[REVIEW]: plotastic: Bridging Plotting and Statistics in Python

[editorialbot]

Submitting author: @markur4 (Martin Kuric)
Repository: https://github.com/markur4/plotastic
Branch with paper.md (empty if default branch):
Version: 0.1.1
Editor: @rkurchin
Reviewers: @gmrandazzo, @SunnyXu
Archive: 10.5281/zenodo.10775033

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Reviewers and authors:

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Reviewer instructions & questions

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @rkurchin know.

✨ 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 @SunnyXu

📝 Checklist for @gmrandazzo

[editorialbot]

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (715.6 files/s, 173540.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          49           1835           2843           4696
SVG                              1              0              0           2671
HTML                            13            294             39           1750
Markdown                         4            235              0            995
JavaScript                      12            131            221            880
CSS                              4            190             35            780
Jupyter Notebook                13              0           8915            522
TeX                              1              5              0             92
reStructuredText                 8             59            106             77
TOML                             1             16             49             71
YAML                             2              4              0             36
DOS Batch                        1              8              1             26
JSON                             1              0              0             10
make                             1              4              7              9
INI                              1              0              0              8
Bourne Shell                     2              9             12              7
-------------------------------------------------------------------------------
SUM:                           114           2790          12228          12630
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.5281/ZENODO.7213391 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.01026 is OK
- 10.21105/joss.03021 is OK
- 10.18637/jss.v059.i10 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1662

[editorialbot]

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

[rkurchin]

@gmrandazzo and @SunnyXu, let me know if you have any questions about how to get your reviews started!

[SunnyXu]

Review checklist for @SunnyXu

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/markur4/plotastic?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@markur4) 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?

[SunnyXu]

@rkurchin @markur4
plotastic is a solid Python package bridging the gap between seaborn and pingouin to offer a unified environment for plotting and statistical analysis. It is good that there are the testing section and codecov on GitHub. Please see my comments (linked to issues) below to improve. Please let me know if anything is unclear.

1. Manuscript improvement
   (Manuscript improvement markur4/plotastic#1)
2. PYPI
   (PYPI markur4/plotastic#2)
3. Data of Example Gallery in the section of Documentations (Data of Example Gallery in the section of Documentations markur4/plotastic#3)
4. Some parts of the Documentation are empty (Some parts of the Documentation are empty markur4/plotastic#4)
5. Quick Example
   (Quick Example  markur4/plotastic#5)
6. fix the point of “Community guidelines” in my review checklist (Fix the point of “Community guidelines” in the review checklist markur4/plotastic#6)

[markur4]

@SunnyXu Thanks a lot for the great feedback! I appreciate the detail!

@rkurchin I worked through all points. Should I close them once the reviewer is satisfied?

[editorialbot]

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

[SunnyXu]

@markur4 Thanks for the improvement. I like your improvement regarding issue 3 and issue 6 especially.
@rkurchin Martin has addressed all the issues except the second one (PYPI) which might get improved later. Please let me know if I need to do anything else. Thanks again for considering me as a reviewer. Hope to help with another review again in the future.

[rkurchin]

@SunnyXu, are you satisfied on the community guidelines point? If so, please check off that last box. If not, please leave any additional comments/feedback necessary.

@gmrandazzo, do you think you'll be able to start your review fairly soon?

[SunnyXu]

@rkurchin Thanks for the reminder. I am satisfied and checked the last box. I do not have additional comments regarding.

[editorialbot]

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

[gmrandazzo]

Review checklist for @gmrandazzo

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/markur4/plotastic?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@markur4) 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?

[gmrandazzo]

@markur4 and @rkurchin

Thanks for the chance to review this paper. Here are my comments:

1. The summary is OK; however, there needs to be a reason why it would be good to use plastic instead of seaborn+pingouin. This important statement is written in lines 54, 55, and 56 of the manuscript. Please report them also in the summary. The rest of the manuscripts seem fine to me.

2. Installation is fine. However, this package works only for Python >=3.11, and I need clarification on why older Python, i.e., 3.9, is not OK. If there is any specific reason, please state this in the installation document, specifying also the minimum Python version. Can you please fix that?

from pyproject.toml

[...]
#' Specify version only if concrete incompatibilities exist
requires-python = ">=3.11"

Is there any specific incompatibility? If yes, state this. If not, please fix that.

3. I have opened a shell. I copied and pasted the script you presented in the paper, and the Python shell became unusable. I'm not able to see the final plot. Can you check what is going on?

