search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
725 stars 38 forks source link

[REVIEW]: svFSI: A Multiphysics Package for Integrated Cardiac Modeling #4118

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@CZHU20<!--end-author-handle-- (Chi Zhu) Repository: https://github.com/SimVascular/svFSI Branch with paper.md (empty if default branch): Version: 2022.09.26 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @chennachaos, @JaroslavHron, @axel-loewe Archive: 10.5281/zenodo.7113485

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83"><img src="https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83/status.svg)](https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83)

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:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 2 years ago

Wordcount for paper.md is 1210

whedon commented 2 years 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.jelectrocard.2003.09.017 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

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 2 years ago

PDF failed to compile for issue #4118 with the following error: 

 [WARNING] Citeproc: citation axel-loewe not found
Error producing PDF.
! Undefined control sequence.
\hyper@@link ->\let \Hy@reserved@a 
                                   \relax \@ifnextchar [{\hyper@link@ }{\hyp...
l.356 }

Looks like we failed to compile the PDF
whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=3.70 s (107.1 files/s, 46964.6 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
Fortran 77                              79           6159           7485          37515
C                                      121           8078           7418          32300
C++                                      5           3117           6762          27459
C/C++ Header                            50           2780           4050          12528
Fortran 90                               5           1081            353           6067
make                                    46            419            585           2621
CMake                                   35            436            928           2118
Bourne Shell                            35            255            260            680
Markdown                                 5            237              0            680
CSS                                      1             92             47            217
TeX                                      1             16              0            160
Tcl/Tk                                   3             50            110            150
Bourne Again Shell                       7             66             90            142
Windows Module Definition                1              1              6             53
WiX source                               1             10              0             23
HTML                                     1              0              0             12
---------------------------------------------------------------------------------------
SUM:                                   396          22797          28094         122725
---------------------------------------------------------------------------------------

Statistical information for the repository 'e26e085a5a0b9d4a326f71d9' was
gathered on 2022/02/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Chi                              1             6              2            0.00
Vijay Vedula                     7           257            205            0.27
alexkaiser                       1             0          50067           29.37
osmsc                            1        119931              0           70.35

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Chi Zhu                       4          100.0          0.6                0.00
Vijay Vedula                256           99.6          8.3               18.75
osmsc                     69660           58.1          0.0               19.87
Kevin-Mattheus-Moerman commented 2 years ago

@whedon re-invite @axel-loewe as reviewer

whedon commented 2 years ago

OK, the reviewer has been re-invited.

@axel-loewe please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

Kevin-Mattheus-Moerman commented 2 years ago

@axel-loewe apologies for the second invite. I had added you initially as @ @axel-loewe by mistake. It should be fixed now.

Kevin-Mattheus-Moerman commented 2 years ago

@chennachaos, @JaroslavHron, @axel-loewe thanks for your help with this review!!!! :partying_face: You may now start. Let me know if you have any questions.

axel-loewe 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:

JaroslavHron commented 2 years ago

Hi @Kevin-Mattheus-Moerman - it seems that i have missed the invitation, and its now expired - could you reinvite me.

Kevin-Mattheus-Moerman commented 2 years ago

@whedon re-invite @JaroslavHron a reviewer

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
axel-loewe commented 2 years ago

Zhu et al. present svFSI, a simulation software for cardiac physiology. It covers multiple cardiac functions (physics): solid mechanics, hemodynamics and apparently cardiac electrophysiology. The effort of developing a software for this challenging coupled problem and making if publicly available is appreciated.

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

While there is no LICENSE file, there is Copyright-Simvasscular.txt which holds a license. Renaming might help to make this information more easily findable. The text seems to be the MIT license, I recommend mentioning this explicitly and also adding this information to the metadate of the GitHub project.

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?

From the commit history, this does not seem to be the case (3 minor commits only). I am aware that the public commits may not be representative of the entire history of the project. Please comment on it.

Installation: Does installation proceed as outlined in the documentation?

