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

[whedon]

Submitting author: @thecraigoneill (Craig O'Neill)
Repository: https://github.com/thecraigoneill/planet_LB
Branch with paper.md (empty if default branch):
Version: V1.1
Editor: @nicoguaro
Reviewers: @brmather, @jfpa
Archive: 10.5281/zenodo.8226562

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/483df4a80d8cb5d9e3fd5a6d9d7fa136"><img src="https://jose.theoj.org/papers/483df4a80d8cb5d9e3fd5a6d9d7fa136/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/483df4a80d8cb5d9e3fd5a6d9d7fa136/status.svg)](https://jose.theoj.org/papers/483df4a80d8cb5d9e3fd5a6d9d7fa136)

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:

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

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

• 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 code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v1.0.0)?
• Authorship: Has the submitting author (@thecraigoneill) made substantial 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? (and documentation is sufficient?) #214
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function 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 #213

Software paper

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

Review checklist for @jfpa

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 code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v1.0.0)?
• Authorship: Has the submitting author (@thecraigoneill) made substantial 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? (and documentation is sufficient?) #218
• 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.) #219

Documentation

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

Software paper

• Authors: Does the paper.md file include a list of authors with their affiliations? #217
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

⚠️ JOSE reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/jose-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1041

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (221.6 files/s, 54174.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           4            121             94            568
Jupyter Notebook                 5              0           1704            508
Markdown                         2             35              0             56
TeX                              1              4              0             49
YAML                             1              6              4             29
-------------------------------------------------------------------------------
SUM:                            13            166           1802           1210
-------------------------------------------------------------------------------


Statistical information for the repository 'a819d866c8c5ec4ec4340762' was
gathered on 2023/04/17.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Craig O'Neill                    6            70             14           10.26
thecraigoneill                   3           731              4           89.74

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
Craig O'Neill                56           80.0          0.6               10.71
thecraigoneill              727           99.5          4.6               12.10

[whedon]

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

[whedon]

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

MISSING DOIs

- None

INVALID DOIs

- None

[nicoguaro]

@brmather, @jfpa, this is the space where the review process takes form. Please see the checklist for each one above and tick the boxes when you see that the criterion is satisfied.

I will be here to answer the questions that you might have.

Let us use as a tentative timeframe the third week of May, is that OK for you?

[jfpa]

@nicoguaro , thanks for the update. Makes sense to me.
Cheers!

[jfpa]

@whedon generate pdf

[whedon]

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

[whedon]

👋 @jfpa, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @brmather, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @brmather, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @jfpa, please update us on how your review is going (this is an automated reminder).

[nicoguaro]

@brmather, @jfpa, would you mind giving us an update on how your review is going? Is there something that @thecraigoneill or I can do to help you move forward?

[jfpa]

Dear Dr. Guarín-Zapata, I'm making progress toward completing the review. I hope to have it ready by the end of the week. Cheers, Pani

…

On Mon, May 29, 2023 at 9:07 AM Nicolás Guarín-Zapata < ***@***.***> wrote: @brmather <https://github.com/brmather>, @jfpa <https://github.com/jfpa>, would you mind giving us an update on how your review is going? Is there something that @thecraigoneill <https://github.com/thecraigoneill> or I can do to help you move forward? — Reply to this email directly, view it on GitHub <#205 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AET7TBY7HSDYQVV2HRHIT4TXISUTNANCNFSM6AAAAAAXAPJ744> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Pani

[brmather]

I’m aiming for the end of this week as well!

[jfpa]

Dear Prof. Guarin @nicoguaro, I'm unable to complete the checklist (the boxes are deactivated). Could you please indicate a way to proceed?

[brmather]

Dear @nicoguaro,

I have reviewed the software and found that it is looking spiffy. The Lattice Boltzmann solver works very efficiently and the examples are, indeed, very useful to Earth Science applications. My only issue with the repository is that the installation instructions are not sufficiently outlined in the README. It needs to have a separate subheading titled "Installation" and the dependencies need to be listed.

Minor comments

• I was initially confused that there is no setup.py file included in the repository, yet installing planet_LB via pip is supported. I suppose that means the package is manually created by the author and pushed to PyPI. If so, there is an opportunity to set up a GitHub action to handle this package deployment whenever a new release is published.
• The tests within planet_LB are not exhaustive to say the least. Maybe a few more tests could be included in there to benchmark numerical solutions against analytical solutions. FYI, GitHub actions can test software on a range of python versions and system architectures.
• Community guidelines for contributions need to be included.

[nicoguaro]

@jfpa, the problem checking te boxes persists or are you able to check them now?

[jfpa]

@jfpa, the problem checking te boxes persists or are you able to check them now?

No, I'm not able to check them.

[labarba]

@whedon re-invite @jfpa as reviewer

[whedon]

OK, the reviewer has been re-invited.

@jfpa please accept the invite by clicking this link: https://github.com/openjournals/jose-reviews/invitations

[editorialbot]

Done! archive is now 10.5281/zenodo.8226562

[nicoguaro]

@editorialbot recomend-accept

[editorialbot]

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

@editorialbot commands

[nicoguaro]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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]

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

Check final proof 👉📄 Download article

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

[nicoguaro]

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

[labarba]

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]

@editorialbot generate pdf

[editorialbot]

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

[thecraigoneill]

@editorialbot generate pdf

[editorialbot]

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

[thecraigoneill]

@editorialbot generate pdf

[editorialbot]

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

[thecraigoneill]

@editorialbot generate pdf

[editorialbot]

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

[thecraigoneill]

@editorialbot generate pdf

[editorialbot]

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

[thecraigoneill]

@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]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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:
- 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"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

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

Here's what you must now do:

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

Any issues? Notify your editorial technical team...

[labarba]

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

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

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://jose.theoj.org/papers/10.21105/jose.00205/status.svg)](https://doi.org/10.21105/jose.00205)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00205">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00205/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00205/status.svg
   :target: https://doi.org/10.21105/jose.00205

This is how it will look in your documentation:

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