[REVIEW]: deepCR: Cosmic Ray Rejection with Deep Learning

[whedon]

Submitting author: @kmzzhang (Keming Zhang)
Repository: https://github.com/profjsb/deepCR
Version: v0.2.0
Editor: @terrytangyuan
Reviewer: @shreyasbapat, @DanielLenz
Archive: 10.5281/zenodo.3383309

Status

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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

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

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @terrytangyuan know.

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

Review checklist for @shreyasbapat

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.2.0
• Authorship: Has the submitting author (@kmzzhang) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @DanielLenz

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.2.0
• Authorship: Has the submitting author (@kmzzhang) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

⭐ 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:

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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]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[DanielLenz]

I really enjoyed the package and the paper, thanks for providing that! I'll wrap up the review shortly.

In the meantime, could you add the software acknowledgements that you have included in our AAS submission here as well?

[shreyasbapat]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kmzzhang]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kmzzhang]

@DanielLenz I have included the software acknowledgements.

[shreyasbapat]

Can the network architecture diagram be also included in the paper? Or maybe in the README as it is in the https://arxiv.org/pdf/1907.09500.pdf ?

[shreyasbapat]

Though, it's really amazing! I loved reviewing the submission. The paper is awesome, and the package is definitely awesome :D

[terrytangyuan]

@kmzzhang Could you take a look at @shreyasbapat's suggestion? We should be ready to move on after that.

[kmzzhang]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kmzzhang]

@shreyasbapat I've added the network architecture figure in the paper. I also added both figure caption to the main text because they're not showing up as figure captions. Please let me know if this is the optimal way to do it. Thanks!

[DanielLenz]

Thanks for adding the figures! I'm sure there is a more optimal way to adjust the alignment/spacing and the caption; do you have any pointers, @terrytangyuan ?

[terrytangyuan]

cc @openjournals/joss-eics who might have a better idea on how to fix it.

[kyleniemeyer]

@kmzzhang if you put the figures on their own lines, the positioning should be better; you can also add captions:

``deepCR`` is a Python package ...
... at left) is concatenated with the original image as the input.

![Figure 1](https://raw.githubusercontent.com/profjsb/deepCR/master/imgs/network.png)

Since ``deepCR`` ... 
...pixels replaced with deepCR predictions  (last row).

![Figure 2](https://raw.githubusercontent.com/profjsb/deepCR/master/imgs/postage-sm.jpg)
 
In the paper accompanying ``deepCR`` [@deepcr], the authors showed that ...

[kmzzhang]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

@terrytangyuan - this looks to be ready for you to accept I think?

[terrytangyuan]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1086/323894 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.1482019 is OK
- 10.7717/peerj.453 is OK
- 10.3847/1538-3881/aabc4f is OK

MISSING DOIs

- None

INVALID DOIs

- None

[terrytangyuan]

@kmzzhang @arfon Thanks!

@kmzzhang At this point 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.

[kmzzhang]

@terrytangyuan DOI: 10.5281/zenodo.3383309. Thanks!

[terrytangyuan]

@whedon set v0.2.0 as version

[whedon]

OK. v0.2.0 is the version.

[terrytangyuan]

@whedon set 10.5281/zenodo.3383309 as archive

[whedon]

OK. 10.5281/zenodo.3383309 is the archive.

[terrytangyuan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#940

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#940, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[terrytangyuan]

Looks good to me. @arfon Could you handle the next steps?

[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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01651 joss-papers#941
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01651
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...

[arfon]

@shreyasbapat, @DanielLenz - many thanks for your reviews here and to @terrytangyuan for editing this submission ✨

@kmzzhang - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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[kmzzhang]

@arfon I just realized that the title in the paper is incorrect. It should be “deepCR: Cosmic Ray Rejection with Deep Learning,” while the published paper has the word “Ray" missing. I may have omitted it in the paper source file — the title in the paper submission metadata is correct. Is there a way to fix this error?

[arfon]

@kmzzhang - I can fix this for you.

[arfon]

OK that should be fixed now. It might take a few hours for the updated paper to show up online as there's caching in place for the PDFs.