I did not manage to compile the code with clang 13.0 (Undefined identifiers in METISLib). Do you see an option to increase compatibility with other compilers or to provide a container? In the current form, I cannot evaluate svFSI's functionality.

Functionality: Have the functional claims of the software been confirmed?

svFSI is introduced as a multi-physics simulator including electrophysiology, tissue mechanics and blood dynamics. Unfortunately, I could not find any information on electrophysiology in the paper or the documentation (http://simvascular.github.io/docssvFSI.html). As such, I suggest to either document these features or to remove these aspects from the paper. Later on I found this link at the bottom of the README file: http://simvascular.github.io/docsSimCardio.html#cep-modeling It's not entirely clear to me how SimCardio relates to svFSI and I strongly recommend to provide a comprehensive overview of all relevant documentation for svFSI at a central place.

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

The website lists them but there is no automated way of installing them. Later on, I discovered more detailed information in the INSTALL-DEPS.md file in the repository. Would be good to sync this information with the web page documentation. Given the high number of dependencies and very specific versions being referred to in the documentation, I encourage you to consider providing a containerized version.

State of the field: Do the authors describe how this software compares to other commonly-used packages?

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

As coupling multiple physics is a complex problem and also multiplies the number of user-chosen parameters, types of boundary conditions, pre- and postprocessing steps etc., I assume that svFSI probably provides only a subset of features of established single-physics simulators. I believe it would be important for potential new users to learn about which features are supported. The brief paper remains rather vagues and does not mention the concrete scope. The documentation I found on the website is a tutorial for setting up a fluid-structure simulation (which I believe will be valuable for new users). However, I could not find a comprehensive user manual. The Documentation folder only contains a Doxygen configuration file. I feel that a proper user documentation is a prerequisite for svFSI to be really useful beyond the group of developers.

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

Could not find such information. There are no CI pipelines implemented as GitHub actions. Cannot judge on external CI.

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

Could not find such information in the repository or the svFSI part of the SimVascular webpage.

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?

Line 27: Please change the reference to openCARP to this one: https://dx.doi.org/10.1016/j.cmpb.2021.106223

JaroslavHron commented 2 years ago

@Kevin-Mattheus-Moerman - it seems that there was some typo in the re-invitation and it failed

danielskatz commented 2 years ago

@whedon re-invite @JaroslavHron as reviewer

whedon commented 2 years ago

OK, the reviewer has been re-invited.

@jaroslavhron please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

whedon commented 2 years ago

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

whedon commented 2 years ago

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

Kevin-Mattheus-Moerman commented 2 years ago

@chennachaos, @JaroslavHron, can you given an update on review progress? Thanks.

Kevin-Mattheus-Moerman commented 2 years ago

@CZHU20 can you respond to the issues raised above by Axel Loewe? :point_up:

chennachaos commented 2 years ago

Hi @Kevin-Mattheus-Moerman. I have not started yet. I will start it next week.

CZHU20 commented 2 years ago

Hi @Kevin-Mattheus-Moerman, I will discuss the issues raised by Axel with my coauthors and post the formal response as soon as possible. Thank you.

Kevin-Mattheus-Moerman commented 2 years ago

@CZHU20 I hope you are doing well. I am just checking in to see how you are getting on addressing those issues. Can you provide an update? No worries if you need more time.

CZHU20 commented 2 years ago

@Kevin-Mattheus-Moerman Thanks for the reminder and sorry for the delay. I am afraid that it will take a little bit longer. This is my first time submitting to JOSS. May I ask if I can revise the manuscript based on first reviewer's comments now? Will this affect other reviewers? Thank you.

JaroslavHron commented 2 years ago

Hi, just to let you know - I should be able to submit my review by the end of this week.

Kevin-Mattheus-Moerman commented 2 years ago

@Kevin-Mattheus-Moerman Thanks for the reminder and sorry for the delay. I am afraid that it will take a little bit longer. This is my first time submitting to JOSS. May I ask if I can revise the manuscript based on first reviewer's comments now? Will this affect other reviewers? Thank you.

@CZHU20 yes you can keep responding/fixing as the comments/issues come in. There is no former review round system. So yes people do start addressing reviewer comments and continue to do so.

