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[REVIEW]: Qiskit Experiments: A Python package to characterize and calibrate quantum computers #5329

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editorialbot opened this issue Apr 2, 2023 · 61 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Shell Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Apr 2, 2023

Submitting author: @eggerdj (Daniel Egger)
Repository: https://github.com/Qiskit/qiskit-experiments
Branch with paper.md (empty if default branch): paper
Version: 0.5.1
Editor: @danielskatz
Reviewers: @nunezco2, @goerz, @TejasAvinashShetty
Archive: 10.5281/zenodo.7844174

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/db68fcbca2c6abd4a31d3fb87d82690b"><img src="https://joss.theoj.org/papers/db68fcbca2c6abd4a31d3fb87d82690b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/db68fcbca2c6abd4a31d3fb87d82690b/status.svg)](https://joss.theoj.org/papers/db68fcbca2c6abd4a31d3fb87d82690b)

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

@nunezco2 & @goerz & @TejasAvinashShetty, 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 @nunezco2

📝 Checklist for @goerz

📝 Checklist for @TejasAvinashShetty

@editorialbot editorialbot added Python review Shell Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Apr 2, 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=0.76 s (562.5 files/s, 96686.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         260          10801          18732          33559
YAML                           101            110              4           2141
reStructuredText                38            874           1396            982
Markdown                        10            245              0            788
HTML                             3             51              5            309
TeX                              1             22              0            228
Jupyter Notebook                 2              0           2865            218
CSS                              3             20              8            206
INI                              1             11              0             67
Bourne Shell                     2             15             28             28
Jinja Template                   1              0              0              9
JSON                             6              0              0              6
TOML                             1              1              0              5
-------------------------------------------------------------------------------
SUM:                           429          12150          23038          38546
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 867

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

OK DOIs

- 10.1088/2058-9565/aba404 is OK
- 10.48550/ARXIV.2303.02108 is OK
- 10.1103/PhysRevA.100.032328 is OK
- 10.1103/PhysRevA.61.010304 is OK
- 10.1103/PhysRevResearch.4.033027 is OK
- 10.48550/ARXIV.2211.16439 is OK
- 10.5281/zenodo.3455847 is OK
- 10.48550/ARXIV.2209.00678 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.2573505 is OK
- 10.5281/zenodo.4091470 is OK
- 10.1103/PhysRevLett.106.180504 is OK
- 10.48550/ARXIV.2208.00576 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.11813 is OK
- 10.1088/2058-9565/ab8e92 is OK
- 10.1103/PhysRevApplied.17.064061 is OK
- 10.48550/ARXIV.2207.11268 is OK
- 10.5281/zenodo.6363115 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@danielskatz
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danielskatz commented Apr 2, 2023

👋 @nunezco2, @goerz, and @TejasAvinashShetty - 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#5329 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.

@goerz
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goerz commented Apr 2, 2023

Review checklist for @goerz

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/Qiskit/qiskit-experiments?
  • 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 (@eggerdj) 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?

@nunezco2
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nunezco2 commented Apr 3, 2023

Review checklist for @nunezco2

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/Qiskit/qiskit-experiments?
  • 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 (@eggerdj) 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?

@TejasAvinashShetty
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TejasAvinashShetty commented Apr 4, 2023

Review checklist for @TejasAvinashShetty

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/Qiskit/qiskit-experiments?
  • 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 (@eggerdj) 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?

@TejasAvinashShetty
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TejasAvinashShetty commented Apr 5, 2023

The github handles and the actual author names required effort to verify. Also it would be better if the code to reproduce the example in the paper is added to the paper for the benefit of the reader

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eggerdj commented Apr 6, 2023

Dear @TejasAvinashShetty ,

In response to #5329 (comment) regarding the code of the QV experiment (comment Qiskit-Extensions/qiskit-experiments#1129). I would avoid including the code in the paper itself in the unlikely event of changes to the code. You can find an example of the QV experiment here: https://qiskit.org/documentation/experiments/manuals/verification/quantum_volume.html . What I think would make sense is to amend the paper with an extra sentence that points to the experiment manuals. We could also explicitly call out the quantum volume manual.

@danielskatz
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@eggerdj - this seems reasonable to me

@eggerdj
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eggerdj commented Apr 7, 2023

@danielskatz This PR Qiskit-Extensions/qiskit-experiments#1131 adds a link to the experiment manuals in the docs. It also addresses Qiskit-Extensions/qiskit-experiments#1124

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eggerdj commented Apr 7, 2023

@editorialbot generate pdf

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

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TejasAvinashShetty commented Apr 8, 2023

@danielskatz Can the reviewers discuss with each other or is it against JoSS rules? I mean only converse on Github and on this thread only.

@TejasAvinashShetty
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TejasAvinashShetty commented Apr 8, 2023

@eggerdj Just as an aside, is qiskit-experiments installable via conda package manager?

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eggerdj commented Apr 8, 2023

@TejasAvinashShetty you can pip install it

@danielskatz
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@danielskatz Can the reviewers discuss with each other or is it against JoSS rules? I mean only converse on Github and on this thread only.

Open discussion in this issue is fine

@nunezco2
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@eggerdj Thank you for the revisions on the article. @danielskatz I am satisfied with the extent of the changes in the new version.

@danielskatz
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@TejasAvinashShetty - it looks like you are also satisfied with the submission?

@danielskatz
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@goerz - there's no hurry, but I'm just checking that nothing is currently blocking your review progress...

