Joss-reviews: [REVIEW]: DetectorChecker: analyzing patterns of defects in detector screens

[whedon]

Submitting author: @tomaslaz (Tomas Lazauskas)
Repository: https://github.com/alan-turing-institute/DetectorChecker
Version: 1.0.8
Editor: @fboehm
Reviewers: @janfreyberg, @craddm
Archive: Pending

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Status

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Markdown: [![status](https://joss.theoj.org/papers/b6b67cd22d488e7bfa42b4074bc4eda8/status.svg)](https://joss.theoj.org/papers/b6b67cd22d488e7bfa42b4074bc4eda8)

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

@janfreyberg, 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
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

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

Review checklist for @janfreyberg

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 (@tomaslaz) 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).
• [ ] 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?
• [ ] 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?

@craddm , 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
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

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

Review checklist for @craddm

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 (@tomaslaz) 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?
• [ ] 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).
• [ ] 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. @janfreyberg 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]

Reference check summary:

OK DOIs

- 10.1088/0031-9155/42/1/001 is OK
- 10.1002/9781118658222 is OK
- 10.1002/bimj.201600178 is OK

MISSING DOIs

- https://doi.org/10.1038/146150e0 may be missing for title: Statistical method from the viewpoint of quality control

INVALID DOIs

- None

[whedon]

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

[fboehm]

Thank you, @janfreyberg ! Please feel free to mention me if you have questions or difficulties. Thanks again!!

[fboehm]

@tomaslaz - it looks like you're missing a doi according to the examination from whedon.

MISSING DOIs

• https://doi.org/10.1038/146150e0 may be missing for title: Statistical method from the viewpoint of quality control

Please be sure to verify that this doi is accurate, then add it to your manuscript.

[fboehm]

@tomaslaz - I'm struggling to find a second reviewer. Are there any scholars whom you can suggest as reviewers? Thanks again!

[fboehm]

@tomaslaz - please disregard the last message. I've found a second reviewer.

[fboehm]

@whedon add @craddm as reviewer

[whedon]

OK, @craddm is now a reviewer

[tomaslaz]

@tomaslaz - it looks like you're missing a doi according to the examination from whedon.

MISSING DOIs

• https://doi.org/10.1038/146150e0 may be missing for title: Statistical method from the viewpoint of quality control

Please be sure to verify that this doi is accurate, then add it to your manuscript.

The suggested DOI is for a paper, however, we cite a book.

[fboehm]

Thanks for double-checking the doi, @tomaslaz. We'll proceed without a doi for that reference.

[fboehm]

@craddm and @janfreyberg - just wanted to check in to see how the review is going. Please let me know if there's something that I can do to help. Thanks again!!

[fboehm]

Thank you, @craddm for mentioning the issue. @tomaslaz - Do you have any questions on how to proceed with revisions based on the open issue from @craddm?

@janfreyberg Is there anything that I can do to help as you review the submission? Do you have any questions about the checklist? Thanks again!!

[janfreyberg]

Hi all - apologies for the long delay in my review, I should have updated you earlier. I've just updated the checklist and created an issue on the DetectorChecker repo!

[fboehm]

Excellent - thanks @janfreyberg ! @tomaslaz - please let me know if you have any questions about the opened issues. Thanks again!!

[fboehm]

@tomaslaz - I see that the issue from @janfreyberg remains open. Do you have any questions on how to resolve it? I think that it's one of the last hurdles before we can publish this.

[fboehm]

@craddm - It looks like three boxes remain unchecked in your checklist. If you haven't had a chance to suggest improvements for the documentation and functionality claims, please feel free to do so. Thanks again!

[tomaslaz]

thank you @fboehm and @janfreyberg @craddm for the suggestions and recommendations! We are planning to work on the changes and resolve the raised issues soon.

[fboehm]

Thank you, @tomaslaz ! Please let us know when you have addressed the issues.

Thanks again!!

[fboehm]

@tomaslaz - I've added the "paused' label to give you time to address the issues. Do you anticipate that you can address the concerns within the next month, ie, by Nov 23? I don't want to keep the reviewers on hold for too long. Thanks again!

[tomaslaz]

@fboehm - apologies for taking our time addressing the concerns. @OscartGiles, any updates?

[OscartGiles]

Dear @fboehm and @tomaslaz - I'm planning to work through these this week so we should have a response soon. Sorry for the delay. All the best.

[fboehm]

Thanks so much, @tomaslaz and @OscartGiles ! Please let me know if you have any questions, and please feel free to use this review thread to discuss and clarify the needed edits.

[fboehm]

Hi, @OscartGiles and @tomaslaz - I just wanted to check in to see how you are progressing through the issues from reviewers. Is there anything that I might help with right now?

[OscartGiles]

Hi @fboehm, 18 days went fast. I'm partway through the revisions now and we'll have them finished and submitted next week. All the best

[fboehm]

@OscartGiles - excellent! Thank you again! Please know that I'm happy to discuss any edits that you're about to make, especially if you're unsure about how to proceed.