[REVIEW]: QuantumACES.jl: Design noise characterisation experiments for quantum computers

[editorialbot]

Submitting author: @evanhockings (Evan T. Hockings)
Repository: https://github.com/evanhockings/QuantumACES.jl
Branch with paper.md (empty if default branch):
Version: v0.1.1
Editor: @phibeck
Reviewers: @obliviateandsurrender, @meandmytram, @pkairys
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/685c96388439611a9efa78dd9521648c/status.svg)](https://joss.theoj.org/papers/685c96388439611a9efa78dd9521648c)

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

@obliviateandsurrender & @meandmytram & @pkairys, 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 @phibeck 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 @meandmytram

[editorialbot]

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

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[editorialbot]

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

✅ OK DOIs

- 10.1103/PhysRevA.70.052328 is OK
- 10.1017/CBO9781139034807.007 is OK
- 10.1103/PhysRevLett.121.190501 is OK
- 10.5281/zenodo.3945249 is OK
- 10.1137/141000671 is OK
- 10.1103/PhysRevLett.128.110504 is OK
- 10.5281/zenodo.3455848 is OK
- 10.1063/1.1499754 is OK
- 10.4230/LIPIcs.TQC.2022.4 is OK
- 10.1103/PhysRevA.86.032324 is OK
- 10.22331/q-2021-07-06-497 is OK
- 10.1090/psapm/068 is OK
- 10.7907/rzr7-dt72 is OK
- 10.1103/PhysRevX.13.031007 is OK
- 10.1016/S0003-4916(02)00018-0 is OK
- 10.1038/nature03350 is OK
- 10.22331/q-2021-10-05-557 is OK
- 10.5281/zenodo.594712 is OK
- 10.1109/SFCS.1996.548464 is OK
- 10.1038/s41467-023-38247-5 is OK
- 10.1103/RevModPhys.87.307 is OK
- 10.22331/q-2023-09-26-1123 is OK
- 10.1103/PhysRevLett.124.130501 is OK
- 10.1103/PhysRevA.94.052325 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Quantum Codes on a Lattice with Boundary
- No DOI given, and none found for title: The Error Reconstruction and Compiled Calibration ...
- No DOI given, and none found for title: Scalable Noise Characterisation of Syndrome Extrac...
- No DOI given, and none found for title: Quantum Computing with Qiskit

❌ MISSING DOIs

- 10.1145/3505637 may be a valid DOI for title: PyMatching: A Python Package for Decoding Quantum ...
- 10.22331/q-2025-01-20-1600 may be a valid DOI for title: Sparse Blossom: Correcting a Million Errors per Co...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.15 s (491.7 files/s, 140273.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           34            876           3526          14551
Markdown                        28            309              0           1177
TeX                              1             29              0            391
YAML                             6              1              8            162
TOML                             5              3              0             76
-------------------------------------------------------------------------------
SUM:                            74           1218           3534          16357
-------------------------------------------------------------------------------

Commit count by author:

    47	evanhockings
     5	Evan Hockings
     2	dependabot[bot]
     1	Dilum Aluthge

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 742

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[evanhockings]

Wow, how can I get this reference check tool? Would be useful for other papers! I'll update the bibliography with non-arXiv citations for those two papers.

[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/evanhockings/QuantumACES.jl?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@evanhockings) 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?

[phibeck]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1103/PhysRevA.70.052328 is OK
- 10.1017/CBO9781139034807.007 is OK
- 10.1103/PhysRevLett.121.190501 is OK
- 10.5281/zenodo.3945249 is OK
- 10.1137/141000671 is OK
- 10.1103/PhysRevLett.128.110504 is OK
- 10.5281/zenodo.3455848 is OK
- 10.1063/1.1499754 is OK
- 10.4230/LIPIcs.TQC.2022.4 is OK
- 10.1103/PhysRevA.86.032324 is OK
- 10.22331/q-2021-07-06-497 is OK
- 10.1090/psapm/068 is OK
- 10.7907/rzr7-dt72 is OK
- 10.1103/PhysRevX.13.031007 is OK
- 10.1145/3505637 is OK
- 10.22331/q-2025-01-20-1600 is OK
- 10.1016/S0003-4916(02)00018-0 is OK
- 10.1038/nature03350 is OK
- 10.22331/q-2021-10-05-557 is OK
- 10.5281/zenodo.594712 is OK
- 10.1109/SFCS.1996.548464 is OK
- 10.1038/s41467-023-38247-5 is OK
- 10.1103/RevModPhys.87.307 is OK
- 10.22331/q-2023-09-26-1123 is OK
- 10.1103/PhysRevLett.124.130501 is OK
- 10.1103/PhysRevA.94.052325 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Quantum Codes on a Lattice with Boundary
- No DOI given, and none found for title: The Error Reconstruction and Compiled Calibration ...
- No DOI given, and none found for title: Scalable Noise Characterisation of Syndrome Extrac...
- No DOI given, and none found for title: Quantum Computing with Qiskit

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[phibeck]

Wow, how can I get this reference check tool? Would be useful for other papers! I'll update the bibliography with non-arXiv citations for those two papers.

Hi @evanhockings I asked the other editors and here's what I learned:

The editorialbot is an instance of the Buffy Ruby app. I don't know Ruby but grepping around in the code for key statements pointed me to the DOIChecker object, which seems to be where the work of checking the DOIs is done. It looks like the logic (some of which is in the DOIChecker caller) is, wildly paraphrasing,

• grab the DOIs from the BibTeX
• if there's a DOI, check it doesn't have any common prefixes and looks standard,
• make an API call to resolve the DOI to validate it
• if there's no DOI, query the title on CrossRef and try to find close matches (via the Levenshtein distance?)

[phibeck]

@obliviateandsurrender, @meandmytram, @pkairys thanks again for reviewing! For those who haven't already, please go ahead and create your checklist first using the command @editorialbot generate my checklist. Feel free to create issues in project repository directly or write them down as comments here, but please do link the issues in this review so it's easy to follow for everyone. Please let me know if you have any questions about the review process.

[evanhockings]

Ah okay, thanks @phibeck!