Joss-reviews: [PRE REVIEW]: PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK)

[whedon]

Submitting author: @banesullivan (C. Bane Sullivan)
Repository: https://github.com/pyvista/pyvista/
Version: 0.18.1
Editor: @leouieda
Reviewers: @Chilipp, @nicoguaro

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Thanks for submitting your paper to JOSS @banesullivan. Currently, there isn't an JOSS editor assigned to your paper.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1382 with the following error:

Can't find any papers to compile :-(

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[labarba]

👋 @leouieda — the submitting author suggested you as handling editor, and indeed it looks like this is your cup of tea! I'll assign you now, but do let me know if you are disinclined for any reason.

[labarba]

@whedon assign @leouieda as editor

[whedon]

OK, the editor is @leouieda

[banesullivan]

Thanks, @labarba! It looks like whedon successfully rendered the PDF!

From the preview, it seems I may need to change a few things in the Markdown:

• [x] One code snippet runs off the page - I'll try to fix this.
• [x] I'm wondering if I added the figure captions in the correct way in Markdown?
• [x] I may need to shift the figures around. Is there a way to specify the width in markdown that the latex compiler will recognize?

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[leouieda]

@labarba I'd be happy to edit this and the PVGeo paper :+1:

[leouieda]

Hi @banesullivan, I've been going through the paper and I think it's a bit out of our usual format. Quoting from our guidelines:

... JOSS papers are only permitted to contain a limited set of metadata (see header below), Statement of Need, Summary, Acknowledgements, and References sections. ... software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation.

Could you please reformat the paper before we proceed with the review? The information is already in the paper so it's only a matter of cutting and reorganizing. You don't have to remove all the figures. In particular, make sure there are:

• A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience
• A clear statement of need that illustrates the purpose of the software

It would also help if you clarified wether the citations in Mentions are actually using vtki or if they are examples of possible applications of vtki.

[banesullivan]

Thank you for the feedback @leouieda. I have made updates to the paper addressing your concerns.

1. On the note of the paper's format:

   • I have significantly trimmed the content and made sure the paper only contains: Statement of Need, Summary, Mentions, and References sections
   • I have removed all code examples to adhere to JOSS' criteria that "software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation"

2. On the note of ensuring there is a "summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience":

   • I have rewritten the summary to describe the high-level purpose of why we built vtki and what need it fills. Particularly, the paper now focuses on what vtki achieves and what that looks like for a novice programmer/new user rather than the nuances of how it is implemented.

3. On the note of ensuring there is a "clear statement of need that illustrates the purpose of the software"

   • The paper now conveys a more clear narrative of the current state of 3D visualization in Python and what role vtki fills in that space.
   • Specifically, I focused on including this in the first paragraph of the summary:
     > The availability of software for 3D visualization in Python is limited to libraries that are either not capable of handling large, spatially referenced datasets or have inherently complex application programming interfaces (APIs). One of these software libraries is the Visualization Toolkit (VTK) [@vtkbook]; a powerful scientific visualization software library, and with Python bindings, it combines the speed of C++ with the rapid prototyping of Python. Despite this, VTK code programmed in Python using the base VTK python package is unnecessarily complicated as its API merely binds existing C++ calls. The vtki Python package provides a concise, well-documented interface exposing VTK’s powerful visualization backend; enabling researchers to rapidly explore large datasets, communicate their spatial findings, and facilitate reproducibility.

4. I have clarified the mentions to state that the listed publications do indeed leverage vtki for 3D visualization.

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[leouieda]

:wave: Hi @rgmyr @Chilipp would you be interested in reviewing this submission for JOSS?

[Chilipp]

Hey @leouieda and @banesullivan!

I am looking forward to review this during the next week. Looks very interesting.

[leouieda]

@Chilipp thanks for the quick response! Can I just get a confirmation that you're agreeing to review this submission? (just to make sure)

[Chilipp]

sure, my apologies @leouieda . Yes, I agree to review it

[banesullivan]

👋 Hi @Chilipp, thanks for taking the time to review vtki!!

[leouieda]

@whedon assign @Chilipp as reviewer

[whedon]

OK, the reviewer is @Chilipp

[leouieda]

@Chilipp sorry this is taking so long. @banesullivan is in the process of renaming the vtki package to vista (see pyvista/vista#208). We'll need to update this issue before we can start the review.

[leouieda]

:wave: Hi @RcSepp would be interested in reviewing this submission for JOSS?

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[banesullivan]

We have settled on PyVista as the new name of this software - sorry for the delay!

[Chilipp]

We'll need to update this issue before we can start the review.

All right @leouieda, just tell me when I can start the review

[banesullivan]

Please note, @akaszynski and I have changed the paper title to "PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK)"

@whedon generate pdf

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[banesullivan]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[leouieda]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[leouieda]

OK, I just renamed the issue and updated the link in the description to the new package. Everything seems to work and the link inserted in the PDF is the correct one now. I'm just waiting on some reviewer invitations to start the review. Hopefully that can be resolved within a week or so.

[leouieda]

@whedon add @nicoguaro as reviewer

[whedon]

OK, @nicoguaro is now a reviewer

[leouieda]

@JonathanReardon as I said on twitter @nicoguaro beat you to it this time :slightly_smiling_face: Thanks again for volunteering and I hope you'll consider doing so again the future.

[leouieda]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1450. Feel free to close this issue now!

[leouieda]

@banesullivan @Chilipp @nicoguaro please head on over to #1450 for the actual review. Please feel free to post any comments there and open issues in the software repository. Don't hesitate to ask if you have any questions.