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[REVIEW]: fibergen: An introductory tool for FFT-based material homogenization #1027

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whedon opened this Issue Oct 18, 2018 · 130 comments

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whedon commented Oct 18, 2018

Submitting author: @fospald (Felix Ospald)
Repository: https://github.com/fospald/fibergen
Version: v1.0
Editor: @jedbrown
Reviewer: @tisaac, @ctdegroot
Archive: 10.5281/zenodo.2556861

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/add4f02dcedfaae8f81da200000d64ee"><img src="http://joss.theoj.org/papers/add4f02dcedfaae8f81da200000d64ee/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/add4f02dcedfaae8f81da200000d64ee/status.svg)](http://joss.theoj.org/papers/add4f02dcedfaae8f81da200000d64ee)

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) 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

@tisaac & @ctdegroot, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @jedbrown know.

Please try and complete your review in the next two weeks

Review checklist for @tisaac

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?
  • Version: v1.0
  • Authorship: Has the submitting author (@fospald) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @ctdegroot

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?
  • Version: v1.0
  • Authorship: Has the submitting author (@fospald) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Oct 18, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tisaac, it looks like you're currently assigned as the reviewer for 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:

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
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whedon commented Oct 18, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 18, 2018

PDF failed to compile for issue #1027 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1027 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/bin/whedon:98:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

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jedbrown commented Oct 18, 2018

@whedon generate pdf

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whedon commented Oct 18, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 18, 2018

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jedbrown commented Oct 18, 2018

@arfon Do you know why this review issue was created with the repository linked to https://fospald.github.io/fibergen/ instead of the repository from the pre-review issue #986? (I edited it before asking whedon to regenerate.)

@tisaac @ctdegroot Welcome! The comments from whedon above outline the review process. I'll be watching this thread if you have any questions. Thanks!

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tisaac commented Oct 18, 2018

@jedbrown, is a github release version necessary (submission has no tagged releases)? I think it should have a release, but as I understand it, the reviewed version will get a zenodo doi or similar which is what is actually important to identifying what was reviewed.

@tisaac tisaac referenced this issue Oct 18, 2018

Closed

A tagged release #1

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jedbrown commented Oct 18, 2018

@tisaac A tag should be made after the review (which may include new commits to the software), as part of archiving (using Zenodo or similar). It isn't necessary at this stage.

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tisaac commented Oct 18, 2018

I'm checking off "Does the full list of paper authors seem appropriate and complete?", but the second commit (fospald/fibergen@c6a91c9) appears to be an import an existing project, so I'm relying on the honesty of the submitting author.

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fospald commented Oct 18, 2018

I'm the original author of every line of the code and all demos, etc.
I did not use github right from the beginning for the project. I'm adding the project because research and publications are done.

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fospald commented Nov 8, 2018

Hi, what to do next?

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jedbrown commented Nov 8, 2018

@ctdegroot How is your review going?

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ctdegroot commented Nov 9, 2018

@jedbrown Working on the review. Hope to finish next week.

@fospald I am supposed to check "Does the release version given match the GitHub release (2018.1)?", but the GitHub repo shows no releases tagged. Can you clarify this for me?

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ctdegroot commented Nov 9, 2018

@fospald I read the review above and can see that the release issue has already been discussed.

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ctdegroot commented Nov 9, 2018

Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). I don't see any examples of how to use the code. If there are some, can you please tell me where they are and please put something in the README about these.

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 I don't see any guidelines for how third parties can contribute to the software. Can you add something to the README?

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ctdegroot commented Nov 9, 2018

@fospald Where are the test cases located? To what extent do they cover the code?

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ctdegroot commented Nov 10, 2018

I cannot find any documentation of the code API. It seems that all of the core code is stuffed into the 27,000 line fibergen.cpp. How would one go about understanding the code and potentially working with it, without the GUI? Maybe try Doxygen to at least give a basic bit of documentation?

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fospald commented Nov 12, 2018

@fospald I am supposed to check "Does the release version given match the GitHub release (2018.1)?", but the GitHub repo shows no releases tagged. Can you clarify this for me?

I will make only minor changes to the project and keep everything compatible. I don't want to maintain several branches. There will be no future releases with big changes.

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fospald commented Nov 12, 2018

Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). I don't see any examples of how to use the code. If there are some, can you please tell me where they are and please put something in the README about these.

You run the GUI and then you can select one of the demos (located in the demo directory).
See here
The editor gives help about the available settings in the project file.
See here

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 I don't see any guidelines for how third parties can contribute to the software. Can you add something to the README?

Ok. I added a "Contributing" section in the README.

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fospald commented Nov 12, 2018

@fospald Where are the test cases located? To what extent do they cover the code?

@ctdegroot The test cases are located in fibergen.cpp at line 23113 to 24194.
The tests cover core math operations, functions to compute geometric intersections, material laws (derivatives), solver operators for various methods.

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fospald commented Nov 12, 2018

I cannot find any documentation of the code API. It seems that all of the core code is stuffed into the 27,000 line fibergen.cpp. How would one go about understanding the code and potentially working with it, without the GUI? Maybe try Doxygen to at least give a basic bit of documentation?

