[REVIEW]: WulffPack: A Python package for Wulff constructions

whedon commented 4 years ago

Submitting author: @magnusrahm (Magnus Rahm) Repository: https://gitlab.com/materials-modeling/wulffpack Version: v1.1 Editor: @drvinceknight Reviewer: @EduPH, @mzszym, @corybrunson Archive: 10.5281/zenodo.3600252

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Reviewers and authors:

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Reviewer instructions & questions

@EduPH & @mzszym & @corybrunson, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @EduPH

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@magnusrahm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @mzszym

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@magnusrahm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @corybrunson

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@magnusrahm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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

[ ] 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @EduPH, @mzszym, @corybrunson it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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@whedon generate pdf

whedon commented 4 years ago

Attempting to check references...

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

PDF failed to compile for issue #1944 with the following error:

Can't find any papers to compile :-(

drvinceknight commented 4 years ago

@whedon generate pdf from branch joss-pape

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-pape. Reticulating splines etc...

whedon commented 4 years ago

PDF failed to compile for issue #1944 with the following error:

error: pathspec 'joss-pape' did not match any file(s) known to git. Can't find any papers to compile :-(

drvinceknight commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon commented 4 years ago


OK DOIs

- 10.1524/zkri.1901.34.1.449 is OK
- 10.1016/0022-0248(83)90184-7 is OK
- https://doi.org/10.1016/0001-6160(67)90206-4 is OK
- https://doi.org/10.1016/j.commatsci.2012.10.028 is OK
- 10.1007/s10853-012-6739-x is OK
- 10.1016/S0927-0256(97)00167-5 is OK
- 10.1145/235815.235821 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1088/1361-648X/aa680e is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

mzszym commented 4 years ago

I believe that I am done with the review. I think it is a very good small module with a well defined function and a rather complete description. It is well implemented and I found no important issues. I could run the examples without problems. Constructed nanoparticles seem to be according to my expectations. The only thing I missed was the description how "this software compares to other commonly-used packages?", which I understand as a comparison with other packages offering the same or similar functionality.

Edit: I found the sentence about it. It seems to have a missing citation: Screenshot 2019-12-14 at 17 57 10 I would appreciate slightly more information, but I think, a very basic comparison is provided.

magnusrahm commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

magnusrahm commented 4 years ago

Thank you, @mzszym! The comparison to other packages was indeed very short. It is updated (and the missing reference has been fixed) in the latest version of the paper, like so:

The regular Wulff construction has been implemented in several software packages, including a submodule of the Python package pymatgen (Ong et al., 2013), a no longer maintained C++ package (Roosen, McCormack, & Carter, 1998), and a Wolfram Mathematica implementation with a graphical user interace (Zucker, Chatain, Dahmen, Hagège, & Carter, 2012). While the latter code has support for Winterbottom constructions, we have found no publicly available software that implements the icosahedral and decahedral Wulff construction. The aforementioned codes also seem to lack the ability to transform the created shapes into an atomistic representation, a feature of critical importance if the Wulff construction is to be used for atomistic simulations.

mzszym commented 4 years ago

@magnusrahm Well done. I am confident that the package fulfills all requirements.

drvinceknight commented 4 years ago

I will be checking GitHub in a limited capacity over the next couple of weeks.

corybrunson commented 4 years ago

@drvinceknight and @magnusrahm thank you for your patience. I'm beginning my review now.

corybrunson commented 4 years ago

@magnusrahm thank you for the elegant software and thorough documentation behind this submission. In most respects i think it quite meets the needs of JOSS, and the few issues i've raised should be quick to resolve. I had no problems along the way other than those raised in the issues. The concepts are quite new to me, but i hope that i've grasped them well enough to give useful feedback. I'll be quick to respond to any questions about it, and i'll check off the remaining items as the issues are addressed.

EduPH commented 4 years ago

I agree with the other two reviewers. The package fulfils all the requirements.

drvinceknight commented 4 years ago

(Me closing the issue was a miss click)

Thank you very much for your work reviewing @EduPH, @mzszym, @corybrunson!

I'll be looking through this later today with any final minor editorial requests :+1:

drvinceknight commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

PDF failed to compile for issue #1944 with the following error:

Can't find any papers to compile :-(

drvinceknight commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

drvinceknight commented 4 years ago

@whedon check references from branch joss-paper

whedon commented 4 years ago

Attempting to check references... from custom branch joss-paper

whedon commented 4 years ago


OK DOIs

- 10.1524/zkri.1901.34.1.449 is OK
- 10.1016/0022-0248(83)90184-7 is OK
- 10.1016/0001-6160(67)90206-4 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1007/s10853-012-6739-x is OK
- 10.1016/S0927-0256(97)00167-5 is OK
- 10.1145/235815.235821 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1088/1361-648X/aa680e is OK

MISSING DOIs

- None

INVALID DOIs

- None

drvinceknight commented 4 years ago

@magnusrahm everything looks good to me, would you be able to make a Zenodo archive, and report the DOI in the review thread (here).

Could you make sure the Zenodo deposit has the correct metadata (title and author list should match the paper).

magnusrahm commented 4 years ago

@drvinceknight I have uploaded a Zenodo archive (10.5281/zenodo.3600252, https://doi.org/10.5281/zenodo.3600252). I have also merged the joss-paper branch into the master branch and deleted the former. Some very minor additions were made to the paper (https://gitlab.com/materials-modeling/wulffpack/commit/82b4e1771798733a6022ff292982bc17ea7b6310).

drvinceknight commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

drvinceknight commented 4 years ago

@whedon set 10.5281/zenodo.3600252 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3600252 is the archive.

drvinceknight commented 4 years ago

@openjournals/joss-eics this paper is ready to be accepted :+1:

danielskatz commented 4 years ago

@magnusrahm - it looks like this is now version 1.1 - correct?

magnusrahm commented 4 years ago

Yes, that's correct.

danielskatz commented 4 years ago

@whedon set v1.1 as version

whedon commented 4 years ago

OK. v1.1 is the version.

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1088/0953-8984/28/5/053001 is OK
- 10.1524/zkri.1901.34.1.449 is OK
- 10.1016/0022-0248(83)90184-7 is OK
- 10.1016/0001-6160(67)90206-4 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1007/s10853-012-6739-x is OK
- 10.1016/S0927-0256(97)00167-5 is OK
- 10.1145/235815.235821 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1088/1361-648X/aa680e is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1205

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1205, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1206
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01944
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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