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[REVIEW]: Kanapy: A Python package for generating complex synthetic polycrystalline microstructures. #1732

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whedon opened this issue Sep 16, 2019 · 90 comments
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@whedon whedon commented Sep 16, 2019

Submitting author: @mrgprasad (Mahesh R. G. Prasad)
Repository: https://github.com/mrgprasad/kanapy
Version: v1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @heprom, @KedoKudo, @chennachaos
Archive: 10.5281/zenodo.3529591

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790"><img src="https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790/status.svg)](https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790)

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

@heprom & @KedoKudo & @chennachaos, 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 @Kevin-Mattheus-Moerman know.

Please try and complete your review in the next two weeks

Review checklist for @heprom

Conflict of interest

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 (@mrgprasad) 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 @KedoKudo

Conflict of interest

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 (@mrgprasad) 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 @chennachaos

Conflict of interest

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 (@mrgprasad) 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 Sep 16, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @heprom, @KedoKudo, @chennachaos 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:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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For a list of things I can do to help you, just type:

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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 Sep 16, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Sep 16, 2019

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Sep 16, 2019

@mrgprasad @heprom, @KedoKudo, @chennachaos 👋 this is where the review will take place. The instructions and the checklists at the top will guide you through the process. Let me know if you have questions. Let the reviewing begin 🎉

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Sep 16, 2019

@putanowr now that I have 3 reviewers it is okay if you are not able to join us. The review has now started. However if you are keen to help and the review process is still ongoing mid-October (which is when you said you might have time over at #1634), I can still add you here.

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@putanowr putanowr commented Sep 16, 2019

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@KedoKudo KedoKudo commented Oct 1, 2019

@Kevin-Mattheus-Moerman
After carefully reviewing kanapy, I think the following aspects of kanapy could be improved:

The writing of the summary is adequate, but I hope the author could add a few sentences to compare kanapy with existing synthetic microstructure construction softwares (Dream.3D for example) to highlight the innovative aspect of kanapy. Also, I noticed that the acknowledge part of paper.md is empty, which I am not sure whether this is intentional or not.

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@mrgprasad mrgprasad commented Oct 2, 2019

@KedoKudo
Thank you for taking time and reviewing the repo and the paper. I will make the necessary changes and get back to you soon.

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@chennachaos chennachaos commented Oct 2, 2019

Hi @mrgprasad. I have started the review for Kanapy.
I have a remark related to State of the field in the Software paper section.

The paper discusses the issues with a couple of techniques used for generating synthetic microstructures, and then presents algorithms used in Kanapy, which is good. But, it does not mention anything about the need for Kanapy package. To convince the reader about Kanapy, it is important to address the following questions.
1.) What is motivation behind developing Kanapy?
2.) What are the advantages of Kanapy over other software libraries used for the generation of microstructures, for example, Dream.3D and Neper?
3.) Does Kanapy address any limitations of the existing libraries?
4.) Are there any specific features in Kanapy that are not available in other libraries? If so, what are they?

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@mrgprasad mrgprasad commented Oct 2, 2019

@chennachaos
Thank you for the paper review and pointing out that I have skipped over the actual motivation for developing Kanapy. I will address this and the related questions and push a new version of the paper soon.

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@mrgprasad mrgprasad commented Oct 4, 2019

@whedon generate pdf

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@whedon whedon commented Oct 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 4, 2019

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@mrgprasad mrgprasad commented Oct 4, 2019

@Kevin-Mattheus-Moerman, @KedoKudo, @chennachaos and @heprom
I have pushed an update to the Kanapy repo based on KedoKudo's review.

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@mrgprasad mrgprasad commented Oct 4, 2019

@KedoKudo
I have updated the software paper based on your comments. Do let me know if you have any further suggestions. Also, I have removed the acknowledgement section.

@chennachaos
With this update I have also tried to address our queries. I hope the motivation for Kanapy's development, its design and unique features and how it addresses the limitations of other software libraries is clear now.

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@KedoKudo KedoKudo commented Oct 9, 2019

@mrgprasad @Kevin-Mattheus-Moerman
I am happy with the current state of kanapy, and I would like to recommend this package for publication.

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Oct 10, 2019

@KedoKudo thanks for your help here 🎉

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Oct 10, 2019

@heprom can you give us an indication as to when you will be able to complete this review?

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@chennachaos chennachaos commented Oct 10, 2019

Hi @mrgprasad. The automated tests work. However, there are some warning messages at the end (see the attached image) that has the potential to confuse the users.

I suggesting fixing this issue.

tests-warning-messages

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@chennachaos chennachaos commented Oct 10, 2019

@mrgprasad
A statement of need for Documentation is missing.

Consider adding a paragraph on 'motivation' behind Kanapy in the Overview section of the documentation.

I will open these two as issues in your Github repo so we can track them.

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@mrgprasad mrgprasad commented Oct 10, 2019

@chennachaos
I have pushed an update to Kanapy's repo based on your review. I have also updated the issues you have opened on Kanapy's repo. Do let me know if additional changes are necessary.

