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[REVIEW]: HNN-core: A Python software for cellular and circuit-level interpretation of human MEG/EEG #5848

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editorialbot opened this issue Sep 15, 2023 · 53 comments
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accepted Jupyter Notebook Makefile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Sep 15, 2023

Submitting author: @ntolley (Nicholas Tolley)
Repository: https://github.com/jonescompneurolab/hnn-core
Branch with paper.md (empty if default branch): joss_paper
Version: v0.3.1
Editor: @bmcfee
Reviewers: @isdanni, @neurofractal
Archive: 10.5281/zenodo.10289164

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c"><img src="https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c/status.svg)](https://joss.theoj.org/papers/0ed15ebe93ce4177edb3542fd24d0f7c)

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

@isdanni & @neurofractal, 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 @bmcfee 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 @isdanni

📝 Checklist for @neurofractal

@editorialbot editorialbot added Jupyter Notebook Makefile Python review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 15, 2023
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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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (483.0 files/s, 128732.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          51           2742           5392          10508
reStructuredText                11            402            169            821
JSON                             3              0              0            663
YAML                             6             36              7            276
TeX                              1             25              0            263
Markdown                         2             60              0            212
HTML                             3             10              0             94
Jupyter Notebook                 3              0            733             66
make                             2             19              9             61
Dockerfile                       1             19              2             58
INI                              1              0              0              3
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            85           3313           6312          13028
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 2215

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Failed to discover a Statement of need section in paper

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

OK DOIs

- 10.7554/eLife.51214 is OK
- 10.1152/jn.00535.2009 is OK
- 10.1007/s10548-021-00838-0 is OK
- 10.1093/cercor/bhab221 is OK
- 10.3389/fpsyg.2018.02117 is OK
- 10.1016/j.neuroimage.2021.118479 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1371/journal.pcbi.1008386 is OK
- 10.7554/eLife.44494 is OK
- 10.1371/journal.pcbi.1011003 is OK
- 10.1016/b978-012264841-0/50054-8 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1155/2011/852961 is OK
- 10.3389/fninf.2013.00041 is OK
- 10.3389/fninf.2013.00010 is OK
- 10.1016/j.pneurobio.2023.102490 is OK
- 10.1101/2021.10.11.463545 is OK
- 10.1101/2023.04.17.537118 is OK
- 10.1103/RevModPhys.65.413 is OK
- 10.21105/joss.02505 is OK
- 10.1101/2023.06.16.545371 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1162/neco.1997.9.6.1179 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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isdanni commented Sep 15, 2023

Review checklist for @isdanni

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/jonescompneurolab/hnn-core?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@ntolley) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@bmcfee
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bmcfee commented Oct 6, 2023

👋 just checking in on how this one is going. It appears that @isdanni is nearly done with the review checklist - thanks!

@neurofractal do you have a sense of your timeline for this one?

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isdanni commented Oct 12, 2023

👋 just checking in on how this one is going. It appears that @isdanni is nearly done with the review checklist - thanks!

@neurofractal do you have a sense of your timeline for this one?

Thanks! I just finished the initial round of review. Will follow up if I have any questions.

@ntolley
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ntolley commented Oct 23, 2023

Hi everyone! Just pinging this thread to see if there's anything we can do to help with the review process.

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bmcfee commented Oct 23, 2023

I've sent an email ping to check in - sometimes github thread updates don't make it to folks' inboxes.

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bmcfee commented Oct 24, 2023

Reviewer wrote back indicating that we should expect some updates by next week.

@neurofractal
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neurofractal commented Oct 24, 2023

Review checklist for @neurofractal

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/jonescompneurolab/hnn-core?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@ntolley) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@ntolley
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ntolley commented Nov 2, 2023

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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ntolley commented Nov 2, 2023

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@Kevin-Mattheus-Moerman
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@bmcfee thanks for editing here, will you check in and see how this review is progressing?

@ntolley
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ntolley commented Nov 21, 2023

@Kevin-Mattheus-Moerman @bmcfee apologies the hold up is on our end. We've been a bit preoccupied with conference/paper deadlines the last few weeks but have been preparing our revisions for @neurofractal's comments. The response should be ready before the end of today.

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ntolley commented Nov 21, 2023

@editorialbot generate pdf

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ntolley commented Dec 7, 2023

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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ntolley commented Dec 7, 2023

@bmcfee that all sounds good! I have fixed the bulleted list formatting and added explicit figure references at L37, L162, and L164. It is indeed directly related to the code example, as the simulation outputs are displayed in the right panel (as indicated in the figure reference added).

