[REVIEW]: PyKronecker: A Python Library for the Efficient Manipulation of Kronecker Products and Related Structures

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@nickelnine37@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @JulianKarlBauer, @nicoguaro Archive: 10.5281/zenodo.7566803

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0946dc0f465819544e228a6acb96bf24"><img src="https://joss.theoj.org/papers/0946dc0f465819544e228a6acb96bf24/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0946dc0f465819544e228a6acb96bf24/status.svg)](https://joss.theoj.org/papers/0946dc0f465819544e228a6acb96bf24)

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

@JulianKarlBauer & @nicoguaro, 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 @Kevin-Mattheus-Moerman 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 @JulianKarlBauer

📝 Checklist for @nicoguaro

editorialbot commented 2 years 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 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (847.2 files/s, 109897.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0             17           1360
Python                          14            624            399           1113
Markdown                        18            438              0            903
TeX                              1             22              0            180
YAML                             4             13              5             82
INI                              1              2              0             21
TOML                             1              2              0              8
-------------------------------------------------------------------------------
SUM:                            40           1101            421           3667
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1471

editorialbot commented 2 years ago

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

OK DOIs

- 10.1109/TNNLS.2017.2727545 is OK
- 10.1016/S0377-0427(00)00393-9 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.softx.2019.100361 is OK
- 10.21105/jcon.00015 is OK
- 10.48550/arXiv.1502.05767 is OK
- 10.1137/141000671 is OK
- 10.2307/3609497 is OK
- 10.1090/s0025-5718-1973-0395196-6 is OK
- 10.1145/355826.355831 is OK
- 10.1109/TC.1981.6312174 is OK
- 10.1145/225545.225548 is OK
- 10.1145/3291041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

JulianKarlBauer commented 2 years ago

Review checklist for @JulianKarlBauer

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/nickelnine37/pykronecker?
[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 (@nickelnine37) 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?

JulianKarlBauer commented 2 years ago

@Kevin-Mattheus-Moerman during the first steps of the review process, I created a merge-request with some small changes instead of raising an issue describing what to change. As this merge-request now has been merged, I am listed as contributor to pykronecker. Formally, does this induce a COI? This question might be a bit pedantic, as such a situation is probably common during the review process. But I am a bit in doubt and therefore ask, following https://github.com/openjournals/joss/blob/main/COI.md .

JulianKarlBauer commented 2 years ago

Review Result JKB

General checks

General checks are passed.

Functionality

Kronecker product of two random matrices of homogeneous dimension have been calculated by pykronecker.KroneckerProduct([np.random.rand(n, n), np.random.rand(n, n)]) with values of n up to 150 in this script. Equality check with np.kron and pylops.Kronecker pass.

Performance claims of the paper can not be reproduced due to limited hardware performance. However, perfplot has been used in this script to compare pykronecker with alternative Python libraries mentioned in the paper. pykronecker performs well within these checks.

Documentation

The structure and scope of the documentation are good and appropriate for the size of the package. Installation are given. Examples are given and cover essential use cases. Tests are automated and pass on multiple Python versions. However, a note on how to run the tests, e.g., placed in directory tests/README.md could be an improvement. This file might point towards this Github-actions file. Currently, contributing instructions are missing.

Software paper

The manuscript is well structured. The formulations are precise and catchy. For readers without direct prior knowledge, a basic understanding is created and the subject matter is well motivated. For example, a reader with knowledge on tensor algebra but without direct prior experience with the Kronkecker product or the Kronecker sum of matrices is picked up on the content. PyKronecker is comprehensibly motivated as an efficient implementation of basic operations with a user-friendly interface. Formal and linguistic requirements are met and the list of references is diverse and appears to be complete.

Improvements / Recommendations

[x] See merge-requests and issues mentioned above.
[x] Please extend community guidelines on contributing and bug reporting.

Kevin-Mattheus-Moerman commented 2 years ago

@Kevin-Mattheus-Moerman during the first steps of the review process, I created a merge-request with some small changes instead of raising an issue describing what to change. As this merge-request now has been merged, I am listed as contributor to pykronecker. Formally, does this induce a COI? This question might be a bit pedantic, as such a situation is probably common during the review process. But I am a bit in doubt and therefore ask, following https://github.com/openjournals/joss/blob/main/COI.md .

@JulianKarlBauer this would not be seen as a COI. If however the contribution is large enough to warrant co-authorship then it would be.

JulianKarlBauer commented 2 years ago

...

@JulianKarlBauer this would not be seen as a COI. If however the contribution is large enough to warrant co-authorship then it would be.

Thank you for your assessment. The contributions are minimal, so no COI.

nickelnine37 commented 2 years ago

Thanks @JulianKarlBauer for your time reviewing this. I have now added contributing guidelines here https://github.com/nickelnine37/pykronecker/pull/7

nickelnine37 commented 2 years ago

I have also now added testing instructions in a tests/README file. https://github.com/nickelnine37/pykronecker/pull/8

JulianKarlBauer commented 2 years ago

Thanks @JulianKarlBauer for your time reviewing this. I have now added contributing guidelines here nickelnine37/pykronecker#7

@nickelnine37 Thanks again for adding the contributing guidelines. @Kevin-Mattheus-Moerman All boxes of my review-checklist are ticked.

