search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

[REVIEW]: BlueCelluLab: Biologically Detailed Neural Network Experimentation API #7026

Closed editorialbot closed 2 months ago

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@anilbey<!--end-author-handle-- (Mustafa Anıl Tuncel) Repository: https://github.com/BlueBrain/BlueCelluLab Branch with paper.md (empty if default branch): joss-paper Version: 2.6.32 Editor: !--editor-->@mooniean<!--end-editor-- Reviewers: @finsberg, @ryEllison Archive: 10.5281/zenodo.13325726

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff"><img src="https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg)](https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff)

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

@finsberg & @ryEllison, 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 @mooniean 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 @finsberg

📝 Checklist for @ryEllison

editorialbot commented 3 months ago

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
editorialbot commented 3 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/neuro.11.001.2009 is OK
- 10.3389/fninf.2017.00046 is OK
- 10.3389/fninf.2019.00063 is OK
- 10.3389/fninf.2022.884046 is OK
- 10.1002/spe.4380090102 is OK
- 10.1371/journal.pcbi.1007696 is OK
- 10.1002/pfi.21408 is OK
- 10.1007/978-3-642-59412-0_26 is OK
- 10.5281/zenodo.10809263 is OK

MISSING DOIs

- No DOI given, and none found for title: Pep 484–type hints
- No DOI given, and none found for title: Adapting dynamic object-oriented languages to mixe...
- No DOI given, and none found for title: Pydantic

INVALID DOIs

- None
editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.25 s (637.4 files/s, 182223.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            29              1              0          25703
Python                          99           2228           1809           8357
reStructuredText                 8            354            192           1939
Jupyter Notebook                 8              0           4422            576
YAML                             5             21             15            168
TeX                              1              9              0            152
Markdown                         5             34              0            100
TOML                             1              8              0             71
INI                              1              5              0             63
DOS Batch                        1              8              1             26
make                             2              4              7             17
CSV                              1              0              0             11
Bourne Shell                     1              4              0              8
-------------------------------------------------------------------------------
SUM:                           162           2676           6446          37191
-------------------------------------------------------------------------------

Commit count by author:

    74  Anil Tuncel
    56  anilbey
     9  Werner Van Geit
     6  dependabot[bot]
     5  ilkilic
     3  Alexis Arnaudon
     3  Aurélien Jaquier
     3  Eduard Šubert
     2  MikeG
     1  A Sato
     1  Darshan Mandge
     1  Kiliç Ilkan Fabrice
     1  eduard.subert
editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1268

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 3 months ago

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

mooniean commented 3 months ago

Hi @anilbey and reviewers @finsberg and @ryEllison - this is the review thread for the submission. All of our communications will happen here from now on.

Meanwhile, please check the post at the top of the issue for instructions on how to generate your own review checklist. 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@mooniean) if you have any questions or concerns. Thanks!

finsberg commented 3 months ago

Review checklist for @finsberg

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

finsberg commented 3 months ago

@mooniean I am done with my review on this software and can recommend it for publication in JOSS. The authors did an excellent job preparing this software for JOSS.

mooniean commented 3 months ago

@finsberg thank you so much, that is great to hear!

As soon as @ryEllison also checks the paper/software, I'll then make final checks!

ryEllison commented 3 months ago

Review checklist for @ryEllison

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ryEllison commented 3 months ago

Good morning, @mooniean! I have now finished my review of the paper/software. It's a rather nice frontend API to the NEURON simulation engine, facilitating quick neuron-model development. There's certainly an off-the-shelf compatibility during installation for Unix-like OS over Windows. With that said, however, I can make the recommendation for publication in JOSS.

mooniean commented 3 months ago

This is excellent, thank you both for your reviews!

Before going to the post-review checklist, @anilbey: in the paper, can you add a small explanation for Figure 1? It is not mentioned at any point in the text, it's only for clarification!

After, I'll be happy to advance to the next steps.

anilbey commented 3 months ago

Thanks reviewers for taking your time and reviewing BlueCelluLab. @mooniean I just added it the explanation here https://github.com/BlueBrain/BlueCelluLab/pull/199 let me regenerate the pdf.

anilbey commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

mooniean commented 3 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

mooniean commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/neuro.11.001.2009 is OK
- 10.3389/fninf.2017.00046 is OK
- 10.3389/fninf.2019.00063 is OK
- 10.3389/fninf.2022.884046 is OK
- 10.1002/spe.4380090102 is OK
- 10.1371/journal.pcbi.1007696 is OK
- 10.1002/pfi.21408 is OK
- 10.1007/978-3-642-59412-0_26 is OK
- 10.5281/zenodo.10809263 is OK

MISSING DOIs

- No DOI given, and none found for title: Pep 484–type hints
- No DOI given, and none found for title: Adapting dynamic object-oriented languages to mixe...
- No DOI given, and none found for title: Pydantic

INVALID DOIs

- None
mooniean commented 3 months ago

@anilbey I've started the post-review checklist. Can you please follow the tasks in my previous comment?