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@chennachaos chennachaos commented Oct 11, 2019

Hi @mrgprasad. Thank you for the updates.

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@chennachaos chennachaos commented Oct 11, 2019

Hi @Kevin-Mattheus-Moerman, I have completed the review. @mrgprasad has been prompt in responding to my questions and remarks. I am happy with the current state of the Kanapy package.

I recommend the Kanapy software package for publication in the JOSS.

Thank you for the opportunity.

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@heprom heprom commented Oct 19, 2019

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@heprom heprom commented Oct 19, 2019

Hi @Kevin-Mattheus-Moerman I have done a first pass at reading the paper and testing the code. There is a small bug in the examples (I thing after moving to json input files): the input file in ellipsoid_pack.py has not been changed which result in an error when running the example.

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@whedon whedon commented Nov 5, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 5, 2019

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@mrgprasad mrgprasad commented Nov 5, 2019

@Kevin-Mattheus-Moerman
Thanks for the pointer. I have changed this in the paper.

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Nov 5, 2019

@mrgprasad great. Thanks looks good to me now. Can you now do the following:

  • Archive a copy of the reviewed software on Zenodo and list the DOI of the archived version here. Make sure that as you do this that the meta data (e.g. the title and author list) will match that of the paper.
  • Can you please confirm the version of the reviewed and archived software? Is it still v0.0.1 or have you changed the version?
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@mrgprasad mrgprasad commented Nov 5, 2019

@Kevin-Mattheus-Moerman
I have created the archive on Zenodo, here's the DOI: 10.5281/zenodo.3529591
Both the reviewed and the archived software are v1.0.0

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Nov 5, 2019

@whedon set 10.5281/zenodo.3529591 as archive

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@whedon whedon commented Nov 5, 2019

OK. 10.5281/zenodo.3529591 is the archive.

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Nov 5, 2019

@openjournals/joss-eics I recommend this submission for acceptance in JOSS

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Nov 5, 2019

@whedon set v1.0.0 as version

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@whedon whedon commented Nov 5, 2019

OK. v1.0.0 is the version.

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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

Hi @mrgprasad, just a few fixes needed in the paper:

  • missing period in i.e in second paragraph: "i.e," -> "i.e.,"
  • in the 3rd paragraph, the sentence beginning with "Thus addressing" is incomplete, or at least awkward. Perhaps something like "This addresses the limitations..."
  • last sentence of 3rd paragraph: change "in-built" to "built-in"
  • The URL isn't showing up in the pybind11 citation, please try this instead:
@misc{pybind11,
   author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
   year = {2017},
   howpublished = {\url{https://github.com/pybind/pybind11}},
   title = {pybind11 -- Seamless operability between {C++11} and {Python}}
}

Please let me know back here when you've made those changes and I'll finish the last few steps of acceptance.

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@mrgprasad mrgprasad commented Nov 8, 2019

@whedon generate pdf

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@whedon whedon commented Nov 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 8, 2019

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@mrgprasad mrgprasad commented Nov 8, 2019

@kyleniemeyer
I have made all the changes based on your suggestions. Thank you.

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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@whedon accept

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@whedon whedon commented Nov 8, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 8, 2019


OK DOIs

- 10.1186/2193-9772-3-5 is OK
- 10.1016/j.cma.2011.01.002 is OK
- 10.1016/j.commatsci.2014.04.011 is OK
- 10.1016/S0167-8396(01)00049-8 is OK
- 10.1103/PhysRevE.88.053312 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 8, 2019

Check final proof 👉 openjournals/joss-papers#1093

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1093, 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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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@whedon accept deposit=true

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@whedon whedon commented Nov 8, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Nov 8, 2019
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@whedon whedon commented Nov 8, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Nov 8, 2019

🚨🚨🚨 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#1094
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01732
  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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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@mrgprasad congrats on your article's publication in JOSS!

Many thanks to @Kevin-Mattheus-Moerman for editing, and @heprom, @KedoKudo, @chennachaos for reviewing this submission.

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@whedon whedon commented Nov 8, 2019

🎉🎉🎉 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.01732/status.svg)](https://doi.org/10.21105/joss.01732)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01732">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01732/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01732/status.svg
   :target: https://doi.org/10.21105/joss.01732

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@mrgprasad mrgprasad commented Nov 8, 2019

I would like to thank @KedoKudo, @chennachaos & @heprom for reviewing Kanapy. Your suggestions have made the software better.
@Kevin-Mattheus-Moerman thank you for taking time and editing!
And final thanks to @kyleniemeyer for accepting the submission.

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@mrgprasad mrgprasad commented Nov 8, 2019

@kyleniemeyer
We are working on extending Kanapy to include other important features with respect to microstructure generation. In this regard, can we submit the software for review again? If not, is it possible to update the current JOSS paper to reflect this?

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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@mrgprasad if the software functionality changes substantially, then you can submit later for a new review.

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