[REVIEW]: PyNeuroTrace - Python code for neural activity time series

[editorialbot]

Submitting author: !--author-handle-->@peter-hogg<!--end-author-handle-- (Peter William Hogg) Repository: https://github.com/padster/pyNeuroTrace Branch with paper.md (empty if default branch): Version: 1.0.1 Editor: !--editor-->@adamltyson<!--end-editor-- Reviewers: @stephenlenzi, @danielmk Archive: 10.5281/zenodo.13312905

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/338dbf8284b80de945d30d971f43efb3"><img src="https://joss.theoj.org/papers/338dbf8284b80de945d30d971f43efb3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/338dbf8284b80de945d30d971f43efb3/status.svg)](https://joss.theoj.org/papers/338dbf8284b80de945d30d971f43efb3)

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

@stephenlenzi & @danielmk, 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 @adamltyson 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 @danielmk

📝 Checklist for @stephenlenzi

[editorialbot]

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

[adamltyson]

Hi @Peter-Hogg should the DOI be 10.5281/zenodo.13312904? The DOI above seems to be for something different.

[adamltyson]

Hi again @Peter-Hogg, would you also be able to update the zenodo title to match the paper title? They're just very slightly different. Then I think we're finally ready to go!

[Peter-Hogg]

@adamltyson sorry for that. Updated the title

10.5281/zenodo.13312905

[adamltyson]

@editorialbot set 10.5281/zenodo.13312905 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13312905

[adamltyson]

@editorialbot set 1.0.1 as version

[editorialbot]

Done! version is now 1.0.1

[adamltyson]

@editorialbot generate pdf

[adamltyson]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.7554/eLife.38173 is OK
- 10.1371/journal.pcbi.1005423 is OK
- 10.1038/s41467-024-47515-x is OK
- 10.1038/s43586-022-00147-1 is OK
- 10.1371/journal.pone.0157595 is OK
- 10.1002/jbio.201100133 is OK
- 10.1038/nprot.2010.169 is OK
- 10.1038/s41592-019-0597-2 is OK
- 10.1109/embc.2018.8512983 is OK
- 10.3389/fncir.2020.00033 is OK
- 10.1016/s0896-6273(01)00235-5 is OK
- 10.1101/061507 is OK
- 10.1101/pdb.prot106831 is OK
- 10.1038/s41598-017-02301-2 is OK

MISSING DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...
- No DOI given, and none found for title: SLAP2 – Two Photon Microscope Kit

INVALID DOIs

- None

[editorialbot]

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

[adamltyson]

Thanks @Peter-Hogg, this all looks good to me. I'll hand it over to the EiC for the final checks.

[adamltyson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.7554/eLife.38173 is OK
- 10.1371/journal.pcbi.1005423 is OK
- 10.1038/s41467-024-47515-x is OK
- 10.1038/s43586-022-00147-1 is OK
- 10.1371/journal.pone.0157595 is OK
- 10.1002/jbio.201100133 is OK
- 10.1038/nprot.2010.169 is OK
- 10.1038/s41592-019-0597-2 is OK
- 10.1109/embc.2018.8512983 is OK
- 10.3389/fncir.2020.00033 is OK
- 10.1016/s0896-6273(01)00235-5 is OK
- 10.1101/061507 is OK
- 10.1101/pdb.prot106831 is OK
- 10.1038/s41598-017-02301-2 is OK

MISSING DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...
- No DOI given, and none found for title: SLAP2 – Two Photon Microscope Kit

INVALID DOIs

- None

[editorialbot]

: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/5769, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@Peter-Hogg 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 final points that require your attention:

On the paper:

• [x] senstive should read sensitive

On the archive:

• [x] You currently list two licenses, the default CC-BY one, and your proper license. I suggest you edit this to only have your software license, unless you have a good reason to also have the CC-BY for non-software content.

[Peter-Hogg]

@Kevin-Mattheus-Moerman, thanks for catching the typo; I've edited the paper with the most recent push. I've also removed the default license from the archive. Thanks everyone who has helped with the review process.

Cheers,

Peter

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Coleman given-names: Patrick orcid: "https://orcid.org/0009-0001-5216-7748" - family-names: Hogg given-names: Peter William orcid: "https://orcid.org/0000-0003-2176-4977" - family-names: Toth given-names: Tristan Dellazizzo orcid: "https://orcid.org/0009-0001-3239-6930" - family-names: Haas given-names: Kurt orcid: "https://orcid.org/0000-0003-4754-1560" contact: - family-names: Hogg given-names: Peter William orcid: "https://orcid.org/0000-0003-2176-4977" doi: 10.5281/zenodo.13312905 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Coleman given-names: Patrick orcid: "https://orcid.org/0009-0001-5216-7748" - family-names: Hogg given-names: Peter William orcid: "https://orcid.org/0000-0003-2176-4977" - family-names: Toth given-names: Tristan Dellazizzo orcid: "https://orcid.org/0009-0001-3239-6930" - family-names: Haas given-names: Kurt orcid: "https://orcid.org/0000-0003-4754-1560" date-published: 2024-08-15 doi: 10.21105/joss.06877 issn: 2475-9066 issue: 100 journal: Journal of Open Source Software publisher: name: Open Journals start: 6877 title: PyNeuroTrace - Python code for neural activity time series type: article url: "https://joss.theoj.org/papers/10.21105/joss.06877" volume: 9 title: PyNeuroTrace - Python code for neural activity time series ```

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5775
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06877
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@Peter-Hogg et al. congratulations on this JOSS paper!

@adamltyson thanks for editing!

And a special thanks to the reviewers: @stephenlenzi, @danielmk !!

[editorialbot]

: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.06877/status.svg)](https://doi.org/10.21105/joss.06877)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06877">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06877/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06877/status.svg
   :target: https://doi.org/10.21105/joss.06877

This is how it will look in your documentation:

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[adamltyson]

Congrats @Peter-Hogg, and thanks @stephenlenzi, @danielmk, @Kevin-Mattheus-Moerman!