[PRE 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 Version: 0.2 Editor: @meg-simula Reviewers: @martejulie, @blbentley Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d47fbf887ce21cf686a56bac1b36817e"><img src="https://joss.theoj.org/papers/d47fbf887ce21cf686a56bac1b36817e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d47fbf887ce21cf686a56bac1b36817e/status.svg)](https://joss.theoj.org/papers/d47fbf887ce21cf686a56bac1b36817e)

Author instructions

Thanks for submitting your paper to JOSS @cgurrr. Currently, there isn't an JOSS editor assigned to your paper.

@cgurrr if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

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.

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]

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

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (476.8 files/s, 124313.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            465            586           1321
Jupyter Notebook                10              0           5690            477
Markdown                         2             19              0             54
reStructuredText                 4             33             39             44
TeX                              1              9              0             37
YAML                             1              5              4             27
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            34            543           6327           1995
-------------------------------------------------------------------------------

Statistical information for the repository '101082f254699460241a82a1' was
gathered on 2021/11/02.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Claire                          10           423            263            7.27
Claire Guerrier                 66          5259           3149           89.16
Nicolas                          1             1              1            0.02
Nicolas Galtier                  4           176            103            2.96
Niko                             4            45             10            0.58

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         19.0                5.00
Claire Guerrier            2252           42.8          4.3                9.90
Nicolas                       1          100.0          0.3                0.00
Nicolas Galtier              53           30.1         21.5               50.94
Niko                          6           13.3         25.1                0.00

[whedon]

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

[danielskatz]

👋 @meg-simula - would you be able to edit this submission?

[danielskatz]

@whedon invite @meg-simula as editor

[whedon]

@meg-simula has been invited to edit this submission.

[meg-simula]

Sure, right up my alley.

[meg-simula]

@whedon assign @meg-simula as editor

[whedon]

OK, the editor is @meg-simula

[meg-simula]

@whedon generate pdf

[whedon]

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

[meg-simula]

@whedon check references

[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 Thanks for this submission and my apologies for the delay in handling.

If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

[meg-simula]

:wave: @martejulie would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[martejulie]

@meg-simula Absolutely!

[meg-simula]

@whedon assign @martejulie as reviewer

[whedon]

OK, @martejulie is now a reviewer

[meg-simula]

Great @martejulie! I've assigned you as a reviewer now. At least one more reviewer is needed, so feel free to just stay put and await further information.

[cgurrr]

@meg-simula Thanks for accepting to be an editor for our submission. I apologize for the late reply.

Follow three names coming from the reviewer suggestion list, that could be a good match: ryEllison, for his expertise in both computational neuroscience and biophysics, It seems that blbentley and woolfeh could also be good match.

[meg-simula]

:wave: @ryEllison @woolfeh @blbentley would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[blbentley]

Hello @meg-simula, I would be happy to review this.

[woolfeh]

Hi @meg-simula, I would also be happy to review this submission but wouldn't be able to start for a couple of weeks. Is that OK?

[ryEllison]

Hey, @meg-simula, I would be happy to review this!

[meg-simula]

Wow @blbentley @woolfeh @ryEllison - thank you all for the positive and quick responses! We just need one more reviewer on this, and since @blbentley was first (in addition to @martejulie), I'll assign you now and get this review started.

[meg-simula]

@whedon add @blbentley as reviewer

[whedon]

OK, @blbentley is now a reviewer

[meg-simula]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4012.