[PRE REVIEW]: PyMedPhys: A community effort to develop an open standard library for Medical Physics in Python

[editorialbot]

Submitting author: !--author-handle-->@Matthew-Jennings<!--end-author-handle-- (Matthew Jennings) Repository: https://github.com/pymedphys/pymedphys Branch with paper.md (empty if default branch): Version: 0.38.0 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @ProfLeao, @gbaltz Managing EiC: Arfon Smith

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Thanks for submitting your paper to JOSS @Matthew-Jennings. Currently, there isn't an JOSS editor assigned to your paper.

@Matthew-Jennings if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.60 s (845.7 files/s, 173480.2 lines/s)
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Language                     files          blank        comment           code
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Python                         384          11927          10787          33300
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Markdown                        12            851              0           2680
Jupyter Notebook                12              0           2873            970
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JavaScript                       7            104            222            255
TeX                              1             14              0            145
DOS Batch                        1             20              0             45
CSS                              1              3              4             31
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INI                              1              0              0              5
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                           510          13691          14747          76182
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 578

[editorialbot]

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

OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.4103/jmp.JMP_51_19 is OK
- 10.48550/arXiv.2109.03951 is OK
- 10.1088/1361-6560/abb71b is OK
- 10.1002/acm2.13430 is OK
- 10.1109/SMC52423.2021.9658879 is OK
- 10.1002/mp.15164 is OK
- 10.1002/mp.13491 is OK
- 10.3389/fphy.2020.567300 is OK
- 10.3389/fphy.2021.741453 is OK
- 10.1002/acm2.13556 is OK
- 10.1016/j.ejmp.2021.08.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[SimonBiggs]

@Matthew-Jennings if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Reading from the bottom of the list, we have the following person:

username: ProfLeao Preferred Programming Languages: Python Domains/topic areas you are comfortable reviewing: Chemistry, Physics, Chemical Engineering, Medical Physics Google Scholar: https://scholar.google.com/citations?user=GcjoCaMAAAAJ

---

@Matthew-Jennings, I suspect you need to write a comment saying "ProfLeao"

[Matthew-Jennings]

ProfLeao

[arfon]

@editorialbot – invite @danasolav as editor

:wave: @danasolav – would you be able to edit this submission for us?

[editorialbot]

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

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[arfon]

@editorialbot invite @danasolav as editor

👋 @danasolav – would you be able to edit this submission for us?

[editorialbot]

Invitation to edit this submission sent!

[danasolav]

Hi @arfon, I could not understand from the readme file what this software does. Medical physics is extremely broad. According to the paper it looks like it focuses on radiation, but the paper also lacks some key information that it should contain. Perhaps the authors can revise the readme and paper to be more specific and informative? In any case, radiation is not my area of expertise, so it looks like I'm going to have to decline this one.

[Kevin-Mattheus-Moerman]

@SimonBiggs @Matthew-Jennings can you address these comments? :point_up: i.e. clarify software application in the readme and paper?

[SimonBiggs]

Yup, thanks @Kevin-Mattheus-Moerman.

@sjswerdloff and @Matthew-Jennings have begun the discussion over at:

https://github.com/pymedphys/pymedphys/issues/1667

[SimonBiggs]

@Kevin-Mattheus-Moerman, does the following proposed changes to the paper appropriately address the concerns raised?

https://github.com/pymedphys/pymedphys/suites/7052584802/artifacts/277878183

[Kevin-Mattheus-Moerman]

@SimonBiggs the readme appears unchanged, is that correct? On the paper

The summary reads:

PyMedPhys is an open-source medical physics library built for Python by a diverse community that values and prioritizes code sharing, review, continuous improvement, and peer development.

This seems to simply say, this is open source software and we follow the open source philosophy. This is of course standard and a requirement of JOSS. However it does not say much about what the software is for. You can consider shortening this if you like.

PyMedPhys aims to simplify and enhance both research and clinical work related to medical physics. It is inspired by the Astropy Project (Astropy Collaboration, 2013); a highly successful collaborative work of our physics peers in astronomy.

I read this as: PyMedPhys enhances research/clinical work in "medical physics". Medical physics can be anything at this point (MRI, radiation, simulation of cardiac ablation therapy,...) so the reader is unsure. The next sentence then points to Astropy, and it says it is a "highly successful collaborative work of our physics peers in astronomy.". After looking at the paper a bit more I think I now understand that you were inspired by Astropy in the sense that it seems to be a collection of methods and algorithms used in astrophysics. And Astropy aspires to be standard/canonical open source and library used by astrophysicists. So anything useful to astrophysicists will be contained in this one open source ecosystem. So it looks like you want PyMedPhys to be like Astropy in that way but to instead be an open source library that collects all matter of methods and algorithms relevant to the medical physics community. And medical physics is kept broad/general there and includes radiation work. I think I get it now but perhaps your text can be improved. This is only a recommendation but perhaps this would help (please feel completely free to reject this recommendation or change it completely): PyMedPhys aims to simplify and enhance both research and clinical work related to medical physics. It is inspired by the Astropy Project (Astropy Collaboration, 2013); which forms a common core package for Astronomy in Python. Similarly PyMedPhys aspires to be a canonical open source library, but instead for medical physics. PyMedPhys currently includes [insert some functionality description], and aims to cover X, Y, Z and other medical physics software utilities in future work. Something like the above clarifies the goal of the package and the functionality more clearly. Again, just a recommendation.

