[REVIEW]: PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design #6586

editorialbot · 2024-04-05T21:35:29Z

Submitting author: @jonbmartin (Jonathan Martin)
Repository: https://github.com/jonbmartin/pulpy
Branch with paper.md (empty if default branch):
Version: v1.8.8
Editor: @emdupre
Reviewers: @bwheelz36, @curtcorum
Archive: 10.5281/zenodo.13963346

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516"><img src="https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516/status.svg"></a>
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

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-04-05T21:35:33Z

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

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2024-04-05T21:35:56Z

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 · 2024-04-05T21:36:02Z

Paper file info:

📄 Wordcount for paper.md is 1352

✅ The paper includes a Statement of need section

editorialbot · 2024-04-05T21:36:05Z

License info:

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

editorialbot · 2024-04-05T21:36:19Z

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 · 2024-04-05T21:36:36Z

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

emdupre · 2024-04-05T21:42:59Z

👋 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 · 2024-04-15T22:16:25Z

👋 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 · 2024-04-16T22:48:18Z

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 · 2024-04-17T01:32:48Z

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?

openjournals/joss-reviews#6586

emdupre · 2024-04-30T17:33:14Z

👋 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 · 2024-05-01T09:14:44Z

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 · 2024-05-07T21:38:19Z

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

jonbmartin · 2024-05-14T02:06:00Z

Thank you for the feedback! I agree that more documentation would be helpful. I have been traveling but will address these issues within the next 1-2 weeks.

jonbmartin · 2024-05-21T20:40:57Z

Hello all,

Thank you again for the initial review- it was very helpful, and I've made some changes to address the points raised. These correspond to a new release, release 1.8.2

Comments response:

unittests are now running, and are set to automatically run in response to opened pull requests via a github workflow.
Documentation has been increased. I have added more documentation in the README to help users get started. More comprehensive tutorials are linked to in a separate tutorial repository . I would appreciate any further feedback on this from the reviewers.
@curtcorum very helpfully addressed an issue with figures not displaying properly on the github page with a pull request. Sphinx and Github have annoying contradictions in how they handle images which seems to be an unresolved issue. My plan is to migrate to a more modern documentation package than Sphinx soon, but in the meantime I've created a separate README.rst and README.md for Sphinx and github respectively.
@bwheelz36 made several helpful structural/cleanliness suggestions. I deleted some unnecessary clutter (e.g. pulpy.egg-info) and migrated the functionality in the shell script to Github workflows (one shell script is still called, but this is done by a workflow - keeps things a little more collected. This is again needed because of Sphinx, more motivation to move away from it in the future).
I have not yet taken the step of consolidating config files to a single pyproject.toml, but this was listed as a non-dealbreaker.
@bwheelz36 wanted clarity about the scope of the toolbox, especially vs. PyPulseq. PyPulseq is a more high level tool, good for building entire pulse sequences but with little focus on design/optimization of individual pulses. For example, I would recommend PyPulseq to build a full spin-echo pulse sequence. In contrast, PulPy would be a good tool to, for example, design a very specific refocusing RF pulse. That specific, optimized component could then be used in a higher-level toolbox like PyPulseq.
@bwheelz36 pointed out that PulPy is not a dependency of Pulseq or PyPulseq, as was stated in the paper. This is correct and was stated in error - the predecessor of PulPy, SigPy, was incorporated as a dependency in those packages. The manuscript has been updated to clarify this with: "The previous iteration of this toolbox, SigPy.RF, has already been incorporated into open-source sequence development software such as Pulseq [@Layton2017] and PyPulseq [@SravanRavi2019] to provide RF pulses critical to the performance of various pulse sequences. We feel that PulPy, with its' more specific focus on pulse design, will be able to even more easily integrated into other MRI acquisition software toolboxes, and we encourage other MRI software developers to incorporate PulPy as a component of MRI acquisition software."

I hope that this addresses the issues raised - please let me know if there is anything you would like further work on or clarification of.

emdupre · 2024-05-22T18:08:22Z

Thank you, @jonbmartin ! I'll note that it looks like these changes are partially in response to jonbmartin/pulpy#1, so I've cross-linked the discussion there.

@bwheelz36 and @curtcorum, please let us know if these changes help to address your initial concerns ! If you feel like a given review item has been sufficiently address, please mark it as completed on your reviewer checklist. This helps us to track overall progress on the review. And thank you again for your work reviewing PulPy to date 💐

jonbmartin · 2024-05-22T20:29:44Z

That's correct @emdupre, sorry for the confusion - thank you for linking things!

emdupre · 2024-05-29T01:08:53Z

👋 Hi everyone !

I just wanted to follow-up on this and check how this re-review of PulPy is going. @curtcorum and @bwheelz36, please let me know if you have any questions or concerns on process at this point ! And thank you again for your work in reviewing 🌻

jonbmartin · 2024-10-22T22:06:28Z

@editorialbot check references

editorialbot · 2024-10-22T22:06:50Z

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
- 10.13140/RG.2.2.25014.34881 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

🟡 SKIP 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: 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...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-22T22:08:47Z

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

jonbmartin · 2024-10-22T22:13:07Z

@editorialbot generate pdf

editorialbot · 2024-10-22T22:14:30Z

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

emdupre · 2024-10-24T15:49:41Z

Thank you, @jonbmartin ! I saw only a few small remaining formatting changes ; I've proposed a pull request to address these here : jonbmartin/pulpy#25

emdupre · 2024-10-24T16:29:56Z

@editorialbot generate pdf

editorialbot · 2024-10-24T16:31:18Z

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

emdupre · 2024-10-24T16:37:27Z

Thank you, @jonbmartin ! The paper now looks correct to me.

