[REVIEW]: simcardems: A FEniCS-based cardiac electro-mechanics solver

[editorialbot]

Submitting author: @finsberg (Henrik Nicolay Topnes Finsberg)
Repository: https://github.com/ComputationalPhysiology/simcardems
Branch with paper.md (empty if default branch): master
Version: v2023.0.0
Editor: @AoifeHughes
Reviewers: @mbarzegary, @sdelandtsheer
Archive: https://doi.org/10.5281/zenodo.7503468

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/28986461c27b8a76c8ac5a43dc57e8dc/status.svg)](https://joss.theoj.org/papers/28986461c27b8a76c8ac5a43dc57e8dc)

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

@mbarzegary & @sdelandtsheer, 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 @AoifeHughes 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 @mbarzegary

📝 Checklist for @sdelandtsheer

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (536.7 files/s, 80367.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          36           1100            573           5870
Markdown                        13            472              0           1527
YAML                             5             33              5            182
TeX                              2             11              0            124
make                             3             34              7             95
JSON                             5              0              0             47
reStructuredText                 3             27             28             37
Dockerfile                       1              3              1              7
-------------------------------------------------------------------------------
SUM:                            68           1680            614           7889
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 509

[editorialbot]

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

OK DOIs

- 10.21105/joss.01539 is OK
- 10.21105/joss.00224 is OK
- 10.3389/fphys.2018.01431 is OK
- 10.21105/joss.01848 is OK
- 10.1016/j.yjmcc.2017.03.008 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[mbarzegary]

Review checklist for @mbarzegary

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/ComputationalPhysiology/simcardems?
• 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 (@finsberg) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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?

[AoifeHughes]

Good morning, @mbarzegary, @sdelandtsheer, can I check how the reviews are getting on?

[sdelandtsheer]

Hi, looking good, the documentation is really nice. Will post my review by Saturday latest.

[mbarzegary]

Hi. I will finish the review by the end of next week.

[AoifeHughes]

Excellent, thanks both

[sdelandtsheer]

Review checklist for @sdelandtsheer

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/ComputationalPhysiology/simcardems?
• 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 (@finsberg) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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?

[sdelandtsheer]

Hello all, I am nearly done, sorry for the delay, other things keep popping up.
I'll finish this up tomorrow, but it seems that everything is fine from my side, the code is excellent

[sdelandtsheer]

Hello, I am having issues with the testing. With conda it seems that everything is set up except dolfin. I tried with Docker but my machine is refusing to cooperate although the image is pulled. I use windows 10, that might be the problem.
The project is interesting and the code seems to be of very good quality, however I am unable to run the tests and reproduce the plots.
I will be traveling over the next week and I don't have any more time to review this project, the install might be too complex for my IT skills. It might be a good idea to designate another reviewer if possible.

[AoifeHughes]

@sdelandtsheer No problem, don't stress about it too much. I can see you've made it a significant way through the checklist - if I can just check if you've updated it as much as possible, that would be wonderful.

If you've any comments or ideas, please do share with the authors, as I'm sure they'd be appreciated.

@mbarzegary how is your review going? 😊

[mbarzegary]

dear @AoifeHughes,

I confirm the quality of the software and the effort the authors have put in to develop it. Moreover, I know about the SimCardioTest project and its goals, so what the software tries to target as part of the project endeavor is clear to me. However, I believe there are some concerns that should be addressed before accepting the submission, elaborated in a couple of issues I have opened on the software repo (listed above). In my opinion, these are crucial to be fixed, allowing less-technical users to grab the code and use it (especially when the authors have pointed out that the code can be used for learning cardiac electro-mechanics). Advanced users can always enjoy and take advantage of the discretization schemes and model coupling in their codes.

I tried to be expressive since I know the value of the submitted work. I hope the authors find the comments useful.

[finsberg]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "title" (NAME) ["@", #<BibTeX::Entry >, {:doi=>["10.1007/978-3-642-23099-8"]}]

[finsberg]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/978-3-642-23099-8 is OK
- 10.21105/joss.01539 is OK
- 10.21105/joss.00224 is OK
- 10.3389/fphys.2018.01431 is OK
- 10.21105/joss.01848 is OK
- 10.1371/journal.pcbi.1002061 is OK
- 10.1016/j.yjmcc.2017.03.008 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1016/j.cmpb.2021.106223 is OK
- 10.1016/j.pbiomolbio.2011.06.015 is OK
- 10.21105/joss.01848 is OK
- 10.1080/10255842.2012.704368 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[finsberg]

@AoifeHughes I have now added the missing DOIs

[danielskatz]

@AoifeHughes & @finsberg - JOSS practice is to provide DOIs for anything that has a DOI, but not for things that don't 🙂

[danielskatz]

@finsberg - please add spaces before your citations - I'll proofread this more carefully later and may have other issues as well

[finsberg]

@editorialbot generate pdf

[finsberg]

@danielskatz I have now added spaces before the citations.

[danielskatz]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[danielskatz]

@finsberg - please change the metadata in the zenodo archive so that the the title matches the title of the paper. The authors also should match, and they almost do, but you could change the last author to have a full name, and add ORCIDs if you wanted. (this does not require a new deposit or does not create a new DOI)

[danielskatz]

@finsberg - I've also created a PR (ComputationalPhysiology/simcardems#132) with a few very minor changes - please merge this, or let me know what you disagree with

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1007/978-3-642-23099-8 is OK
- 10.21105/joss.01539 is OK
- 10.21105/joss.00224 is OK
- 10.3389/fphys.2018.01431 is OK
- 10.21105/joss.01848 is OK
- 10.1371/journal.pcbi.1002061 is OK
- 10.1016/j.yjmcc.2017.03.008 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1016/j.cmpb.2021.106223 is OK
- 10.1016/j.pbiomolbio.2011.06.015 is OK
- 10.21105/joss.01848 is OK
- 10.1080/10255842.2012.704368 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3862, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@finsberg - I think this is ready to publish, once the archive metadata issue is fixed. Please let me know when that is

[finsberg]

@danielskatz I have now updated the title and the author list to match the paper (the original metadata was generated directly from a GitHub release).

[danielskatz]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04753 joss-papers#3863
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04753
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

@danielskatz I have now updated the title and the author list to match the paper (the original metadata was generated directly from a GitHub release).

@AoifeHughes - you might want add this in your instructions to future submitters. See https://joss.readthedocs.io/en/latest/editing.html#message-to-authors-at-the-end-of-a-review for suggested language

[danielskatz]

Congratulations to @finsberg (Henrik Nicolay Topnes Finsberg) and co-authors!!

And thanks to @mbarzegary & @sdelandtsheer for reviewing, and to @AoifeHughes for editing!
We couldn't do this without you

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04753

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