4. Functional documentation seems poor. Please improve it.

Thanks!
Best regards

[gmrandazzo]

@markur4 Ah last comment. Please clean the package directory from .vscode and .DS_Store and other garbage files. Add them to the .gitignore

[markur4]

@gmrandazzo @rkurchin

Thank you very much for the valuable feedback!

1.

That's a good point, I included the rationale in the last sentence of the summary:

Before: [...]This approach streamlines the process, translating seaborn parameters into statistical terms, providing researchers and data scientists with a cohesive and user-friendly solution in python.

After: [...] This approach streamlines the process, translating seaborn parameters into statistical terms, allowing researchers to focus on correct statistical testing and less about specific syntax and implementations.

2.

I haven't tested plotastic on any other version than 3.11. I revised pyproject.toml to reduce confusion:

### Python version
#' Lower versions than 3.11 have not been tested
requires-python = ">=3.11"

Please let me know if testing on older python versions is required to pass the review.

3.

Interesting, I have never executed plotastic in a shell. Here's what I did:

• Made "tests/_paper_test.py" and copy pasted example code from paper
• Executed "tests/_paper_test.py" in vscode interactive mode (venv editable mode): this worked!
• opened terminal, ran this:
  python _paper_test.py
  this worked! (no plot shows up, but shell remains usable)
• Made a fresh venv, installed from github according to readme
• Ran python _paper_test.py in both shell and vscode: this worked, too
• Opened a python shell, copy pasted code: this worked! (but no plot shows up!)
• In the same python shell, I ran:

import seaborn as sns
sns.catplot(data=DF, **_dims)

• this worked! but also did NOT open a plot!

Summary:

• Sadly, I can not reproduce your shell getting unresponsive
• Since seaborn code also does not open plots when running from the python shell, I don't think that plotastic should be able to do this, too.
• plotastic was designed to be used with ipython, I would not recommend execution in python shell at all.
• Could you please retry using ipython / jupyter notebooks / vscode interactive mode?

4.

The screenshots do not refer to the correct documentation, but preliminary experiments with sphinx. I git removed them completely to prevent confusion.

Please use the documentations and examples found in the README.md as a guide to use plotastic. Let me know if they are clear!

5.

Thanks for pointing out the garbage files! I git removed them from src, if you find any more, let me know!

[gmrandazzo]

@markur4 ok for point 2. State the minimum version in the README in the section "REQUIREMENTS" or something like that. Try to harmonize everything. Remember that someone landing your GitHub page should be able to install the software without somersault.

Then @rkurchin fine to me. Accepted.

[markur4]

@gmrandazzo @rkurchin

Ok, I'm happy that it's working! Also, I've added a requirements section to the README.md!
Thanks a lot!

[rkurchin]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[rkurchin]

Thanks again reviewers! @markur4, you can see above a few things you'll need to do (and in some cases, send me info in a comment here) to finalize this submission. I'll do a read over the manuscript itself and send any editorial comments shortly!

[rkurchin]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5281/ZENODO.7213391 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.01026 is OK
- 10.21105/joss.03021 is OK
- 10.18637/jss.v059.i10 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[rkurchin]

@editorialbot generate pdf

[editorialbot]

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

[markur4]

@rkurchin

Here's what I did:

• Built current repo, uploaded on PyPi,
  Version: 0.1.1
• Cloned repo, zipped it and uploaded on Zenodo,
  DOI: 10.5281/zenodo.10775033
• Checked that license (GPLv3), ORCIDs and authors are the same as in the archive

Let me know if I missed something!

[rkurchin]

@editorialbot set 0.1.1 as version

[editorialbot]

Done! version is now 0.1.1

[rkurchin]

@editorialbot set 10.5281/zenodo.10775033 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10775033

[rkurchin]

Apologies that this took a little while!

Editorial comments:

• line 9: I think you can remove the "a" before "syntax" since I usually parse that as a collective noun
• line 12-13: I'm not sure if "analyses" is the plural of "analysis" (and hence an additional object of the verb "conducts") or the British English spelling of the third-person singular of the verb "analyzes" – in any case, the parallelization of the sentence is a bit broken. I would suggest rewriting/splitting it. One possibility: "The library systematically groups the data according to the needs of statistical tests and plots. It can perform these analyses and visualize the results and also supports extensive customization options"
• 22-25: not sure what's going on with the line spacing thing here, but perhaps double-check if there's anything goofy about your source file?
• 28: remove extra period before citation
• 31: missing a "with" before seaborn
• figure 1: Why is the whole of the plotting block in parentheses?
• 42: I think the apostrophe after seaborn is a ` instead of a '
• 67: "per axes" --> "per axis"
• 71-72: add "a" after "initializes"
• 77, 91: plotastic --> plotastic
• 78: remove "in"
• 82: there's a word missing in this sentence...statistical what? Perhaps information? Indicators? Parameters?
• References: pandas requests two particular things be cited when acknowledging it, please replace your citation with those two

[markur4]

@rkurchin

No problem, thanks for the feedback!