The version number of the release is v0.3.1 https://github.com/jonescompneurolab/hnn-core/releases/tag/v0.3.1

Lastly this is the DOI associated with the Zenodo archive: 10.5281/zenodo.10289164

And the direct web link: https://zenodo.org/records/10289164

(the title, license, and author list have been updated accordingly)

Please let me know if you need anything else!

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bmcfee commented Dec 8, 2023

@editorialbot set v0.3.1 as version

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Done! version is now v0.3.1

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bmcfee commented Dec 8, 2023

@editorialbot set 10.5281/zenodo.10289164 as archive

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Done! archive is now 10.5281/zenodo.10289164

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bmcfee commented Dec 8, 2023

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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bmcfee commented Dec 8, 2023

Thanks @ntolley ! Everything looks good on my end here. Just to confirm, since you hadn't mentioned it explicitly, have you verified the author names/affiliations and ORCID links?

@ntolley
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ntolley commented Dec 8, 2023

That's correct! We have confirmed with all the authors their preferred affiliations/ORCID and the records match between the JOSS paper and the Zenodo archive.

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bmcfee commented Dec 8, 2023

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.7554/eLife.51214 is OK
- 10.1152/jn.00535.2009 is OK
- 10.1007/s10548-021-00838-0 is OK
- 10.1093/cercor/bhab221 is OK
- 10.3389/fpsyg.2018.02117 is OK
- 10.1016/j.neuroimage.2021.118479 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1371/journal.pcbi.1008386 is OK
- 10.7554/eLife.44494 is OK
- 10.1371/journal.pcbi.1011003 is OK
- 10.1016/b978-012264841-0/50054-8 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1155/2011/852961 is OK
- 10.3389/fninf.2013.00041 is OK
- 10.3389/fninf.2013.00010 is OK
- 10.1016/j.pneurobio.2023.102490 is OK
- 10.1101/2021.10.11.463545 is OK
- 10.1101/2023.04.17.537118 is OK
- 10.1103/RevModPhys.65.413 is OK
- 10.21105/joss.02505 is OK
- 10.1101/2023.06.16.545371 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1162/neco.1997.9.6.1179 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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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#4821, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 8, 2023
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Kevin-Mattheus-Moerman commented Dec 15, 2023

@ntolley As AEiC I will now help to process final steps. I have checked your repository, this review, the paper, and the archive link. Most seems to be in order. I only have the below point that needs your attention:

  • It looks like the following author that is on the paper is not listed on the archive link: Carmen Kohl. Please add this person, and in the right location, so the author sets match.

@ntolley
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ntolley commented Dec 15, 2023

Thanks @Kevin-Mattheus-Moerman for catching that! Apologies I was almost certain I had verified everyone's names. The Zenodo link should be updated with Carmen's information. Please let me know if there's anything else you need me to do.

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@editorialbot accept

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

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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