CZHU20 commented 2 years ago

Just a quick update on the revision. We are still addressing some of the comments, especially those related to software documentations. Thank you for your help and patience.

chennachaos commented 2 years ago

Hi @Kevin-Mattheus-Moerman, I started the review for this but I am not able to check the boxes. Could you please assist me in this regard?

Kevin-Mattheus-Moerman commented 2 years ago

@chennachaos thanks. We've since also moved to a new editorial bot system. Can you call the following to generate you a new checklist: @editorialbot generate my checklist

chennachaos commented 2 years ago

Review checklist for @chennachaos

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

chennachaos commented 2 years ago

Thanks, @Kevin-Mattheus-Moerman!

chennachaos commented 2 years ago

After going through the repository and the paper, I have almost the same set of concerns as those raised by @axel-loewe. I think, at this point, it is better to wait until @CZHU20 addresses those comments.

Kevin-Mattheus-Moerman commented 2 years ago

@CZHU20 can you provide an update on how you are getting on addressing those reviewer comments? :point_up:

CZHU20 commented 2 years ago

@Kevin-Mattheus-Moerman Dear Kevin, thanks for the reminder and I apologize for the delay. From Feb to late April is our "proposal-writing" season, I didn't think I could address those comments adequately. Now with all proposals submitted, this is on top of my to-do list. Thank you and the reviewers for your patience.

Kevin-Mattheus-Moerman commented 2 years ago

@CZHU20 I hope you are doing well and that your survived the "proposal-writing" season. For me it is "exam paper correction season" :) Let me know if there are any updates on addressing the review comments. It would be good to pick this up soon to avoid losing track of the reviewers.

CZHU20 commented 2 years ago

@Kevin-Mattheus-Moerman Dear Kevin, thank you for the reminder and I am glad we all survived :) We are steadily making progress in addressing the reviewer's comments. We think one of the most important issue is that the reviewer couldn't build the software and evaluate its functionality. We have created a Dockerfile to automate the build process and to increase its cross-platform compatibility. The Docker repository is located here: https://github.com/CZHU20/Docker-svFSI We have successfully tested it on macOS Big Sur, Ubuntu 18.04 and Window 10 with WSL 2, and is in the process of merging it into the main svFSI repository.

@axel-loewe Thank you very much for your comments and sorry for the delay. Would you please try to build svFSI with the above Dockerfile and review its functions? We are still addressing your other comments, especially those on documentations. We really appreciate your patience.

Kevin-Mattheus-Moerman commented 2 years ago

@axel-loewe thanks again for your help here. Have you tested @CZHU20 's suggestion? :point_up:

Kevin-Mattheus-Moerman commented 2 years ago

@axel-loewe thanks again for your help here. Have you tested @CZHU20 's suggestion? :point_up:

axel-loewe commented 2 years ago

I‘m currently on parental leave. Might find some time next week or the week after. Maybe some of the other reviewers can have a look in the meantime.

Am 08.06.2022 um 10:13 schrieb Kevin Mattheus Moerman @.***>:



@axel-loewehttps://github.com/axel-loewe thanks again for your help here. Have you tested @CZHU20https://github.com/CZHU20 's suggestion? ☝️

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/4118#issuecomment-1149603418, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMMXMXCEOUW6XRZAPSA425DVOBI23ANCNFSM5NJFW6LQ. You are receiving this because you were mentioned.Message ID: @.***>

axel-loewe commented 2 years ago

I can confirm that the Docker container is working and reproduces the example that I tried (04/06) :+1:

08/03 did start but seems to be a rather big simulation, did not complete within a couple of hours.

I'll proceed with the review when the responses to all comments are ready.

CZHU20 commented 2 years ago

Dear @axel-loewe, thanks for the feedback. We are in the process of overhauling the SimVascular website. This is the last item on our checklist. All responses will be ready in a week or so. Thank you for your patience.

CZHU20 commented 2 years ago

Dear all, thank you very much for your patience. We have finally completed all revisions. Here are our responses to @axel-loewe 's comments.

