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[PRE REVIEW]: VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data #4222

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@baxmittens<!--end-author-handle-- (maximilian bittens) Repository: https://github.com/baxmittens/VTUFileHandler Branch with paper.md (empty if default branch): Version: 0.1.3 Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @dmbates, @mkitti Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/d0b4c4084b6c7ce45ff84cf01a50fbe0/status.svg)](https://joss.theoj.org/papers/d0b4c4084b6c7ce45ff84cf01a50fbe0)

Author instructions

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

@baxmittens if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

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editorialbot commented 2 years ago

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@editorialbot commands

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

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editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (508.8 files/s, 43297.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           11            115             44            822
XML                              4              0              0            420
Markdown                         2             30              0            133
TeX                              1              3              0             33
TOML                             1              2              0             15
-------------------------------------------------------------------------------
SUM:                            19            150             44           1423
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 948

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.23919/eucap.2017.7928679 may be a valid DOI for title: Surrogate models for uncertainty quantification: An overview
- 10.1109/38.865875 may be a valid DOI for title: Visualizing with VTK: a tutorial
- 10.21105/joss.03673 may be a valid DOI for title: ogs6py and VTUinterface: streamlining OpenGeoSys workflows in Python

INVALID DOIs

- None
editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot query scope

editorialbot commented 2 years ago

Submission flagged for editorial review.

Kevin-Mattheus-Moerman commented 2 years ago

@baxmittens thanks for this submision, I am the AEiC for JOSS on call the coming week. I've briefly reviewed this submission and have just triggered an additional scope review by our editorial board. This is normal for submissions of this size (in terms of lines of code and functionality). This scope review should take about 2 weeks to complete. In the mean time, perhaps you can check and address these potentially missing DOIs :point_up:, you can call @editorialbot generate pdf here to update the paper and you can check the references using @editorialbot check references.

baxmittens commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

baxmittens commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

Checking the BibTeX entries failed with the following error: 

Failed to parse BibTeX on value "pages" (NAME) [#<BibTeX::Bibliography data=[2]>, "@", #<BibTeX::Entry >, {:title=>["Visualizing with VTK: a tutorial"], :author=>["Schroeder, William J and Avila, Lisa Sobierajski and Hoffman, William"], :journal=>["IEEE Computer graphics and applications"], :volume=>["20"], :number=>["5"], :doi=>["10.1109/38.865875"]}]
editorialbot commented 2 years ago

:warning: An error happened when generating the pdf.

baxmittens commented 2 years ago

@editorialbot generate pdf

baxmittens commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.23919/EuCAP.2017.7928679 is OK
- 10.1109/38.865875 is OK
- 10.21105/joss.03673 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kthyng commented 2 years ago

Hi @pdebuyl! Is this submission a good fit for you?

kthyng commented 2 years ago

@editorialbot invite @pdebuyl as editor

editorialbot commented 2 years ago

Invitation to edit this submission sent!

kthyng commented 2 years ago

Oops, forgot to tell @baxmittens that this submission was deemed to be in scope, so we will proceed with the review.

pdebuyl commented 2 years ago

Hi @kthyng may I deflect this? I am interested but got a lot of delay on other work items, including my JOSS editorial duties, since january and would like to focus on those in the short term.

danielskatz commented 2 years ago

Yes, we'll find another editor

danielskatz commented 2 years ago

👋 @jbytecode - Would you be able to edit this submission?

danielskatz commented 2 years ago

@editorialbot invite @jbytecode as editor

editorialbot commented 2 years ago

Invitation to edit this submission sent!

jbytecode commented 2 years ago

@danielskatz gladly, thanks!

jbytecode commented 2 years ago

@editorialbot assign me as editor

editorialbot commented 2 years ago

Assigned! @jbytecode is now the editor

jbytecode commented 2 years ago

@baxmittens - Thank you for this submission.

If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @ - because we don't want to bother them with unnecessary notifications). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

baxmittens commented 2 years ago

@jbytecode thank you for editing my submission.

pdebuyl commented 2 years ago

Thank you @danielskatz

jbytecode commented 2 years ago

@baxmittens - any suggestions for potential reviewers?

baxmittens commented 2 years ago

@jbytecode - unfortunately, this link with the list of reviewers from above is not working. If you tell me, where to find this list, I would be glad to look for potential reviewers.

jbytecode commented 2 years ago

@baxmittens - how about this: https://docs.google.com/spreadsheets/d/1PAPRJ63yq9aPC1COLjaQp8mHmEq3rZUzwUYxTulyu78/edit#gid=856801822

baxmittens commented 2 years ago

@jbytecode I did not look over the entire list but here are some suggestions. Hope this helps.

