[REVIEW]: Manim Slides: A Python package for presenting Manim content anywhere

[whedon]

Submitting author: @jeertmans (Jérome Eertmans)
Repository: https://github.com/jeertmans/manim-slides
Branch with paper.md (empty if default branch):
Version: v4.15.0
Editor: @magsol
Reviewers: @behollister, @bryanwweber
Archive: 10.5281/zenodo.8215167

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/6cea80a2e0854602e095da04908cfdb9"><img src="https://jose.theoj.org/papers/6cea80a2e0854602e095da04908cfdb9/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/6cea80a2e0854602e095da04908cfdb9/status.svg)](https://jose.theoj.org/papers/6cea80a2e0854602e095da04908cfdb9)

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

@behollister & @bryanwweber, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

Review checklist for @behollister

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: v4.13.2
• Authorship: Has the submitting author (@jeertmans) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @bryanwweber

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: v4.13.2
• Authorship: Has the submitting author (@jeertmans) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function of the software can be verified? #207
• 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @behollister, @bryanwweber it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSE reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 786

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (839.1 files/s, 86285.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            659            293           2531
Markdown                        19            284              0            688
YAML                            13             60             57            469
HTML                             1             68              5            218
TOML                             1             11              0             81
TeX                              1              5              0             48
DOS Batch                        1              8              1             26
Bourne Shell                     1             10              0             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            54           1109            363           4081
-------------------------------------------------------------------------------


Statistical information for the repository 'db2d887a27b587ca985b537f' was
gathered on 2023/04/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Fairlight8                       2            50             10            0.84
Federico Galatolo               22           505             35            7.59
Jérome Eertmans                113          4623           1406           84.78
Linus Heck                       6            75             43            1.66
MikeGillotti                     1            15              4            0.27
Tomasz Dądela                    1            15            192            2.91
Wu Tingfeng                      1            53             34            1.22
Wucheng Zhang                    1             3              0            0.04
pre-commit-ci[bot]               4            24             22            0.65
yang-fighter                     1             1              1            0.03

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Fairlight8                   48           96.0          0.7               10.42
Federico Galatolo            94           18.6          1.2                0.00
Jérome Eertmans            3273           70.8          4.5                5.16
Linus Heck                   16           21.3         22.0               12.50
MikeGillotti                 11           73.3          5.5                0.00
Tomasz Dądela                 9           60.0          4.3               33.33
Wu Tingfeng                  20           37.7          5.9               15.00
pre-commit-ci[bot]           11           45.8          5.5                0.00
yang-fighter                  1          100.0          3.2                0.00

[whedon]

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[bryanwweber]

@jeertmans Thanks for the paper and the package! I've created several issues in the repository related to my review:

• Suggestions from JOSE review jeertmans/manim-slides#168
• [DOC] Improve installation documentation with a full end-to-end procedure jeertmans/manim-slides#169
• [FEATURE] Add wheel to PyPI and declare dependencies on Manim/ManimGL jeertmans/manim-slides#170
• [DOC] JOSE Paper: Improve statement of need jeertmans/manim-slides#171
• [DOC] Improve contributions documentation jeertmans/manim-slides#172

Aside from those issues, the version that is tagged here for the paper is not the most current release. @magsol How should that version be updated? Thank you! I look forward to the responses.

[jeertmans]

Thanks for your review @bryanwweber! Indeed, the package has evolved quite a bit since the pre-review process was started. Most importantly, I have added a feature that converts Manim Slides presentations into PowerPoint files, which is pretty convenient for presenting in conferences for example.

I did not want to update the paper prior to the first review, but I can’t surely update the paper so it matches the latest version of Manim Slides.

For the rest of your review, I will address the comments directly in the PRs.

[jeertmans]

Hello @bryanwweber, I have opened a series of PRs to address each of your comments.
I hope they answer your concerns correctly, and I hope open to any new suggestion you might have :-)

Already, thank you for your time!

[magsol]

@whedon set v4.12.0 as version

[whedon]

OK. v4.12.0 is the version.

[bryanwweber]

@jeertmans Thank you! I've left one comment on one of the PRs and otherwise they look good!

[jeertmans]

Thanks @bryanwweber! I've merged all the PRs and released the changes under v4.13.0, which also contains more debugging messages (explaining the bump in minor version).

