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[REVIEW]: Planet_LB: Lattice-Boltzmann solutions for planetary geodynamics problems #205

Closed whedon closed 11 months ago

whedon commented 1 year ago

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

Status

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:

  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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @jfpa

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 1 year ago

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 :tada:.

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whedon commented 1 year ago

Wordcount for paper.md is 1041

whedon commented 1 year ago 
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 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 
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 commented 1 year ago

@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 commented 1 year ago

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

jfpa commented 1 year ago

@whedon generate pdf

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

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

whedon commented 1 year ago

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

whedon commented 1 year ago

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

whedon commented 1 year ago

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

nicoguaro commented 1 year ago

@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 commented 1 year ago

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 https://github.com/openjournals/jose-reviews/issues/205#issuecomment-1567186326, or unsubscribe https://github.com/notifications/unsubscribe-auth/AET7TBY7HSDYQVV2HRHIT4TXISUTNANCNFSM6AAAAAAXAPJ744 . You are receiving this because you were mentioned.Message ID: @.***>

-- Pani

brmather commented 1 year ago

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

jfpa commented 1 year ago

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

brmather commented 1 year ago

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

nicoguaro commented 1 year ago

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

jfpa commented 1 year ago

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

No, I'm not able to check them.

labarba commented 1 year ago

@whedon re-invite @jfpa as reviewer

whedon commented 1 year ago

OK, the reviewer has been re-invited.

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

labarba commented 1 year ago

@jfpa — Please accept the invitation: this will give you the access required to edit the comment, to be able to click the boxes. Do let me know here that you've accepted, because we have a pending upgrade to the system that will solve this very problem for the future!

jfpa commented 1 year ago

Dear colleagues, Prof. Barba @labarba, Prof. Guarín-Zapata @nicoguaro et al.,

Here are some "issues" related to the checklist above. Thanks for the opportunity of reviewing this submission. Please, let me know if this formatting works or if there is a different way of presenting the issues.

Functionality/Performance I suggest either optimizing the examples for use in the classroom or stating that they're intended for asynchronous activities.

For example, the ‘Lid-driven flow example’ (‘LB_id_flow.ipynb’) is relatively inefficient in the calculation of the cell [3]. For 40,000 steps it takes too long to calculate the benchmark case in my laptop (likely the way a student would use it in class). If these cases are intended for use in the classroom, I’d suggest using a different approach to explore Mohamad's (2011) example. Currently, it is ~120 minutes for 40,000 steps. However, a cool perk is that you can visualize the cavity flow velocity for any quantity of steps. In this vein, would it be useful to save the steps to create a visualization of the evolution?

Documentation I suggest including the installation requirements (packages) in the README to make the test easier, explicitly stating that those are the needed packages (i.e., expanding on the ‘requirements.txt’ file).

Software paper I suggest expanding the references on the implementation of Lattice-Boltzmann modeling to geodynamics and providing key references beyond Mohamad (2011), intended for undergraduate students. For example, Chen & Doolen (1998), Dong et al. (2008), Guo et al. (2000), and D’Humieres (1992).

Suggested references Chen, S., & Doolen, G. D. (1998). Lattice Boltzmann Method for Fluid Flows. Annual Reviews of Fluid Mechanics, 30, 329–364.

D’Humieres, D. (1992). Generalized Lattice-Boltzmann Equations. In B. D. Shizgal & D. P. Weaver (Eds.), Rarefied Gas Dynamics - Theory and Simulations (Vol. 159, pp. 450–458). Progress in Astronautics and Aeronautics.

Dong, Y.-H., Sagaut, P., & Marie, S. (2008). Inertial consistent subgrid model for large-eddy simulation based on the lattice Boltzmann method. Physics of Fluids, 20(035104), 1–13. https://doi.org/10.1063/1.2842379.