I did, though, just catch an issue on the archive : It seems that rather than editing the Zenodo archive, a new DOI was created in modifying the title. This is problematic as the version on the archive (v2) no longer matches the version on the software (v1.8.8).

Are you able to directly edit the existing archive, or create a new matching software version and archive version ?

jonbmartin · 2024-10-24T22:33:31Z

Ah, I apologize for that! I just edited the existing archive (DOI: 10.5281/zenodo.13963346, URL: https://zenodo.org/records/13963346) to have the correct title. This is v1.8.8. Unfortunately I don't believe Zenodo allows me to delete the published v2 record. Does that resolve the issue?

emdupre · 2024-10-26T00:03:44Z

I believe it does resolve the issue ! I will advance this now.

emdupre · 2024-10-26T00:06:08Z

Thank you, @jonbmartin, for these edits ! The paper and archive now look correct to me.

I am now happy to recommend PulPy to the EiC team for publication in JOSS 🚀

Thank you, too, to @bwheelz36 and @curtcorum for your work in reviewing this submission ! JOSS only works because of your work 💐

emdupre · 2024-10-26T00:08:27Z

@editorialbot recommend-accept

editorialbot · 2024-10-26T00:08:29Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-10-26T00:08:56Z

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
- 10.13140/RG.2.2.25014.34881 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

🟡 SKIP 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: 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...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-26T00:10:10Z

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6059, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-10-31T10:43:49Z

jonbmartin · 2024-10-31T14:41:54Z

Done! See the revised zenodo repository: https://zenodo.org/records/13963346

Kevin-Mattheus-Moerman · 2024-11-01T09:38:41Z

@editorialbot accept

editorialbot · 2024-11-01T09:38:43Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-11-01T09:45:52Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Martin
  given-names: Jonathan B.
  orcid: "https://orcid.org/0000-0002-9384-8056"
- family-names: Sun
  given-names: Heng
- family-names: Albert
  given-names: Madison
- family-names: Johnson
  given-names: Kevin M.
- family-names: Grissom
  given-names: William A.
  orcid: "https://orcid.org/0000-0002-3289-1827"
contact:
- family-names: Grissom
  given-names: William A.
  orcid: "https://orcid.org/0000-0002-3289-1827"
doi: 10.5281/zenodo.13963346
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Martin
    given-names: Jonathan B.
    orcid: "https://orcid.org/0000-0002-9384-8056"
  - family-names: Sun
    given-names: Heng
  - family-names: Albert
    given-names: Madison
  - family-names: Johnson
    given-names: Kevin M.
  - family-names: Grissom
    given-names: William A.
    orcid: "https://orcid.org/0000-0002-3289-1827"
  date-published: 2024-11-01
  doi: 10.21105/joss.06586
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6586
  title: "PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06586"
  volume: 9
title: "PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design"

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editorialbot · 2024-11-01T09:45:57Z

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editorialbot · 2024-11-01T09:45:58Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

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Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06586 joss-papers#6077
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Kevin-Mattheus-Moerman · 2024-11-01T15:10:47Z

@jonbmartin congratulations on this publication!!!!!

Thanks for editing @emdupre !!!

And a special thank you to the reviewers: @bwheelz36, @curtcorum !!!!

editorialbot · 2024-11-01T15:10:50Z

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editorialbot added Python review Shell Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Apr 5, 2024

editorialbot assigned emdupre Apr 5, 2024

editorialbot mentioned this issue Apr 5, 2024

[PRE REVIEW]: PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design #6482

Closed

bwheelz36 mentioned this issue Apr 16, 2024

Initial JOSS review jonbmartin/pulpy#1

Closed

curtcorum mentioned this issue Apr 17, 2024

JOSS review (in-progress) jonbmartin/pulpy#2

Closed

curtcorum added a commit to curtcorum/pulpy that referenced this issue Apr 17, 2024

Update README.rst

daa0f46

openjournals/joss-reviews#6586

This was referenced Apr 17, 2024

Update README.rst curtcorum/pulpy#1

Merged

PulPy Logo fix in README.rst jonbmartin/pulpy#3

Merged

bwheelz36 mentioned this issue May 29, 2024

PyPi package does not install dependencies jonbmartin/pulpy#11

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 26, 2024

editorialbot added accepted published Papers published in JOSS labels Nov 1, 2024

Kevin-Mattheus-Moerman closed this as completed Nov 1, 2024

[REVIEW]: PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design #6586

[REVIEW]: PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design #6586

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editorialbot commented Apr 5, 2024 • edited Loading

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bwheelz36 commented Apr 16, 2024 • edited Loading

Review checklist for @bwheelz36

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curtcorum commented Apr 17, 2024 • edited Loading

Review checklist for @curtcorum

Conflict of interest

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Functionality

Documentation

Software paper

emdupre commented Apr 30, 2024

bwheelz36 commented May 1, 2024

curtcorum commented May 7, 2024

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emdupre commented May 22, 2024

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Kevin-Mattheus-Moerman commented Oct 31, 2024 • edited Loading

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jonbmartin commented Oct 31, 2024

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