[REVIEW]: Paraqus: Exporting Finite Element Simulation Results from Abaqus to VTK

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@tmfrlm@prashjha<!--end-editor-- Reviewers: @Huzaifg, @lelaus Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9ab64c645825e0d56d84512c4cac597e"><img src="https://joss.theoj.org/papers/9ab64c645825e0d56d84512c4cac597e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9ab64c645825e0d56d84512c4cac597e/status.svg)](https://joss.theoj.org/papers/9ab64c645825e0d56d84512c4cac597e)

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

@alizma & @KParas, 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 @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 ✨

Checklists

📝 Checklist for @lelaus

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

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

OK DOIs

- 10.5281/zenodo.50550 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.cageo.2016.11.008 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (563.6 files/s, 114036.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          27           1621           2512           3549
Fortran 77                       1            164             98            608
YAML                             5             27              4            130
reStructuredText                 6             81             21            123
Markdown                         2             21              0             45
DOS Batch                        1              8              1             26
TOML                             1              3              0             25
TeX                              1              2              0             16
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            45           1931           2643           4531
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 539

editorialbot commented 1 year ago

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

prashjha commented 1 year ago

Dear @alizma and @KParas, please read the first couple of comments in this thread and create your review checklist if not done already. You can read the 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!

KParas commented 1 year ago

Review checklist for @KParas

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 https://github.com/tmfrln/paraqus?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@tmfrlm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

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

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] 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, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] 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?

KParas commented 1 year ago

@prashjha How do we verify this checkpoint in case there seem to be no commits from an author but?

"Does the full list of paper authors seem appropriate and complete?"

Does JOSS also require/recommend an author contribution section like some other journals?

prashjha commented 1 year ago

@KParas, good point. You can ask the author, @tmfrln, for clarification. While the "Contributions" section is not mandatory, as a reviewer, you can request authors to have one in the draft.

prashjha commented 1 year ago

Hi @alizma, Could you please update how the review is progressing? I see that you have not yet created a checklist. I would appreciate it if you could get started soon. Thanks!! :)

alizma commented 1 year ago

Review checklist for @alizma

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 https://github.com/tmfrln/paraqus?
[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 (@tmfrlm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] 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, who the target audience is, and its relation to other work?
[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?

tmfrln commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

tmfrln commented 1 year ago

Hi everyone, we added a contributions section to the paper to address the question @KParas asked. If you need any additional information please let me know. We also fixed an invalid doi for one of the references.

alizma commented 1 year ago

Hi @tmfrln, could you add a CONTRIBUTING.md file that discusses "guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support"?

Also I know the dependencies are minimal, but nevertheless, these should be listed somewhere in the Installation section of your documentation, and ideally also provided as a requirements.txt or equivalent for completeness sake.

Also @prashjha, could you suggest how I should confirm end-to-end functionality of the provided examples if I do not have access to Abaqus?

tmfrln commented 1 year ago

Hi @alizma,

I added the file that you requested to the repository.
The dependencies are indeed minimal, only numpy is required to run Paraqus. This dependency is specified in the file pyproject.toml (without a version number, since we are not aware of a specific requirement). The python interpreter shipped with Abaqus has numpy preinstalled, and if Paraqus is installed standalone via pip, numpy should be automatically installed also. I updated the documentation with this information as well, but think that a requirements.txt would conflict with the pyproject.toml.

prashjha commented 1 year ago

Hi @tmfrln, could you add a CONTRIBUTING.md file that discusses "guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support"?

Also I know the dependencies are minimal, but nevertheless, these should be listed somewhere in the Installation section of your documentation, and ideally also provided as a requirements.txt or equivalent for completeness sake.

Also @prashjha, could you suggest how I should confirm end-to-end functionality of the provided examples if I do not have access to Abaqus?

@alizma, it looks like the library comes with the Abaqus-produced files to test the scripts. You do not need to run Abaqus to test this library. The authors do provide instructions to reproduce the Abaqus output file in case anyone is interested. But for the review, you can assume that the Abaqus output file is given and the scripts work as intended. @tmfrln, does it sound right?

tmfrln commented 1 year ago

@prashjha The library is split up in two parts: The vtk writers and a general data model are independent of Abaqus and can be used/tested in any python environment. The second part is supposed to be run in Abaqus and implements the interface of the Abaqus database to the data model. So for some of the examples, Abaqus in indeed required to test them. One of the main ideas of this package is to export results from Abaqus once, and have them in a format that can be shared with people who do not use Abaqus afterwards. If this would be helpful, i could offer to showcase the Abaqus-related examples on a zoom call or similar. I am however not sure if that is ok with JOSS's requirements for peer review. If the group of @KParas has access to Abaqus, maybe it would be an option for him to share if the examples worked for him?

prashjha commented 1 year ago

@KParas, could you please provide an update on your review? Thanks!

prashjha commented 1 year ago

Hi @KParas, please provide an update on your review. It has been too long, and we need to speed up the review, please. There are a lot of items remaining in your checklist.

prashjha commented 1 year ago

@alizma, could you please provide an update on your review? Thanks!

