[REVIEW]: OpenCCM: An Open-Source Continuous Compartmental Modelling Package

editorialbot commented 2 weeks ago

Submitting author: !--author-handle-->@nasserma@philipcardiff<!--end-editor-- Reviewers: @luohancfd, @speth Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b63c31c74a6055cd2ec19402826b08cb"><img src="https://joss.theoj.org/papers/b63c31c74a6055cd2ec19402826b08cb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b63c31c74a6055cd2ec19402826b08cb/status.svg)](https://joss.theoj.org/papers/b63c31c74a6055cd2ec19402826b08cb)

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

@luohancfd & @speth, 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 @speth

📝 Checklist for @luohancfd

editorialbot commented 2 weeks ago

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editorialbot commented 2 weeks ago

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

OK DOIs

- 10.5281/zenodo.8137090 is OK
- 10.21105/joss.03742 is OK
- 10.1016/j.compchemeng.2024.108650 is OK
- 10.1016/j.ces.2019.115196 is OK
- 10.1002/9781119176817.ecm2110 is OK
- 10.1515/9783110499001 is OK

MISSING DOIs

- No DOI given, and none found for title: Compartment Modelling Software
- No DOI given, and none found for title: OpenFOAM v10 User Guide
- No DOI given, and none found for title: The paraview guide: a parallel visualization appli...

INVALID DOIs

- None

editorialbot commented 2 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (771.5 files/s, 139402.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          37           1344           2995           3594
Markdown                         6            153              0            369
GLSL                             3             80            114            204
TeX                              1              9              0            100
YAML                             2              8             11             51
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            50           1594           3120           4321
-------------------------------------------------------------------------------

Commit count by author:

    56  Alex Vasile
    15  Nasser M. Abukhdeir
     8  Matthew Peres Tino
     6  yuvraj-aseri
     2  nasserma
     1  Nasser Mohieddin Abukhdeir

editorialbot commented 2 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1691

✅ The paper includes a Statement of need section

editorialbot commented 2 weeks ago

License info:

🟡 License found: GNU Lesser General Public License v2.1 (Check here for OSI approval)

editorialbot commented 2 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

speth commented 2 weeks ago

Review checklist for @speth

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/uw-comphys/openccm?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@nasserma) 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?

editorialbot commented 2 weeks ago

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

luohancfd commented 2 weeks ago

Review checklist for @luohancfd

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/uw-comphys/openccm?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@nasserma) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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?
[ ] 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).
[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?
[ ] 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, who the target audience is, and its relation to other work?
[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?

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