[REVIEW]: kep_solver: A Python package for kidney exchange programme exploration

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@WPettersson@jmschrei<!--end-editor-- Reviewers: @arianesasso, @igarizio Archive: 10.5281/zenodo.7369472

Status

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Markdown: [![status](https://joss.theoj.org/papers/46198c037f6e26fbb0e098a15cf730af/status.svg)](https://joss.theoj.org/papers/46198c037f6e26fbb0e098a15cf730af)

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

@arianesasso & @igarizio, 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 @jmschrei 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 @igarizio

📝 Checklist for @arianesasso

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:

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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 commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.87 s (90.1 files/s, 444574.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            38              5              0         377130
Python                          15            828            967           3446
XML                              8              0              0            476
Markdown                         5            154              0            379
reStructuredText                 4             78            192            237
Jupyter Notebook                 2              0            580            170
TeX                              1              8              0             77
YAML                             2             10              1             52
make                             1              4              7              9
TOML                             1              1              0              3
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                            78           1088           1747         381981
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 983

editorialbot commented 2 years ago

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

OK DOIs

- 10.1111/ajt.14702 is OK
- 10.1111/ajt.14124 is OK
- 10.1111/j.1600-6143.2010.03021.x is OK
- 10.1016/j.cor.2022.105707 is OK
- j.geb.2015.01.001 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/2615731.2617407 is INVALID

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:

jmschrei commented 2 years ago

Howdy @arianesasso and @igarizio!

Thanks for agreeing to review this submission.

The process for conducting a review is outlined above. Please run the command shown above to have @editorialbot generate your checklist, which will give a step-by-step process for conducting your review. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.

Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html And here is a checklist, similar to above: https://joss.readthedocs.io/en/latest/review_checklist.html

Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!

igarizio commented 1 year ago

Review checklist for @igarizio

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://gitlab.com/wpettersson/kep_solver?
[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 (@WPettersson) 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?

jmschrei commented 1 year ago

Hi @arianesasso, just checking to make sure this is still on your radar.

arianesasso commented 1 year ago

Hi @jmschrei, sorry, I will add my checklist before the end of this week.

jmschrei commented 1 year ago

Great, thanks!

arianesasso commented 1 year ago

Review checklist for @arianesasso

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://gitlab.com/wpettersson/kep_solver?
[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 (@WPettersson) 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?

arianesasso commented 1 year ago

Dear @WPettersson,

First, thank you for submitting your software/paper to JOSS! I am honored to be its reviewer :). It takes a lot of effort to build something like this.

I am adding my review issues to your GitLab issue tracker page. You can follow a summary of them here: GitLab Issues

I just finished my review for now and listed the issues. Please, feel free to comment here or on any of the issues in your repository. I am happy to discuss any of those with you!

WPettersson commented 1 year ago

Dear @arianesasso I've responded to all your comments on the Gitlab issues page - thank you for the excellent feedback and I have incorporated your suggested changes and hopefully addressed all the issues.

arianesasso commented 1 year ago

@WPettersson thank you for the great work! I just checked all the changes, and I have nothing else to add :).

@jmschrei I believe my checklist is finished and I am satisfied with the changes made by @WPettersson.

jmschrei commented 1 year ago

Great, thanks @arianesasso !

igarizio commented 1 year ago

Hi everyone! My checklist is complete. Thanks again @WPettersson for the submission! 🎉

jmschrei commented 1 year ago

Great, thanks!

jmschrei commented 1 year ago

@WPettersson do you have a DOI (e.g. from Zenodo) for the project and a specific version of the code you want tagged?

jmschrei 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

- 10.1111/ajt.14702 is OK
- 10.1111/ajt.14124 is OK
- 10.1111/j.1600-6143.2010.03021.x is OK
- 10.1016/j.cor.2022.105707 is OK
- j.geb.2015.01.001 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/2615731.2617407 is INVALID

jmschrei 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:

jmschrei commented 1 year ago

Would you also mind looking into the invalid DOI?

