[REVIEW]: kuibit: Analyzing Einstein Toolkit simulations with Python

whedon commented 3 years ago

Submitting author: @sbozzolo (Gabriele Bozzola) Repository: https://github.com/Sbozzolo/kuibit/ Version: 1.0.0 Editor: @eloisabentivegna Reviewer: @yurlungur, @eloisabentivegna Archive: 10.5281/zenodo.4681119

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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

@yurlungur & @eloisabentivegna, 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 @eloisabentivegna 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 @yurlungur

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 (@sbozzolo) 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 @eloisabentivegna

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 (@sbozzolo) 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?

whedon commented 3 years ago

Attempting PDF compilation from custom branch joss-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:

eloisabentivegna commented 3 years ago

@sbozzolo, one more request: could you change the Zenodo archive title to match this submission title (see https://joss.readthedocs.io/en/latest/editing.html#after-reviewers-recommend-acceptance)? The author list should also match the submission's author list. (But thanks for the credit! :) )

Sbozzolo commented 3 years ago

How do I do it? Everything was generated automatically by Zenodo

EDIT: I found out: I have to add a zenodo.json to my repo. I'll regenerate the archive.

Sbozzolo commented 3 years ago

Okay, I think I got it (even if I had to regenerate the archive 3 times)!

The new DOI is 10.5281/zenodo.4681119

eloisabentivegna commented 3 years ago

@whedon set 10.5281/zenodo.4681119 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4681119 is the archive.

eloisabentivegna commented 3 years ago

@whedon generate pdf from branch joss-paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch joss-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:

eloisabentivegna commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

PDF failed to compile for issue #3099 with the following error:

 Can't find any papers to compile :-(

eloisabentivegna commented 3 years ago

@whedon accept from branch joss-paper

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/2222

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2222, 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 joss-paper

whedon commented 3 years ago

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

OK DOIs

- 10.5281/zenodo.3866075 is OK
- 10.1007/3-540-36569-9_13 is OK
- doi:10.1088/0264-9381/29/11/115001 is OK
- 10.1103/PhysRevD.72.024028 is OK
- 10.1088/1361-6382/aa9cad is OK
- 10.1145/3311790.3396656 is OK

MISSING DOIs

- None

INVALID DOIs

- None

eloisabentivegna commented 3 years ago

Thanks @Sbozzolo for the nice package, and thanks @Yurlungur for an exceptionally thorough review! I appreciate your collaboration.

Yurlungur commented 3 years ago

My pleasure. I'm very excited to see Kuibit enter the Einstein Toolkit ecosystem!

kyleniemeyer commented 3 years ago

Hi @Sbozzolo, I am the AEIC on duty this week doing some final checks before accepting.

I noticed that the Guercilena citation might have the incorrect title or URL, can you double check that one? I think it should be rugutils.

Sbozzolo commented 3 years ago

Thank you very much, @eloisabentivegna and @Yurlungur !

@kyleniemeyer, yes, thanks, I just pushed a new version. I also took the chance to add the Cactus citation inline when I mention Cactus.

kyleniemeyer commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #3099 with the following error:

 Can't find any papers to compile :-(

kyleniemeyer commented 3 years ago

@whedon generate pdf from branch joss-paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch joss-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 from branch joss-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

- 10.5281/zenodo.3866075 is OK
- 10.1007/3-540-36569-9_13 is OK
- doi:10.1088/0264-9381/29/11/115001 is OK
- 10.1103/PhysRevD.72.024028 is OK
- 10.1088/1361-6382/aa9cad is OK
- 10.1145/3311790.3396656 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/2224

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2224, 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 joss-paper

kyleniemeyer commented 3 years ago

@whedon accept deposit=true from branch joss-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/2225
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03099
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 3 years ago

Congratulations @Sbozzolo on your article's publication in JOSS!

Many thanks to @Yurlungur for reviewing this, and @eloisabentivegna for editing (and reviewing).

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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03099/status.svg)](https://doi.org/10.21105/joss.03099)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03099">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03099/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03099/status.svg
   :target: https://doi.org/10.21105/joss.03099

This is how it will look in your documentation:

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