Kevin-Mattheus-Moerman commented 2 years ago

@JulianKarlBauer great, thanks for your help!

nicoguaro commented 2 years ago

Review checklist for @nicoguaro

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/nickelnine37/pykronecker?
[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 (@nickelnine37) 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?

Kevin-Mattheus-Moerman commented 2 years ago

@JulianKarlBauer, @nicoguaro could you provide an update on review progress? Let me know if you have any questions. Thanks again for your help!

JulianKarlBauer commented 2 years ago

@Kevin-Mattheus-Moerman Review from my side is finished, I recommend acceptance.

Kevin-Mattheus-Moerman commented 2 years ago

Thanks @JulianKarlBauer!

nickelnine37 commented 1 year ago

Hi @Kevin-Mattheus-Moerman, @nicoguaro. I was just wondering whether there are any updates on your side with regard to this. Please let me know if you require any additional information from us.

nicoguaro commented 1 year ago

@nickelnine37, I am running a bit late on paper reviews. I should be getting up to date in the next week.

nickelnine37 commented 1 year ago

@nicoguaro No problem, thank you again for your time.

danielskatz commented 1 year ago

@nicoguaro - how is your review coming?

nicoguaro commented 1 year ago

@danielskatz, I have checked almost all the boxes. I need to go to a different computer to check the tests since they do not work on Windows, which I have on my office computer.

I would also like to play a little bit more... I think I can manage it this week.

nicoguaro commented 1 year ago

@danielskatz, I just successfully ran the tests in a workstation with Linux Mint. I think that we are good to go.

danielskatz commented 1 year ago

@nicoguaro - Can you then check the remaining boxes in your review?

nicoguaro commented 1 year ago

@danielskatz - Done, I forgot last time.

danielskatz commented 1 year ago

Thanks. @Kevin-Mattheus-Moerman - over to you for the last pre-acceptance steps, though I can do the final processing if you want

Kevin-Mattheus-Moerman commented 1 year ago

@nickelnine37 both reviewers now recommend acceptance in JOSS so we are good to move on to formal acceptance. There are a couple of steps needed before we can proceed:

[x] Can you please archive a copy of the software on ZENODO. You can do this manually or using these automated steps: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
[x] Once you have created the ZENODO archive, please report back here with the ZENODO DOI

Please check, and if needed manually edit, the ZENODO archive such that:

[x] The ZENODO archive license matches the software license
[x] The ZENODO archive title matches the JOSS paper title
[x] The author set and order is the same as the JOSS paper
[x] You may edit the author descriptions on ZENODO to include ORCID information (recommended, but not required)
[x] Please let us know if the version tag has moved on, e.g. this review is currently for 0.1.1, but if this needs to be changed let us know. The version tag should match one on your repository and the one listed on the ZENODO archive.

On the paper:

[x] In your affiliation(s) please spell out USA and the UK as United States of America and the United Kingdom.

Kevin-Mattheus-Moerman 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:

nickelnine37 commented 1 year ago

@Kevin-Mattheus-Moerman

Thanks a lot. The DOI is 10.5281/zenodo.7566803. I have moved the version tag on to 0.1.2. The code has not changed at all from v0.1.1, but I believe I had to create a new release in order for it to be registered by Zenodo. I have also just pushed a change to correct the UK/USA issue.

nickelnine37 commented 1 year ago

I have also completed all the items on your checklist, although I am not sure how to mark them as completed (I thought I did last night, but they are unchecked now I look this morning)

nickelnine37 commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

nickelnine37 commented 1 year ago

@Kevin-Mattheus-Moerman @danielskatz Please let me know if there are any further steps I should take at this time.

Kevin-Mattheus-Moerman commented 1 year ago

@nickelnine37 no steps on your end. I'll pick this up shortly. Apologies for the delay.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 10.5281/zenodo.7566803 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7566803

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 0.1.2 as version

editorialbot commented 1 year ago

Done! version is now 0.1.2

Kevin-Mattheus-Moerman 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:

Kevin-Mattheus-Moerman 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

- 10.1109/TNNLS.2017.2727545 is OK
- 10.1016/S0377-0427(00)00393-9 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.softx.2019.100361 is OK
- 10.21105/jcon.00015 is OK
- 10.48550/arXiv.1502.05767 is OK
- 10.1137/141000671 is OK
- 10.2307/3609497 is OK
- 10.1090/s0025-5718-1973-0395196-6 is OK
- 10.1145/355826.355831 is OK
- 10.1109/TC.1981.6312174 is OK
- 10.1145/225545.225548 is OK
- 10.1145/3291041 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/3921, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

openjournals / joss-reviews