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

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whedon opened this issue Sep 13, 2021 · 92 comments
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accepted CMake published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Shell TeX

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@whedon
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whedon commented Sep 13, 2021

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2cbf53837479d66e53519db2ee14bea7"><img src="https://joss.theoj.org/papers/2cbf53837479d66e53519db2ee14bea7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2cbf53837479d66e53519db2ee14bea7/status.svg)](https://joss.theoj.org/papers/2cbf53837479d66e53519db2ee14bea7)

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:

  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/joss-reviews/invitations

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

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@tiburoch) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • 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 what problems the software is designed to solve 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 (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

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

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@tiburoch) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • 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 what problems the software is designed to solve 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 (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
@whedon
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whedon commented Sep 13, 2021

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 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-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/joss-reviews:

watching

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

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
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whedon commented Sep 13, 2021

Wordcount for paper.md is 1411

@whedon
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whedon commented Sep 13, 2021

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
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whedon commented Sep 13, 2021

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
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whedon commented Sep 13, 2021

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

@whedon
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whedon commented Sep 27, 2021

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

@whedon
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whedon commented Sep 27, 2021

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

@diehlpk
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diehlpk commented Oct 4, 2021

@whedon remind @srmnitc in 2 weeks

@whedon
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whedon commented Oct 4, 2021

Reminder set for @srmnitc in 2 weeks

@diehlpk
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diehlpk commented Oct 4, 2021

@whedon remind @KParas in 2 weeks

@whedon
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whedon commented Oct 4, 2021

Reminder set for @KParas in 2 weeks

@diehlpk
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diehlpk commented Oct 29, 2021

@KParas How is your review going?

@KParas
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KParas commented Nov 3, 2021

@KParas How is your review going?

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

@diehlpk
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diehlpk commented Nov 15, 2021

@KParas, @srmnitc how is your review going?

@srmnitc
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srmnitc commented Nov 16, 2021

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

@diehlpk
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diehlpk commented Nov 29, 2021

@KParas, @srmnitc how is your review going?

@srmnitc
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srmnitc commented Dec 2, 2021

@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
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diehlpk commented Dec 2, 2021

@srmnitc Thanks for your review.

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

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

@diehlpk
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diehlpk commented Dec 13, 2021

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

@helgee
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helgee commented Dec 13, 2021

Sorry, bit too far outside my comfort zone.

@kylebeggs
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@diehlpk I'd be willing.

@whedon whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 18, 2022
@whedon
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whedon commented Jan 18, 2022

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Jan 18, 2022

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
- 10.1029/2021GL094901 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

- 10.1016/j.jmps.2021.104607 may be a valid DOI for title: Velocity-driven frictional sliding: Coarsening and steady-state pulses

INVALID DOIs

- None

@diehlpk
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diehlpk commented Jan 18, 2022

@srmnitc, @kylebeggs thanks for your reviews. We can not run JOSS without your help.

@whedon
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whedon commented Jan 18, 2022

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

Check final proof 👉 openjournals/joss-papers#2892

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2892, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@diehlpk
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diehlpk commented Jan 18, 2022

MISSING DOIs

  • 10.1016/j.jmps.2021.104607 may be a valid DOI for title: Velocity-driven frictional sliding: Coarsening and steady-state pulses

@tiburoch can you please add this DOI to the paper? I am not sure why I missed that before accepting the paper.

@tiburoch
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@diehlpk sorry this slips in when I updated this publication from its arxiv version to the published one. It is fixed now.

@kyleniemeyer
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@whedon generate pdf

@whedon
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whedon commented Jan 18, 2022

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

@kyleniemeyer
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Hi @tiburoch, I am the AEIC on duty this week, and just did some final checks before accepting.

I submitted a small PR to fix a few small things, could you please merge this?

@tiburoch
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Hi @kyleniemeyer , thank you for the additional corrections. I accepted the merge request and it will be automatically merged when the CI is done (should take less than 1h).

@kyleniemeyer
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@whedon generate pdf

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whedon commented Jan 18, 2022

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

@kyleniemeyer
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@tiburoch bah, I missed one citation fix! Could you please change [@geubelle_spectral_1995], [@breitenfeld_numerical_1998] to [@geubelle_spectral_1995; @breitenfeld_numerical_1998] in the second sentence of the Statement of Need section?

After that, we should be ready to publish. Thanks!

@tiburoch
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@kyleniemeyer : it's done, the master branch is updated.

@kyleniemeyer
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@whedon generate pdf

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whedon commented Jan 19, 2022

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

@kyleniemeyer
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@whedon accept deposit=true

@whedon
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whedon commented Jan 19, 2022

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

@whedon whedon added accepted published Papers published in JOSS labels Jan 19, 2022
@whedon
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whedon commented Jan 19, 2022

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented Jan 19, 2022

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03724 joss-papers#2895
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03724
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@kyleniemeyer
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@tiburoch congratulations on your article's publication in JOSS!

Many thanks to @srmnitc and @kylebeggs for reviewing this, and @diehlpk for editing.

@whedon
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whedon commented Jan 19, 2022

🎉🎉🎉 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://joss.theoj.org/papers/10.21105/joss.03724/status.svg)](https://doi.org/10.21105/joss.03724)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03724">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03724/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03724/status.svg
   :target: https://doi.org/10.21105/joss.03724

This is how it will look in your documentation:

DOI

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