PyMedPhys

[SimonBiggs]

Submitting Author: Simon Biggs (@SimonBiggs)
Package Name: PyMedPhys One-Line Description of Package: A python library providing tools for Medical Physicists. Repository Link (if existing): https://github.com/pymedphys/pymedphys

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Description

• Include a brief paragraph describing what your package does:

Provides a central hub for Medical Physicists to share and review each others code that improves their day-to-day job. It also provides analysis tools that supports Medical Physics research.

Scope

• Please indicate which category or categories this package falls under:
  • [ ] Data retrieval
  • [ ] Data extraction
  • [ ] Data munging
  • [ ] Data deposition
  • [ ] Data visualization
  • [ ] Reproducibility
  • [ ] Geospatial
  • [ ] Education
  • [x] Unsure/Other (explain below)

See description above.

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of:

• Who is the target audience and what are scientific applications of this package?

Medical Physicists.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?

Similar tools, pylinac and pydicom. PyMedPhys complements these packages often builds on top of them.

• Any other questions or issues we should be aware of?:

P.S. *Have feedback/comments about our review process? Leave a comment here

[lwasser]

hi there @SimonBiggs ! Welcome to pyopensci! Can you tell us a bit more about this submission? It doesn't look to me like this is a python package on it's own, rather a community / subset of packages similar maybe to astropy? please let me know what you are looking for here. And perhaps you can provide some more information about the peer review part of things as that is what we do here at pyopensci!

[SimonBiggs]

Hi @lwasser,

We're in an interesting scenario where people are using the code within publications:

• https://docs.pymedphys.com/lib/ref/gamma.html
• https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=pymedphys+gamma&btnG=

But we don't actually have a paper out there. I began to attempt to write a JOSS paper (https://joss.theoj.org/) for the gamma implementation, but it appears that one repo can't have multiple papers, it'd be handy to be able to have just a pymedphys.gamma paper, and then have ways where other contributors can spin off papers/get peer review, for sub-modules.

I saw that for a JOSS submission it can be easier if it has gone through the pyOpenSci process first. Might it be possible to attempt to have the above pymedphys.gamma module to go through review here? And then see how easy it would be to submit a JOSS paper just for that subsection of PyMedPhys? This would then pave the way for others within the PyMedPhys community to follow a similar process...

Cheers, Simon

[lwasser]

hi again @SimonBiggs help me understand this a bit better. we currently review python packages which would follow the JOSS model that there is one package within a single repo that is curated, citable etc. It sounds as if this may be a set of submodules which similar to JOSS, we don't have the infrastructure right now to support review for as the citation would be on the repo rather than sub sections of the repo. Some issues would come up because:

• any archive of this would be for the entire repo yet it sounds like the review would only be for a subset of the repo
• how do you track citation for a submodule within a larger repo - tools like zenodo are repo focused not submodule focused
• tracking maintenance over time of a sub module would get challenging.

Do i understand this correctly? We may have to put this on hold if that is the case for the time being until we figure out a way that this type of review could be implemented in a sustainable way. But please do let me know if i am mis understanding the goal here.

[lwasser]

i will say that we are planning to work with other communities to implement uniform standards and such - pangeo being one of them - so perhaps there is a way we can work together in the future even if we can't perform a review right now.

[SimonBiggs]

Do i understand this correctly? We may have to put this on hold if that is the case for the time being until we figure out a way that this type of review could be implemented in a sustainable way.

Yup, I think you've got it to a tee. I'm all for making sure which ever way it occurs it is sustainable. Happy to just stay on the radar for now until the approach is more supported.

Cheers :slightly_smiling_face:, Simon

[lwasser]

@SimonBiggs of course. i am going to close this issue for the time being but please do keep in touch with us. Cheers! :)

[SimonBiggs]

Awesome :) thanks @lwasser