cff-version: "1.2.0"
authors:
- family-names: Jas
  given-names: Mainak
  orcid: "https://orcid.org/0000-0002-3199-9027"
- family-names: Thorpe
  given-names: Ryan
  orcid: "https://orcid.org/0000-0003-2491-8599"
- family-names: Tolley
  given-names: Nicholas
  orcid: "https://orcid.org/0000-0003-0358-0074"
- family-names: Bailey
  given-names: Christopher
  orcid: "https://orcid.org/0000-0003-3318-3344"
- family-names: Brandt
  given-names: Steven
- family-names: Caldwell
  given-names: Blake
  orcid: "https://orcid.org/0000-0002-6882-6998"
- family-names: Cheng
  given-names: Huzi
- family-names: Daniels
  given-names: Dylan
  orcid: "https://orcid.org/0009-0008-1958-353X"
- family-names: Pujol
  given-names: Carolina Fernandez
  orcid: "https://orcid.org/0009-0003-0611-1270"
- family-names: Khalil
  given-names: Mostafa
- family-names: Kanekar
  given-names: Samika
  orcid: "https://orcid.org/0000-0002-6111-4461"
- family-names: Kohl
  given-names: Carmen
  orcid: "https://orcid.org/0000-0001-7585-595X"
- family-names: Kolozsvári
  given-names: Orsolya
  orcid: "https://orcid.org/0000-0002-1619-6314"
- family-names: Lankinen
  given-names: Kaisu
  orcid: "https://orcid.org/0000-0003-2210-2385"
- family-names: Loi
  given-names: Kenneth
- family-names: Neymotin
  given-names: Sam
  orcid: "https://orcid.org/0000-0003-3646-5195"
- family-names: Partani
  given-names: Rajat
  orcid: "https://orcid.org/0000-0002-6863-7046"
- family-names: Pelah
  given-names: Mattan
- family-names: Rockhill
  given-names: Alex
  orcid: "https://orcid.org/0000-0003-3868-7453"
- family-names: Sherif
  given-names: Mohamed
  orcid: "https://orcid.org/0000-0002-8951-1645"
- family-names: Hamalainen
  given-names: Matti
  orcid: "https://orcid.org/0000-0001-6841-112X"
- family-names: Jones
  given-names: Stephanie
  orcid: "https://orcid.org/0000-0001-6760-5301"
contact:
- family-names: Jones
  given-names: Stephanie
  orcid: "https://orcid.org/0000-0001-6760-5301"
doi: 10.5281/zenodo.10289164
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jas
    given-names: Mainak
    orcid: "https://orcid.org/0000-0002-3199-9027"
  - family-names: Thorpe
    given-names: Ryan
    orcid: "https://orcid.org/0000-0003-2491-8599"
  - family-names: Tolley
    given-names: Nicholas
    orcid: "https://orcid.org/0000-0003-0358-0074"
  - family-names: Bailey
    given-names: Christopher
    orcid: "https://orcid.org/0000-0003-3318-3344"
  - family-names: Brandt
    given-names: Steven
  - family-names: Caldwell
    given-names: Blake
    orcid: "https://orcid.org/0000-0002-6882-6998"
  - family-names: Cheng
    given-names: Huzi
  - family-names: Daniels
    given-names: Dylan
    orcid: "https://orcid.org/0009-0008-1958-353X"
  - family-names: Pujol
    given-names: Carolina Fernandez
    orcid: "https://orcid.org/0009-0003-0611-1270"
  - family-names: Khalil
    given-names: Mostafa
  - family-names: Kanekar
    given-names: Samika
    orcid: "https://orcid.org/0000-0002-6111-4461"
  - family-names: Kohl
    given-names: Carmen
    orcid: "https://orcid.org/0000-0001-7585-595X"
  - family-names: Kolozsvári
    given-names: Orsolya
    orcid: "https://orcid.org/0000-0002-1619-6314"
  - family-names: Lankinen
    given-names: Kaisu
    orcid: "https://orcid.org/0000-0003-2210-2385"
  - family-names: Loi
    given-names: Kenneth
  - family-names: Neymotin
    given-names: Sam
    orcid: "https://orcid.org/0000-0003-3646-5195"
  - family-names: Partani
    given-names: Rajat
    orcid: "https://orcid.org/0000-0002-6863-7046"
  - family-names: Pelah
    given-names: Mattan
  - family-names: Rockhill
    given-names: Alex
    orcid: "https://orcid.org/0000-0003-3868-7453"
  - family-names: Sherif
    given-names: Mohamed
    orcid: "https://orcid.org/0000-0002-8951-1645"
  - family-names: Hamalainen
    given-names: Matti
    orcid: "https://orcid.org/0000-0001-6841-112X"
  - family-names: Jones
    given-names: Stephanie
    orcid: "https://orcid.org/0000-0001-6760-5301"
  date-published: 2023-12-15
  doi: 10.21105/joss.05848
  issn: 2475-9066
  issue: 92
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5848
  title: "HNN-core: A Python software for cellular and circuit-level
    interpretation of human MEG/EEG"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05848"
  volume: 8
title: "HNN-core: A Python software for cellular and circuit-level
  interpretation of human MEG/EEG"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05848 joss-papers#4843
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05848
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Dec 15, 2023
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@ntolley congratulations on this JOSS publication!

Thanks for editing @bmcfee, and a special thanks to the reviewers: @isdanni, @neurofractal ! 🥳

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.05848/status.svg)](https://doi.org/10.21105/joss.05848)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05848">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05848/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05848/status.svg
   :target: https://doi.org/10.21105/joss.05848

This is how it will look in your documentation:

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bmcfee commented Dec 16, 2023

Thanks again @isdanni and @neurofractal , and congrats to @ntolley (and many coauthors)!

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