[REVIEW]: GXBeam: A Pure Julia Implementation of Geometrically Exact Beam Theory

whedon commented 2 years ago

Submitting author: !--author-handle-->@taylormcd@prashjha<!--end-editor-- Reviewers: @Kevin-Mattheus-Moerman, @PetrKryslUCSD Archive: 10.5281/zenodo.6558458

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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

@Kevin-Mattheus-Moerman & @PetrKryslUCSD, 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 @prashjha 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 @Kevin-Mattheus-Moerman

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@taylormcd) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @PetrKryslUCSD

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@taylormcd) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Kevin-Mattheus-Moerman, @PetrKryslUCSD it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 2 years ago

Wordcount for paper.md is 822

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (386.2 files/s, 191412.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           13           1729           1069           7310
Markdown                         7            751              0           3076
SVG                              6              6              6           2656
TeX                              1             10              0            119
YAML                             4              5              0             71
TOML                             3              2              0             41
-------------------------------------------------------------------------------
SUM:                            34           2503           1075          13273
-------------------------------------------------------------------------------

Statistical information for the repository 'bef385b8dd4c87a3022f9756' was
gathered on 2021/12/17.
No commited files with the specified extensions were found.

whedon commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.4404703 is OK
- 10.5281/zenodo.5633646 is OK
- 10.5334/jors.151 is OK
- 10.2514/5.9781600866821.0103.0142 is OK
- 10.1002/sapm197352287 is OK
- 10.1016/j.compstruct.2012.04.007 is OK
- 10.1063/1.4985091 is OK
- 10.2514/5.9781600866821.0059.0102 is OK

MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing

INVALID DOIs

- None

whedon 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:

prashjha commented 2 years ago

Thank you @Kevin-Mattheus-Moerman and @PetrKryslUCSD for agreeing to be reviewers. Please read the first couple of comments in this thread and also reviewer guidelines here. Also, you can browse the closed "REVIEW" issues on the "joss-reviews" repository to get some ideas on how to complete the reviews. Good luck!

whedon commented 2 years ago

:wave: @PetrKryslUCSD, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @Kevin-Mattheus-Moerman, please update us on how your review is going (this is an automated reminder).

PetrKryslUCSD commented 2 years ago

Waiting on responses to my suggestions/questions.

taylormcd commented 2 years ago

Sorry for the delay. Had the holidays, then a conference, and am now dealing with being sick. I should be able to address suggestions/questions starting next week.

PetrKryslUCSD commented 2 years ago

No worries.

PetrKryslUCSD commented 2 years ago

@whedon generate pdf

whedon 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:

whedon 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:

PetrKryslUCSD commented 2 years ago

@whedon help

whedon commented 2 years ago

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

@whedon commands

PetrKryslUCSD commented 2 years ago

@whedon commands

whedon commented 2 years ago

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

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

PetrKryslUCSD commented 2 years ago

@prashjha I am sorry, I can't figure out how to submit the review. Is there a whedon command?

prashjha commented 2 years ago

Hi @PetrKryslUCSD, to review, you need to look at the checklists provided, open issues in the software repository to fix issues that you have in mind, and add comments here to the corresponding authors if any. Once your issues have been addressed and you are satisfied with the response and overall quality of the submission, you will simply let me know your decision here.

PetrKryslUCSD commented 2 years ago

OK. In that case I would like to report the review is finished. Recommendation: publish.

prashjha commented 2 years ago

@PetrKryslUCSD, got it. Thank you for taking the time to review this.

Kevin-Mattheus-Moerman commented 2 years ago

@prashjha I'll get to my review in the coming week. Apologies for the delay so far.

Kevin-Mattheus-Moerman commented 2 years ago

@taylormcd I've started the review process. Here are some initial comments. I'll resume work early next week.

