[REVIEW]: matscipy: materials science at the atomic scale with Python #5668
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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: For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type: |
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Hi @rashatwi how is your review going? |
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Sorry for my delayed response. I'll complete the review this upcoming week. Thanks for your patience. |
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@editorialbot generate my checklist |
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** General checks
** Functionality
** Documentation
** Software paper
Summarizing: I would like to see the tests on my machine pass, other than that I am very happy with this contribution. Will definitely incorporate this into my own work. As for the documentation issue: Maybe the authors have examples for more usage that are not easily findable for me and they could point me to the right example/folder/whatever to have a look at them. |
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Hi @pastewka please take a look at the comments above. |
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Will work on those, thanks @diehlpk and @mastricker for the comments. |
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Hi @diehlpk and @pastewka |
Review checklist for @mbarzegaryConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Dear @mastricker, thank you very much for your review and comments. Here I will try to answer your questions about To generate dislocations the module relies on anisotropic elasticity solution within Stroh formalism as implemented in atomman package. Unfortunately this package has an insane number of dependencies and thus we prefer not to include it as a default dependency of Another reason why most of test are skipped is related to the use of DXA algorithm for testing. We simply tests if the DXA algorithm from ovito package detects the same dislocation that we want to create. This requires Finally, some of the tests rely on calling Normally I use these tests to verify a fresh installation of In the plasticity section of the documentation I have added few examples how to build dislocations in Building cylindrical configurations with dislocations section. At the moment it is only for the case of BCC metals, I will add FCC and Diamond structure this week. I was thinking to add a section to show how one can add a new types of structures and dislocations to the set. If you have any particularly interesting system in mind, I would be happy to try to use it for this example. |
Review checklist for @rashatwiConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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I finished my review of the code and paper. It is clear to me that matscipy is well suited for JOSS and will be very useful to the computational materials science community. In terms of the paper, I think the authors did a good job in terms of describing clearly what the functionalities of matscipy are and in terms of citing the relevant and commonly used packages in the field. In terms of the checklist items, I have checked off most of them, but I think there are a few things that need to be addressed before acceptance of this work in JOSS. Most of my comments are minor, except for the fact that there is very limited/not enough examples or tutorials on how to use the different functionalities explained in the paper. I think the availability of detailed and clear tutorials will make it more accessible and much easier for new users to adopt the methods implemented in matscipy. Paper-related comments:
Package-related comments:
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@pastewka It worked :) The editor-in-chief will do a final check and it should be published soon. |
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@editorialbot set v1.0.0 as version |
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Done! version is now v1.0.0 |
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@diehlpk some minor things slipped the net here, it is easy to forget a minor thing or two, it really helps to call |
Post-Review Checklist for Editor and AuthorsAdditional Author Tasks After Review is Complete
Editor Tasks Prior to Acceptance
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@pastewka As AEiC I will now help to process final steps. I have checked this review, the archive link, your repository, and the paper. I have only the below minor points that require your attention:
Suggestion/comment (no action required):
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@Kevin-Mattheus-Moerman @diehlpk We addressed these final issues in current master. |
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@editorialbot generate pdf |
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@editorialbot generate pdf |
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@pastewka I've reviewed the changes and all looks good now. I will now proceed to process this work for acceptance. |
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@editorialbot recommend-accept |
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👋 @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#4959, then you can now move forward with accepting the submission by compiling again with the command |
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@editorialbot accept |
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Perfect, thanks everyone @diehlpk @Kevin-Mattheus-Moerman @mastricker @xuanxu @rashatwi @mbarzegary |
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Congratulations on this JOSS publication @pastewka! Thanks for editing @diehlpk And a special Thank you to the reviewers: @rashatwi, @mbarzegary, @mastricker |
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Submitting author: @pastewka (Lars Pastewka)
Repository: https://github.com/libAtoms/matscipy
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @diehlpk
Reviewers: @rashatwi, @mbarzegary, @mastricker
Archive: 10.5281/zenodo.10564956
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Checklists
📝 Checklist for @mbarzegary
📝 Checklist for @rashatwi
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