[REVIEW]: SeismicMesh: Triangular meshing for seismology

[whedon]

Submitting author: @krober10nd (Keith Roberts)
Repository: https://github.com/krober10nd/SeismicMesh
Version: v3.3.1
Editor: @meg-simula
Reviewers: @nschloe, @jorgensd
Archive: 10.5281/zenodo.4447042

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/ba94127ebbd0ca13c841f047fb5077bd/status.svg)](https://joss.theoj.org/papers/ba94127ebbd0ca13c841f047fb5077bd)

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

@nschloe, 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 @meg-simula 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 @nschloe

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

• I confirm that I read and will adhere to the JOSS 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 (@krober10nd) 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: Do the authors clearly state 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 @jorgensd

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

• I confirm that I read and will adhere to the JOSS 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 (@krober10nd) 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: Do the authors clearly state 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @nschloe 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:

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

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s00366-006-0014-1 is OK
- 10.1016/j.cageo.2007.06.014 is OK
- 10.1145/2998441 is OK
- 10.1007/s00158-018-1950-2 is OK
- 10.1007/s12665-015-4537-x is OK
- 10.1073/pnas.93.4.1591 is OK
- 10.5194/gmd-12-1847-2019 is OK
- 10.1016/j.jcp.2014.01.005 is OK
- 10.1109/SC.2014.86 is OK
- 10.1002/nme.2579 is OK
- 10.1145/2629697 is OK
- 10.1093/gji/ggv380 is OK
- 10.1190/1.3238367 is OK
- 10.1137/S0036144503429121 is OK
- 10.1190/1.1441754 is OK
- 10.1190/1.1437283 is OK

MISSING DOIs

- 10.1007/978-3-642-04319-2_10 may be a valid DOI for title: Perturbing slivers in 3D Delaunay meshes

INVALID DOIs

- None

[whedon]

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

[meg-simula]

Issue started by whedon before proper assignment of reviewers, closing this and trying again.

[arfon]

@whedon add @jorgensd as reviewer

[whedon]

OK, @jorgensd is now a reviewer

[arfon]

OK, you should be good to go here now @meg-simula!

[meg-simula]

Ok, thanks @arfon!

@nschloe @jorgensd @krober10nd Thanks for your patience - ready for the review now.

[krober10nd]

Thanks could you correct the title please? It says ERR ..

[jorgensd]

@arfon I am not able to tick the checklist boxes above, and when trying to accept the invitation I get that it is expired.

[jorgensd]

@whedon generate pdf

[whedon]

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

[jorgensd]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

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

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

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

# 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

[jorgensd]

@arfon I am not able to tick the checklist boxes above, and when trying to accept the invitation I get that it is expired.

@arfon Im still not able to tick the boxes above (even now that Im assigned as reveiwer), is it possible to resend an invitiation to me?

[arfon]

@whedon re-invite @jorgensd as reviewer

[meg-simula]

@krober10nd Happy New Year! Thanks for your patience and nudging here.

In the paper, could you please address the following minor comment:

• Core functionality - item 2. This sentence is unclear (something about the "in either" bit), please improve.

After resolving this, could you please

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[krober10nd]

Hey @meg-simula ...Okay, I edited the text in the paper in the Core functionality- item 2 (it was a typo).

I then made a tagged release V3.3.1 https://github.com/krober10nd/SeismicMesh/releases/tag/V3.3.1 and archived it in Zenodo and edited the metadata on Zenodo to reflect and match the paper. https://zenodo.org/record/4447042#.YAWQvS1h1pQ

The doi is 10.5281/zenodo.4447042

[meg-simula]

@whedon set 10.5281/zenodo.4447042 as archive

[whedon]

OK. 10.5281/zenodo.4447042 is the archive.

[meg-simula]

@whedon set v3.3.1 as version

[whedon]

OK. v3.3.1 is the version.

[meg-simula]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2030

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2030, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1142/9789811202124_0004 is OK
- 10.1007/s00366-006-0014-1 is OK
- 10.1016/j.cageo.2007.06.014 is OK
- 10.1145/2998441 is OK
- 10.1007/s00158-018-1950-2 is OK
- 10.1007/s12665-015-4537-x is OK
- 10.1073/pnas.93.4.1591 is OK
- 10.5194/gmd-12-1847-2019 is OK
- 10.1016/j.jcp.2014.01.005 is OK
- 10.1142/9789811202124_0004 is OK
- 10.1109/sc.2014.86 is OK
- 10.1002/nme.2579 is OK
- 10.1145/2629697 is OK
- 10.1093/gji/ggv380 is OK
- 10.1190/1.3238367 is OK
- 10.1137/s0036144503429121 is OK
- 10.1190/1.1441754 is OK
- 10.1007/978-3-642-04319-2_10 is OK
- 10.1190/1.1437283 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[krober10nd]

Thanks! Does the chief editor have to approve this now or is good to go?

[meg-simula]

This is now with the Editor(s) in Chief, yes.

…

-- Marie

On Mon, 18 Jan 2021, 16:37 Keith Roberts, ***@***.***> wrote: Thanks! Does the chief editor have to approve this now or is good to go? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2687 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFPEST2H6GDOOA264F6YSDS2RIU5ANCNFSM4RUQHQKA> .

[kthyng]

@krober10nd Hi! I'll be taking over from here. I see your Zenodo archive is set up, and the version of your software is set.

Paper comments:

• Your #1 under Core Functionality — the last reference should not have ().
• your #3 — I'm outside this field but in ocean meshes, 2d meshes can have bad quality shape (e.g. really narrow triangles). Could you state briefly why 2d meshes don't have degenerate elements?
• Parallelism first sentence: no () around reference.

[krober10nd]

@kthyng Thanks! I fixed up the two citations to be in-text rather than parenthetical. In regard to your comment about degenerate element quality, indeed I meant so-called sliver elements which occur only in 3D meshes. I edited the text minimally to be more specific what I meant by degenerate elements in this case.

[kthyng]

@whedon generate pdf

[whedon]

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

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02687 joss-papers#2036
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02687
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congratulations on your new publication @krober10nd! Thanks to editor @meg-simula and reviewers @nschloe and @jorgensd for your time and expertise!!

[whedon]

🎉🎉🎉 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.02687/status.svg)](https://doi.org/10.21105/joss.02687)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02687">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02687/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02687/status.svg
   :target: https://doi.org/10.21105/joss.02687

This is how it will look in your documentation:

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