[REVIEW]: PyVBMC: Efficient Bayesian inference in Python #5428

editorialbot · 2023-05-01T14:19:34Z

Submitting author: @Bobby-Huggins (Bobby Huggins)
Repository: https://github.com/acerbilab/pyvbmc
Branch with paper.md (empty if default branch): joss-submission
Version: 1.0.1
Editor: @rkurchin
Reviewers: @matt-graham, @isdanni
Archive: 10.5281/zenodo.7966315

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/cfa9269922f94c81d1bfcb0733365a19/status.svg)](https://joss.theoj.org/papers/cfa9269922f94c81d1bfcb0733365a19)

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 & @isdanni, 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 @isdanni

📝 Checklist for @matt-graham

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-05-01T14:19:36Z

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 · 2023-05-01T14:19:46Z

Software report:

github.com/AlDanial/cloc v 1.88  T=1.07 s (165.2 files/s, 480635.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         109           3579           4894          16418
TeX                              3             73             16            732
SVG                              1              0              0            539
Jupyter Notebook                 6              0         485913            411
INI                              4              0              0            380
reStructuredText                27            231            179            367
Markdown                        12            114              0            344
YAML                             6             31              5            224
MATLAB                           3             21             14            126
TOML                             1              9              3             57
DOS Batch                        1             10              1             39
make                             2             11             15             30
CSS                              2              6              0             29
-------------------------------------------------------------------------------
SUM:                           177           4085         491040          19696
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-05-01T14:19:47Z

Wordcount for paper.md is 1345

editorialbot · 2023-05-01T14:19:50Z

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

OK DOIs

- 10.7554/eLife.55365 is OK
- 10.1016/j.anucene.2020.108046 is OK
- 10.1007/s40857-022-00277-2 is OK
- 10.3390/pharmaceutics14040749 is OK
- 10.1162/neco_a_01127 is OK
- 10.1214/20-BA1200 is OK
- 10.1016/0378-3758(91)90002-V is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-01T14:21:16Z

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

isdanni · 2023-05-01T19:32:05Z

Review checklist for @isdanni

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/acerbilab/pyvbmc?
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 (@Bobby-Huggins) 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?

matt-graham · 2023-05-02T09:50:59Z

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/acerbilab/pyvbmc?
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 (@Bobby-Huggins) 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 · 2023-05-12T21:53:57Z

🔔 Hi all, checking in on progress here!

isdanni · 2023-05-12T22:30:50Z

🔔 Hi all, checking in on progress here!

Thanks for the reminder! I will finish the initial round of review by this weekend.

matt-graham · 2023-05-19T07:34:41Z

🔔 Hi all, checking in on progress here!

Hi @rkurchin. I've now completed my review checklist and all the issues I raised while reviewing the code and documentation have now been addressed by the authors, so from my perspective no further changes needed.

isdanni · 2023-05-19T14:58:48Z

I also have no further questions. Functionality and performance features are confirmed as well.

rkurchin · 2023-05-23T20:12:35Z

rkurchin · 2023-05-23T20:12:47Z

@editorialbot check references

editorialbot · 2023-05-23T20:13:10Z

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

OK DOIs

- 10.7554/eLife.55365 is OK
- 10.1016/j.anucene.2020.108046 is OK
- 10.1007/s40857-022-00277-2 is OK
- 10.3390/pharmaceutics14040749 is OK
- 10.1162/neco_a_01127 is OK
- 10.1214/20-BA1200 is OK
- 10.1016/0378-3758(91)90002-V is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin · 2023-05-23T20:15:19Z

@editorialbot generate pdf

editorialbot · 2023-05-23T20:17:08Z

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

rkurchin · 2023-05-23T20:37:23Z

Some final steps here (see checklist above):

Does Mikko J. Arnos have an ORCID and if so, could you add it to the manuscript?
Please 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!)
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.
Post a comment here with the version number and DOI.

I'll post some editorial feedback on the manuscript itself shortly.

rkurchin · 2023-05-23T20:55:42Z

Editorial comments on manuscript (very nicely written, this is by far the fewest editorial comments I've ever given! 🤩):

line 39: sample efficiency doesn't need to be hyphenated here
59: the bit starting from "For example:" is a sentence fragment. Could just join to previous sentence with commas, or perhaps break out into a bulleted list?
62: unfeasible -> infeasible

As a separate remark, this looks like really cool software and actually may be just the tool I need for some of my own work, so I'll likely start playing around with it myself! 😁

Bobby-Huggins · 2023-05-24T08:12:37Z

Thanks @matt-graham and @isdanni for the review, and thanks @rkurchin for the feedback and kind remarks! Glad to hear we might have found another user 🙂 I have just updated the paper with your comments.

Mikko does not have an ORCID, but I will complete the other steps shortly and comment with the DOI + version number.

Bobby-Huggins · 2023-05-25T06:41:02Z

@editorialbot generate pdf

Bobby-Huggins · 2023-05-25T06:42:13Z

@rkurchin no problem, thanks for catching these, they should be fixed now.

editorialbot · 2023-05-25T06:42:21Z

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

rkurchin · 2023-05-25T19:10:49Z

@editorialbot recommend-accept

editorialbot · 2023-05-25T19:10:51Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-25T19:11:09Z

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

OK DOIs

- 10.7554/eLife.55365 is OK
- 10.1016/j.anucene.2020.108046 is OK
- 10.1007/s40857-022-00277-2 is OK
- 10.3390/pharmaceutics14040749 is OK
- 10.1162/neco_a_01127 is OK
- 10.1214/20-BA1200 is OK
- 10.1016/0378-3758(91)90002-V is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-25T19:12:58Z

