[REVIEW]: ASIMTools: A lightweight workflow and simulation manager for reproducible atomistic simulations

[editorialbot]

Submitting author: @mkphuthi (Mgcini Keith Phuthi)
Repository: https://github.com/BattModels/asimtools.git
Branch with paper.md (empty if default branch):
Version: v0.0.2
Editor: @HaoZeke
Reviewers: @abhishektiwari, @imtambovtcev
Archive: https://dx.doi.org/10.5281/zenodo.13952433

Status

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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

@abhishektiwari & @imtambovtcev, 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 @HaoZeke 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 @abhishektiwari

📝 Checklist for @imtambovtcev

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (2214.3 files/s, 129165.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          53            771           1399           4417
YAML                            73             44             95           1414
reStructuredText                19            279            557            430
Markdown                         3             86              0            385
TeX                              1             13              0            203
Bourne Shell                    29             89            159            100
DOS Batch                        1              8              1             26
make                             1              5              7             12
-------------------------------------------------------------------------------
SUM:                           180           1295           2218           6987
-------------------------------------------------------------------------------

Commit count by author:

   152	mkphuthi
     6	emilannevelink
     3	Keith Phuthi

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1038/s41563-023-01699-7 is OK
- 10.1002/cpe.3505 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1021/acsomega.3c10014 is OK

MISSING DOIs

- No DOI given, and none found for title: Vibrational Entropy and Free Energy of Solid Lithi...

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1690

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[abhishektiwari]

Review checklist for @abhishektiwari

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/BattModels/asimtools.git?
• 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 (@mkphuthi) 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?

[imtambovtcev]

Review checklist for @imtambovtcev

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/BattModels/asimtools.git?
• 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 (@mkphuthi) 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?

[imtambovtcev]

Review of "ASIMTools: A lightweight framework for scalable and reproducible atomic simulations"

Summary:

The manuscript presents ASIMTools, a flexible and lightweight workflow manager designed for reproducible atomic simulations. The tool's ability to handle different atomic structures, computing environments, and simulation protocols with minimal setup is well-explained. The software's potential to simplify and enhance the reproducibility of simulation workflows is evident.

Comments and Suggestions:

Highlighting the Advantages: While the paper effectively outlines the capabilities of ASIMTools, I suggest further emphasizing the specific advantages of this tool over existing solutions. It would be beneficial to clarify in the documentation what unique contributions ASIMTools offers compared to what already exists. This could involve a more direct explanation of how ASIMTools enhances current workflows and addresses challenges that other tools may not fully resolve.

Installation via PyPI: The installation instructions are clear; however, adding a PyPI installation option would be a valuable enhancement.

Conclusion:

I find the manuscript well-prepared, with the suggestions provided to further strengthen the clarity and accessibility of the tool.

[mkphuthi]

Hi @abhishektiwari and @imtambovtcev,

Thank you for the suggestions. Let me know if there are any other edits you would like me to make.

Best,
Keith

[imtambovtcev]

Hi @mkphuthi,

No additional edits are required from me.

Best,
@imtambovtcev

[mkphuthi]

Hi @HaoZeke ,@abhishektiwari,

Bumping this so that I know next steps.

Best,
@mkphuthi

[abhishektiwari]

@HaoZeke completed review from my side and marked checklist completed.

[HaoZeke]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[HaoZeke]

@mkphuthi apologies for the delay, the paper reads well, I've left an issue about setting the version and archive, which should bring us almost to the end of the process.

[HaoZeke]

@editorialbot check references

[HaoZeke]

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1038/s41563-023-01699-7 is OK
- 10.1002/cpe.3505 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1021/acsomega.3c10014 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Vibrational Entropy and Free Energy of Solid Lithi...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[HaoZeke]

@editorialbot set https://dx.doi.org/10.5281/zenodo.13942780 as archive

[editorialbot]

Done! archive is now https://dx.doi.org/10.5281/zenodo.13942780

[editorialbot]

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

[HaoZeke]

@editorialbot set v0.0.1 as version

[editorialbot]

Done! version is now v0.0.1

[HaoZeke]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1038/s41563-023-01699-7 is OK
- 10.1002/cpe.3505 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1021/acsomega.3c10014 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Vibrational Entropy and Free Energy of Solid Lithi...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-gjerding_atomic_2021 already defined
ID ref-huber_aiida_2020 already defined

[HaoZeke]

@mkphuthi could you make a new release (zenodo and version only should be fine, no need to update PyPI for now) with the updated bibliography?

[mkphuthi]

@HaoZeke Done!

[HaoZeke]

@editorialbot set v0.0.2 as version

[editorialbot]

Done! version is now v0.0.2

[HaoZeke]

@mkphuthi sorry but the zenodo release is v2 but it should be v0.0.2, please update / reissue it.

[mkphuthi]

@HaoZeke Ah good catch. I've updated it.

[HaoZeke]

@editorialbot set https://dx.doi.org/10.5281/zenodo.13952433 as archive

[editorialbot]

Done! archive is now https://dx.doi.org/10.5281/zenodo.13952433

[HaoZeke]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.commatsci.2021.110731 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1038/s41563-023-01699-7 is OK
- 10.1002/cpe.3505 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1021/acsomega.3c10014 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Vibrational Entropy and Free Energy of Solid Lithi...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6019, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept