[REVIEW]: pypulseq: A Python Package for MRI Pulse Sequence Design

whedon commented 5 years ago

Submitting author: @imr-framework (Sairam Geethanath) Repository: https://github.com/imr-framework/pypulseq Version: 1.2.2r1 Editor: @Kevin-Mattheus-Moerman Reviewers: @grlee77, @mathieuboudreau, @spinicist Archive: 10.5281/zenodo.3479527

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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

@grlee77, @mathieuboudreau, and @spinicist, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @grlee77

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
[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 (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @mathieuboudreau

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
[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 (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @spinicist

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
[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 (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

sravan953 commented 4 years ago

@sravan953, once you've made the above change, can you run @whedon generate pdf here? Also can you do the following:

[ ] Please archive the reviewed software on Zenodo and report the DOI here in this review thread. Make sure the Zenodo deposit has the correct metadata (same title and author list as the paper).

[ ] Can you confirm that the version of the reviewed (and archived) software is 1.2.2, or has the version tag moved on? Please provide the latest version tag for the reviewed software.

I am not sure what you mean. Right now, I signed into Zenodo via my Github account. Searching for 'PyPulseq' does not return any results.
Are you suggesting I publish another release with the latest commit? We submitted it at 1.2.2, and that is the latest release so far.

sravan953 commented 4 years ago

@sravan953, once you've made the above change, can you run @whedon generate pdf here? Also can you do the following:

[ ] Please archive the reviewed software on Zenodo and report the DOI here in this review thread. Make sure the Zenodo deposit has the correct metadata (same title and author list as the paper).

[ ] Can you confirm that the version of the reviewed (and archived) software is 1.2.2, or has the version tag moved on? Please provide the latest version tag for the reviewed software.

@Kevin-Mattheus-Moerman Oops, I now follow what you were saying. There have been some minor fixes since version 1.2.2. was submitted to JOSS for review. Would you recommend publishing a new release with the latest commit?

sravan953 commented 4 years ago

@Kevin-Mattheus-Moerman -

DOI - 10.5281/zenodo.3479527
Latest release - 1.2.2r1 (published on Zenodo)

Kevin-Mattheus-Moerman commented 4 years ago

@whedon set 1.2.2r1 as version

whedon commented 4 years ago

OK. 1.2.2r1 is the version.

Kevin-Mattheus-Moerman commented 4 years ago

@whedon set 10.5281/zenodo.3479527 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3479527 is the archive.

Kevin-Mattheus-Moerman commented 4 years ago

@openjournals/joss-eics I recommend this paper for acceptance in JOSS.

@sravan953 the editor in chief on call will take over now. They might have additional comments on your paper.

Kevin-Mattheus-Moerman commented 4 years ago

@sravan953 one last point from me. I would recommend that you update your paper title (and also the matched Zenodo archive title) to be a bit more descriptive, e.g.: PyPulseq: A Python Package for MRI Pulse Sequence Design Something like that would help make your paper more discoverable. @arfon is this something that we can change just in the PDF or do we need to propagate the title change anywhere else?

arfon commented 4 years ago

@arfon is this something that we can change just in the PDF or do we need to propagate the title change anywhere else?

Just the paper.md should do it.

sravan953 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

sravan953 commented 4 years ago

@Kevin-Mattheus-Moerman @arfon Updated the title on the README.md, Zenodo archive and on paper.md.

labarba commented 4 years ago

I fixed in-text citation syntax and a terminology issue in https://github.com/imr-framework/pypulseq/pull/23

labarba commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago


OK DOIs

- 10.1002/mrm.26235 is OK
- 10.1016/j.mri.2018.03.008 is OK
- 10.1016/j.jmr.2004.05.021 is OK
- 10.1002/mrm.25640 is OK
- 10.1002/mrm.26990 is OK
- 10.1615/CritRevBiomedEng.2019029380 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1023

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1023, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

labarba commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1024
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01725
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

labarba commented 4 years ago

Congratulations, @imr-framework, your JOSS paper is published! 🚀

Huge thanks to our editor: @Kevin-Mattheus-Moerman, and the reviewers: @grlee77, @mathieuboudreau, @spinicist — your contributions to JOSS are greatly appreciated 🙏

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01725/status.svg)](https://doi.org/10.21105/joss.01725)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01725">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01725/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01725/status.svg
   :target: https://doi.org/10.21105/joss.01725

This is how it will look in your documentation:

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sairamgeethanath commented 4 years ago

Congratulations, @imr-framework, your JOSS paper is published! 🚀

Huge thanks to our editor: @Kevin-Mattheus-Moerman, and the reviewers: @grlee77, @mathieuboudreau, @spinicist — your contributions to JOSS are greatly appreciated 🙏

Many thanks to all the reviewers @mathieuboudreau @spinicist @grlee77, the editor @Kevin-Mattheus-Moerman and the associate editor in chief @labarba for the time and inputs to make our work better.

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