[REVIEW]: SALSA: A Python Package for Constructing Synthetic Quasar Absorption Line Catalogs from Astrophysical Hydrodynamic Simulations

[whedon]

Submitting author: @biboyd (Brendan Boyd)
Repository: https://github.com/biboyd/SALSA
Version: v1.0.0
Editor: @danielskatz
Reviewer: @olebole, @zpace
Archive: 10.5281/zenodo.4002067

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Status

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Markdown: [![status](https://joss.theoj.org/papers/57e7093a8aeb101332be1e1e53dc2793/status.svg)](https://joss.theoj.org/papers/57e7093a8aeb101332be1e1e53dc2793)

Reviewers and authors:

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Reviewer instructions & questions

@olebole & @zpace, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 @olebole

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@biboyd) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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 @zpace

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@biboyd) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

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

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

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.

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For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- 10.1146/annurev-astro-091916-055240 is OK
- 10.3847/1538-4357/aa7d04 is OK
- 10.3847/1538-4357/aa7e2d is OK
- 10.3847/1538-4357/aadd03 is OK
- 10.3847/1538-4357/aa87b4 is OK
- 10.1088/0004-637X/731/1/6 is OK
- 10.1088/0004-637X/791/1/64 is OK
- 10.3847/1538-4357/ab0654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

👋 @olebole & @zpace - thanks again for agreeing to review!

This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/2581 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

[olebole]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[olebole]

I am now happy with the paper and would recommend to accept it.

[danielskatz]

Thanks @olebole!

[danielskatz]

👋 @zpace - it looks like you are close to finishing as well, other than the references checkbox

Is this correct?

[zpace]

@danielskatz everything looks good to me, as well. The authors have addressed my relatively few suggestions. I recommend accepting this submission.

[danielskatz]

Thanks @olebole and @zpace - that was remarkably fast and easy

[danielskatz]

👋 @biboyd (Brendan Boyd) - At this point could you:

• 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.

[biboyd]

@danielskatz I made a new release and archived on zenodo. Here is the information

Release: v1.0.0

zenodo archive: https://zenodo.org/record/4002068#.X0aJKxl7lhE

DOI: 10.5281/zenodo.4002067

[danielskatz]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[danielskatz]

@whedon set 10.5281/zenodo.4002067 as archive

[whedon]

OK. 10.5281/zenodo.4002067 is the archive.

[danielskatz]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1146/annurev-astro-091916-055240 is OK
- 10.3847/1538-4357/aa7d04 is OK
- 10.1088/0067-0049/192/1/9 is OK
- 10.3847/1538-4357/aa7e2d is OK
- 10.3847/1538-4357/aadd03 is OK
- 10.3847/1538-4357/aa87b4 is OK
- 10.1088/0004-637X/731/1/6 is OK
- 10.1088/0004-637X/791/1/64 is OK
- 10.3847/1538-4357/ab0654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

I found a few small fixes needed in the paper - biboyd/SALSA#5

Otherwise, this looks ready to go to me

Please let me know when you have merged this, or what you disagree with

[biboyd]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[biboyd]

I merged in your small changes. I also reopened one of the reviewers issues biboyd/SALSA#2 because it wasn't properly addressed. I just added a short snippet referencing the yt software in the paper and then edited the annotations accordingly.

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1146/annurev-astro-091916-055240 is OK
- 10.3847/1538-4357/aa7d04 is OK
- 10.1088/0067-0049/192/1/9 is OK
- 10.3847/1538-4357/aa7e2d is OK
- 10.3847/1538-4357/aadd03 is OK
- 10.3847/1538-4357/aa87b4 is OK
- 10.1088/0004-637X/731/1/6 is OK
- 10.1088/0004-637X/791/1/64 is OK
- 10.3847/1538-4357/ab0654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1676

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1676, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02581 joss-papers#1677
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02581
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Thanks to @olebole & @zpace for reviewing!

And congratulations to @biboyd (Brendan Boyd) and co-authors!!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[danielskatz]

👋 @biboyd - sorry I forgot to ask you this before - is this submission associated with an AAS publication?

[biboyd]

@danielskatz No it is not

[danielskatz]

Thanks - there's a slightly more complicated process that links the two publications together in that case, and it was pointed out to me that we might have missed it - great to know!