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

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@kungfugo@jarvist<!--end-editor-- Reviewers: @meandmytram, @Roger-luo Archive: 10.5281/zenodo.7575767

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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

@meandmytram & @Roger-luo, 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 @jarvist 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 @Roger-luo

📝 Checklist for @meandmytram

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

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 commented 1 year ago

Wordcount for paper.md is 707

editorialbot commented 1 year ago

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 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:

jarvist commented 1 year ago

^-- Those Biblio errors definitely need fixing @kungfugo

kungfugo commented 1 year ago

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

Roger-luo commented 1 year ago

Review checklist for @Roger-luo

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/kungfugo/BellDiagonalQudits.jl?
[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 (@kungfugo) 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?

meandmytram commented 1 year ago

Review checklist for @meandmytram

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/kungfugo/BellDiagonalQudits.jl?
[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 (@kungfugo) 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?

Roger-luo commented 1 year ago

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 commented 1 year ago

@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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

meandmytram commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

meandmytram commented 1 year ago

@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 commented 1 year ago

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

Roger-luo commented 1 year ago

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 commented 1 year ago

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

kungfugo commented 1 year ago

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.

Roger-luo commented 1 year ago

I understand the issue, however, the output of the manual is not deterministic due to the random sampling.

You can set up seed at the beginning of doctest, just copy-paste the following to your runtests.jl

using Documenter
DocMeta.setdocmeta!(BellDiagonalQudits, :DocTestSetup, :(using BellDiagonalQudits, Random;Random.seed!(123)); recursive=true)
doctest(BellDiagonalQudits)

This reminds me that you should have an explicit argument for RNG for methods calling rand etc, e.g this line https://github.com/kungfugo/BellDiagonalQudits.jl/blob/main/src/BellStates/bellStates.jl#L16 should have an argument rng::AbstractRNG otherwise one will not be able to set RNG state explicitly thus issues like the above in a doctest will appear.

But you can do it later, while this package still seems to require a lot of improvements. I think the minimum requirements are met now.

kungfugo commented 1 year ago

@jarvist , seems like all the requirements are met. What's the next step?

jarvist commented 1 year ago

Great! Do you want to make any further edits based on what Roger is suggesting above?

jarvist commented 1 year ago

@editorialbot check repository

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1002.3 files/s, 136284.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           14            457             52           1623
TOML                             6            297              3           1247
Markdown                         6            135              0            370
YAML                             4              7              0             86
TeX                              1              5              0             60
Lisp                             1              1              0              8
-------------------------------------------------------------------------------
SUM:                            32            902             55           3394
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 714

jarvist commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

jarvist 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:

kungfugo commented 1 year ago

Great! Do you want to make any further edits based on what Roger is suggesting above?

I will incorporate those suggestions in the next major release. For now I'd like to publish with JOSS based on the current version.

jarvist commented 1 year ago

OK! I made a minor suggestion for the paper.

Have you generated a DOI for the code yet? Probably easiest would be to use Zenodo to publish a tagged version of your code.

Upon successful completion of the review, authors will make a tagged release of the software, and deposit a copy of the repository with a data-archiving service such as Zenodo or figshare, get a DOI for the archive, and update the review issue thread with the version number and DOI.

kungfugo commented 1 year ago

Sorry, but what suggestion do you mean?

If there are no more changes required, I will create a new release that will be registered by Zenodo to generate the DOI

jarvist commented 1 year ago

Sorry, but what suggestion do you mean?

https://github.com/kungfugo/BellDiagonalQudits.jl/compare/main...jarvist:patch-1?expand=1

kungfugo commented 1 year ago

Allright! Included your suggestions, created release v0.1.5 and registered with Zenodo, https://doi.org/10.5281/zenodo.7575767

jarvist commented 1 year ago

@editorialbot set 10.5281/zenodo.7575767 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7575767

jarvist commented 1 year ago

@editorialbot set v0.1.5 as version

editorialbot commented 1 year ago

Done! version is now v0.1.5

jarvist commented 1 year ago

@editorialbot recommend-accept

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

- 10.1038/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 commented 1 year ago

:wave: @openjournals/pe-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/3909, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jarvist commented 1 year ago

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 commented 1 year ago

@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 commented 1 year ago

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

[x] 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.
[x] 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.
[x] 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 commented 1 year ago

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

openjournals / joss-reviews