Joss-reviews: [PRE REVIEW]: PVGeo: an open-source Python package for geoscientific visualization in VTK and ParaView

[whedon]

Submitting author: @banesullivan (C. Bane Sullivan)
Repository: https://github.com/OpenGeoVis/PVGeo
Version: 2.0.0
Editor: @leouieda
Reviewers: @gassmoeller, @leguark

Author instructions

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

@banesullivan if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@whedon commands

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1384 with the following error:

Can't find any papers to compile :-(

[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

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[labarba]

👋 @leouieda — it looks like this is a companion package to the submission I assigned you earlier today. It makes sense for you to edit both?

EDIT: I mean this one: https://github.com/openjournals/joss-reviews/issues/1382

[whedon]

PDF failed to compile for issue #1384 with the following error:

Can't find any papers to compile :-(

[banesullivan]

Whoops, forgot to merge the paper into the master branch... on it.

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[labarba]

@leouieda — I will assign you as editor on this one, but do let me know if you have any qualms.

[labarba]

@whedon assign @leouieda as editor

[whedon]

OK, the editor is @leouieda

[banesullivan]

Please note that there is a citation for vtki in this paper: #1382

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1384 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 278 0 --:--:-- --:--:-- --:--:-- 282
Error producing PDF.
! Argument of \caption@ydblarg has an extra }.

\par
l.367 ...dary, and interpreted faulting surfaces.}

Looks like we failed to compile the PDF

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[banesullivan]

How would I go about making sure Figure 2 isn't forced onto its own page? Ideally, I'd like it to be at the top of that page and then have the Mentions section start right under it.

I'm not familiar with the markdown to LaTeX converter used here and how I might implement a fix for this.

[leouieda]

Hi @banesullivan, just an update: I'm trying to find reviewers for your two submissions but I'm having a hard time tracking down people with the right balance of skills. I'm still waiting on a few replies but I'm hoping to get this started soon.

I'm also not too familiar with the manuscript building pipeline. Try moving the figure higher up in the document. You can ask Whedon to compile the PDF from a branch so you don't have to make broken commits to master: @whedon generate pdf from branch custom-branch-name

[banesullivan]

Thank you for the update, @leouieda!

I'll experiment on another branch with the figure layouts - thanks for the tip!

[leouieda]

:wave: Hi @ngoldbaum @rowanc1 would you be interested in reviewing this submission for JOSS?

[ngoldbaum]

I can't, I'm sorry.

[leouieda]

@ngoldbaum thanks for the quick reply :tada: No worries.

[leouieda]

@whedon assign @gassmoeller as reviewer

[whedon]

OK, the reviewer is @gassmoeller

[leouieda]

@gassmoeller thank you agreeing to review :tada: I just wanted to add a disclaimer that @gassmoeller @banesullivan and I have recently been part on the same conference session proposals. However, this does not constitute a conflict of interest according to our policies.

[gassmoeller]

I am looking forward to review this @leouieda. Do I need to do anything to create the actual review issue or will you do that?

[leouieda]

Hi @gassmoeller happy to have you on board! I'll create the review. We're just waiting on a second reviewer. I'm having a hard time finding someone with the right skills and time. Do you have any suggestions?

[banesullivan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[leouieda]

@whedon add @leguark as reviewer

[whedon]

OK, @leguark is now a reviewer

[leouieda]

@banesullivan let us know when things are stable after the rename of vtki/pyvista so we can start this review.

[banesullivan]

@leouieda All is stable and PVGeo is released on version 2.0.0 which is the version I'd like to submit for review (not 1.2.3 mentioned above)

[leouieda]

OK, I'll let whedon do its magic and start the review :+1:

[leouieda]

@whedon set 2.0.0 as version

[whedon]

OK. 2.0.0 is the version.

[leouieda]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[leouieda]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1451. Feel free to close this issue now!

[leouieda]

:wave: @banesullivan @gassmoeller @Leguark please head on over to #1451 for the review. Please don't hesitate to ask if you have any questions about the review process. We encourage reviewers to open issues/PRs in the software repo as well as leave comments on the review thread. As a reminder, if you create any issues/PRs please include openjournals/joss-reviews#1451 in the description so that it will link back to the review. This helps me keep track of what is happening.

[alexgarciac]

hi. as this is python and a py package there should be some sample data so that anyone could test that the package and all the assertions being made in the paper do really work. I read the paper and there is a lot about a lot but there is no sample data to test the package.

[leouieda]

Hi @alexgarciac, the JOSS paper should not contain documentation or data. These are expect to be included in the software documentation, which the submission does. For example: https://pvgeo.org/examples/filters-general/voxelize-points.html