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[REVIEW]: PXO (Poly-XTAL Operations): Free MATLAB codebase to generate and analyse complex 2D grain structures #3190

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whedon opened this issue Apr 18, 2021 · 122 comments
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accepted M Matlab Objective-C published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Apr 18, 2021

Submitting author: @SunilAnandatheertha (sunil anandatheertha)
Repository: https://github.com/SunilAnandatheertha/PXO
Version: V10.1.1
Editor: @Kevin-Mattheus-Moerman
Reviewer: @yangbai90, @ksyang2013, @littlelazy6
Archive: 10.5281/zenodo.5142160

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7e7206fe84bfcc3062f1a76f68bea3b1"><img src="https://joss.theoj.org/papers/7e7206fe84bfcc3062f1a76f68bea3b1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7e7206fe84bfcc3062f1a76f68bea3b1/status.svg)](https://joss.theoj.org/papers/7e7206fe84bfcc3062f1a76f68bea3b1)

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

@yangbai90 & @ksyang2013 & @littlelazy6, 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 start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest

Review checklist for @yangbai90

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 (@SunilAnandatheertha) 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

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 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 @ksyang2013

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 (@SunilAnandatheertha) 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

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 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 @littlelazy6

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 (@SunilAnandatheertha) 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

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 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?
@whedon
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whedon commented Apr 18, 2021

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @yangbai90, @ksyang2013, @littlelazy6 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

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

@whedon generate pdf

@whedon
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whedon commented Apr 18, 2021

Failed to discover a Statement of need section in paper

@whedon
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whedon commented Apr 18, 2021

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

OK DOIs

- 10.1016/S0081-1947(08)60603-7 is OK
- 10.1016/0001-6160(84)90151-2 is OK
- 10.1016/0036-9748(89)90525-5 is OK
- 10.1016/0001-6160(84)90089-0 is OK
- 10.2355/isijinternational.38.913 is OK
- 10.1016/0956-7151(90)90177-I is OK
- 10.1016/j.actamat.2009.10.058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Apr 18, 2021

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.59 s (362.7 files/s, 34721.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                         205           1236           3423          15420
Markdown                         7             65              0            184
XML                              1              1              0            146
TeX                              1              7              0             89
YAML                             1              1              1             10
-------------------------------------------------------------------------------
SUM:                           215           1310           3424          15849
-------------------------------------------------------------------------------


Statistical information for the repository 'ed33fcbd1250117096d9d5d1' was
gathered on 2021/04/18.
No commited files with the specified extensions were found.

@whedon
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whedon commented Apr 18, 2021

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

@Kevin-Mattheus-Moerman
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@yangbai90, @ksyang2013, @littlelazy6 this is where the review takes place. Could you provide an indication as to the time you need to provide your initial review? FYI we can be flexible and it is okay if you need to take quite a bit of time. Thanks again for your help!!!!

@ksyang2013
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ksyang2013 commented Apr 28, 2021 via email

@littlelazy6
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littlelazy6 commented Apr 29, 2021 via email

@yangbai90
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I will return the comments within two weeks. Thanks!

@whedon
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whedon commented May 2, 2021

👋 @yangbai90, please update us on how your review is going (this is an automated reminder).

@whedon
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whedon commented May 2, 2021

👋 @ksyang2013, please update us on how your review is going (this is an automated reminder).

@whedon
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whedon commented May 2, 2021

👋 @littlelazy6, please update us on how your review is going (this is an automated reminder).

@yangbai90
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@SunilAnandatheertha
Hi sunil, except for the Limitations in the wiki, is there any more text about the performance part for your code?

@ksyang2013
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ksyang2013 commented May 14, 2021 via email

@SunilAnandatheertha
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@yangbai90 Thank you for the comment. Will include the performance related limitations in the code in the wiki page and will update here.

@SunilAnandatheertha
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@ksyang2013 Thank you for the update. I think @Kevin-Mattheus-Moerman would be the best person to help you in this issue.

