editorialbot commented 1 year ago

Submitting author: !--author-handle-->@eggerdj@danielskatz<!--end-editor-- Reviewers: @nunezco2, @goerz, @TejasAvinashShetty Archive: 10.5281/zenodo.7844174

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 commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

Wordcount for paper.md is 867

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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

danielskatz commented 1 year ago

👋 @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 commented 1 year ago

Review checklist for @goerz

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Qiskit/qiskit-experiments?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

Review checklist for @nunezco2

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Qiskit/qiskit-experiments?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

Review checklist for @TejasAvinashShetty

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Qiskit/qiskit-experiments?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

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

eggerdj commented 1 year ago

Dear @TejasAvinashShetty ,

In response to https://github.com/openjournals/joss-reviews/issues/5329#issuecomment-1497114965 regarding the code of the QV experiment (comment https://github.com/Qiskit/qiskit-experiments/issues/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 commented 1 year ago

@eggerdj - this seems reasonable to me

eggerdj commented 1 year ago

@danielskatz This PR https://github.com/Qiskit/qiskit-experiments/pull/1131 adds a link to the experiment manuals in the docs. It also addresses https://github.com/Qiskit/qiskit-experiments/issues/1124

eggerdj commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

TejasAvinashShetty commented 1 year ago

@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 commented 1 year ago

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

eggerdj commented 1 year ago

@TejasAvinashShetty you can pip install it

danielskatz commented 1 year ago

@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 commented 1 year ago

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

danielskatz commented 1 year ago

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

danielskatz commented 1 year ago

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

goerz commented 1 year ago

No, I just haven't had time to look at it

goerz commented 1 year ago

Ok, I finished my review. Overall, the software package and its documentation are of very high quality, and I have no fundamental objections to publication.

I came across two minor issues that should be fixed:

First, there are some small technical issues with the reproducibility of the tutorial, cf. https://github.com/Qiskit/qiskit-experiments/issues/1136. I've left the "Installation instructions" checkmark open until the issue is closed.

Second, the "Example usage" in the paper could be improved. I somewhat agree with @TejasAvinashShetty's comment. I think JOSS' intent for the "Example usage" is to actually show some code, and the first three code blocks of the online QV examples wouldn't be much to add here. As for @eggerdj's comment that the example code could change in future versions, you could just say "using v0.5 of qiskit-experiments". That being said, everybody is probably just going to look at the documentation, not the JOSS paper, to get a usage example, so I'm not sure if I care that much ;-)

Without the code, though, the section in the paper needs some editing. The first two sentences in particular sound like they lead up to a code example. You could rephrase this as, e.g.,

Qiskit Experiments can run, for example, a Quantum Volume (QV) measurement. Evaluating the QV of a quantum backend requires executing random SU(4) circuits on a noisy simulator of the backend to quantify the largest quantum circuit with equal width and depth that can be successfully run. A depth d QV circuit is successful if it has …. Qiskit Experiments only requires a few lines of code to run this standardized yet complex experiment, see the online documentation [url]. The analysis classes of existing experiments … Figure 2."

I've left the "Quality of writing" checkmark open for this. Please either add the code for the example or rephrase the text.

eggerdj commented 1 year ago

Dear @goerz , thank you for the review. I have amended the paper according to your suggestion here: https://github.com/Qiskit/qiskit-experiments/pull/1138

eggerdj commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

eggerdj commented 1 year ago

@danielskatz and @goerz I believe the two following PRs should address the points raised by Michael. Thanks again for pointing this out!

Tutorials: https://github.com/Qiskit/qiskit-experiments/pull/1137
Paper: https://github.com/Qiskit/qiskit-experiments/pull/1138

goerz commented 1 year ago

Looks good to me! This is ready for publication, as far as I'm concerned

danielskatz commented 1 year ago

thanks @goerz and @eggerdj

danielskatz commented 1 year ago

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

danielskatz commented 1 year ago

👋 @eggerdj - in case it wasn't clear, the top set of items above 👆 are for you to do, then I will do the bottom set and we'll be about done.

eggerdj commented 1 year ago

@danielskatz Thanks for the reminder. We are preparing a 0.5.1 release which will have the PR's that we merged during this review.

eggerdj commented 1 year ago

@editorialbot generate pdf

eggerdj commented 1 year ago

Author and affiliation check done: https://github.com/Qiskit/qiskit-experiments/pull/1146

editorialbot commented 1 year ago

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

coruscating commented 1 year ago

@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

danielskatz commented 1 year ago

@editorialbot set 10.5281/zenodo.7844174 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7844174

danielskatz commented 1 year ago

@editorialbot set 0.5.1 as version

editorialbot commented 1 year ago

Done! version is now 0.5.1

danielskatz commented 1 year ago

@editorialbot recommend-accept

This will generate a proof that I will then proofread

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4142, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

👋 @eggerdj - I've suggested some minor changes in https://github.com/Qiskit/qiskit-experiments/pull/1152 - please merge this, or let me know what you disagree with, then we can continue to acceptance and publication

eggerdj commented 1 year ago

@danielskatz edits look good. Thank you.

danielskatz commented 1 year ago

@editorialbot recommend-accept

Another proof, for final check

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

openjournals / joss-reviews

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

Status

Reviewer instructions & questions

Checklists

Review checklist for @goerz

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @nunezco2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @TejasAvinashShetty

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance