Closed editorialbot closed 1 month ago
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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
MISSING DOIs
- None
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.88 T=1.70 s (105.6 files/s, 31142.2 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 104 5692 4648 19852
HTML 25 1334 75 7703
Markdown 12 1193 0 5535
SVG 2 1 1 2996
JavaScript 12 131 221 880
CSS 4 190 35 779
reStructuredText 7 169 159 351
XML 4 0 336 256
TeX 1 19 0 236
R 1 25 8 77
YAML 3 6 4 57
TOML 1 5 0 47
DOS Batch 2 8 1 28
make 1 4 7 9
Bourne Shell 1 0 0 1
-------------------------------------------------------------------------------
SUM: 180 8777 5495 38807
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1025
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
π Hi @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega, and thank you again for agreeing to review this submission for MIRP !
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
.
In working through the checklist, you're likely to have specific feedback on MIRP. Whenever possible, please open relevant issues on the software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !
If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@alexzwanenburg Can you please clarify if Sebastian Starke and Steffan Lock are the same person. I do not see any code contributions from a Steffan Lock. This may be fine if he helped make the package, but please clarify. Or maybe Steffan Leger as mentioned in the thank you at the bottom is the same as Steffan Lock?
@drcandacemakedamoore Steffen LΓΆck is my professor and advised on the paper and the package. Stefan Leger contributed to early in-house versions of MIRP, prior to moving GitHub. Sebastian Starke also made minor contributions to an earlier version of MIRP.
@alexzwanenburg preferably module names should be all lower case (and super-best is single word or if no other choice with underscore). I notice you have modules that are camelcase. Different file systems have different case conventions. The real point is that it could be possible to import these modules in two different ways then cause problems on different files systems where case conventions are different. I will get to more substantial issues soon, but this already pops out for my eyes, before I even started the real review. But since I'm on superficial issues right now, some badges would not hurt (it's nice to have the pypi version badge and also Anaconda if you released it there, and I can't tell at first glance here.)
@alexzwanenburg on a less superficial issue, I note there is no developer's documentation. Many people may want to tinker with what you have done, and hopefully even contribute to the package. I am looking for documentation somewhere that tells people how to run the testing, so they can test new stuff before sending it. I am also looking for this, because it is not clear if you have any automated testing that runs in CI (did I miss it?) so instead of figuring out how to run it from there I would need instructions to run your tests properly . Update: I see from my Windows machine it is python -m pytest
but I have no idea what it will be from a Mac
Thank you, @drcandacemakedamoore !
If you could please open subsequent review comments as issues on the MIRP repository, this will help to make sure there is sufficient space for follow-up discussion and that action items are trackable across reviewers. I know that @alexzwanenburg has started to respond in-thread, but we'll generally ask to keep only high-level discussions in the general review thread and re-direct all other comments to the project issue tracker.
If you have any other questions, of course, please don't hesitate to ask.
π Hi everyone, happy Monday !
I just wanted to check-in on the status of this review and make sure that there weren't any current blockers in working through the reviewer checklists.
I did notice that @drcandacemakedamoore has opened https://github.com/oncoray/mirp/issues/66, https://github.com/oncoray/mirp/issues/67, and https://github.com/oncoray/mirp/issues/68 -- thank you ! I'm cross-linking them here, so they're easier for myself (and other reviewers) to track.
Hello! Thank you very much for the invitation to review this paper. I will finalize the review later this week (only the "functionality" section is missing). For now, I've left my comments on issue #69 .
@emdupre Feel free to let me know if my comments are appropriate, this is my first time reviewing for JOSS so I'm learning, thanks!
π Hi everyone ! Thank you for your comments on MIRP to date !
I just wanted to note that we have now passed the four week review window. If you could please work on finalizing your initial reviews as soon as possible, I would appreciate it.
Once you have finalized your initial reviews, you can let me know by responding directly in this thread. Of course, if you have any questions or blockers, please don't hesitate to let me know !
π @surajpaib @Matthew-Jennings @drcandacemakedamoore @theanega
π Hello again,
I just wanted to follow up on the previous message as I know if created some concern and confusion :
Apologies for being unclear on these points in my previous message. If there's anything else I can clarify, please let me know. And thank you again for your work in reviewing MIRP !
Thanks, @emdupre! No worries.
@alexzwanenburg can you confirm the most up to date branch we should be looking at is dev2.2.1 for everything?
@drcandacemakedamoore I can confirm that the most up-to-date branch is dev2.2.1. I have been working on this branch to address your comments and suggestions. This does not include the paper itself, which lives in the paper branch.
Hi @emdupre! I will cross off the remainder of the checklist by the end of this week. I hope that timeline works.
π Hi everyone, thanks for the updates !
