[REVIEW]: Digital Twins for Ocean Robots

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@gaelforget@luraess<!--end-editor-- Reviewers: @jonathanlilly, @Alexander-Barth Archive: Pending

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Reviewers and authors:

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Reviewer instructions & questions

@jonathanlilly & @Alexander-Barth, 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:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @luraess 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 @Alexander-Barth

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.11 s (364.3 files/s, 206720.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           19           3720          12837           3206
TeX                              8            302            181           2576
Markdown                         6             69              0            131
YAML                             4              4              0            119
TOML                             3              4              0             57
Ruby                             1              8              4             45
-------------------------------------------------------------------------------
SUM:                            41           4107          13022           6134
-------------------------------------------------------------------------------

Commit count by author:

   307  gaelforget
    11  Gael Forget
     2  CompatHelper Julia
     1  Julia TagBot
     1  ggebbie
     1  github-actions[bot]

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.tex is 2782

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 1 month ago

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

OK DOIs

- 10.3389/fmars.2018.00328 is OK
- 10.3389/fmars.2017.00128 is OK
- 10.1137/141000671 is OK
- 10.17226/26894 is OK
- 10.21105/joss.03349 is OK
- 10.21105/joss.00602 is OK
- 10.5281/zenodo.11144554 is OK
- 10.21105/joss.02018 is OK
- 10.21105/joss.04207 is OK
- 10.21105/joss.02813 is OK
- 10.5194/gmd-8-939-2015 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.3389/fmars.2019.00439 is OK
- 10.21105/joss.03814 is OK
- 10.1175/JPO-D-14-0023.1 is OK
- 10.5194/gmd-8-3071-2015 is OK
- 10.5194/os-11-839-2015 is OK
- 10.1016/j.pocean.2015.06.002 is OK
- 10.1175/2009JPO4043.1 is OK
- 10.1175/JPO3072.1 is OK

MISSING DOIs

- No DOI given, and none found for title: MITgcm.jl: a Julia Interface to the MITgcm
- 10.21203/rs.3.rs-3979671/v1 may be a valid DOI for title: Energy Imbalance in the Sunlit Ocean Layer
- 10.1029/96jc02775 may be a valid DOI for title: A finite-volume, incompressible Navier Stokes mode...
- 10.1016/s1463-5003(03)00009-x may be a valid DOI for title: Conservation of properties in a free surface model
- 10.1016/j.future.2004.11.010 may be a valid DOI for title: An efficient exact adjoint of the parallel MIT gen...

INVALID DOIs

- None

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

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

Alexander-Barth commented 1 month ago

Review checklist for @Alexander-Barth

Conflict of interest

[x] I confirm that I have read the JuliaCon conflict of interest policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JCon for the purpose of this review.

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/JuliaOcean/OceanRobots.jl?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@gaelforget) made major 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?
[ ] 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

Paper format

[x] Authors: Does the paper.tex file include a list of authors with their affiliations?
[ ] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Content

[ ] Context: is the scientific context motivating the work correctly presented?
[ ] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[ ] Results: are the results presented and compared to approaches with similar goals?

Alexander-Barth commented 1 month ago

Hi @gaelforget, this is a nice paper!

I try to run the first code snipped on the your paper (Code 1).

using OceanRobots , ArgoData , CairoMakie
files_list = GDAC.files_list() ; wmo = 6900900
argo = read(ArgoFloat() , wmo = wmo , files_list = lst )
fig = plot(argo , option = : standard , pol = pol )

It it seems that lst should be files_list. Also pol is undefined. Should such issues be discussed here, or rather directly in https://github.com/JuliaOcean/OceanRobots.jl ?

Alexander-Barth commented 1 month ago

Concerning "Does installation proceed as outlined in the documentation?": I did not see any specific instruction (or did I miss them?), but I can confirm that package can be installed as any julia package.

Alexander-Barth commented 1 month ago

I am trying to run the notebook Buoy_NWP_NOAA.jl, but I cannot change the station number. It will always show 41046 even if I select 44065.

