[REVIEW]: PLIP: A hybrid python/C++ package for linearized machine learning interatomic potentials

[editorialbot]

Submitting author: @aksam432 (Akshay Krishna Ammothum Kandy)
Repository: https://github.com/LAM-GROUP/PLIP
Branch with paper.md (empty if default branch): paper
Version: v0.3.4
Editor: @phibeck
Reviewers: @Materials-Informatics-Laboratory, @RainierBarrett, @jakryd
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3eeaf11617d88637e5aafac01ca9329a"><img src="https://joss.theoj.org/papers/3eeaf11617d88637e5aafac01ca9329a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3eeaf11617d88637e5aafac01ca9329a/status.svg)](https://joss.theoj.org/papers/3eeaf11617d88637e5aafac01ca9329a)

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

@Materials-Informatics-Laboratory & @RainierBarrett & @jakryd, 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 @phibeck 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 @RainierBarrett

📝 Checklist for @Materials-Informatics-Laboratory

[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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (268.1 files/s, 33728.7 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                               6            197             43           1223
TeX                               1              0              0            215
HTML                              1              2              5            120
Python                            1             37             21            119
C/C++ Header                      4             41            287            105
Markdown                          4             34              0             70
JSON                              1              0              0             52
YAML                              1              1              4             18
Bourne Again Shell                2             11             28              9
--------------------------------------------------------------------------------
SUM:                             21            323            388           1931
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1088/2632-2153/abc9fd is OK
- 10.1103/PhysRevB.107.174106 is OK
- 10.1016/j.commatsci.2019.03.049 is OK
- 10.1103/PhysRevB.87.184115 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1063/1.3553717 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/acs.jctc.8b00770 is OK
- 10.1016/j.cpc.2018.03.016 is OK
- 10.21105/joss.05118 is OK
- 10.1103/PhysRevLett.104.136403 is OK
- 10.1038/s41467-022-29939-5 is OK
- 10.1103/PhysRevB.99.014104 is OK
- 10.1088/2632-2153/abc9fd is OK
- 10.1021/acs.jpcc.2c06341 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 911

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

[RainierBarrett]

Review checklist for @RainierBarrett

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/LAM-GROUP/PLIP?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@aksam432) 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?

[phibeck]

Thank you @RainierBarrett for getting the review started!

@Materials-Informatics-Laboratory, @jakryd, please go ahead and create your checklist first using the command @editorialbot generate my checklist.

As you work through your checklists, please feel free to comment and ask questions in this thread. You are encouraged to create issues in the repository directly. When you do, please mention openjournals/joss-reviews#5715 so that it creates a link in this thread and we can keep track of it.

We aim for reviews to be completed within 2-4 weeks. Please let me know if you have any questions, or if either of you need more time.

Meanwhile, @aksam432 feel free to get started working on the issues linked above.

[Materials-Informatics-Laboratory]

Review checklist for @Materials-Informatics-Laboratory

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/LAM-GROUP/PLIP?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@aksam432) 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?

[Materials-Informatics-Laboratory]

@aksam432 quick question regarding the paper. When you say that your method represents an "interpretable MLIP", what exactly does interpretable mean in this context? The only portion I could find that might fall into this category is the use of LASSO, but I'm not sure if I would go so far as to say it gives you an "interpretable" MLIP.

[phibeck]

👋 @aksam432 feel free to get started working on the issues and comments linked here. @jakryd, are you still willing to do the review? Please let me know should you need more time.

[aksam432]

@phibeck I will work on the comments and issues this week.

[phibeck]

👋 @aksam432 could you let us know where you stand with responding to the comments of the reviewers and how much more time you will need?

[aksam432]

@phibeck Sorry for the delay. I will be done by begining of next week.

[phibeck]

Hi @aksam432, checking in on your progress.

@jakryd, it would be great to get an update from your side as well regarding the review, thanks.

[phibeck]

👋 @aksam432 could you please provide an update when you plan to address the reviewers comments?

[aksam432]

Hello everyone,
I regret to inform that I can only provide the corrections by November 10th 2023 due to personal reasons. Thanks

[phibeck]

@editorialbot remind @aksam432 in twelve days

[editorialbot]

Reminder set for @aksam432 in twelve days

[editorialbot]

👋 @aksam432, please update us on how things are progressing here (this is an automated reminder).

[phibeck]

Hi @aksam432, can you please let me know if you are able to address the issues and comments within the next two weeks?

If you are not able to within that time, we will need to place the submission on hold, so that we can address the substantial number of submissions that need attention. If you are not able to work on this in the foreseeable future, we will need to withdraw it.

[kyleniemeyer]

@editorialbot withdraw

Due to a lack of responsiveness from the author, we are withdrawing this submission.

[editorialbot]

Paper withdrawn.

[kyleniemeyer]

Thanks to @phibeck for editing this, and thank you to @Materials-Informatics-Laboratory, @RainierBarrett, and @jakryd for helping with the review.