[x] On the documentation site under Limitations it says ..More details about the convergence of this package may be found in the examples.... The example link there is broken (it goes here which gives a 404: https://flow.byu.edu/GXBeam.jl/dev/@ref%20Nonlinear%20Analysis%20of%20a%20Cantilever%20Subjected%20to%20a%20Constant%20Moment)
[x] The examples in the documentation appear encoded in a mardown file (i.e. https://github.com/byuflowlab/GXBeam.jl/blob/master/docs/src/examples.md). It would be great however if these could be executed e.g. as jupyter notebooks. Could the authors consider facilitating this? It should largely be a copy-paste excercise to make these executable Jupyter notebooks, whereas currently, as a new user, I find myself having to copy paste a lot to reproduce the examples.
[x] I got an error running the tests, can you assist/investigate? https://github.com/byuflowlab/GXBeam.jl/issues/68

taylormcd commented 2 years ago

@Kevin-Mattheus-Moerman

The broken link is fixed now.
I used for the documentation and examples, which is pretty standard practice in Julia. I would rather not have two versions of the same examples due to the headaches that causes for maintenance. That being said, using might be a good long term solution for supporting Jupyter notebooks as well.
The error is now fixed.

taylormcd commented 2 years ago

@Kevin-Mattheus-Moerman Jupyter notebook versions of the examples are now available.

Kevin-Mattheus-Moerman commented 2 years ago

@taylormcd thanks for adding those. I'll have a look later the coming week. Where can I find the new Jupyter notebook versions?

taylormcd commented 2 years ago

They're linked from the relevant pages in the documentation. Note that I haven't yet created a new release with the changes, so the notebooks are only linked from the development version of the documentation..

prashjha commented 2 years ago

Hi @Kevin-Mattheus-Moerman, just checking if you are close to finishing this review. No worries if you need further time.

Kevin-Mattheus-Moerman commented 2 years ago

@prashjha thanks for the reminder. I reinstalled the software and have been testing it again this week. In particular the jupyter notebooks referred to by @taylormcd. There some some minor issues remaining :point_down:

@taylormcd below are some remaining points:

[x] I get some errors during testing, see; https://github.com/byuflowlab/GXBeam.jl/issues/77
[x] Perhaps I missed them but I cannot see clear community guidelines (instructions on how one might contribute). Can you add these? You can simply add a section on how folks should contribute to your readme or link to a detailed CONTRIBUTING.md file for instance. The basic info should cover how you'd like them to contribute e.g. post issues, or fork and create a pull request. A more detailed approach would be to also state where help is needed and what role folks could play. Perhaps you could even refer to a roadmap.md so potential contributors can see where they might fit in. The level of detail I leave up to you. On detail, you can also consider adding a code of conduct (e.g. a COC.md) if you think your community will grow (see here for templates: https://www.contributor-covenant.org/).

Side note (not a requirement), it would be nice if the software did not rely on vtk for visualization, e.g. if it could use GLMakie for instance.

prashjha commented 2 years ago

@Kevin-Mattheus-Moerman thanks for the update!

taylormcd commented 2 years ago

I added a short contributing section to README.md. I'll probably create a more detailed one later, but this should suffice for now.

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot check references

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot generate pdf

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

@taylormcd @prashjha all issues have now been addressed and I recommend acceptance in JOSS. I wanted to check references, see above, however it seems our bot is not responding to references checking requests this morning. But I am sure you'll check this during the potential acceptance process. Thanks for the opportunity to review this interesting package. All the best.

