[REVIEW]: PreliZ: A tool-box for prior elicitation

[editorialbot]

Submitting author: @aleicazatti (Alejandro Icazatti)
Repository: https://github.com/arviz-devs/preliz
Branch with paper.md (empty if default branch):
Version: v0.3.4
Editor: @olexandr-konovalov
Reviewers: @jungtaekkim, @djmannion
Archive: 10.5281/zenodo.8368516

Status

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Markdown: [![status](https://joss.theoj.org/papers/f1dadc218c75287b631c0313afb64b1f/status.svg)](https://joss.theoj.org/papers/f1dadc218c75287b631c0313afb64b1f)

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Checklists

📝 Checklist for @djmannion

📝 Checklist for @jungtaekkim

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (679.0 files/s, 155762.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          31           1712           2343           5134
Markdown                         8             84              0            224
Jupyter Notebook                 6              0           2690            144
TeX                              1             12              0            142
YAML                             4             14              2            115
TOML                             1              9              0             51
reStructuredText                 2             40             29             38
DOS Batch                        1              8              1             26
make                             1              6              7             13
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            56           1885           5072           5890
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 815

[editorialbot]

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

OK DOIs

- 10.21105/joss.01143 is OK
- 10.1145/3313831.3376377 is OK
- 10.1007/s11104-022-05329-0 is OK
- 10.1016/j.envsoft.2013.10.010 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[djmannion]

Review checklist for @djmannion

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/arviz-devs/preliz?
• 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 (@aleicazatti) 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?

[jungtaekkim]

Review checklist for @jungtaekkim

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/arviz-devs/preliz?
• 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 (@aleicazatti) 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?

[djmannion]

Thanks to the authors for this very useful package! I have opened a few minor issues that would require consideration prior to the completion of my review:

• [paper] ppa model definition + typos arviz-devs/preliz#253
• [docs] statement of need arviz-devs/preliz#254
• notebook dependency arviz-devs/preliz#255

[djmannion]

Each of my issues has been resolved by the authors and my review is complete.

[olexandr-konovalov]

Thank you @djmannion! I can already see some ticked boxes in @jungtaekkim's review - hope we may have the 2nd review soon!

[jungtaekkim]

@editorialbot generate pdf

[editorialbot]

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

[jungtaekkim]

I reviewed this paper and the issue raised was resolved.

• JOSS reviews for a paper arviz-devs/preliz#260

I think this paper is ready to publish.

[aloctavodia]

Do we need to do something else? How can we help?

[aloctavodia]

@olexandr-konovalov any update on this?

[olexandr-konovalov]

Thanks for your reviews @jungtaekkim and @djmannion! @jungtaekkim could you please check again and tick all the remaining boxes in your review, if they don't require further actions, or act accordingly.

[jungtaekkim]

@olexandr-konovalov I did it.

[olexandr-konovalov]

@editorialbot generate pdf

[editorialbot]

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

[olexandr-konovalov]

@aloctavodia @aleicazatti sorry it took a while to get back to you. I've made another check of the PDF:

• line 43 of paper.md - missing "to" in "helping practitioners choose prior distributions"
• bibliography: the new name of jupyter-matplotlib is ipympl https://matplotlib.org/ipympl/
• page 4 only has a figure and a code snippet. Perhaps some reaarangement or adding some textual "glue" might help to avoid that. Otherwise, it's quite unclear what the code belongs to.

Could you please fix that and I will then recommend it for acceptance.

[aloctavodia]

@olexandr-konovalov thanks for the feedback, the 3 issues you mentioned have been addressed.

[olexandr-konovalov]

@editorialbot generate pdf

[editorialbot]

Done! archive is now 10.5281/zenodo.8368036

[olexandr-konovalov]

@aloctavodia also, please edit the title at https://zenodo.org/record/8368036: it should be

PreliZ: A tool-box for prior elicitation

instead of

arviz-devs/preliz: 0.3.3

[olexandr-konovalov]

P.S. @aloctavodia I think the correct order would be to

• merge Fix LaTeX umlaut arviz-devs/preliz#277
• make new release to keep in sync with the repository
• let me know new version number and DOI

It seems like everything else is in a good shape, so hopefully no more quick releases will be needed (until it will go to the EiC).

[aloctavodia]

I tick them, but they get unticked when I refresh the page. I tried from my laptop and from my mobile phone.

[olexandr-konovalov]

@aloctavodia ah, ok, then verbal confirmation is enough :) - let's get actual stuff done.

[aloctavodia]

PreliZ's release 0.3.4
Zenodo all versions https://doi.org/10.5281/zenodo.8368035
Zenodo version 0.3.4 https://doi.org/10.5281/zenodo.8368516

[olexandr-konovalov]

@editorialbot set v0.3.4 as version

[editorialbot]

Done! version is now v0.3.4

[olexandr-konovalov]

@editorialbot set 10.5281/zenodo.8368516 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8368516

[olexandr-konovalov]

@editorialbot generate pdf

[editorialbot]

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

[olexandr-konovalov]

@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

- 10.21105/joss.01143 is OK
- 10.1145/3313831.3376377 is OK
- 10.1201/9781003019169 is OK
- 10.1007/s11104-022-05329-0 is OK
- 10.1201/b16018 is OK
- 10.1016/j.envsoft.2013.10.010 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1214/23-BA1381 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#4594, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[olexandr-konovalov]

Thanks @aloctavodia! Looking at https://zenodo.org/record/8368516, you can also edit metadata, so that it will have some short abstract instead of "What's Changed" and "New Contributors" - this version will be linked from the article, so it would be more informative and appropriate.

[aloctavodia]

I updated the metadata, thanks for the recomendation

[gkthiruvathukal]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Icazatti
  given-names: Alejandro
  orcid: "https://orcid.org/0000-0003-1491-7330"
- family-names: Abril-Pla
  given-names: Oriol
  orcid: "https://orcid.org/0000-0002-1847-9481"
- family-names: Klami
  given-names: Arto
  orcid: "https://orcid.org/0000-0002-7950-1355"
- family-names: Martin
  given-names: Osvaldo A
  orcid: "https://orcid.org/0000-0001-7419-8978"
contact:
- family-names: Martin
  given-names: Osvaldo A
  orcid: "https://orcid.org/0000-0001-7419-8978"
doi: 10.5281/zenodo.8368516
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Icazatti
    given-names: Alejandro
    orcid: "https://orcid.org/0000-0003-1491-7330"
  - family-names: Abril-Pla
    given-names: Oriol
    orcid: "https://orcid.org/0000-0002-1847-9481"
  - family-names: Klami
    given-names: Arto
    orcid: "https://orcid.org/0000-0002-7950-1355"
  - family-names: Martin
    given-names: Osvaldo A
    orcid: "https://orcid.org/0000-0001-7419-8978"
  date-published: 2023-09-22
  doi: 10.21105/joss.05499
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5499
  title: "PreliZ: A tool-box for prior elicitation"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05499"
  volume: 8
title: "PreliZ: A tool-box for prior elicitation"

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]

🐘🐘🐘 👉 Toot 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.05499 joss-papers#4596
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05499
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...

[aloctavodia]

Everything LGTM!

[arfon]

@jungtaekkim, @djmannion – many thanks for your reviews here and to @olexandr-konovalov 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 ✨

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

[editorialbot]

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