Joss-reviews: [REVIEW]: AstroPaint: A Python Package for Painting Halo Catalogs into Celestial Maps

[whedon]

Submitting author: @syasini (Siavash Yasini)
Repository: https://github.com/syasini/AstroPaint
Version: 0.1.1
Editor: @harpolea
Reviewer: @AshKelly, @zpace
Archive: 10.5281/zenodo.4243176

: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.

Status

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Markdown: [![status](https://joss.theoj.org/papers/fb0e63372a0ada00083300ca5f2cba19/status.svg)](https://joss.theoj.org/papers/fb0e63372a0ada00083300ca5f2cba19)

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

@AshKelly & @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 @AshKelly

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 (@syasini) 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: 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 @zpace

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 (@syasini) 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: 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. @AshKelly, @zpace 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.

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@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]

Reference check summary:

OK DOIs

- 10.1088/0004-637X/709/2/920 is OK
- 10.2172/1556957 is OK
- 10.3847/2041-8213/ab0bfe is OK
- 10.1093/mnras/stw2035 is OK
- 10.21105/joss.01298 is OK
- 10.1038/302315a0 is OK
- 10.1093/mnras/sty3226 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[zpace]

After having reviewed this submission, I am happy to recommend it for acceptance into JOSS. The developers have responded to my handful of comments and suggestions to my satisfaction.

[syasini]

Thanks, @zpace. Your comments and feedback were incredibly helpful. We appreciate your assistance and guidance in creating the documentation and all the time you spent on reviewing our software in detail.

[AshKelly]

I would like to apologise for the delay in my review and thank you for your continued patience. I will complete my review before the end of the week!

[syasini]

Thanks @AshKelly! We appreciate it.

[AshKelly]

I am happy to recommend this submission for acceptance into JOSS. The developers have responded positively to all of my comments and suggestions.

I would also like to add that I really like the library and the simplicity of the API. Notably, the abstraction into three main components Catalog, Canvas and Painter. I found that after just a short period experimenting with examples given in the docs, I was able to produce quite involved catalogues with relative ease. I anticipate this is a library I will use in the future. Great job!

I'd also like to thank @zpace as I benefited from the documentation that they helped produce. The RTD is a really great addition!

[syasini]

Thanks for your feedback @AshKelly! I sincerely appreciate your kind comment regarding the API. I'm glad you liked it and found it easy to use.
We're grateful for your all help and really appreciate the time you took to review our work.

[arfon]

@whedon generate pdf

[arfon]

@whedon check references

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[whedon]

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

OK DOIs

- 10.1088/0004-637X/709/2/920 is OK
- 10.2172/1556957 is OK
- 10.3847/2041-8213/ab0bfe is OK
- 10.1093/mnras/stw2035 is OK
- 10.21105/joss.01298 is OK
- 10.1038/302315a0 is OK
- 10.1093/mnras/sty3226 is OK

MISSING DOIs

- 10.1088/1475-7516/2020/10/012 may be a valid DOI for title: The Websky Extragalactic CMB Simulations

INVALID DOIs

- None

[arfon]

:wave: @syasini - I'm going to help out @harpolea to get this paper across the line and published.

[arfon]

@syasini - I made a tiny formatting fix in https://github.com/syasini/AstroPaint/pull/85. After merging (assuming you like the change), could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[syasini]

Thanks for your help @arfon. I just commented on issue #85. I sincerely appreciate your suggestion.

After you submit the PR to develop I will go ahead with the new version release and submission to Zenodo and will report back here with the updates.

[arfon]

@syasini https://github.com/syasini/AstroPaint/pull/86

[syasini]

@arfon, I published a new release on (v1.0.0) on Zenodo. You can find it here. Let me know if further actions are needed on my side.

And thanks for resubmitting the PR to develop. I merged it earlier today :)

[arfon]

@whedon set 10.5281/zenodo.4243176 as archive

[whedon]

OK. 10.5281/zenodo.4243176 is the archive.

[arfon]

@whedon check references

[whedon]

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

OK DOIs

- 10.1088/0004-637X/709/2/920 is OK
- 10.2172/1556957 is OK
- 10.3847/2041-8213/ab0bfe is OK
- 10.1093/mnras/stw2035 is OK
- 10.21105/joss.01298 is OK
- 10.1038/302315a0 is OK
- 10.1093/mnras/sty3226 is OK

MISSING DOIs

- 10.1088/1475-7516/2020/10/012 may be a valid DOI for title: The Websky Extragalactic CMB Simulations

INVALID DOIs

- None

[arfon]

@syasini - did you check if 10.1088/1475-7516/2020/10/012 was a valid DOI for one of your references? If so, please add it to your BibTeX please.

[syasini]

Thanks for pointing that our @arfon. That's indeed the valid DOI for the reference. I just added it to the paper.bib file.

[arfon]

@whedon check references

[whedon]

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

OK DOIs

- 10.1088/0004-637X/709/2/920 is OK
- 10.1088/1475-7516/2020/10/012 is OK
- 10.2172/1556957 is OK
- 10.3847/2041-8213/ab0bfe is OK
- 10.1093/mnras/stw2035 is OK
- 10.21105/joss.01298 is OK
- 10.1038/302315a0 is OK
- 10.1093/mnras/sty3226 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1088/0004-637X/709/2/920 is OK
- 10.1088/1475-7516/2020/10/012 is OK
- 10.2172/1556957 is OK
- 10.3847/2041-8213/ab0bfe is OK
- 10.1093/mnras/stw2035 is OK
- 10.21105/joss.01298 is OK
- 10.1038/302315a0 is OK
- 10.1093/mnras/sty3226 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/1894

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1894, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1895
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02608
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...

[arfon]

@AshKelly, @zpace - many thanks for your reviews here and for @harpolea help editing ✨

@syasini - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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  <img src="https://joss.theoj.org/papers/10.21105/joss.02608/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02608/status.svg
   :target: https://doi.org/10.21105/joss.02608

This is how it will look in your documentation:

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[syasini]

Thanks for the great news @arfon! This is very exciting.

And many thanks again to @zpace and @AshKelly for their insightful feedback and their positive reviews and to @harpolea for editing.

Publishing with JOSS was a great experience and we'll be looking forward to hopefully do it again in the future!

Thank you all 🙏