[REVIEW]: svFSI: A Multiphysics Package for Integrated Cardiac Modeling

whedon commented 2 years ago

Submitting author: !--author-handle-->@CZHU20@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @chennachaos, @JaroslavHron, @axel-loewe Archive: 10.5281/zenodo.7113485

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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

@chennachaos & @JaroslavHron & @ @axel-loewe, 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 @Kevin-Mattheus-Moerman 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 @JaroslavHron

✨ 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 (@CZHU20) 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 @axel-loewe

✨ 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 (@CZHU20) 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?

CZHU20 commented 2 years ago

@axel-loewe Thank you so much for your review! It really helped improving our work.

JaroslavHron commented 2 years ago

Hi, I have looked at the current state and it looks good - nice work.

The docker image makes it easy to run the tests. I was able to compile/run the code without any problem (ubuntu, gcc).
May be I would recommend to mention/cite in the text of the paper that for parallel solvers the trilinos library is used for the parallel linear solvers/preconditioners (or required/recommended for some of the examples - https://github.com/SimVascular/svFSI-Tests/tree/master/07-fsi/ale/03-pipe_3D)

CZHU20 commented 2 years ago

@JaroslavHron Thank you very much for your comment.

I have revised the paper by adding the following sentence.

"It [svFS] also provides several built-in iterative linear solvers and preconditioners, along with many other options through Trilinos(Heroux et al., 2005)."

Kevin-Mattheus-Moerman commented 2 years ago

@chennachaos I think it looks like you can pick up the review again.

chennachaos commented 2 years ago

Hi @Kevin-Mattheus-Moerman. Sorry for the delay. I have been busy with a lot of stuff going on at the moment. I will complete the review by the end of next week.

Kevin-Mattheus-Moerman commented 2 years ago

Hi @chennachaos I removed the one on top since you created the new checklist type above in a comment: https://github.com/openjournals/joss-reviews/issues/4118#issuecomment-1099385011

Let me know if you can use that, if not I'll put the one on top back.

chennachaos commented 2 years ago

I think the one already there is fine.

chennachaos commented 2 years ago

Hi @CZHU20, I have the following comments regarding the software paper.

1.) Literature on the topic from Prof. Alfio Quarteroni's group, e.g. the iHEART project and the associated software (https://arxiv.org/pdf/2201.03303.pdf), is missing. Consider adding a couple of relevant references from this group.

2.) If possible, remove/merge the duplicates equal contributions to the paper and "Corresponding author" in the authors' details.

Kevin-Mattheus-Moerman commented 2 years ago

@CZHU20 you can start addressing these right away if you can/like :point_up:

CZHU20 commented 2 years ago

@chennachaos Thank you very much for your comment. We have addressed both in the new commit:

We have added the following sentence to the manuscript:

Recently, Quarteroni et al. have also been developing an open-source simulator for the cardiac function, and the fiber generation module (Africa et al., 2022) and electromechanics (Fedele et al., 2022) have been announced so far.

Proper ways to assign equal contribution and corresponding authors have been adopted.

- name: Chi Zhu
orcid: 0000-0002-1099-8893
equal-contrib: true
affiliation: "1, 2"
- name: Vijay Vedula
affiliation: 3
equal-contrib: true
- name: Dave Parker
affiliation: 4
- name: Nathan Wilson
affiliation: 5
- name: Shawn Shadden
affiliation: 1
corresponding: true
- name: Alison Marsden
affiliation: 4
corresponding: true

Please let me know if you have other comments. Thank you.

CZHU20 commented 2 years ago

@Kevin-Mattheus-Moerman I have followed the JOSS guideline to assign equal contribution and corresponding author. However, the generated pdf does not reflect both changes. I used the following docker command to generate the pdf

docker run --rm \
    --volume $PWD:/data \
    --user $(id -u):$(id -g) \
    --env JOURNAL=joss \
    openjournals/paperdraft

Is this because it's currently in draft state? Thank you.

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

@CZHU20 it seems to be working here though right :point_up: ?

CZHU20 commented 2 years ago

Yes. It looks good. Thank you very much.

chennachaos commented 2 years ago

Hi @CZHU20, Some nice examples are provided in svFSI-Tests to help the users verify the software. However, it looks like README files for some of the examples need to be updated. For example, all three ALE FSI examples point to the same YouTube tutorial (on pressure pulse inside the aorta).

I recommend checking all the examples thoroughly and updating them as necessary. I would also recommend adding comparisons of results, either as graphs or tables, to the corresponding README files so that the user knows straightway what to expect when the input files are executed, instead of navigating through lengthy journal papers.

CZHU20 commented 2 years ago

Hi @chennachaos Thank you very much for your comments. Regarding the YouTube tutorials, we currently only recorded some most common cases to demonstrate the main features of svFSI. Hence, all the README files of FSI cases pointed to this tutorial. I agree it's confusing, so we have added a clarification (see here):

This video is for flow inside a modeled aorta, but the general idea is also applicable to this case.

We will gradually upload more tutorials to our channel.

We have also followed your suggestion and updated all of our README files to make them more self-explanatory. For those cases with a reference, we have added problem configuration and some results so that the readers can get all the information at once. Here are some examples: Fluid: https://github.com/SimVascular/svFSI-Tests/tree/master/04-fluid/03-driven-cavity-2D Structure: https://github.com/SimVascular/svFSI-Tests/tree/master/05-struct/02-LV-Guccione-passive FSI: https://github.com/SimVascular/svFSI-Tests/tree/master/07-fsi/ale/03-pipe_3D For some other cases without a reference, we have included some form of the results. For example: Heat conduction: https://github.com/SimVascular/svFSI-Tests/tree/master/01-heat/01-diffusion-line-source Electrophysiology: https://github.com/SimVascular/svFSI-Tests/tree/master/08-cep/05-Purkinje

I hope these changes address your concerns. Thank you again for your time. Please let me know if you have other comments.

chennachaos commented 2 years ago

Hi @Kevin-Mattheus-Moerman, I finished my review. This is a very well-written library. I recommend it for publication in the JOSS.

