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[REVIEW]: spiketools: a Python package for analyzing single-unit neural activity #5268
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
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👋🏼 @rly, @neuromusic, @djsaunde this is the review thread for the paper. All of our communications will happen here from now on. As a reviewer, the first step is to create a checklist for your review by entering @editorialbot generate my checklist as the top of a new comment in this thread. These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines. 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #5268 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. We aim for reviews to be completed within about 2-4 weeks. Please let me know if any 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. Please feel free to ping me (@AJQuinn) if you have any questions/concerns. |
Hi @rly, @neuromusic, @djsaunde - it's been around a week. I'd like to quickly check in and make sure that you all have what you need to start the review and aren't facing any issues? Please let me know if so and we can try to sort something! Cheers |
Review checklist for @djsaundeConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Review checklist for @rlyConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Hi @neuromusic - have you been able to get started with the checklist and review? We're hoping to get all reviews in over the next couple of weeks. No problem if you need a bit more time, just let me know here or via an email. |
Hi @djsaunde - Thanks for filling out the checklist. Are there still open issues that need to be resolved before you can sign off on the remaining sections? If so, could you add a link to this thread in the issue description so that I can keep a track of them from here? Thank you! |
This issue is currently blocking " Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)." Otherwise, the checklist is complete (apologies for the delay). |
Hey all - first thing, thank you to everyone's work on this review, we greatly appreciate it! @rly : thanks for your review, and suggestions you made - we have made those updates through the issues! @djsaunde : thanks also for the review and for your comments. For the specifics of the spiketools issue you opened (spiketools/spiketools#171) this has been addressed in a literal way by removing the broken link (there some notes here contextualizing that that broken link was due to adapting materials from another project and not because there is a page that could not be navigated to). For this project, our main set of examples are in the tutorials, which covers examples of key sub-modules (as well as having doctest examples within a large number of function docstrings). For the purpose of the review, do you find the available materials sufficient for confirming the "example usage" topic, or are you leaving this topic open because you think the project should have some additional examples / doc pages? @AJQuinn - thank you for handling this submission! |
@TomDonoghue Yup, that will do, thanks. I've updated my checklist s.t. it is complete. |
@TomDonoghue Thanks for making those updates! The work is solid. I appreciated the tutorials. There are no blocking issues from my standpoint. |
Fantastic, thanks @djsaunde and @rly! Much appreciated. @TomDonoghue, I've been in touch with @neuromusic off-thread and there should be a final review coming in early next week. Apologies for the delay on this, should be able to move quickly from next week. |
Hey @AJQuinn - any updates from @neuromusic? |
Sorry for the delay. I'll get it done later today. |
Review checklist for @neuromusicConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@editorialbot check references |
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@editorialbot set 10.5281/zenodo.10076024 as archive |
Done! archive is now 10.5281/zenodo.10076024 |
@editorialbot generate pdf |
Hi @TomDonoghue looks good to me, happy to recommend to accept. A final check will be carried out by an Editor in Chief who may raise additional points if anything has been missed. One point that might come up (not certain how strict the policy is here) is that the Zenodo repo name for v0.2.0 now doesn't match the paper title - you can update this in the metadata and might want to do that now. |
@editorialbot recommend-accept |
1 similar comment
@editorialbot recommend-accept |
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👋 @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#4767, then you can now move forward with accepting the submission by compiling again with the command |
@TomDonoghue as AEiC I am here to help process this work for acceptance in JOSS. I have check the paper, this review, the repository, and the archive link. Most seems in order. However, I do have the points below that require your attention:
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@Kevin-Mattheus-Moerman - I have updated the title on Zenodo and our affiliations on the paper! Let me know if there is anything else I should do / update! |
@editorialbot generate pdf |
@TomDonoghue all looks good now. Thanks. |
@editorialbot accept |
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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
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. |
🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘 |
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨 Here's what you must now do:
Any issues? Notify your editorial technical team... |
Congratulations on this paper @TomDonoghue ! Thanks for editing @AJQuinn! And a special thanks to the reviewers: @rly, @neuromusic, @djsaunde |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
This is how it will look in your documentation: We need your help! The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
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Submitting author: @TomDonoghue (Thomas Donoghue)
Repository: https://github.com/spiketools/spiketools
Branch with paper.md (empty if default branch):
Version: 0.2.0
Editor: @AJQuinn
Reviewers: @rly, @neuromusic, @djsaunde
Archive: 10.5281/zenodo.10076024
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
@rly & @neuromusic & @djsaunde, 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 @AJQuinn 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 @rly
📝 Checklist for @djsaunde
📝 Checklist for @neuromusic
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