[REVIEW]: SeismicMesh: Triangular meshing for seismology

whedon commented 4 years ago

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

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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

@nschloe, 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 @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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

krober10nd commented 3 years ago

I would like to check with @nschloe if you have any more comments and suggestions for revision to move this forward. Thank you.

meg-simula commented 3 years ago

@nschloe: How is the final bits of this review going? Any additional comments/issues to be resolved?

@jorgensd Thanks for your efforts on this - I note that all your boxes are checked - is this good to go from your side?

nschloe commented 3 years ago

How is the final bits of this review going

I will check as soon as I have time.

jorgensd commented 3 years ago

@nschloe: How is the final bits of this review going? Any additional comments/issues to be resolved?

@jorgensd Thanks for your efforts on this - I note that all your boxes are checked - is this good to go from your side?

This is good to go from my side.

krober10nd commented 3 years ago

I've dealt with one more issue pertaining to the paper (https://github.com/krober10nd/SeismicMesh/pull/170) @nschloe brought up and I've independently improved parallel performance in 2d/3d by a significant margin in https://github.com/krober10nd/SeismicMesh/pull/171 and https://github.com/krober10nd/SeismicMesh/pull/172 and updated the figure and text accordingly regarding 3d parallel performance.

I'd like to know please where this paper stands.

Thanks

nschloe commented 3 years ago

I might have time to look at the revisions later tonight, otherwise tomorrow.

nschloe commented 3 years ago

@whedon generate pdf

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:

nschloe commented 3 years ago

@whedon generate pdf

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:

nschloe commented 3 years ago

This is good to go from my point of view.

Just for the record, let me add a few remarks.

@krober10nd was exceptionally responsive to the remarks, and I think the software and the article have greatly improved in the process.
I'm not a big fan of how the software targets seismologists only. SeismicMesh is a parallel implementation of distmesh, and as such is general-purpose mesh generator. There is a function that converts seismology data into a density function, but that part is actually separate and can be used with any other mesh generator. I also wouldn't like to see another mesh generator next year that only adapts that small part for medicine and calls it CellMesh.
For anyone interested, as part of the review process, I compiled a more extensive mesh generator comparison at https://github.com/nschloe/meshgen-comparison (including SeismicMesh).
I love the JOSS review process and I'll hopefully start writing up some articles for it myself next year.

Happy holidays everyone!

krober10nd commented 3 years ago

Thank you Nico! It has been a great pleasure to work on this with these reviewers. I agree with your comments as well.

I've learned a tremendous amount from you guys and I really enjoyed this review process especially the open nature of it! Look forward to seeing your articles appear on here @nschloe!

meg-simula commented 3 years ago

Great, thanks @nschloe, @jorgensd, and @krober10nd! I will follow up from here early next week.

krober10nd commented 3 years ago

@whedon generate pdf

just running Nico's betterbib package to add as much information to the papers bibliography as possible.

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:

meg-simula commented 3 years ago

Early next week will have to be first thing after Jan 4 2021 - Happy Holidays to all of you in the meanwhile!

meg-simula commented 3 years ago

/ooo Dec 22 until Jan 7

krober10nd commented 3 years ago

Hope the time off was relaxing! Please let me know if there’s anything else to be done. Thank you. @meg-simula

krober10nd commented 3 years ago

Hi @meg-simula any updates on this process?

meg-simula commented 3 years ago

@whedon generate pdf

meg-simula commented 3 years ago

@whedon check references

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:

meg-simula commented 3 years ago

@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 commented 3 years ago

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 commented 3 years ago

@whedon set 10.5281/zenodo.4447042 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4447042 is the archive.

meg-simula commented 3 years ago

@whedon set v3.3.1 as version

whedon commented 3 years ago

OK. v3.3.1 is the version.

meg-simula commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 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/2030

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

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 commented 3 years ago

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

meg-simula commented 3 years ago

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

-- Marie

On Mon, 18 Jan 2021, 16:37 Keith Roberts, notifications@github.com 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 https://github.com/openjournals/joss-reviews/issues/2687#issuecomment-762324859, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFPEST2H6GDOOA264F6YSDS2RIU5ANCNFSM4RUQHQKA .

kthyng commented 3 years ago

@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 commented 3 years ago

@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 commented 3 years ago

@whedon generate pdf

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:

kthyng commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

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

Here's what you must now do:

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

Any issues? Notify your editorial technical team...

kthyng commented 3 years ago

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

whedon commented 3 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:
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HTML:
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  <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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