CZHU20 commented 2 years ago

@chennachaos Thank you very much!

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Paper is not ready for acceptance yet, the archive is missing

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

@CZHU20 since all reviewers are now happy we are ready to process this work for acceptance in JOSS. There a couple of steps remaining.

On the paper, I have read it and it looks good, I only have the following minor editorial comments:

[x] Please add the city and country to each of your affiliations. Do not use acronyms for countries, e.g. please spell out USA as United States of America.
[x] You may use open source rather than open-source throughout the paper.

Other points:

[x] Please can you conform what the version for the reviewed software should be? Are you still at v1.0.0 or has the version tag changed?
[x] Please can you archive a copy of the software on ZENODO. You can do this manually or use these automated steps: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
[x] Once the ZENODO archive is create please report back here with the ZENODO DOI.
[x] Please manually edit the ZENODO archive where needed to ensure that the title and authors match those on the JOSS paper title. Furthermore please check that the license listed there is correct.

CZHU20 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:

CZHU20 commented 2 years ago

@Kevin-Mattheus-Moerman Thank you. I have fixed the affliction problem and used "open source" everywhere.

Regarding software version and ZENODO archive, the development on the public repository has been frozen since the JOSS paper was submitted. After discussing with other authors, we intend to create a new tag for the current version and archive the same version in ZENODO. But we don't want to include the JOSS material (paper.md, paper.bib etc) as they are not part of the software. Can we merge changes (made according to reviewers' comments) in the JOSS branch to the main branch, and archive the main branch instead of the JOSS branch?

Thank you very much!

Kevin-Mattheus-Moerman commented 1 year ago

@CZHU20 Yes, what you suggest regarding the archiving and leaving out the paper.md etc is fine.

CZHU20 commented 1 year ago

@Kevin-Mattheus-Moerman Dear Kevin, I have made all the changes. We have created a new release (2022.09.26) based on the reviewed version of svFSI. The DOI of the ZENODO archive is 10.5281/zenodo.6673060. All records on ZENODO has been made consistent with the JOSS submission. Please let me know if there are other issues. Thank you very much.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 10.5281/zenodo.6673060 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.6673060

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 10.5281/zenodo.7113485 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7113485

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 2022.09.26 as version

editorialbot commented 1 year ago

Done! version is now 2022.09.26

Kevin-Mattheus-Moerman commented 1 year ago

@CZHU20 I think your text listed the wrong ZENODO archive so I fixed it, since it seems it should have been: 10.5281/zenodo.7113485.

Can you check what the version tag should be, are you happy with what I set just now 2022.09.26, I am just checking since it was submitted as v1.0.0 which is a different version tagging format. This tag is up to you so just let me know if 2022.09.26 is good.

CZHU20 commented 1 year ago

@Kevin-Mattheus-Moerman Thank you very much for the help. Sorry about the ZENODO archive DOI. Yes, I am happy with 2022.09.26 as the tag.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot recommend accept

editorialbot commented 1 year ago

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

@editorialbot commands

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.jcp.2015.11.022 is OK
- 10.1161/CIRCRESAHA.110.223610 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1115/1.4005694 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1371/journal.pcbi.1005828 is OK
- 10.1371/journal.pcbi.1009331 is OK
- 10.1016/j.jbiomech.2018.03.034 is OK
- 10.1002/cnm.3351 is OK
- 10.1615/Int.J.UncertaintyQuantification.2020033068 is OK
- 10.1007/s10237-020-01294-8 is OK
- 10.1115/1.4048032 is OK
- 10.48550/ARXIV.2201.03303 is OK
- 10.48550/ARXIV.2207.12460 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.cmpb.2021.106223 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/j.cmpb.2021.106223' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

Kevin-Mattheus-Moerman commented 1 year ago

@CZHU20 this PR should fix these issues with the DOIs: https://github.com/SimVascular/svFSI/pull/92

CZHU20 commented 1 year ago

@Kevin-Mattheus-Moerman this pull request has been merged. Thank you.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.jcp.2015.11.022 is OK
- 10.1161/CIRCRESAHA.110.223610 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1115/1.4005694 is OK
- 10.1016/j.cmpb.2021.106223 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1371/journal.pcbi.1005828 is OK
- 10.1371/journal.pcbi.1009331 is OK
- 10.1016/j.jbiomech.2018.03.034 is OK
- 10.1002/cnm.3351 is OK
- 10.1615/Int.J.UncertaintyQuantification.2020033068 is OK
- 10.1007/s10237-020-01294-8 is OK
- 10.1115/1.4048032 is OK
- 10.48550/ARXIV.2201.03303 is OK
- 10.48550/ARXIV.2207.12460 is OK

MISSING DOIs

- Errored finding suggestions for "The LifeV library: engineering mathematics beyond ...", please try later

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 1 year ago

@CZHU20 one more pull request: https://github.com/SimVascular/svFSI/pull/93 to fix that missing DOI

CZHU20 commented 1 year ago

@Kevin-Mattheus-Moerman Done.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot check references

openjournals / joss-reviews