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[REVIEW]: WulffPack: A Python package for Wulff constructions #1944

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whedon opened this issue Dec 12, 2019 · 54 comments
Closed

[REVIEW]: WulffPack: A Python package for Wulff constructions #1944

whedon opened this issue Dec 12, 2019 · 54 comments
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@whedon whedon commented Dec 12, 2019

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

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f0887de96e6adf8e7ee3c0989b4003ed"><img src="https://joss.theoj.org/papers/f0887de96e6adf8e7ee3c0989b4003ed/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f0887de96e6adf8e7ee3c0989b4003ed/status.svg)](https://joss.theoj.org/papers/f0887de96e6adf8e7ee3c0989b4003ed)

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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @drvinceknight know.

Please try and complete your review in the next two weeks

Review checklist for @EduPH

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@magnusrahm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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

Review checklist for @mzszym

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@magnusrahm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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

Review checklist for @corybrunson

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@magnusrahm) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?
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@whedon whedon commented Dec 12, 2019

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 🎉.

⭐️ Important ⭐️

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 commands

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

@whedon generate pdf
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@whedon whedon commented Dec 12, 2019

Attempting to check references...
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@whedon whedon commented Dec 12, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 12, 2019

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

Can't find any papers to compile :-(

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@drvinceknight drvinceknight commented Dec 12, 2019

@whedon generate pdf from branch joss-pape

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@whedon whedon commented Dec 12, 2019

Attempting PDF compilation from custom branch joss-pape. Reticulating splines etc...
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@whedon whedon commented Dec 12, 2019

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 :-(

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@drvinceknight drvinceknight commented Dec 12, 2019

@whedon generate pdf from branch joss-paper

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@whedon whedon commented Dec 12, 2019

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
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@whedon whedon commented Dec 12, 2019


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
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@whedon whedon commented Dec 12, 2019

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@mzszym mzszym commented Dec 14, 2019

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.

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@magnusrahm magnusrahm commented Dec 18, 2019

@whedon generate pdf from branch joss-paper

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@whedon whedon commented Dec 18, 2019

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
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@whedon whedon commented Dec 18, 2019

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@magnusrahm magnusrahm commented Dec 18, 2019

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.

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@mzszym mzszym commented Dec 19, 2019

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

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@drvinceknight drvinceknight commented Dec 20, 2019

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

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@corybrunson corybrunson commented Dec 27, 2019

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

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@corybrunson corybrunson commented Dec 27, 2019

@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.

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@EduPH EduPH commented Dec 29, 2019

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

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@drvinceknight drvinceknight commented Jan 6, 2020

(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 👍

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@whedon whedon commented Jan 6, 2020

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
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@whedon whedon commented Jan 6, 2020

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@drvinceknight drvinceknight commented Jan 6, 2020

@whedon check references from branch joss-paper

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@whedon whedon commented Jan 6, 2020

Attempting to check references... from custom branch joss-paper
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@whedon whedon commented Jan 6, 2020


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
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@drvinceknight drvinceknight commented Jan 6, 2020

@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).

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@magnusrahm magnusrahm commented Jan 7, 2020

@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).

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@drvinceknight drvinceknight commented Jan 7, 2020

@whedon generate pdf

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@whedon whedon commented Jan 7, 2020

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@drvinceknight drvinceknight commented Jan 7, 2020

@whedon set 10.5281/zenodo.3600252 as archive

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@whedon whedon commented Jan 7, 2020

OK. 10.5281/zenodo.3600252 is the archive.

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@drvinceknight drvinceknight commented Jan 7, 2020

@openjournals/joss-eics this paper is ready to be accepted 👍

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@danielskatz danielskatz commented Jan 7, 2020

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

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@magnusrahm magnusrahm commented Jan 7, 2020

Yes, that's correct.

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@danielskatz danielskatz commented Jan 7, 2020

@whedon set v1.1 as version

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@whedon whedon commented Jan 7, 2020

OK. v1.1 is the version.

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@danielskatz danielskatz commented Jan 7, 2020

@whedon accept

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@whedon whedon commented Jan 7, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Jan 7, 2020

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
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@whedon whedon commented Jan 7, 2020

Check final proof 👉 openjournals/joss-papers#1205

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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
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@danielskatz danielskatz commented Jan 7, 2020

@whedon accept deposit=true

@whedon whedon added the accepted label Jan 7, 2020
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@whedon whedon commented Jan 7, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Jan 7, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Jan 7, 2020

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

Here's what you must now do:

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

Any issues? notify your editorial technical team...

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@danielskatz danielskatz commented Jan 7, 2020

Thanks to @EduPH, @mzszym, @corybrunson for reviewing!
And @drvinceknight for editing!
And congratulations to @magnusrahm and co-authors!

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@danielskatz danielskatz commented Jan 7, 2020

I'm now waiting for the DOI to resolve, after which I will close this issue

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@magnusrahm magnusrahm commented Jan 7, 2020

Thank you! 😃

@danielskatz danielskatz closed this Jan 7, 2020
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@whedon whedon commented Jan 7, 2020

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01944/status.svg)](https://doi.org/10.21105/joss.01944)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01944">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01944/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01944/status.svg
   :target: https://doi.org/10.21105/joss.01944

This is how it will look in your documentation:

DOI

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