[REVIEW]: PeriDEM - High-fidelity modeling of granular media consisting of deformable complex-shaped particles

[editorialbot]

Submitting author: @prashjha (Prashant K Jha)
Repository: https://github.com/prashjha/PeriDEM
Branch with paper.md (empty if default branch): joss
Version: v0.2.1
Editor: @matthewfeickert
Reviewers: @divijghose, @nrichart, @ziyixi
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5"><img src="https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5/status.svg)](https://joss.theoj.org/papers/dd0c52ad995d506dc88c4cc9b79416d5)

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

@divijghose & @nrichart, 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 @matthewfeickert 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 @divijghose

📝 Checklist for @nrichart

📝 Checklist for @ziyixi

[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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.53 s (710.5 files/s, 342625.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              4              4          41380
C/C++ Header                   158          11551          22547          36252
Python                          38           5991           6508          15856
C++                             57           3590           2435          13231
Markdown                        19           1879              0           6697
YAML                            23            155            184           3862
CSS                              5            506            169           2269
CMake                           34            315            566           1060
CSV                              8              0              0            901
Bourne Shell                    14            151            122            674
JavaScript                       6             72            124            280
Jupyter Notebook                 1              0            512            236
TeX                              1             15              0            168
XML                              2              0              0             36
make                             2             15              6             33
reStructuredText                 1              0              0              2
Bazel                            1              0              0              1
-------------------------------------------------------------------------------
SUM:                           374          24244          33177         122938
-------------------------------------------------------------------------------

Commit count by author:

   182	Prashant K. Jha
    14	prashjha

[editorialbot]

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

✅ OK DOIs

- 10.1680/geot.1979.29.1.47 is OK
- 10.1016/j.jmps.2021.104376 is OK
- 10.1016/S0022-5096(99)00029-0 is OK
- 10.1137/17M1112236 is OK
- 10.1016/j.cma.2019.03.024 is OK
- 10.1002/nme.5791 is OK
- 10.1007/s10704-020-00480-0 is OK
- 10.1007/s42102-019-00010-0 is OK
- 10.3934/dcdsb.2020178 is OK
- 10.1007/s10659-013-9463-0 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1016/j.powtec.2018.09.047 is OK
- 10.1109/TPDS.2021.3104255 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Introduction to peridynamics
- No DOI given, and none found for title: METIS: A software package for partitioning unstruc...
- No DOI given, and none found for title: nanoflann: a C++ header-only fork of FLANN, a libr...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2040

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Boost Software License 1.0 (Valid open source OSI approved license)

[editorialbot]

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

[matthewfeickert]

@divijghose @nrichart @ziyixi Thanks for agreeing to review this submission! This is the review thread for the paper. All of our communications will happen here from now on. 👍

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied (and if you leave notes on each item that's even better). There are also links to the JOSS reviewer guidelines. I find it particularly helpful to also use the JOSS review criteria and review checklist docs as supplement/guides to the reviewer checklist @editorialbot will make for you.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7525 so that a link is created to this Issue 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 4 weeks. Please let me know if either of you require some more time (that's perfectly okay). We can also use @editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@matthewfeickert) if you have any questions/concerns.

[matthewfeickert]

@editorialbot add @ziyixi as reviewer

[editorialbot]

@ziyixi added to the reviewers list!

[matthewfeickert]

As mentioned in #7392 (comment), we have had some additional potential reviewers respond to agree to also contribute reviews, and I like to accept 3 reviewers when possible. So @ziyixi will be joining as a reviewer (thanks!).

@ziyixi, please check out #7525 (comment) for additional information, and if you have any questions please let me know.

[matthewfeickert]

👋 @divijghose, @nrichart, @ziyixi don't forget to create your review checklists with

@editorialbot generate my checklist

before starting your review.

[divijghose]

Review checklist for @divijghose

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/prashjha/PeriDEM?
• 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 (@prashjha) 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?

[matthewfeickert]

@nrichart, @ziyixi Please make sure to generate your checklists soon.

[nrichart]

Review checklist for @nrichart

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/prashjha/PeriDEM?
• 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 (@prashjha) 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?

[matthewfeickert]

As at least two reviewers have their checklist generated now I'll have @editorialbot give us reminders in 3 weeks to follow up on the initial state of the review.

[matthewfeickert]

@editorialbot remind @divijghose in 3 weeks

[editorialbot]

Reminder set for @divijghose in 3 weeks

[matthewfeickert]

@editorialbot remind @nrichart in 3 weeks

[editorialbot]

Reminder set for @nrichart in 3 weeks

[matthewfeickert]

@editorialbot remind @ziyixi in 3 weeks

[editorialbot]

Reminder set for @ziyixi in 3 weeks

[ziyixi]

Review checklist for @ziyixi

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/prashjha/PeriDEM?
• 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 (@prashjha) 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?