[REVIEW]: svZeroDSolver: A modular package for lumped-parameter cardiovascular simulations

[editorialbot]

Submitting author: @menon-karthik (Karthik Menon)
Repository: https://github.com/SimVascular/svZeroDSolver.git
Branch with paper.md (empty if default branch): paper
Version: v2.0
Editor: @philipcardiff
Reviewers: @TS-CUBED, @marchirschvogel
Archive: Pending

Status

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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

@TS-CUBED & @marchirschvogel, 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 @philipcardiff 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 @TS-CUBED

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1007/s10439-010-0083-6 is OK
- 10.1002/cnm.3639 is OK
- 10.1007/s10439-021-02796-x is OK
- 10.1016/j.wavemoti.2003.12.009 is OK
- 10.1017/flo.2024.5 is OK
- 10.1101/2023.08.17.23294242 is OK
- 10.1007/s10439-009-9760-8 is OK
- 10.1146/ANNUREV-FLUID-010313-141341 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.21105/joss.04118 is OK
- 10.1016/j.cma.2005.04.014 is OK
- 10.1115/1.4042184 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A generalized-alpha method for integrating the fil...
- No DOI given, and none found for title: Computational Fluid-Structure Interaction
- No DOI given, and none found for title: Predictors of Myocardial Ischemia in Patients with...
- No DOI given, and none found for title: Bayesian Windkessel calibration using optimized 0D...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: Personalized and uncertainty-aware coronary hemody...

❌ MISSING DOIs

- 10.1007/s10237-018-1098-4 may be a valid DOI for title: The importance of the pericardium for cardiac biom...
- 10.1007/s10439-012-0579-3 may be a valid DOI for title: Patient-specific multiscale modeling of blood flow...
- 10.1007/s10439-006-9212-7 may be a valid DOI for title: Coupling of a 3D finite element model of cardiac v...
- 10.1016/j.compbiomed.2024.109420 may be a valid DOI for title: Hybrid Physics-Based and Data-Driven Modeling of V...

❌ INVALID DOIs

- https://doi.org/10.1016/j.cma.2023.116414 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/cnm.3820 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cma.2024.117119 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/B978-0-323-95484-6.00016-6 is INVALID because of 'https://doi.org/' prefix

[philipcardiff]

Hi @menon-karthik, please address the missing and invalid DOIs above. Thanks!

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=5.78 s (34.3 files/s, 46691.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            72              0              0         249009
C++                             37            662           1538           3640
CSS                              2            414            166           1953
JavaScript                       5            452            256           1650
Python                          15            356            487           1474
C/C++ Header                    34            374           3805           1099
Markdown                         7            150              0            449
TeX                              2             32              0            376
CMake                           11             85            261            258
YAML                             8             20             19            231
XML                              1              6              9            226
HTML                             1             13              3            148
Dockerfile                       1              4              1             27
TOML                             1              1              0              8
Bourne Shell                     1              1              0              4
-------------------------------------------------------------------------------
SUM:                           198           2570           6545         260552
-------------------------------------------------------------------------------

Commit count by author:

    42	Karthik Menon
    29	Martin R. Pfaller
    25	Jonathan Pham
    19	Jakob Richter
    15	menon-karthik
    13	mrp089
    11	Martin Pfaller
     8	Dave Parker
     3	Nick Dorn
     2	emilinmathew

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1716

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

[TS-CUBED]

Review checklist for @TS-CUBED

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/SimVascular/svZeroDSolver.git?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@menon-karthik) 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?

[TS-CUBED]

The license follows the MIT license, but does not specify it. It may be useful to include the name "MIT License" in the License file to make it clear to the user that it is using this common license.