[REVIEW]: brains-py: A framework to support research on energy-efficient unconventional hardware for machine learning

[editorialbot]

Submitting author: @ualegre (Unai Alegre-Ibarra)
Repository: https://github.com/braiNEdarwin/brains-py
Branch with paper.md (empty if default branch): master
Version: 1.0.2
Editor: @arfon
Reviewers: @wob86, @sisco0
Archive: 10.5281/zenodo.8410268

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/af9dc02733d17cac673fd042ac514272/status.svg)](https://joss.theoj.org/papers/af9dc02733d17cac673fd042ac514272)

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

@wob86, 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 @arfon 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 @wob86

📝 Checklist for @sisco0

[editorialbot]

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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.23 s (630.3 files/s, 104261.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          80           2388           8297          10834
reStructuredText                52            990            462            207
Markdown                         2             57              0            148
TeX                              1             10              0            107
YAML                             6              7             22             71
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           143           3464           8789          11402
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1038/s41586-019-1901-0 is OK
- 10.1088/2634-4386/ac1a7f is OK
- 10.1038/s41565-020-00779-y is OK
- 10.1109/CTEMS.2018.8769211 is OK
- 10.5281/zenodo.3828935 is OK
- 10.1103/PhysRevApplied.17.064025 is OK
- 10.1002/smsc.202000014 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 2141

[arfon]

@wob86 This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my 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 and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5573 so that a link is created to this thread (and I can keep an eye on what is happening). 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

[wob86]

Review checklist for @wob86

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 https://github.com/braiNEdarwin/brains-py?
• 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 (@ualegre) 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?

[arfon]

👋 @wob86 – how are you getting along with your review? It looks like you've made it most of the way through the checklist but there are a few ones left unchecked still?

[wob86]

Paper looks good as does supporting documentation in repo and gives a good introduction to the software and explanation of its need and usage.
I have two main issues one with readability of help sections which I have raised as issue number 67 on the repo and the installation guide not being correct which is why I have left the installatioon step unchecked in the checklist, this is issue. 66

[arfon]

Got it, thanks @wob86. @ualegre – how are you getting along incorporating @wob86's feedback?

[arfon]

@miesli @GregaVrbancic – would you be willing to review this submission for JOSS? The submission under consideration is brains-py: A framework to support research on energy-efficient unconventional hardware for machine learning (https://github.com/braiNEdarwin/brains-py).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks
Arfon

[ualegre]

Got it, thanks @wob86. @ualegre – how are you getting along incorporating @wob86's feedback?

@arfon finished implementing @wob86's feedback.

[wob86]

@arfon I am now happy with this paper and approve it from my side.

[arfon]

@ljvmiranda921 @sisco0 – would you be willing to review this submission for JOSS? The submission under consideration is brains-py: A framework to support research on energy-efficient unconventional hardware for machine learning (https://github.com/braiNEdarwin/brains-py).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks
Arfon

[sisco0]

I have performed a pre-analysis of the current project research area and it matches my experience.
The review would be performed without inconvenience @arfon.

[arfon]

Excellent, thanks so much @sisco0!

[arfon]

@editorialbot add @sisco0 as reviewer

[editorialbot]

@sisco0 added to the reviewers list!

[arfon]

@sisco0 This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my 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 and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5573 so that a link is created to this thread (and I can keep an eye on what is happening). 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[arfon]

👋 @sisco0 – just checking in that you're still ok to complete this review for us?

[sisco0]

Agree. I am doing the review during today.

[sisco0]

Review checklist for @sisco0

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 https://github.com/braiNEdarwin/brains-py?
• 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 (@ualegre) 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?

[sisco0]

The current review is complete.
The whole set of points have been reviewed and verified.
No expected modification to perform over the paper nor the Git repository.

[arfon]

@ualegre – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• I can then move forward with accepting the submission.

[ualegre]

@arfon, the DOI of the archive is: 10.5281/zenodo.8410268

[ualegre]

The Zenodo page is available here: https://zenodo.org/record/8410268

[arfon]

@editorialbot set 10.5281/zenodo.8410268 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8410268

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/dsais-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#4660, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Alegre-Ibarra
  given-names: Unai
  orcid: "https://orcid.org/0000-0001-5957-7945"
- family-names: Euler
  given-names: Hans-Christian Ruiz
- family-names: A.Mollah
  given-names: Humaid
- family-names: Petrov
  given-names: Bozhidar P.
- family-names: Sastry
  given-names: Srikumar S.
- family-names: Boon
  given-names: Marcus N.
- family-names: Jong
  given-names: Michel P.
  name-particle: de
- family-names: Zolfagharinejad
  given-names: Mohamadreza
- family-names: Uitzetter
  given-names: Florentina M. J.
- family-names: Ven
  given-names: Bram
  name-particle: van de
- family-names: Almeida
  given-names: António J. Sousa
  name-particle: de
- family-names: Kinge
  given-names: Sachin
- family-names: Wiel
  given-names: Wilfred G.
  name-particle: van der
doi: 10.5281/zenodo.8410268
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Alegre-Ibarra
    given-names: Unai
    orcid: "https://orcid.org/0000-0001-5957-7945"
  - family-names: Euler
    given-names: Hans-Christian Ruiz
  - family-names: A.Mollah
    given-names: Humaid
  - family-names: Petrov
    given-names: Bozhidar P.
  - family-names: Sastry
    given-names: Srikumar S.
  - family-names: Boon
    given-names: Marcus N.
  - family-names: Jong
    given-names: Michel P.
    name-particle: de
  - family-names: Zolfagharinejad
    given-names: Mohamadreza
  - family-names: Uitzetter
    given-names: Florentina M. J.
  - family-names: Ven
    given-names: Bram
    name-particle: van de
  - family-names: Almeida
    given-names: António J. Sousa
    name-particle: de
  - family-names: Kinge
    given-names: Sachin
  - family-names: Wiel
    given-names: Wilfred G.
    name-particle: van der
  date-published: 2023-10-08
  doi: 10.21105/joss.05573
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5573
  title: brains-py, A framework to support research on energy-efficient
    unconventional hardware for machine learning
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05573"
  volume: 8
title: brains-py, A framework to support research on energy-efficient
  unconventional hardware for machine learning

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]

🐘🐘🐘 👉 Toot 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.05573 joss-papers#4661
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05573
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]

Looks like the DOI is being slow to resolve. I'll keep this issue open until it's registered and resolving.

[arfon]

Looks like the DOI is resolving now ⚡

@wob86, @sisco0 – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@ualegre – 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.05573/status.svg)](https://doi.org/10.21105/joss.05573)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05573">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05573/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05573/status.svg
   :target: https://doi.org/10.21105/joss.05573

This is how it will look in your documentation:

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