[REVIEW]: ADI.jl: A Julia Package for High-Contrast Imaging

[whedon]

Submitting author: @mileslucas (Miles Lucas)
Repository: https://github.com/JuliaHCI/ADI.jl
Version: v0.5.3
Editor: @dfm
Reviewer: @giordano, @semaphoreP
Archive: 10.5281/zenodo.4323554

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Status

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Markdown: [![status](https://joss.theoj.org/papers/32605be405e024fcbd15cd81dfdf9985/status.svg)](https://joss.theoj.org/papers/32605be405e024fcbd15cd81dfdf9985)

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

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

1. Make sure you're logged in to your GitHub account
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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 @giordano

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 (@mileslucas) 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 @semaphoreP

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 (@mileslucas) 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. @giordano, @semaphoreP 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:

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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]

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

OK DOIs

- 10.1088/1538-3873/128/968/102001 is OK
- 10.1126/science.1102929 is OK
- 10.1086/500401 is OK
- 10.1088/2041-8205/755/2/L28 is OK
- 10.3847/1538-4357/aaa1f2 is OK
- 10.1137/141000671 is OK
- 10.1051/0004-6361/201834136 is OK
- 10.1109/TPDS.2018.2872064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[whedon]

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

[mileslucas]

@whedon preview

[whedon]

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

@whedon commands

[mileslucas]

@whedon generate pdf

[whedon]

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

[semaphoreP]

Just finished the checklist. I am done reviewing I believe. Let me know if there's anything else.

[dfm]

@semaphoreP: Yes it looks like you're all set. Thank you very much for your review!!

[giordano]

I also just finished the checklist. I'd like to mention that I had left some comments in ADI.jl bug tracker:

• Make ADIAlgorithm <: Any? JuliaHCI/ADI.jl#26 about subtyping of a data structure
• UndefVarError: head not defined in the documentation JuliaHCI/ADI.jl#27 about an error experienced while going through examples in the documentation
• Possible improvements to documentation JuliaHCI/ADI.jl#30 more general suggestions about the documentation
• Error during benchmarks JuliaHCI/ADI.jl#32 and Another error duing benchmarks JuliaHCI/ADI.jl#34 reporting errors while running benchmarks

All reported issues have been resolved already. I also opened a couple of pull requests with trivial changes:

• Fix typo in documentation JuliaHCI/ADI.jl#29 to fix a typo in documentation
• Do not ]dev ADI in bench/Manifest.toml JuliaHCI/ADI.jl#31 to make it possible to load the Julia environment for benchmarks

[mileslucas]

I'll mention, too, I have the working changes on the master branch ready to release, which will change the version to 0.5.3 (rather than the 0.5.2 when I initiated the submission).

[dfm]

@giordano and @semaphoreP: Thanks for reviews! I really appreciate your time and your constructive suggestions.

@mileslucas: There are two things for you to do before we do the final processing:

1. I submitted a PR with some small edits to the manuscript. Take a look at that, merge it, and double check the manuscript to see if there are any other edits that you want to make. Then, comment @whedon generate pdf on this thread and double check the proofs. In particular, check that the author names and affiliations are correct. This is harder to change later!
2. Release v0.5.3 and create an archive for the version using Zenodo or similar. Note: the title and author list on that archive must exactly match the manuscript. Report the DOI of that archive to this thread.

Thanks all!!

[mileslucas]

@whedon generate pdf

[whedon]

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

[mileslucas]

@dfm All released and updated, the Zenodo link is https://zenodo.org/deposit/4323554 with the doi 10.5281/zenodo.4323554

[dfm]

@mileslucas: Please update the metadata on the Zenodo archive to match the manuscript (as requested above in bold text :D). The title should be ADI.jl: A Julia Package for High-Contrast Imaging and the author list should be you and Michael Bottom. You don't need to make a new archive - you should be able to edit the metadata for the existing archive.

[mileslucas]

@dfm I don't know what to say: every time I edit the DOI it says it has the correct information.

Saving doesn't change anything and when I try to publish I get a server error

[dfm]

@mileslucas: Bizarre! It looks like you used some sort of GitHub actions workflow to publish your release? Perhaps it has something to do with that. Can you try uploading a new snapshot of the code with the right metadata to Zenodo directly? Thanks!

[mileslucas]

Yeah, I'm using the zenodo feature that automatically updates with each github release. I sent a support request to zenodo to see if that can be resolved before I upload a new version. I'll ping here when I've got it figured out.

[dfm]

Ok thanks! Ping me when you have it sorted and I'll take it from there.

[mileslucas]

I was told to turn it off and back on again discard the changes and re-submit and it seems to have worked-
https://zenodo.org/record/4323554

[mileslucas]

@dfm

[dfm]

@mileslucas: Excellent - Looks good now!

[dfm]

@whedon check references

[whedon]

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

OK DOIs

- 10.1088/1538-3873/128/968/102001 is OK
- 10.1126/science.1102929 is OK
- 10.1086/500401 is OK
- 10.1088/2041-8205/755/2/L28 is OK
- 10.3847/1538-4357/aaa1f2 is OK
- 10.1137/141000671 is OK
- 10.1051/0004-6361/201834136 is OK
- 10.1109/TPDS.2018.2872064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[dfm]

@whedon set 10.5281/zenodo.4323554 as archive

[whedon]

OK. 10.5281/zenodo.4323554 is the archive.

[dfm]

@whedon set v0.5.3 as version

[whedon]

OK. v0.5.3 is the version.

[dfm]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1088/1538-3873/128/968/102001 is OK
- 10.1126/science.1102929 is OK
- 10.1086/500401 is OK
- 10.1088/2041-8205/755/2/L28 is OK
- 10.3847/1538-4357/aaa1f2 is OK
- 10.1137/141000671 is OK
- 10.1051/0004-6361/201834136 is OK
- 10.1109/TPDS.2018.2872064 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#1992

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1992, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[dfm]

@mileslucas: I've handed this off to the Editors-in-Chief to handle the final processing. They might have some last edits for the manuscript and once that's been sorted we'll have this published!

@giordano, @semaphoreP: Thanks for your reviews!! I really appreciate the time that you've put in and for your constructive recommendations for the code. Thanks again!!

[kthyng]

Everything looks to be in order! @mileslucas the summary in your paper is excellent! This is uncommon.

We can proceed.

[kthyng]

@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.02843 joss-papers#1993
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02843
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...

[kthyng]

Congrats on your new publication @mileslucas! Thanks to editor @dfm and reviewers @giordano and @semaphoreP for your time and expertise!!

[whedon]

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

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reStructuredText:
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