[REVIEW]: Pylinac: Image analysis for routine quality assurance in radiotherapy

[editorialbot]

Submitting author: !--author-handle-->@jrkerns<!--end-author-handle-- (James Kerns) Repository: https://github.com/jrkerns/pylinac Branch with paper.md (empty if default branch): joss_paper Version: v3.17 Editor: !--editor-->@kellyrowland<!--end-editor-- Reviewers: @ProfLeao, @SimonBiggs Archive: 10.5281/zenodo.10145069

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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

@ProfLeao & @SimonBiggs, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ 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 ✨

Checklists

📝 Checklist for @SimonBiggs

📝 Checklist for @ProfLeao

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.50 s (274.5 files/s, 116141.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          83           5316           7355          29759
reStructuredText                30           3932           3070           6005
YAML                             7             24             21            496
TeX                              1              0              0            374
HTML                             8             64              0            280
DOS Batch                        1             34              2            227
make                             1             30              6            156
SVG                              1              9              0            133
Markdown                         3             40              0            132
TOML                             1              8              1             69
-------------------------------------------------------------------------------
SUM:                           136           9457          10455          37631
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1012

[editorialbot]

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

[SimonBiggs]

Review checklist for @SimonBiggs

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 https://github.com/jrkerns/pylinac?
• [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 (@jrkerns) 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
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• [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?

[ProfLeao]

Review checklist for @ProfLeao

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 https://github.com/jrkerns/pylinac?
• [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 (@jrkerns) 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
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• [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?

[SimonBiggs]

@editorialbot commands

[editorialbot]

Hello @SimonBiggs, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[SimonBiggs]

@kellyrowland, I have completed my review and approve the submission.

[kellyrowland]

Thanks @SimonBiggs !

[ProfLeao]

Hi @jrkerns, I believe you've already seen it, but several links in your main README file are broken, However, this has no impact on the package functionality nor on the revision level required by JOSS. If you like, I can mark them for easy identification.

[ProfLeao]

Just for record, I would like to note that no explicit "community guidelines" were found. However, I considered the code highlighted below to be sufficient.

https://github.com/jrkerns/pylinac/blob/c6286ca6c86e90a995a0cad674572991fcc5d30e/docs/source/overview.rst?plain=1#L46-L104

[kellyrowland]

Thanks; I might suggest adding instructions on how to contribute to the project in this section (i.e., are folks welcome to open issues/PRs that follow in this philosophy?).

[ProfLeao]

@kellyrowland, is there a standard way of highlighting parts of the article that need revision?

[kellyrowland]

@ProfLeao you can comment here in the issue and reference the line numbers in the paper file or by quoting the language in the paper.

[ProfLeao]

@ProfLeao you can comment here in the issue and reference the line numbers in the paper file or by quoting the language in the paper.

Thanks.

[SimonBiggs]

Also, if it helps @ProfLeao, I made the following issue here:

https://github.com/jrkerns/pylinac/issues/468#issue-1973303026

[ProfLeao]

Also, if it helps @ProfLeao, I made the following issue here:

jrkerns/pylinac#468 (comment)

Great! Thanks.

[jrkerns]

Hi @ProfLeao and @SimonBiggs; thanks for taking the time to review the submission. Simon created two issues which I recently addressed: https://github.com/jrkerns/pylinac/issues/468 (contribution guide) and https://github.com/jrkerns/pylinac/issues/467 (RTD badge link). @ProfLeao I also fixed the links in the headline sections from stable to latest which was causing broken links. These are fixed and pushed already so should be live. I poked around and didn't find any other broken links, but if there are any others you had run into please let me know. @kellyrowland I added a bit to the contributing section. If this needs further elaboration please let me know. Thanks all!

[kellyrowland]

Contributing updates look great, thanks.

[ProfLeao]

Hi @jrkerns , I'll leave some "suggestions" for improving the text. Please note that my native language is not English, so any suggestions that are not relevant can be disregarded.

Summary

1. Line: 6

Original text: "Pylinac is a python library (...)"

Suggested text: "Pylinac is a Python library (...)"

2. Line: 9

Original text: "required by the medical physics society."

Suggested text: "required by the Medical Physics Society."

3. Line: 10

Original text: as the target audience is not developers. Thus, most workflows can be executed in a few lines (...)"

Suggested text: "as the target audience is not developers. Thus, most workflows can be implemented in a few lines of code."

Statement of need

4. Line: 23

Original text: "multileaf collimator that shape the radiation (Calvo-Ortega et al., 2014) These images and (...)"

