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[REVIEW]: QAOA.jl: Toolkit for the Quantum and Mean-Field Approximate Optimization Algorithms #5364

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editorialbot opened this issue Apr 13, 2023 · 55 comments
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accepted Julia published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Apr 13, 2023

Submitting author: @timbode (Tim Bode)
Repository: https://github.com/FZJ-PGI-12/QAOA.jl
Branch with paper.md (empty if default branch):
Version: v1.0.1
Editor: @danielskatz
Reviewers: @babreu-ncsa, @pkairys, @Abinashbunty
Archive: 10.5281/zenodo.8086187

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/727b3c5b6b91eb6d30b2a8f4cbdaeaaa"><img src="https://joss.theoj.org/papers/727b3c5b6b91eb6d30b2a8f4cbdaeaaa/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/727b3c5b6b91eb6d30b2a8f4cbdaeaaa/status.svg)](https://joss.theoj.org/papers/727b3c5b6b91eb6d30b2a8f4cbdaeaaa)

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

@babreu-ncsa & @pkairys & @Abinashbunty, 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 @danielskatz 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 @pkairys

📝 Checklist for @Abinashbunty

📝 Checklist for @babreu-ncsa

@editorialbot editorialbot added Julia review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Apr 13, 2023
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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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1885.2 files/s, 220188.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           12            288             77            703
TOML                             3            146              1            644
Markdown                         9             76              0            373
Jupyter Notebook                 6              0           1213            293
YAML                             4              5             16            148
TeX                              1             10              0             95
-------------------------------------------------------------------------------
SUM:                            35            525           1307           2256
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 526

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

OK DOIs

- 10.48550/ARXIV.2303.00329 is OK
- 10.22331/q-2018-08-06-79 is OK
- 10.1137/141000671 is OK
- 10.48550/arxiv.1907.07587 is OK
- 10.48550/arxiv.1811.04968 is OK
- 10.5281/zenodo.2573505 is OK

MISSING DOIs

- 10.22331/q-2020-10-11-341 may be a valid DOI for title: Yao.jl: Extensible, Efficient Framework for Quantum Algorithm Design

INVALID DOIs

- None

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

@danielskatz
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@babreu-ncsa, @pkairys, and @Abinashbunty - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#5364 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 reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

@danielskatz
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👋 @timbode - Please fix the missing DOI that editorialbot suggests. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

@Abinashbunty
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Abinashbunty commented Apr 13, 2023

Review checklist for @Abinashbunty

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/FZJ-PGI-12/QAOA.jl?
  • 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 (@timbode) 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?

@pkairys
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pkairys commented Apr 13, 2023

Review checklist for @pkairys

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/FZJ-PGI-12/QAOA.jl?
  • 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 (@timbode) 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?

@Abinashbunty
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Abinashbunty commented Apr 15, 2023

  • Contribution and authorship: Has the submitting author (@timbode) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

For the referenced checklist item, I am going to mark it as ☑️ based on #5347 (comment) and the reaction to it by @danielskatz

@timbode
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timbode commented Apr 19, 2023

Thanks @Abinashbunty for catching that typo! I'll fix the missing DOI asap.

@timbode
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timbode commented Apr 19, 2023

@editorialbot generate pdf

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

@danielskatz
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@editorialbot check references

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

OK DOIs

- 10.48550/ARXIV.2303.00329 is OK
- 10.22331/q-2018-08-06-79 is OK
- 10.1137/141000671 is OK
- 10.22331/q-2020-10-11-341 is OK
- 10.48550/arxiv.1907.07587 is OK
- 10.48550/arxiv.1811.04968 is OK
- 10.5281/zenodo.2573505 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@Abinashbunty
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  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

For this item of checklist, my review + #5347 (comment) suffices for this to be marked as checked. 👍🏼

@babreu-ncsa
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babreu-ncsa commented May 2, 2023

Review checklist for @babreu-ncsa

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/FZJ-PGI-12/QAOA.jl?
  • 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 (@timbode) 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?

@danielskatz
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👋 @babreu-ncsa, @pkairys, @Abinashbunty - Can I get an update from each of you on how your reviews are coming, and what is needed to move them forward?

@Abinashbunty
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@danielskatz Some components I'll have to execute on my machine and then my review will be over. Major part of my review is over. In case things run well, it'll be quicker else I'll advise the author(s) to make the necessary changes.

@babreu-ncsa
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@danielskatz thanks for the push, I'm running behind. I'll expedite the review this week.

