[REVIEW]: qujax: Simulating quantum circuits with JAX

[editorialbot]

Submitting author: @SamDuffield (Samuel Duffield)
Repository: https://github.com/CQCL/qujax
Branch with paper.md (empty if default branch): paper
Version: v1.0.0
Editor: @lucydot
Reviewers: @jmiszczak, @amitkumarj441, @meandmytram
Archive: 10.5281/zenodo.8268973

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bd448465a308f0897c35e56fe7ca2740"><img src="https://joss.theoj.org/papers/bd448465a308f0897c35e56fe7ca2740/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bd448465a308f0897c35e56fe7ca2740/status.svg)](https://joss.theoj.org/papers/bd448465a308f0897c35e56fe7ca2740)

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

@jmiszczak & @amitkumarj441 & @meandmytram, 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 @lucydot 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 @jmiszczak

📝 Checklist for @meandmytram

📝 Checklist for @amitkumarj441

[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:

@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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1334.0 files/s, 198038.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            491            474           1272
Jupyter Notebook                 7              0           3889            595
Markdown                         3             66              0            249
TeX                              1             50              0            151
YAML                             5             14              4            151
reStructuredText                21             64             49             52
-------------------------------------------------------------------------------
SUM:                            51            685           4416           2470
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1131

[editorialbot]

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

OK DOIs

- 10.48550/ARXIV.1811.04968 is OK
- 10.5281/zenodo.2573505 is OK
- 10.1088/2058-9565/ab8e92 is OK
- 10.21105/joss.00819 is OK
- 10.48550/ARXIV.2003.02989 is OK
- 10.48550/ARXIV.2205.05190 is OK
- 10.22331/q-2021-10-06-559 is OK
- 10.22331/q-2023-02-02-912 is OK
- 10.5281/zenodo.7465577 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[lucydot]

@SamDuffield I can see that the paper is already exceeding the (not completely strict) word limit of ~1000 words. Please bear this in mind when making amendments - if you want to add something to the paper, something else may need to come out. I suggest prioritising (keeping in) your high level summary at the start of the paper, and the statement of need section. The tensor descriptions I think are fine for the paper at its current length.

[meandmytram]

Review checklist for @meandmytram

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/CQCL/qujax?
• 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 (@SamDuffield) 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?

[jmiszczak]

Review checklist for @jmiszczak

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/CQCL/qujax?
• 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 (@SamDuffield) 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?

[jmiszczak]

@editorialbot commands

[editorialbot]

Hello @jmiszczak, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[lucydot]

Dear @jmiszczak and @meandmytram - I can see you have both started your reviews. This is a reminder to keep going - and please update this thread (or raise an issue on the qujax repo) with points as they arise.

[jmiszczak]

OK, thanks for the reminder.

[jmiszczak]

Hi @lucydot, I made some tests, played with the code, and everything looks perfect. So, should I just finish the form and that's it?

[lucydot]

@jmiszczak If you are happy that each point in the checklist is met, then yes go ahead and check each point off. A brief description of what you have tested (e.g. worked through the tutorials) would be useful, and anything that your review has raised that is not an acceptance-blocker, but would improve the quality of the software, is encouraged.

@meandmytram, a reminder for your review.

[jmiszczak]

Package installation is handled via pip. Basic examples with variational quantum algorithms are provided in notebooks. To run notebooks, one has to additionally instal Jupyter.

The paper provides a good explanation of the provided functionality. Delivered documentation and usage examples are sufficient to start working with the package.

The major advantage of qujax is the ability to use just-in-time compilation. Another nice feature is the functional approach. These two are the major features distinguishing it among other packages.

I highly recommend publication in JOSS.

[amitkumarj441]

Review checklist for @amitkumarj441

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/CQCL/qujax?
• 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 (@SamDuffield) 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?

[lucydot]

Hello, pleased to see all reviews are underway.
Just to let you all know that I am at a conference for the next week; will check in again w/c 10th July.

[meandmytram]

Hey everyone, just dropping my quick review here.

I was able to install the package through the use of pip and play with all the provided tutorials as well as digging a bit through the API. I found the paper well written and the statement of need the state clearly justifying the fact that the package fills in a specific niche. In addition, the paper offers a comprehensive elucidation of the available functionality. The provided documentation and usage examples are make starting work with the package easy. I totally agree with @jmiszczak on the point of the two distinguishing features of qujax and I do think that it fulfils the need of the community in this area.

