[REVIEW]: OGRe: An Object-Oriented General Relativity Package for Mathematica

whedon commented 3 years ago

Submitting author: @bshoshany (Barak Shoshany) Repository: https://github.com/bshoshany/OGRe Version: v1.6 Editor: @VivianePons Reviewer: @kostunin, @amelialdrew Archive: 10.5281/zenodo.5168868

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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

@kostunin & @amelialdrew, 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 @VivianePons 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 @kostunin

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 (@bshoshany) 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: 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?
[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 @amelialdrew

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 (@bshoshany) 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: 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?
[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?

kostunin commented 3 years ago

Dear @bshoshany, thanks for the comprehensive answers!

The points on papers and tests are understandable and I think that your explanation are acceptable and fulfill the requirements for publication.

A comment regarding automated tests (hopefully you or your students can implement them later): at the present moment only developer can verify the calculations performed by the software (manually, as it is described), but the end used is not able to do so, especially if not an expert in the field. So, the explicit comparison of calculation results would be a great advantage, but taking into account the target audience of your software, the current documentation is sufficient.

Regarding parallelization -- I think it is indeed platform/memory/CPU/etc related issue and unavoidable taking into account diversity of Mathematica installations. Could you please send me a short notebook, which tests only parallelization, so I can run and troubleshoot it? I think it is just a minor bug and can be discussed just in your github and should not postpone the publication.

I am happy with summary corrections, I think it is sufficient to modify text in this way.

@VivianePons I recommend to give a green light to a paper, the software clearly represents scholarly effort and is very well documented. The minor improvements can be implemented in upcoming versions.

VivianePons commented 3 years ago

Thank you very much @kostunin , with your green light, I can now take it to next step toward publication :)

VivianePons commented 3 years ago

@whedon generate paper

whedon commented 3 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

VivianePons commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #3416 with the following error:

 Can't find any papers to compile :-(

VivianePons commented 3 years ago

@whedon generate pdf from branch paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

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:

VivianePons commented 3 years ago

@whedon check references

VivianePons commented 3 years ago

@whedon check references from branch paper

whedon commented 3 years ago

Attempting to check references... from custom branch paper

whedon commented 3 years ago

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

OK DOIs

- 10.1007/s41114-018-0015-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kostunin commented 3 years ago

@VivianePons I guess @bshoshany did not introduce the corrected paragraph in the final version, let us wait for his confirmation.

VivianePons commented 3 years ago

No problem, @bshoshany let me know when the paper is in its final state for publication

bshoshany commented 3 years ago

@kostunin Thank you so much for green-lighting the publication!

Thanks for your help with the potential bug - I've attached a parallelization test notebook here, please let me know if it doesn't work for you (perhaps by opening an issue in the package repository): Test.zip.

Now that I have your approval, I updated paper.md with the new paragraph.

@VivianePons The paper is now ready for publication! Thanks :)

bshoshany commented 3 years ago

@whedon generate pdf from branch paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

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:

VivianePons commented 3 years ago

@whedon check references

VivianePons commented 3 years ago

@whedon check references from branch paper

whedon commented 3 years ago

Attempting to check references... from custom branch paper

whedon commented 3 years ago

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

OK DOIs

- 10.1007/s41114-018-0015-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

VivianePons commented 3 years ago

@bshoshany thanks! Can you make a tagged release of the paper / software (on Zenodo, figshare, or other) and send me the DOI? Be careful to use the same metadata (title, author) as for the paper itself

bshoshany commented 3 years ago

@VivianePons I'm not sure I understand, doesn't JOSS generate its own DOI for the paper? The paper proof shows 10.21105/joss.03416 as the DOI.

VivianePons commented 3 years ago

JOSS does but I need a tagged release of the software

bshoshany commented 3 years ago

I see, no problem. The software already has a DOI from Zenodo: doi:10.5281/zenodo.4742935

Is that okay, or do I need to create a separate one with the same title as the paper?

VivianePons commented 3 years ago

I see that this one is from August 8, has there been no change since then?

In any case, I need the same title indeed. I believe you can change it without making a new one

bshoshany commented 3 years ago

The latest version of OGRe is indeed v1.6 from 2021-08-07. I did change paper.md a few days ago due to @kostunin's comments, but that's not reflected in Zenodo since it only refers to the software and not the paper.

I changed the title now. Please let me know if you also need the paper to be included in the tagged release, or if just the software is enough.

VivianePons commented 3 years ago

That's perfect, thanks!

VivianePons commented 3 years ago

@whedon set 10.5281/zenodo.5168868 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5168868 is the archive.

VivianePons commented 3 years ago

@whedon set v1.6 as version

whedon commented 3 years ago

OK. v1.6 is the version.

VivianePons commented 3 years ago

Hi @kostunin you forgot to check the "Performance" box. The box needs to be checked even if there is no performance claim.

kostunin commented 3 years ago

Hi @kostunin you forgot to check the "Performance" box. The box needs to be checked even if there is no performance claim.

done

VivianePons commented 3 years ago

I can now propose the paper for publication! Congratulation @bshoshany and thank you @kostunin and @amelialdrew for the reviews

VivianePons commented 3 years ago

@whedon recommend-accept from branch paper

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1007/s41114-018-0015-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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/2552

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2552, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch paper

kyleniemeyer commented 3 years ago

Hi @bshoshany, I'm the AEIC on duty this week, doing some final checks. I just have a few minor edits for your paper before accepting:

[ ] Could you add a bit more to your affiliation? Usually we see at least department/unit in addition to institution
[ ] Throughout the article, you used hyphens (-) as em-dashes (—). Can you replace those with the latter? For example, in the first paragraph, "...general relativity - the field..." should be "...general relativity—the field...".
[ ] At the end of the statement of need section, if you are including the references in the actual sentence, then I think you should use the @author:2001 citation format rather than [@author:2001]. This would change (e.g.) "differential geometry in (Kobayashi & Nomizu, 1996a)" to "differential geometry in Kobayashi & Nomizu (1996a)". The other option is to remove the "in" before the references and combine, like "differential geometry (Kobayashi & Nomizu, 1996a; Kobayashi & Nomizu, 1996b)" by changing the text to differential geometry [@Kobayashi1; @Kobayashi2].

bshoshany commented 3 years ago

Hi @kyleniemeyer, thanks for the comments! I have applied all of your suggestions to the paper. Please let me know if any other changes are needed.

bshoshany commented 3 years ago

@whedon generate pdf from branch paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

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:

kyleniemeyer commented 3 years ago

@whedon accept deposit=true from branch paper

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/2564
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03416
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

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