[REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox

whedon commented 4 years ago

Submitting author: @maieroli2010 (Oliver Maier) Repository: https://github.com/IMTtugraz/PyQMRI Version: v1.0.0 Editor: @Kevin-Mattheus-Moerman Reviewer: @grlee77, @agahkarakuzu, @DARSakthi Archive: 10.5281/zenodo.4313301

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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 & @agahkarakuzu & @DARSakthi, 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 start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @grlee77

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 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 (@maieroli2010) 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: 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 @agahkarakuzu

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 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 (@maieroli2010) 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: 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 @DARSakthi

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 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 (@maieroli2010) 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: 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 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

MaierOli2010 commented 3 years ago

Due to security concerns I've temporarily disabled the link to the Jenkins server. Working with our IT Security to get an official solution but it might take some time.

MaierOli2010 commented 3 years ago

@agahkarakuzu I've moved the CI from Jenkins to the University GitLab site. This should provide similar functionality but without the security vulnerabilities of exposing my own workstation to the public. The GitLab repo is synced with GitHub and all changes to GitLab will be mirrored to GitHub as well. I've updated the Contributing section to point to GitLab for Code development.

agahkarakuzu commented 3 years ago

@MaierOli2010 I made a small PR to fix a typo. Other than that, looks like all my comments have been resolved, thank you so much for addressing them and making this amazing tool publicly available!

I checked all the remaining boxes, all good on my end.

Kevin-Mattheus-Moerman commented 3 years ago

Thanks for your help @agahkarakuzu !

Kevin-Mattheus-Moerman commented 3 years ago

@whedon generate pdf

Kevin-Mattheus-Moerman commented 3 years ago

@grlee77 all boxes are ticked but you addressed some typos/paper changes. Let me know if you are happy to recommend acceptance at this point.

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 3 years ago

@DARSakthi can you also review the latest paper and let us know if you are happy with it as it stands. Thanks!

DARSakthi commented 3 years ago

Looks good to me -- all comments have been addressed. Well done @MaierOli2010 and team. Cheers

DS

MaierOli2010 commented 3 years ago

Had to update affiliations. Should be all set now from my side. I thought about increasing the version number to 1.0, i.e., first release if the paper is accepted. Should I do that prior or post to the published paper?

MaierOli2010 commented 3 years ago

@whedon generate pdf from branch JOSS_pub

whedon commented 3 years ago

Attempting PDF compilation from custom branch JOSS_pub. Reticulating splines etc...

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

MaierOli2010 commented 3 years ago

@Kevin-Mattheus-Moerman Are there any blockers left which should be addressed?

Kevin-Mattheus-Moerman commented 3 years ago

@MaierOli2010 apologies for the delay. I'll start processing this for acceptance shortly.

Kevin-Mattheus-Moerman commented 3 years ago

@MaierOli2010 At this point could you do the following:

[x] Archive a copy of the software on ZENODO (some find these steps useful: https://guides.github.com/activities/citable-code/)? Please ensure that the metadata, in particular the author information, names, and order match the information for the JOSS paper. Can you also make sure the title matches the JOSS paper? You may need to manually edit this information. Once you've archived a copy please report back here with the archive DOI. Thanks.
[x] Can you confirm what the latest version tag is for this work? Is it still at v0.3.1?
[x] Since your paper is about to be accepted I recommend you read through it once more yourself and make any final edits if needed.

MaierOli2010 commented 3 years ago

@Kevin-Mattheus-Moerman I've archived the software. The associated DOI is: 10.5281/zenodo.4313301 Further, I decided to push the version to "first release", i.e. v1.0.0 as the acceptance of the paper marks the first release in my opinion. This is also the archived version tag.

There were some minor edits to affiliations and I've shortened a sentence in the introduction as its meaning was the same as of the one beforehand.

Finally, I would like to thank all of you for reviewing our work :)

Kevin-Mattheus-Moerman commented 3 years ago

@whedon set 10.5281/zenodo.4313301 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4313301 is the archive.

Kevin-Mattheus-Moerman commented 3 years ago

@whedon set v1.0.0 as version

whedon commented 3 years ago

OK. v1.0.0 is the version.

Kevin-Mattheus-Moerman commented 3 years ago

@whedon generate pdf

Kevin-Mattheus-Moerman commented 3 years ago

@whedon generate pdf from branch JOSS_pub

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 3 years ago

@MaierOli2010 I have two minor points about the paper:

[x] For consistency, can you add "Austria" to the 3rd affiliation?
[x] Should the heading "Algorithmic" be "Algorithms" instead?

MaierOli2010 commented 3 years ago

@Kevin-Mattheus-Moerman Added "Austria" to the 3rd affiliation and renamed "Algorithmic" to "Algorithms" Both changes are done to "master" branch as I've merged everything there.

Kevin-Mattheus-Moerman commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1978

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1978, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 3 years ago

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

OK DOIs

- 10.1137/090769521 is OK
- 10.1002/mrm.27502 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1016/j.parco.2011.09.001 is OK
- 10.1016/0167-2789(92)90242-F is OK
- 10.1109/TMI.2016.2564989 is OK
- 10.1002/mrm.22595 is OK
- 10.1109/TMI.2009.2023119 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1002/mrm.22483 is OK
- 10.1007/978-3-642-54774-4_3 is OK
- 10.24355/dbbs.084-201305311128-0 is OK
- 10.1002/ima.22196 is OK
- 10.1137/16M1092015 is OK
- 10.1007/s10589-012-9476-9 is OK
- 10.1002/mrm.20283 is OK
- 10.1016/j.neuroimage.2019.01.029 is OK
- 10.21105/joss.00656 is OK
- 10.21105/joss.02343 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1038/nm.3390 is OK
- 10.1016/B978-012372560-8/50002-4 is OK
- 10.1186/s12968-019-0570-3 is OK
- 10.1002/mrm.26726 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 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/1979
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02727
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 3 years ago

Congratulations @MaierOli2010!

Thanks for another excellent review @grlee77, @agahkarakuzu, @DARSakthi!!!

whedon commented 3 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.02727/status.svg)](https://doi.org/10.21105/joss.02727)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02727">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02727/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02727/status.svg
   :target: https://doi.org/10.21105/joss.02727

This is how it will look in your documentation:

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