[REVIEW]: mpl-interactions: A Python package for Interactive Matplotlib Figures

[editorialbot]

Submitting author: @ianhi (Ian Hunt-Isaak)
Repository: https://github.com/mpl-extensions/mpl-interactions
Branch with paper.md (empty if default branch): joss
Version: 0.24.1
Editor: @ppxasjsm
Reviewers: @flekschas, @rgerum
Archive: 10.5281/zenodo.10211397

Status

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Markdown: [![status](https://joss.theoj.org/papers/532b30e11db3c14503f5d6e2f5561004/status.svg)](https://joss.theoj.org/papers/532b30e11db3c14503f5d6e2f5561004)

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

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✨ 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 @rgerum

📝 Checklist for @flekschas

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.19 s (434.5 files/s, 312898.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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JSON                             5              0              0          48403
Python                          24            677           1437           2905
Jupyter Notebook                26              0           4314           1513
Markdown                        14            254              0            549
YAML                             8             27              7            204
INI                              1              6              0             70
DOS Batch                        1              8              1             26
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make                             1              6              7             15
CSS                              1              1              2              9
HTML                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            84            985           5768          53740
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gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1322

[editorialbot]

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

[rgerum]

Review checklist for @rgerum

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/mpl-extensions/mpl-interactions?
• 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 (@ianhi) 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?

[rgerum]

The authors provide an extension for matplotlib to add interactivity to plots by providing parametersliders. While this is not exactly a new idea as both matplotlib and ipyhon already feature sider widgets, the authors point out that these solutions are not handling the plot update in a performant maner and are also rather difficult to use.
The API seems well tought through and offers different options on how to add sliders, have joined sliders to inlucence multiple plots, so I think the package has a substantial size and therefore meets the scope of JOSS. The package has automatic test, although they are currently (according to Github) failing for mpl-latest, but for the stable versions of matplotlib they seem to run well.

The only checkmark I haven't set yet is about the list of authors (Contribution and authorship). There are a good number of other contributors listed in the github repository readme that do not appear as authors of the paper. Also Doeke Hekstra does not appear in the contributor list in the reposiotires readme. Could the author elaborate on the reasons for this?

[ianhi]

Hi @ppxasjsm quick question about process.

If i'm understanding the instructions in the first comment correctly:

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.)

Then to address the comments from rgerum we should open a new issue on mpl-interactions? Or is that only for detailed difficult issue?

[rgerum]

If you think it will be a length discussion you can open an issue I guess, but I think its not a major technical problem that needs to be addressed with a lot of back and forth. I think in this case you can directly answer me here.

[flekschas]

Review checklist for @flekschas

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/mpl-extensions/mpl-interactions?
• 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 (@ianhi) 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?

[flekschas]

General comment

mpl-interactions is an extension for matplotlib for automating the creation of interactive sliders, inputs, radio buttons for configuring a visualization. While the extension does not seem to offer general interactions/interactivity (like view manipulations or selections), being able to rapidly adjust plotting and function parameters could be to be useful to help scientist to better understand their data and methods.
The paper is well written and contains easy to understand examples. The software itself is extensively document and seems to be in a well-maintained state.

Below I list why I cannot yet check every box:

Contribution and authorship

I agree with @rgerum here. Several contributors with substantial contributions (e.g., with more than 10 commits) are not listed as an author but Doeke Hekstra with zero code contributions is listed as an author. Clarification is needed.

State of the field:

The authors have commented on the shortcomings of interactive figures with matplotlib and ipywidgets but they left out the shortcomings of mpl-interactions: ipywidgets can easily be integrated with other widgets while from the documentation and code samples, it looks like mpl-interactions can really only be used to interactively plot matplotlib figures faster. Moreover, the extension does not offer view manipulations like pan&zoom or selections. It'd be great to clarify this. Also, why is ipympl not mentioned?

And finally, on a broader level, one might also wonder how mpl-interactions compares to other interactive plotting libraries like altair, holoviz, plotly, etc. Providing a broader perspective would be really useful to the reader.

Installation & Functionality

I followed https://mpl-interactions.readthedocs.io/en/stable/install.html#setup-for-jupyterlab-3 and tried to run the Basic Example from https://mpl-interactions.readthedocs.io/en/stable/index.html#basic-example with JupyterLab v4.0.2 on a M1 MacBook but can't get it to work.

Not sure what I might have done wrong or missing, but unfortunately, I didn't get mpl-interactions to work.

Minor writing comments

the choices it makes are not always optimal for scientific plotting

This statement is fairly strong but unjustified. The authors should either give a definition + example of what optimality for scientific plotting means and why ipywidgets does not support it. Or alternatively remove this statement.

y_data = logistic_growth(t_data, L=5, k=1, t0=1) + rng.normal(size=t_data.size, scale=0.

