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[REVIEW]: PyMedPhys: A community effort to develop an open standard library for Medical Physics in Python
Submitting author: @Matthew-Jennings (Matthew Jennings) Repository: https://github.com/pymedphys/pymedphys Branch with paper.md (empty if default branch): Version: 0.38.0 Editor: @osorensen Reviewers: @ProfLeao, @gbaltz Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/2992a30f426890227839e1c19f697356"><img src="https://joss.theoj.org/papers/2992a30f426890227839e1c19f697356/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/2992a30f426890227839e1c19f697356)
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 & @gbaltz, 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 @osorensen 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
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.81 s (625.1 files/s, 126614.2 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
JSON 16 0 0 33359
Python 383 11897 10707 32965
SVG 19 11 282 3041
Markdown 13 509 0 1653
TOML 6 96 58 975
Jupyter Notebook 12 0 2873 970
reStructuredText 36 399 314 620
YAML 8 158 100 585
JavaScript 7 104 222 255
TeX 1 14 0 145
DOS Batch 1 20 0 45
Starlark 1 19 15 32
CSS 1 3 4 31
INI 1 0 0 5
Bourne Shell 1 0 0 2
-------------------------------------------------------------------------------
SUM: 506 13230 14575 74683
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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/pymedphys/pymedphys?
- [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 (@Matthew-Jennings) 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, 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?
Hi @ProfLea, yes, you're welcome to add suggestions to the text here. Alternatively you can also open an issue in the source repository. The latter would be easier if you have a larger number of suggested changes.
Hi @ProfLea, yes, you're welcome to add suggestions to the text here. Alternatively you can also open an issue in the source repository. The latter would be easier if you have a larger number of suggested changes.
ok thanks.
Hi @Matthew-Jennings, how are you? I'm not a big expert on Apache licenses, but I think the lines below need some adjustments. Right ?
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright [yyyy] [name of copyright owner]
https://github.com/pymedphys/pymedphys/blob/17c9d93f4f9deef51003f0f86773ac506cd62693/LICENSE#L178-L189
Hi @ProfLeao,
Thanks for jumping in to review PyMedPhys 🙂
I don't believe we need to edit that guidance component of the original license file. Instead, we just make sure to include that boilerplate at the top of each source file:
https://github.com/pymedphys/pymedphys/blob/main/lib/pymedphys/main.py#L1-L13
Hi @ProfLeao,
Thanks for jumping in to review PyMedPhys 🙂
I don't believe we need to edit that guidance component of the original license file. Instead, we just make sure to include that boilerplate at the top of each source file:
https://github.com/pymedphys/pymedphys/blob/main/lib/pymedphys/main.py#L1-L13
Hello @SimonBiggs . Thanks for the clarification. Today I will continue to study the software, I will let you know if any other questions arise.
Hello @SimonBiggs . I noticed that some features were migrated in the directory tree and the examples still do not include some of these changes. With the expansion of software visibility that JOSS can offer in mind, it would be good to update this.
Take, for example, the case of pinnacle.
old:
from pymedphys.labs.pinnacle import PinnacleExport
Now:
from pymedphys._experimental.pinnacle import PinnacleExport
Sorry if it's exhausting, but I'm looking to reproduce as much of your tool's functionality as possible.
Hi @ProfLeao,
Indeed that is a good find. Thank you!
@pchlap, might you be in a position to fix this? One difference from the recommendation is that the docs need to utilise the public interface to pinnacle:
from pymedphys.experimental.pinnacle import PinnacleExport
(No underscore prior to experimental)
Sorry if it's exhausting
Don't be sorry at all, we really appreciate the review and your time. Thankyou!
Review checklist for @gbaltz
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/pymedphys/pymedphys?
- [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 (@Matthew-Jennings) 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, 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?
Hi, Looks like several of the links in the documentation section of the readme are broken, namely: "getting started", "library users guide", "CLI users guide", and "General".
Additionally I think the README file is missing a couple of the required sections as part of my Documentation review checklist. Currently missing sections are "Statement of Need" and "Automated Tests". I also think an "Examples" section is maybe missing as it takes a couple clicks digging in the documentation to find examples.
Looks like several of the links in the documentation section of the readme are broken, namely: "getting started", "library users guide", "CLI users guide", and "General".
Hi @Matthew-Jennings, would you be able to take this one?
Additionally I think the README file is missing a couple of the required sections as part of my Documentation review checklist. Currently missing sections are "Statement of Need" and "Automated Tests". I also think an "Examples" section is maybe missing as it takes a couple clicks digging in the documentation to find examples.
@nlambriICH might you be able to take this one?
Looks like several of the links in the documentation section of the readme are broken, namely: "getting started", "library users guide", "CLI users guide", and "General".
Hi @Matthew-Jennings, would you be able to take this one?
@SimonBiggs: Yep, will try to tonight.
Additionally I think the README file is missing a couple of the required sections as part of my Documentation review checklist. Currently missing sections are "Statement of Need" and "Automated Tests". I also think an "Examples" section is maybe missing as it takes a couple clicks digging in the documentation to find examples.
@nlambriICH might you be able to take this one?
@SimonBiggs Sure, I can take it.
@SimonBiggs Sure, I can take it.
@guanfada would you be interested in giving @nlambriICH a hand? Potentially @nlambriICH you might be able to delegate some to @guanfada?
@SimonBiggs Sure, I can take it.
@guanfada would you be interested in giving @nlambriICH a hand? Potentially @nlambriICH you might be able to delegate some to @guanfada?
Sure thing. Please let me know what I can do for the revision. @SimonBiggs @nlambriICH
Currently missing sections are "Statement of Need" and "Automated Tests". I also think an "Examples" section is maybe missing as it takes a couple clicks digging in the documentation to find examples.
@guanfada Can you start adding a draft for these required sections in the README?. We can then work together for the final version.
@Matthew-Jennings, can you please update us on how it's going addressing the points raised by the reviewers?
can you please update us on how it's going addressing the points raised by the reviewers?
Still underway, sorry. But we do have persons assigned to each of the items raised. I'll poke.
can you please update us on how it's going addressing the points raised by the reviewers?
Still underway, sorry. But we do have persons assigned to each of the items raised. I'll poke.
Thank! It's no problem if it takes some time to address the issues, but please keep us posted.
About the text:
In the Statement of need section, isolated in-house development efforts are mentioned several times. I understand that initiatives of this nature are common in several Medical Physics services, but as it is a scientific publication, I believe that the statement should be endorsed by some bibliographic source or by examples that make it more consistent. Do the authors believe this would be possible? Could the quotes in line 55 and following exemplify this?
Sorry for the delay in continuing the review, I've been working away for several days.
@ProfLeao We are going to make adjustments according to your comments! Thank you so much!
@ProfLeao @SimonBiggs We have added references for "in-house development" Thanks.