@yangbai90
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@whedon commands

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whedon commented May 17, 2021

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

@yangbai90
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@whedon check references

@whedon
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whedon commented May 17, 2021

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

OK DOIs

- 10.1016/S0081-1947(08)60603-7 is OK
- 10.1016/0001-6160(84)90151-2 is OK
- 10.1016/0036-9748(89)90525-5 is OK
- 10.1016/0001-6160(84)90089-0 is OK
- 10.2355/isijinternational.38.913 is OK
- 10.1016/0956-7151(90)90177-I is OK
- 10.1016/j.actamat.2009.10.058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@yangbai90
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@whedon check repository

@openjournals openjournals deleted a comment from whedon Jul 28, 2021
@Kevin-Mattheus-Moerman
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@whedon generate pdf

@whedon
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whedon commented Jul 28, 2021

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

@Kevin-Mattheus-Moerman
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@whedon set 10.5281/zenodo.5142160 as archive

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whedon commented Jul 28, 2021

OK. 10.5281/zenodo.5142160 is the archive.

@SunilAnandatheertha
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@Kevin-Mattheus-Moerman Thank you. I am not able to tick the checkboxes.

@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Jul 28, 2021

@SunilAnandatheertha that is okay, I'll check them when ready. Note they remain unchecked now since those steps appear not to have been changed in the latest paper. I repeat them again below:

  • Check softwares this should read software
  • The acronym FEA is not explained please fix or avoid its use. Again it is also used in full as finite element analysis, after its first use so please be consistent again or remove.
  • ...to help the users to getting started -> ...to help users to get started.

@SunilAnandatheertha
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@Kevin-Mattheus-Moerman Thank you for this. I have updated it.

@whedon generate pdf

@Kevin-Mattheus-Moerman
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@whedon generate pdf

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whedon commented Jul 28, 2021

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

@Kevin-Mattheus-Moerman
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@whedon recommend-accept

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whedon commented Jul 29, 2021

Attempting dry run of processing paper acceptance...

@whedon whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 29, 2021
@whedon
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whedon commented Jul 29, 2021

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

OK DOIs

- 10.1016/j.actamat.2014.08.063 is OK
- 10.1107/S0021889808030112 is OK
- 10.21105/joss.02094 is OK
- 10.1177/14644207211010836 is OK
- 10.1186/2193-9772-3-5 is OK
- 10.1016/S0081-1947(08)60603-7 is OK
- 10.1016/0001-6160(84)90151-2 is OK
- 10.1016/0036-9748(89)90525-5 is OK
- 10.1016/0001-6160(84)90089-0 is OK
- 10.2355/isijinternational.38.913 is OK
- 10.1016/0956-7151(90)90177-I is OK
- 10.1016/j.actamat.2009.10.058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Jul 29, 2021

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2487

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2487, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@Kevin-Mattheus-Moerman
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@whedon accept deposit=true

@whedon whedon added accepted published Papers published in JOSS labels Jul 29, 2021
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whedon commented Jul 29, 2021

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

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whedon commented Jul 29, 2021

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented Jul 29, 2021

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.03190 joss-papers#2488
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03190
  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...

@Kevin-Mattheus-Moerman
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Congratulations on your accepted paper @SunilAnandatheertha (sunil anandatheertha) 🎉

Thank you @yangbai90, @ksyang2013, @littlelazy6 for reviewing this work! We really appreciate your help!!

@whedon
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whedon commented Jul 29, 2021

🎉🎉🎉 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.03190/status.svg)](https://doi.org/10.21105/joss.03190)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03190">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03190/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03190/status.svg
   :target: https://doi.org/10.21105/joss.03190

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:

@SunilAnandatheertha
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@Kevin-Mattheus-Moerman and the entire JOSS team: JOSS is a very good initiative. Thank you for this platform. Thank you also for considering the work in your journal. I am happy to see the acceptance. @ksyang2013 @yangbai90 @littlelazy6 Thank you so much for your review comments, they have been really helpful. Thank you all.

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