[REVIEW]: BellDiagonalQudits: A package for entanglement analyses of mixed maximally entangled qudits #4924

editorialbot · 2022-11-11T08:56:42Z

Submitting author: @kungfugo (Christopher Popp)
Repository: https://github.com/kungfugo/BellDiagonalQudits.jl
Branch with paper.md (empty if default branch):
Version: v0.1.5
Editor: @jarvist
Reviewers: @meandmytram, @Roger-luo
Archive: 10.5281/zenodo.7575767

Status

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📝 Checklist for @Roger-luo

📝 Checklist for @meandmytram

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-11-11T08:56:44Z

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editorialbot · 2022-11-11T08:56:46Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (369.5 files/s, 50455.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           14            457             52           1614
TOML                             6            294              3           1219
Markdown                         5             74              0            249
YAML                             3              4              0             59
TeX                              1              5              0             58
Lisp                             1              1              0              8
-------------------------------------------------------------------------------
SUM:                            30            835             55           3207
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-11-11T08:56:48Z

Wordcount for paper.md is 707

editorialbot · 2022-11-11T08:57:36Z

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

OK DOIs

- 10.48550/ARXIV.2209.15267 is OK
- 10.21105/joss.00615 is OK
- 10.21105/jcon.00097 is OK

MISSING DOIs

- 10.1038/s41598-022-16225-z may be a valid DOI for title: Almost complete solution for the NP-hard separability problem of Bell diagonal qutrits
- 10.1038/s41598-021-98523-6 may be a valid DOI for title: Free versus bound entanglement, a NP-hard problem tackled by machine learning

INVALID DOIs

- https://doi.org/10.1088/1751-8113/40/28/S03 is INVALID because of 'https://doi.org/' prefix

editorialbot · 2022-11-11T08:58:05Z

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

jarvist · 2022-11-11T08:58:25Z

^-- Those Biblio errors definitely need fixing @kungfugo

kungfugo · 2022-11-15T16:06:43Z

@jarvist Thanks for pointing out. .bib now contains the correct DOIs.

Roger-luo · 2022-11-15T20:10:59Z

Review checklist for @Roger-luo

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.

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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/kungfugo/BellDiagonalQudits.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 (@kungfugo) 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.
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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?

meandmytram · 2022-11-16T09:01:13Z

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/kungfugo/BellDiagonalQudits.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 (@kungfugo) 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?

Roger-luo · 2022-11-30T19:01:42Z

Before heading to the details of the package I have some general comments on the basic quality of the software:

please consider putting an installation section in the README, e.g

https://github.com/Roger-luo/Configurations.jl#installation

and please also set up some basic things for the above package as the following:

CI tests and CI badges in README (should be at least on Julia 1.6 and Julia 1.x)
Test coverage and coverage badge in README, and test coverage should be above 90%
Since you are taking this piece of software seriously, I'd suggest adding Aqua tests, but not required
please setup community guidelines line and code of conduct (as required by JOSS)
please consider following the style guide of Julia, it is not required but strongly recommended, e.g
- use snake case for functions
- camel case for types
- follow other conventions in Julia/Base module

kungfugo · 2022-12-02T18:56:15Z

@Roger-luo thank you for your help! I just addressed your comments. In particular:

An installation section is now part of the README
CI tests are set up including the badge
Test coverage is set up including the badge (there seems to be some issue with codecov, but following the link in the badge verifies coverage >90%)
CODE_OF_CONDUCT.md is in the root directory
A contribution section is now part of the README
Functions and Types follow the style guide

meandmytram · 2022-12-14T16:59:08Z

Hey @kungfugo, the example shown in the documentation doesn't work for me. However, it works if I call CreateStandardIndexbasis(d,n) instead of create_standard_indexbasis(d,n). Can you update the documentation on https://kungfugo.github.io/BellDiagonalQudits.jl/dev/manual/ please?

meandmytram · 2022-12-14T17:08:32Z

Also, the first phrase of the paper's summary bugs me a little.

