[REVIEW]: The MFrontGallery project

[editorialbot]

Submitting author: @thelfer (Thomas Helfer)
Repository: https://github.com/thelfer/MFrontGallery
Branch with paper.md (empty if default branch): master
Version: 2.1
Editor: @srmnitc
Reviewers: @mrbuche, @likask
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/df14924ef6b0619487f482165d8930b7"><img src="https://joss.theoj.org/papers/df14924ef6b0619487f482165d8930b7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/df14924ef6b0619487f482165d8930b7/status.svg)](https://joss.theoj.org/papers/df14924ef6b0619487f482165d8930b7)

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

@mrbuche & @likask, 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 @srmnitc 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 @mrbuche

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1016/j.anucene.2024.110577 is OK
- 10.1016/j.camwa.2015.06.027 is OK
- 10.21105/joss.02003 is OK
- 10.1007/s12665-012-1546-x is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.13140/RG.2.2.15996.77444 is OK
- 10.13140/RG.2.2.13453.05609 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: TFEL/MFront website
- No DOI given, and none found for title: Zur Modellierung und Simulation geothermischer Tra...
- No DOI given, and none found for title: Ein Strömungs- und Transportmodell für klüftiges G...
- No DOI given, and none found for title: Simulation von Transportvorgängen im klüftigen Ges...
- No DOI given, and none found for title: Theorie und Numerik der Mehrphasenströmungen in ge...
- No DOI given, and none found for title: Implementation of clay rock and bentonite models u...
- No DOI given, and none found for title: The Burger_EDF_CIWAP_2021 constitutive law for con...
- No DOI given, and none found for title: Introducing small strain legacy Abaqus/UMAT implem...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.13 s (1086.0 files/s, 324309.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             12             42             12          22595
Markdown                        17           1235            240           4634
CMake                           80            269            803           4481
C++                              3            365            767           2166
XML                              2              0              6            928
Text                             3            335              0            866
CSS                              3            197            270            608
TeX                              2             57              0            575
C/C++ Header                     3             60            101            306
HTML                             1              1              7            136
XSLT                             1              6              0            113
JavaScript                       6             45             62             88
Fortran 95                       1              0              6             70
Fortran 77                       3              0             44             66
YAML                             2             10             11             66
Fortran 90                       1              0              5             37
MATLAB                           2              0              0             10
Python                           1              0              0              2
-------------------------------------------------------------------------------
SUM:                           143           2622           2334          37747
-------------------------------------------------------------------------------

Commit count by author:

   136	Thomas Helfer
    37	Helfer Thomas
     9	tnagel
     4	HELFER Thomas 202608
     4	Thomas Nagel
     3	Reinhard
     3	maxence-wz
     1	cbsilver
     1	thelfer

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1775

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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

[srmnitc]

👋🏼 @thelfer @mrbuche @likask this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@srmnitc ) if you have any questions/concerns, thanks again for the submission, and for the reviews!

[srmnitc]

@thelfer editorialbot is complaining that it could not find a license. This is probably because the license is not in a file named LICENSE. Is this something you could do? Thanks!

[thelfer]

@srmnitc I do this ASAP

[thelfer]

@srmnitc I copied LGPL-3.0.txt in LICENSE

[mrbuche]

Review checklist for @mrbuche

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/thelfer/MFrontGallery?
• 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 (@thelfer) 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?

[mrbuche]

@editorialbot generate pdf

[editorialbot]

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

[mrbuche]

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

The paper is successful in explaining how this software fits in with compatible software, but perhaps not how it compares to equivalent software that may already be out there. Maybe there is no comparable alternatives, but that could then be stated. @srmnitc is this what is meant from this bullet?

[srmnitc]

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

The paper is successful in explaining how this software fits in with compatible software, but perhaps not how it compares to equivalent software that may already be out there. Maybe there is no comparable alternatives, but that could then be stated. @srmnitc is this what is meant from this bullet?

Yes, that point is meant to ensure that it is compared to other available tools. I agree with your assessment that if none exists, that could be stated.

[mrbuche]

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

The paper is successful in explaining how this software fits in with compatible software, but perhaps not how it compares to equivalent software that may already be out there. Maybe there is no comparable alternatives, but that could then be stated. @srmnitc is this what is meant from this bullet?

Yes, that point is meant to ensure that it is compared to other available tools. I agree with your assessment that if none exists, that could be stated.

Okay thank you! @thelfer that is my only criticism on the writing currently. I have gotten through most things except trying to install and use the software myself, things look great overall!

[thelfer]

@mrbuche Thanks for this review. Concerning the state of the field, the question is somehow difficult because the project is really focused on QA issues related to material knowledge management which is seldom a major concern in most open-source thermomechanical solvers.

Don't be mistaken by the last sentence. Open-source solvers are very concerned by quality issues regarding code, verifications tests, etc.. and do a wonderful job.

However, most (thermomechanical) solvers delegate material management issues to their users and for what I know, helping to set a proper material knowledge management strategy is not really dealt with in details.

The major benefit of the project (and the paper) is to highlight the need and to propose, thanks to MFront, a solution that can be used in a wide variety of context (languages, solvers, etc..)

[mrbuche]

@mrbuche Thanks for this review. Concerning the state of the field, the question is somehow difficult because the project is really focused on QA issues related to material knowledge management which is seldom a major concern in most open-source thermomechanical solvers.

Don't be mistaken by the last sentence. Open-source solvers are very concerned by quality issues regarding code, verifications tests, etc.. and do a wonderful job.

However, most (thermomechanical) solvers delegate material management issues to their users and for what I know, helping to set a proper material knowledge management strategy is not really dealt with in details.

The major benefit of the project (and the paper) is to highlight the need and to propose, thanks to MFront, a solution that can be used in a wide variety of context (languages, solvers, etc..)

@thelfer that is definitely true I feel, the material management side of things is usually totally outside the software used to do numerical solutions, which is then usually put on the user to handle somehow, which is then usually something that doesn't have any sense of QA.

Maybe this is all technically clear in the paper, in places like "... the originality of the MFrontGallery project is to..." but just not the recipe that JOSS gives, which could be more like guidelines than requirements? Could point out that the software is "first of its kind" or something too. I am happy either way and am checking that box!

[thelfer]

@mrbuche What about adding the following section at the end of the paper, after the conclusion and before the references ?

# State of the field

The project is focused on Quality Assurance issues related to material
knowledge management which is, in the authors' experience, seldom a
major concern in most open-source thermomechanical solvers. Several
libraries providing high quality implementations of constitutive
equations are available, but generally dedicated to one specific solver.
The implementations are generally generic (as opposed to
self-contained). The `MFrontGallery` project thus provide a unique
approach.

[mrbuche]

@mrbuche What about adding the following section at the end of the paper, after the conclusion and before the references ?

# State of the field

The project is focused on Quality Assurance issues related to material
knowledge management which is, in the authors' experience, seldom a
major concern in most open-source thermomechanical solvers. Several
libraries providing high quality implementations of constitutive
equations are available, but generally dedicated to one specific solver.
The implementations are generally generic (as opposed to
self-contained). The `MFrontGallery` project thus provide a unique
approach.

@thelfer perfect!

[thelfer]

@thelfer perfect!

Merged !

[mrbuche]

@editorialbot generate pdf

[editorialbot]

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