[REVIEW]: strucscan: A lightweight Python-based framework for high-throughput material simulation

[editorialbot]

Submitting author: @thohamm (Thomas Hammerschmidt)
Repository: https://github.com/ICAMS/strucscan
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @ppxasjsm
Reviewers: @mturiansky, @wcwitt
Archive: 10.5281/zenodo.7313602

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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

@mturiansky & @wcwitt, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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✨ 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 @mturiansky

📝 Checklist for @wcwitt

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (673.6 files/s, 97655.0 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           26            907           1978           3374
Markdown                          9            203              0            910
TeX                               1             12              0            123
Jupyter Notebook                  4              0           1763            121
reStructuredText                  6             37             41             76
YAML                              8             20            135             65
Bourne Again Shell               14             25            137             57
make                              1              5              5              9
--------------------------------------------------------------------------------
SUM:                             69           1209           4059           4735
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1016/0927-0256(96)00008-0 is OK
- 10.1103/PhysRevB.59.1758 is OK
- 10.1103/physrevb.54.11169 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1016/j.commatsci.2018.07.043 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1002/cpe.3505 is OK
- 10.1109/CCGRID.2001.923173 is OK
- 10.1007/10968987_3 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1088/1367-2630/15/11/115016 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1016/j.commatsci.2012.10.028 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1446

[editorialbot]

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

[ppxasjsm]

@mturiansky, @wcwitt, Please go ahead and start your review by generating your checklist. Do let me know if you have any problems/issues in the meantime.

[mturiansky]

Review checklist for @mturiansky

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/ICAMS/strucscan?
• 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 (@thohamm) 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?

[wcwitt]

Review checklist for @wcwitt

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/ICAMS/strucscan?
• 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 (@thohamm) 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?

[ppxasjsm]

/ooo October 4 until October 13

[thohamm]

issues fixed and closed

[mturiansky]

I opened one last issue. Once this is addressed, I can tick off the functionality checkbox and am okay with publication. The test coverage is a bit low in my opinion (see below), but I think it does cover the basic functionality.

Name                                Stmts   Miss  Cover
-------------------------------------------------------
strucscan/__init__.py                  10      0   100%
strucscan/_version.py                 337    213    37%
strucscan/cli.py                       35     35     0%
strucscan/core/__init__.py              0      0   100%
strucscan/core/collector.py            28      0   100%
strucscan/core/datatree.py             37      4    89%
strucscan/core/jobmaker.py            138     66    52%
strucscan/core/jobmanager.py          252     61    76%
strucscan/core/jobobject.py            50      5    90%
strucscan/core/statusmanager.py        28     11    61%
strucscan/engine/__init__.py            0      0   100%
strucscan/engine/dummy.py             115     70    39%
strucscan/engine/generalengine.py      63     22    65%
strucscan/engine/vasp.py              244    215    12%
strucscan/error/__init__.py             0      0   100%
strucscan/error/errorhandler.py       107     93    13%
strucscan/error/errormanager.py        27     24    11%
strucscan/properties/__init__.py        0      0   100%
strucscan/properties/bulk.py           11      8    27%
strucscan/properties/eos.py            41     25    39%
strucscan/resources/__init__.py         0      0   100%
strucscan/resources/atomicdata.py       2      0   100%
strucscan/resources/inputyaml.py       22      0   100%
strucscan/resources/properties.py      32      5    84%
strucscan/scheduler.py                168    119    29%
strucscan/utils.py                    236    108    54%
-------------------------------------------------------
TOTAL                                1983   1084    45%

[thohamm]

Thank you for the careful testing of our code and your feedback! We fixed and closed the issue, see comment in github repo.

[wcwitt]

Sorry to be a bit slow here - will finish ASAP

[thohamm]

Thank you also for your comment on the test coverage. The reason is that several parts of the code rely on operating with a scheduler system and are therefore a bit hard to test in a standalone run.

[mturiansky]

I'm all done with my review now, @ppxasjsm . All my concerns were addressed, and I'm okay with publication.

[thohamm]

@mturiansky Thank you for reviewing our work and for your constructive comments.