In the field of quantum information and technology, entanglement of quantum states called qudits is regarded as resource for quantum and classical information processing tasks and allows the use of algorithms with better performance than any classical algorithm for certain applications like superdense coding, teleportation or computing.

Qudits are not quantum states but rather quantum systems.
"Entanglement as a resource for classical information processing task" sounds a bit weird I think.
I'd rather say "any known classical algorithm".
It's not really clear what a classical algorithm for quantum teleportation would be. In order to evade confusion, I would say something like "Entanglement of quantum states is often regarded as a computational resource for quantum computers opening possibilities for speedups in a variety of algorithms."

kungfugo · 2022-12-14T17:13:41Z

Hey @kungfugo, the example shown in the documentation doesn't work for me. However, it works if I call CreateStandardIndexbasis(d,n) instead of create_standard_indexbasis(d,n). Can you update the documentation on https://kungfugo.github.io/BellDiagonalQudits.jl/dev/manual/ please?

Hey @meandmytram, have you pulled the latest changes? The source code only contains the function create_standard_indexbasis. createStandardIndexBasis() should not exist anymore.

kungfugo · 2022-12-14T21:08:15Z

@meandmytram thank you very much for your comments! I will adjust the paper accordingly soon.

meandmytram · 2022-12-15T06:01:12Z

Hey @kungfugo, the example shown in the documentation doesn't work for me. However, it works if I call CreateStandardIndexbasis(d,n) instead of create_standard_indexbasis(d,n). Can you update the documentation on https://kungfugo.github.io/BellDiagonalQudits.jl/dev/manual/ please?

Hey @meandmytram, have you pulled the latest changes? The source code only contains the function create_standard_indexbasis. createStandardIndexBasis() should not exist anymore.

I installed the package via Pkg, should I rather pull the package from GitHub?

kungfugo · 2022-12-15T16:15:50Z

Hey @kungfugo, the example shown in the documentation doesn't work for me. However, it works if I call CreateStandardIndexbasis(d,n) instead of create_standard_indexbasis(d,n). Can you update the documentation on https://kungfugo.github.io/BellDiagonalQudits.jl/dev/manual/ please?

Hey @meandmytram, have you pulled the latest changes? The source code only contains the function create_standard_indexbasis. createStandardIndexBasis() should not exist anymore.

I installed the package via Pkg, should I rather pull the package from GitHub?

This is my mistake. The latest version has not been tagged correctly. I will fix this asap. In the meanwhile you could pull from GitHub. There were no functional changes, only CI, tests and styling. Sorry for this problem.

kungfugo · 2022-12-15T17:20:39Z

@meandmytram I released a new version (v0.1.2) compatible with the documentation and including your suggestions for the paper.

meandmytram · 2022-12-15T21:00:29Z

@kungfugo Thanks for the changes, everything now seems to work according to documentation. One last but not the least thing I am a bit confused about is what it is exactly you're doing in the example. There is a lot of terminology I am not familiar with, sorry. From my understanding, you are building something like an ensemble of states from which you are then sampling and then analysing the entanglement, is this right? If that's something not too hard, could you please add a bit more explanations so that the content is more accessible.

kungfugo · 2023-01-02T17:39:16Z

@meandmytram , thanks for your comment. I agree.
I have released a new version (v.0.1.3) with a more detailed manual.

Roger-luo · 2023-01-03T20:57:00Z

Hi @kungfugo I have some minor comments on the APIs and manual,

mode selection it might be better and more consistent with other Julia packages to just use Symbol for mode selection, e.g

myCoordStates = uniform_bell_sampler(100, d, "enclosurePolytope")

can be

myCoordStates = uniform_bell_sampler(100, d, :enclosurePolytope)

it is not a big difference tho, but you can see this discussion to understand why

tovrep is not (re)exported, this causing manual example to fail. Tho, this is a method from LazySets but I believe you should re-export this function, otherwise, you need to show your user they need to using LazySets. Please consider putting a doc test in your tests to prevent an example from failing again.

