[REVIEW]: SGMCMCJax: a lightweight JAX library for stochastic gradient Markov chain Monte Carlo algorithms

[whedon]

Submitting author: @jeremiecoullon (Jeremie Coullon)
Repository: https://github.com/jeremiecoullon/SGMCMCJax
Branch with paper.md (empty if default branch):
Version: v0.2.12
Editor: @dfm
Reviewers: @canyon289, @ColCarroll
Archive: 10.5281/zenodo.6460681

⚠️ JOSS reduced service mode ⚠️

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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

@canyon289 & @ColCarroll, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @canyon289

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@jeremiecoullon) 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 and who the target audience is?
• 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?

Review checklist for @ColCarroll

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@jeremiecoullon) 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @canyon289, @ColCarroll it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 704

[whedon]

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

OK DOIs

- 10.18637/jss.v091.i03 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.29 s (146.1 files/s, 15822.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          22            319            139           1151
Jupyter Notebook                 7              0           1769            334
reStructuredText                 6            226             92            266
TeX                              1              5              0            123
Markdown                         2             47              0            108
DOS Batch                        1              8              1             26
INI                              2              6              0             13
make                             2              5              7             13
-------------------------------------------------------------------------------
SUM:                            43            616           2008           2034
-------------------------------------------------------------------------------


Statistical information for the repository '90cd66425854a5c498f05574' was
gathered on 2022/01/30.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jeremie Coullon                 66          3010           1471           97.39
Kevin Murphy                     3            95             25            2.61

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Jeremie Coullon            1520           50.5          1.2                6.45
Kevin Murphy                 89           93.7          0.1                8.99

[whedon]

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

[dfm]

@ColCarroll, @canyon289, @jeremiecoullon — This is the review thread for the paper. All of our communications will happen here from now on. Thanks again for agreeing to participate!

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4113 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[canyon289]

@jeremiecoullon
I left my initial set of comments. Do know that the issue tickets are biased towards issues. Overall the library is quite easy to navigate and understand given all the code examples. I also am quite excited to see a comprehensive library of SHGMCMC implementations, and the hope that others will contribute more as the field advances.

For the issues reported I see no major deficiencies, just smaller additions or fixes that are needed in a couple of spots. I'm happy add any additional feedback if you need it, or to discuss further if you would find that helpful.

Remaining in my review is the assessment of functionality. I plan to get to it soon but am not anticipating any issues.

Thanks for contributing such a nice library to the open source statistics community

[jeremiecoullon]

@canyon289 : thanks very much for these comments! I will start addressing these today.

[whedon]

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

[whedon]

👋 @canyon289, please update us on how your review is going (this is an automated reminder).

[canyon289]

👋 @canyon289, please update us on how your review is going (this is an automated reminder).

I plan on assessing functionality this week. With all the examples and documentation I am not concerned at all, the library looks great

[dfm]

@canyon289: Thanks! And sorry about the bot reminder - it sends that regardless of the fact that you only just commented.

[ColCarroll]

+1 started, and hoping to be done this week!

[ColCarroll]

Update: I've completed my first round of reviews, and will wait for @jeremiecoullon to address the opened issues. No rush from me there, but I will not be imminently opening new issues, and will just be watching for discussion on the open ones!

[jeremiecoullon]

@whedon generate pdf

[editorialbot]

My name is now @editorialbot

[editorialbot]

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

[dfm]

@jeremiecoullon — I just wanted to check in to make sure that you don't have any questions wrt the final steps listed above. Let me know if you run into any issues!

[jeremiecoullon]

@dfm Thanks for checking in! I just never got round to it (stuff piled on recently..). I'll get to it soon so we can finish this up :)

[jeremiecoullon]

@dfm : I finally finished this :)

1. I read through the paper a final time; looks good
2. Release version: 0.2.12
3. Zenodo DOI: 10.5281/zenodo.6460681

Zenodo archived link: https://zenodo.org/record/6460681

Let me know if something is missing!

[dfm]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.18637/jss.v091.i03 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[dfm]

@editorialbot generate pdf

[dfm]

@editorialbot set 10.5281/zenodo.6460681 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6460681

[editorialbot]

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

[dfm]

@editorialbot set v0.2.12 as version

[editorialbot]

Done! version is now v0.2.12

[dfm]

@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

- 10.18637/jss.v091.i03 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3131

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3131, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[dfm]

@jeremiecoullon — I've now handed this off to the managing editors to do the final processing. There may be some final edits or other changes, but the process should be fairly quick. Thanks again for your submission and for your responses to all the suggestions from @canyon289 and @ColCarroll!

@canyon289, @ColCarroll — Thanks again for your reviews of this submission. Thanks for the time that you took and the thorough and constructive comments that you made. We couldn't do this without you, and I really appreciate you volunteering your time!!

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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.04113 joss-papers#3137
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04113
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]

@canyon289, @ColCarroll – many thanks for your reviews here and to @dfm 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 ✨

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

[editorialbot]

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