[REVIEW]: deeplenstronomy: A dataset simulation package for strong gravitational lensing

[whedon]

Submitting author: @rmorgan10 (Robert Morgan)
Repository: https://github.com/deepskies/deeplenstronomy
Version: v0.0.1.2
Editor: @pdebuyl
Reviewer: @shreyasbapat, @jiwoncpark
Archive: 10.5281/zenodo.4479712

⚠️ 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.

Status

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Markdown: [![status](https://joss.theoj.org/papers/e978dd566d1f290055a02d76288e95e1/status.svg)](https://joss.theoj.org/papers/e978dd566d1f290055a02d76288e95e1)

Reviewers and authors:

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Reviewer instructions & questions

@shreyasbapat & @jiwoncpark, 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 @shreyasbapat

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 (@rmorgan10) 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 @jiwoncpark

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 (@rmorgan10) 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. @shreyasbapat, @jiwoncpark 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.

⭐ Important ⭐

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:

2. 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

[pdebuyl]

@shreyasbapat @jiwoncpark make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines linked to at the top of this review page.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here.

[whedon]

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

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1086/301513 is OK
- 10.1103/PhysRevD.98.043526 is OK
- 10.3847/1538-4357/ab042c is OK

MISSING DOIs

- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data structures for statistical computing in python
- 10.1016/j.dark.2018.11.002 may be a valid DOI for title: Lenstronomy: multi-purpose gravitational lens modelling software package

INVALID DOIs

- None

[shreyasbapat]

There are a few DOIs missing !

[rmorgan10]

There are a few DOIs missing !

The pandas DOI has been added, and the lenstronomy citation has been updated to the journal article (including the DOI) instead of ArXiv.

deepskies/deeplenstronomy@e9ae93b

[pdebuyl]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.25080/majora-92bf1922-00a is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.dark.2018.11.002 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1086/301513 is OK
- 10.1103/PhysRevD.98.043526 is OK
- 10.3847/1538-4357/ab042c is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @jiwoncpark, please update us on how your review is going.

[whedon]

👋 @shreyasbapat, please update us on how your review is going.

[pdebuyl]

@jiwoncpark @shreyasbapat gentle reminder

[jiwoncpark]

@pdebuyl Apologies for the delay in my update. I should be finished with my review by tomorrow.

[pdebuyl]

Thank you for the reply @jiwoncpark . Since the spring, the timeframe for a JOSS review is 6 weeks maximum. I update the review regularly to make sure that the review will happen but there is no emergency for tomorrow.

[pdebuyl]

@shreyasbapat @jiwoncpark gentle reminder

There are several ways to proceed with the review. You can check the items and proceed with direct feedback to the author or prepare a bulk review. Either way is fine, feel free to ask questions here about it.

[rmorgan10]

@pdebuyl I would like to put the deeplenstronomy paper on arXiv at some point, but this is the first time I've worked with JOSS. Would you recommend waiting until after the review process for any reason?

[pdebuyl]

Hi @rmorgan10 I would recommend waiting for the publication here to save you the trouble of updating the arXiv version. You are free to proceed however (see https://joss.readthedocs.io/en/latest/submitting.html?highlight=arxiv#preprint-policy ).

Just make sure to not reference the paper as published in joss yet (mention of submission is fine of course).

[rmorgan10]

@pdebuyl If I wait until after the review process (and deeplenstronomy is accepted), does JOSS release the TeX for the paper to me?

[pdebuyl]

No. Officially, JOSS only sees the input .md file and the pdf output. It is possible to execute our code locally of course. It uses pandoc. It is also possible to use pandoc directly, provided you have the template and logo. I can help if you wish (not anymore today however).

[arfon]

@rmorgan10 - you might be able to make a TeX version using this script: https://github.com/mattpitkin/psrqpy/blob/master/paper/Makefile

[pdebuyl]

@shreyasbapat @jiwoncpark any news on this?

[shreyasbapat]

I promise to review this in next 2 days😀

[pdebuyl]

@whedon set 10.5281/zenodo.4479712 as archive

[whedon]

OK. 10.5281/zenodo.4479712 is the archive.

[pdebuyl]

@whedon set v0.0.1.2 as version

[whedon]

OK. v0.0.1.2 is the version.

[rmorgan10]

@pdebuyl I've updated the bibliography with your recommendations, thanks! deepskies/deeplenstronomy@032f6a5

[pdebuyl]

@whedon generate pdf

[whedon]

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

[pdebuyl]

Thank you. Can you edit the archive's title to match the paper? It should read "deeplenstronomy: A dataset simulation package for strong gravitational lensing"

[rmorgan10]

Yup! Sorry about that, it's now updated

[pdebuyl]

Thanks :-) The paper will now go the the editor in chief.

Thank you @shreyasbapat and @jiwoncpark , with special mention for the text changes proposed by @jiwoncpark :-)

[pdebuyl]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.4480392 is OK
- 10.5281/zenodo.4476822 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-92bf1922-00a is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.dark.2018.11.002 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1086/301513 is OK
- 10.1103/PhysRevD.98.043526 is OK
- 10.3847/1538-4357/ab042c 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#2071

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2071, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[pdebuyl]

@rmorgan10 please check the final pdf https://raw.githubusercontent.com/openjournals/joss-papers/7b45a09803a630144e588ffe8f36aa033e3dbd66/joss.02854/10.21105.joss.02854.pdf

The editor-in-chief in rotation will pick up the process from here. Thanks for submitting to JOSS :-)

[rmorgan10]

It looks good to me! Thanks @pdebuyl, @jiwoncpark, and @shreyasbapat for your reviews and for helping deeplenstronomy get to this point!

[kyleniemeyer]

Looks good to me, publishing now!

[kyleniemeyer]

@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.02854 joss-papers#2073
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02854
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]

Congrats @rmorgan10 on your article's publication in JOSS!

Many thanks to @shreyasbapat and @jiwoncpark for reviewing this, and @pdebuyl for editing.

[whedon]

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

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