[REVIEW]: colorspace: A Python Toolbox for Manipulating and Assessing Colors and Palettes

[editorialbot]

Submitting author: @retostauffer (Reto Stauffer)
Repository: https://github.com/retostauffer/python-colorspace
Branch with paper.md (empty if default branch):
Version: v0.5.0
Editor: @jromanowska
Reviewers: @hollowscene, @dmreagan
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/94041eecfa4b186c7c07252875817578"><img src="https://joss.theoj.org/papers/94041eecfa4b186c7c07252875817578/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/94041eecfa4b186c7c07252875817578/status.svg)](https://joss.theoj.org/papers/94041eecfa4b186c7c07252875817578)

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

@hollowscene & @dmreagan, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

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

📝 Checklist for @dmreagan

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.23 s (360.1 files/s, 108731.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          55           4134           7429           9260
CSV                              1              0              0           1058
TeX                              2            129             15            986
Markdown                         4            157              0            459
YAML                             6             54             79            344
JSON                             6             13              0            318
SVG                              3              2              2            233
Sass                             2             17             14            134
make                             1             22             32             65
R                                2             31             18             46
INI                              1              1              0              7
-------------------------------------------------------------------------------
SUM:                            83           4560           7589          12910
-------------------------------------------------------------------------------

Commit count by author:

   499	Reto Stauffer
    54	=
    34	Achim Zeileis
     6	github-actions[bot]

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1582

✅ The paper includes a Statement of need section

[editorialbot]

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

OK DOIs

- 10.1038/s41467-020-19160-7 is OK
- 10.18637/jss.v096.i01 is OK
- 10.1109/tvcg.2009.113 is OK
- 10.1109/mcse.2007.55 is OK
- 10.21105/joss.03021 is OK
- 10.5281/zenodo.10957263 is OK
- 10.5281/zenodo.12514964 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- 10.1016/0306-4573(91)90096-5 may be a valid DOI for title: Envisioning Information
- No DOI given, and none found for title: Color Use Guidelines for Data Representation
- No DOI given, and none found for title: Color
- No DOI given, and none found for title: Fundamentals of Data Visualization
- No DOI given, and none found for title: What’s New in Matplotlib 2.0 (Jan 17, 2017), Chang...
- No DOI given, and none found for title: Colour for Presentation Graphics
- No DOI given, and none found for title: Colormap
- No DOI given, and none found for title: Colormaps
- No DOI given, and none found for title: palettable: Color Palettes for Python
- No DOI given, and none found for title: cmcrameri: Python Wrapper around Fabio Crameri’s P...

INVALID DOIs

- None

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

[jromanowska]

👋🏼 @retostauffer @hollowscene @dmreagan 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

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7120 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

I encourage you to over-communicate and let everyone know that you're on the task every now and then, instead of waiting several weeks to collect all your comments, questions, or suggestions.

Please feel free to ping me (@jromanowska) if you have any questions/concerns.

[hollowscene]

Review checklist for @hollowscene

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/retostauffer/python-colorspace?
• 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 (@retostauffer) 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?

[hollowscene]

Hey everyone, just thought I'd make an early start to some of the housekeeping tickboxes. As a heads up - I'll most likely hold off on actually installing and playing around with the package until I've got a bit more time this weekend.

I hate to be nitpicky but just for the statement of need tickboxes, I feel like I'm not getting an explicit designation of who the target audience is. I definitely acknowledge it does feel a bit redundant for this package considering how ubiquitous its usage should be, and it sort of is implied within the current statement of need. But just wanted to double check this before ticking it off as I'm not entirely sure how strict we need to be!

[jromanowska]

Good point! The tickboxes are very general - to suit all the different types of software submitted to JOSS. As long as you feel that the "Statement of need" section in the paper is alright, you can check off the box. However, you could also ask the authors to have a second look at it and improve if you feel something is missing.

And thanks for starting right off - we encourage here over-commenting, so let's keep it like that 👍

[dmreagan]

Review checklist for @dmreagan

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/retostauffer/python-colorspace?
• 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 (@retostauffer) 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?

[hollowscene]

Hello, just to update, I've made a bit more of a dent into my checklist. Hoping to be able to work through the rest over the week ahead

[dmreagan]

I also wondered about the explicit target audience as in #7120 (comment). But I think it is implied that the intended users are the same users of the "most graphics packages" the authors refer to in the second paragraph. It's a ✅ for me.