@timbode
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timbode commented May 23, 2023

Thanks for your efforts - I'll address all shortcomings once you're done.

@danielskatz
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@timbode - At this point could you:

  • Make a tagged release of your software, and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

@timbode
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timbode commented Jun 27, 2023

@danielskatz I will try doing all of the above from a mobile device. Let’s see if it’s possible. If not, it will have to wait until the week after next.

@timbode
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timbode commented Jun 27, 2023

  • Make a tagged release of your software, and list the version tag of the archived version here.

The version tag is v1.0.1.

@timbode
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timbode commented Jun 27, 2023

  • Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

https://doi.org/10.5281/zenodo.8086187

@timbode
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timbode commented Jun 27, 2023

@danielskatz I will try doing all of the above from a mobile device. Let’s see if it’s possible. If not, it will have to wait until the week after next.

Seems it all worked!

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@editorialbot set v1.0.1 as version

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Done! version is now v1.0.1

@danielskatz
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@editorialbot set 10.5281/zenodo.8086187 as archive

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Done! archive is now 10.5281/zenodo.8086187

@danielskatz
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@editorialbot recommend-accept

(I will proofread the version that this produces, and let you know if I see anything that should be changed.)

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.48550/ARXIV.2303.00329 is OK
- 10.22331/q-2018-08-06-79 is OK
- 10.1137/141000671 is OK
- 10.22331/q-2020-10-11-341 is OK
- 10.48550/arxiv.1907.07587 is OK
- 10.48550/arxiv.1811.04968 is OK
- 10.5281/zenodo.2573505 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/csism-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#4353, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 27, 2023
@danielskatz
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👋 @timbode - I'm suggesting some small changes in FZJ-PGI-12/QAOA.jl#31

In addition, there's something wrong with the first reference. The DOI doesn't match the title, while the DOI that does match the title seems to be https://doi.org/10.5281/zenodo.2562111 but the authors don't match this archive, so I'm not sure what should be done to fix this.

Please go ahead and merge my PR (or let me know what you disagree with, and fix the first reference, then ping me here and I'll create a new proof.

@timbode
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timbode commented Jun 27, 2023

@danielskatz I’ve switched to the Zenodo reference you found. I hope it works now in spite of me doing this via mobile. I’ve also merged your corrections in the paper, thanks for that.

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.48550/ARXIV.2303.00329 is OK
- 10.22331/q-2018-08-06-79 is OK
- 10.1137/141000671 is OK
- 10.22331/q-2020-10-11-341 is OK
- 10.48550/arxiv.1907.07587 is OK
- 10.48550/arxiv.1811.04968 is OK
- 10.5281/zenodo.2562111 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/csism-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#4356, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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@editorialbot accept

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

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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: Bode
  given-names: Tim
  orcid: "https://orcid.org/0000-0001-8280-3891"
- family-names: Bagrets
  given-names: Dmitry
- family-names: Misra-Spieldenner
  given-names: Aditi
- family-names: Stollenwerk
  given-names: Tobias
- family-names: Wilhelm
  given-names: Frank K.
contact:
- family-names: Bode
  given-names: Tim
  orcid: "https://orcid.org/0000-0001-8280-3891"
doi: 10.5281/zenodo.8086187
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bode
    given-names: Tim
    orcid: "https://orcid.org/0000-0001-8280-3891"
  - family-names: Bagrets
    given-names: Dmitry
  - family-names: Misra-Spieldenner
    given-names: Aditi
  - family-names: Stollenwerk
    given-names: Tobias
  - family-names: Wilhelm
    given-names: Frank K.
  date-published: 2023-06-28
  doi: 10.21105/joss.05364
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5364
  title: "QAOA.jl: Toolkit for the Quantum and Mean-Field Approximate
    Optimization Algorithms"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05364"
  volume: 8
title: "QAOA.jl: Toolkit for the Quantum and Mean-Field Approximate
  Optimization Algorithms"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05364 joss-papers#4357
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05364
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 28, 2023
@danielskatz
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Congratulations to @timbode (Tim Bode) and co-authors on your publication!!

And thanks to @babreu-ncsa, @pkairys, and @Abinashbunty for reviewing!
We depend on volunteers, and really appreciate your willing to help make this process work

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🎉🎉🎉 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.05364/status.svg)](https://doi.org/10.21105/joss.05364)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05364">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05364/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05364/status.svg
   :target: https://doi.org/10.21105/joss.05364

This is how it will look in your documentation:

DOI

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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:

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