Closed whedon closed 2 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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Wordcount for paper.md
is 1411
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
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @srmnitc, please update us on how your review is going (this is an automated reminder).
:wave: @KParas, please update us on how your review is going (this is an automated reminder).
@whedon remind @srmnitc in 2 weeks
Reminder set for @srmnitc in 2 weeks
@whedon remind @KParas in 2 weeks
Reminder set for @KParas in 2 weeks
@KParas How is your review going?
@KParas How is your review going?
@diehlpk It is going good. I will try to submit soon.
@KParas, @srmnitc how is your review going?
@diehlpk Thanks for the reminder. I will finish it next week.
@KParas, @srmnitc how is your review going?
@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:
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.
@srmnitc Thanks for your review.
@tiburoch Please have a look at @srmnitc's comments and address them in a timely manner.
Thank you @srmnitc for your time and your encouraging review. I will try to address your points by next week.
@helgee @kylebeggs @mkhoshbin1 would you be interested in reviewing this paper?
Sorry, bit too far outside my comfort zone.
@diehlpk I'd be willing.
@whedon add @kylebeggs as reviewer
OK, @kylebeggs is now a reviewer
@diehlpk Sorry. I don't have enough domain knowledge.
@whedon remove @KParas as reviewer
OK, @KParas is no longer a reviewer
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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,
@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.
hi @kylebeggs how is your review going?
@diehlpk going good, haven't made much progress lately due to holiday season. Will be finishing this next week.
@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:
@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.
@diehlpk My issues have been addressed and thus the review is complete and submission is accepted!
@diehlpk My issues have been addressed and thus the review is complete and submission is accepted!
@kylebeggs Thank you!
@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.
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.
@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!
@whedon generate pdf
@whedon check references
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@tiburoch
I would recommend the following changes before, I can recommend the paper for acceptance
and suited to study a broad class of problems (fracture and friction)
Can you please put a link to the examples here? Like problemsthe Fourier transforms and the convolutions are computed within a shared-memory parallel framework using FFTW3/OpenMP
I assume you reference to Figure 1 here? If so, could you add the used software versions to the paper? Also, which compilers did you used? I believe that this information is important for reproducibility.512 GiB RAM
You specified the amount of memory here, but not in Figure 1. Can you make this consistent?@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.
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,
@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.
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.
@tiburoch Could you please reply, so we can finalize the paper.
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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