I just wanted to summarize status:
@theanega : I see that you've completed your checklist, but you've also created issue https://github.com/oncoray/mirp/issues/69 which is still open. Could you please confirm the status of your review ?
@Matthew-Jennings : I see that you've not yet completed your checklist and that you've created the following open issues https://github.com/oncoray/mirp/issues/72, https://github.com/oncoray/mirp/issues/73, and https://github.com/oncoray/mirp/issues/75. I assume you've currently finished the initial review and are now waiting on the resolution of these issues, but if you're instead still working on the initial review,please let me know.
@drcandacemakedamoore and @surajpaib : I know that you were not expecting to finish the initial review until this week. Please let us know when you are able to do so !
I'll also cross-link all of the other associated issues to date, in case this helps in finalizing initial reviews:
@emdupre: Yep, that's correct!
I released version 2.2.1. This also includes updates to the documentation and a new tutorial: https://oncoray.github.io/mirp/tutorial_compute_radiomics_features_mr.html
I am looking forward to your feedback on these updates.
Hi @emdupre I've opened an issue on the MIRP repo with more of my observations and with that I'm done with my initial review.
Much thanks for your patience
π Hi everyone, and happy Monday !
I wanted to update with my understanding of the current status of this review for MIRP.
Currently, the following JOSS associated issues are open:
At this point, it appears that @alexzwanenburg is actively addressing these comments.
Please let me know, though, if there are any review-related discussions I am not capturing here and should be aware of. And thank you all again for your work in reviewing MIRP to date ! π
I have released version 2.2.2 which resolved the linked issues. Thanks for all the feedback!
Hi @alexzwanenburg, would you mind keeping these Issues open until we've re-reviewed?
In my mind, they're not closed until either the reviewers have confirmed the recommendations/suggestions have been met, or where they're not met, agreement has been reached that those items need not preclude publication.
π Hi everyone !
I just wanted to follow-up on this and check how this re-review of MIRP is going. @Matthew-Jennings, @drcandacemakedamoore, @surajpaib, and @theanega, 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 π»
I will endeavour to complete my review in the next few days.
I will take a look this weekend.
On Thu, Jun 6, 2024, 1:59 AM Matthew Jennings @.***> wrote:
I will endeavour to complete my review in the next few days.
β Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6413#issuecomment-2151197978, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHMYSANAWGFIYSMWWV5CJWTZF6X6RAVCNFSM6AAAAABD2TTWCWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJRGE4TOOJXHA . You are receiving this because you were mentioned.Message ID: @.***>
I will re-review the paper over the next couple of days and close all relevant issues.
I am happy that you addressed the open issue I had, and ready to close it. I would encourage you, while it is not strictly required, to put some badges on your repo (here is an example repo with badges: https://github.com/ReSurfEMG/ReSurfEMG) before JOSS publication . You, or whoever will maintain this software, will always have some technical issues to work on. I see some things that could be further developed, but what you really need to sustain the software is a community of users willing to pitch in and support that. Adding some badges helps people quickly see your software is citable, what version you are on, and so forth. The upcoming publication moment is the moment you may get the most eyeballs on your software. Take the opportunity to make it "look good". Anyways, from my perspective, I am happy to close my issue, and OK moving forward.
Hi @emdupre, I am happy to consider my review complete and to see this published. Thank you, @alexzwanenburg for your patience and work to address review items. Well done on producing an excellent radiomics resource.
Thank you for confirming, @Matthew-Jennings and @drcandacemakedamoore !
It looks like all reviewer checklists are now completed. @surajpaib, you mentioned that you were planning to re-review ; if this is not yet complete, please let me know. If I don't hear from you in the next couple of days, I'll assume you're OK to move forward as-is.
After confirmed reviewer sign-off, the next step is that I'll complete a few editorial checks to continue processing the submission π
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
π Hi @alexzwanenburg, I've asked editorialbot to generate our post-review checklist, which provides action items for both the authors as well as the editor.
I'll work on getting paper comments to you as soon as possible. In the meantime, could you please address the "additional author tasks" listed here?
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
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
Again, thanks for the excellent peer-reviews. I think it greatly helped making MIRP a better software in all aspects.
A to-do list for me:
I fixed an ORCID and updated a table with the most recent information.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I uploaded the release on Zenodo, with the following DOI: 10.5281/zenodo.12493595 The release version is 2.2.4
Submitting author: !--author-handle-->@alexzwanenburg<!--end-author-handle-- (Alex Zwanenburg) Repository: https://github.com/oncoray/mirp Branch with paper.md (empty if default branch): paper Version: v2.2.4 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega Archive: 10.5281/zenodo.12493595
Status
Status badge code:
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
@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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @emdupre know.
β¨ 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 β¨
Checklists
π Checklist for @surajpaib
π Checklist for @Matthew-Jennings
π Checklist for @drcandacemakedamoore
π Checklist for @theanega