[PRE REVIEW]: Digital Twins for Ocean Robots

[editorialbot]

Submitting author: !--author-handle-->@gaelforget<!--end-author-handle-- (Gael Forget) Repository: https://github.com/JuliaOcean/OceanRobots.jl Branch with paper.md (empty if default branch): JuliaConProceedings2023 Version: v0.2.0 Editor: !--editor-->@luraess<!--end-editor-- Reviewers: Pending Managing EiC: Mathieu Besançon

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Thanks for submitting your paper to JCON @gaelforget. Currently, there isn't a JCON editor assigned to your paper.

The AEiC suggestion for the handling editor is @luraess.

@gaelforget if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.11 s (357.5 files/s, 207432.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           19           3720          12837           3206
TeX                              8            303            184           2575
Markdown                         6             69              0            131
YAML                             4              4              0            119
TOML                             3              4              0             57
-------------------------------------------------------------------------------
SUM:                            40           4100          13021           6088
-------------------------------------------------------------------------------

Commit count by author:

   280  gaelforget
    10  Gael Forget
     2  CompatHelper Julia
     1  Julia TagBot
     1  ggebbie
     1  github-actions[bot]

[editorialbot]

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
- 10.21105/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
- 10.5194/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

- https://doi.org/10.17226/26894 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1175/JPO-D-14-0023.1 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Paper file info:

📄 Wordcount for paper.tex is 2793

🔴 Failed to discover a Statement of need section in paper

[editorialbot]

License info:

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

[editorialbot]

:warning: An error happened when generating the pdf.

[luraess]

@editorialbot assign @me as editor

[editorialbot]

Assigned! @me is now the editor

[luraess]

@gaelforget Thanks for submitting your draft to the JuliaCon Proceedings! I will be the managing editor of your paper. Could you please suggest me a succinct list of relevant reviewers.

Also, your paper failed to compile in the system with following error https://github.com/JuliaCon/proceedings-papers/actions/runs/9501383592/job/26186778694 . Please try getting it to compile - it seems to be related to missing reference or similar. To re-trigger PDF generation, use @editorialbot generate pdf. Thanks!

[gaelforget]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[gaelforget]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[gaelforget]

@gaelforget Thanks for submitting your draft to the JuliaCon Proceedings! I will be the managing editor of your paper. Could you please suggest me a succinct list of relevant reviewers.

Will do. Thanks @luraess for handling this submission.

Also, your paper failed to compile in the system with following error https://github.com/JuliaCon/proceedings-papers/actions/runs/9501383592/job/26186778694 . Please try getting it to compile - it seems to be related to missing reference or similar. To re-trigger PDF generation, use @editorialbot generate pdf. Thanks!

I don't understand how to reproduce the issue that needs fixing.

• The paper compiles on my laptop without problem, incl for the BibTeX part.
• The log generated by the GitHub action suggests to look at paper.log and paper.blg but I don't have access to those files.
• I see that there are warnings related to BibTeX in the GitHub action log but I am not sure this is actually related to the 2 errors mentioned.
• I tried docker run ghcr.io/xu-cheng/texlive-full:latest on my laptop to see if I could reproduce the environment used by the GitHub action to reproduce the issue, but then I get an error message from docker.

So how am I supposed to proceed to figure out what the error is, so I can try figure out to fix it?

Please advise

[gaelforget]

ps. I did a couple things that did not affect the outcome : 1. fixe the INVALID DOIs 2. move docs/paper to paper

pps. the docker error message suggest that the image from @xu-cheng does not support ARM. I confirmed that I can run the docker image on an older Mac. But then I dont know how to use it interactively to compile tex, bibtex, etc.

docker run ghcr.io/xu-cheng/texlive-full:latest
Unable to find image 'ghcr.io/xu-cheng/texlive-full:latest' locally
latest: Pulling from xu-cheng/texlive-full
docker: no matching manifest for linux/arm64/v8 in the manifest list entries.
See 'docker run --help'.

[luraess]

Thanks for digging into the issue @gaelforget. I will take a look and advice.

[luraess]

@editorialbot commands

[editorialbot]

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[luraess]

@editorialbot remove editor

[editorialbot]

Editor removed!

[luraess]

@editorialbot assign @luraess as editor

[editorialbot]

Assigned! @luraess is now the editor

[luraess]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[luraess]

@gaelforget seem when comparing to other recently submitted papers (e.g. https://github.com/kaipartmann/Peridynamics.jl/tree/paper_juliacon_2023/paper), you may be missing the .latexmkrc, prep.rb files in your paper folder https://github.com/JuliaOcean/OceanRobots.jl/tree/JuliaConProceedings2023/paper

[gaelforget]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[gaelforget]

I added the files in https://github.com/JuliaOcean/OceanRobots.jl/commit/bcd75310d7e41480cf0d12ac5c1a8c7b85d667b5

but does not seem sufficient (see https://github.com/JuliaCon/proceedings-review/issues/149#issuecomment-2177358642)

[gaelforget]

@editorialbot generate pdf

[editorialbot]

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

[gaelforget]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[gaelforget]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[gaelforget]

@editorialbot generate pdf

[editorialbot]

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

[gaelforget]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[luraess]

It now partly seems to build, with missing refs I guess. Did you manage to get any further insights @gaelforget ?

[gaelforget]

It now partly seems to build, with missing refs I guess. Did you manage to get any further insights @gaelforget ?

Yes, build completed without the refs or with one ref. So I'll need to keep probing to find which ones may be the issue. Adding back a few at a time & call editorialbot each time I guess.

[luraess]

I guess this may be the most efficient for now. Unfortunately, I also have an ARM machine which would hit similar issues with running the Docker image.

[gaelforget]

@editorialbot generate pdf

[gaelforget]

@editorialbot generate pdf

to CMIP6

[editorialbot]

:warning: An error happened when generating the pdf.

[gaelforget]

@editorialbot generate pdf

to bezanson2017julia

[editorialbot]

:warning: An error happened when generating the pdf.

[editorialbot]

:warning: An error happened when generating the pdf.

[gaelforget]

@editorialbot generate pdf

[editorialbot]

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

[gaelforget]

@editorialbot generate pdf