[REVIEW]: UltraNest - a robust, general purpose Bayesian inference engine

[whedon]

Submitting author: @JohannesBuchner (Johannes Buchner)
Repository: https://github.com/JohannesBuchner/UltraNest/
Version: v3.2.0
Editor: @fboehm
Reviewer: @mattpitkin, @ziatdinovmax
Archive: 10.5281/zenodo.4653423

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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.)

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Review checklist for @mattpitkin

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 (@JohannesBuchner) 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: Do the authors clearly state 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 @ziatdinovmax

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 (@JohannesBuchner) 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: Do the authors clearly state 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. @mattpitkin, @ziatdinovmax 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.

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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 a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3001 with the following error:

Can't find any papers to compile :-(

[mattpitkin]

@JohannesBuchner for the conda installation instructions in the documentation can you add that you need to explicitly specify the conda-forge channel, e.g., either:

conda install -c conda-forge ultranest

or

conda config --add channels conda-forge
conda install ultranest

[mattpitkin]

@JohannesBuchner can you merge the joss-paper branch of the ultranest repo into master so that the paper can be compiled?

[JohannesBuchner]

I'd rather not, I understood I can use a branch https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements

Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository together with your software (although they may be in a short-lived branch which is never merged with the default).

[JohannesBuchner]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

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

[mattpitkin]

@JohannesBuchner thanks for regenerating. I hadn't realised there was a method to generate it from a different branch!

[mattpitkin]

@JohannesBuchner can you add the DOI https://doi.org/10.1021/acs.jctc.9b00567 for the Griffiths & Wales paper? Can you also update the Higson, Handley, Hobson & Lasenby paper to the published version as given here?

[mattpitkin]

Minor paper comments:

• line 16: typo "contraining" to "constraining"
• line 17: remove comma after "open source"
• line 31: either remove "also" or move it to read "also performs well"
• line 32: maybe change to say "The variants include developments related to: ..." or something similar.
• line 46: remove "also"
• line 49: explain what a "live point" is.
• line 49: "A inverse" to "An inverse"
• line 50: "converts" to "converts these live points", and "and the likelihood L evaluated." to "and the likelihood L is evaluated at each point."
• line 69: "estimate" to "estimates"
• line 71: should "integrators" be "integrator"? If not change "integrators is" to "integrators are".

[fboehm]

Hello, @ziatdinovmax - How is the review going? Please feel free to make comments in this thread. Also, please feel free to "@" mention me. I can try to help with any issues or clarifications.

thanks again!

[ziatdinovmax]

@fboehm My apologies for the delay on my end. I will add my comments shortly.

[whedon]

👋 @ziatdinovmax, please update us on how your review is going.

[whedon]

👋 @mattpitkin, please update us on how your review is going.

[mattpitkin]

@whedon @fboehm I'm just waiting on @JohannesBuchner to address my above minor comments on the paper and then I can sign-off the review.

[whedon]

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

@whedon commands

[ziatdinovmax]

@fboehm

Here you go:

In their package/paper, J. Buchner introduces a general-purpose Bayesian-inference approach for parameter estimation and model comparison. I was able to easily install the package and reproduce the examples in tutorials. The paper itself is written in a clear and concise manner. My only suggestion is to improve documentation of individual functions according to one of the accepted styles (reST, Google-style, Numpydoc, etc.). For example, currently, most of the package's functions just have this

"""This function does this and that"""

But it should be expanded to something like this:

"""
This function does this and that.

Args:
    param1: This is the first param.
    param2: This is a second param.

Returns:
    This is a description of what is returned.
"""

After this I will be happy to recommend the acceptance of this paper.

[JohannesBuchner]

I haven't had time yet to address Matt's comment, but just as a quick reply: This convention is from PEP 257, section "One-line Docstrings". I use it for simple functions where I believed the function name, the argument names and the one-line docstring give sufficient documentation. If you have a list of functions which are unclear, I am happy to expand the documentation.

[fboehm]

@JohannesBuchner - Would it be feasible to update the documentation as suggested by @ziatdinovmax? I get the impression that the suggestion is more comprehensive than what is currently written. THanks!

[mattpitkin]

@JohannesBuchner thanks for the updates. If you could just address #3001 (comment) I'll sign-off my final tick box for the review.

[whedon]

I'm sorry @JohannesBuchner, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[JohannesBuchner]

Ah ok, wasn't sure if that was for me. All ready from my side.

[kthyng]

So why is there a giant pile of missing or invalid dois?

[kthyng]

@JohannesBuchner I'm looking at your Zenodo archives and they look out of order. The most recent one is associated with an older version of the code. Can I verify this is the correct DOI even though Zenodo tells me there is a more recent one when I click on it: 10.5281/zenodo.4636924.

[kthyng]

@JohannesBuchner Just a couple of notes for your paper:

• there is a typo in the 2nd paragraph: chose > choose.
• why are there extra periods in the [2] affiliation line?

[fboehm]

So why is there a giant pile of missing or invalid dois?

@kthyng - I verified that the dois in the generated pdf work. Should I also be concerned with the output of whedon's check on references? I had thought that it was imperfect. I don't know the algorithm that whedon uses for reference check. Does it look a the bib file? Do we need the bib file to contain only those references that are used in paper.md? Or is it ok if the bib file has unused references?

[JohannesBuchner]

@JohannesBuchner I'm looking at your Zenodo archives and they look out of order. The most recent one is associated with an older version of the code. Can I verify this is the correct DOI even though Zenodo tells me there is a more recent one when I click on it: 10.5281/zenodo.4636924.

Thanks, I think zenodo got confused there because I did a bunch at the same time.

The latest version is now 3.2.0.
doi: 10.5281/zenodo.4653423

[JohannesBuchner]

@whedon set v3.2.0 as version

[whedon]

I'm sorry @JohannesBuchner, I'm afraid I can't do that. That's something only editors are allowed to do.

[JohannesBuchner]

@JohannesBuchner Just a couple of notes for your paper:

* there is a typo in the 2nd paragraph: chose > choose.

* why are there extra periods in the [2] affiliation line?

Thank you, these are fixed in the updated branch.

[JohannesBuchner]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

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

[fboehm]

@whedon set v3.2.0 as version

[whedon]

OK. v3.2.0 is the version.

[fboehm]

@whedon set 10.5281/zenodo.4653423 as archive

[whedon]

OK. 10.5281/zenodo.4653423 is the archive.

[kthyng]

@fboehm @JohannesBuchner As long as the DOIs in the paper are ok, it is fine. I would be remiss not to check in though with the unusual listing of doi's coming through our whedon check.

[kthyng]

Looks like everything is in order now!

[kthyng]

@whedon accept deposit=true from branch joss-paper

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03001 joss-papers#2176
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.03001
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...

[kthyng]

Congrats on your new publication @JohannesBuchner! Thanks to editor @fboehm and reviewers @mattpitkin and @ziatdinovmax for your hard work, time, and expertise!!

[whedon]

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

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[JohannesBuchner]

Many thanks @mattpitkin and @ziatdinovmax for your useful comments, and @fboehm for the guidance through the process. It helped me a lot, as this was my first submission!