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[REVIEW]: A Modularised Java library for 3D Euclidean geometry #4283

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@agdturner<!--end-author-handle-- (Andy Turner) Repository: https://github.com/agdturner/ccg-v3d Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @abhishekvp, @behollister Archive: Pending

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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

@abhishekvp, @behollister 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:

@editorialbot generate my checklist

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

📝 Checklist for @abhishekvp

editorialbot commented 2 years ago

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

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editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.31 s (160.4 files/s, 104185.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                            38           1502          10763          18723
XML                              2              7             45            237
Maven                            1              7             36            195
Markdown                         2             32              0            163
YAML                             2              4              4             48
TeX                              1              3              0             32
JSON                             2              0              0             30
JavaScript                       1              0              0              1
-------------------------------------------------------------------------------
SUM:                            49           1555          10848          19429
-------------------------------------------------------------------------------

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

Wordcount for paper.md is 1204

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

OK DOIs

- None

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:

VivianePons commented 2 years ago

@editorialbot add @behollister as reviewer

editorialbot commented 2 years ago

@behollister added to the reviewers list!

behollister commented 2 years ago

Review checklist for @behollister

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

behollister commented 2 years ago

Posted issue for submission review: https://github.com/agdturner/ccg-v2d/issues/1

VivianePons commented 2 years ago

Hi, @behollister and @agdturner can you update me the state of the review / requests?

Also, @abhishekvp I see you haven't generated your checklist, when do you think you can start the review?

Thanks

agdturner commented 2 years ago

Hi @VivianePons. @behollister has identified an issue to do with getting started with the library using Maven. There was a slight confusion, but I believe I have addressed the issue. The library is organised along Maven guidelines which place all the test classes in a similar but separate directory structure to the source code. @behollister had suggested to reorganise this along the lines of a standard Eclipse project which I don't think is necessary. Hopefully loading the project as a Maven project in Eclipse has made things easier. I have not used Eclipse for a number of years preferring Apache NetBeans. I assume it is just as easy to open a Maven project in Eclipse as it is in Netbeans so that all the unit tests are easy to run. Since submitting to JOSS I have found a further Use Case scenario for the library. It is a physics problem which I hope to work on over the summer. This could help strengthen the statement of need - especially if I succeed in using the library to solve the problem that Joe Barker of @stonerlab set me which is along the following lines: Toon Verstraelen (https://scicomp.stackexchange.com/users/156/toon-verstraelen), Minimum image convention for triclinic unit cell, URL (version: 2012-09-01): https://scicomp.stackexchange.com/q/3107. I can provide further details of this if wanted, but essentially there should be a general solution that is more efficient than a brute force search in order to find the minimum distance from one point to a regular set of other points in some kind of parallelepiped tessellation as is common in crystalline/metallic materials... Thanks everyone for your efforts with this review.

behollister commented 2 years ago

Sorry for the delay. Very busy at the moment.

The academic term is in its final week, and I have duties of grading and student presentations to attend. I'll return to this review and have it completed next week.

Again, thank you for all of the information provided. It will surely facilitate my review's completion next week and is greatly appreciated.

behollister commented 2 years ago

Build issue using Maven project via Eclipse IDE: https://github.com/agdturner/ccg-v3d/issues/2

behollister commented 2 years ago

@VivianePons, @agdturner, according to https://github.com/openjournals/joss-reviews/issues/4283#issuecomment-1124573068, it might be prudent for @agdturner to expand on unchecked items (@behollister 'checklist') as of Jun 3, before a possible acceptance of the submission.

@agdturner, you mention additional work this summer that will strengthen the submission in terms of "statement of need."

behollister commented 2 years ago

Hi @VivianePons. Can you please answer @agdturner 's question here: https://github.com/agdturner/ccg-v3d/issues/4#issuecomment-1146891572

Also, before any decision can be made, I believe we need feedback from @abhishekvp as well.

VivianePons commented 2 years ago

Dear @agdturner and @behollister

If I understand correctly, @behollister has raised an issue and @agdturner is asking if it's better to withdraw and resubmit. This really depends on how much time is needed to "fix" the issue in a way that would be sufficient for the the reviewer to be satisfied. From what I read, it does not concern directly the software but more the paper itself and in particular the use cases.

I'd say, it's really up to you @agdturner . If you believe you can make this change in the coming days / weeks, then we can continue with this process. On the other hand, if you prefer to have more time and to prepare a better, more complete, submission, this is also possible.

About @abhishekvp : he hasn't answered my emails. If we continue to the process, I will contact him again and if still no response, I'll look for another reviewer. For the paper to get published, we indeed need 2 completed reviews

agdturner commented 2 years ago

I don't have time in the next two months to develop a scientific use case that proves the utility of the software in providing a new capability. There are many general applications for processing tetrahedra (https://en.wikipedia.org/wiki/Tetrahedron#Applications) and this is one thing that the library supports, for example, calculating the minimum distance between two tetrahedrons, which could be useful for physical object collision avoidance...

VivianePons commented 2 years ago

Yes I perfectly understand.

From what I read in the comment, the original question was about the "References" check box but somehow, it drifted and now it seems to me we are discussing the "Substancial scholarly effort"

So my questions would be for @behollister : in the current state of the paper and with the explanation from @agdturner , do you believe you can check those two boxes? If not, can you be a bit more specific about what is missing? For example, what part of the paper would require more citations in your opinion?

behollister commented 2 years ago

Hi @VivianePons and @agdturner,

Currently there are only unit tests and one reference.