Guo, Z., Shi, B., & Wang, N. (2000). Lattice BGK Model for Incompressible Navier-Stokes Equation. Journal of Computational Physics, 165, 288–306. https://doi.org/10.1006/jcph.2000.6616.

nicoguaro commented 1 year ago

@thecraigoneill, both reviewers have marked the checklist for your submission. Nevertheless, they left some comments related to "minor issues". Can you address them?

thecraigoneill commented 1 year ago

Thanks @nicoguaro - can do. I'll get onto these revisions.

nicoguaro commented 1 year ago

@thecraigoneill, did you have a chance to check this out? Is there anything that we can do to help you with the process?

thecraigoneill commented 11 months ago

@whedon generate pdf

editorialbot commented 11 months ago

My name is now @editorialbot

thecraigoneill commented 11 months ago

@editorialbot generate pdf

thecraigoneill commented 11 months ago

@editorialbot commands

editorialbot commented 11 months ago

Hello @thecraigoneill, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set jose-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
thecraigoneill commented 11 months ago

@editorialbot check references

editorialbot commented 11 months 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

MISSING DOIs

- 10.2514/5.9781600866319.0450.0458 may be a valid DOI for title: Generalized Lattice Boltzmann Equations

INVALID DOIs

- None
thecraigoneill commented 11 months ago

@editorialbot check repository

editorialbot commented 11 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (376.8 files/s, 115102.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           5            172            135            817
Jupyter Notebook                 6              0           2467            730
TeX                              1              8              0            103
Markdown                         2             46              0             65
YAML                             1              6              4             29
-------------------------------------------------------------------------------
SUM:                            15            232           2606           1744
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 11 months ago

Wordcount for paper.md is 1041

thecraigoneill commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

thecraigoneill commented 11 months ago

@nicoguaro I've completed the modifications requested by the reviewers. I'm attaching my comments regarding what was done below:

Comments from @brmather:

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.

Both of these requests are done.

_I was initially confused that there is no setup.py file included in the repository, yet installing planetLB 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.

This is a good point. I’ve included the setup file in the repository now, but haven’t automated the pip push call, as I’m a little more conservative with that distribution than github, but this is certainly a possibility once the code base is more mature.

_The tests within planetLB 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.

There are two things here – the benchmarks themselves, and the commit tests. I think the benchmarks test the core functionality of the code fairly well, though, for time-dependent problems, they can take a while to run. I’ve added some more geothermal testing in a new ipynb as well. Regarding implementing the commit tests (in tests.py): The benchmarks generally run through time and so can make for a slow commit if the full suite are run. I’ve opted to test the basic core functionality instead. I’ve updated with some more tests to make sure the 2D structures are behaving each commit.

Community guidelines for contributions need to be included. Community guidelines included!

Comments from @jfpa

I suggest either optimizing the examples for use in the classroom or stating that they're intended for asynchronous activities.

Good point. Some of these are for robust benchmarking, and probably aren’t best suited for the classroom. I’ve updated the ipynb to note this, particularly for the lid problem.

However, a cool perk is that you can visualize the cavity flow velocity for any quantity of steps. In this vein, would it be useful to save the steps to create a visualization of the evolution? Absolutely! I had the functionality hidden away in there. I’ve now made this more explicit, with its own section and a revised codeblock in the ipynb.

I suggest including the installation requirements (packages) in the README to make the test easier, explicitly stating that those are the needed packages (i.e., expanding on the ‘requirements.txt’ file). This has been done.

I suggest expanding the references on the implementation of Lattice-Boltzmann modeling to geodynamics and providing key references beyond Mohamad (2011), intended for undergraduate students. For example, Chen & Doolen (1998), Dong et al. (2008), Guo et al. (2000), and D’Humieres (1992).

Added the suggested references.

thecraigoneill commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

thecraigoneill commented 11 months ago

@editorialbot check references

editorialbot commented 11 months 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
thecraigoneill commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

thecraigoneill commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

thecraigoneill commented 11 months ago

@nicoguaro the paper pdf in the github repo is now up to date too (as you no doubt saw from my preceding 10 comment wall-of-shame editing effort!). I think this takes care of the revisions on my end. I'll await your feedback before thinking about zenodo or somesuch for DOIs. cheers Craig

nicoguaro commented 11 months 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?