[REVIEW]: Planet_LB: Lattice-Boltzmann solutions for planetary geodynamics problems

whedon commented 1 year ago

Submitting author: !--author-handle-->@thecraigoneill@nicoguaro<!--end-editor-- Reviewers: @brmather, @jfpa Archive: 10.5281/zenodo.8226562

Status

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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

@brmather & @jfpa, 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://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @nicoguaro 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 @brmather

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 code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v1.0.0)?
[x] Authorship: Has the submitting author (@thecraigoneill) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] #214
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state the need for this software and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies? (Ideally these should be handled with an automated package management solution.)
[x] Example usage: Do the authors include examples of how to use the software?
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] #213

Software paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state the need for this software and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jfpa

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 code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v1.0.0)?
[x] Authorship: Has the submitting author (@thecraigoneill) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] #218
[x] Functionality: Have the functional claims of the software been confirmed?
[x] #219

Documentation

[x] A statement of need: Do the authors clearly state the need for this software and who the target audience is?
[x] #215
[x] Example usage: Do the authors include examples of how to use the software?
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] #216

Software paper

[x] #217
[x] A statement of need: Do the authors clearly state the need for this software and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

jfpa commented 1 year ago

@jfpa and @brmather, did @thecraigoneill address your concerns regarding planet_LB?

If so, and seeing that you both already marked all the boxes, would you recommend the work for publication?

@nicoguaro Prof. O'Neill addressed all comments fully. I recommend the work for publication. Thanks for the opportunity of reviewing this work.

brmather commented 1 year ago

@nicoguaro indeed, I recommend publication.

nicoguaro commented 1 year ago

@editorialbot generate pdf

editorialbot 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:

nicoguaro commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1017/CBO9780511807442 is OK
- 10.1007/978-1-4471-7423-3 is OK
- 10.1016/j.pepi.2007.06.009 is OK
- 10.1146/annurev.fluid.30.1.329 is OK
- 10.1063/1.2842379 is OK
- 10.1006/jcph.2000.6616 is OK
- 10.2514/5.9781600866319.0450.0458 is OK

MISSING DOIs

- None

INVALID DOIs

- None

nicoguaro commented 1 year ago

@thecraigoneill, I have created a PR with some style suggestions. Also, I think that you can change the bib file to get the right capitalization for Cambridge University Press.

Regarding the figures in the paper, I have some questions/suggestions:

You are using a colormap that is divergent (I think that it is RdGY). These colormaps are commonly used when one has a particular value that want to highlight and present results above/below it. In the case of figure 1, this seems to be the value of 400. Is there anything special about 400 there?
I suggest that the figures are explicitly mentioned in the text of the paper.
The labels for the vertical axes of the figures are present but the horizontal ones are missing. Also, what are the units?
I am guessing that the color represents temperature (T) but it is not explicitly stated in the caption. It is also missing the units.

thecraigoneill commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

thecraigoneill commented 1 year ago

@editorialbot generate pdf

editorialbot 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:

thecraigoneill commented 1 year ago

Hi @nicoguaro

_I have created a https://github.com/thecraigoneill/planet_LB/pull/3 with some style suggestions. Also, I think that you can change the bib file to get the right capitalization for Cambridge University Press._ I've updated the reference.

_Regarding the figures in the paper, I have some questions/suggestions:

You are using a colormap that is divergent (I think that it is RdGY). These colormaps are commonly used when one has a particular value that want to highlight and present results above/below it. In the case of figure 1, this seems to be the value of 400. Is there anything special about 400 there?_

The base is at 800C, so 400C is halfway point. In convection literature/geodynamics (my background) it's pretty common to use diverging colorpalets as they show the thermal boundary layers well, and the RdGY is a nice modern version.

_I suggest that the figures are explicitly mentioned in the text of the paper._

I've dropped mention in the relevant places.

_The labels for the vertical axes of the figures are present but the horizontal ones are missing. Also, what are the units?_

Added units/labels to update figures.

_I am guessing that the color represents temperature (T) but it is not explicitly stated in the caption. It is also missing the units._

On top of the Figure changes, I updated the captions to reflect this information.

Ok - I think that is it? cheers C

nicoguaro commented 1 year ago

@thecraigoneill, I think that you need to create a new release at the repo. That way, we can link the publication to that version.

thecraigoneill commented 1 year ago

Hi @nicoguaro Created a new release as requested, its tab is V1.1. Linked here: https://github.com/thecraigoneill/planet_LB/releases/tag/V1.1

nicoguaro commented 1 year ago

@editorialbot set V1.1 as version

editorialbot commented 1 year ago

Done! version is now V1.1

nicoguaro commented 1 year ago

@thecraigoneill can you archive the current release into Zenodo?

thecraigoneill commented 1 year ago

Hi @nicoguaro - done. https://doi.org/10.5281/zenodo.8226562

nicoguaro commented 1 year ago

@editorialbot set https://doi.org/10.5281/zenodo.8226562 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8226562

nicoguaro commented 1 year ago

@editorialbot recomend-accept

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

nicoguaro commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1017/CBO9780511807442 is OK
- 10.1007/978-1-4471-7423-3 is OK
- 10.1016/j.pepi.2007.06.009 is OK
- 10.1146/annurev.fluid.30.1.329 is OK
- 10.1063/1.2842379 is OK
- 10.1006/jcph.2000.6616 is OK
- 10.2514/5.9781600866319.0450.0458 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/jose-papers/pull/132, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

nicoguaro commented 1 year ago

@labarba, I think that from here we need your help!

labarba commented 1 year ago

hi @thecraigoneill — please check your proof for final adjustments. I noticed that the caption under Figures 1 and 2 are repeated in the text, with italics. Also, in parentheticals, replace the string "eg." with "e.g.," (including the comma). For Figure 3 move the caption text into an actual caption.

thecraigoneill commented 1 year ago

@editorialbot generate pdf

editorialbot 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:

thecraigoneill commented 1 year ago

@editorialbot generate pdf

editorialbot 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:

thecraigoneill commented 1 year ago

@editorialbot generate pdf

editorialbot 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:

thecraigoneill commented 1 year ago

@editorialbot generate pdf

editorialbot 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:

thecraigoneill commented 1 year ago

@editorialbot generate pdf

editorialbot 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:

thecraigoneill commented 1 year ago

@labarba @nicoguaro - thanks guys. Manuscript has been cross-checked for all "eg". Captions inserted into each Figure instance (and removed from text). The final pdf generated looks.... reasonable (?!) to me, I don't see any more grammatical or formatting issues, so I think that's it?

labarba commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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.

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CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: O'Neill given-names: Craig J orcid: "https://orcid.org/0000-0002-6034-1881" doi: 10.5281/zenodo.8226562 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: O'Neill given-names: Craig J orcid: "https://orcid.org/0000-0002-6034-1881" date-published: 2023-08-10 doi: 10.21105/jose.00205 issn: 2577-3569 issue: 66 journal: Journal of Open Source Education publisher: name: Open Journals start: 205 title: "Planet_LB: Lattice-Boltzmann solutions for planetary geodynamics problems" type: article url: "https://jose.theoj.org/papers/10.21105/jose.00205" volume: 6 title: "Planet_LB: Lattice-Boltzmann solutions for planetary geodynamics problems" ```

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editorialbot commented 1 year ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/jose-papers/pull/133
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00205
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

labarba commented 1 year ago

Congratulations, @thecraigoneill, your JOSE paper is published! 🎉

Huge thanks to our Editor: @nicoguaro and the Reviewers: @brmather, @jfpa — you make all this possible 🙏

editorialbot commented 1 year ago

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