prashjha 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

- 10.1137/141000671 is OK
- 10.1016/0020-7683(90)90060-9 is OK
- 10.1115/1.3171871 is OK
- 10.1016/0045-7825(88)90073-4 is OK
- 10.1016/0045-7825(85)90050-7 is OK
- 10.5281/zenodo.2682214 is OK
- 10.5281/zenodo.3722891 is OK
- 10.5334/jors.151 is OK
- 10.2514/4.866821 is OK
- 10.1002/sapm197352287 is OK
- 10.1002/sapm197352287 is OK
- 10.1016/j.compstruct.2012.04.007 is OK
- 10.1063/1.4985091 is OK
- 10.1002/nme.532 is OK
- 10.1002/(SICI)1097-0207(19980315)41:5<781::AID-NME308>3.0.CO;2-9 is OK
- 10.1016/0045-7825(94)00056-s is OK
- 10.1002/nme.1620382107 is OK
- 10.1002/nme.1620261105 is OK
- 10.1016/0045-7949(88)90355-0 is OK
- 10.1002/nme.1620260710 is OK
- 10.1002/nme.487 is OK
- 10.1016/0045-7825(95)00724-F is OK

MISSING DOIs

- 10.1002/(sici)1097-0207(19980315)41:5<781::aid-nme308>3.0.co;2-9 may be a valid DOI for title: Finite rotations in dynamics of beams and implicit time-stepping schemes

INVALID DOIs

- None

prashjha commented 2 years ago

@editorialbot generate pdf

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:

prashjha commented 2 years ago

Hi, @Kevin-Mattheus-Moerman, thanks for completing the review.

prashjha commented 2 years ago

Hello @taylormcd, I am reading the draft one last time. If I have any edits or suggestions, I will let you know soon. Meanwhile, could you check the following reference flagged by editorialbot:

Ibrahimbegović, A., & Mikdad, M. A. (1998). Finite rotations in dynamics of beams and implicit time-stepping schemes. International Journal for Numerical Methods in Engineer- ing, 41(5), 781–814. https://doi.org/10.1002/(SICI)1097-0207(19980315)41:5%3C781:: AID-NME308%3E3.0.CO;2-9

prashjha commented 2 years ago

Hi, @taylormcd, see if these suggestions for the draft makes sense:

Line 16: missing space between "researchers" and "(Betsch".
Line 33: "that it is written ..."?
Line 53: "... accelerations are also provided" is better as you use word "support" in the beginning of this sentence.
Line 65: "... sectional analysis"?

After you have updated the draft and also fixed the reference I mentiond, can you also do (if not done already) a 'tagged' release of your code, archive the release using zenedo or other methods? Make sure that the title of zenedo archive matches with the title of this JOSS submission.

Once you are done, I will hand your paper to EiC for the final decision.

taylormcd commented 2 years ago

I adopted the first three changes, but not the last one because multiple section analyses may be necessary for a single GXBeam run. I also tagged a new release and archived it with Zenodo: https://doi.org/10.5281/zenodo.6558458. Let me know if there's anything else that needs to be done.

prashjha 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

- 10.1137/141000671 is OK
- 10.1016/0020-7683(90)90060-9 is OK
- 10.1115/1.3171871 is OK
- 10.1016/0045-7825(88)90073-4 is OK
- 10.1016/0045-7825(85)90050-7 is OK
- 10.5281/zenodo.2682214 is OK
- 10.5281/zenodo.3722891 is OK
- 10.5334/jors.151 is OK
- 10.2514/4.866821 is OK
- 10.1002/sapm197352287 is OK
- 10.1002/sapm197352287 is OK
- 10.1016/j.compstruct.2012.04.007 is OK
- 10.1063/1.4985091 is OK
- 10.1002/nme.532 is OK
- 10.1002/(SICI)1097-0207(19980315)41:5<781::AID-NME308>3.0.CO;2-9 is OK
- 10.1016/0045-7825(94)00056-s is OK
- 10.1002/nme.1620382107 is OK
- 10.1002/nme.1620261105 is OK
- 10.1016/0045-7949(88)90355-0 is OK
- 10.1002/nme.1620260710 is OK
- 10.1002/nme.487 is OK
- 10.1016/0045-7825(95)00724-F is OK

MISSING DOIs

- None

INVALID DOIs

- None

prashjha commented 2 years ago

@editorialbot generate pdf

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:

prashjha commented 2 years ago

@editorialbot set 10.5281/zenodo.6558458 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6558458

openjournals / joss-reviews