Zhu et al. present svFSI, a simulation software for cardiac physiology. It covers multiple cardiac functions (physics): solid mechanics, hemodynamics and apparently cardiac electrophysiology. The effort of developing a software for this challenging coupled problem and making if publicly available is appreciated.

We thank the reviewer for the thorough evaluation of the software, and we have used these comments to improve our software.

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

While there is no LICENSE file, there is Copyright-Simvasscular.txt which holds a license. Renaming might help to make this information more easily findable. The text seems to be the MIT license, I recommend mentioning this explicitly and also adding this information to the metadate of the GitHub project.

Per the reviewer’s recommendation, we have renamed Copyright-Simvasscular.txt to Licence.txt. Since multiple parities were involved in the development of this software at different phases, we have to put our license file into the metadata of GitHub to reflect that. We have modified the README to clearly state that the main body of svFSI follows MIT style license

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?

From the commit history, this does not seem to be the case (3 minor commits only). I am aware that the public commits may not be representative of the entire history of the project. Please comment on it.

Chi Zhu and Vijay Vedula share co-first authorship of the submission. Due to the submitting author’s account settings, some of the commits from CZHU20 are not automatically registered by GitHub, e.g. commit 1f24ab5fe513a1aa48b962e64e9718db6bb1d046 on Jun 30, 2021. Also, many changes made by the submitting author were added to svFSI through methods like diff-patch.

Installation: Does installation proceed as outlined in the documentation?

I did not manage to compile the code with clang 13.0 (Undefined identifiers in METISLib). Do you see an option to increase compatibility with other compilers or to provide a container? In the current form, I cannot evaluate svFSI's functionality.

We are sorry that the reviewer was not able to compile the code. We have followed the reviewer’s suggestion and created a dockerfile to automate the build process. It is now included in the svFSI repository, and you can follow the instructions here to build and test it. https://github.com/SimVascular/svFSI/tree/JOSS_paper/Docker

Functionality: Have the functional claims of the software been confirmed?

svFSI is introduced as a multi-physics simulator including electrophysiology, tissue mechanics and blood dynamics. Unfortunately, I could not find any information on electrophysiology in the paper or the documentation (http://simvascular.github.io/docssvFSI.html). As such, I suggest to either document these features or to remove these aspects from the paper. Later on I found this link at the bottom of the README file: http://simvascular.github.io/docsSimCardio.html#cep-modeling It's not entirely clear to me how SimCardio relates to svFSI and I strongly recommend to provide a comprehensive overview of all relevant documentation for svFSI at a central place.

We appreciate the reviewer’s effort to locate these documents. The SimCardio project aims to develop a complete software suite that can cover all aspects of cardiac modeling from image segmentation to computational modeling. svFSI is a major part of SimCardio as it performs multi-physics cardiac simulations. Following changes have been made in svFSI/README.md to better explain the scope of svFSI:

  • In the Introduction section, we added, “It[svFSI] is a major component of the ongoing SimVascular SimCardio project that aims to provide the complete pipeline for cardiac modeling, from image segmentation to computational modeling.”
  • Following the reviewer’s suggestion, we have also overhauled the svFSI website where all relevant documentation for svFSI is now hosted. In the Main features section, we also provide direct links to documentations of fluid, structure, electrophysiology and fluid-structure interaction.
  • Meanwhile, we have modified the Documentation and Tutorial section in svFSI/README.md to better direct users to the right resource.

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

The website lists them but there is no automated way of installing them. Later on, I discovered more detailed information in the INSTALL-DEPS.md file in the repository. Would be good to sync this information with the web page documentation. Given the high number of dependencies and very specific versions being referred to in the documentation, I encourage you to consider providing a containerized version.

We have followed the reviewer’s suggestion and created a dockerfile to automate the build process. Please follow the instruction here to build the Docker image and test the software. https://github.com/SimVascular/svFSI/tree/JOSS_paper/Docker

Clear build/installation instruction is also provided on the website.

