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[REVIEW]: cRacklet: a spectral boundary integral method library for interfacial rupture simulation #3724

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @tiburoch (Thibault Roch) Repository: https://gitlab.com/cracklet/cracklet.git Version: v1.0.0 Editor: @diehlpk Reviewers: @srmnitc, @kylebeggs Archive: 10.5281/zenodo.5865617

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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

@kylebeggs & @srmnitc, 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 @diehlpk 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 @kylebeggs

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @srmnitc

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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

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whedon commented 3 years ago

Wordcount for paper.md is 1411

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/0022-5096(60)90013-2 is OK
- 10.1016/S0065-2156(08)70121-2 is OK
- 10.1029/JB084iB05p02161 is OK
- 10.1029/JB088iB12p10359 is OK
- 10.1016/0022-5096(95)00043-I is OK
- 10.1023/A:1007535703095 is OK
- 10.1007/s10704-014-9967-z is OK
- 10.1002/2013JB010586 is OK
- 10.1103/PhysRevLett.119.144101 is OK
- 10.1103/PhysRevE.98.063002 is OK
- 10.1103/PhysRevLett.121.234302 is OK
- 10.1103/PhysRevX.9.041043 is OK
- 10.1016/j.jmps.2019.103806 is OK
- 10.1016/j.epsl.2019.115978 is OK
- 10.1016/j.jmps.2020.103967 is OK
- 10.1115/1.2834197 is OK
- 10.1038/s41467-021-22806-9 is OK
- 10.25080/Majora-4af1f417-011 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.18 s (917.1 files/s, 125884.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             56           1612           2219           5106
C/C++ Header                    42            876           2485           3200
CMake                           35            242           1053            838
MATLAB                           8            256           1074            659
SVG                              1              0              0            565
Python                           8            291            251            542
Fortran 77                       1             50             57            305
TeX                              1             22              0            273
reStructuredText                10            206            128            270
Markdown                         2            101              0            251
YAML                             1             13              2            111
Bourne Shell                     2              7              0             69
Dockerfile                       1              5              3             36
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           169           3685           7279          12234
-------------------------------------------------------------------------------

Statistical information for the repository 'a8312b57321b95788c3385ed' was
gathered on 2021/09/13.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Fabian Barras                   15         12034           2321           62.90
Thibault Roch                   99          6698           1596           36.34
Thibault.Roch                    6           150             23            0.76

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
Fabian Barras             10741           89.3         39.9               22.87
Thibault Roch              5841           87.2          8.5               41.31
whedon commented 3 years ago

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

whedon commented 2 years ago

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

whedon commented 2 years ago

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

diehlpk commented 2 years ago

@whedon remind @srmnitc in 2 weeks

whedon commented 2 years ago

Reminder set for @srmnitc in 2 weeks

diehlpk commented 2 years ago

@whedon remind @KParas in 2 weeks

whedon commented 2 years ago

Reminder set for @KParas in 2 weeks

diehlpk commented 2 years ago

@KParas How is your review going?

KParas commented 2 years ago

@KParas How is your review going?

@diehlpk It is going good. I will try to submit soon.

diehlpk commented 2 years ago

@KParas, @srmnitc how is your review going?

srmnitc commented 2 years ago

@diehlpk Thanks for the reminder. I will finish it next week.

diehlpk commented 2 years ago

@KParas, @srmnitc how is your review going?

srmnitc commented 2 years ago

@diehlpk I have finished my review at this point. I apologize for the delay. This code is quite nice, well written and has already been employed in a number of publications. As such, I believe it will be useful and hence should be published in JOSS.