WPettersson commented 1 year ago

Oh, totally forgot about that DOI thing, I was going to mention it earlier. That's from this paper which (as best I can tell) does not have a DOI, but is also the recommended citation for the particular repository mentioned in the paper (the repository in question). If I remove the DOI completely, it'll still warn about a missing DOI - should I remove the citation and link to repository completely instead? Or is it okay to have a reference that doesn't have a DOI.

For versioning, version 2.1.1 is the latest and is the version the reviewers approved, so makes most sense to use that.

Also I don't have a DOI at the moment - I didn't know whether that would conflict with what JoSS does. I can obtain one if that'd help.

jmschrei commented 1 year ago

Hm. I'll leave that DOI question to the EiC.

Yeah, we need a DOI to publish the work. It should contain the entire repository and the paper.

WPettersson commented 1 year ago

Okay, I have a DOI now: 10.5281/zenodo.7369472

jmschrei commented 1 year ago

@editorialbot set v2.1.1 as version

editorialbot commented 1 year ago

Done! version is now v2.1.1

jmschrei commented 1 year ago

@editorialbot set https://doi.org/10.5281/zenodo.7369472 as archive

editorialbot commented 1 year ago

Done! Archive is now https://doi.org/10.5281/zenodo.7369472

jmschrei 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

- 10.1111/ajt.14702 is OK
- 10.1111/ajt.14124 is OK
- 10.1111/j.1600-6143.2010.03021.x is OK
- 10.1016/j.cor.2022.105707 is OK
- j.geb.2015.01.001 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/2615731.2617407 is INVALID

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'j.geb.2015.01.001' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

WPettersson commented 1 year ago

Huh, odd that it failed that but not earlier. Anyway, I can add 10.1016/ to the front of that DOI in the references if needed?

jmschrei commented 1 year ago

Yes, that would be helpful. Thanks!

WPettersson commented 1 year ago

Okay, I've pushed commits to fix that DOI, and to remove that invalid DOI. Seeing as the bot didn't complain about the other paper without a DOI, I figured that it should still work.

However, the zenodo data is now very-slightly out of date. Is that going to cause problems?

jmschrei commented 1 year ago

I don't think so, but if you'd like to get a new DOI I can assign that one.

WPettersson commented 1 year ago

I think it's best to leave it with the current DOI then, I don't really want two DOIs when the difference is so small.

arfon 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

- 10.1111/ajt.14702 is OK
- 10.1111/ajt.14124 is OK
- 10.1111/j.1600-6143.2010.03021.x is OK
- 10.1016/j.cor.2022.105707 is OK
- 10.1016/j.geb.2015.01.001 is OK

MISSING DOIs

- 10.1097/00007890-201407151-02779 may be a valid DOI for title: Price of Fairness in Kidney Exchange

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/bcm-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/3761, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 1 year ago

Looks like the DOIs are looking good now 👍

WPettersson commented 1 year ago

Huh, I never knew that that journal accepted such short papers. Anyway, if people want me to, I can now change that citation to the new one from the journal, which has a DOI. I'll probably do so anyway, but in case it messes up submission processes I'll hold off for the time being.

Kevin-Mattheus-Moerman commented 1 year ago

@WPettersson I am the AEiC of this track and here to help process this work for acceptance. Can you clarify what you mean by:

Anyway, if people want me to, I can now change that citation to the new one from the journal, which has a DOI.

If there is an update needed to a citation/DOI please do so now before we proceed. I also have one minor comment, see below:

[x] In your affiliation, please write United Kingdom instead of UK.

WPettersson commented 1 year ago

I've pushed two commits, one to updated the affiliation, and a second that changes the citation to one from a journal with a DOI. The short version is the cited paper has two possible citations; the first of these does not have a DOI and I did not realise it was also accepted a second time.

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

@WPettersson all looks good now. I will proceed now with formal acceptance.

openjournals / joss-reviews