An application (short) need not be an original use case, but something complementary to existing literature -- @abhishekvp may have less/more requirements. Select an existing publication suggesting a calculation using the submission library for completeness. Include the application (and reference paper) with the JOSS submission. Relates to: https://github.com/agdturner/ccg-v3d/issues/4.

I don't believe this should require a withdraw and resubmit.

VivianePons commented 2 years ago

Update: I have contacted the other reviewer, he had been busy these past months but he will be doing the review soon.

I will be on leave for the next few weeks and will follow things when I come back.

VivianePons commented 2 years ago

/ooo July 16 until August 4

abhishekvp commented 2 years ago

Review checklist for @abhishekvp

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

abhishekvp commented 2 years ago

Apologies for the late review. Please find my review comments below:

The paper proposes and implements the ccg-v3d - an extensible Java library for working with 3D Euclidian Geometry.

Thanks to @agdturner for considering to submit to the Journal of Open Source Software. The author's contribution to the open source community are appreciated.

Although the code contributions in the repository seem complete and useful, the research paper has significant room for improvement. As per the reviewer checklist - specific comments to each of the checklist items are as follows:

On the documentation aspect of the code-repository -

Overall the code repository is mature, but the paper has room for improvement. It is recommended that author refer the guidelines for submitting to JOSS here. Sincerely appreciate the author's efforts towards sharing this work with the open-source community.

arfon commented 1 year ago

@VivianePons – it seems like this submission is making slow (but steady) progress towards being ready to accept at some point soonish?

@agdturner – how are you getting along making changes based on the reviewer feedback?

agdturner commented 1 year ago

Hi @arfon, everyone. Thanks for the message and for the reviews which seem fair. I am making slow (and hopefully steady progress) to address reviewer feedback, and refactoring the code to make it better and make the development more sustainable. I developed some rendering code in a very similarly named repository (ccg-r3d) and had some success in visualising a Utah Teapot (a sort of "Hello World" program equivalent for 3D model graphics rendering). I'm currently working on rendering models from different camera angles and distances. There have been some structural changes to classes in the refactoring work. I will update the paper and documentation to reflect this. I will also spend some more time exploring other open source 3D Modelling software as suggested whilst developing science use case scenarios... Sorry for being slow with this...

VivianePons commented 1 year ago

Thank you for the update. @arfon : what do you think the best course of action is? Should we pause the submission and come back to it in a few months? Or should we ask the author to resubmit whenever it is ready? Since we started the review, I have stepped back as an editor for JOSS. So whatever we decide, as this is not going to be finish soon, it would be better to assign a new editor for the paper.

arfon commented 1 year ago

@agdturner – I'm going to mark this as paused for now and let's revisit in a couple of months?

Since we started the review, I have stepped back as an editor for JOSS. So whatever we decide, as this is not going to be finish soon, it would be better to assign a new editor for the paper.

Yes, of course. No problem at all. I can take this one on from here. Thank you @VivianePons!

arfon commented 1 year ago

@editorialbot assign me as editor

editorialbot commented 1 year ago

Assigned! @arfon is now the editor

agdturner commented 1 year ago

Hi @arfon Thanks for taking over the editing role for this. Let me see what I can get around to in the next couple of months. I have improved my 3D rendering code and am working on some science use case scenarios.

behollister commented 1 year ago

@agdturner, @arfon: Glad to hear of progress. Let me know when I should continue my review.

arfon commented 1 year ago

:wave: @agdturner – it's a month since we last heard from you – how are you getting along here with your updates?

agdturner commented 1 year ago

Hi @arfon, I have improved the rendering code and applied this to visualise a few other data sets going beyond the Hello World Utah Teapot. I added more images in the ccg-r3d README. A colleague supplied me with some data for a mountain region that they are studying. It is just the surface triangles and not really volumes, but I am hopeful this will lead to the development of a science use case scenario. I've extended the library so that calculations can be done optionally using IEEE double precision floating point coordinates. This should make it straightforward to compare results and provide examples of differences and where using more heavyweight arbitrary precision numbers for coordinates is useful. I think I might be able to find some examples where it is beneficial to have greater precision and range than is offered by double precision. I've been looking at some open source software with 3D capabilities (Apache Commons Geometry, Blender, MeshLab, three.js and QGIS), and have been thinking about what sort of comparisons to make with ccg-v3d.

arfon commented 1 year ago

OK thanks for the update @agdturner. What's your current estimate for when you might be ready for the reviewers to take another look here?

agdturner commented 1 year ago

Hi @arfon, On the current trajectory I estimate not for several months as I think there is still a lot of work needed to address all the points of the reviewers. Unfortunately, other demanding work is now taking priority and depending on how that goes, I might not find time to concentrate on this much in the coming months. Does it cause a problem if this remains paused? Thanks for your help.

arfon commented 1 year ago

@agdturner – keeping submissions open pending major updates is discouraged in the long run at JOSS, primarily because of the challenge of keeping reviewers 'on the hook'. Given that this submission has been in a hold since October, I'm willing to give this another month but if this isn't ready for reviewers again by then we'll reject and encourage resubmission as and when you're able to make these updates.

arfon commented 1 year ago

:wave: @agdturner – as it looks like you're not going to be able to make these changes in the foreseeable future, I'm going to close this review now but we would welcome a resubmission in the future as and when you're able to respond to reviewer feedback.

@abhishekvp, @behollister – many thanks for your efforts here. Apologies this review didn't work out.

arfon commented 1 year ago

@editorialbot reject

editorialbot commented 1 year ago

Paper rejected.