[REVIEW]: MIRP: A Python package for standardised radiomics

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@alexzwanenburg@emdupre<!--end-editor-- Reviewers: @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega Archive: 10.5281/zenodo.12493595

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Reviewer instructions & questions

@surajpaib & @Matthew-Jennings & @drcandacemakedamoore & @theanega, 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:

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

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emdupre commented 5 months ago

Thank you, @alexzwanenburg ! Confirming that I have received these updates ; I am currently at a conference and so responding more slowly than usual. I will, though, have feedback to you shortly !

emdupre commented 4 months ago

@editorialbot set 2.2.4 as version

editorialbot commented 4 months ago

Done! version is now 2.2.4

emdupre commented 4 months ago

@editorialbot set 10.5281/zenodo.12493595 as archive

editorialbot commented 4 months ago

Done! archive is now 10.5281/zenodo.12493595

emdupre commented 4 months ago

Thank you for your patience, @alexzwanenburg !

I've now finished reviewing the software paper and archive. I only have a few small editorial requests:

On L42, "The latest major version (2)..." I believe intended to denote the 2.x.x series ; however, I found this unclear on first read. I would suggest to amend to either simply "The latest major version" or reword to something like "Updates in the recent major release series"
On L28 and L29, the formatting for these in-line enumerated items is less than ideal. Could you please either convert this to a list or remove "1." and "2." in text ? Rewording L27 from "created reference standards" to "created two reference standards" could help to clarify this point.
In the current reference list, multiple journals are denoted by their abbreviations ; e..g, "Sci. Rep." for "Scientific Reports." Could you please write out the journal names in full ?

alexzwanenburg commented 4 months ago

Thanks for reviewing the paper and archive. I made the suggested corrections.

alexzwanenburg commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

emdupre commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago

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

OK DOIs

- 10.1038/s41571-022-00707-0 is OK
- 10.1038/nrclinonc.2016.162 is OK
- 10.1148/radiol.2020191145 is OK
- 10.1038/s41598-017-13448-3 is OK
- 10.1038/s41598-018-36938-4 is OK
- 10.1038/s41598-022-13967-8 is OK
- 10.1148/radiol.211604 is OK
- 10.1148/radiol.231319 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1038/s41467-023-44591-3 is OK
- 10.1158/0008-5472.CAN-17-0339 is OK
- 10.1002/mp.13046 is OK
- 10.1158/0008-5472.CAN-18-0125 is OK
- 10.1088/0031-9155/60/14/5471 is OK
- 10.1038/s41598-017-10371-5 is OK
- 10.1093/neuonc/now256 is OK

MISSING DOIs

- None

INVALID DOIs

- None

emdupre commented 4 months ago

Thank you, @alexzwanenburg ! I'm now happy to recommend mirp to the EiC team for publication in JOSS ✨🚀

Thank you, too, to @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, and @theanega for your reviews and involvement throughout this process ! JOSS works because of your work 💐

emdupre commented 4 months ago

@editorialbot recommend-accept

editorialbot commented 4 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 4 months ago

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

OK DOIs

- 10.1038/s41571-022-00707-0 is OK
- 10.1038/nrclinonc.2016.162 is OK
- 10.1148/radiol.2020191145 is OK
- 10.1038/s41598-017-13448-3 is OK
- 10.1038/s41598-018-36938-4 is OK
- 10.1038/s41598-022-13967-8 is OK
- 10.1148/radiol.211604 is OK
- 10.1148/radiol.231319 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1038/s41467-023-44591-3 is OK
- 10.1158/0008-5472.CAN-17-0339 is OK
- 10.1002/mp.13046 is OK
- 10.1158/0008-5472.CAN-18-0125 is OK
- 10.1088/0031-9155/60/14/5471 is OK
- 10.1038/s41598-017-10371-5 is OK
- 10.1093/neuonc/now256 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 4 months ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5580, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

alexzwanenburg commented 4 months ago

Aside from an overly wide sentence on page 2 the proof looks fine from my perspective.

emdupre commented 4 months ago

@openjournals/bcm-eics, just re-pinging here in case this notification slipped through ! Thank you 🙏

Kevin-Mattheus-Moerman commented 4 months ago

@editorialbot set version as v2.2.4

editorialbot commented 4 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Kevin-Mattheus-Moerman commented 4 months ago

@editorialbot set v2.2.4 as version

editorialbot commented 4 months ago

Done! version is now v2.2.4

Kevin-Mattheus-Moerman commented 4 months ago

@alexzwanenburg as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

[x] European English is used throughout, except for one occurrence of standardized which should read standardised.
[x] Please edit the Zenodo listed version tag to include the v so it will end up reading version v2.2.4 (I know it seems odd but the thing after the word version there should be the complete version tag as listed for your GitHub release tag, which has the v).

alexzwanenburg commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

alexzwanenburg commented 4 months ago

I made changed standardized to standardised in the paper, and updated the Zenodo listed version to v2.2.4.

Kevin-Mattheus-Moerman commented 4 months ago

@editorialbot accept

editorialbot commented 4 months ago

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

editorialbot commented 4 months ago

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: Zwanenburg given-names: Alex orcid: "https://orcid.org/0000-0002-0342-9545" - family-names: Löck given-names: Steffen orcid: "https://orcid.org/0000-0002-7017-3738" doi: 10.5281/zenodo.12493595 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Zwanenburg given-names: Alex orcid: "https://orcid.org/0000-0002-0342-9545" - family-names: Löck given-names: Steffen orcid: "https://orcid.org/0000-0002-7017-3738" date-published: 2024-07-17 doi: 10.21105/joss.06413 issn: 2475-9066 issue: 99 journal: Journal of Open Source Software publisher: name: Open Journals start: 6413 title: "MIRP: A Python package for standardised radiomics" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06413" volume: 9 title: "MIRP: A Python package for standardised radiomics" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

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editorialbot commented 4 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 4 months 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/5645
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06413
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 4 months ago

Congratulations on this JOSS publication @alexzwanenburg et al. !

Thanks for editing @emdupre !

And a special thank you to the reviewers: @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega !!

editorialbot commented 4 months ago

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

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