[ppxasjsm]

Thank you @mturiansky for your review and your feedback. @wcwitt can you give me an estimate of when you think you'll be able to finish the reveiw by? Thanks.

[wcwitt]

I'll finish this week.

[ppxasjsm]

Brilliant! Thank you.

[ppxasjsm]

I don't have any further comments on this paper and am happy to proceed with acceptance. @thohamm can you confirm you are ok with the proofs of the final article?

[thohamm]

@editorialbot generate pdf

[editorialbot]

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

[thohamm]

I corrected one typo and can confirm that we are ok with the proofs.

[Kevin-Mattheus-Moerman]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[Kevin-Mattheus-Moerman]

@ppxasjsm thanks for editing this submission. A minor feedback point. Please include the v if it is part of the version tag e.g. v1.0.0. So the version tag should match the one shown here: https://github.com/ICAMS/strucscan/tags. I'll also ask the authors to edit the version listed on ZENODO which currently says version 1.0.0.

[Kevin-Mattheus-Moerman]

@thohamm I am an AEiC for this track and here to help process acceptance of this work in JOSS. I've studied your repository, the archived version, and this review. I've also proofread your paper. I have the following minor points that require your attention before we proceed to process this for acceptance (feel free to disagree with language suggestions or to propose your own alternatives if needed):

• I have set the version tag as listed on your repository i.e. v1.0.0, can you please manually edit the ZENODO archive to list this as the version, it currently says version 1.0.0.
• The paper contains both data tree and data-tree, please uses the latter throughout.
• Use past tense in ...calculations in computational materials science lead to the... i.e. ...calculations in computational materials science have lead to the...
• Commas are needed in the locations indicated by square brackets: ...can be extended[,] with basic programming skills[,] to further scheduling systems.... And I suggest actually rephrasing this sentence to the smoother (check if I understood it right, the lack of commas confused me): ...can be extended, by somebody with basic programming skills, with additional scheduling systems, simulation codes and material properties at the atomic scale, and well as other simulation scales.. Feel free to propose a different alternative.
• Commas needed at square bracket locations: ...a large toolbox of features[,] or from a predefined database concept[,] but rather needs...
• Should materials properties be written material properties?

Recommendations (not required):

• If the acronym in the affiliation (ICAMS) is not used elsewhere in the document, you could consider removing it.
• Add commas as shown by square bracket locations
  ...by computational material science relies[,] to a large degree[,] on the prediction...
...different crystal structures[,] or different simulation settings.
• Consider using : after are in ...the required high-throughput calculations are (i) the sampling ...
• It is common practice to use code style text, when referring to software project names. So instead of saying strucscan you may consider using strucscan. i.e. use:

`strucscan`

If you do this, also do it for SunGridEngine and slurm and any other software project names.

• Remove the capital letter when strucscan appears at the start of a sentence, as the project name does not feature one.
• The text mentions Dependencies: as a "feature", however you mean the opposite, i.e. the fact that your package has few dependencies is a bonus. So perhaps consider a different word, or something like Reduced dependencies.

[thohamm]

@editorialbot generate pdf

[editorialbot]

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

[thohamm]

@Kevin-Mattheus-Moerman Thank you for your careful reading and suggestions.

The following points are changed:

• set zenodo version to v1.0.0
• changed to 'data-tree' throughput
• inserted past tense
• inserted all three comma suggestions and simplified sentence 'can be extended ..'
• changed to 'strucscan' in lowercase throughput

The remaining points were not changed as they are common terms or fine in our opinion.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04719 joss-papers#3760
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04719
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@thohamm congratulations for this publication in JOSS!

@ppxasjsm thanks for editing!

Special thanks to the reviewers @mturiansky and @wcwitt!! 🎉

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[ppxasjsm]

@editorialbot set v1.0.0 as version

@Kevin-Mattheus-Moerman Thank you! This was my first one. I'll remember that next time.

[thohamm]

Thank you all for your efforts in editing, reviewing and publishing our paper. We are glad that our work could be published in JOSS!

[wcwitt]

Congrats!