[REVIEW]: AsFem: A simple to use finite element package for phase-field modeling and multiphysics simulation

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@yangbai90@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @vijaysm, @mscroggs, @schruste Archive: Pending

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Reviewers and authors:

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Reviewer instructions & questions

@vijaysm & @mscroggs & @schruste, 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:

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✨ 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 @vijaysm

📝 Checklist for @mscroggs

📝 Checklist for @schruste

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.ijsolstr.2021.111099 is OK
- 10.1016/j.scriptamat.2020.03.027 is OK
- 10.1016/j.cma.2010.04.011 is OK
- 10.1016/0167-2789(93)90120-P is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=2.00 s (1059.5 files/s, 225871.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C/C++ Header                    754          31347          44784         170844
C++                            1008          13335          12571          78227
Fortran 77                       51             17          13727          24137
GLSL                             27             80            391          21663
SWIG                             97            958            207          10384
CMake                            92           1617           1858           7905
C                                21            796           2076           3792
CUDA                             14            795            191           3073
Markdown                          5            516              0           1508
Python                           12            166            178            725
YAML                              3             69             33            704
Bourne Shell                     13            150             69            549
CSS                               2             59             18            217
XML                               1             15             10            210
JavaScript                        3             29             15            205
HTML                              4             12              0            119
XSLT                              1              4              0            116
Bourne Again Shell                4             18             21             77
TeX                               1              4              0             55
DTD                               1              1              0             30
--------------------------------------------------------------------------------
SUM:                           2114          49988          76149         324540
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 590

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

:wave: @vijaysm, @mscroggs, @schruste I hope you are doing well. Can you provide an update on review progress? Let me know if you have any questions. Thanks.

vijaysm commented 2 years ago

Review checklist for @vijaysm

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/M3Group/AsFem?
[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 (@yangbai90) 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)?
[ ] 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?
[ ] 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?

vijaysm commented 2 years ago

@Kevin-Mattheus-Moerman Thanks for the ping. I didn't realize the review for this submission had opened. Do not remember seeing a notification for it. I'll get started on it soon.

Kevin-Mattheus-Moerman commented 2 years ago

@vijaysm that is okay. Hope you are getting on well. Let us know if you have an update. Thanks again for your help!

mscroggs commented 2 years ago

Sorry, I got unexpected busy. I'll get my review done this week

mscroggs commented 2 years ago

Review checklist for @mscroggs

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/M3Group/AsFem?
[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 (@yangbai90) 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

[ ] 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?
[ ] 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?
[ ] 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?

Kevin-Mattheus-Moerman commented 2 years ago

@mscroggs @vijaysm Thanks again for your help with this review. I see you have left several boxes unticked. Could you summarize what points the authors should work on? Or have you perhaps opened issues relating to these on the project repository? If so can you link to them here? Thanks.

vijaysm commented 2 years ago

I had to take a couple of weeks off due to a family emergency. Will get back to this next week. @Kevin-Mattheus-Moerman

ngsxfem commented 2 years ago

@editorialbot generate my checklist

editorialbot commented 2 years ago

@ngsxfem I can't do that because you are not a reviewer

schruste commented 2 years ago

Review checklist for @schruste

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/M3Group/AsFem?
[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 (@yangbai90) 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

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)?
[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

[ ] 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 and who the target audience is?
[ ] 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?

mscroggs commented 2 years ago

Apologies for the delay in my review. I have a few comments and suggestions. I've also opened issues on the AsFem repo for these

Installation. I was able to install and use the library, but it took me a while to work out the correct way to install PETSc. It would be nice if (eg) a Docker image was provided so that new users could run this library more easily (https://github.com/M3Group/AsFem/issues/62). As the library is installable without this, however, I'd be happy for the paper to be published before this is done.
Statement of need. It's not fully clear to me from the paper or the documentation in what way this library is "simple" (https://github.com/M3Group/AsFem/issues/63)
State of the field. There is very little mention of how this library compares to other open FEM libraries. (https://github.com/M3Group/AsFem/issues/64)
References. There's currently no reference for the finite element method. (https://github.com/M3Group/AsFem/issues/65)

Kevin-Mattheus-Moerman commented 2 years ago

@yangbai90 can you inform me on how you are getting on addressing these issues :point_up:

Kevin-Mattheus-Moerman commented 2 years ago

@vijaysm, @schruste can you provide an update from your end? Are you waiting for the author to implement changes? Thanks again for your help.

Kevin-Mattheus-Moerman commented 2 years ago

@vijaysm, @schruste :wave:

vijaysm commented 2 years ago

There are several issues that need to be addressed by the author for both the code and paper. These have been noted down in the AsFem repo. I had similar comments as @mscroggs noted above and a few new ones as well.

Kevin-Mattheus-Moerman commented 2 years ago

@vijaysm okay thanks for the update!

Kevin-Mattheus-Moerman commented 2 years ago

@schruste can you also provide an update?

Kevin-Mattheus-Moerman commented 2 years ago

@schruste can you also provide an update?

:point_up:

schruste commented 2 years ago

@Kevin-Mattheus-Moerman : Sorry for being sooo late! I now found some time to continue my review. I added to two of @mscroggs issues on the AsFem-github and opened another issue.

