[REVIEW]: SeisModels.jl: A Julia package for models of the Earth's interior

whedon commented 4 years ago

Submitting author: @anowacki (Andy Nowacki) Repository: https://github.com/anowacki/SeisModels.jl Version: v1.1.0 Editor: @kbarnhart Reviewers: @daniellivingston, @joa-quim Archive: 10.6084/m9.figshare.11993313

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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

@daniellivingston, @fhorrobin, & @joa-quim please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @kbarnhart know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @daniellivingston

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 (@anowacki) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @fhorrobin

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 (@anowacki) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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

[ ] 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 @joa-quim

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 (@anowacki) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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?

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

anowacki commented 4 years ago

@anowacki is this the most up to date version of the publication? I may have a couple of minor editorial comments on the paper---just want to make sure I'm looking at the right thing.

Hi @kbarnhart—yes, this version is the current one, so please do let me know of any comments you have, the current situation permitting of course.

kbarnhart commented 4 years ago

@whedon generate pdf

kbarnhart commented 4 years ago

@whedon check references

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1111/j.1365-246X.1995.tb03540.x is OK
- 10.1111/j.1365-246X.1991.tb06724.x is OK
- 10.1016/0031-9201(81)90046-7 is OK
- 10.1126/science.1199375 is OK
- 10.1785/gssrl.70.2.154 is OK
- 10.1785/gssrl.81.3.530 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kbarnhart commented 4 years ago

@anowacki I only have a couple of comments. They are meant to improve readability and accessibility for a non-specialist audience.

[ ] In paragraph 2: Define abbreviations: I think this only means writing out PREM as Preliminary Reference Earth Model. If you are aware of better written out names of the other Earth models, I'd recommend using them, but I suspect they will stay as AK135 and iasp91. I think P-wave and S-wave can stay as is.
[ ] In paragraph 4: "appropriate formats" is rather unspecific. Could you revise to state which formats are supported.

Once these changes are in the paper, please do the following:

[ ] Make a tagged release of your software
[ ] 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 (title and author list exactly the same as on the JOSS paper).
[ ] Comment here with:
- The version tag of the archived version
- the DOI of the archived version

I with then move forward with accepting the submission (I will do some final metadata updating and then pass the submission on to the managing editor in chief who will handle final acceptance and publication).

anowacki commented 4 years ago

@whedon generate pdf from branch joss-review

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

anowacki commented 4 years ago

@kbarnhart I have archived v1.1.0 of SeisModels.jl at Figshare with doi 10.6084/m9.figshare.11993313.

kbarnhart commented 4 years ago

@whedon set 10.6084/m9.figshare.11993313 as archive

whedon commented 4 years ago

OK. 10.6084/m9.figshare.11993313 is the archive.

kbarnhart commented 4 years ago

@whedon set v1.1.0 as version

whedon commented 4 years ago

OK. v1.1.0 is the version.

kbarnhart commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1111/j.1365-246X.1995.tb03540.x is OK
- 10.1111/j.1365-246X.1991.tb06724.x is OK
- 10.1016/0031-9201(81)90046-7 is OK
- 10.1126/science.1199375 is OK
- 10.1785/gssrl.70.2.154 is OK
- 10.1785/gssrl.81.3.530 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 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/1371

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1371, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kbarnhart commented 4 years ago

Nice work @anowacki! Thanks to @daniellivingston and @joa-quim for your reviews.

I've now recommended that this be accepted and handed it off to the JOSS Editors in Chief who handle final processing.

arfon commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 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/1372
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02043
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

anowacki commented 4 years ago

Thanks once again, @kbarnhart, @daniellivingston and @joa-quim. The process has been a great pleasure.

arfon commented 4 years ago

@daniellivingston, @joa-quim - many thanks for your reviews and to @kbarnhart for editing this submission ✨

@anowacki - your paper is now published in JOSS :zap::rocket::boom:

whedon commented 4 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:

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