[REVIEW]: 3D Line Radiative Transfer & Synthetic Observations with Magritte

[whedon]

Submitting author: @FredDeCeuster (Frederik De Ceuster)
Repository: https://github.com/Magritte-code/Magritte
Branch with paper.md (empty if default branch): joss_paper_1.0
Version: 0.0.1
Editor: @xuanxu
Reviewers: @gonsie, @CFGrote
Archive: 10.5281/zenodo.6320469

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Review checklist for @gonsie

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@FredDeCeuster) 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: 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?
• 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 @CFGrote

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@FredDeCeuster) 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: 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?
• 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. @gonsie, @CFGrote 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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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:

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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]

👋 @CFGrote, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @gonsie, please update us on how your review is going (this is an automated reminder).

[gonsie]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3905 with the following error:

 Can't find any papers to compile :-(

[xuanxu]

@whedon generate pdf from branch joss_paper_1.0

[whedon]

Attempting PDF compilation from custom branch joss_paper_1.0. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[gonsie]

@FredDeCeuster can you clarify the author list on the paper?

In the readme Atulit Srivastava is listed as a developer, but I can't find any contributions from them in GitHub.

In the readme Ward Homan and Jan Bolte are listed as technical advisors, but they are not included in the author list.

[FredDeCeuster]

@gonsie

Atulit Srivastava developed parts for a future version (currently not public), but also already contributed ideas for this version.

Ward Homan and Jan Bolte mostly contributed to the science done with Magritte (see papers in documentation), but I would be happy to include them as co-authors on this paper.

[CFGrote]

Review started. Installation went ok with minor hickups (will post separate issue later). Running the first example gave me errors, see Magritte-code/Magritte#54. I'd like to see this fixed before I continue.

[gonsie]

Thanks @FredDeCeuster, I think the author list you have now is fine, I just wanted to clarify.

[CFGrote]

Review comments on Documentation and Examples in Magritte-code/Magritte#56

[CFGrote]

@whedon generat pdf from branch joss_paper_1.0

[whedon]

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

@whedon commands

[CFGrote]

@whedon generate pdf from branch joss_paper_1.0

[whedon]

Attempting PDF compilation from custom branch joss_paper_1.0. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[CFGrote]

Software paper review in Magritte-code/Magritte#57

[gonsie]

I find the documentation of the code base somewhat lacking. There is almost no API documentation. While the examples do a decent job of walking someone through creating a model, the text itself is limited and doesn't explain much. A note in the documentation points to the code base... but there are very few comments in the code.

[editorialbot]

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

OK DOIs

- 10.1093/mnras/stz3557 is OK
- 10.1093/mnras/staa3199 is OK
- 10.1126/science.abb1229 is OK
- 10.1051/0004-6361/202037492 is OK
- 10.1007/s41115-019-0004-9 is OK
- 10.1051/0004-6361/202140823 is OK
- 10.1051/0004-6361/202141161 is OK

MISSING DOIs

- 10.1146/annurev-astro-090120-033712 may be a valid DOI for title: Evolution and Mass Loss of Cool Ageing Stars: a Daedalean Story

INVALID DOIs

- None

[xuanxu]

@FredDeCeuster the editorial bot suggests 10.1146/annurev-astro-090120-033712 as the DOI for Decin, L. (2020) reference. Can you check if it is the right one and if so update the paper with it?

[FredDeCeuster]

I've checked and added the doi for Decin (2020).
Magritte-code/Magritte@30b5d08

[xuanxu]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[xuanxu]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1093/mnras/stz3557 is OK
- 10.1093/mnras/staa3199 is OK
- 10.1126/science.abb1229 is OK
- 10.1051/0004-6361/202037492 is OK
- 10.1146/annurev-astro-090120-033712 is OK
- 10.1007/s41115-019-0004-9 is OK
- 10.1051/0004-6361/202140823 is OK
- 10.1051/0004-6361/202141161 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[xuanxu]

OK @FredDeCeuster, everything looks good, here are the next steps:

• Please release a new tagged version from the current stable branch so it includes all the changes made during the review process
• Then archive that latest release in Zenodo or a similar service
• Check the Zenodo deposit has the correct metadata: title and authors names should match the paper; you may also add authors' ORCIDs.

Once you do that please report here the version number and archive DOI

[FredDeCeuster]

Thanks!
version number 0.0.1
Zenodo DOI: 10.5281/zenodo.6320469

[xuanxu]

@editorialbot set 10.5281/zenodo.6320469 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.6320469

[xuanxu]

Thank you @FredDeCeuster. We're all set. Recommending for acceptance.

[xuanxu]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3003

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3003, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.03905 joss-papers#3016
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03905
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...

[kyleniemeyer]

Congratulations @FredDeCeuster on your article's publication in JOSS!5887-8498))

Many thanks to @gonsie and @CFGrote for reviewing this, and @xuanxu for editing.

[editorialbot]

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

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