My main points mostly coincide with @mscroggs assessment:

Installation 1: The installation is still quite painful. With some effort it is not too hard to setup, but the non-smoothness of the installation procedure can be an unnecessary barrier for interested users. There is room for improvement in the build system. CMake allows for more convenience than is used at the moment. Further, the documentation can be improved, see also the corresponding issue
Installation 2: A Docker-image would be a (comparably simple) way to circumvent the setup overhead. At least for users that want to have a quick look and first try/run this would make perfect sense. For users that are convinced of the package the setup overhead may again be acceptable, but for new ones that simply want to try it out a docker-based version would be a good idea, see also the issue opened by @mscroggs .
Statement of need/field: The author has to explain why this additional software package should be prefered in the considered use cases over the more obvious solutions (using established finite element frameworks with a lot of convenience (layers), like mfem, fenics / firedrake, ngsolve, freefem++, ... )´. Neither is this explained in the paper nor are there any proper references to similar libraries or techniques. See also the issue opened by @mscroggs
- There are some more details:
- Is the code only low order and only continuous Lagrange elements?
- The problem with the quadrature rule is only explained where it makes problems. I would recommend discussing the issue of quadrature in the documentation right away.
- It seems to me that only a fixed number of pre-defined PDE-problems can be treated. Could this be (easily) extended to other PDE problems?

Kevin-Mattheus-Moerman commented 2 years ago

@yangbai90 can you address these comments? :point_up:

yangbai90 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:

yangbai90 commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @yangbai90, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers

yangbai90 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

- 10.1016/j.ijsolstr.2021.111099 is OK
- 10.1016/j.scriptamat.2020.03.027 is OK
- 10.1016/j.cma.2010.04.011 is OK
- 10.1016/0167-2789(93)90120-P is OK

MISSING DOIs

- 10.1016/j.jpowsour.2019.03.026 may be a valid DOI for title: Two-level modeling of lithium-ion batteries
- 10.1016/j.camwa.2020.06.009 may be a valid DOI for title: MFEM: A modular finite element methods library

INVALID DOIs

- None

yangbai90 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

- 10.1016/j.ijsolstr.2021.111099 is OK
- 10.1016/j.scriptamat.2020.03.027 is OK
- 10.1016/j.jpowsour.2019.03.026 is OK
- 10.1016/j.cma.2010.04.011 is OK
- 10.1016/0167-2789(93)90120-P is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1016/j.camwa.2020.06.009 is OK
- 10.1515/jnma-2021-0081 is OK
- 10.1063/1.1744102 is OK

MISSING DOIs

- None

INVALID DOIs

- None

yangbai90 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

@yangbai90 how are you getting on? Have you addressed those comments fully? :point_up:

yangbai90 commented 2 years ago

Dear @Kevin-Mattheus-Moerman , I have revised the manuscript according to reviewers' comments, please take a look at the new version. Best, Yang

Kevin-Mattheus-Moerman commented 2 years ago

@vijaysm, @mscroggs, @schruste it looks like @yangbai90 has made quite a few changes. Can you pick up the review again at this point and summarize any remaining issues? Thanks!

vijaysm commented 2 years ago

@Kevin-Mattheus-Moerman I'll review the new changes this week. Thanks for the updates @yangbai90

Kevin-Mattheus-Moerman commented 2 years ago

@vijaysm, @mscroggs, @schruste it looks like @yangbai90 has made quite a few changes. Can you pick up the review again at this point and summarize any remaining issues? Thanks!

Kevin-Mattheus-Moerman commented 1 year ago

@vijaysm, @mscroggs, @schruste :wave:

Kevin-Mattheus-Moerman commented 1 year ago

@vijaysm, @mscroggs, @schruste :wave: please can you resume the review process? Thanks.

vijaysm commented 1 year ago

Yes, sorry. September was a bad month for me. I'll spend some time this weekend to finish up pending items.

schruste commented 1 year ago

Yes, also sorry from my side. I will try to check the update soon.

Kevin-Mattheus-Moerman commented 1 year ago

@mscroggs can you resume the review process again? Thanks

Kevin-Mattheus-Moerman commented 1 year ago

Thanks @vijaysm and @schruste

vijaysm commented 1 year ago

While the statement of need section reads much better now after new changes, I still think you should present some examples of usage and capabilities in the paper. It is quite incomplete without it IMO. It reads more like a proposal at the moment. @yangbai90

I also made more comments in the open issues in the repo. Please address them where appropriate.

yangbai90 commented 1 year ago

Dear @Kevin-Mattheus-Moerman and all reviewers, many thanks for your feedback. They are quite helpful for me to improve the package. However, I have no time to revise the code according to your comments. Therefore, I'd like to cancel this submission.

Many thanks for your work and time. Best, Yang

@editorialbot withdraw

Kevin-Mattheus-Moerman commented 1 year ago

@yangbai90 I understand, but it is very unfortunate. We do expect authors to be committed to improving and maintaining the software, especially during the review process. I understand your decision but would ask you to not submit works to JOSS in the future unless the authors have the bandwidth to maintain the software and respond to review comments.

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