a section with more examples including one very similar to the ArgoStatus

best pedro

I did a git pull of the repo and see that there is a problem in Chapter32.

When I execute the second cell I get a KeyError.

Can the authors please check if this works for them in the freshly pulled repo?

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