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

[whedon]

Submitting author: @drcandacemakedamoore (Candace Makeda Moore)
Repository: https://github.com/drcandacemakedamoore/cleanX
Branch with paper.md (empty if default branch):
Version: v0.1.14
Editor: @cMadan
Reviewers: @henrykironde, @anki-xyz
Archive: 10.5281/zenodo.6331739

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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

• 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

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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 (@drcandacemakedamoore ) 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: 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?
• 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 @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

• 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 (@drcandacemakedamoore ) 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: 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?
• 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. @henrykironde, @anki-xyz 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.

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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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 714

[whedon]

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

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.25 s (186.9 files/s, 160605.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          20            902           1684           3243
Jupyter Notebook                10              0          30961           1031
CSS                              1            192             32            685
Markdown                         5             98              0            259
YAML                             3             12             10            223
TeX                              1              8              0             57
Bourne Shell                     2              3              0             32
reStructuredText                 2             14              8             28
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            46           1241          32703           5593
-------------------------------------------------------------------------------


Statistical information for the repository '1d949d34dfc08c81a0156016' was
gathered on 2021/08/18.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Candace Makeda Moore           192         18316          15433           84.45
Oleg Sivokon                    79          4576           1630           15.53
andrew-f-murphy                  2             5              5            0.03

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Candace Makeda Moore       2143           11.7          2.0                9.24
Oleg Sivokon               3682           80.5          0.7                9.53
andrew-f-murphy               4           80.0          3.6              100.00

[whedon]

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

[henrykironde]

I have requested some suggestions as part of the review drcandacemakedamoore/cleanX#36
drcandacemakedamoore/cleanX#35

[cMadan]

@henrykironde, thanks for the update! I've looked over discussions so far and I really appreciate that you're suggesting more robust software development principles (e.g., branches, workflows).

[whedon]

👋 @anki-xyz, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @henrykironde, please update us on how your review is going (this is an automated reminder).

[anki-xyz]

👋 @anki-xyz, please update us on how your review is going (this is an automated reminder).

Hi, can someone resent me the invite link? It seems to be expired, thanks!

[anki-xyz]

@cMadan can we maybe schedule a five min zoom or something? I feel stupid to not actually can do the things I am supposed to do... I think I need some kind of help. Thank you!

[cMadan]

@whedon re-invite @anki-xyz as reviewer

[whedon]

OK, the reviewer has been re-invited.

@anki-xyz please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[cMadan]

@anki-xyz, let me know if that fixes things!

[anki-xyz]

Things work now, thank you!

[henrykironde]

Here are some recommendations @drcandacemakedamoore, feel free to let me know what is appropriate to add to your software.

1. Combine the Api source docs with other related documentation like Medical professional documentation, include Most of the sections in the README or all of it.
2. Add developer docs. Contributors should be able to set up this development environment with minimal effort and run tests locally. Example for reference https://retriever.readthedocs.io/en/latest/developer.html
3. Add anenvironment.yml to make it simple for users to set up the Conda virtual environment in the installation part.
4. Move all the badges to the top. This makes it easy for users to notice the state of the software.
5. Explain your workflow in the developer docs. (2-3 sentences)
6. Since you are changing the main only at release, I strongly recommend that you create a branch called development for contributors to add patches before the release. Currently, you have several branches and it is hard to see any progress on the software after the release. Why the name development or dev? This is very clear for most users.

[drcandacemakedamoore]

Thank you very much. We will try to implement ALL of these changes, and push them next week along with some additional functions! There may be some technical issues that will come up with the .yml file, but we will try to make one as instructed.

…

On Thu, Sep 30, 2021 at 7:18 AM henry senyondo ***@***.***> wrote: Here are some recommendations @drcandacemakedamoore <https://github.com/drcandacemakedamoore>, feel free to let me know what is appropriate to add to your software. 1. Combine the Api source docs with other related documentation like Medical professional documentation, include Most of the sections in the README or all of it. 2. Add developer docs. Contributors should be able to set up this development environment with minimal effort and run tests locally. Example for reference https://retriever.readthedocs.io/en/latest/developer.html 3. Add anenvironment.yml to make it simple for users to set up the Conda virtual environment in the installation part. 4. Move all the badges to the top. This makes it easy for users to notice the state of the software. 5. Explain your workflow in the developer docs. (2-3 sentences) 6. Since you are changing the main only at release, I strongly recommend that you create a branch called development for contributors to add patches before the release. Currently, you have several branches and it is hard to see any progress on the software after the release. Why the name development or dev? This is very clear for most users. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3632 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHMYSAOIDPMLJZFR54MYBOTUEPXLHANCNFSM5CNBSWDQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[wvxvw]

Add an environment.yml to make it simple for users to set up the Conda virtual environment in the installation part.

@henrykironde

I started working on this, and then I realized that... well, we build the package for number of platforms (you can see them in the readme), the dependencies are different for each platform, so, it's not possible to have a single environment.yml. Even worse, we build the package for platforms neither of us has access to (MacOS).

So, if anyone wanted to develop on, say, a Mac, then they need a different environment.yml than the one I might use for Linux. I can, probably generate all of those environment files in CI, but there are two problems with that:

• We don't use these files in our development process, so, they are likely to get out of sync.
• They are generated, so, we wouldn't add them to the source code. This means that whoever wants to get those files will have to download them from the job artifacts for the platform that they want to work on. (It's really easier to generate the file locally by installing the latest version of the package, than it is to find the artifact in question).

Alternatively, I could simply add a single file for one of my Linux environments... or I could add three, which is more realistic, since I use an environment for Python 3.7, 3.8 and 3.9. And, since Python 3.10 is coming out next week, soon we'll try to support that too. So, there will be four files, just for Linux.

Anyways, if you just want one environment file, what version of Python do you want it for?

[wvxvw]

@henrykironde Can you please look at this branch: https://github.com/drcandacemakedamoore/cleanX/tree/wvxvw/review-fixes and tell me if it helps you with conda environments?

[editorialbot]

My name is now @editorialbot

[cMadan]

@editorialbot generate pdf

[editorialbot]

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

[cMadan]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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]

@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]

⚠️ 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]

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

[cMadan]

@editorialbot check references

[editorialbot]

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]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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]

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

Check final proof 👉📄 Download article

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

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.03632 joss-papers#3408
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03632
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]

@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 ⚡🚀💥

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03632/status.svg)](https://doi.org/10.21105/joss.03632)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03632/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03632/status.svg
   :target: https://doi.org/10.21105/joss.03632

This is how it will look in your documentation:

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