👋 @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#4268, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Bobby-Huggins · 2023-06-04T08:06:59Z

Hi, I just wanted to double-check that you don't need any further action on our end, for the moment (the final proof looks good to me).

gkthiruvathukal · 2023-06-04T14:00:36Z

@Bobby-Huggins Yes, I will be able to take things from here. Thanks!

gkthiruvathukal · 2023-06-21T01:23:38Z

@editorialbot accept

editorialbot · 2023-06-21T01:23:40Z

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

editorialbot · 2023-06-21T01:25:58Z

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: Huggins
  given-names: Bobby
  orcid: "https://orcid.org/0009-0006-3475-5964"
- family-names: Li
  given-names: Chengkun
  orcid: "https://orcid.org/0000-0001-5848-910X"
- family-names: Tobaben
  given-names: Marlon
  orcid: "https://orcid.org/0000-0002-9778-0853"
- family-names: Aarnos
  given-names: Mikko J.
- family-names: Acerbi
  given-names: Luigi
  orcid: "https://orcid.org/0000-0001-7471-7336"
contact:
- family-names: Huggins
  given-names: Bobby
  orcid: "https://orcid.org/0009-0006-3475-5964"
- family-names: Acerbi
  given-names: Luigi
  orcid: "https://orcid.org/0000-0001-7471-7336"
doi: 10.5281/zenodo.7966315
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Huggins
    given-names: Bobby
    orcid: "https://orcid.org/0009-0006-3475-5964"
  - family-names: Li
    given-names: Chengkun
    orcid: "https://orcid.org/0000-0001-5848-910X"
  - family-names: Tobaben
    given-names: Marlon
    orcid: "https://orcid.org/0000-0002-9778-0853"
  - family-names: Aarnos
    given-names: Mikko J.
  - family-names: Acerbi
    given-names: Luigi
    orcid: "https://orcid.org/0000-0001-7471-7336"
  date-published: 2023-06-21
  doi: 10.21105/joss.05428
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5428
  title: "PyVBMC: Efficient Bayesian inference in Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05428"
  volume: 8
title: "PyVBMC: Efficient Bayesian inference in Python"

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 · 2023-06-21T01:26:09Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-06-21T01:26:10Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-06-21T01:26:11Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05428 joss-papers#4329
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05428
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Bobby-Huggins · 2023-06-21T15:44:01Z

Thanks everyone for the smooth review process! Everything looks good to me, but I don't see an option to close the issue on my end.

gkthiruvathukal · 2023-06-24T19:34:19Z

@Bobby-Huggins I will take care of this! Congratulations!!

editorialbot · 2023-06-24T19:34:39Z

🎉🎉🎉 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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  <img src="https://joss.theoj.org/papers/10.21105/joss.05428/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05428/status.svg
   :target: https://doi.org/10.21105/joss.05428

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homerjed · 2025-01-28T08:22:32Z

👋 @Bobby-Huggins, the editorialbot has listed you as a potential reviewer (see here #7634) for my software submission (https://github.com/homerjed/sbgm). If you are available, would you consider reviewing? Cheers!

editorialbot added CSS Makefile review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels May 1, 2023

editorialbot assigned rkurchin May 1, 2023

editorialbot mentioned this issue May 1, 2023

[PRE REVIEW]: PyVBMC: Efficient Bayesian inference in Python #5285

Closed

matt-graham mentioned this issue May 3, 2023

test_minimize_adam_matyas_with_noise intermittently failing acerbilab/pyvbmc#135

Closed

This was referenced May 16, 2023

Some possible mistakes in docstring for VBMC class acerbilab/pyvbmc#136

Closed

ValueError raised in FunctionLogger when target density is zero acerbilab/pyvbmc#137

Closed

Some options appear to not have any effect acerbilab/pyvbmc#139

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 25, 2023

editorialbot added accepted published Papers published in JOSS labels Jun 21, 2023

gkthiruvathukal closed this as completed Jun 24, 2023

editorialbot mentioned this issue Oct 19, 2024

[PRE REVIEW]: hetGPy: Heteroskedastic Gaussian Process Modeling in Python #7374

Closed

editorialbot mentioned this issue Nov 4, 2024

[PRE REVIEW]: sbi reloaded: a toolkit for simulation-based inference workflows #7428

Closed

This was referenced Jan 8, 2025

[PRE REVIEW]: SBGM: Score-based diffusion models in JAX #7634

Open

[PRE REVIEW]: PyBOP: A Python package for battery model optimisation and parameterisation #7653

Closed

editorialbot mentioned this issue Mar 5, 2025

[PRE REVIEW]: PolytopeWalk: Sparse MCMC Sampling over Polytopes #7872

Closed

editorialbot mentioned this issue Mar 15, 2025

[PRE REVIEW]: MultiVae: A Python package for Multimodal Variational Autoencoders on Partial Datasets. #7905

Closed

editorialbot mentioned this issue Apr 25, 2025

[PRE REVIEW]: Bamojax: Bayesian Modelling with JAX #8104

Open

[REVIEW]: PyVBMC: Efficient Bayesian inference in Python #5428

[REVIEW]: PyVBMC: Efficient Bayesian inference in Python #5428

Comments

editorialbot commented May 1, 2023 • edited Loading

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Reviewer instructions & questions

Checklists

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isdanni commented May 1, 2023 • edited Loading

Review checklist for @isdanni

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

matt-graham commented May 2, 2023 • edited Loading

Review checklist for @matt-graham

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented May 12, 2023

isdanni commented May 12, 2023

matt-graham commented May 19, 2023

isdanni commented May 19, 2023

rkurchin commented May 23, 2023 • edited Loading

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

rkurchin commented May 23, 2023

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Bobby-Huggins commented Jun 4, 2023

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