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

whedon commented 2 years ago

Submitting author: !--author-handle-->@cgurrr@meg-simula<!--end-editor-- Reviewers: @martejulie, @meg-simula Archive: 10.5281/zenodo.6540844

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Review checklist for @martejulie

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Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

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 :tada:.

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whedon commented 2 years ago

Wordcount for paper.md is 517

whedon commented 2 years ago

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 commented 2 years ago

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

whedon commented 2 years ago

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 commented 2 years ago

:wave: @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 commented 2 years ago

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 commented 2 years ago

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

martejulie commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

whedon commented 2 years ago

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

whedon commented 2 years ago

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

cgurrr commented 2 years ago

@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 commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

martejulie commented 2 years ago

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 commented 2 years ago

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

cgurrr commented 2 years ago

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

cgurrr commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

cgurrr commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

martejulie commented 2 years ago

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

meg-simula commented 2 years ago

Thanks @martejulie and @cgurrr for the updates! We are now waiting for an update from @blbentley to proceed.

cgurrr commented 2 years ago

Hi @meg-simula, did you get any update from blbentley? Thanks!

meg-simula commented 2 years ago

Thanks for the ping, I have not and will follow-up off-line.

cgurrr commented 2 years ago

Hi @meg-simula , sorry to ask again, but did you get any update from the other reviewer? We are currently in the process of submission for two papers using the library, and we would like to refer to a published version of it. Many thanks!

meg-simula commented 2 years ago

Hi @cgurrr, thanks for the ping! This review is definitely much overdue. Let me check some options and get back to you tomorrow.

meg-simula commented 2 years ago

@editorialbot add @meg-simula as reviewer

editorialbot commented 2 years ago

@meg-simula added to the reviewers list!

meg-simula commented 2 years ago

Review checklist for @meg-simula

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ngltr/sinaps?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] 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?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

meg-simula commented 2 years ago

@cgurrr I've added one issue regarding missing dependencies, let me know if you resolve this (so that I can test the demos).

cgurrr commented 2 years ago

@meg-simula, see https://github.com/ngltr/sinaps/issues/14#issuecomment-1119000622 It seems that you need to upgrade numba. We now have added a minimum version requirement in the install dependencies. You could also simply update sinaps to 0.3.1., and it should work. Let us now if you have any more issues.

meg-simula commented 2 years ago

Thanks @cgurrr for the quick response and updated dependencies instructions. I am still unable to test the sinaps package, now due to errors when importing hvplot: ValueError: The depends decorator only accepts string types referencing a parameter or parameter instances, found bool type instead. Any advice on this point?

ngltr commented 2 years ago

@meg-simula, The installation process works well from scratch ( for example in the automated test, dependencies installation is checked https://github.com/ngltr/sinaps/runs/6341186525?check_suite_focus=true), but it seems we need to add other minimum version requirements for the all dependencies in case the user has old versions already installed. As a temporary solution, can you try to upgrade all dependencies : pip install hvplot pandas networkx datashader numpy --upgrade If sill not working maybe, you can try to install sinaps in a virtualenv : python3 -m venv sinaps_env source sinaps_env/bin/activate pip install sinaps

meg-simula commented 2 years ago

@ngltr Thanks for the patience and follow-up. I still run into issues I'm afraid using the virtual environment option in particular:

Collecting zipp>=0.5
  Downloading zipp-3.8.0-py3-none-any.whl (5.4 kB)
ERROR: panel 0.13.0 has requirement param>=1.12.0, but you'll have param 1.10.0 which is incompatible.
ERROR: numba 0.55.1 has requirement numpy<1.22,>=1.18, but you'll have numpy 1.22.3 which is incompatible.

I appreciate that you add some notes on potential incompatibilities and - if possible - potential fixes in the installation documentation.

As the tests run nicely with the automated tool, I think we can leave it at that.

meg-simula commented 2 years ago

@editorialbot generate pdf

meg-simula commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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 commented 2 years ago

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

meg-simula commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

@editorialbot generate pdf

meg-simula commented 2 years ago

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

editorialbot commented 2 years ago

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

meg-simula commented 2 years ago

@editorialbot set 10.5281/zenodo.6540844 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6540844

meg-simula commented 2 years ago

@editorialbot set v0.3.2 as version

editorialbot commented 2 years ago

Done! version is now v0.3.2

meg-simula commented 2 years ago

@editorialbot recommend-accept

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