I think it is better to make the following example in the manual a self-contained example, the current one seems a bit hand-waving - one cannot directly run that code block without defining
a few things extra

myExtendedKernel = extend_vpolytope_by_densitystates(tovrep(mySepKernel), newSepDensityStates)

A similar issue exists for

myOptimizedEWs = create_random_bounded_ews(
    d,
    myBasis,
    n,
    true,
    50
    )

I'd suggest you to go through these examples and making sure clicking copy-paste buttons gives runnable scripts instead of just a code block.

In summary, I think the functionality is solid, it does what is described.
The documentation requires further improvement as commented above.

And a non-blocking suggestion from a user perspective, the current APIs are too long, and some of them seems to have too much positional arguments, e.g

f(x) = analyse_coordstate(
    d,
    x,
    myAnaSpec,
    myBasis,
    mySepKernel,
    myWeylOperatorBasis,
    myBasisDict,
    missing,
    myOptimizedCoodEWs
)

or

myAnaSpec = AnalysisSpecification(
   true,
   true,
   true,
   true,
   true,
   false,
   true,
   false
)

If you need to specify configuration/options, I'd suggest checking out https://github.com/Roger-luo/Configurations.jl which is designed for the case. But if you are able to make it more automatic, or incremental (instead of putting a bunch of true all in one) it will have a much friendlier UX.

meandmytram · 2023-01-04T09:04:47Z

The example looks way less opaque now, I think once we're done with Roger's comments we'd be all set.

kungfugo · 2023-01-04T13:20:39Z

Hi @Roger-luo,
thank you for your comments. I released v0.1.4 with changes according to your comments. In particular:

Mode selection: Symbols are now used instead of strings.
Exported functions: tovrep is now exported as well
Manual: The manual is now self-contained. All code can now be run by copy-and-paste. minor improvements

Concerning your comments regarding doctest:
I understand the issue, however, the output of the manual is not deterministic due to the random sampling. As far as I understand, this prevents the straightforward use of doctest. For this release, I would prefer to rely on the tested current implementation, but I will consider this issue for the next major release.

Concerning your comments regarding the API:
I agree that there can be significant improvements concerning the UX. However, for this release, I prefer to keep the current implementation for the sake of flexibility of use and stability of code, but I will consider your suggestions for the next major release. The same goes for Configurations.jl, which seems very suitable to improve the UX.

editorialbot · 2023-01-27T11:25:26Z

Done! Archive is now 10.5281/zenodo.7575767

jarvist · 2023-01-27T11:25:50Z

@editorialbot set v0.1.5 as version

editorialbot · 2023-01-27T11:25:52Z

Done! version is now v0.1.5

jarvist · 2023-01-27T11:26:00Z

@editorialbot recommend-accept

editorialbot · 2023-01-27T11:26:02Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-01-27T11:26:03Z

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

OK DOIs

- 10.1038/s41598-022-16225-z is OK
- 10.1088/1751-8113/40/28/S03 is OK
- 10.48550/ARXIV.2209.15267 is OK
- 10.21105/joss.00615 is OK
- 10.21105/jcon.00097 is OK
- 10.1038/s41598-021-98523-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-01-27T11:27:49Z

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3909, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jarvist · 2023-01-27T11:30:34Z

OK! Looking good. That's me, an editor in chief should be along shortly for final checks.

Many thanks @Roger-luo and @meandmytram for such detailed and interactive reviews, thank you @kungfugo for engaging with the process and being so responsive. (And my apologies for not noticing the reviews had finished 3 weeks ago!)

kungfugo · 2023-01-27T11:32:37Z

@jarvist , @Roger-luo , @meandmytram thank you for your efforts! First time publishing with JOSS and it was a nice ecperience. Looking forward to the next ones.

kyleniemeyer · 2023-01-29T18:26:42Z

Hi @kungfugo, just doing some final checks before accepting.