I made these revisions, let me know if I missed something!

* line 9: I think you can remove the "a" before "syntax" since I usually parse that as a collective noun

I removed the "a"

* line 12-13: I'm not sure if "analyses" is the plural of "analysis" (and hence an additional object of the verb "conducts") or the British English spelling of the third-person singular of the verb "analyzes" – in any case, the parallelization of the sentence is a bit broken. I would suggest rewriting/splitting it. One possibility: "The library systematically groups the data according to the needs of statistical tests and plots. It can perform these analyses and visualize the results and also supports extensive customization options"

I agree, the point that I wanted to convey doesn't come across at all.

Before: The library systematically groups the data according to the needs of statistical tests and plots, conducts visualisation, analyses and supports extensive customization options. In essence, plotastic establishes a protocol for configuring statical analyses through plotting parameters. This approach streamlines the process, translating seaborn parameters into statistical terms,
[...].

After: Hence, statistics and plotting are performed on the same set of parameters, so that the strength of seaborn in visualising multidimensional data is extended onto statistical analysis. In essence, plotastic translates seaborn parameters into statistical terms, configures statistical protocols based on intuitive plotting syntax and returns a matplotlib figure with known customization options and more. This approach streamlines data analysis, [...].

* 22-25: not sure what's going on with the line spacing thing here, but perhaps double-check if there's anything goofy about your source file?

I removed unnecessary newlines

* 28: remove extra period before citation

Done

* 31: missing a "with" before `seaborn`

Done

* figure 1: Why is the whole of the plotting block in parentheses?

It's python syntax that allows for methods to be chained in newlines. Without parentheses, the methods need to be in one line and that becomes unreadable very quickly.

* 42: I think the apostrophe after `seaborn` is a ` instead of a '

It's a ', but I rephrased it to prevent confusion:

Before: plotastic was inspired by seaborn's intuitive and consistent usage of the same set of parameters

After: plotastic was inspired by seaborn using the same set of intuitive and consistent parameters

* 67: "per axes" --> "per axis"

Done

* 71-72: add "a" after "initializes"

Done

* 77, 91: plotastic --> `plotastic`

Done

* 78: remove "in"

Done

* 82: there's a word missing in this sentence...statistical what? Perhaps information? Indicators? Parameters?

Done

* References: [pandas requests](https://pandas.pydata.org/about/citing.html) two particular things be cited when acknowledging it, please replace your citation with those two

Done

[rkurchin]

@editorialbot generate pdf

[editorialbot]

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

[rkurchin]

@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

- 10.5281/ZENODO.7213391 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.21105/joss.01026 is OK
- 10.21105/joss.03021 is OK
- 10.18637/jss.v059.i10 is OK

MISSING DOIs

- No DOI given, and none found for title: Pandas: A Foundational Python Library for Data Ana...

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#5105, then you can now move forward with accepting the submission by compiling again with the command @editorialbot 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.

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CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Kuric
  given-names: Martin
  orcid: "https://orcid.org/0009-0009-7292-7714"
- family-names: Ebert
  given-names: Regina
  orcid: "https://orcid.org/0000-0002-8192-869X"
contact:
- family-names: Kuric
  given-names: Martin
  orcid: "https://orcid.org/0009-0009-7292-7714"
doi: 10.5281/zenodo.10775033
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kuric
    given-names: Martin
    orcid: "https://orcid.org/0009-0009-7292-7714"
  - family-names: Ebert
    given-names: Regina
    orcid: "https://orcid.org/0000-0002-8192-869X"
  date-published: 2024-03-09
  doi: 10.21105/joss.06304
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6304
  title: "plotastic: Bridging Plotting and Statistics in Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06304"
  volume: 9
title: "`plotastic`: Bridging Plotting and Statistics in Python"

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[editorialbot]

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[editorialbot]

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[arfon]

@gmrandazzo, @SunnyXu – many thanks for your reviews here and to @rkurchin 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 ✨

@markur4 – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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