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Reviews for the Journal of Open Source Software
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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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Status

status

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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

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

tiburoch commented 2 years ago

@diehlpk : the master has been updated with answers to your comments, including cRacklet and FFTW version number and the compiler that have been used in the Figure legend. A tag has been created in the repository for the version mentioned in the paper. (v1.0.0-alpha-1)

diehlpk 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:

diehlpk commented 2 years ago

@tiburoch Thanks, I can accept the paper as it is.

Please upload the current version to Zenodo or FigShare and provide me with the DOI. Note that the title and the authors on Zenodo or FigShare have to match with the paper.

diehlpk commented 2 years ago

@whedon set v1.0.0-alpha-1 as version

whedon commented 2 years ago

OK. v1.0.0-alpha-1 is the version.

tiburoch commented 2 years ago

@diehlpk . Thank you for your time and for accepting the paper for publication. I have a last question for you before I can upload it to Zenodo: the version that is referenced for Fig 1 (v1.0.0-alpha.1) is the pre-release version, which corresponds to the state of the code before we submitted it to JOSS. Now that publication is accepted, the version number is moving to v1.0.0 as the code has slightly changed to take into account the comments during the review process. Is it possible to have the version number linked to the publication being v1.0.0? I will upload both the pre-release (v1.0.0-alpha.1) and the v.1.0.0 to Zenodo.

Best regards, Thibault

diehlpk commented 2 years ago

@whedon set v1.0.0 as version

whedon commented 2 years ago

OK. v1.0.0 is the version.

diehlpk commented 2 years ago

@diehlpk . Thank you for your time and for accepting the paper for publication. I have a last question for you before I can upload it to Zenodo: the version that is referenced for Fig 1 (v1.0.0-alpha.1) is the pre-release version, which corresponds to the state of the code before we submitted it to JOSS. Now that publication is accepted, the version number is moving to v1.0.0 as the code has slightly changed to take into account the comments during the review process. Is it possible to have the version number linked to the publication being v1.0.0? I will upload both the pre-release (v1.0.0-alpha.1) and the v.1.0.0 to Zenodo.

Best regards, Thibault

@tiburoch The version which includes add edits during the JOSS review needs to be on Zenodo.

I updated the version already.

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

@diehlpk : here is the doi for the software on Zenodo : 10.5281/zenodo.5865477 , And here is the one for the last version (1.0.0) : 10.5281/zenodo.5865617 .

diehlpk commented 2 years ago

@whedon set 10.5281/zenodo.5865617 as archive

diehlpk commented 2 years ago

@whedon commands

whedon commented 2 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon recommend-accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true
diehlpk commented 2 years ago

@whedon set 10.5281/zenodo.5865617 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5865617 is the archive.

diehlpk commented 2 years ago

@tiburoch I can now recommend your paper for acceptance.

diehlpk commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
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
- 10.1029/2021GL094901 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 commented 2 years ago

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

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2892

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 2 years ago

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 commented 2 years ago

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

kyleniemeyer 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:

kyleniemeyer commented 2 years ago

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 commented 2 years ago

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 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:

kyleniemeyer commented 2 years ago

@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 commented 2 years ago

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

kyleniemeyer 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:

kyleniemeyer commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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 commented 2 years ago

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

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

whedon commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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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