[REVIEW]: normflows: A PyTorch Package for Normalizing Flows

[editorialbot]

Submitting author: @VincentStimper (Vincent Stimper)
Repository: https://github.com/VincentStimper/normalizing-flows
Branch with paper.md (empty if default branch):
Version: v1.7.0
Editor: @mstimberg
Reviewers: @matejgrcic, @kazewong
Archive: 10.5281/zenodo.8027667

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/420c214fa37679e4132c39bd9c09f631"><img src="https://joss.theoj.org/papers/420c214fa37679e4132c39bd9c09f631/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/420c214fa37679e4132c39bd9c09f631/status.svg)](https://joss.theoj.org/papers/420c214fa37679e4132c39bd9c09f631)

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

@matejgrcic & @kazewong, 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 @mstimberg 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 @kazewong

📝 Checklist for @matejgrcic

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (671.1 files/s, 93139.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          71           1392           1439           6213
Jupyter Notebook                12              0           1797           1102
Markdown                         3             79              0            268
TeX                              1             26              0            221
YAML                             4              6              4             82
-------------------------------------------------------------------------------
SUM:                            91           1503           3240           7886
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 836

[editorialbot]

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

[mstimberg]

👋🏼 @VincentStimper, @matejgrcic, @kazewong, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

There are additional guidelines in the message at the start of this issue.

Please don't hesitate to ping me (@mstimberg) if you have any questions/concerns.

[editorialbot]

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

OK DOIs

- 10.4310/CMS.2010.v8.n1.a11 is OK
- 10.1109/TPAMI.2020.2992934 is OK

MISSING DOIs

- 10.1002/cpa.21423 may be a valid DOI for title: A family of nonparametric density estimation algorithms

INVALID DOIs

- None

[kazewong]

Review checklist for @kazewong

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/VincentStimper/normalizing-flows?
• 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 (@VincentStimper) 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?

[matejgrcic]

Review checklist for @matejgrcic

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/VincentStimper/normalizing-flows?
• 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 (@VincentStimper) 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?

[mstimberg]

👋 @kazewong, @matejgrcic no rush for performing the actual review of course, but just checking in to see whether there are any questions on your side or anything else I can do to help you with the review? Please be reminded that JOSS reviews can be iterative, i.e. feel free to open issues or comment here as soon as you come across concerns – there is no need to gather everything into a single review text as commonly done for traditional journals. In the same vein, please feel free to tick boxes in your checklist whenever you are sure about them (the two in the beginning – conflict of interest and code of conduct – would be good first candidates 😉 ). Thanks for your time 🙏 !

[mstimberg]

Hi it's me again 😊 @kazewong, @matejgrcic, how are things going from your side, anything I can do to help? Please note that at JOSS we strive to complete a first round of reviews within 6 weeks, and this review issue has been opened about 4 weeks ago. Could you give me some estimate when you think will be able to perform the review? Thanks a lot, and as always, don't hesitate to ask in case anything about the process is unclear 🙏

PS: I will be travelling for the next two weeks, so my replies might take a bit longer than usual. But as I said earlier, reviews here can be iterative, and authors and reviewers are free to discuss and fix issues without my direct involvement 😉

[kazewong]

@mstimberg I just came back from my work travel. There is a submission deadline this coming Friday, but after that I should be able to start putting in review issues in the repo. That should be aligned with the 6 weeks deadline.

[mstimberg]

@kazewong Thanks for the feedback. If you could finish the review in the week after the submission deadline, that would be perfect! I'll set you up a reminder here, given that I might not be available myself to poke you 😊

[mstimberg]

@editorialbot remind @kazewong in 10 days

[editorialbot]

Reminder set for @kazewong in 10 days

[editorialbot]

👋 @kazewong, please update us on how your review is going (this is an automated reminder).

[mstimberg]

👋 Hi @kazewong, how are things going? Could you please let us know whether you found time to have a look at the software and when you will be able to finish your review 🙏 ?

[mstimberg]

👋 Hi @matejgrcic I've seen that you started your review and checked off a few items in the checklist. Could you let us know when you will be able to finish your review 🙏 ?

[kazewong]

@mstimberg I have some comments for the draft which I am going to start putting them in by the end of today.

[matejgrcic]

Hi @mstimberg, I should finish the review this week.

[mstimberg]

@kazewong and @matejgrcic, thanks for your feedback, looking forward to your reviews/comments 👍

[mstimberg]

Hi @VincentStimper, thanks for the changes and the release, we are almost there! I noticed that the Zenodo record lists the licence "Other" instead of MIT, could you change this manually in the archive metadata (no need for a new release)?

[mstimberg]

@editorialbot set version v1.7.0

[editorialbot]

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

@editorialbot commands

[mstimberg]

@editorialbot set v1.7.0 as version

[editorialbot]

Done! version is now v1.7.0

[mstimberg]

@editorialbot set 10.5281/zenodo.8027667 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8027667

[mstimberg]

@editorialbot generate pdf

[editorialbot]

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

[mstimberg]

Oh, and I'm sorry, but I overlooked it before: would you mind also manually editing the author list in the archive so that it matches the author list of the paper? 🙏

[VincentStimper]

Hi @mstimberg,

I changed the author list and the license.

Best regards,
Vincent

[mstimberg]

Thanks for the changes. Apologies for the nitpicking, but it seems that the Zenodo archive incorrectly associates Bernhard Schölkopf's ORCID with José Miguel Hernández-Lobato. As soon as this is fixed we will be ready to go.

[VincentStimper]

Hi @mstimberg,

thanks for spotting this. Now it's changed.

Best regards,
Vincent

[mstimberg]

Great, all looks good from my side! I will now recommend the paper for submission, and an editor-in-chief will launch the final steps for the publication process.

[mstimberg]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.4310/CMS.2010.v8.n1.a11 is OK
- 10.1002/cpa.21423 is OK
- 10.1126/science.aaw1147 is OK
- 10.1109/TPAMI.2020.2992934 is OK
- 10.48550/arXiv.1711.10604 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#4300, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[gkthiruvathukal]

I will process this shortly. Thank you for your patience!

[gkthiruvathukal]

Everything looks good here. I am proceeding with the final acceptance. Congratulations!

[gkthiruvathukal]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Stimper
  given-names: Vincent
  orcid: "https://orcid.org/0000-0002-4965-4297"
- family-names: Liu
  given-names: David
- family-names: Campbell
  given-names: Andrew
- family-names: Berenz
  given-names: Vincent
- family-names: Ryll
  given-names: Lukas
- family-names: Schölkopf
  given-names: Bernhard
  orcid: "https://orcid.org/0000-0002-8177-0925"
- family-names: Hernández-Lobato
  given-names: José Miguel
doi: 10.5281/zenodo.8027667
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Stimper
    given-names: Vincent
    orcid: "https://orcid.org/0000-0002-4965-4297"
  - family-names: Liu
    given-names: David
  - family-names: Campbell
    given-names: Andrew
  - family-names: Berenz
    given-names: Vincent
  - family-names: Ryll
    given-names: Lukas
  - family-names: Schölkopf
    given-names: Bernhard
    orcid: "https://orcid.org/0000-0002-8177-0925"
  - family-names: Hernández-Lobato
    given-names: José Miguel
  date-published: 2023-06-24
  doi: 10.21105/joss.05361
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5361
  title: "normflows: A PyTorch Package for Normalizing Flows"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05361"
  volume: 8
title: "normflows: A PyTorch Package for Normalizing Flows"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05361 joss-papers#4343
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05361
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05361/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05361/status.svg
   :target: https://doi.org/10.21105/joss.05361

This is how it will look in your documentation:

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