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[REVIEW]: Neurosift: DANDI exploration and NWB visualization in the browser #6590

Closed editorialbot closed 5 months ago

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@magland<!--end-author-handle-- (Jeremy Magland) Repository: https://github.com/flatironinstitute/neurosift Branch with paper.md (empty if default branch): paper Version: v0.2.8 Editor: !--editor-->@mstimberg<!--end-editor-- Reviewers: @alexrockhill, @jodeleeuw, @sanjayankur31 Archive: 10.5281/zenodo.11192864

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0b7a6a284076c02bfe5660344d5bb58f"><img src="https://joss.theoj.org/papers/0b7a6a284076c02bfe5660344d5bb58f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0b7a6a284076c02bfe5660344d5bb58f/status.svg)](https://joss.theoj.org/papers/0b7a6a284076c02bfe5660344d5bb58f)

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

@alexrockhill & @jodeleeuw & @sanjayankur31, 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:

@editorialbot generate my checklist

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

📝 Checklist for @sanjayankur31

📝 Checklist for @alexrockhill

sanjayankur31 commented 5 months ago

Many thanks @alexrockhill, @jodeleeuw, and @sanjayankur31 for your detailed and constructive reviews. It seems that you all recommend the publication of the software/paper in its current form (if not, please let me know 😄 ).

Yes :)

@sanjayankur31, one item in your checklist is still unchecked, but I take your earlier comment as indicating that you are happy with everything.

Ah, sorry about that. Checked off now too.

magland commented 5 months ago
  • Double check authors and affiliations (including ORCIDs)

I have double checked these.

  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.

The latest version is 0.2.8

  • Archive the release on Zenodo/figshare/etc and post the DOI here.

Archived on Zenodo: https://zenodo.org/records/11192864

DOI: 10.5281/zenodo.11192864

Note that I did not create an archive release in the traditional way because the source contains a git submodule. So I prepared a .tar.gz of the source code including the submodule and uploaded that to Zenodo.

  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

I double checked this.

  • Make sure that the license listed for the archive is the same as the software license.

It does match (Apache 2.0)

mstimberg commented 5 months ago

@editorialbot generate pdf

mstimberg commented 5 months ago

@editorialbot set 0.2.8 as version

editorialbot commented 5 months ago

Done! version is now 0.2.8

editorialbot commented 5 months ago

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

mstimberg commented 5 months ago

Note that I did not create an archive release in the traditional way because the source contains a git submodule. So I prepared a .tar.gz of the source code including the submodule and uploaded that to Zenodo.

Thanks, the archive looks good to me. While it is not strictly necessary, it would be preferable to also have a corresponding tag/release in the github repo. Note that you can also manually attach your .tar.gz file to the release.

mstimberg commented 5 months ago

@editorialbot set 10.5281/zenodo.11192864 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.11192864

mstimberg commented 5 months ago

I made a few minor edits to the paper in flatironinstitute/neurosift#171, please merge if you agree. Note that you do not need to do a new release/archive, since the changes only concern the paper (which will be archived upon publication).

I also noted two minor things in the Zenodo archive that would be nice to correct (again, no need to do a new release/archive, all changes can be done in the Zenodo metadata):

  1. Jeff Soules is missing his affiliation
  2. The description under the title is typset as verbose/typewriter, this could be normal text instead.
mstimberg commented 5 months ago

@editorialbot generate pdf

mstimberg commented 5 months ago

@editorialbot check references

editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.7554/eLife.78362 is OK
- 10.1016/j.neuron.2015.10.025 is OK
- 10.5281/zenodo.10790679 is OK

MISSING DOIs

- No DOI given, and none found for title: nwbwidgets: Explore the hierarchical structure of ...
- No DOI given, and none found for title: h5wasm: A WebAssembly HDF5 reader/writer library

INVALID DOIs

- None
editorialbot commented 5 months ago

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

mstimberg commented 5 months ago

Thanks, @magland, everything looks good to me now. I am recommending that this submission be accepted for publication. An EiC will review shortly and if all goes well this will go live soon! Thanks to @alexrockhill, @jodeleeuw, and @sanjayankur31 for timely and constructive reviews!

mstimberg commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.7554/eLife.78362 is OK
- 10.1016/j.neuron.2015.10.025 is OK
- 10.5281/zenodo.10790679 is OK

MISSING DOIs

- No DOI given, and none found for title: nwbwidgets: Explore the hierarchical structure of ...
- No DOI given, and none found for title: h5wasm: A WebAssembly HDF5 reader/writer library

INVALID DOIs

- None
editorialbot commented 5 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/5351, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

bendichter commented 5 months ago

Great work all-around. The paper is quite well-written, and the review process was very impressive. The proof looks good to me!

NWB Widgets does not currently have a DOI. If that is critical I can mint one on Zenodo, though I am fine with leaving the citation as-is.

magland commented 5 months ago

Thanks everyone! The review was a very good experience.

Kevin-Mattheus-Moerman commented 5 months ago

@magland 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:

Kevin-Mattheus-Moerman commented 5 months ago

@magland please work on the above and let me know when we can proceed. Thanks!

magland commented 5 months ago

@magland 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] In your affiliations, please spell out USA as United States of America

Done https://github.com/flatironinstitute/neurosift/blob/paper/paper/joss/paper.md

  • [x] Please set 0.2.8 as the version tag on ZENODO

Done https://zenodo.org/records/11192864

  • [x] Please create a tagged release on your repository with the version tag 0.2.8.

Done https://github.com/flatironinstitute/neurosift/releases/tag/v0.2.8

@Kevin-Mattheus-Moerman thanks so much!

Let me know if there's anything else that needs to be done.

Kevin-Mattheus-Moerman commented 5 months ago

@editorialbot set v0.2.8 as version

editorialbot commented 5 months ago

Done! version is now v0.2.8

Kevin-Mattheus-Moerman commented 5 months ago

@magland please edit the Zenodo listed version to include the v in v0.2.8

magland commented 5 months ago

@magland please edit the Zenodo listed version to include the v in v0.2.8

@Kevin-Mattheus-Moerman done

Kevin-Mattheus-Moerman commented 5 months ago

@editorialbot accept

editorialbot commented 5 months ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 5 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: Magland given-names: Jeremy orcid: "https://orcid.org/0000-0002-5286-4375" - family-names: Soules given-names: Jeff orcid: "https://orcid.org/0000-0002-2240-1038" - family-names: Baker given-names: Cody orcid: "https://orcid.org/0000-0002-0829-4790" - family-names: Dichter given-names: Benjamin orcid: "https://orcid.org/0000-0001-5725-6910" contact: - family-names: Magland given-names: Jeremy orcid: "https://orcid.org/0000-0002-5286-4375" doi: 10.5281/zenodo.11192864 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Magland given-names: Jeremy orcid: "https://orcid.org/0000-0002-5286-4375" - family-names: Soules given-names: Jeff orcid: "https://orcid.org/0000-0002-2240-1038" - family-names: Baker given-names: Cody orcid: "https://orcid.org/0000-0002-0829-4790" - family-names: Dichter given-names: Benjamin orcid: "https://orcid.org/0000-0001-5725-6910" date-published: 2024-05-27 doi: 10.21105/joss.06590 issn: 2475-9066 issue: 97 journal: Journal of Open Source Software publisher: name: Open Journals start: 6590 title: "Neurosift: DANDI exploration and NWB visualization in the browser" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06590" volume: 9 title: "Neurosift: DANDI exploration and NWB visualization in the browser" ```

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.

Find more information on .cff files here and here.

editorialbot commented 5 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 5 months ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5395
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06590
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 5 months ago

Congratulations on this JOSS publication @magland ! :partying_face:

Thanks for editing @mstimberg !

And a special thank you to the reviewers: @alexrockhill, @jodeleeuw, @sanjayankur31 !!!!

editorialbot commented 5 months 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.06590/status.svg)](https://doi.org/10.21105/joss.06590)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06590">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06590/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06590/status.svg
   :target: https://doi.org/10.21105/joss.06590

This is how it will look in your documentation:

DOI

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