[REVIEW]: PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design

[editorialbot]

Submitting author: @jonbmartin (Jonathan Martin)
Repository: https://github.com/jonbmartin/pulpy
Branch with paper.md (empty if default branch):
Version: v1.8.1
Editor: @emdupre
Reviewers: @bwheelz36, @curtcorum
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516/status.svg)](https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516)

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

@bwheelz36 & @curtcorum, 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 @emdupre 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 @bwheelz36

📝 Checklist for @curtcorum

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (985.5 files/s, 150449.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          29           1013           1304           3003
TeX                              1              1              0            436
Markdown                         1             21              0             89
reStructuredText                 5             67            134             65
YAML                             2             12             24             41
TOML                             1              2              0             20
make                             1              4              6             10
Bourne Shell                     1              0              0              7
-------------------------------------------------------------------------------
SUM:                            41           1120           1468           3671
-------------------------------------------------------------------------------

Commit count by author:

   119	jonbmartin
    11	Jonathan Martin

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1352

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

OK DOIs

- 10.1016/j.jmr.2008.06.010 is OK
- 10.1002/mrm.27411 is OK
- 10.1007/s10334-023-01134-7 is OK
- 10.1109/42.75611 is OK
- 10.1002/mrm.26235 is OK
- 10.1002/MRM.29686 is OK
- 10.1117/12.3008456 is OK
- 10.1038/s42256-021-00411-1 is OK
- 10.1002/MRM.21013 is OK
- 10.1016/0022-2364(89)90265-5 is OK
- 10.1007/BF02797382 is OK
- 10.1006/JMRE.2001.2340 is OK
- 10.1002/MRM.23152 is OK
- 10.1109/TMI.2008.922699 is OK
- 10.1002/MRM.10493 is OK
- 10.3390/BIOENGINEERING10020158 is OK
- 10.1109/TMI.2022.3161875 is OK
- 10.21105/JOSS.01725 is OK
- 10.1145/2833157.2833162 is OK
- 10.1002/MRM.20978 is OK
- 10.1002/(SICI)1522-2594(199911)42:5<952::AID-MRM16>3.0.CO;2-S is OK
- 10.1002/MRM.26235 is OK
- 10.1002/MRM.22406 is OK
- 10.1002/MRM.29294 is OK
- 10.1002/MRM.29271 is OK

MISSING DOIs

- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox
- No DOI given, and none found for title: Adjustment and Basic Imaging Sequences for the Ope...
- No DOI given, and none found for title: Selective complex pulse design by optimal control ...
- No DOI given, and none found for title: Advanced Normalization Tools (ANTS)
- No DOI given, and none found for title: SigPy: A Python Package for High Performance Itera...
- No DOI given, and none found for title: Berkeley Advanced Reconstruction Toolbox
- No DOI given, and none found for title: Quantitative MRI made easy with qMRLab
- No DOI given, and none found for title: MARIE a MATLAB-based open source software for the ...
- No DOI given, and none found for title: SigPy.RF: Comprehensive Open-Source RF Pulse Desig...
- No DOI given, and none found for title: OCRA : a low-cost, open-source FPGA-based MRI cons...

INVALID DOIs

- None

[editorialbot]

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

[emdupre]

👋 Hi @bwheelz36 and @curtcorum, and thank you for agreeing to review this submission for PulPy !

The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @editorialbot generate my checklist

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #6586 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

As you go over the submission, please check any items on your reviewer checklist that you feel have been satisfied. If you aren't sure how to get started, please see the JOSS reviewer guidelines -- and of course, feel free to ping me (@emdupre) with any questions !

We aim for reviews to be completed within four weeks, or six weeks at latest. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

If you any questions or concerns arise, please feel free to ask here or via email. And thank you again !

[emdupre]

👋 Hi everyone, and happy Monday !

@bwheelz36 and @curtcorum, I noticed you had not yet created your reviewer checklists, so I wanted to make sure you weren't encountering any issues in getting started.

Of course, if you have any questions or concerns, please don't hesitate to let me know ! And thank you again for agreeing to review this submission for PulPy 💐

[bwheelz36]

Review checklist for @bwheelz36

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 https://github.com/jonbmartin/pulpy?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jonbmartin) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

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

[curtcorum]

Review checklist for @curtcorum

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 https://github.com/jonbmartin/pulpy?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jonbmartin) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

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

[emdupre]

👋 Hi everyone ! I just wanted to follow-up on the status of this review, as I see that you have started your checklists, @curtcorum and @bwheelz36, but I'm not clear if you are still working through them or waiting on author / editor feedback.

Please let me know if you're hitting any specific blockers, or if you have any scheduling concerns I should be aware of.

I also noticed that jonbmartin/pulpy#1 is still open ; @jonbmartin, I just wanted to confirm that you are welcome to address issues as they are created, rather than waiting until the initial review is complete ! This can help to keep the review process moving forward.

If you have any questions, of course, please don't hesitate to let me know !

[bwheelz36]

Hi @emdupre; in my initial review I requested additional documentation on the code. When this is addressed I would like to take another look.

[curtcorum]

I will finish the non-doc items. I concur that the documentation is a good start, but more is needed.