Tell me if you need anything else to be done :-)

[magsol]

@whedon set v4.13.0 as version

[whedon]

OK. v4.13.0 is the version.

[magsol]

@behollister 👋 Hey Brad, wanted to check in and see if you needed anything for the review, or what kind of timetable you're looking at. Thanks!

[whedon]

👋 @behollister, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @bryanwweber, please update us on how your review is going (this is an automated reminder).

[bryanwweber]

My review is complete, thanks!

[magsol]

@jeertmans Wanted to keep you informed: we're looking to wrap up this review by early-to-mid next week. Sorry for the delay!

[jeertmans]

No problem at all @magsol :)
Thanks for noticing me!

[labarba]

have a look at this tiny fix: labarba/manim-slides#1

[jeertmans]

Thanks for your suggestion @labarba, this is fixed :-)

As the v4.15.0 was released, and the paper is still not published, maybe it would be possible to update the version to v4.15.0, and the Zenodo to 10.5281/zenodo.8215167?

[labarba]

Ah. Do you have the GitHub Zenodo integration set up to update the archive automatically with each release? We do like to ask authors to edit the metadata of the archive so that the title and author list match the paper. (The auto-archives pull as authors all committers to the repo and use the repo name as title.) Could you do that change for the archive we will attach to the JOSE paper?

[labarba]

@editorialbot set v4.15.0 as version

[editorialbot]

Done! version is now v4.15.0

[labarba]

@editorialbot set 10.5281/zenodo.8215167 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8215167

[jeertmans]

Ah. Do you have the GitHub Zenodo integration set up to update the archive automatically with each release? We do like to ask authors to edit the metadata of the archive so that the title and author list match the paper. (The auto-archives pull as authors all committers to the repo and use the repo name as title.) Could you do that change for the archive we will attach to the JOSE paper?

Done! :-)

[labarba]

Oops. Somewhere we missed something. The archive is now 10.5281/zenodo.8215167 and it doesn't show the paper title.

[jeertmans]

Like so @labarba ?

[labarba]

@editorialbot accept

[editorialbot]

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

[editorialbot]

⚠️ Couldn't acccept/publish paper. An error happened. Could not deposit with Open Journals.

[labarba]

@openjournals/dev 👋
This is our first time accepting a paper here at JOSE with the new editorial workflow and bot, and I'm afraid something has gone awry. Help!

[jeertmans]

@labarba That's weird, even more because I received a ORCID notification asking me the permission to link to that paper... which links to 404 not found https://joss.theoj.org/papers/10.21105/jose.00206

Note: I don't think the @openjournals/dev tag works

[arfon]

@xuanxu any chance you could take a quick look?

[xuanxu]

I think I've fixed the error, retrying 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: Eertmans
  given-names: Jérome
  orcid: "https://orcid.org/0000-0002-5579-5360"
doi: 10.5281/zenodo.8215167
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Eertmans
    given-names: Jérome
    orcid: "https://orcid.org/0000-0002-5579-5360"
  date-published: 2023-08-08
  doi: 10.21105/jose.00206
  issn: 2577-3569
  issue: 66
  journal: Journal of Open Source Education
  publisher:
    name: Open Journals
  start: 206
  title: "Manim Slides: A Python package for presenting Manim content
    anywhere"
  type: article
  url: "https://jose.theoj.org/papers/10.21105/jose.00206"
  volume: 6
title: "Manim Slides: A Python package for presenting Manim content
  anywhere"

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]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSE! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00206 jose-papers#129
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00206
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...

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/jose-papers#130

[labarba]

Congratulations, @jeertmans, your JOSE paper is published! 🎉

Huge thanks to. our Editor: @magsol and the Reviewers: @behollister, @bryanwweber — this is all possible thanks to your generous contributions 🙏

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://jose.theoj.org/papers/10.21105/jose.00206/status.svg)](https://doi.org/10.21105/jose.00206)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00206">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00206/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00206/status.svg
   :target: https://doi.org/10.21105/jose.00206

This is how it will look in your documentation:

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[jeertmans]

Many thanks to all :D

[magsol]

Thank you as always to our fearless leader and EiC @labarba, both for shepherding the paper to its publication as she does so well, and for helping iron out some remaining wrinkles with the new editorial bot.