[REVIEW]: CleanX: A Python library for data cleaning of large sets of radiology images

whedon commented 3 years ago

Submitting author: !--author-handle-->@drcandacemakedamoore@cMadan<!--end-editor-- Reviewers: @henrykironde, @anki-xyz Archive: 10.5281/zenodo.6331739

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@henrykironde & @anki-xyz, 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 @henrykironde

✨ 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

[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 (@drcandacemakedamoore ) 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).
[x] 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: 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?
[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?

Review checklist for @anki-xyz

✨ 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

[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 (@drcandacemakedamoore ) 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?
[ ] 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).
[x] 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: 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?
[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?

andrew-f-murphy commented 2 years ago

Ahh I see no one else has submitted theirs, happy to remove to for uniformity

henrykironde commented 2 years ago

@drcandacemakedamoore Thank you for working on the suggestions and issues that were raised. I have tested the software, specifically using the Linux Docker environment since I had issues with my local MacOS environment. At this point, I recommend accepting the software. I am handing it over to @anki-xyz and @cMadan for further review.

andrew-f-murphy commented 2 years ago

Thanks for all your feedback @henrykironde

andrew-f-murphy commented 2 years ago

hey @anki-xyz , @cMadan anything on our end that you require?

anki-xyz commented 2 years ago

I was going through the software, seems to work on my end. I would also be happy to accept the software as is. The manuscript could be improved in two (minor) ways:

Specify how CleanX speeds up software
The manuscript contains abundant "many", and "some" - if you could be more specific here.

andrew-f-murphy commented 2 years ago

Thanks @anki-xyz for your suggestions, we have made those changes.

andrew-f-murphy commented 2 years ago

Candace et.al are going to be busy for a while but I will be around, please let me know if you require anything else @anki-xyz @cMadan

drcandacemakedamoore commented 2 years ago

@anki-xyz and @cMadan I just added some information on licenses of all the images in the demos. I had overlooked this, but someone else looking at the package found it. If there is anything else we need to update let me or Andrew know.

anki-xyz commented 2 years ago

Good for me - accept.

andrew-f-murphy commented 2 years ago

Thanks for your time and feedback @anki-xyz

arfon commented 2 years ago

:wave: @cMadan – looks like this one is ready for you to do the last few pieces with before handing over to the EiC team 🎉

andrew-f-murphy commented 2 years ago

Thanks @arfon, @cMadan happy to take on any additional feedback.

cMadan commented 2 years ago

@henrykironde and @anki-xyz, thank you for your thorough reviews. We very much appreciate the work you've put in for reviewing this submission!

@drcandacemakedamoore @andrew-f-murphy @wvxvw, I will do some final checks and then we'll be all set!

andrew-f-murphy commented 2 years ago

No worries, I am now away for a while but @drcandacemakedamoore will be around

andrew-f-murphy commented 2 years ago

Hey @cMadan anything we can do to help out?

drcandacemakedamoore commented 2 years ago

@arfon , Did this get handed over to the EiC team yet?

cMadan commented 2 years ago

Apologies for the delay, I've been having a hectic time lately (COVID, heatwave, etc.) and I am very sorry that this has delayed me in finalising the review process here.

cMadan commented 2 years ago

@whedon recommend-accept

editorialbot commented 2 years ago

My name is now @editorialbot

cMadan commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Paper is not ready for acceptance yet, the archive is missing

cMadan commented 2 years ago

@editorialbot set version as v0.1.14

editorialbot commented 2 years ago

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

@editorialbot commands

cMadan commented 2 years ago

@editorialbot set v0.1.14 as version

editorialbot commented 2 years ago

Done! version is now v0.1.14

cMadan commented 2 years ago

@editorialbot set 10.5281/zenodo.6331739 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6331739

cMadan commented 2 years ago

@whedon generate pdf

editorialbot commented 2 years ago

My name is now @editorialbot

cMadan commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

cMadan commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1145/2207243.2207253 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1007/978-3-319-94878-2_6 is OK
- 10.1007/s00330-020-07453-w is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ejmp.2021.02.007 is INVALID because of 'https://doi.org/' prefix

cMadan commented 2 years ago

@drcandacemakedamoore, it looks like one DOI needs to have the url fixed. Can you make this correction and let me know after it's done?

editorialbot commented 2 years ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/j.ejmp.2021.02.007' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

andrew-f-murphy commented 2 years ago

Hey @cMadan totally understand, I have removed https://doi.org/ from that DOI now

cMadan commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1145/2207243.2207253 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1016/j.ejmp.2021.02.007 is OK
- 10.1007/978-3-319-94878-2_6 is OK
- 10.1007/s00330-020-07453-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

cMadan commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1145/2207243.2207253 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1016/j.ejmp.2021.02.007 is OK
- 10.1007/978-3-319-94878-2_6 is OK
- 10.1007/s00330-020-07453-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3407, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3408
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03632
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@henrykironde, @anki-xyz – many thanks for your reviews here and to @cMadan for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@drcandacemakedamoore – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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