Joss-reviews: [REVIEW]: `swiftsimio`: A python library for reading SWIFT data

[whedon]

Submitting author: @JBorrow (Josh Borrow)
Repository: https://github.com/swiftsim/swiftsimio
Version: v4.0.4
Editor: @dfm
Reviewer: @dmentipl, @mtremmel
Archive: 10.5281/zenodo.3969353

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Status

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Markdown: [![status](https://joss.theoj.org/papers/e85c85f49b99389d98f9b6d81f090331/status.svg)](https://joss.theoj.org/papers/e85c85f49b99389d98f9b6d81f090331)

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

@dmentipl & @mtremmel, 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 @dfm know.

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

Review checklist for @dmentipl

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 (@JBorrow) 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 @mtremmel

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 (@JBorrow) 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dmentipl, @mtremmel it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

1. 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]

PDF failed to compile for issue #2430 with the following error:

Can't find any papers to compile :-(

[JBorrow]

@whedon generate pdf from branch joss-paper

[whedon]

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

[whedon]

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

[JBorrow]

@whedon generate pdf from branch joss-paper

[whedon]

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

[whedon]

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

[dmentipl]

All of my comments have been addressed. I'm happy to accept!

[dfm]

Thanks @dmentipl!

[dfm]

Pinging @mtremmel!

I know that you said that you needed a few weeks so no rush, just wanted to keep this on your radar! Let me know if you have any questions during the review.

[mtremmel]

All of my comments have been addressed and I am happy to accept!

[dfm]

@whedon generate pdf from branch joss-paper

[whedon]

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

[whedon]

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

[dfm]

@JBorrow: I opened a pull request with some edits for the .bib file - the manuscript otherwise looks great to me. After you merge that, can you build the paper here to make sure you're happy with the proofs (it will be harder to make too many changes later!)

Then, once you're happy with the proofs, can you bump the version number of the code and archive it (using Zenodo or similar). The archive should have the new version number and it should also have exactly the same title and author list as your paper (with Zenodo you can edit the metadata after the DOI is minted).

Finally, please report the new version number and the DOI for the archive in this thread.

Thanks!

[dfm]

@dmentipl, @mtremmel: Thank you very much for your reviews! I really appreciate that time you took and the constructive suggestions you had for the code!!

[JBorrow]

@whedon generate pdf from branch joss-paper

[whedon]

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

[JBorrow]

Thanks all for your effort on this! Really excited to have this out in JOSS.

[whedon]

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

[JBorrow]

The new version number is 4.0.4 and the DOI is 10.5281/zenodo.3969268.

[dfm]

@JBorrow: It looks like all we got in that archive is the wheel of the Python package. It should be the full source of the repo instead!

[JBorrow]

Apologies, I didn't realise that was what was required - how is 10.5281/zenodo.3969353?

[dfm]

@JBorrow: Looks good - thanks!

[dfm]

@whedon set 10.5281/zenodo.3969353 as archive

[whedon]

OK. 10.5281/zenodo.3969353 is the archive.

[dfm]

@whedon set v4.0.4 as version

[whedon]

OK. v4.0.4 is the version.

[dfm]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #2430 with the following error:

Can't find any papers to compile :-(

[dfm]

@whedon accept from branch joss-paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1088/0067-0049/192/1/9 is OK
- 10.1111/j.1365-2966.2005.09655.x is OK
- 10.21105/joss.00809 is OK
- 10.1145/2929908.2929916 is OK
- 10.1093/mnras/stu2058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

: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/1606

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1606, 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

[JBorrow]

Great, the final proof looks good to me. I'd like to thank all three of you for your work and help on this!

[kthyng]

Everything looks good to me!

[kthyng]

@whedon accept deposit=true from branch joss-paper

[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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1607
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02430
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? Notify your editorial technical team...

[kthyng]

Congrats on your new publication @JBorrow! Thanks to the hard work and expertise of our editor @dfm and reviewers @dmentipl, @mtremmel!!

[whedon]

: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.02430/status.svg)](https://doi.org/10.21105/joss.02430)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02430">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02430/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02430/status.svg
   :target: https://doi.org/10.21105/joss.02430

This is how it will look in your documentation:

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