[REVIEW]: Sinaps: A Python library to simulate voltage dynamic and ionic electrodiffusion in neurons

[whedon]

Submitting author: @cgurrr (Claire Guerrier)
Repository: https://github.com/ngltr/sinaps
Branch with paper.md (empty if default branch):
Version: v0.3.2
Editor: @meg-simula
Reviewers: @martejulie, @meg-simula
Archive: 10.5281/zenodo.6540844

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/d47fbf887ce21cf686a56bac1b36817e/status.svg)](https://joss.theoj.org/papers/d47fbf887ce21cf686a56bac1b36817e)

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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

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Review checklist for @martejulie

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• 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 (@cgurrr) 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

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 and who the target audience is?
• 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?

Review checklist for @blbentley

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• 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 (@cgurrr) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @martejulie, @blbentley it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 517

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (202.6 files/s, 32488.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            505            606           1446
Jupyter Notebook                 6              0           2151            250
Markdown                         2             22              0             58
reStructuredText                 4             33             39             44
TeX                              1              9              0             37
YAML                             1              5              4             28
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            33            586           2808           1898
-------------------------------------------------------------------------------


Statistical information for the repository '135eefc95d9bb21596eb89e4' was
gathered on 2021/12/20.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Claire                          10           423            263            7.08
Claire Guerrier                 66          5259           3149           86.74
Nicolas                          1             1              1            0.02
Nicolas Galtier                 11           400            142            5.59
Niko                             4            45             10            0.57

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Claire                       60           14.2         19.3                5.00
Claire Guerrier            2215           42.1          4.6                9.98
Nicolas                       1          100.0          0.6                0.00
Nicolas Galtier             281           70.2          4.6               13.88

[whedon]

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

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.3389/fncir.2020.00033 may be a valid DOI for title: Comprehensive Imaging of Sensory-Evoked Activity of Entire Neurons Within the Awake Developing Brain Using Ultrafast AOD-Based Random-Access Two-Photon Microscopy
- 10.1371/journal.pcbi.1006485 may be a valid DOI for title: Active dendrites regulate the spatiotemporal spread of signaling microdomains.

INVALID DOIs

- None

[meg-simula]

👋 @cgurrr @martejulie @blbentley this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also 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. 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. Please feel free to ping me (@meg-simula ) if you have any questions/concerns.

[martejulie]

Hi! Very nice work!

I support the publication of this software with minor revisions.

Here comes a few questions and some (minor) suggestions for improvement.

Functionality

• Please see issue #4 in the source code repo.

Documentation

• Please see issue #6, #7, #8, and #9 in the source code repo.

Automated tests

• Please see issue #2 and #3 in the source code repo.

Quality of writing

• Please see my pull request for some minor suggestions.

State of the field/References

• Numerous papers have been published on the modeling of voltage dynamics and ion concentration dynamics in neurons, see Sætra et al. 2020 and the references therein. The novelty of this work is the fast computation of intracellular electrodiffusion of ions for complex neuronal geometries and the development of a Python package that can be used to build custom set-ups. I think it would be appropriate to add a short paragraph (two-three sentences) about this in the paper. A key reference, which I think should be cited, is the paper of Solbrå et al. 2018, A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons, and their simulator KNPsim.

[cgurrr]

Hi @martejulie,
Many thanks for all your suugestions/comments. We will take care of this as soon as possible.

[martejulie]

@whedon generate pdf

[whedon]

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

[whedon]

👋 @blbentley, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @martejulie, please update us on how your review is going (this is an automated reminder).

[cgurrr]

@martejulie Many thanks for your useful comments. We modified/corrected the paper and the code accordingly. We have now completed all the corrections. Please let us know if we need to make any other improvements.

[martejulie]

@whedon generate pdf

[whedon]

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

[martejulie]

Hi, @cgurrr!

Thank you! Very nice to see that you have followed all my suggestions. I have already checked off a few more marks on the review checklist.

It would be great if you could create a new pip release of the current version of the code and update the documentation. (I noticed that 1) the HeavysideCurrent function is still used in the Plotting notebook (on the web page), and 2) the API references are not up to date with the new Hodgkin-Huxley implementation. There might be more.)

This would make it easier to review the documentation and the functionality of the code.

[meg-simula]

@martejulie @cgurrr Thanks for the review, responses and resolution of issues. @blbentley Could you please update us on the status of your review?

[cgurrr]

Hi @martejulie, we now released version 0.3 and updated the documentation (it is now on readthedocs with continuous updates).

[cgurrr]

@whedon generate pdf

[whedon]

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

[cgurrr]

@whedon generate pdf

[whedon]

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

[martejulie]

@meg-simula @cgurrr I have now finished my checklist and I support the publication of this software.

[meg-simula]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1371/journal.pcbi.1007661 is OK
- 10.3389/fncir.2020.00033 is OK
- 10.1371/journal.pcbi.1006485 is OK
- 10.1371/journal.pcbi.1006510 is OK
- 10.1017/CBO9780511541612 is OK
- 10.1146/annurev.neuro.28.061604.135703 is OK
- 10.1086/419236 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[meg-simula]

@cgurrr Would you please take another look at the references in the paper? Last names seems to have gone missing mostly, with only initials remaining.

After this, could you make a tagged release and archive for the software, and report the version number and archive DOI here?

[cgurrr]

@meg-simula Many thanks for your comments.

• We added a note on potential incompatibilities and proposed potential fixes in the documentation: https://sinaps.readthedocs.io/en/stable/installing.html
• We corrected the author name syntax in the references of the paper.
• The tagged release is now 0.3.2,
• Finally, we made an archive in Zenodo. DOI: 10.5281/zenodo.6540844

[meg-simula]

@editorialbot generate pdf

[meg-simula]

@cgurrr Lovely, thanks for the follow-up and response.

[editorialbot]

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

[meg-simula]

@editorialbot set 10.5281/zenodo.6540844 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6540844

[meg-simula]

@editorialbot set v0.3.2 as version

[editorialbot]

Done! version is now v0.3.2

[meg-simula]

@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

- 10.1371/journal.pcbi.1007661 is OK
- 10.3389/fncir.2020.00033 is OK
- 10.1371/journal.pcbi.1006485 is OK
- 10.1371/journal.pcbi.1006510 is OK
- 10.1017/CBO9780511541612 is OK
- 10.1146/annurev.neuro.28.061604.135703 is OK
- 10.1086/419236 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3213

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3213, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot remove @blbentley as reviewer

[editorialbot]

@blbentley removed from the reviewers list!

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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 👉 Creating pull request for 10.21105.joss.04012 joss-papers#3214
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04012
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...

[arfon]

@martejulie, @meg-simula – many thanks for your reviews here and to @meg-simula for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@cgurrr – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 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.04012/status.svg)](https://doi.org/10.21105/joss.04012)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04012">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04012/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04012/status.svg
   :target: https://doi.org/10.21105/joss.04012

This is how it will look in your documentation:

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