This line is cut off

This framework makes it easy generate complex interactive visualizations

A to is missing after easy

Complete Tutorials, Examples, and API documentation are available on https://mpl-interactions.readthedocs.io/en/stable/

Why are Tutorials and Examples examples capitalized here?

[ppxasjsm]

@ianhi can you please take a look at the reviewers comments and address them so that we can move the review forward. Thank you!

[ppxasjsm]

Thank you for the reviews @flekschas and @rgerum so far!

[ppxasjsm]

Hi @ianhi, just to let you know I'll be out of office until the 11th of September and will pick this up again on my return.

[rgerum]

As the question of authorship seems to have been addressed now (mpl-extensions/mpl-interactions#283) I added the check mark to the "authors" item in the check list, which is now complete.

[flekschas]

I checked off "Contribution and authorship" as well for the same reason. I also checked "State of the field" given mpl-extensions/mpl-interactions@52a9ba0#diff-e504eb580b095a7e65428b098183a581e475f0fb316db95287eacd7d4f344424.

The last missing check for me is "References". Once the authors cite "Altair, Holoviz, and plotly" things are good to go on my end.

[ianhi]

The package has automatic test, although they are currently (according to Github) failing for mpl-latest, but for the stable versions of matplotlib they seem to run well.

I forgot to mention but I fixed this a week or sot ago, tests now pass on the master branch of matplotlib.

The last missing check for me is "References". Once the authors cite "Altair, Holoviz, and plotly" things are good to go on my end.

see mpl-extensions/mpl-interactions@8cbc9f7

[flekschas]

Awesome, thanks. I checked all checkboxes now. Good stuff and congrats 🎉

[ianhi]

Hi @ppxasjsm is there anything more the authors need to do here?

[ppxasjsm]

Hi @ianhi, we are almost there now. Sorry for the delay. I'll go through the paper now and will give you a small set of tasks based on that and we should be ready to recommend accept in no time.

[ianhi]

Hi @ppxasjsm I'm very sorry about the delays. I am now officially back to being able to keep track of conversations on github.

• Double check
• release: 0.24.1
• zenodo: https://doi.org/10.5281/zenodo.10211398
• title + author list match
• license: both are 3 clause bsd

[ppxasjsm]

@ianhi, I am sorry now I am the slow one. I am out of office until the 24th Jan, but I'll try and see if I can move this along over the next week or so.

[ppxasjsm]

@editorialbot generate pdf

[editorialbot]

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

[ppxasjsm]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.01057 is OK
- 10.5281/zenodo.3634720 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[ppxasjsm]

@editorialbot set 10.5281/zenodo.10211397 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10211397

[ppxasjsm]

@editorialbot set 0.24.1 as version

[editorialbot]

Done! version is now 0.24.1

[ppxasjsm]

@editorialbot generate pdf

[editorialbot]

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

[ppxasjsm]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.01057 is OK
- 10.5281/zenodo.3634720 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[ppxasjsm]

@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

- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.01057 is OK
- 10.5281/zenodo.3634720 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#4971, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@ianhi – I made a couple of tiny changes to formatting here: mpl-extensions/mpl-interactions#290

Could you please merge this and I can proceed to accept?

[arfon]

@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: Hunt-Isaak
  given-names: Ian
  orcid: "https://orcid.org/0000-0002-7591-083X"
- family-names: Russell
  given-names: John
  orcid: "https://orcid.org/0009-0002-0402-2306"
- family-names: Hekstra
  given-names: Doeke
  orcid: "https://orcid.org/0000-0003-2332-9223"
doi: 10.5281/zenodo.10211397
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hunt-Isaak
    given-names: Ian
    orcid: "https://orcid.org/0000-0002-7591-083X"
  - family-names: Russell
    given-names: John
    orcid: "https://orcid.org/0009-0002-0402-2306"
  - family-names: Hekstra
    given-names: Doeke
    orcid: "https://orcid.org/0000-0003-2332-9223"
  date-published: 2024-01-31
  doi: 10.21105/joss.05651
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5651
  title: "mpl-interactions: A Python Package for Interactive Matplotlib
    Figures"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05651"
  volume: 9
title: "mpl-interactions: A Python Package for Interactive Matplotlib
  Figures"

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.

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[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.05651 joss-papers#4973
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05651
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...

[arfon]

@flekschas, @rgerum - many thanks for your reviews here and to @ppxasjsm for editing this submission.

@ianhi - your paper is now accepted and published in JOSS ⚡️🚀💥

[editorialbot]

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