KParas commented 1 year ago

@prashjha Due to some unforeseen helath issues and othe commitments, it did not go as planned. To be realistic, I will be able to finish the review until January end, in case it still suits you. My sincere appologies for the delay and inconvenience caused.

prashjha commented 12 months ago

Hi @KParas, thank you for letting me know. I sincerely hope everything gets sorted out. Yes, January end will work but it has to be a hard deadline. Please let me know if this is acceptable.

prashjha commented 10 months ago

Dear @alizma and @KParas, we are running significantly behind, and I would greatly appreciate it if you could finish the review soon. Please share the update and realistic timeline by which you could finish the reviews. Again, I appreciate your help in reviewing this submission.

prashjha commented 8 months ago

Hi, @alizma and @KParas. We are now significantly behind schedule. I have not heard from both of you, and you have ignored my pings. Please let me know if you can complete the reviews. It is unfair to the authors that the review has been stuck for so long.

jstollberg commented 4 months ago

Hi @prashjha, could you give us a small update since the review process got stuck for some time now?

jstollberg commented 2 months ago

Dear @prashjha, the last update on the review was already one year ago in September 2023. This seems quite a long time to me. When can we expect the review process to be finished?

prashjha commented 2 months ago

Howdy, @Huzaifg, @lelaus, @Brookluo, @jannisteunissen, would you be interested in reviewing the JOSS submission above (pdf link)? The corresponding software is at this link.

This link covers almost everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

prashjha commented 2 months ago

Hi @jstollberg, the delay is due to two reviewers ghosting us completely. I will try to find one more reviewer, and based on their assessment and @alizma's partial assessment, it should be sufficient to make a decision.

jannisteunissen commented 2 months ago

@prashjha I might not be the best reviewer since I have never used abaqus and don't have access to it

Huzaifg commented 2 months ago

Hello Prashant,

I don't currently have access to Abaqus. Can I do the review without it? If yes, I would be happy to review

Best Huzaifa

On Wed, Sep 18, 2024, 3:43 PM Prashant K. Jha @.***> wrote:

Hi @jstollberg https://github.com/jstollberg, the delay is due to two reviewers ghosting us completely. I will try to find one more reviewer, and based on their assessment and @alizma https://github.com/alizma's partial assessment, it should be sufficient to make a decision.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5729#issuecomment-2359369668, or unsubscribe https://github.com/notifications/unsubscribe-auth/APONE5R5QQ7TRDC6OQTHOUTZXHQXXAVCNFSM6AAAAAA3BQSOT2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJZGM3DSNRWHA . You are receiving this because you were mentioned.Message ID: @.***>

prashjha commented 2 months ago

Thank you for your positive response, @Huzaifg. Let me confirm with the authors.

Hi @tmfrln and @jstollberg, please let us know if the review of your repository is possible without access to Abaqus.

prashjha commented 2 months ago

@jannisteunissen, thank you for letting me know.

Brookluo commented 2 months ago

Hello, I'm not suitable for the review of this paper, but I hope you can find other reviewers.

lelaus commented 2 months ago

Hello @prashjha ,

Thank you for contacting me. I would be very happy to participate in this review.

However, I have never used Abaqus and have no licence to use it at the moment.

In your opinion, is it possible to do a full review despite these limitations? In case of a positive answer, I would be available.

I look forward to your reply.

tmfrln commented 1 month ago

Hi everyone,

first of all, thanks @lelaus and @Huzaifg for your interest in taking part in the review.

I think a complete review is not possible without access to Abaqus. However, there is a learning edition that can be downloaded for free here, but is only available on Windows. A registration on the Simulia site may also be required.

With this edition, reviewers can run the complete test suite for paraqus, but only some of the examples: example_abaqus_aluminum_bending.py, example_abaqus_rivet_forming.py. and example_abaqus_extrusion.py will not work with the learning version.

From my point of view, the remaining tests and examples should be enough to review the package though.

P.S.: Since this has been up for review for quite some time now, i would like to kindly ask reviewers to only participate if they can review the package in the near future - thanks!

prashjha commented 1 month ago

@tmfrln, thank you for clarifying the abaqus requirement.

@lelaus and @Huzaifg, thank you for your positive response. I am adding you both as reviewers. Please complete the reviews without abaqus. @tmfrln should be able to help with any problems.

prashjha commented 1 month ago

@editorialbot add @Huzaifg as reviewer

editorialbot commented 1 month ago

@Huzaifg added to the reviewers list!

prashjha commented 1 month ago

@editorialbot add @lelaus as reviewer

editorialbot commented 1 month ago

@lelaus added to the reviewers list!

prashjha commented 1 month ago

@editorialbot remove @alizma as reviewer

editorialbot commented 1 month ago

@alizma removed from the reviewers list!

prashjha commented 1 month ago

@editorialbot remove @KParas as reviewer

editorialbot commented 1 month ago

@KParas removed from the reviewers list!

prashjha commented 1 month ago

Dear @Huzaifg and @lelaus, please create your review checklist using the command below

@editorialbot generate my checklist

You can read the 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!

As @tmfrln said, this submission has been delayed due to unresponsive reviewers, which I just removed. I would appreciate it if you could complete the review soon. You can also look at the progress the two reviewers made by looking at their checklists.

tmfrln commented 4 weeks ago

@prashjha Thanks for updating the reviewers! @lelaus @Huzaifg If you need any assistance, especially if you decide to install the learning version of abaqus, I will be happy to help.

lelaus commented 4 weeks ago

Hi @prashjha and @tmfrln, thanks for adding me as reviewer. I'll do my best. Before start, I just want to advice you that unfortunately my review will not be based on the usage of the learning version of Abaqus since I have only Linux Debian OS.

lelaus commented 3 weeks ago

Review checklist for @lelaus

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 https://github.com/tmfrln/paraqus?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@tmfrlm) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

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

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] 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, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] 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?

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