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[REVIEW]: Swalbe.jl: A lattice Boltzmann solver for thin film hydrodynamics #4312

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@Zitzeronion<!--end-author-handle-- (Stefan Zitz) Repository: https://jugit.fz-juelich.de/compflu/swalbe.jl/ Branch with paper.md (empty if default branch): master Version: 0.1.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @mbernaschi, @lnacquaroli Archive: 10.5281/zenodo.7030890

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HTML: <a href="https://joss.theoj.org/papers/414a5b53a41e05a250a352360a7da337"><img src="https://joss.theoj.org/papers/414a5b53a41e05a250a352360a7da337/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/414a5b53a41e05a250a352360a7da337/status.svg)](https://joss.theoj.org/papers/414a5b53a41e05a250a352360a7da337)

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

@mbernaschi, 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:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon 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 @mbernaschi

📝 Checklist for @lnacquaroli

editorialbot commented 2 years ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (529.6 files/s, 134543.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           31           1243            761           6707
TOML                             4            263              2           1072
Markdown                         6            144              0            727
TeX                              1              3              1            399
YAML                             3              3              2            105
-------------------------------------------------------------------------------
SUM:                            45           1656            766           9010
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1734

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/RevModPhys.81.739 is OK
- 10.1017/jfm.2019.595 is OK
- 10.1137/141000671 is OK
- 10.5281/zenodo.4907285 is OK
- 10.1103/RevModPhys.69.931 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1103/PhysRevE.100.033313 is OK
- 10.1103/PhysRevE.104.034801 is OK
- 10.1103/PhysRevFluids.1.073901 is OK
- 10.1103/PhysRevLett.119.204501 is OK
- 10.1103/PhysRevE.63.011208 is OK
- 10.1073/pnas.1820487116 is OK
- 10.1063/1.4863318 is OK
- 10.1021/la301353f is OK
- 10.1017/jfm.2015.590 is OK
- 10.1103/PhysRevLett.111.144502 is OK
- 10.1103/PhysRevLett.109.184502 is OK
- 10.1103/PhysRevLett.95.164503 is OK
- 10.1103/PhysRevLett.124.194502 is OK
- 10.1063/1.5119014 is OK
- 10.1063/1.4824108 is OK

MISSING DOIs

- 10.1038/nmat788 may be a valid DOI for title: Complex dewetting scenarios captured by thin-film models
- 10.1016/j.advengsoft.2019.02.002 may be a valid DOI for title: Rapid software prototyping for heterogeneous and distributed platforms
- 10.1007/s002110000197 may be a valid DOI for title: Nonnegativity preserving convergent schemes for the thin film equation
- 10.1017/jfm.2015.590 may be a valid DOI for title: Displacement flows under elastic membranes. Part 1. Experiments and direct numerical simulations
- 10.1017/jfm.2013.375 may be a valid DOI for title: Modelling the suppression of viscous fingering in elastic-walled Hele-Shaw cells
- 10.1038/144993a0 may be a valid DOI for title: The mathematical theory of non-uniform gases

INVALID DOIs

- doi:10.1357/002224099764805174 is INVALID (failed connection)
editorialbot commented 2 years ago

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

arfon commented 2 years ago

@mbernaschi – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing: 

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/4312 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

arfon commented 2 years ago

:wave: @mbernaschi – just checking in here to see if you'll be starting your review soon?

arfon commented 2 years ago

:wave: @lnacquaroli – would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

The submission under review is Swalbe.jl: A lattice Boltzmann solver for thin film hydrodynamics

mbernaschi commented 2 years ago

Sorry, I am busy till next Thursday (April 28). All the best, Massimo Bernaschi

Il giorno gio 21 apr 2022 alle ore 11:20 Arfon Smith < @.***> ha scritto:

👋 @mbernaschi https://github.com/mbernaschi – just checking in here to see if you'll be starting your review soon?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4312#issuecomment-1104937131, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDMCGJ36VINOO5JSAR524LVGEMUDANCNFSM5TCV3IZQ . You are receiving this because you were mentioned.Message ID: @.***>

-- --- Massimo Bernaschi: Istituto Applicazioni del Calcolo ---- | IAC-CNR | e-mail: @.*** | | Via dei Taurini, 19 | phone: +39 06 49937350 | | 00185 Roma - ITALY | fax: +39 06 4404306 |

Skype nickname: m.bernaschi
See http://www.iac.cnr.it/~massimo for my GPG public key or check
GnuPG Public Key Fingerprint (keyserver.linux.it)
pub 1024/CAA3FB48 2001/01/04 Massimo Bernaschi @.***>
Key fingerprint = 3EFF 7AFF F8A4 F34E 382B DD81 57F3 700A CAA3 FB48
lnacquaroli commented 2 years ago

Hi there, I could start next week if it's OK for you.

It's the first time I would take a review in JOSS so I am unaware of where to leave the comments or to check the items on the checklist above.

Do I need to mention them just here in a comment with a small text around or is there any checklist I can copy in here and check them as I go through the article?

Sorry for the inconvenience, if you feel, just pick someone else...

Zitzeronion commented 2 years ago

👋 @mbernaschi and @lnacquaroli, thanks for accepting to review our contribution.

Looking forward to your feedback 😃

arfon commented 2 years ago

Hi there, I could start next week if it's OK for you.

Apologies for the slow reply. Yes, that would be amazing, thank you @lnacquaroli!

arfon commented 2 years ago

@editorialbot add @lnacquaroli as reviewer

editorialbot commented 2 years ago

@lnacquaroli added to the reviewers list!

arfon commented 2 years ago

@lnacquaroli, please create your checklist typing: @editorialbot generate my checklist and this will generate your review checklist for you to work through.

Any questions, don't hesitate to ask!

lnacquaroli commented 2 years ago

Review checklist for @lnacquaroli

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lnacquaroli commented 2 years ago

Hi @arfon, the review is done. Sorry for the delay, I started actually a couple of days ago to finish it this week. It's a very nice job.

(I think there is a small typo in line 91, "revcovers" should read "recovers").

Please, let me know if there is anything else to do.

Cheers!

arfon commented 2 years ago

Thanks for the update @lnacquaroli!

@mbernaschi – looks like we're just waiting for your review at this point. When do you think you might be able to complete it by?

Zitzeronion commented 2 years ago

@mbernaschi is there anything I can do to help with the process, please let me know.

Thanks for the very positive review @lnacquaroli and thanks for taking the time to run and test the package 😄

arfon commented 2 years ago

FYI I've just followed up with @mbernaschi over email to ask when they might be able to complete their review by.

Zitzeronion commented 2 years ago

@arfon sorry to bother you, but is it possible to get an update?

mbernaschi commented 2 years ago

Review checklist for @mbernaschi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mbernaschi commented 2 years ago

Sorry I opened it by mistake

mbernaschi commented 2 years ago

@arfon Hello, I completed my review. I believe it is a pretty good package although I don't consider Julia as so "necessary" to accomplish the same tasks. I could not find explicit performance claims so I did not check the corresponding box. As to the state of field and references, I believe the authors should add some recent packages. Let me self-cite TLBfind (https://github.com/FrancescaPelusi/TLBfind). It is not at the fault of the authors. TLBfind has been released quite recently. Also a bit of proof-reading of the paper could help. However, all in all, I believe the work should be accepted. Once again, please excuse me for the delay of my review

arfon commented 2 years ago

Thanks @mbernaschi! @Zitzeronion – could you take a look at the feedback from @mbernaschi and let us know your response/changes?

Zitzeronion commented 2 years ago

@mbernaschi thank you a lot for taking the time to review the package and awarding it your approval.

I do agree with @mbernaschi that Julia is not the only language to code a solver similar to Swalbe.jl. The decision in favor of Julia over C++, Fortran or Rust is in fact a question of taste. I think that writing good (documented and tested) Julia code is much easier than writing good C++ code. I also think that the syntax of Julia makes it easier to learn than C++, but again this is my taste. Spending less time on coding and more time on research is a net gain of Julia.

When we first submitted the paper TLBfind was indeed not yet on github. In the revised version of the paper we included TLBfind in the State of the field section among waLBerla, OpenLB and PALABOS.

Zitzeronion commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Zitzeronion commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @Zitzeronion, 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 joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers
Zitzeronion commented 2 years ago

@editorialbot set JOSS as branch

editorialbot commented 2 years ago

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

@editorialbot commands

Zitzeronion commented 2 years ago

@editorialbot set JOSS as branch

editorialbot commented 2 years ago

Done! branch is now JOSS

Zitzeronion commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Zitzeronion commented 2 years ago

@arfon sorry for making a mess with the editorialbot. May I ask one question which I already raised in the prereview issue, is it possible to add an Author's contribution section to the paper?

arfon commented 1 year ago

May I ask one question which I already raised in the prereview issue, is it possible to add an Author's contribution section to the paper?

Sure, that's fine 👍

Zitzeronion commented 1 year ago

@arfon I added short Authors contribution section, thanks for allowing it 😃. I was wondering if there is now the possibility to converge towards a final stage and a publication. To my understanding, @lnacquaroli has given his approval as well as @mbernaschi. Please let me know what is missing and how I can improve the package.

Zitzeronion 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:

arfon commented 1 year ago

@Zitzeronion – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

I can then move forward with accepting the submission.

Zitzeronion commented 1 year ago

@arfon I've created a Zenodo copy/archive after merging the JOSS branch and a version update with the feedback from the reviewers. The zenodo DOI is: 10.5281/zenodo.7030890

Zitzeronion commented 1 year ago

@editorialbot set master as branch

editorialbot commented 1 year ago

Done! branch is now master

Zitzeronion 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:

arfon commented 1 year ago

@editorialbot set 10.5281/zenodo.7030890 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7030890

arfon commented 1 year ago

@editorialbot recommend-accept