[Kevin-Mattheus-Moerman]

@osorensen do you think you can help edit this Python submission relating to medical physics? I thought of you given your links to medical (neuro)imaging, however it may be somewhat off topic. If you cannot take this one, then I can take it but I would prefer if you could since I have quite a full plate at the moment.

[Kevin-Mattheus-Moerman]

@editorialbot invite @osorensen as editor

[editorialbot]

Invitation to edit this submission sent!

[osorensen]

@editorialbot assign @osorensen as editor

[editorialbot]

Assigned! @osorensen is now the editor

[osorensen]

That's fine @Kevin-Mattheus-Moerman. It's not 100 % my field, but I'll find reviewers who are experts.

[osorensen]

@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:

[osorensen]

:wave: @ProfLeao @hannesUlrich @michaelberks, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[ProfLeao]

would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines:

@osorensen, of course. It will be a pleasure

[ProfLeao]

@editorialbot commands

[editorialbot]

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

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

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

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@editorialbot check repository

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[ProfLeao]

@editorialbot generate my checklist

[editorialbot]

@ProfLeao I can't do that because you are not a reviewer

[osorensen]

@ProfLeao thanks! I'll add you to the reviewer list. Once I get a second reviewer confirmed, I'll start a new review issue, in which you can generate your checklist. You will be notified when this happens.

[osorensen]

@editorialbot add @ProfLeao as reviewer

[editorialbot]

@ProfLeao added to the reviewers list!

[hannesUlrich]

Unfortunately I have to decline, that is outside my field of expertise.

[osorensen]

That's ok. Thanks for the quick response @hannesUlrich.

[ProfLeao]

@ProfLeao thanks! I'll add you to the reviewer list. Once I get a second reviewer confirmed, I'll start a new review issue, in which you can generate your checklist. You will be notified when this happens.

Ok thanks.

[SimonBiggs]

@SimonBiggs the readme appears unchanged, is that correct? On the paper

The summary reads:

PyMedPhys is an open-source medical physics library built for Python by a diverse community that values and prioritizes code sharing, review, continuous improvement, and peer development.

This seems to simply say, this is open source software and we follow the open source philosophy. This is of course standard and a requirement of JOSS. However it does not say much about what the software is for. You can consider shortening this if you like.

PyMedPhys aims to simplify and enhance both research and clinical work related to medical physics. It is inspired by the Astropy Project (Astropy Collaboration, 2013); a highly successful collaborative work of our physics peers in astronomy.

I read this as: PyMedPhys enhances research/clinical work in "medical physics". Medical physics can be anything at this point (MRI, radiation, simulation of cardiac ablation therapy,...) so the reader is unsure. The next sentence then points to Astropy, and it says it is a "highly successful collaborative work of our physics peers in astronomy.". After looking at the paper a bit more I think I now understand that you were inspired by Astropy in the sense that it seems to be a collection of methods and algorithms used in astrophysics. And Astropy aspires to be standard/canonical open source and library used by astrophysicists. So anything useful to astrophysicists will be contained in this one open source ecosystem. So it looks like you want PyMedPhys to be like Astropy in that way but to instead be an open source library that collects all matter of methods and algorithms relevant to the medical physics community. And medical physics is kept broad/general there and includes radiation work. I think I get it now but perhaps your text can be improved. This is only a recommendation but perhaps this would help (please feel completely free to reject this recommendation or change it completely): PyMedPhys aims to simplify and enhance both research and clinical work related to medical physics. It is inspired by the Astropy Project (Astropy Collaboration, 2013); which forms a common core package for Astronomy in Python. Similarly PyMedPhys aspires to be a canonical open source library, but instead for medical physics. PyMedPhys currently includes [insert some functionality description], and aims to cover X, Y, Z and other medical physics software utilities in future work. Something like the above clarifies the goal of the package and the functionality more clearly. Again, just a recommendation.

@JacobMcAloney, I really like the suggestion above. Would you up for another adjustment taking into account that recommendation?

[Matthew-Jennings]

Thank you, @Kevin-Mattheus-Moerman, for your helpful initial review.

@SimonBiggs the readme appears unchanged, is that correct?

So far, yes, though we do see the merit of fleshing it out as per @danasolav's feedback. Would the README in its current form preclude publication in JOSS? If so, what specifically would need to be included from JOSS' perspective? One point that comes to my mind is that, unlike a JOSS paper summary, the README's missing content probably ought to be (primarily) targeted at a specialist audience.

I'd say that we're willing to cater to your/the reviewers' preferences here, just noting that it might take some time (perhaps a week or two) for those edits to be reflected in the README.

[osorensen]

@Matthew-Jennings, no, the README in its current form does not preclude publication in JOSS. I am looking for reviewers now, and once I find three reviewers, these will have a look at the README and everything else.

[osorensen]

:wave: @eteq, would you be willing to review this submission for the Journal of Open Source Software? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I realize might this seems far from your field of work, however, this is a medical physics tool which is directly inspired by the Astropy Project. Given your key role in Astropy, if you would be able to do a review with a focus on the software rather than the particular applications, it would be much appreciated.

[osorensen]

@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:

[osorensen]

:wave: @jasqs would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[osorensen]

:wave: @brechmos @grlee77 @7omasz would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[osorensen]

@editorialbot add @gbaltz as reviewer

[editorialbot]

@gbaltz added to the reviewers list!

[osorensen]

I'll start the review now, as we got two reviewers.

[osorensen]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4555.