@ctdegroot End users should use the GUI and should not do any coding.
But I understand the issue. I will try my best add some documentation with Doxygen and reply when I'm done. Also I know that the single file concept is not ideal. Limited time for the project...

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fospald commented Nov 13, 2018

@ctdegroot I added a Doxygen documentation. You have to
git pull
cd doc/doxygen
make (or just doxygen)
firefox html/index.html
(also added this to the README.md)

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whedon commented Feb 5, 2019

OK. 10.5281/zenodo.2556861 is the archive.

@jedbrown jedbrown added the accepted label Feb 5, 2019

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jedbrown commented Feb 5, 2019

@openjournals/joss-eics Over to you. Thanks, @tisaac and @ctdegroot for reviewing.

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fospald commented Feb 5, 2019

@jedbrown I annotated the tag.

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jedbrown commented Feb 5, 2019

If you want an annotated tag on the server, you'd have to delete it and re-push, something like

git push origin :refs/tags/v1.0
git push --tags origin
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fospald commented Feb 5, 2019

@jedbrown Now it should be fine.

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kyleniemeyer commented Feb 6, 2019

@whedon generate pdf

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whedon commented Feb 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 6, 2019

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kyleniemeyer commented Feb 6, 2019

@whedon check references

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whedon commented Feb 6, 2019

Attempting to check references...
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whedon commented Feb 6, 2019


OK DOIs

- http://doi.org/10.1016/j.jnnfm.2010.12.010 is OK
- http://doi.org/10.1007/s00466-014-1071-8 is OK
- http://doi.org/10.1016/j.cma.2015.06.003 is OK
- http://doi.org/10.1007/s00466-015-1227-1 is OK
- http://doi.org/10.1002/nme.5008 is OK
- http://doi.org/10.1002/pamm.201410320 is OK
- http://doi.org/https://doi.org/10.1016/j.cma.2016.06.021 is OK
- http://doi.org/10.1002/nme.5371 is OK
- http://doi.org/10.1016/j.crme.2014.12.005 is OK

MISSING DOIs

- https://doi.org/10.1016/s1387-1609(99)80001-2 may be missing for title: A fast numerical method for computing the linear and nonlinear mechanical properties of composites

INVALID DOIs

- None
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kyleniemeyer commented Feb 6, 2019

It looks like that missing DOI is a fluke, so we can ignore that and proceed.

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kyleniemeyer commented Feb 6, 2019

@whedon accept

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whedon commented Feb 6, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Feb 6, 2019

Check final proof 👉 openjournals/joss-papers#476

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#476, 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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whedon commented Feb 6, 2019


OK DOIs

- http://doi.org/10.1016/j.jnnfm.2010.12.010 is OK
- http://doi.org/10.1007/s00466-014-1071-8 is OK
- http://doi.org/10.1016/j.cma.2015.06.003 is OK
- http://doi.org/10.1007/s00466-015-1227-1 is OK
- http://doi.org/10.1002/nme.5008 is OK
- http://doi.org/10.1002/pamm.201410320 is OK
- http://doi.org/https://doi.org/10.1016/j.cma.2016.06.021 is OK
- http://doi.org/10.1002/nme.5371 is OK
- http://doi.org/10.1016/j.crme.2014.12.005 is OK

MISSING DOIs

- https://doi.org/10.1016/s1387-1609(99)80001-2 may be missing for title: A fast numerical method for computing the linear and nonlinear mechanical properties of composites

INVALID DOIs

- None
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kyleniemeyer commented Feb 6, 2019

@whedon accept deposit=true

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whedon commented Feb 6, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Feb 6, 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#477
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01027
  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 commented Feb 6, 2019

@fospald congrats, your article is now published in JOSS! Thanks for submitting a solid article and piece of software.

@tisaac & @ctdegroot thank you for reviewing this submission, and thanks to @jedbrown for editing it.

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whedon commented Feb 6, 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](http://joss.theoj.org/papers/10.21105/joss.01027/status.svg)](https://doi.org/10.21105/joss.01027)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01027">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01027/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01027/status.svg
   :target: https://doi.org/10.21105/joss.01027

This is how it will look in your documentation:

DOI

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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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fospald commented Feb 6, 2019

@kyleniemeyer @jedbrown Looking at some published papers (including mine)
http://joss.theoj.org/papers/10.21105/joss.01027
http://joss.theoj.org/papers/10.21105/joss.01168
it seems in the section "Cite as:" (on the left) the first name is missing.
"Ospald, (2019)."
Can this be fixed?

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jedbrown commented Feb 6, 2019

@fospald I believe that is the intended formatting, but it's unusual that the accepted papers list shows a URL https://fospald.github.io/fibergen/ instead of the usual fospald / fibergen. http://joss.theoj.org/papers/accepted

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fospald commented Feb 6, 2019

@jedbrown How to change the URL?

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jedbrown commented Feb 6, 2019

I don't know; might be a question for @arfon.
joss

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arfon commented Feb 6, 2019

@jedbrown How to change the URL?

I can fix this.

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arfon commented Feb 6, 2019

OK, fixed.

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jedbrown commented Feb 6, 2019

Thanks!

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