Suggested text: "multileaf collimator that shape the radiation (Calvo-Ortega et al., 2014). These images and (...)"

Example usage

5. Line: 56

Original text: "where 𝐼 is the ROI of the contrast region in question (...)"

Suggested text: "where 𝐼 is the ROI of the contrast region of interest (...)"

6. Line: 58

Original text: "This corresponds to the circular ROIs on the outer edge (...)"

Suggested text: "This corresponds to the circular ROIs at the outer edge (...)"

7. Line: 69

Original text: "69 be saved as records that may be audited by state authorities. (...)"

Suggested text: "69 be stored as records that can be audited by government authorities. (...)"

[ProfLeao]

When I receive feedback about the above suggestions, I'll complete my checklist.

[jrkerns]

@editorialbot generate pdf

[editorialbot]

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

[jrkerns]

@ProfLeao Thank you for the suggestions. I implemented all of them except for the Summary Line 9 about medical physics society. In the US, there is a society called the AAPM, and there are several other "societies" internationally (e.g. EFOMP). I didn't think it would be helpful to list out the specific societies, so I purposely used an informal term here for the community-as-a-whole. If this is acceptable, then I believe everything was addressed. The updated proof is above and the commit itself. Thank you for taking the time to review the submission.

[ProfLeao]

I understand. I apologize for not understanding the generic term mentioned. Satisfied with the modifications. @kellyrowland I have completed my review.

[jrkerns]

Hi @kellyrowland Is there anything else I need to do to complete the submission? Thanks

[kellyrowland]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
• [x] Check the references in the paper for corrections (e.g. capitalization)
• [x] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [x] Recommend acceptance with @editorialbot recommend-accept

[kellyrowland]

@jrkerns please issue a new tagged release of the software (if changed since the start of the review), and archive it (on Zenodo, figshare, or elsewhere). Then, please then post the version number and archive DOI here in the review issue, and I'll follow some subsequent wrap-up steps from there based on the checklist above.

[kellyrowland]

@editorialbot generate pdf

[kellyrowland]

@editorialbot check references

[editorialbot]

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

[jrkerns]

V 3.17 GH release: https://github.com/jrkerns/pylinac/releases/tag/v3.17 pypi: https://pypi.org/project/pylinac/3.17.0/ zenodo: https://zenodo.org/records/10145069

[kellyrowland]

@editorialbot set v3.17 as version

[editorialbot]

Done! version is now v3.17

[kellyrowland]

@editorialbot set 10.5281/zenodo.10145069 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10145069

[kellyrowland]

@editorialbot check references

[kellyrowland]

@editorialbot check references

[kellyrowland]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

:wave: @openjournals/bcm-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/4791, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot check references

[Kevin-Mattheus-Moerman]

@jrkerns As AEiC I will now help to process this work for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however I do have the below points that need your attention:

• [x] Your archive currently says 3.17.0 for the version, however this should be edited to match v3.17, i.e. drop the 0 and include the v so it will say end up listing it as Version v3.17.
• [x] Please edit your affiliation by adding the town, and state as well. Also, please spell out the USA as United States of America.
• [x] Check (I am unsure) if this sentence Conceptualization, coding, development and paper writing by James Kerns. needs an Oxford comma, i.e. Conceptualization, coding, development, and paper writing by James Kerns..
• [x] Recommendation (no action required): The acronym ROI is defined as regions of interest (ROI), i.e. using the plural "regions". Later though it is both used as ROI and ROIs. Would it be less confusing to rewrite it to introduce it in a singular form e.g. region of interest ROI, and then to add the s when you want the plural form?

[jrkerns]

Hi @Kevin-Mattheus-Moerman,

Thanks for taking the time to look this over. I have edited the zenodo listing to reflect the first change (to my understanding): https://zenodo.org/records/10145069. I adjusted the paper to reflect the last 3 changes: https://github.com/jrkerns/pylinac/commit/35c94407ba64dcb8d77953024a66e333da39a73c

Let me know if there's anything else that needs adjusting. Thanks!

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@jrkerns thanks for making those changes. The version tag is now correctly set for the archive. One remaining issue is the title for the archive, it should match the paper title Pylinac: Image analysis for routine quality assurance in radiotherapy. Can you please edit the archive to do this?

[jrkerns]

Edited: https://zenodo.org/records/10145069

[Kevin-Mattheus-Moerman]

@editorialbot accept