[dmreagan]

Question about references: is it OK to have web links in the body of the paper? The authors have included direct URLs to a few of their own web resources while putting all 3rd-party links down in the References section.

[jromanowska]

Question about references: is it OK to have web links in the body of the paper? The authors have included direct URLs to a few of their own web resources while putting all 3rd-party links down in the References section.

For me, that seems logical. However, if you think it doesn't suit, go ahead and suggest another way of doing it. JOSS does not have strict formatting rules for the papers.

[hollowscene]

Just finished my review checklist.

I did encounter one issue with some tests failing due to some Windows OS discrepancies which I've raised a GitHub issue for. Regardless, automated tests are thorough and well documented so I've still ticked it off in the checklist.

Regarding references, adding 3rd-party links seems reasonable and is more quickly accessible so I've also given it a tick.

Overall, the paper is well written and the package has had significant work dedicated to it. I have no doubt this package will be incredibly useful for both casual and veteran data vizzers. Amazing work :)

[zeileis]

Andrew @hollowscene, thank you so much for the positive and constructive feedback along with the issues and pull requests in the GitHub project. Reto is currently on vacation but we'll incorporate all your helpful suggestions in the software and paper when he's back! Thanks & best wishes, Achim

[jromanowska]

@zeileis , @retostauffer - how is it going? Let us know when you're done with the modifications.

[zeileis]

Julia @jromanowska, thanks for the reminder and apologies for the delay. Reto will be back from his vacations this week. I already took some notes and I expect that we will have a revision and response to the helpful reviews very soon.

[zeileis]

Another follow-up, unfortunately just to say that we will need a bit more time because corona had other plans for us this week. But we promise that we will get back to this as soon as possible. Apologies again!

[jromanowska]

Another follow-up, unfortunately just to say that we will need a bit more time because corona had other plans for us this week. But we promise that we will get back to this as soon as possible. Apologies again!

Thanks for letting us know and stay safe. Get healthy while we're waiting patiently :)

[retostauffer]

Dear @jromanowska, @hollowscene, and @dmreagan,

First of all, we would like to sincerely thank you for handling our submission, as well as for the constructive and valuable feedback on our work. We apologize for the delayed response due to vacations and covid.

We have thoroughly addressed all comments from the review as well as the pre-review (handled by Daniel S. Katz).

We have also updated the README to acknowledge the contributions of the reviewers and editors involved in this process. Your efforts in enhancing the quality of our work are greatly appreciated.

Paper

• Highlight the target audience as well as the research scope of the software. Specifically, we have updated the end of the "Summary" (see paper.md#L34-L37) and the last paragraph of the 'Statement of need' (paper.md#L77-L80).
• Minor touch-ups for layouting purposes.

Software

Key Changes

• New release (v0.5.2) available on PyPI.
• Updated the Installation guidelines to address two issues reported by @dmreagan (see Issue 23 and Issue 24), with the corresponding pull request by @zeileis (see PR 25).
• Fixed an issue where tests using temporary files failed on Windows, as reported by @hollowscene (see Issue 21, addressed in PR 22).
• Addressed the issue that installation from source, as described in the documentation, failed on systems where setuptools was not installed (reported by @dmreagan in Issue 23):
  • Updated the documentation to ensure setuptools is installed when needed.
  • Included setuptools in the Makefile and requirements_devel.txt to ensure it is available when installing colorspace from source.
  • Added a check to verify that setuptools is installed when running setup.py.

Additional Changes

• Fixed a few bugs affecting 32-bit systems in statshelper.py and colorlib.py.
• Adjusted colorspace to function correctly even when the standard library tkinter is missing.
• Fixed a minor visualization bug in demos.Spectrum.
• Replaced the deprecated python setup.py install command with pip install ..
• Streamlined the Installation
  and Community guidelines sections in the documentation.
• Added dedicated rules to run tests for hard and soft dependencies (make hardtest, make softtest).

Once again, thank you for your time and thoughtful feedback. We look forward to your further comments and suggestions.

Best regards,
@retostauffer and @zeileis

[retostauffer]

@editorialbot generate pdf

[editorialbot]

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