State of the field: Do the authors describe how this software compares to other commonly-used packages?

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

As coupling multiple physics is a complex problem and also multiplies the number of user-chosen parameters, types of boundary conditions, pre- and postprocessing steps etc., I assume that svFSI probably provides only a subset of features of established single-physics simulators. I believe it would be important for potential new users to learn about which features are supported. The brief paper remains rather vagues and does not mention the concrete scope. The documentation I found on the website is a tutorial for setting up a fluid-structure simulation (which I believe will be valuable for new users). However, I could not find a comprehensive user manual. The Documentation folder only contains a Doxygen configuration file. I feel that a proper user documentation is a prerequisite for svFSI to be really useful beyond the group of developers.

We agree with the reviewer that it is important to properly document the features of svFSI. To achieve this goal, we have first overhauled our website to properly present the scope, features, theory, implementation and options of svFSI as well as its major components (fluid, structure, fsi, electrophysiology).

Furthermore, we have prepared a comprehensive list of examples to demonstrate almost all functionalities of svFSI, including physics solved, parameter selections, types of boundary conditions etc. From svFSI repository or website, users will be directed to https://github.com/SimVascular/svFSI-Tests. In each case, we have documented the problem it solves and key aspects of the software configuration. All cases have been tested and are ready to run by the user. Here are some examples:

We have established a new repository svFSI-Tools to host all the pre/post-processing tools and added a new section Pre/Post Processing Tool to svFSI/README.md.

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

Could not find such information. There are no CI pipelines implemented as GitHub actions. Cannot judge on external CI.

We have significantly enhanced the svFSI-Tests by including established simulation results in most of the examples (highlighted in bold in svFSI-Tests README), which can be used by the users to manually verify the functionality of the software. The following sentence has been added to Section Features in svFSI/README.md: “… the GitHub repository svFSI-Tests to get a detailed insight into the capability of the code. Also, most of the examples contain established simulation results, which users can use to verify the functionality of svFSI.”

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

Could not find such information in the repository or the svFSI part of the SimVascular webpage.

We have added new sections in both svFSI README and svFSI website to provide clear guideline for these scenarios.

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?

Line 27: Please change the reference to openCARP to this one: https://dx.doi.org/10.1016/j.cmpb.2021.106223

The suggested change has been made.

  • Is the Readme.md file required? Seems it does not hold relevant information for users/developers and might be confused with README.md. Will also cause trouble on non-case-sensitive file systems.

This problem has been fixed by renaming Readme.md to README_JOSS.md.

Thank you all again.

axel-loewe commented 2 years ago

I suggest mentioning the Docker container also in the INSTALL.md file

The authors markedly improved the documentation. For the future it would be great if there was also a complete user manual / documentation of parameters besides the examples.

CZHU20 commented 2 years ago

Hi @axel-loewe, thanks for the quick feedback. We have added the following sentence to INSTALL.md to include Docker container information.

If you are interested in testing the new features in the most recent commit, we recommend you to build and run svFSI in Docker container. Otherwise, please follow the instructions below to build svFSI on Ubuntu and MacOS.

A complete user manual and developer guide are definitely planned for the future. But users are always welcome to reach out to us with any usage/development questions.

Meanwhile, please let me know if you have any other comments. Thank you.

Kevin-Mattheus-Moerman commented 2 years ago

@axel-loewe thanks for your help here. If you can, can you comment on @CZHU20 's response :point_up: ? Let me know, since you appear to have all boxes ticked, if you recommend this work for acceptance in JOSS or if there are still open issues. Thanks.

Kevin-Mattheus-Moerman commented 2 years ago

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

Kevin-Mattheus-Moerman commented 2 years ago

@JaroslavHron can you provide an update on the review? Are there still open issues for you? Thanks.

axel-loewe commented 2 years ago

@axel-loewe thanks for your help here. If you can, can you comment on @CZHU20 's response ☝️ ? Let me know, since you appear to have all boxes ticked, if you recommend this work for acceptance in JOSS or if there are still open issues. Thanks.

Yes, I recommend this work for publication!