[REVIEW]: PxMCMC: A Python package for proximal Markov Chain Monte Carlo

[editorialbot]

Submitting author: @auggiemarignier (Augustin Marignier)
Repository: https://github.com/auggiemarignier/pxmcmc
Branch with paper.md (empty if default branch): joss_paper
Version: v1.0.0
Editor: @mstimberg
Reviewers: @jeremiecoullon, @mattpitkin
Archive: 10.5281/zenodo.8185139

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Checklists

📝 Checklist for @mattpitkin

📝 Checklist for @jeremiecoullon

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1189.4 files/s, 111479.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24            608            532           2049
reStructuredText                15            178             60            633
TeX                              1             13              0            152
Markdown                         2             19              0             70
YAML                             3              7             16             67
TOML                             1              5              0             35
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            48            842            616           3041
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 608

[editorialbot]

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

OK DOIs

- 10.1093/MNRAS/STY2004 is OK
- 10.1016/j.acha.2010.10.002 is OK
- 10.1086/670067 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1051/0004-6361/201220729 is OK
- 10.1093/rasti/rzac010 is OK
- 10.1561/2400000003 is OK
- 10.1007/s11222-015-9567-4 is OK
- 10.1137/19m1283719 is OK
- 10.1093/mnras/stz3453 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[mstimberg]

👋🏼 @auggiemarignier, @jeremiecoullon, @mattpitkin, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

at the top of a new comment in this thread.

There are additional guidelines in the message at the start of this issue.

Please don't hesitate to ping me (@mstimberg) if you have any questions/concerns.

[mattpitkin]

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 https://github.com/auggiemarignier/pxmcmc?
• 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 (@auggiemarignier) 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?

[mattpitkin]

@auggiemarignier when looking at the examples scripts in https://github.com/auggiemarignier/pxmcmc/tree/main/experiments, there are no (or very few) comments in the codes. To make these far more useful as examples, could you please comment the major steps in each, in particular the set up of the sampler and the various inputs required.

Could you also please add come "Community guidelines" to the README/docs - see https://joss.readthedocs.io/en/latest/review_checklist.html#documentation.

[auggiemarignier]

@mattpitkin thanks for your comments. I've opened a PR in the main repo where I'll implement the various changes suggested during the review.

I've added comments throughout the example scripts (data still needs to be added so that they run), and added the community guidelines to README and docs CONTRIBUTING page.

[jeremiecoullon]

Review checklist for @jeremiecoullon

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/auggiemarignier/pxmcmc?
• 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 (@auggiemarignier) 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?

[jeremiecoullon]

@auggiemarignier: I'm having trouble instaling the package from source. I opened an issue on github describing my setup and the error I get.
I wonder if you have thoughts on this?

Thanks!

[mattpitkin]

I've opened an issue about the internal package version string not matching the current package version auggiemarignier/pxmcmc#17.

[mattpitkin]

For the Donoho (2006) paper, add the DOI https://doi.org/10.1109/TIT.2006.871582

[mattpitkin]

In terms of "State of the field", you might want to mention this package https://github.com/astro-informatics/proxnest, which uses the proximal method for nested sampling.

[auggiemarignier]

@editorialbot generate pdf

[editorialbot]

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

[auggiemarignier]

@editorialbot generate pdf

[editorialbot]

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

[auggiemarignier]

@mattpitkin just chasing up on the last few things on your checklist

• Functionality - Functionality : is there anything I need to change for this? I recommend simply running the Earth topography example.
• Documentation - Statement of need : see the docs build for the PR
• Software Paper - State of the field : I've added the proxnest package as you suggested (see latest proof)
• Software Paper - References : I believe everything is there and the syntax is correct.

Let me know if there's anything else!

[auggiemarignier]

@jeremiecoullon Let me know if there's anything I can do to help you tick off things on your checklist!

[jeremiecoullon]

@auggiemarignier Sorry for the delay!
I opened an issue in your repo, and I'll continue going through the list :)

[jeremiecoullon]

I finished my review: I think it's very good! 


The examples are nice, the code is well structured, and the UX (ie: running the quickstart, interacting with the repo & documentation) is good.

By the way, I suggested some small edits which I think would further reduce friction in getting a first example up and running.

But this is all great! Congrats on this great package! 🎉 ✅

[mattpitkin]

I've also finished my review and am happy to sign-off on the paper.

[auggiemarignier]

thank you both! :)

[editorialbot]

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

[mstimberg]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1093/MNRAS/STY2004 is OK
- 10.48550/arXiv.2106.03646 is OK
- 10.1016/j.acha.2010.10.002 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1086/670067 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1051/0004-6361/201220729 is OK
- 10.1093/rasti/rzac010 is OK
- 10.1561/2400000003 is OK
- 10.1007/s11222-015-9567-4 is OK
- 10.1137/19m1283719 is OK
- 10.1093/mnras/stz3453 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mstimberg]

@editorialbot set 10.5281/zenodo.8185139 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8185139

[mstimberg]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[mstimberg]

@auggiemarignier All looks in excellent shape to me, I will now recommend acceptance and an editor-in-chief will take over for the final step. Congrats and thanks again @mattpitkin and @jeremiecoullon for your time 🎉 !

[mstimberg]

@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

- 10.1093/MNRAS/STY2004 is OK
- 10.48550/arXiv.2106.03646 is OK
- 10.1016/j.acha.2010.10.002 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1086/670067 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1051/0004-6361/201220729 is OK
- 10.1093/rasti/rzac010 is OK
- 10.1561/2400000003 is OK
- 10.1007/s11222-015-9567-4 is OK
- 10.1137/19m1283719 is OK
- 10.1093/mnras/stz3453 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[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#4433, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[auggiemarignier]

@mstimberg @mattpitkin @jeremiecoullon thank you all for your feedback and time! It's much appreciated.

[gkthiruvathukal]

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[gkthiruvathukal]

Everything looks great here. I'm moving to final acceptance now!

[gkthiruvathukal]

@editorialbot accept

[editorialbot]

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

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

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CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Marignier
  given-names: Augustin
  orcid: "https://orcid.org/0000-0001-6778-1399"
contact:
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  given-names: Augustin
  orcid: "https://orcid.org/0000-0001-6778-1399"
doi: 10.5281/zenodo.8185139
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Marignier
    given-names: Augustin
    orcid: "https://orcid.org/0000-0001-6778-1399"
  date-published: 2023-07-26
  doi: 10.21105/joss.05582
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5582
  title: "PxMCMC: A Python package for proximal Markov Chain Monte
    Carlo"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05582"
  volume: 8
title: "PxMCMC: A Python package for proximal Markov Chain Monte Carlo"

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