I am wondering if there is not an issue with this line:

https://github.com/JuliaOcean/OceanRobots.jl/blob/c5179c048d504366ba2175161759261a4242ceb7/examples/Buoy_NWP_NOAA.jl#L69

Should it not be: buoy=read(NOAAbuoy(),sta) (rather than hard coding the station number) ?

Alexander-Barth commented 1 month ago

The notebook Buoy_NWP_NOAA_monthly.jl: can you add unit to the x and y axis? It it in °Fahrenheit ?

Drifter_GDP.jl:

it would be useful to define ve and vn ( zonal and meridional velocity I guess :-) )
the y axis is just time and the labels number like 300. Can you add more information about the time unit and origin (like "days since 2000-01-01" ?)

References of the PDF paper:

please check capitalization of reference 1 (e.g. co2 -> CO2,...), 3 (cmip6 - CMIP6), 6 (argo -> Argo), 11 (mitgcm -> MITgcm)... see https://stackoverflow.com/questions/2800527/preserving-all-capitalization-in-bibtex

luraess commented 1 month ago

Should such issues be discussed here, or rather directly in https://github.com/JuliaOcean/OceanRobots.jl ?

@Alexander-Barth Issues specific to the code, OceanRobots.jl, could be directly discussed in the respective repo (as issue) which can reference this Review issue. Issues, comments and suggestions related to the manuscript and the revision should be discussed here. Hope this helps - thanks!

gaelforget commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

gaelforget commented 1 month ago

updated code snippet in https://github.com/JuliaCon/proceedings-review/issues/164#issuecomment-2265768841

addresses https://github.com/JuliaCon/proceedings-review/issues/164#issuecomment-2252988030

Good points! Thank you

gaelforget commented 1 month ago

I am trying to run the notebook Buoy_NWP_NOAA.jl, but I cannot change the station number. It will always show 41046 even if I select 44065.

I am wondering if there is not an issue with this line:

https://github.com/JuliaOcean/OceanRobots.jl/blob/c5179c048d504366ba2175161759261a4242ceb7/examples/Buoy_NWP_NOAA.jl#L69

Should it not be: buoy=read(NOAAbuoy(),sta) (rather than hard coding the station number) ?

Done.

gaelforget commented 1 month ago

The notebook Buoy_NWP_NOAA_monthly.jl: can you add unit to the x and y axis? It it in °Fahrenheit ?

Done

Drifter_GDP.jl:

it would be useful to define ve and vn ( zonal and meridional velocity I guess :-) )

the y axis is just time and the labels number like 300. Can you add more information about the time unit and origin (like "days since 2000-01-01" ?)

Done

References of the PDF paper:

please check capitalization of reference 1 (e.g. co2 -> CO2,...), 3 (cmip6 - CMIP6), 6 (argo -> Argo), 11 (mitgcm -> MITgcm)... see https://stackoverflow.com/questions/2800527/preserving-all-capitalization-in-bibtex

Done in https://github.com/JuliaOcean/OceanRobots.jl/commit/6bb4d8e8e64af1fa42d63de1e11e8e239e04ec7c

Alexander-Barth commented 1 month ago

For people not familiar with Pluto (or Julia), I think it would be nice to mention somewhere that all you need to do is to install julia and Pluto. The installation of OceanRobots.jl and other will be done automatically when you run the notebook. Is this information already somewhere?

gaelforget commented 6 days ago

For people not familiar with Pluto (or Julia), I think it would be nice to mention somewhere that all you need to do is to install julia and Pluto. The installation of OceanRobots.jl and other will be done automatically when you run the notebook. Is this information already somewhere?

Good point! Thanks for the suggestion.

I added on this in the new How-To section , https://juliaocean.github.io/OceanRobots.jl/dev/examples/#How-To

gaelforget commented 6 days ago

Concerning "Does installation proceed as outlined in the documentation?": I did not see any specific instruction (or did I miss them?), but I can confirm that package can be installed as any julia package.

I added installation docs in the new How-To section , https://juliaocean.github.io/OceanRobots.jl/dev/examples/#How-To

gaelforget commented 6 days ago

@editorialbot generate pdf

editorialbot commented 6 days ago

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

JuliaCon / proceedings-review