Could you clean up the Zenodo metadata? The author list does not have your real name, and @jarvist is listed as a contributor—generally this should match the paper.
Can you remove the "These authors contributed equally." bit from the author block of the paper? It doesn't really make sense for a single-author paper.
In a few places, you use a reference as part of a sentence, but with the parenthetical format. Could you replace this with the "Author et al. (year)" format? For example, rather than "summarized in (Baumgartner et al., 2007)", replace with "summarized by Baumgartner et al. (2007)". This is done with the @author:year syntax.

kungfugo · 2023-01-30T16:40:04Z

Hi @kyleniemeyer ,

thank you for your comments. I have a released a new version v0.1.6 including your requests and registered it with zenodo.

In particular:

New DOI with corrected Zenodo metadata: DOI: https://zenodo.org/record/7585987
The author block does not the 'equal contribution' part anymore
References cited without parentheses when part of a sentence

kyleniemeyer · 2023-01-30T16:50:49Z

@editorialbot generate pdf

editorialbot · 2023-01-30T16:52:11Z

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

kyleniemeyer · 2023-01-30T17:12:34Z

@kungfugo looks good, thank you!

kyleniemeyer · 2023-01-30T17:12:47Z

@editorialbot accept

editorialbot · 2023-01-30T17:12:49Z

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

editorialbot · 2023-01-30T17:14:42Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-01-30T17:14:43Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-01-30T17:14:44Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04924 joss-papers#3920
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04924
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kyleniemeyer · 2023-01-30T17:42:19Z

Congratulations @kungfugo on your article's publication in JOSS!

Many thanks to @meandmytram and @Roger-luo for reviewing this submission, and @jarvist for editing.

editorialbot · 2023-01-30T17:42:21Z

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kyleniemeyer · 2023-01-30T18:28:09Z

(I'm going to reopen because it looks like the PDF is not yet appearing—I saw there were some systemic issues with GitHub Actions earlier.)

arfon · 2023-01-31T09:44:24Z

(I'm going to reopen because it looks like the PDF is not yet appearing—I saw there were some systemic issues with GitHub Actions earlier.)

Should be fixed now!

editorialbot · 2023-01-31T09:44:27Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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editorialbot added Emacs Lisp Julia review TeX Track: 3 (PE) Physics and Engineering labels Nov 11, 2022

editorialbot assigned jarvist Nov 11, 2022

editorialbot mentioned this issue Nov 11, 2022

[PRE REVIEW]: BellDiagonalQudits: A package for entanglement analyses of mixed maximally entangled qudits #4826

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 27, 2023

editorialbot added accepted published Papers published in JOSS labels Jan 30, 2023

kyleniemeyer closed this as completed Jan 30, 2023

kyleniemeyer reopened this Jan 30, 2023

arfon closed this as completed Jan 31, 2023

[REVIEW]: BellDiagonalQudits: A package for entanglement analyses of mixed maximally entangled qudits #4924

[REVIEW]: BellDiagonalQudits: A package for entanglement analyses of mixed maximally entangled qudits #4924

Comments

editorialbot commented Nov 11, 2022 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Nov 11, 2022

editorialbot commented Nov 11, 2022

editorialbot commented Nov 11, 2022

editorialbot commented Nov 11, 2022

editorialbot commented Nov 11, 2022

jarvist commented Nov 11, 2022 • edited

kungfugo commented Nov 15, 2022

Roger-luo commented Nov 15, 2022 • edited

Review checklist for @Roger-luo

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

meandmytram commented Nov 16, 2022 • edited

Review checklist for @meandmytram

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Roger-luo commented Nov 30, 2022

kungfugo commented Dec 2, 2022

meandmytram commented Dec 14, 2022

meandmytram commented Dec 14, 2022

kungfugo commented Dec 14, 2022

kungfugo commented Dec 14, 2022

meandmytram commented Dec 15, 2022

kungfugo commented Dec 15, 2022

kungfugo commented Dec 15, 2022

meandmytram commented Dec 15, 2022 • edited

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editorialbot commented Nov 11, 2022 •

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meandmytram commented Dec 15, 2022 •

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edited