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

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@danielskatz We've made the 0.5.1 release which contains the changes from reviews. Here's the DOI: https://doi.org/10.5281/zenodo.7844174

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@editorialbot set 10.5281/zenodo.7844174 as archive

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Done! Archive is now 10.5281/zenodo.7844174

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@editorialbot set 0.5.1 as version

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Done! version is now 0.5.1

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@editorialbot recommend-accept

This will generate a proof that I will then proofread

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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

- 10.1088/2058-9565/aba404 is OK
- 10.48550/ARXIV.2303.02108 is OK
- 10.1088/2058-9565/abdca6 is OK
- 10.1103/PhysRevA.100.032328 is OK
- 10.1103/PhysRevA.61.010304 is OK
- 10.1103/PhysRevResearch.4.033027 is OK
- 10.48550/ARXIV.2211.16439 is OK
- 10.5281/zenodo.3455847 is OK
- 10.48550/ARXIV.2209.00678 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.2573505 is OK
- 10.5281/zenodo.4091470 is OK
- 10.1103/PhysRevLett.106.180504 is OK
- 10.48550/ARXIV.2208.00576 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.11813 is OK
- 10.1088/2058-9565/ab8e92 is OK
- 10.1103/PhysRevApplied.17.064061 is OK
- 10.48550/ARXIV.2207.11268 is OK
- 10.5281/zenodo.6363115 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#4142, 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 Apr 19, 2023
@danielskatz
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👋 @eggerdj - I've suggested some minor changes in Qiskit-Extensions/qiskit-experiments#1152 - please merge this, or let me know what you disagree with, then we can continue to acceptance and publication

@eggerdj
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eggerdj commented Apr 19, 2023

@danielskatz edits look good. Thank you.

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@editorialbot recommend-accept

Another proof, for final check

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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

- 10.1088/2058-9565/aba404 is OK
- 10.48550/ARXIV.2303.02108 is OK
- 10.1088/2058-9565/abdca6 is OK
- 10.1103/PhysRevA.100.032328 is OK
- 10.1103/PhysRevA.61.010304 is OK
- 10.1103/PhysRevResearch.4.033027 is OK
- 10.48550/ARXIV.2211.16439 is OK
- 10.5281/zenodo.3455847 is OK
- 10.48550/ARXIV.2209.00678 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.2573505 is OK
- 10.5281/zenodo.4091470 is OK
- 10.1103/PhysRevLett.106.180504 is OK
- 10.48550/ARXIV.2208.00576 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.11813 is OK
- 10.1088/2058-9565/ab8e92 is OK
- 10.48550/arXiv.1608.03355 is OK
- 10.1103/PhysRevApplied.17.064061 is OK
- 10.48550/ARXIV.2207.11268 is OK
- 10.5281/zenodo.6363115 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#4146, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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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: Kanazawa
  given-names: Naoki
  orcid: "https://orcid.org/0000-0002-4192-5558"
- family-names: Egger
  given-names: Daniel J.
  orcid: "https://orcid.org/0000-0002-5523-9807"
- family-names: Ben-Haim
  given-names: Yael
- family-names: Zhang
  given-names: Helena
  orcid: "https://orcid.org/0000-0002-7813-7133"
- family-names: Shanks
  given-names: William E.
  orcid: "https://orcid.org/0000-0002-5045-8808"
- family-names: Aleksandrowicz
  given-names: Gadi
- family-names: Wood
  given-names: Christopher J.
  orcid: "https://orcid.org/0000-0001-7606-7349"
contact:
- family-names: Egger
  given-names: Daniel J.
  orcid: "https://orcid.org/0000-0002-5523-9807"
doi: 10.5281/zenodo.7844174
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kanazawa
    given-names: Naoki
    orcid: "https://orcid.org/0000-0002-4192-5558"
  - family-names: Egger
    given-names: Daniel J.
    orcid: "https://orcid.org/0000-0002-5523-9807"
  - family-names: Ben-Haim
    given-names: Yael
  - family-names: Zhang
    given-names: Helena
    orcid: "https://orcid.org/0000-0002-7813-7133"
  - family-names: Shanks
    given-names: William E.
    orcid: "https://orcid.org/0000-0002-5045-8808"
  - family-names: Aleksandrowicz
    given-names: Gadi
  - family-names: Wood
    given-names: Christopher J.
    orcid: "https://orcid.org/0000-0001-7606-7349"
  date-published: 2023-04-19
  doi: 10.21105/joss.05329
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5329
  title: "Qiskit Experiments: A Python package to characterize and
    calibrate quantum computers"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05329"
  volume: 8
title: "Qiskit Experiments: A Python package to characterize and
  calibrate quantum computers"

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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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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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.05329 joss-papers#4147
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05329
  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 Apr 19, 2023
@danielskatz
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Congratulations to @eggerdj (Daniel Egger) and co-authors!!

And thanks to @nunezco2, @goerz, and @TejasAvinashShetty on a remarkably simple and quick review, which was also due in part to the quality of the submission!

We couldn't do this without your voluntary help and support

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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.05329/status.svg)](https://doi.org/10.21105/joss.05329)

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<a style="border-width:0" href="https://doi.org/10.21105/joss.05329">
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@TejasAvinashShetty
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Congratulations to @eggerdj (Daniel Egger) and co-authors!!

And thanks to @nunezco2, @goerz, and @TejasAvinashShetty on a remarkably simple and quick review, which was also due in part to the quality of the submission!

We couldn't do this without your voluntary help and support

Thank you @danielskatz

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eggerdj commented Apr 20, 2023

@danielskatz @goerz @nunezco2 and @TejasAvinashShetty thanks a lot for handling the submission and for the reviews which helped us improve our work.

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