[REVIEW]: flowMC: Normalizing-flow enhanced sampling package for probabilistic inference in Jax

[editorialbot]

Submitting author: @kazewong (Kaze W. K. Wong)
Repository: https://github.com/kazewong/flowMC
Branch with paper.md (empty if default branch): 40-joss-paper
Version: 0.1
Editor: @rkurchin
Reviewers: @matt-graham, @daniel-dodd
Archive: 10.5281/zenodo.7706605

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5b60695b2a844550730dd104150d11f1"><img src="https://joss.theoj.org/papers/5b60695b2a844550730dd104150d11f1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5b60695b2a844550730dd104150d11f1/status.svg)](https://joss.theoj.org/papers/5b60695b2a844550730dd104150d11f1)

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

@matt-graham & @daniel-dodd, 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 @rkurchin 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 @Daniel-Dodd

📝 Checklist for @matt-graham

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (416.5 files/s, 58964.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            473            451           1625
Jupyter Notebook                 6              0           2277            681
reStructuredText                10            182            159            244
Markdown                         3             64              0            192
TeX                              1              0              0            179
YAML                             3              6              8             55
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            47            737           2903           3014
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1268

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1073/pnas.2109420119 is OK
- 10.1103/PhysRevD.100.034515 is OK
- 10.1109/TPAMI.2020.2992934 is OK
- 10.1103/PhysRevE.101.023304 is OK
- 10.1103/PhysRevE.101.053312 is OK
- 10.1007/s11222-008-9110-y is OK
- 10.1137/17M1134640 is OK

MISSING DOIs

- 10.1093/mnras/stac2272 may be a valid DOI for title: Accelerating astronomical and cosmological inference with Preconditioned Monte Carlo

INVALID DOIs

- None

[rkurchin]

@kazewong do fix that one missing DOI when you have a moment

Reviewers @matt-graham and @daniel-dodd, let me know if you have any questions about getting your reviews started!

[daniel-dodd]

@editorialbot generate my checklist

[editorialbot]

@daniel-dodd I can't do that because you are not a reviewer

[daniel-dodd]

@daniel-dodd I can't do that because you are not a reviewer

Hi @rkurchin, is there something I should have done before running @editorialbot generate my checklist? Thanks. :)

[danielskatz]

Something seems broken here - let me try a couple of things....

[danielskatz]

@editorialbot remove @daniel-dodd as reviewer

[editorialbot]

@daniel-dodd is not in the reviewers list

[danielskatz]

@editorialbot add @daniel-dodd as reviewer

[editorialbot]

@daniel-dodd added to the reviewers list!

[danielskatz]

@xuanxu - can you see what's going on here with the reviewer list?

[danielskatz]

@daniel-dodd - can you try to generate your checklist again?

[xuanxu]

The problem was that the reviewer added initially in the pre-review issue was @daniel-dodd instead of @Daniel-Dodd, and for the bot those are two different usernames (GitHub shows both cases as the canonical form so it's difficult to see the difference unless you edit the comment)

[daniel-dodd]

Review checklist for @daniel-dodd

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/kazewong/flowMC?
• 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 (@kazewong) 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)?
  • Opened PR (first-pass) edits Joss paper typo edits kazewong/flowMC#80
• 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?

[daniel-dodd]

Thank you, @danielskatz and @xuanxu. :)

[matt-graham]

Review checklist for @matt-graham

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/kazewong/flowMC?
• 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 (@kazewong) 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?

[rkurchin]

Happy New Year, everyone! Hope you had a great holiday. Just a friendly reminder to reviewers @daniel-dodd and @matt-graham to keep working on these reviews and let me know if you have any questions about the process or anything. :)

[rkurchin]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1073/pnas.2109420119 is OK
- 10.1103/PhysRevD.100.034515 is OK
- 10.1109/TPAMI.2020.2992934 is OK
- 10.1103/PhysRevE.101.023304 is OK
- 10.1103/PhysRevE.101.053312 is OK
- 10.1007/s11222-008-9110-y is OK
- 10.1093/mnras/stac2272 is OK
- 10.1137/17M1134640 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[rkurchin]

@editorialbot generate pdf

[editorialbot]

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

[rkurchin]

@editorialbot recommend-accept

[editorialbot]

Paper is not ready for acceptance yet, the archive is missing

[rkurchin]

Thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

1. Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)
2. Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.
3. Post a comment here with the version number and DOI.

@kazewong, make sure to follow these steps so that I can finalize acceptance of this paper!

[kazewong]

@rkurchin The version number is v0.1 https://github.com/kazewong/flowMC/releases/tag/latest and the DOI on zenodo is https://doi.org/10.5281/zenodo.7706605

[rkurchin]

@editorialbot set 0.1 as version

[editorialbot]

Done! version is now 0.1

[rkurchin]

@editorialbot set 10.5281/zenodo.7706605 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7706605

[rkurchin]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[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#4036, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1073/pnas.2109420119 is OK
- 10.1103/PhysRevD.100.034515 is OK
- 10.1109/TPAMI.2020.2992934 is OK
- 10.1103/PhysRevE.101.023304 is OK
- 10.1103/PhysRevE.101.053312 is OK
- 10.1007/s11222-008-9110-y is OK
- 10.1093/mnras/stac2272 is OK
- 10.1137/17M1134640 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.05021 joss-papers#4043
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05021
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...

[arfon]

@matt-graham, @daniel-dodd – many thanks for your reviews here and to @rkurchin 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 ✨

@kazewong – your paper is now accepted and published in JOSS ⚡🚀💥

[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:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05021/status.svg" alt="DOI badge" >
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reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05021/status.svg
   :target: https://doi.org/10.21105/joss.05021

This is how it will look in your documentation:

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