[REVIEW]: GRAPL: A computational library for nonparametric structural causal modelling, analysis and inference

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@max-little@Nikoleta-v3<!--end-editor-- Reviewers: @Athene-ai, @fAndreuzzi Archive: 10.5281/zenodo.6959433

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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

@Athene-ai & @fAndreuzzi, 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 @Nikoleta-v3 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 @Athene-ai

📝 Checklist for @fAndreuzzi

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

:wave: @openjournals/joss-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/3412, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 2 years ago

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

OK DOIs

- 10.1017/S0266466603004109 is OK
- 10.1145/3501714.3501743 is OK
- 10.3389/fnagi.2020.553635 is OK

MISSING DOIs

- None

INVALID DOIs

- None

max-little commented 2 years ago

Great, thanks @Nikoleta-v3 . Is there anything I need to do at this point?

Nikoleta-v3 commented 2 years ago

Nothing else you can do for now 😃 I pinged the editorial board. One of the editors will check that everything is okay with the paper, and then publish it. They might have a few more comments but at this point they will be very minor.

max-little commented 2 years ago

Excellent, thank you!

arfon commented 2 years ago

@Nikoleta-v3 @Athene-ai – can you confirm that @Athene-ai completed a full review here? I don't see a checklist for them anywhere in this thread.

Athene-ai commented 2 years ago

Review checklist for @Athene-ai

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/max-little/GRAPL?
[ ] 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 (@max-little) 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

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?

Athene-ai commented 2 years ago

Review checklist for @Athene-ai

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/max-little/GRAPL?
[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 (@max-little) 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

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?
[ ] 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?

arfon commented 2 years ago

@Nikoleta-v3 @Athene-ai – can you confirm that @Athene-ai completed a full review here? I don't see a checklist for them anywhere in this thread.

...and now we have one. Thanks @Athene-ai!

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/3415
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04534
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@Athene-ai, @fAndreuzzi – many thanks for your reviews here and to @Nikoleta-v3 for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@max-little – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 2 years ago

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max-little commented 2 years ago

Thanks @Nikoleta-v3 , @fAndreuzzi , @Athene-ai , @arfon , very much appreciated. Happy to contribute as a reviewer, if you can use my help, do let me know. All the best Max

Athene-ai commented 2 years ago

Happy to contribute as a reviewer, if you can use my help, do let me know !😉

max-little commented 1 year ago

Yes, most meaning what is going to be used by the user. You should document also classes, as they support docstrings too.

OK I'll do that, it's basically going to be all methods/functions and classes.

I would also suggest to split functions into smaller, more maintainable ones, it looks quite weird and dangerous to me that you don't have functions which are not going to be used by the user. Even if you do not share any code among different functions, you should try to pack your logic into smaller, single-responsibility functions.

As I've said, there are no functions/methods which should not be accessed by the user. This is the logic of structural causal modelling and inference. Can you perhaps explain to me which parts of the functionality of the software shouldn't be accessed by the user, and give a convincing reason why, in terms of the logic of structural causal modelling and inference?

Best Max

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

-- Max Little (www.maxlittle.net) Associate Professor, University of Birmingham Turing Fellow, Alan Turing Institute TED Fellow (fellows.ted.com/profiles/max-little) Visiting Associate Professor, MIT Author: Machine Learning for Signal Processing, Oxford University Press global.oup.com/academic/product/machine-learning-for-signal-processing-9780198714934 Room 138, School of Computer Science University of Birmingham Birmingham B15 2TT UK +44 7710 609564 Skype: dr.max.little

fandreuz commented 1 year ago

So let's start another review round @max-little ? :smile:

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