[REVIEW]: pyforce: Python Framework for data-driven model Order Reduction of multi-physiCs problEms

[editorialbot]

Submitting author: @Steriva (Stefano Riva) Repository: https://github.com/ERMETE-Lab/ROSE-pyforce Branch with paper.md (empty if default branch): Version: v0.1.2 Editor: @Fei-Tao Reviewers: @ShimingYIN, @damar-wicaksono, @alberto743 Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b3bc9aaecef1a8e0919310833eb76c2c"><img src="https://joss.theoj.org/papers/b3bc9aaecef1a8e0919310833eb76c2c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b3bc9aaecef1a8e0919310833eb76c2c/status.svg)](https://joss.theoj.org/papers/b3bc9aaecef1a8e0919310833eb76c2c)

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

@ShimingYIN & @damar-wicaksono & @alberto743, 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 @Fei-Tao 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 @damar-wicaksono

📝 Checklist for @alberto743

📝 Checklist for @ShimingYIN

[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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1016/j.nucengdes.2024.113105 is OK
- 10.1063/1.168744 is OK
- 10.48550/arXiv.2401.07300 is OK
- 10.5281/zenodo.10447666 is OK
- 10.1515/9783110671490 is OK
- 10.48550/arXiv.1905.05982 is OK
- 10.1016/j.cma.2015.01.018 is OK
- 10.1016/j.cma.2022.115773 is OK
- 10.1002/nme.4747 is OK
- 10.1016/j.anucene.2022.109538 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (569.8 files/s, 166008.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          29           1335           2238           2938
Jupyter Notebook                17              0           9305           2921
SVG                              1              0              0            708
TeX                              2             41              0            378
Markdown                         4             86              0            270
GLSL                             3             34             73            129
reStructuredText                10             86            166            104
YAML                             3             11             12             80
DOS Batch                        1              8              1             26
make                             1              4              7              9
Bourne Shell                     1              0              1              5
-------------------------------------------------------------------------------
SUM:                            72           1605          11803           7568
-------------------------------------------------------------------------------

Commit count by author:

    38	Stefano Riva
    35	Steriva
     5	Neko-tan

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 663

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[alberto743]

Review checklist for @alberto743

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/ERMETE-Lab/ROSE-pyforce?
• [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 (@Steriva) 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
• [ ] 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.
• [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

• [ ] 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

• [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?
• [ ] 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?

[damar-wicaksono]

Review checklist for @damar-wicaksono

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/ERMETE-Lab/ROSE-pyforce?
• [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 (@Steriva) 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?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] 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?
• [x] 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?

[ShimingYIN]

Review checklist for @ShimingYIN

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/ERMETE-Lab/ROSE-pyforce?
• [ ] 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 (@Steriva) 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?

[alberto743]

Fix license text: https://github.com/ERMETE-Lab/ROSE-pyforce/issues/6

[Steriva]

License text has been fixed with pull request #7

[damar-wicaksono]

@editorialbot commands

[editorialbot]

Hello @damar-wicaksono, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[damar-wicaksono]

@editorialbot generate pdf

[editorialbot]

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

[alberto743]

@Fei-Tao Sorry, I am very late with this review. I hope to complete in the next weeks.

[Fei-Tao]

No problem. Thanks for your update. Looking forward to your reviews.

On Mon, Oct 14, 2024 at 12:49 PM Alberto @.***> wrote:

@Fei-Tao https://github.com/Fei-Tao Sorry, I am very late with this review. I hope to complete in the next weeks.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6950#issuecomment-2411772160, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2NSR3XESKWWDKLSZ6K4UZ3Z3PYYNAVCNFSM6AAAAABKIBZMWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJRG43TEMJWGA . You are receiving this because you were mentioned.Message ID: @.***>

[damar-wicaksono]

Hi @Fei-Tao,

I've completed my portion of the review. I raised several comments and suggestions regarding the package, its documentation and accompanying paper (please refer to the linked Issues in this thread). The authors have addressed these points satisfactorily.

The package implements a range of DDROM techniques that I believe will be valuable to its target audience. The documentation includes detailed tutorials that showcase the package's capabilities, particularly in the context of nuclear engineering and related fields (as advertised), making them well-suited to its intended users. The documentation is well-structured and comprehensive, and the paper is well-written.

I am pleased to support the publication of this package in JOSS.

[Fei-Tao]

Hi @damar-wicaksono, thanks for your effort in helping improve this submission. Appreciate your time.

@ShimingYIN and @alberto743, would you please complete your reviewing at your convenience? Thanks again for agreeing to review this submission.

[ShimingYIN]

Hi @damar-wicaksono, thanks for your effort in helping improve this submission. Appreciate your time.

@ShimingYIN and @alberto743, would you please complete your reviewing at your convenience? Thanks again for agreeing to review this submission.

@Fei-Tao Sorry for being so late. I've started with this review and hope to finish it within the coming week.

[Steriva]

Dear all,

I hope this message finds you well. I wanted to kindly ask if there are any updates regarding the status of the submission. Please let me know if there's anything else required from my side to assist with the review process.

Thank you for your time and support! Best regards

[ShimingYIN]

Dear all,

I hope this message finds you well. I wanted to kindly ask if there are any updates regarding the status of the submission. Please let me know if there's anything else required from my side to assist with the review process.

Thank you for your time and support! Best regards

@Steriva Hi Stefano, sorry for the delay in the review process due to some deadlines recently. I am currently working on it and aim to provide my feedback shortly.

[alberto743]

Issue raised on "statement of need" https://github.com/ERMETE-Lab/ROSE-pyforce/issues/20

[alberto743]

@Steriva Is conda needed for the installation? Or is it just suggested?

[Steriva]

@Steriva Is conda needed for the installation? Or is it just suggested?

@alberto743, I would say it's strongly recommended since it's the easiest way to install dolfinx.

Moreover, to ensure a quicker and easier installation, it is suggested to change the conda-solver to libmamba.

[alberto743]

@Steriva Thank you for the answer. Does it apply to developers as well? I guess it would be useful to specify in the documentation the instructions for both users and developers. It would ease my task to verify whether I may reproduce the compilation step from scratch.

[Steriva]

The installation procedure is the same for both users and developers, I will specify it in the installation notes file.

[Steriva]

Greetings, I wanted to kindly ask if there are any updates regarding the status of the submission. Please let me know if there's anything else required from my side to assist with the review process.

Thank you for your time in improving the pyforce package! Best regards

[Neko-tan]

Greetings to all, I am Carolina, the second developer and the supervisor of the pyforce package. First of all, I would like to thank you all for your time and the suggestions you have given us, they have been very helpful in improving our package!

I would like to know if there are any updates regarding the status of the revisions. Of course, we will be glad to answer any questions and assist in the review process!

Thank you again, and best regards, Carolina

[alberto743]

@Neko-tan @Steriva sorry for the long delay. I plan to resume working on this review with the upcoming summer break.