Would be cool to see its comparison with QC simulation packages using other backends, but this can be left as a direction for future research.

I endorse the publication of this work in JOSS.

[lucydot]

Excellent - thank you for your time and expertise in reviewing @meandmytram and @jmiszczak 🎈

@amitkumarj441, do you have a timescale for review completion? ☑️

All the best,

Lucy

[lucydot]

Hello @SamDuffield and @amitkumarj441,

A heads up that I am going on annual leave until the 8th of August. I will check back on this ASAP when I return as I think we are getting close to finalising this review. @amitkumarj441 please let us know if you need longer than this timeframe to complete your review (8th July).

Best,

Lucy

[lucydot]

@editorialbot generate pdf

[editorialbot]

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

[lucydot]

@SamDuffield @amitkumarj441 -

Given we have had two reviewers with a clear, strong positive consensus I'm happy for this to proceed without a third reviewer. I'll ask our editorial bot to generate a post-review checklist for us both to work through @SamDuffield. You won't be able to tick off yourself, just let me know in the thread when each point is complete.

[lucydot]

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.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[lucydot]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[lucydot]

@editorialbot set 10.5281/zenodo.8268973 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8268973

[lucydot]

Hello,

Just to let you know that I will be away on leave for two weeks, so my replies will be slower than usual. Seeing as we are so close to this completing, I will check in on it!

Best,

Lucy

[lucydot]

Hello, just updated PR @gamatos once that it is merged I can pass onto the editors-in-chief team for final checks...

[gamatos]

Hi @lucydot, just updated and merged your pull request CQCL/qujax#91!

[lucydot]

@editorialbot generate pdf

[lucydot]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.48550/ARXIV.1811.04968 is OK
- 10.5281/zenodo.2573505 is OK
- 10.1088/2058-9565/ab8e92 is OK
- 10.21105/joss.00819 is OK
- 10.48550/ARXIV.2003.02989 is OK
- 10.48550/ARXIV.2205.05190 is OK
- 10.22331/q-2021-10-06-559 is OK
- 10.22331/q-2023-02-02-912 is OK
- 10.5281/zenodo.7465577 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1017/CBO9780511976667 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[lucydot]

@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

- 10.48550/ARXIV.1811.04968 is OK
- 10.5281/zenodo.2573505 is OK
- 10.1088/2058-9565/ab8e92 is OK
- 10.21105/joss.00819 is OK
- 10.48550/ARXIV.2003.02989 is OK
- 10.48550/ARXIV.2205.05190 is OK
- 10.22331/q-2021-10-06-559 is OK
- 10.22331/q-2023-02-02-912 is OK
- 10.5281/zenodo.7465577 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1017/CBO9780511976667 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/pe-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#4543, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

@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: Duffield
  given-names: Samuel
  orcid: "https://orcid.org/0000-0002-8656-8734"
- family-names: Matos
  given-names: Gabriel
  orcid: "https://orcid.org/0000-0002-3373-0128"
- family-names: Johannsen
  given-names: Melf
contact:
- family-names: Duffield
  given-names: Samuel
  orcid: "https://orcid.org/0000-0002-8656-8734"
doi: 10.5281/zenodo.8268973
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Duffield
    given-names: Samuel
    orcid: "https://orcid.org/0000-0002-8656-8734"
  - family-names: Matos
    given-names: Gabriel
    orcid: "https://orcid.org/0000-0002-3373-0128"
  - family-names: Johannsen
    given-names: Melf
  date-published: 2023-09-12
  doi: 10.21105/joss.05504
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5504
  title: "qujax: Simulating quantum circuits with JAX"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05504"
  volume: 8
title: "qujax: Simulating quantum circuits with JAX"

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.05504 joss-papers#4555
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05504
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...

[kyleniemeyer]

Congratulations @SamDuffield on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @jmiszczak, @amitkumarj441, and @meandmytram for reviewing this, and @lucydot for editing.

[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.05504/status.svg)](https://doi.org/10.21105/joss.05504)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05504">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05504/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05504/status.svg
   :target: https://doi.org/10.21105/joss.05504

This is how it will look in your documentation:

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