ChrisRackauckas juliohm dmbates jarvist Datseris wkearn rowanc1

jbytecode commented 2 years ago

👋👋👋 Dear @ChrisRackauckas 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/4222).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

jbytecode commented 2 years ago

👋👋👋 Dear @juliohm 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/4222).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

juliohm commented 2 years ago

I would love to help but I am super busy in the following the months. Please feel free to contact another potential reviewer 🙏🏽

Thank you for the great contribution @baxmittens 🎆 Hopefully we can provide integrations with Meshes.jl in the future.

jbytecode commented 2 years ago

@juliohm - thank you for the quick response, hope we will work together in later submissions.

jbytecode commented 2 years ago

👋👋👋 Dear @dmbates 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/4222).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

dmbates commented 2 years ago

I just glanced at the repository for this package and there are several issues that I think should be addressed before the paper is considered for publication in JOSS. As it stands the repository is not in the standard form for a Julia package.

I would recommend that the authors first revise the package to follow the Julia package standards, add documentation for the exported functions and structs, and submit the package for inclusion in the general package registry, then reconsider the paper. It is not a particularly onerous task to get a Julia package registered but it is not trivial either. There are some resources such as the PackageTemplates package and the JuliaRegistrator bot but it still takes some effort the first time through. There is a slack channel dedicated to questions on package registration.

jbytecode commented 2 years ago

@dmbates - thank you so much for the quick reply. You can review the paper in light of those comments when you are assigned as a reviewer, and I think those changes can be applied by the authors. Do you accept to be a reviewer?

dmbates commented 2 years ago

Yes, I can be a reviewer but my comments are primarily regarding Julia packaging. I don't do finite-element methods and have no experience with VTU or similar formats. Thus I can only comments on Julia programming and packaging aspects.

jbytecode commented 2 years ago

@dmbates I think you are a suitable reviewer for this project and in light of your ideas, we can improve this package. Thank you!

jbytecode commented 2 years ago

@editorialbot add @dmbates as reviewer

editorialbot commented 2 years ago

@dmbates added to the reviewers list!

jbytecode commented 2 years ago

@dmbates thank you, you are assigned. Whenever we assign the 2nd reviewer, a new thread will be created with task lists. I will inform you, please keep in touch.

baxmittens commented 2 years ago

hello @dmbates thank you for reviewing and providing some initial feedback.

I just glanced at the repository for this package and there are several issues that I think should be addressed before the paper is considered for publication in JOSS. As it stands the repository is not in the standard form for a Julia package.

I don't think my package it should be a standard julia package at this point. There is WriteVTK.jl and ReadVTK.jl. I did not really want to use those packages at the moment but I would consider it in the future. As I wrote in the paper, my project is mainly about automation of stochastic postprocessing and therefore the need to implement a basic algebra on a result file format.

  • I personally don't know what a VTU file is - from the example I assume the V stands for Voxel but that is about all I can figure out. The purpose of the package should be explained more clearly and a reference to the definition of the VTU file format included.

I included that in the Readme.md

  • One very trivial issue is that the name of the repository should be VTUFileHandler.jl not VTUFileHandler.

Changed.

  • At present there is no docs directory and no inline documentation in the code. This means there will be no documentation available using the help system in Julia.

You're right. I will add some inline documentation.

  • The include statements in src/VTUFileHandler.jl are not in the standard form, using relative paths that can become unreliable

Could you please give me a short example how this would look like for a project with subfolders? I looked for it but couldn't find any. I thought that something like include(joinpath(".","VTUFileHandler","utils.jl")) should work for Apple/Windows/Linux.

  • It is more of a stylistic issue but burying directives like import TranscodingStreams and import Dates way down in the source code tree is unusual. It is more common to put these in src/VTUFileHandler.jl - in most cases right after the declaration of the module name.

I'll change this.

I would recommend that the authors first revise the package to follow the Julia package standards, add documentation for the exported functions and structs, and submit the package for inclusion in the general package registry, then reconsider the paper. It is not a particularly onerous task to get a Julia package registered but it is not trivial either. There are some resources such as the PackageTemplates package and the JuliaRegistrator bot but it still takes some effort the first time through. There is a slack channel dedicated to questions on package registration.

I think I can fix these issues rather quickly. But as I said I do not plan to publish this as a official julia package at this stage of the project.

The VTUFileHandler is just one part of a stochastic toolbox for geoscience applications I am developing, consisting of:

AdaptiveSparseGrids.jl and OGSUQ.jl could serve for two additional joss papers. My plan was to upload these projects later this year and subsequently submit two additional papers, here. I'll think if this is all finished, I'll reconsider publishing the whole project as standard julia package.

jbytecode commented 2 years ago

👋👋👋 Dear @jarvist 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/4222).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.