[REVIEW]: Variational Solvers for Irreversible Evolutionary Systems

[editorialbot]

Submitting author: !--author-handle-->@kumiori<!--end-author-handle-- (Andrés A. León Baldelli) Repository: https://github.com/kumiori/irrevolutions Branch with paper.md (empty if default branch): andres-paper Version: 0.1.0 Editor: !--editor-->@majensen<!--end-editor-- Reviewers: @jorgensd, @jhale Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/bd8a379864dd513dcd8787c21ae4420c/status.svg)](https://joss.theoj.org/papers/bd8a379864dd513dcd8787c21ae4420c)

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

@jorgensd & @jhale, 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 @majensen 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 @jhale

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=1.20 s (357.8 files/s, 91024.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                           280             76            102          28035
Python                          78           4266           2744          12863
Jupyter Notebook                31              0          44943          11933
TeX                              2             44              8           1202
XML                              1              0              0            720
GLSL                             4             27            459            498
CSV                              3              1              0            432
Markdown                         4            122              0            252
Dockerfile                       2             34              8             37
TOML                             1              6              8             22
JSON                            19              0              0             19
Bourne Shell                     2              0              4              7
INI                              1              1              0              4
-------------------------------------------------------------------------------
SUM:                           428           4577          48276          56024
-------------------------------------------------------------------------------

Commit count by author:

   259  andres
   155  Andrés A León Baldelli
    91  kumiori
    51  Andrés A León Baldelli
    23  Ayoub RHOUSNI
    22  SarahTACHET
     6  mbilynsky
     4  jaedong2019
     2  WissamY97
     1  assalaTrabelsi
     1  francoisfernet
     1  igorassist
     1  ueuzj

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.10447666 is OK
- 10.2172/2205494 is OK
- 10.1016/j.advwatres.2011.04.013 is OK
- 10.1007/s10589-008-9167-8 is OK

MISSING DOIs

- No DOI given, and none found for title: dolfiny: Python wrappers for DOLFINx
- 10.5802/crmeca.156 may be a valid DOI for title: La mécanique de l’endommagement au secours de la m...
- No DOI given, and none found for title: PETSc Web page
- No DOI given, and none found for title: PETSc Users Manual
- 10.1016/j.jmps.2011.03.010 may be a valid DOI for title: The issues of the uniqueness and the stability of ...
- No DOI given, and none found for title: The variational approach to fracture
- No DOI given, and none found for title: SLEPc: A scalable and flexible toolkit for the sol...
- 10.1016/s0022-5096(99)00028-9 may be a valid DOI for title: Numerical experiments in revisited brittle fractur...
- No DOI given, and none found for title: Numerical optimization
- No DOI given, and none found for title: Décomposition orthogonale d’un espace hilbertien s...

INVALID DOIs

- https://doi.org/10.1016/j.jmps.2021.104424 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1739

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[jhale]

Review checklist for @jhale

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/kumiori/irrevolutions?
• [ ] 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 (@kumiori) 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?

[jhale]

GNU recommends/instructs that LGPLv3 files should be named COPYING and COPYING.LESSER.