I have few issues which I opened in the repository:

  1. In order to check the boxes Installation, functionality and Installation instructions: I ran into few problems with installation and tests [1, 2, 3]. Although not blocking of acceptance, a more detailed set of instructions for dependencies could be useful [5]. When these issues are addressed, I would be happy to check the points.
  2. Functionality documentation : The API documentation for C++ side is good. However, there is no documentation on the Python side [4]. The tutorials provided are using Python, the Python API is also mentioned in the paper. Thus I think providing API documentation on the Python side is also necessary.
  3. References: The summary section of the paper has a number of statements that need the support of a citation. For example, the first sentence The study of ..., could be strengthened with a reference.

Once the issues are addressed, I would be happy to check the remaining boxes. Thank you for the chance to review this nice software, and sorry for the delay.

diehlpk commented 2 years ago

@srmnitc Thanks for your review.

@tiburoch Please have a look at @srmnitc's comments and address them in a timely manner.

tiburoch commented 2 years ago

Thank you @srmnitc for your time and your encouraging review. I will try to address your points by next week.

diehlpk commented 2 years ago

@helgee @kylebeggs @mkhoshbin1 would you be interested in reviewing this paper?

helgee commented 2 years ago

Sorry, bit too far outside my comfort zone.

kylebeggs commented 2 years ago

@diehlpk I'd be willing.

diehlpk commented 2 years ago

@whedon add @kylebeggs as reviewer

whedon commented 2 years ago

OK, @kylebeggs is now a reviewer

mkhoshbin1 commented 2 years ago

@diehlpk Sorry. I don't have enough domain knowledge.

diehlpk commented 2 years ago

@whedon remove @KParas as reviewer

whedon commented 2 years ago

OK, @KParas is no longer a reviewer

tiburoch commented 2 years ago

@whedon generate pdf

whedon 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:

tiburoch commented 2 years ago

@srmnitc : the master branch has been updated, taking account of your comments:

I just need more information regarding this issue as I cannot reproduce it.

Best,

srmnitc commented 2 years ago

@tiburoch Thanks! Everything looks good. I have closed the issues and I am unable to tick some of the remaining points. The issue with tests is likely something on my side. I will check again in the next two days and hopefully that will allow me to check the remaining points. Thank you for addressing the points promptly.

diehlpk commented 2 years ago

hi @kylebeggs how is your review going?

kylebeggs commented 2 years ago

@diehlpk going good, haven't made much progress lately due to holiday season. Will be finishing this next week.

kylebeggs commented 2 years ago

@diehlpk Review is complete, but there are a couple minor updates I'd like to see before fully accepting.

Overall the software is great. There is a well-defined purpose for the software and it has been demonstrated to be useful in marching science forward through multiple publications. There is an easy to use API and clean code style. Accessibility through Python is great and will encourage more adoption where the scientists/engineers may not be adept in programming. I accept for publication after these revisions for which I have opened an issue in the repository:

  1. No comparison / mention of other commonly used softwares (#6)
  2. Add tutorial of user-defined interface behavior, constitutive laws, etc. (#7)
diehlpk commented 2 years ago

@diehlpk Review is complete, but there are a couple minor updates I'd like to see before fully accepting.

Overall the software is great. There is a well-defined purpose for the software and it has been demonstrated to be useful in marching science forward through multiple publications. There is an easy to use API and clean code style. Accessibility through Python is great and will encourage more adoption where the scientists/engineers may not be adept in programming. I accept for publication after these revisions for which I have opened an issue in the repository:

1. No comparison / mention of other commonly used softwares ([#6](https://gitlab.com/cracklet/cracklet/-/issues/6))

2. Add tutorial of user-defined interface behavior, constitutive laws, etc. ([#7](https://gitlab.com/cracklet/cracklet/-/issues/7))

@tiburoch please have a look at these comments.

kylebeggs commented 2 years ago

@diehlpk My issues have been addressed and thus the review is complete and submission is accepted!

diehlpk commented 2 years ago

@diehlpk My issues have been addressed and thus the review is complete and submission is accepted!