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Furthermore, there seems to be 3 DOIs missing, could you try to address those please?

AurelienJaquier commented 2 months ago

Here is the DOI for the latest release on zenodo: https://doi.org/10.5281/zenodo.13304365 Edit: I updated the link to have the list of authors consistent with the paper

anilbey commented 2 months ago

Hi @mooniean

Furthermore, there seems to be 3 DOIs missing, could you try to address those please?

This was also mentioned during the pre-review https://github.com/openjournals/joss-reviews/issues/6956#issuecomment-2211381582.

Those 3 references do not have the DOI. If all references require a DOI, can we turn those three into footnotes instead (if the markdown template supports it)?

mooniean commented 2 months ago

That's ok! I knew I had seen it somewhere. I'll proceed now with the next steps

mooniean commented 2 months ago

@editorialbot set https://doi.org/10.5281/zenodo.13304365 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.13304365

mooniean commented 2 months ago

@editorialbot set v2.6.28 as version

editorialbot commented 2 months ago

Done! version is now v2.6.28

mooniean commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

mooniean commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/neuro.11.001.2009 is OK
- 10.3389/fninf.2017.00046 is OK
- 10.3389/fninf.2019.00063 is OK
- 10.3389/fninf.2022.884046 is OK
- 10.1002/spe.4380090102 is OK
- 10.1371/journal.pcbi.1007696 is OK
- 10.1002/pfi.21408 is OK
- 10.1007/978-3-642-59412-0_26 is OK
- 10.5281/zenodo.10809263 is OK

MISSING DOIs

- No DOI given, and none found for title: Pep 484–type hints
- No DOI given, and none found for title: Mypy-optional static typing for python
- No DOI given, and none found for title: Pydantic

INVALID DOIs

- None
editorialbot commented 2 months ago

: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/5761, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot set 2.6.28 as version

editorialbot commented 2 months ago

Done! version is now 2.6.28

Kevin-Mattheus-Moerman commented 2 months ago

@anilbey 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 points that require your attention:

anilbey commented 2 months ago

Hi @Kevin-Mattheus-Moerman, yes please update the version to be 2.6.32 since it contains changes related to the copyright and citation.

anilbey commented 2 months ago

The following is a recommendation, not a requirement. I would remove the text at the top of you LICENSE (which mentions the 3rd party/dependency licenses), since you already mention this in your README. This way you LICENSE file can fully match the normal Apache 2.0 text and GitHub (and our systems too) would easily recognise it then as such.

I totally agree. Especially because those 3rd party code/data are not part of the package. Those are only used in the example directory to demonstrate some real world use cases. I created this issue here to address it. https://github.com/BlueBrain/BlueCelluLab/issues/206

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot set 2.6.32 as version

editorialbot commented 2 months ago

Done! version is now 2.6.32

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot set 10.5281/zenodo.13325726 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.13325726

Kevin-Mattheus-Moerman commented 2 months ago

@anilbey I think all looks good to proceed now.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot accept

editorialbot commented 2 months ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 2 months ago

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: Tuncel given-names: Anıl - family-names: Geit given-names: Werner Van - family-names: Gevaert given-names: Mike - family-names: Torben-Nielsen given-names: Benjamin - family-names: Mandge given-names: Darshan - family-names: Kılıç given-names: İlkan - family-names: Jaquier given-names: Aurélien - family-names: Muller given-names: Eilif - family-names: Kanari given-names: Lida - family-names: Markram given-names: Henry doi: 10.5281/zenodo.13325726 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Tuncel given-names: Anıl - family-names: Geit given-names: Werner Van - family-names: Gevaert given-names: Mike - family-names: Torben-Nielsen given-names: Benjamin - family-names: Mandge given-names: Darshan - family-names: Kılıç given-names: İlkan - family-names: Jaquier given-names: Aurélien - family-names: Muller given-names: Eilif - family-names: Kanari given-names: Lida - family-names: Markram given-names: Henry date-published: 2024-08-17 doi: 10.21105/joss.07026 issn: 2475-9066 issue: 100 journal: Journal of Open Source Software publisher: name: Open Journals start: 7026 title: "BlueCelluLab: Biologically Detailed Neural Network Experimentation API" type: article url: "https://joss.theoj.org/papers/10.21105/joss.07026" volume: 9 title: "BlueCelluLab: Biologically Detailed Neural Network Experimentation API" ```

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 commented 2 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 2 months ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/5778
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07026
  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...

Kevin-Mattheus-Moerman commented 2 months ago

@anilbey congratulations on this JOSS publication!

Thanks for editing @mooniean !

And a special thank you to the reviewers: @finsberg, @ryEllison !!

editorialbot commented 2 months ago

: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.07026/status.svg)](https://doi.org/10.21105/joss.07026)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07026">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07026/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07026/status.svg
   :target: https://doi.org/10.21105/joss.07026

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following: