Joss-reviews: [REVIEW]: ArviZ a unified library for exploratory analysis of Bayesian models in Python

[whedon]

Submitting author: @canyon289 (Ravin Kumar)
Repository: https://github.com/arviz-devs/arviz
Version: v.31
Editor: @arfon
Reviewer: @malmaud , @mattpitkin
Archive: 10.5281/zenodo.2540945

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/83e0e4048aa30a256a89f3b35b90f065/status.svg)](http://joss.theoj.org/papers/83e0e4048aa30a256a89f3b35b90f065)

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) 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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @malmaud

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v.31)?
• [x] Authorship: Has the submitting author (@canyon289) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @mattpitkin

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v.31)?
• [x] Authorship: Has the submitting author (@canyon289) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @canyon289, it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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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1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arfon]

@malmaud , @mattpitkin - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

[malmaud]

OK, I've played with all the functionality of the software on my own device - everything works well, the utility is clear, and the documentation is comprehensive (albeit with a few minor typos). I think this is an easy accept after just a few tiny fixes:

• Fix https://github.com/arviz-devs/arviz/issues/481
• In the paper, Rabin's affiliation is listed as 'None'. Is that really true, or is there a workplace you could list?
• Period missing after '...analyzes"', and I think you want 'analyses' there.
• A figure showing a gallery of plot types would be a useful addition to the paper.
• Figure 1 isn't referenced in the text of the paper and its caption isn't particularly informative. The paragraph that talks about soring datasets on disks should reference that figure and its caption should be made informative.

[canyon289]

@malmaud

Thanks for the feedback. A PR is open, just waiting for feedback internally before we submit it again for review to you.

https://github.com/arviz-devs/arviz/pull/483

[canyon289]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[canyon289]

@malmaud The content is ready to review but the example plots seems to have rendered oddly. Is there a way I can see what command whedon is running to compile the pdf so I can test locally?

Also do you have a suggestion on where to place the example gallery, relative to the other headings?

[mattpitkin]

@canyon289 you can see a Makefile with an example of how you can locally generate a LaTeX file and pdf from the markdown doc here.

[canyon289]

Tried getting the PDF to render correctly I think we might have figured it out

PR for reference
https://github.com/arviz-devs/arviz/pull/484

Here it goes

@whedon generate pdf

[canyon289]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[canyon289]

Well this failed. Will try something else. Sorry for all the spam guys

[canyon289]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[canyon289]

Still not correct. I will revisit the way I'm rendering these to see if I can test more effectively in my local environment.

[canyon289]

@malmaud and @mattpitkin

All feedback has been addressed, except example gallery which I'm struggling with tremendously.

I'm having issues generating a PDF with the make file, my tex output displays errors.

I can get a PDF to render with the command

pandoc --filter pandoc-citeproc --bibliography=paper.bib  --variable papersize=a4paper -s paper.md -o paper.pdf

But while the output of this command may look good, the whedon generated pdf does not.

Lastly I tried looking for other JOSS papers with two or more figures but my random search was fruitless.

Here are two versions of the paper with Example gallery. Any suggestions on how to get them to render nicely? I realize this may be outside of the normal review role, I apologize for the trouble.

Multiple Figures
https://github.com/arviz-devs/arviz/commit/4d5d6319c8b80872292ab2589606ca6d4a9b183a

Two Figures
https://github.com/arviz-devs/arviz/commit/714bc2d3d0b852e477ef87c6460c3413411aa128

[arfon]

@canyon289 - could you share the PDF you've compiled locally here? I'd like to bette understand what you're trying to accomplish.

[canyon289]

We're trying to add a local gallery per the review feedback In other words we'd like to meet the intent of the review, but struggling to get nice formatting while doing so.

Here's the two approaches we tried.

2+ Figures
Here's a local render with multiple figures. Unfortunately this render required a "hack" to get it to work locally, so not a great solution
https://github.com/arviz-devs/arviz/files/2722319/paper.pdf

Header hack
https://github.com/arviz-devs/arviz/pull/484/files#diff-e2778e7674f45b806282a9611faa7220R100

Two Figures
We also tried a version with just two figures. In the local render it seems to work, but not in JOSS.
https://github.com/arviz-devs/arviz/files/2722350/paper.pdf
https://github.com/arviz-devs/arviz/pull/485/files

Let me know if I explained this poorly and I can clarify any details

[arfon]

Ah OK. The problem here is that Pandoc + Markdown offers very little in terms of document flow/layout control.

Based on version https://github.com/arviz-devs/arviz/commit/4d5d6319c8b80872292ab2589606ca6d4a9b183a, I've generated the PDF locally by moving the # Example plots section _below_ the # Acknowledgments section and slightly tweaking the width of the figures i.e.:

# Example plots  

A portion of ArviZ's functionality is shown in Figure 2 through Figure 5.  
ArviZ supports more plotting and inference diagnostics, in addition to the ones shown here. Additional examples can be found ArviZ documentation gallery

![Bivariate hexbin plot with marginal distributions](plot_joint.png){width=80%}

![2D Kernel Density estimation](plot_kde_2d.png){width=80%}

![Markov Chain Monte Carlo Trace Plot](plot_trace.png){width=80%}  

![John Kruschke styled posterior distribution plots](plot_posterior.png){width=80%}  

This gives the resulting output: 10.21105.joss.01143.pdf

What do you think?

[canyon289]

Looks good. We made the changes in our paper. Hopefully this works

[canyon289]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[canyon289]

This looks ready for rereview. Thank you all for the help

[mattpitkin]

Hi @canyon289, everything looks good, but I just have a few comments:

• the API documentation appears complete for the methods, but doesn't have any class documentation. In particular, I think it would be useful to have the documentation for the InferenceData class, with that containing some examples or descriptions of what the class can store.
• for the _Pyro: Deep Universal Probabilistic Programming_ reference could you add the arXiv link https://arxiv.org/abs/1810.09538 as it doesn't seem to be released in JMLR yet.
• for the _A Widely Applicable Bayesian Information Criterion_ maybe also add a link to the arXiv version of the paper https://arxiv.org/abs/1208.6338, or the JMLR webpage http://www.jmlr.org/papers/v14/watanabe13a.html

[canyon289]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[canyon289]

@mattpitkin Thank you for the feedback. We made some changes based on your suggestions. Let me know if there's anything else you notice

[mattpitkin]

@canyon289 thanks for the changes. Would it be possible to include the InferenceData class in the API documentation, or is there a specific reason for not doing this? I think it would be good to have it included even if the docstring mainly just adds a link to the page https://arviz-devs.github.io/arviz/notebooks/XarrayforArviZ.html. Also, could that notebook also contain the plot from Figure 1 of the paper?

[canyon289]

@mattpitkin
My (subjective) reasoning for not including az.InferenceData in the api docs was because all the methods in the api docs are intended to be callable by the user. For InferenceData the users don't directly instantiate an az.InferenceData. This is why I after some debate I opted not to include it in api docs, however this reasoning is largely subjective but would love to get your thoughts.

In terms of notebook, here is an updated version in a PR https://github.com/arviz-devs/arviz/pull/510. If you like it I'll merge so we can close that particular item!

https://github.com/arviz-devs/arviz/blob/8b9528ac046843ffd84f2429caff6fe0ce1c76da/doc/notebooks/XarrayforArviZ.ipynb

[canyon289]

Please let me know if there's any remaining actions that I should take. I don't mean to rush this, just want to be sure I'm not holding anyone up

[mattpitkin]

Hi @canyon289, @arfon, sorry for the delay. I'm happy to sign-off on the review and have completed all the tick boxes.

[canyon289]

@mattpitkin No problem, I didn't feel delayed! What are next steps?

[arfon]

Thanks @mattpitkin.

@canyon289 - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[canyon289]

Thank you. We're prepping a release this week which will generate a DOI

[canyon289]

@arfon

Please see the DOI archive here
https://zenodo.org/record/2540945#.XD4csN-YXmE

[arfon]

@whedon set 10.5281/zenodo.2540945 as archive

[whedon]

OK. 10.5281/zenodo.2540945 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/433

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/433, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/434
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01143
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[arfon]

@malmaud , @mattpitkin - many thanks for your reviews here ✨

@canyon289 - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01143/status.svg)](https://doi.org/10.21105/joss.01143)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01143">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01143/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01143/status.svg
   :target: https://doi.org/10.21105/joss.01143

This is how it will look in your documentation:

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