@kylebeggs Thank you!

diehlpk commented 2 years ago

@tiburoch Thanks! Everything looks good. I have closed the issues and I am unable to tick some of the remaining points. The issue with tests is likely something on my side. I will check again in the next two days and hopefully that will allow me to check the remaining points. Thank you for addressing the points promptly.

@tiburoch Could you please have a look, since the review is quite done.

tiburoch commented 2 years ago

Thank you @kylebeggs for your time and the positive review. The answers to your issues are currently in the way to be merged into the master. @diehlpk : I mentionned to @srmnitc that I cannot reproduce the issue and thus need additional informations to tackle the problem.

srmnitc commented 2 years ago

@tiburoch Thanks once again, sorry for the delay as I was on holidays. I followed the installation instructions using a new environment and everything works fine for me now. I have checked the remaining points. @diehlpk I am glad to recommend this software for acceptance!

diehlpk commented 2 years ago

@whedon generate pdf

diehlpk commented 2 years ago

@whedon check references

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

OK DOIs

- 10.1103/RevModPhys.85.529 is OK
- 10.1029/2008RG000260 is OK
- 10.1016/0005-1098(94)90209-7 is OK
- 10.1016/0022-5096(60)90013-2 is OK
- 10.1016/S0065-2156(08)70121-2 is OK
- 10.1029/JB084iB05p02161 is OK
- 10.1029/JB088iB12p10359 is OK
- 10.1016/0022-5096(95)00043-I is OK
- 10.1023/A:1007535703095 is OK
- 10.1007/s10704-014-9967-z is OK
- 10.1002/2013JB010586 is OK
- 10.1103/PhysRevLett.119.144101 is OK
- 10.1103/PhysRevE.98.063002 is OK
- 10.1103/PhysRevLett.121.234302 is OK
- 10.1103/PhysRevX.9.041043 is OK
- 10.1016/j.jmps.2019.103806 is OK
- 10.1016/j.epsl.2019.115978 is OK
- 10.1016/j.jmps.2020.103967 is OK
- 10.1115/1.2834197 is OK
- 10.1038/s41467-021-22806-9 is OK
- 10.25080/Majora-4af1f417-011 is OK
- 10.1016/j.softx.2021.100785 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon 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:

diehlpk commented 2 years ago

@tiburoch

I would recommend the following changes before, I can recommend the paper for acceptance

diehlpk commented 2 years ago

@tiburoch

The above changes are major changes and the following one is a minor one:

In the last part of the paper, you have a bullet list with all the publications, which is good. However, do you need the bullet list? I think if you do not provide details about the paper, a simple list with ref1, ref2, ,,,,, and refN would be better. Currently, it takes a lot of space with not so much details.

tiburoch commented 2 years ago

Thank you @diehlpk for your comments. There is a merge request pending with modifications for the first and third major changes as well as the reformatting of the references to reduce the paper length. (https://gitlab.com/cracklet/cracklet/-/merge_requests/21).

Regarding your second point: the citation describes the architecture of cRacklet itself (any simulations using cRacklet will compute a time convolution using FFTW3), and Fig1 illustrates the scalability of the code when using more than one thread. I added information on the compiler for both Figures, but I'm not sure if I should add the version number for cRacklet itself (I will update the 1.0.0 version tag to match the version to the state of the master when the paper is formally accepted) or for FFTW3 in the first figure?

Best,

diehlpk commented 2 years ago

@tiburoch

but I'm not sure if I should add the version number for cRacklet itself (I will update the 1.0.0 version tag to match the version to the state of the master when the paper is formally accepted)

I would recommend adding the cRacklet version number and mention that the scaling runs were done with it. I think if one would like to compare your results with some other software, this information is valuable.

diehlpk commented 2 years ago

or for FFTW3 in the first figure?

Yes, I would add that for the scaling plot. I still believe having all this information is valuable for others to reproduce your results.

diehlpk commented 2 years ago

@tiburoch Could you please reply, so we can finalize the paper.